From 9da78d7dc1e01668202a6ff1648671c23a471fb9 Mon Sep 17 00:00:00 2001 From: egli Date: Mon, 11 Jun 2018 15:41:06 +0200 Subject: [PATCH 001/147] Update version in develop branch --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index cbb84e0f..b5adf880 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "dacat-api", - "version": "2.7.0", + "version": "2.8.0", "main": "server/server.js", "scripts": { "lint": "eslint common/models", From f620baa601ba253a8cc5e52308fe71847b47ccf5 Mon Sep 17 00:00:00 2001 From: egli Date: Wed, 13 Jun 2018 13:54:15 +0200 Subject: [PATCH 002/147] Upgraded to latest loopback package version and linked packages --- common/models/dataset.js | 60 +- package-lock.json | 10811 ++++++++++++++++++------------------- package.json | 101 +- test/Dataset.js | 4 +- 4 files changed, 5402 insertions(+), 5574 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 49b866dc..fad151ae 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -160,7 +160,14 @@ module.exports = function(Dataset) { Object.keys(fields).map(function(key) { if (facets.indexOf(key) < 0) { if (key === "text") { - match["$or"] = [{$text: searchExpression(key, fields[key])},{sourceFolder: {$regex: fields[key], $options:'i'}}] + match["$or"] = [{ + $text: searchExpression(key, fields[key]) + }, { + sourceFolder: { + $regex: fields[key], + $options: 'i' + } + }] } else if (key === "userGroups") { if (fields[key].length > 0) match["ownerGroup"] = searchExpression(key, fields[key]) @@ -208,11 +215,13 @@ module.exports = function(Dataset) { Dataset.getDataSource().connector.connect(function(err, db) { var collection = db.collection('Dataset'); var res = collection.aggregate(pipeline, - function(err, res) { - if (err) { - console.log("Facet err handling:", err); - } - cb(err, res); + function(err, cursor) { + cursor.toArray(function(err, res) { + if (err) { + console.log("Facet err handling:", err); + } + cb(err, res); + }); }); }); }; @@ -234,7 +243,14 @@ module.exports = function(Dataset) { Object.keys(fields).map(function(key) { if (fields[key] && fields[key] !== 'null') { if (key === "text") { - match["$or"] = [{$text: searchExpression(key, fields[key])},{sourceFolder: {$regex: fields[key], $options:'i'}}] + match["$or"] = [{ + $text: searchExpression(key, fields[key]) + }, { + sourceFolder: { + $regex: fields[key], + $options: 'i' + } + }] } else if (key === "ownerGroup") { // ownerGroup is handled in userGroups parts } else if (key === "userGroups") { @@ -285,7 +301,10 @@ module.exports = function(Dataset) { } }) pipeline.push({ - $unwind: {path: "$datasetlifecycle", preserveNullAndEmptyArrays: true} + $unwind: { + path: "$datasetlifecycle", + preserveNullAndEmptyArrays: true + } }) if (Object.keys(matchJoin).length > 0) { @@ -326,18 +345,21 @@ module.exports = function(Dataset) { Dataset.getDataSource().connector.connect(function(err, db) { var collection = db.collection('Dataset'); var res = collection.aggregate(pipeline, - function(err, res) { - if (err) { - console.log("Facet err handling:", err); - } - // console.log("Query result:", res) - // rename _id to pid - res.map(ds => { - Object.defineProperty(ds, 'pid', Object.getOwnPropertyDescriptor(ds, '_id')); - delete ds['_id'] - }) - cb(err, res); + function(err, cursor) { + cursor.toArray(function(err, res) { + if (err) { + console.log("Facet err handling:", err); + } + // console.log("Query result:", res) + // rename _id to pid + res.map(ds => { + Object.defineProperty(ds, 'pid', Object.getOwnPropertyDescriptor(ds, '_id')); + delete ds['_id'] + }) + cb(err, res); + }); }); + }); }; diff --git a/package-lock.json b/package-lock.json index fbe877fa..e635fba0 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,5650 +1,5453 @@ { - "name": "dacat-api", - "version": "2.6.3", - "lockfileVersion": 1, - 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b5adf880..490a8f22 100644 --- a/package.json +++ b/package.json @@ -1,51 +1,54 @@ { - "name": "dacat-api", - "version": "2.8.0", - "main": "server/server.js", - "scripts": { - "lint": "eslint common/models", - "start": "node .", - "posttests": "npm run lint && nsp check", - "test": "./node_modules/mocha/bin/mocha --timeout=10000 --reporter spec --exit 2>/dev/null" - }, - "dependencies": { - "compression": "1.7.1", - "cors": "2.8.4", - "helmet": "3.9.0", - "loopback": "3.16.2", - "loopback-boot": "2.27.0", - "loopback-component-explorer": "5.2.0", - "loopback-component-model-diagram": "0.3.0", - "loopback-component-mq": "^2.2.5", - "loopback-component-passport": "3.4.1", - "loopback-component-visualizer": "1.2.1", - "loopback-connector-kafka": "^0.2.1", - "loopback-connector-mongodb": "3.3.0", - "loopback-ds-timestamp-mixin": "^3.4.1", - "moment": "^2.20.1", - "moment-timezone": "^0.5.14", - "nodemailer": "^4.3.1", - "passport-ldapauth": "2.0.0", - "passport-local": "1.0.0", - "passport-openidconnect": "0.0.2", - "serve-favicon": "2.4.5", - "strong-error-handler": "2.3.0", - "uuid": "^3.2.1" - }, - "devDependencies": { - "@mean-expert/loopback-sdk-builder": "2.1.0", - "chai": "^4.1.2", - "chai-http": "^3.0.0", - "eslint": "4.10.0", - "eslint-config-loopback": "8.0.0", - "mocha": "^4.1.0", - "nsp": "2.8.1", - "supertest": "^3.0.0" - }, - "repository": { - "type": "", - "url": "" - }, - "license": "GPL-3.0", - "description": "dacat-api" + "name": "dacat-api", + "version": "2.8.1", + "main": "server/server.js", + "engines": { + "node": ">=4" + }, + "scripts": { + "lint": "eslint common/models", + "start": "node .", + "posttests": "npm run lint && nsp check", + "test": "./node_modules/mocha/bin/mocha --timeout=10000 --reporter spec --exit 2>/dev/null" + }, + "dependencies": { + "compression": "^1.0.3", + "cors": "^2.5.2", + "helmet": "^3.10.0", + "loopback-boot": "^2.6.5", + "serve-favicon": "2.4.5", + "strong-error-handler": "2.3.0", + "loopback-component-explorer": "^6.0.0", + "loopback": "^3.19.0", + "loopback-component-model-diagram": "^0.3.0", + "loopback-component-mq": "^2.2.5", + "loopback-component-passport": "^3.4.1", + "loopback-component-visualizer": "^1.2.1", + "loopback-connector-kafka": "^0.2.1", + "loopback-connector-mongodb": "^3.3.0", + "loopback-ds-timestamp-mixin": "^3.4.1", + "moment": "^2.20.1", + "moment-timezone": "^0.5.14", + "nodemailer": "^4.3.1", + "passport-ldapauth": "^2.0.0", + "passport-local": "^1.0.0", + "passport-openidconnect": "^0.0.2", + "uuid": "^3.2.1" + }, + "devDependencies": { + "eslint": "^3.17.1", + "eslint-config-loopback": "^8.0.0", + "nsp": "^2.1.0", + "@mean-expert/loopback-sdk-builder": "^2.1.0", + "chai": "^4.1.2", + "chai-http": "^3.0.0", + "mocha": "^4.1.0", + "supertest": "^3.0.0" + }, + "repository": { + "type": "", + "url": "" + }, + "license": "GPL-3.0", + "description": "dacat-api" } diff --git a/test/Dataset.js b/test/Dataset.js index a42a8b31..a7b14862 100644 --- a/test/Dataset.js +++ b/test/Dataset.js @@ -111,9 +111,9 @@ describe('Simple Dataset tests', () => { .expect(200) .expect('Content-Type', /json/) .end((err, res) => { - res.body.should.be.an('array'); if(err) - done(err); + return done(err); + res.body.should.be.an('array'); done(); }); }); From 834adf9c20095dfdbc90f0e062d47512fd4cdca0 Mon Sep 17 00:00:00 2001 From: murphy_g Date: Wed, 13 Jun 2018 14:33:45 +0200 Subject: [PATCH 003/147] Update server.js --- server/server.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/server/server.js b/server/server.js index 03bd30c4..7ad1d5b6 100644 --- a/server/server.js +++ b/server/server.js @@ -60,7 +60,7 @@ passportConfigurator.buildUserLdapProfile = function(user, options) { } if (!profile.id) { profile.id = user['uid']; - if (!(uid in user)){ + if (!('uid' in user)){ const MY_NAMESPACE = '1b671a64-40d5-491e-99b0-da01ff1f3341'; const generated_id = uuidv3( user['mail'], MY_NAMESPACE); profile.id = generated_id; From b1f2e7ab315e8d74455ad11f5da2602498b783df Mon Sep 17 00:00:00 2001 From: murphy_g Date: Mon, 18 Jun 2018 11:39:58 +0200 Subject: [PATCH 004/147] Update Dockerfile.proxy --- CI/ESS/Dockerfile.proxy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CI/ESS/Dockerfile.proxy b/CI/ESS/Dockerfile.proxy index 86deee26..6e7fab9f 100644 --- a/CI/ESS/Dockerfile.proxy +++ b/CI/ESS/Dockerfile.proxy @@ -31,7 +31,7 @@ COPY CI/ESS/envfiles/middleware.json /usr/src/app/server/ #COPY CI/ESS/envfiles/providers.json /usr/src/app/server/ #COPY CI/ESS/envfiles/datasources.json /usr/src/app/server/ #COPY CI/ESS/envfiles/component-config.json /usr/src/app/server/ -COPY CI/ESS/start.sh /usr/src/app/start.sh +#COPY CI/ESS/start.sh /usr/src/app/start.sh #COPY CI/ESS/settings.json /usr/src/app/test/config/ RUN NODE_ENV=dev # Start the app From 9adc6013107fe23a8bb9b29be09b79e610661bd1 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 20 Jun 2018 11:02:22 +0200 Subject: [PATCH 005/147] Fixed proposalIngest 500 code for missing measurement period --- common/models/proposal.js | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/common/models/proposal.js b/common/models/proposal.js index 939c573a..78a10dd8 100644 --- a/common/models/proposal.js +++ b/common/models/proposal.js @@ -6,19 +6,25 @@ module.exports = function(Proposal) { // put Proposal.beforeRemote('replaceOrCreate', function(ctx, instance, next) { // handle embedded datafile documents - utils.updateAllTimesToUTC(["start", "end"], ctx.args.data.MeasurementPeriodList) + if ("MeasurementPeriodList" in ctx.args.data) { + utils.updateAllTimesToUTC(["start", "end"], ctx.args.data.MeasurementPeriodList) + } next(); }); //patch Proposal.beforeRemote('patchOrCreate', function(ctx, instance, next) { - utils.updateAllTimesToUTC(["start", "end"], ctx.args.data.MeasurementPeriodList) + if ("MeasurementPeriodList" in ctx.args.data) { + utils.updateAllTimesToUTC(["start", "end"], ctx.args.data.MeasurementPeriodList) + } next(); }); //post Proposal.beforeRemote('create', function(ctx, unused, next) { - utils.updateAllTimesToUTC(["start", "end"], ctx.args.data.MeasurementPeriodList) + if ("MeasurementPeriodList" in ctx.args.data) { + utils.updateAllTimesToUTC(["start", "end"], ctx.args.data.MeasurementPeriodList) + } next(); }); From 097a4a89296f4b5608cced680f4546b5d1206d4c Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 25 Jun 2018 15:07:06 +0200 Subject: [PATCH 006/147] Additional mocha tests for issue #501 --- test/Proposal.js | 82 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 test/Proposal.js diff --git a/test/Proposal.js b/test/Proposal.js new file mode 100644 index 00000000..972420c4 --- /dev/null +++ b/test/Proposal.js @@ -0,0 +1,82 @@ +/* jshint node:true */ +/* jshint esversion:6 */ +'use strict'; + +// process.env.NODE_ENV = 'test'; + +var chai = require('chai'); +var chaiHttp = require('chai-http'); +var request = require('supertest'); +var app = require('../server/server'); +var should = chai.should(); +var utils = require('./LoginUtils'); + +var accessToken = null, + proposalId = null; + +var testdataset = { + "proposalId": "20170266", + "email": "proposer%40uni.edu", + "title": "A test proposal", + "abstract": "Abstract of test proposal", + "ownerGroup": "20170251-group" + +} + +describe('Simple Proposal tests', () => { + before((done) => { + utils.getToken(app, { + 'username': 'proposalIngestor', + 'password': 'aman' + }, + (tokenVal) => { + accessToken = tokenVal; + done(); + }); + }); + + it('adds a new proposal', function(done) { + request(app) + .post('/api/v2/Proposals?access_token=' + accessToken) + .send(testdataset) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + res.body.should.have.property('ownerGroup').and.be.string; + res.body.should.have.property('proposalId').and.be.string; + proposalId = encodeURIComponent(res.body['proposalId']); + done(); + }); + }); + + it('should fetch this new proposal', function(done) { + request(app) + .get('/api/v2/Proposals/' + proposalId + '?access_token=' + accessToken) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + it('should delete this proposal', function(done) { + request(app) + .delete('/api/v2/Proposals/' + proposalId + '?access_token=' + accessToken) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + +}); From e6238b6d180aac56bb869274c75257984df4a92b Mon Sep 17 00:00:00 2001 From: egli Date: Wed, 27 Jun 2018 11:45:18 +0200 Subject: [PATCH 007/147] Initial changes to the model logic to allow for automated job creation, not ready yet --- common/models/job.js | 1 + common/models/orig-datablock.js | 4 +- common/models/utils.js | 112 ++++++++++++++++++++++++++++++-- 3 files changed, 109 insertions(+), 8 deletions(-) diff --git a/common/models/job.js b/common/models/job.js index 54a5eb1c..5807c7d9 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -26,6 +26,7 @@ module.exports = function (Job) { // make some consistency checks: // - ensure that all wanted datasets exist already // - TODO: for archive jobs all datasetslifecycle should be in an "archiveable" state + // TODO ensure that job is created by user who has read access to all datasets in case of retrieve JOBS var Dataset = app.models.Dataset; // create array of all pids // console.log("Verifying datasets:",ctx.options) diff --git a/common/models/orig-datablock.js b/common/models/orig-datablock.js index fef6a976..8b4da21e 100644 --- a/common/models/orig-datablock.js +++ b/common/models/orig-datablock.js @@ -35,8 +35,8 @@ module.exports = function(Origdatablock) { // transfer size info to dataset Origdatablock.observe('after save', (ctx, next) => { var OrigDatablock = app.models.OrigDatablock + utils.createArchiveJob(app.models.UserIdentity, app.models.Policy, app.models.Job, ctx) utils.transferSizeToDataset(OrigDatablock, 'size', ctx, next) - }) Origdatablock.isValid = function(instance, next) { @@ -54,4 +54,4 @@ module.exports = function(Origdatablock) { } }); } -}; +} diff --git a/common/models/utils.js b/common/models/utils.js index e6885015..c51e622c 100644 --- a/common/models/utils.js +++ b/common/models/utils.js @@ -128,22 +128,47 @@ exports.createNewFacetPipeline = function(name, type, query) { const pipeline = []; if (type.constructor === Array) { - pipeline.push({ $unwind: '$'+name }); + pipeline.push({ + $unwind: '$' + name + }); } // add all conditions from "other" facets, exclude own conditions if (query && Object.keys(query).length > 0) { //console.log("createFacet query:",query); var q = Object.assign({}, query); delete q[name]; - if(Object.keys(q).length > 0) - pipeline.push({$match: q}); + if (Object.keys(q).length > 0) + pipeline.push({ + $match: q + }); } - let grp = {$group: {_id: '$' + name, count: {$sum: 1}}}; + let grp = { + $group: { + _id: '$' + name, + count: { + $sum: 1 + } + } + }; if (type === 'date') { - grp.$group._id = {year: {$year: '$' + name}, month: {$month: '$' + name}, day: {$dayOfMonth: '$' + name}} + grp.$group._id = { + year: { + $year: '$' + name + }, + month: { + $month: '$' + name + }, + day: { + $dayOfMonth: '$' + name + } + } } pipeline.push(grp); - const sort = {$sort: {_id: -1}}; + const sort = { + $sort: { + _id: -1 + } + }; pipeline.push(sort); return pipeline; } @@ -213,3 +238,78 @@ exports.handleOwnerGroups = function(ctx, next) { } }); } + +// TODO minimize number of parabers: +exports.createArchiveJob = function(UserIdentity, Policy, Job, ctx) { + var instance = ctx.instance + if (!instance) { + instance = ctx.currentInstance + } + console.log("Instance:", JSON.stringify(instance)) + + const token = ctx.options && ctx.options.accessToken; + const userId = token && token.userId; + + console.log("options, userid:", ctx.options, userId) + //const user = userId ? 'user#' + userId : ''; + UserIdentity.findOne({ + where: { + userId: userId + } + }, function(err, user) { + console.log("UserIdentity Instance:", user) + // TODO: get it from User models + // TODO get proper emails in case of unctional accounts + // TODO remove console.log messages + // TODO add test cases + // TODO add creationTime (should not be needed any more) + var email + var login + if (user && user.profile) { + login = user.profile.login + email = user.profile.email + } else { + login = Object.keys(ctx.options.authorizedRoles)[0] + email = login + } + console.log("Email:", email) // check if a normal user or an internal ROLE + Policy.findOne({ + where: { + ownerGroup: instance.ownerGroup + } + }, function(err2, policyInstance) { + // get policy values for the instance.ownerGroups + if (err2) { + console.log("Error when looking for Policy of pgroup ", instance.ownerGroup, err2) + } else { + var jobParams = {} + jobParams.username = login + if (policyInstance) { + jobParams.autoArchive = (autoArchive in policyInstance) ? policyInstance.autoArchive : false + jobParams.tapeCopies = (tapeCopies in policyInstance) ? policyInstance.tapeCopies : "one" + } else { + console.log("No policy settings found for ownerGroup", instance.ownerGroup) + console.log("Assuming default values") + jobParams.autoArchive = false + jobParams.tapeCopies = "one" + } + var body = { + emailJobInitiator: email, + type: "archive", + jobParams: jobParams, + datasetList: [{ + pid: instance.datasetId, + files: [] + }] + } + console.log("Job body:", body) + if (jobParams.autoArchive) { + Job.create(body, function(err, jobmodel) { + console.log("Created Job:", err, jobmodel) + }) + } + } + + }) + }) +}; From 0455c3701b72b2145f90bc75932504c4a4abc38e Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 27 Jun 2018 14:30:09 +0200 Subject: [PATCH 008/147] added additional properties to policy model --- common/models/policy.json | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/common/models/policy.json b/common/models/policy.json index a7dcba92..70513b29 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -8,7 +8,11 @@ "validateUpsert": true }, "properties": { - "availability": { + "manager": { + "type": "string", + "description": "Defines the users that can modify the policy parameters" + }, + "tapeRedundancy": { "type": "string", "description": "Defines the level of redundancy in storage to minimize loss of data. Allowed values are low, medium, high. Low could e.g. mean one tape copy only, medium could mean two tape copies and high two geo-redundant tape copies", "default": "low" @@ -22,6 +26,24 @@ "type": "number", "description": "Number of days after dataset creation that (remaining) datasets are archived automatically", "default": 7 + }, + "archiveEmailNotification": { + "type": "boolean", + "description": "Flag is true when an email notification should be sent to archiveEmailsToBeNotified upon an archive job creation", + "default": false + }, + "archiveEmailsToBeNotified": { + "type": "string", + "description": "Array of additional email addresses that should be notified up an archive job creation" + }, + "retrieveEmailNotification": { + "type": "boolean", + "description": "Flag is true when an email notification should be sent to retrieveEmailsToBeNotified upon a retrieval job creation", + "default": false + }, + "retrieveEmailsToBeNotified": { + "type": "string", + "description": "Array of additional email addresses that should be notified up a retrieval job creation" } }, "validations": [], From 837a42ae24987224087d2e5525d00538f86729b2 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 27 Jun 2018 15:11:12 +0200 Subject: [PATCH 009/147] added additional properties to policy model --- common/models/policy.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/common/models/policy.json b/common/models/policy.json index 70513b29..fe5d98a5 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -9,7 +9,7 @@ }, "properties": { "manager": { - "type": "string", + "type": "array", "description": "Defines the users that can modify the policy parameters" }, "tapeRedundancy": { @@ -33,7 +33,7 @@ "default": false }, "archiveEmailsToBeNotified": { - "type": "string", + "type": "array", "description": "Array of additional email addresses that should be notified up an archive job creation" }, "retrieveEmailNotification": { @@ -42,7 +42,7 @@ "default": false }, "retrieveEmailsToBeNotified": { - "type": "string", + "type": "array", "description": "Array of additional email addresses that should be notified up a retrieval job creation" } }, From a2415a06309ea95c86126ca109c605a41cc7dd08 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Thu, 28 Jun 2018 10:23:59 +0200 Subject: [PATCH 010/147] corrected loopback array syntax --- common/models/policy.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/common/models/policy.json b/common/models/policy.json index fe5d98a5..e8d8be79 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -9,7 +9,7 @@ }, "properties": { "manager": { - "type": "array", + "type": ["array"], "description": "Defines the users that can modify the policy parameters" }, "tapeRedundancy": { @@ -33,7 +33,7 @@ "default": false }, "archiveEmailsToBeNotified": { - "type": "array", + "type": ["array"], "description": "Array of additional email addresses that should be notified up an archive job creation" }, "retrieveEmailNotification": { @@ -42,7 +42,7 @@ "default": false }, "retrieveEmailsToBeNotified": { - "type": "array", + "type": ["array"], "description": "Array of additional email addresses that should be notified up a retrieval job creation" } }, From f057e96b578c87826c5efa02fcd7450fd4c34e2d Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Thu, 28 Jun 2018 10:24:37 +0200 Subject: [PATCH 011/147] corrected loopback array syntax again --- common/models/policy.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/common/models/policy.json b/common/models/policy.json index e8d8be79..8e9adf16 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -9,7 +9,7 @@ }, "properties": { "manager": { - "type": ["array"], + "type": ["string"], "description": "Defines the users that can modify the policy parameters" }, "tapeRedundancy": { @@ -33,7 +33,7 @@ "default": false }, "archiveEmailsToBeNotified": { - "type": ["array"], + "type": ["string"], "description": "Array of additional email addresses that should be notified up an archive job creation" }, "retrieveEmailNotification": { @@ -42,7 +42,7 @@ "default": false }, "retrieveEmailsToBeNotified": { - "type": ["array"], + "type": ["string"], "description": "Array of additional email addresses that should be notified up a retrieval job creation" } }, From a649064a3733522044bf9b7511e4e93fd0bbf4b1 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Fri, 6 Jul 2018 10:13:33 +0200 Subject: [PATCH 012/147] minor edit --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 21aa78dc..ff0087dd 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ -# Data Catalog Backend +# SciCat Data Catalog Backend + The data catalog backend is based on [NoSQL database MongoDB](https://www.mongodb.com/), [the Node based web application framework Express](http://expressjs.com/) and [the API framework Loopback](http://loopback.io/) technology stack (the "MEL" part of the "MELANIE" technology stack). It provides a REST based API which allows to store information about datasets and to allow to answer queries about the stored meta data for these datasets # Getting started From b52a001b64ee388e049967d33b0d8e39c9359f2f Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Fri, 6 Jul 2018 14:48:22 +0200 Subject: [PATCH 013/147] Update issue templates --- .github/ISSUE_TEMPLATE/issue-.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/issue-.md diff --git a/.github/ISSUE_TEMPLATE/issue-.md b/.github/ISSUE_TEMPLATE/issue-.md new file mode 100644 index 00000000..60f04d42 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/issue-.md @@ -0,0 +1,19 @@ +--- +name: 'Issue ' +about: Describe this issue purpose here. + +--- + +## Issue Name + +### Summary + +### Steps to Reproduce + +### Current Behaviour + +### Expected Behaviour + +### Extra Details + +Here you should include details about the system (if it is unique) and possible information about a fix (feel free to link to code where relevant). Screenshots/GIFs are also fine here. From 5734ce4c4856385859d5ce2f478830a9337c46b2 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 9 Jul 2018 11:36:48 +0200 Subject: [PATCH 014/147] work in progress, includes temp bug fix to be removed --- common/models/policy.js | 35 +++++++++++++++++++++++++++++++++++ common/models/policy.json | 9 ++++++++- 2 files changed, 43 insertions(+), 1 deletion(-) diff --git a/common/models/policy.js b/common/models/policy.js index 621ec5de..c7972527 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -3,3 +3,38 @@ module.exports = function(Policy) { }; + +//model extension file + +/*var config = require('../../server/config.local'); +var p = require('../../package.json'); +var utils = require('./utils'); +var dsl = require('./dataset-lifecycle.json'); +var ds = require('./dataset.json'); +var dsr = require('./raw-dataset.json'); +var dsd = require('./derived-dataset.json'); +var own = require('./ownable.json'); + +module.exports = function(Policy) { + var app = require('../../server/server'); + console.log("Log: policy.js 1!"); + + // check logged in user email is a member of policy.manager + Policy.observe('before save', (ctx, next) => { + console.log("I am her!!!!!!!!"); + if (ctx.instance) { + var email + var login + if (user && user.profile) { + login = user.profile.login + email = user.profile.email + } else { + login = Object.keys(ctx.options.authorizedRoles)[0] + email = login + } + + } + next(); + }); + }; +*/ diff --git a/common/models/policy.json b/common/models/policy.json index 8e9adf16..6f0382b8 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -48,6 +48,13 @@ }, "validations": [], "relations": {}, - "acls": [], + "acls": [ + { + "accessType": "*", + "principalType": "ROLE", + "principalId": "$authenticated", + "permission": "ALLOW" + } + ], "methods": {} } From ff4a1d0b673d013729cd768d09b2b268e484b6d9 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 16 Jul 2018 13:27:00 +0200 Subject: [PATCH 015/147] adding published data --- common/models/published-data.js | 20 +++++++++ common/models/published-data.json | 67 ++++++++++++++++++++++++++++ common/models/published-dataset.js | 20 +++++++++ common/models/published-dataset.json | 67 ++++++++++++++++++++++++++++ 4 files changed, 174 insertions(+) create mode 100644 common/models/published-data.js create mode 100644 common/models/published-data.json create mode 100644 common/models/published-dataset.js create mode 100644 common/models/published-dataset.json diff --git a/common/models/published-data.js b/common/models/published-data.js new file mode 100644 index 00000000..63def396 --- /dev/null +++ b/common/models/published-data.js @@ -0,0 +1,20 @@ +'use strict'; +var utils = require('./utils'); + +module.exports = function(PublishedData) { + + // put + PublishedData.beforeRemote('replaceOrCreate', function(ctx, instance, next) { + // convert base64 image + + next(); + }); + + //patch + PublishedData.beforeRemote('patchOrCreate', function(ctx, instance, next) { + next(); + }); + +} + + diff --git a/common/models/published-data.json b/common/models/published-data.json new file mode 100644 index 00000000..0d72c303 --- /dev/null +++ b/common/models/published-data.json @@ -0,0 +1,67 @@ +{ + "name": "PublishedData", + "idInjection": false, + "base": "PersistedModel", + "strict": false, + "options": { + "validateUpsert": true, + "mongodb": { + "collection": "PublishedData" + } + }, + "description": "Digital Object Identifier (DOI) mandatory fields, URL for making dataset metadata accessible online", + "properties": { + "doi": { + "type": "string", + "required": true, + "description": "Digitial Object Identifier", + "default": "retrieve" + }, + "affiliation": { + "type": "string", + "required": true, + "description": "Creator Affiliation", + "default": "retrieve" + }, + "creator": { + "type": "string", + "required": true, + "description": "Creator of dataset/dataset collection", + "default": "retrieve" + }, + "publisher": { + "type": "string", + "required": true, + "description": "Dataset publisher", + "default": "retrieve" + }, + "publicationYear": { + "type": "string", + "required": true, + "description": "YEar of publication ", + "default": "retrieve" + }, + "title": { + "type": "string", + "required": true, + "description": "Title", + "default": "retrieve" + }, + "creationTime": { + "type": "date", + "index": true, + "description": "Time when publication is created. Format according to chapter 5.6 internet date/time format in RFC 3339" + } + }, + "validations": [], + "relations": { + "dataset": { + "type": "belongsTo", + "model": "Dataset", + "foreignKey": "", + "required": true + } + }, + "acls": [], + "methods": {} +} diff --git a/common/models/published-dataset.js b/common/models/published-dataset.js new file mode 100644 index 00000000..91f22b94 --- /dev/null +++ b/common/models/published-dataset.js @@ -0,0 +1,20 @@ +'use strict'; +var utils = require('./utils'); + +module.exports = function(PublishedDataset) { + + // put + PublishedDataset.beforeRemote('replaceOrCreate', function(ctx, instance, next) { + // convert base64 image + + next(); + }); + + //patch + PublishedDataset.beforeRemote('patchOrCreate', function(ctx, instance, next) { + next(); + }); + +} + + diff --git a/common/models/published-dataset.json b/common/models/published-dataset.json new file mode 100644 index 00000000..4d2d39e3 --- /dev/null +++ b/common/models/published-dataset.json @@ -0,0 +1,67 @@ +{ + "name": "PublishedDataset", + "idInjection": false, + "base": "PersistedModel", + "strict": false, + "options": { + "validateUpsert": true, + "mongodb": { + "collection": "PublishedDataset" + } + }, + "description": "Digital Object Identifier (DOI) mandatory fields, URL for making dataset metadata accessible online", + "properties": { + "doi": { + "type": "string", + "required": true, + "description": "Digitial Object Identifier", + "default": "retrieve" + }, + "affiliation": { + "type": "string", + "required": true, + "description": "Creator Affiliation", + "default": "retrieve" + }, + "creator": { + "type": "string", + "required": true, + "description": "Creator of dataset/dataset collection", + "default": "retrieve" + }, + "publisher": { + "type": "string", + "required": true, + "description": "Dataset publisher", + "default": "retrieve" + }, + "publicationYear": { + "type": "string", + "required": true, + "description": "YEar of publication ", + "default": "retrieve" + }, + "title": { + "type": "string", + "required": true, + "description": "Title", + "default": "retrieve" + }, + "creationTime": { + "type": "date", + "index": true, + "description": "Time when publication is created. Format according to chapter 5.6 internet date/time format in RFC 3339" + } + }, + "validations": [], + "relations": { + "dataset": { + "type": "belongsTo", + "model": "Dataset", + "foreignKey": "", + "required": true + } + }, + "acls": [], + "methods": {} +} From 2f96a8cebb926b9a93e8d6728bc20b37efd14519 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 16 Jul 2018 13:28:58 +0200 Subject: [PATCH 016/147] deleting unneeded files --- common/models/published-dataset.js | 20 --------- common/models/published-dataset.json | 67 ---------------------------- 2 files changed, 87 deletions(-) delete mode 100644 common/models/published-dataset.js delete mode 100644 common/models/published-dataset.json diff --git a/common/models/published-dataset.js b/common/models/published-dataset.js deleted file mode 100644 index 91f22b94..00000000 --- a/common/models/published-dataset.js +++ /dev/null @@ -1,20 +0,0 @@ -'use strict'; -var utils = require('./utils'); - -module.exports = function(PublishedDataset) { - - // put - PublishedDataset.beforeRemote('replaceOrCreate', function(ctx, instance, next) { - // convert base64 image - - next(); - }); - - //patch - PublishedDataset.beforeRemote('patchOrCreate', function(ctx, instance, next) { - next(); - }); - -} - - diff --git a/common/models/published-dataset.json b/common/models/published-dataset.json deleted file mode 100644 index 4d2d39e3..00000000 --- a/common/models/published-dataset.json +++ /dev/null @@ -1,67 +0,0 @@ -{ - "name": "PublishedDataset", - "idInjection": false, - "base": "PersistedModel", - "strict": false, - "options": { - "validateUpsert": true, - "mongodb": { - "collection": "PublishedDataset" - } - }, - "description": "Digital Object Identifier (DOI) mandatory fields, URL for making dataset metadata accessible online", - "properties": { - "doi": { - "type": "string", - "required": true, - "description": "Digitial Object Identifier", - "default": "retrieve" - }, - "affiliation": { - "type": "string", - "required": true, - "description": "Creator Affiliation", - "default": "retrieve" - }, - "creator": { - "type": "string", - "required": true, - "description": "Creator of dataset/dataset collection", - "default": "retrieve" - }, - "publisher": { - "type": "string", - "required": true, - "description": "Dataset publisher", - "default": "retrieve" - }, - "publicationYear": { - "type": "string", - "required": true, - "description": "YEar of publication ", - "default": "retrieve" - }, - "title": { - "type": "string", - "required": true, - "description": "Title", - "default": "retrieve" - }, - "creationTime": { - "type": "date", - "index": true, - "description": "Time when publication is created. Format according to chapter 5.6 internet date/time format in RFC 3339" - } - }, - "validations": [], - "relations": { - "dataset": { - "type": "belongsTo", - "model": "Dataset", - "foreignKey": "", - "required": true - } - }, - "acls": [], - "methods": {} -} From 3d230e27f9282ac8d13a295d21f017020b73a43d Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 16 Jul 2018 13:43:08 +0200 Subject: [PATCH 017/147] adding fields from workflow discussion --- common/models/published-data.json | 16 ++++++++++++++++ server/model-config.json | 4 ++++ 2 files changed, 20 insertions(+) diff --git a/common/models/published-data.json b/common/models/published-data.json index 0d72c303..37f0e4b2 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -47,6 +47,22 @@ "description": "Title", "default": "retrieve" }, + "pidArray": { + "type": "string", + "required": true, + "description": "Array of one or more PIDS which make up the published data", + "default": "retrieve" + }, + "doiPostedSuccessfullyTime": { + "type": "date", + "index": true, + "description": "time when doi is successfully posted" + }, + "lastModificationTime": { + "type": "date", + "index": true, + "description": "time when last modified" + }, "creationTime": { "type": "date", "index": true, diff --git a/server/model-config.json b/server/model-config.json index 59e9b601..591888ea 100644 --- a/server/model-config.json +++ b/server/model-config.json @@ -55,6 +55,10 @@ "dataSource": "mongo", "public": true }, + "PublishedData": { + "dataSource": "mongo", + "public": true + }, "Datafile": { "dataSource": "transient", "public": false From b8648ab60938b0ee18573b0333460e40118b0b1f Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 16 Jul 2018 13:44:33 +0200 Subject: [PATCH 018/147] add array for PIDs --- common/models/published-data.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 37f0e4b2..aaa0295f 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -48,7 +48,7 @@ "default": "retrieve" }, "pidArray": { - "type": "string", + "type":[ "string"], "required": true, "description": "Array of one or more PIDS which make up the published data", "default": "retrieve" From 32b4542903bca41586d93a7831446ee71999b648 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 16 Jul 2018 13:49:06 +0200 Subject: [PATCH 019/147] update description --- common/models/published-data.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index aaa0295f..07ecb31a 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -9,7 +9,7 @@ "collection": "PublishedData" } }, - "description": "Digital Object Identifier (DOI) mandatory fields, URL for making dataset metadata accessible online", + "description": "Stores the meta data information for an accessible, published and DOI-identified collection of datasets. It defines a list of mandatory and optional metadata fields to be included. DataCite mandatory fields are included also a full URL and modification times ", "properties": { "doi": { "type": "string", From b5525b4c84701670029b06846c885e2ef428d76a Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 16 Jul 2018 13:49:58 +0200 Subject: [PATCH 020/147] update description --- common/models/published-data.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 07ecb31a..48694f9f 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -51,7 +51,7 @@ "type":[ "string"], "required": true, "description": "Array of one or more PIDS which make up the published data", - "default": "retrieve" + "default": ["retrieve"] }, "doiPostedSuccessfullyTime": { "type": "date", From 29306479bf8eae199a341fa0c130098dd269d258 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 16 Jul 2018 13:59:40 +0200 Subject: [PATCH 021/147] Adding published data model (see issue #34) --- common/models/published-data.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 48694f9f..89cb5312 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -9,7 +9,7 @@ "collection": "PublishedData" } }, - "description": "Stores the meta data information for an accessible, published and DOI-identified collection of datasets. It defines a list of mandatory and optional metadata fields to be included. DataCite mandatory fields are included also a full URL and modification times ", + "description": "Stores the meta data information for an accessible, published and DOI-identified collection of datasets. It defines a list of mandatory and optional metadata fields to be included. DataCite mandatory fields, a full URL and modification times are included.", "properties": { "doi": { "type": "string", From 4907257cddc282340db3cd29d8c8456f2ff944d9 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 16 Jul 2018 14:22:48 +0200 Subject: [PATCH 022/147] add owner array --- common/models/published-data.json | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 89cb5312..b01163bc 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -36,10 +36,10 @@ "default": "retrieve" }, "publicationYear": { - "type": "string", + "type": "number", "required": true, - "description": "YEar of publication ", - "default": "retrieve" + "description": "Year of publication ", + "default": "2018" }, "title": { "type": "string", @@ -53,6 +53,12 @@ "description": "Array of one or more PIDS which make up the published data", "default": ["retrieve"] }, + "owner": { + "type":[ "string"], + "required": true, + "description": "Array of one or more owners who can publish data", + "default": ["owner"] + }, "doiPostedSuccessfullyTime": { "type": "date", "index": true, From 8d0ba5c4b2e9d7c243255140cc9ff5837bc5613c Mon Sep 17 00:00:00 2001 From: egli Date: Wed, 18 Jul 2018 11:56:45 +0200 Subject: [PATCH 023/147] Solve issue #39, allow authenticated users to create ownable objects --- common/models/dataset.json | 6 -- common/models/ownable.json | 6 ++ common/models/utils.js | 2 +- test/LoginUtils.js | 14 ++++ test/SITES_PSI/Ownable.js | 144 +++++++++++++++++++++++++++++++++++++ 5 files changed, 165 insertions(+), 7 deletions(-) create mode 100644 test/SITES_PSI/Ownable.js diff --git a/common/models/dataset.json b/common/models/dataset.json index da469bc1..637fd515 100644 --- a/common/models/dataset.json +++ b/common/models/dataset.json @@ -168,12 +168,6 @@ "principalId": "ingestor", "permission": "ALLOW", "property": ["facet","fullquery","fullfacet"] - }, - { - "principalType": "ROLE", - "principalId": "$authenticated", - "permission": "ALLOW", - "property": ["create"] } ], "methods": { diff --git a/common/models/ownable.json b/common/models/ownable.json index 57ac00fe..ea0ba293 100644 --- a/common/models/ownable.json +++ b/common/models/ownable.json @@ -57,6 +57,12 @@ "principalId": "$everyone", "permission": "ALLOW", "property": "isValid" + }, + { + "principalType": "ROLE", + "principalId": "$authenticated", + "permission": "ALLOW", + "property": "create" } ], "methods": { diff --git a/common/models/utils.js b/common/models/utils.js index c51e622c..fd1d3781 100644 --- a/common/models/utils.js +++ b/common/models/utils.js @@ -239,7 +239,7 @@ exports.handleOwnerGroups = function(ctx, next) { }); } -// TODO minimize number of parabers: + exports.createArchiveJob = function(UserIdentity, Policy, Job, ctx) { var instance = ctx.instance if (!instance) { diff --git a/test/LoginUtils.js b/test/LoginUtils.js index c7ad6f71..8b6d8177 100644 --- a/test/LoginUtils.js +++ b/test/LoginUtils.js @@ -16,3 +16,17 @@ exports.getToken = function (app, user, cb) { } }); }; + +exports.getTokenAD = function (app, user, cb) { + request(app) + .post('/auth/msad') + .send(user) + .set('Accept', 'application/json') + .end((err, res) => { + if (err) { + cb(err) + } else { + cb(res.body.access_token); + } + }); +}; diff --git a/test/SITES_PSI/Ownable.js b/test/SITES_PSI/Ownable.js new file mode 100644 index 00000000..d1cbeac2 --- /dev/null +++ b/test/SITES_PSI/Ownable.js @@ -0,0 +1,144 @@ +/* jshint node:true */ +/* jshint esversion:6 */ +'use strict'; + +// process.env.NODE_ENV = 'test'; +var config = require('../config/settings') +var chai = require('chai'); +var chaiHttp = require('chai-http'); +var request = require('supertest'); +var app = require('../../server/server'); +var should = chai.should(); +var utils = require('../LoginUtils'); + +var accessToken = null, + pid = null; + +var testraw = { + "principalInvestigator": "bertram.astor@grumble.com", + "endTime": "2011-09-14T06:31:25.000Z", + "creationLocation": "/SU/XQX/RAMJET", + "dataFormat": "Upchuck pre 2017", + "scientificMetadata": { + "beamlineParameters": { + "Monostripe": "Ru/C", + "Ring current": { + "v": 0.402246, + "u": "A" + }, + "Beam energy": { + "v": 22595, + "u": "eV" + } + }, + "detectorParameters": { + "Objective": 20, + "Scintillator": "LAG 20um", + "Exposure time": { + "v": 0.4, + "u": "s" + } + }, + "scanParameters": { + "Number of projections": 1801, + "Rot Y min position": { + "v": 0, + "u": "deg" + }, + "Inner scan flag": 0, + "File Prefix": "817b_B2_", + "Sample In": { + "v": 0, + "u": "m" + }, + "Sample folder": "/ramjet/817b_B2_", + "Number of darks": 10, + "Rot Y max position": { + "v": 180, + "u": "deg" + }, + "Angular step": { + "v": 0.1, + "u": "deg" + }, + "Number of flats": 120, + "Sample Out": { + "v": -0.005, + "u": "m" + }, + "Flat frequency": 0, + "Number of inter-flats": 0 + } + }, + "owner": "Bertram Astor", + "ownerEmail": "bertram.astor@grumble.com", + "orcidOfOwner": "unknown", + "contactEmail": "bertram.astor@grumble.com", + "sourceFolder": "/iramjet/tif/", + "size": 0, + "creationTime": "2011-09-14T06:08:25.000Z", + "description": "None", + "doi": "not yet defined", + "isPublished": false, + "ownerGroup": "p10021", + "accessGroups": [], + "proposalId": "10.540.16635/20110123" +} + + +describe('TestCreation', () => { + before((done) => { + utils.getTokenAD(app, { + 'username': config.users.user.username, + 'password': config.users.user.password + }, + (tokenVal) => { + accessToken = tokenVal; + done(); + }); + }); + it('adds a new raw dataset', function(done) { + request(app) + .post('/api/v2/RawDatasets?access_token=' + accessToken) + .send(testraw) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + res.body.should.have.property('owner').and.be.string; + res.body.should.have.property('type').and.equal('raw'); + res.body.should.have.property('pid').and.be.string; + pid = encodeURIComponent(res.body['pid']); + done(); + }); + }); + + + it('should fetch this raw dataset', function(done) { + request(app) + .get('/api/v2/RawDatasets/' + pid + '?access_token=' + accessToken) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + it('should not delete this raw dataset', function(done) { + request(app) + .delete('/api/v2/RawDatasets/' + pid + '?access_token=' + accessToken) + .set('Accept', 'application/json') + .expect(401) + .expect('Content-Type', /json/) + .end((err, res) => { + res.body.should.have.property('error'); + done(); + }); + }); + +}); From 5cd3dc1327c66f29ab421052c30af86834534719 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 18 Jul 2018 15:14:26 +0200 Subject: [PATCH 024/147] Issue #41 work in progress --- common/models/policy.js | 61 ++++++++++++++++++++++------------------- 1 file changed, 33 insertions(+), 28 deletions(-) diff --git a/common/models/policy.js b/common/models/policy.js index c7972527..3ab1a585 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -1,40 +1,45 @@ 'use strict'; -module.exports = function(Policy) { - -}; - //model extension file -/*var config = require('../../server/config.local'); +var config = require('../../server/config.local'); var p = require('../../package.json'); var utils = require('./utils'); -var dsl = require('./dataset-lifecycle.json'); -var ds = require('./dataset.json'); -var dsr = require('./raw-dataset.json'); -var dsd = require('./derived-dataset.json'); var own = require('./ownable.json'); module.exports = function(Policy) { - var app = require('../../server/server'); - console.log("Log: policy.js 1!"); + var app = require('../../server/server'); - // check logged in user email is a member of policy.manager - Policy.observe('before save', (ctx, next) => { - console.log("I am her!!!!!!!!"); - if (ctx.instance) { - var email - var login - if (user && user.profile) { - login = user.profile.login - email = user.profile.email - } else { - login = Object.keys(ctx.options.authorizedRoles)[0] - email = login - } + // for policy interactions + // check logged in user email is a member of policy.manager + Policy.observe('before save', (ctx, next) => { - } + if (ctx.currentInstance) { + //is a partial update currentInstance rather than instance + var UserIdentity = app.models.UserIdentity; + var userId = ctx.options.accessToken.userId; + + //PersistedModel Static Method call + UserIdentity.findOne({ + //json filter + where: { + userId: userId + } + }, function(err, instance) { + var email = instance.profile.email; + //console.log("email:", email); + //console.log("manager: ", ctx.currentInstance.manager); + if (!ctx.currentInstance.manager.includes(email)) { + var e = new Error('Access Not Allowed - policy manager action'); + e.statusCode = 401; + next(e); + } + else next(); + }); + } else { + //is an full update/insert/delete + //should only be proposalingestor next(); - }); - }; -*/ + } + }); +}; From 011bf357fee96074d048bc325b2cd42f904f02a8 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Thu, 19 Jul 2018 12:05:27 +0200 Subject: [PATCH 025/147] Issue #41 added test for policy model --- test/Policy.js | 96 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 test/Policy.js diff --git a/test/Policy.js b/test/Policy.js new file mode 100644 index 00000000..76bb1539 --- /dev/null +++ b/test/Policy.js @@ -0,0 +1,96 @@ +/* jshint node:true */ +/* jshint esversion:6 */ +'use strict'; + +// process.env.NODE_ENV = 'test'; + +var chai = require('chai'); +var chaiHttp = require('chai-http'); +var request = require('supertest'); +var app = require('../server/server'); +var should = chai.should(); +var utils = require('./LoginUtils'); + +var accessToken = null, + id = null; + +var testdataset = { + "manager": [ + "stephan.egli@psi.ch" + ], + "tapeRedundancy": "low", + "tapeRetentionTime": 3, + "autoArchiveDelay": 7, + "archiveEmailNotification": false, + "archiveEmailsToBeNotified": [ + "none" + ], + "retrieveEmailNotification": false, + "retrieveEmailsToBeNotified": [ + "none" + ], + "ownerGroup": "p10021", + "accessGroups": [ + "none" + ] +} + + + +describe('Simple Policy tests', () => { + before((done) => { + utils.getToken(app, { + 'username': 'ingestor', + 'password': 'aman' + }, + (tokenVal) => { + accessToken = tokenVal; + done(); + }); + }); + + it('adds a new policy', function(done) { + request(app) + .post('/api/v2/Policies?access_token=' + accessToken) + .send(testdataset) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + res.body.should.have.property('manager').and.be.string; + res.body.should.have.property('ownerGroup').and.be.string; + id = encodeURIComponent(res.body['id']); + done(); + }); + }); + + it('should fetch this new policy', function(done) { + request(app) + .get('/api/v2/Policies/' + id + '?access_token=' + accessToken) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + it('should delete this policy', function(done) { + request(app) + .delete('/api/v2/Policies/' + id + '?access_token=' + accessToken) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + +}); From 888ed0e01c0b3eb7546941ded6c1fd0aa6b5bec5 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Thu, 19 Jul 2018 14:41:47 +0200 Subject: [PATCH 026/147] Issue #41 added additional field to policy --- common/models/policy.json | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/common/models/policy.json b/common/models/policy.json index 6f0382b8..6541c8e2 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -10,17 +10,16 @@ "properties": { "manager": { "type": ["string"], - "description": "Defines the users that can modify the policy parameters" + "description": "Defines the emails of users that can modify the policy parameters" }, "tapeRedundancy": { "type": "string", "description": "Defines the level of redundancy in storage to minimize loss of data. Allowed values are low, medium, high. Low could e.g. mean one tape copy only, medium could mean two tape copies and high two geo-redundant tape copies", "default": "low" }, - "tapeRetentionTime": { - "type": "number", - "description": "Number of years after creation time, where datasets are subject to retention policies, possibly leading to deletion of data on tape.", - "default": 10 + "autoArchive": { + "type": "boolean", + "description": "automatically archive dataset" }, "autoArchiveDelay": { "type": "number", From 91f067ed12376bb893481437f9f01386f321167f Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 19 Jul 2018 15:17:35 +0200 Subject: [PATCH 027/147] changing owner to author --- common/models/published-data.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index b01163bc..15f2ffec 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -53,7 +53,7 @@ "description": "Array of one or more PIDS which make up the published data", "default": ["retrieve"] }, - "owner": { + "author": { "type":[ "string"], "required": true, "description": "Array of one or more owners who can publish data", From 6c5a39a9d124d07464c26fdc9d57045a7ddb6d8d Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 19 Jul 2018 15:21:03 +0200 Subject: [PATCH 028/147] changing posted->registered and removing defaults (Issue #34) --- common/models/published-data.json | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 15f2ffec..2e589090 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -14,26 +14,22 @@ "doi": { "type": "string", "required": true, - "description": "Digitial Object Identifier", - "default": "retrieve" + "description": "Digitial Object Identifier" }, "affiliation": { "type": "string", "required": true, - "description": "Creator Affiliation", - "default": "retrieve" + "description": "Creator Affiliation" }, "creator": { "type": "string", "required": true, - "description": "Creator of dataset/dataset collection", - "default": "retrieve" + "description": "Creator of dataset/dataset collection" }, "publisher": { "type": "string", "required": true, - "description": "Dataset publisher", - "default": "retrieve" + "description": "Dataset publisher" }, "publicationYear": { "type": "number", @@ -44,8 +40,12 @@ "title": { "type": "string", "required": true, - "description": "Title", - "default": "retrieve" + "description": "Title" + }, + "url": { + "type": "string", + "required": true, + "description": "Full local URL" }, "pidArray": { "type":[ "string"], @@ -59,7 +59,7 @@ "description": "Array of one or more owners who can publish data", "default": ["owner"] }, - "doiPostedSuccessfullyTime": { + "doiRegisteredSuccessfullyTime": { "type": "date", "index": true, "description": "time when doi is successfully posted" From 5c75b3d5a6a56f8353ec97339587b7d9c12fd7ad Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 19 Jul 2018 15:23:55 +0200 Subject: [PATCH 029/147] removing created/updated fields as they will be populated by mixins (See #Issue 34) --- common/models/published-data.json | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 2e589090..b78ba8fe 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -63,16 +63,6 @@ "type": "date", "index": true, "description": "time when doi is successfully posted" - }, - "lastModificationTime": { - "type": "date", - "index": true, - "description": "time when last modified" - }, - "creationTime": { - "type": "date", - "index": true, - "description": "Time when publication is created. Format according to chapter 5.6 internet date/time format in RFC 3339" } }, "validations": [], From 98c4364f66b62a67463b49d73a2e6ef15d7a17a4 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 9 Aug 2018 14:09:30 +0200 Subject: [PATCH 030/147] Some suggested changes to the new data model --- common/models/published-data.js | 26 +++++++++++++------------- common/models/published-data.json | 23 +++++++---------------- 2 files changed, 20 insertions(+), 29 deletions(-) diff --git a/common/models/published-data.js b/common/models/published-data.js index 63def396..57adff64 100644 --- a/common/models/published-data.js +++ b/common/models/published-data.js @@ -1,20 +1,20 @@ 'use strict'; -var utils = require('./utils'); +// var utils = require('./utils'); module.exports = function(PublishedData) { - // put - PublishedData.beforeRemote('replaceOrCreate', function(ctx, instance, next) { - // convert base64 image - - next(); - }); + // TODO add logic that give authors privileges to modify data - //patch - PublishedData.beforeRemote('patchOrCreate', function(ctx, instance, next) { - next(); - }); + // // put + // PublishedData.beforeRemote('replaceOrCreate', function(ctx, instance, next) { + // // convert base64 image + // + // next(); + // }); + // + // //patch + // PublishedData.beforeRemote('patchOrCreate', function(ctx, instance, next) { + // next(); + // }); } - - diff --git a/common/models/published-data.json b/common/models/published-data.json index b78ba8fe..44dbcd2c 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -9,7 +9,7 @@ "collection": "PublishedData" } }, - "description": "Stores the meta data information for an accessible, published and DOI-identified collection of datasets. It defines a list of mandatory and optional metadata fields to be included. DataCite mandatory fields, a full URL and modification times are included.", + "description": "Stores the meta data information for an accessible, published and DOI-identified collection of datasets. It defines a list of mandatory and optional metadata fields to be included. DataCite mandatory fields, a full URL to the landing page and modification times are included.", "properties": { "doi": { "type": "string", @@ -34,8 +34,7 @@ "publicationYear": { "type": "number", "required": true, - "description": "Year of publication ", - "default": "2018" + "description": "Year of publication " }, "title": { "type": "string", @@ -45,7 +44,7 @@ "url": { "type": "string", "required": true, - "description": "Full local URL" + "description": "Full URL to the landing page for this DOI" }, "pidArray": { "type":[ "string"], @@ -53,27 +52,19 @@ "description": "Array of one or more PIDS which make up the published data", "default": ["retrieve"] }, - "author": { + "authors": { "type":[ "string"], "required": true, - "description": "Array of one or more owners who can publish data", - "default": ["owner"] + "description": "Array of one or more persons who are able to update this entry of published data" }, "doiRegisteredSuccessfullyTime": { "type": "date", "index": true, - "description": "time when doi is successfully posted" + "description": "Time when doi is successfully registered" } }, "validations": [], - "relations": { - "dataset": { - "type": "belongsTo", - "model": "Dataset", - "foreignKey": "", - "required": true - } - }, + "relations": {}, "acls": [], "methods": {} } From 11c1e5037526cc5f7e3a2a87af4eca9c529ec84d Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 9 Aug 2018 14:11:26 +0200 Subject: [PATCH 031/147] Removed one dafault value --- common/models/published-data.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 44dbcd2c..3548d49e 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -49,8 +49,7 @@ "pidArray": { "type":[ "string"], "required": true, - "description": "Array of one or more PIDS which make up the published data", - "default": ["retrieve"] + "description": "Array of one or more PIDS which make up the published data" }, "authors": { "type":[ "string"], From e299f905639edbf1a082a309ca781c8430f6c3d9 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 13 Aug 2018 17:04:29 +0200 Subject: [PATCH 032/147] Issue #41 added autoArchive to model --- common/models/policy.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/common/models/policy.json b/common/models/policy.json index 6f0382b8..deaf329e 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -22,6 +22,11 @@ "description": "Number of years after creation time, where datasets are subject to retention policies, possibly leading to deletion of data on tape.", "default": 10 }, + "autoArchive": { + "type": "boolean", + "description": "Flag to indicate that a dataset should be automatically archived after ingest. If false then archive delay is ignored", + "default": true + }, "autoArchiveDelay": { "type": "number", "description": "Number of days after dataset creation that (remaining) datasets are archived automatically", From 1352558cb7dabf5989174419c79659ea94de5364 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Thu, 16 Aug 2018 17:24:15 +0200 Subject: [PATCH 033/147] Issue 41 modified test --- test/Policy.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/Policy.js b/test/Policy.js index 76bb1539..38c32e42 100644 --- a/test/Policy.js +++ b/test/Policy.js @@ -19,7 +19,7 @@ var testdataset = { "stephan.egli@psi.ch" ], "tapeRedundancy": "low", - "tapeRetentionTime": 3, + //"tapeRetentionTime": 3, "autoArchiveDelay": 7, "archiveEmailNotification": false, "archiveEmailsToBeNotified": [ From 95dc89abb19796aadcc660337c174c96267f7324 Mon Sep 17 00:00:00 2001 From: "greenkeeper[bot]" Date: Fri, 17 Aug 2018 19:05:20 +0000 Subject: [PATCH 034/147] chore(package): update dependencies --- package.json | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/package.json b/package.json index 490a8f22..ecdc16e6 100644 --- a/package.json +++ b/package.json @@ -16,11 +16,11 @@ "cors": "^2.5.2", "helmet": "^3.10.0", "loopback-boot": "^2.6.5", - "serve-favicon": "2.4.5", - "strong-error-handler": "2.3.0", + "serve-favicon": "2.5.0", + "strong-error-handler": "3.1.0", "loopback-component-explorer": "^6.0.0", "loopback": "^3.19.0", - "loopback-component-model-diagram": "^0.3.0", + "loopback-component-model-diagram": "^0.4.2", "loopback-component-mq": "^2.2.5", "loopback-component-passport": "^3.4.1", "loopback-component-visualizer": "^1.2.1", @@ -36,13 +36,13 @@ "uuid": "^3.2.1" }, "devDependencies": { - "eslint": "^3.17.1", - "eslint-config-loopback": "^8.0.0", - "nsp": "^2.1.0", + "eslint": "^5.3.0", + "eslint-config-loopback": "^11.0.0", + "nsp": "^3.2.1", "@mean-expert/loopback-sdk-builder": "^2.1.0", "chai": "^4.1.2", - "chai-http": "^3.0.0", - "mocha": "^4.1.0", + "chai-http": "^4.0.0", + "mocha": "^5.2.0", "supertest": "^3.0.0" }, "repository": { From ee380666aafc2c608dd8f9393684224e70998162 Mon Sep 17 00:00:00 2001 From: "greenkeeper[bot]" Date: Fri, 17 Aug 2018 19:05:22 +0000 Subject: [PATCH 035/147] docs(readme): add Greenkeeper badge --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index ff0087dd..646db569 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # SciCat Data Catalog Backend +[![Greenkeeper badge](https://badges.greenkeeper.io/SciCatProject/catamel.svg)](https://greenkeeper.io/) + The data catalog backend is based on [NoSQL database MongoDB](https://www.mongodb.com/), [the Node based web application framework Express](http://expressjs.com/) and [the API framework Loopback](http://loopback.io/) technology stack (the "MEL" part of the "MELANIE" technology stack). It provides a REST based API which allows to store information about datasets and to allow to answer queries about the stored meta data for these datasets # Getting started From 7eedfa5857c516d044c4f3a435298b78d8bc88d5 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Fri, 17 Aug 2018 21:30:46 +0200 Subject: [PATCH 036/147] Update package.json --- package.json | 1 - 1 file changed, 1 deletion(-) diff --git a/package.json b/package.json index ecdc16e6..5b67488d 100644 --- a/package.json +++ b/package.json @@ -38,7 +38,6 @@ "devDependencies": { "eslint": "^5.3.0", "eslint-config-loopback": "^11.0.0", - "nsp": "^3.2.1", "@mean-expert/loopback-sdk-builder": "^2.1.0", "chai": "^4.1.2", "chai-http": "^4.0.0", From b631dee2d0f29d5591ef3f3bbd134f22a0f7227c Mon Sep 17 00:00:00 2001 From: egli Date: Wed, 22 Aug 2018 09:23:00 +0200 Subject: [PATCH 037/147] Disable functionality which is still WIP and was committed to develop erroneously on June 27th --- common/models/orig-datablock.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/orig-datablock.js b/common/models/orig-datablock.js index 8b4da21e..9696a035 100644 --- a/common/models/orig-datablock.js +++ b/common/models/orig-datablock.js @@ -35,7 +35,7 @@ module.exports = function(Origdatablock) { // transfer size info to dataset Origdatablock.observe('after save', (ctx, next) => { var OrigDatablock = app.models.OrigDatablock - utils.createArchiveJob(app.models.UserIdentity, app.models.Policy, app.models.Job, ctx) + // not yet ready utils.createArchiveJob(app.models.UserIdentity, app.models.Policy, app.models.Job, ctx) utils.transferSizeToDataset(OrigDatablock, 'size', ctx, next) }) From 519a95cccd055a5248a24d021262e9d2f57c225b Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Fri, 24 Aug 2018 10:23:05 +0200 Subject: [PATCH 038/147] published data now accessible without login --- common/models/published-data.json | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 3548d49e..ad03865a 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -64,6 +64,13 @@ }, "validations": [], "relations": {}, - "acls": [], + "acls": [ + { + "accessType": "READ", + "principalType": "ROLE", + "principalId": "$unauthenticated", + "permission": "ALLOW" + } + ], "methods": {} } From a1f25c6332cb1764125e415fadec1d1c24c3bdc1 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Fri, 24 Aug 2018 10:42:49 +0200 Subject: [PATCH 039/147] adding access control to published data model (see Issue #47) --- common/models/published-data.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index ad03865a..995a6245 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -68,7 +68,7 @@ { "accessType": "READ", "principalType": "ROLE", - "principalId": "$unauthenticated", + "principalId": "$everyone", "permission": "ALLOW" } ], From a7df693844af4c87c3f657c6ffd6a56736482344 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Fri, 24 Aug 2018 10:46:11 +0200 Subject: [PATCH 040/147] Create PULL_REQUEST_TEMPLATE.md --- PULL_REQUEST_TEMPLATE.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 PULL_REQUEST_TEMPLATE.md diff --git a/PULL_REQUEST_TEMPLATE.md b/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 00000000..c20589b1 --- /dev/null +++ b/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,23 @@ +## Description + +## Motivation + +Link to any open issues here + +## Fixes: + +* +* + +## Changes: + +* +* + +## Tests included/Docs Updated? + +- [ ] Included for each change/fix? +- [ ] Passing? (Merge will not be approved unless this is checked) +- [ ] Docs updated? + +## Extra Information/Screenshots From 5be730ecaa8fd2c6ccf05fa2931453412a1a03de Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 27 Aug 2018 06:42:56 +0200 Subject: [PATCH 041/147] add extra fields to published data --- common/models/published-data.json | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/common/models/published-data.json b/common/models/published-data.json index 995a6245..65d071e3 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -46,6 +46,22 @@ "required": true, "description": "Full URL to the landing page for this DOI" }, + "resourceType": { + "type": "string", + "required": true, + "description": "Type of files, format etc" + }, + "numberOfFiles": { + "type": "number", + "required": true, + "description": "Number of files" + }, + "sizeOfArchive": { + "type": "number", + "required": true, + "description": "Number of files" + }, + "pidArray": { "pidArray": { "type":[ "string"], "required": true, From c814849600780c38f9c9fd7d6509bc62316e6c4a Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 27 Aug 2018 11:44:14 +0200 Subject: [PATCH 042/147] add extra fields to publsihed data (See issue #50) --- common/models/published-data.json | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 65d071e3..3175ea57 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -46,6 +46,11 @@ "required": true, "description": "Full URL to the landing page for this DOI" }, + "abstract": { + "type": "string", + "required": true, + "description": "Abstract text for published datasets" + }, "resourceType": { "type": "string", "required": true, @@ -61,7 +66,6 @@ "required": true, "description": "Number of files" }, - "pidArray": { "pidArray": { "type":[ "string"], "required": true, From 8897b5b01e95f277eb74f4cff50dc9afb3cbe878 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 27 Aug 2018 11:49:36 +0200 Subject: [PATCH 043/147] move mongodb for travis tests --- docker-compose.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yaml b/docker-compose.yaml index 2891a0c0..c70d57bd 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -7,7 +7,7 @@ services: ports: - "27017:27017" volumes: - - './mongodb:/bitnami' + - 'mongodb_data:/bitnami' catamel: From 70107d7c14c778822093d52861884be098c67855 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 27 Aug 2018 14:49:15 +0200 Subject: [PATCH 044/147] make doi field key --- common/models/published-data.json | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/common/models/published-data.json b/common/models/published-data.json index 3175ea57..7c6a9647 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -13,8 +13,9 @@ "properties": { "doi": { "type": "string", - "required": true, - "description": "Digitial Object Identifier" + "id": true, + "description": "Digital Object Identifier", + "defaultFn": "uuidv4" }, "affiliation": { "type": "string", @@ -64,7 +65,7 @@ "sizeOfArchive": { "type": "number", "required": true, - "description": "Number of files" + "description": "Size of archive" }, "pidArray": { "type":[ "string"], From f268adb9041df77838450382083abc81894789c7 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Tue, 28 Aug 2018 13:54:55 +0200 Subject: [PATCH 045/147] add thumbnail image --- common/models/published-data.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/common/models/published-data.json b/common/models/published-data.json index 7c6a9647..ef5d0714 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -52,6 +52,11 @@ "required": true, "description": "Abstract text for published datasets" }, + "thumbnail": { + "type": "string", + "required": true, + "description": "Small, less than 16 MB base 64 image preview of dataset" + }, "resourceType": { "type": "string", "required": true, From 1c5ff72178eda3a33ce8fb19965a9c6cbe0a31c4 Mon Sep 17 00:00:00 2001 From: "greenkeeper[bot]" Date: Wed, 29 Aug 2018 20:03:09 +0000 Subject: [PATCH 046/147] chore(package): update eslint-config-loopback to version 12.0.0 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 5b67488d..7e9ab273 100644 --- a/package.json +++ b/package.json @@ -37,7 +37,7 @@ }, "devDependencies": { "eslint": "^5.3.0", - "eslint-config-loopback": "^11.0.0", + "eslint-config-loopback": "^12.0.0", "@mean-expert/loopback-sdk-builder": "^2.1.0", "chai": "^4.1.2", "chai-http": "^4.0.0", From a79c966b54dfa4b958c0920b5d4d480dc3cacdca Mon Sep 17 00:00:00 2001 From: "greenkeeper[bot]" Date: Thu, 30 Aug 2018 17:58:38 +0000 Subject: [PATCH 047/147] fix(package): update strong-error-handler to version 3.2.0 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 5b67488d..22749588 100644 --- a/package.json +++ b/package.json @@ -17,7 +17,7 @@ "helmet": "^3.10.0", "loopback-boot": "^2.6.5", "serve-favicon": "2.5.0", - "strong-error-handler": "3.1.0", + "strong-error-handler": "3.2.0", "loopback-component-explorer": "^6.0.0", "loopback": "^3.19.0", "loopback-component-model-diagram": "^0.4.2", From dc0a520d0ee2a41880d33313210db063ef24616d Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 6 Sep 2018 16:25:38 +0200 Subject: [PATCH 048/147] Initial commit of changes, not yet complete --- common/models/dataset-lifecycle.json | 286 ++++++++++--------- common/models/job.js | 31 +- common/models/job.json | 27 +- common/models/message.js | 5 + common/models/message.json | 49 ++++ package.json | 100 ++++--- server/model-config.json | 236 +++++++-------- test/Job.js | 413 +++++++++++++++++++++++++++ 8 files changed, 831 insertions(+), 316 deletions(-) create mode 100644 common/models/message.js create mode 100644 common/models/message.json create mode 100644 test/Job.js diff --git a/common/models/dataset-lifecycle.json b/common/models/dataset-lifecycle.json index 42022be1..c035f470 100644 --- a/common/models/dataset-lifecycle.json +++ b/common/models/dataset-lifecycle.json @@ -1,146 +1,156 @@ { - "name": "DatasetLifecycle", - "description":"For each dataset there exists exactly one dataset lifecycle document which describes the current status of the dataset during its lifetime with respect to the storage handling systems", - "base": "Ownable", - "idInjection": false, - "strict": true, - "indexes": { - "datasetId_index": { - "keys": { - "datasetId": 1 - } - } - }, - "options": { - "validateUpsert": true - }, - "replaceOnPUT": false, - "mixins": { - "TimeStamp": { - "createdAt": "createdAt", - "updatedAt": "updatedAt", - "required": false, - "validateUpsert": true, - "silenceWarnings": false - } - }, - "properties": { - "id": { - "type": "string", - "id": true, - "required": true, - "description": "ID of status information. This must be the ID of the associated dataset" - }, - "isOnDisk": { - "type": "boolean", - "description": "Flag which is true, if full dataset is available on disk. Warning: will be obsoleted in coming versions" - }, - "isOnTape": { - "type": "boolean", - "description": "Flag which is true, if full dataset has been stored to tape. Warning: will be obsoleted in coming versions" - }, - "archivable": { - "type": "boolean", - "description": "Flag which is true, if dataset is available to be archived and no archive job for this dataset exists yet" - }, - "retrievable": { - "type": "boolean", - "description": "Flag which is true, if dataset is stored on archive system and is ready to be retrieved" - }, - "archiveStatusMessage": { - "type": "string", - "description": "Current status of Dataset with respect to storage on disk/tape" - }, - "retrieveStatusMessage": { - "type": "string", - "description": "Latest message for this dataset concerning retrieve from archive system" - }, - "lastUpdateMessage": { - "type": "string", - "description": "Latest status update / transition message for this dataset" - }, - "archiveReturnMessage": { - "type": "string", - "description": "Detailed status or error message returned by archive system when treating this dataset" - }, - "dateOfLastMessage": { - "type": "date", - "description": "Time when last status message was sent. Format according to chapter 5.6 internet date/time format in RFC 3339. This will be filled automatically if not provided. Local times without timezone/offset info are automatically transformed to UTC using the timezone of the API server" - }, - "dateOfDiskPurging": { - "type": "date", - "description": "Day when dataset will be removed from disk, assuming that is already stored on tape." - }, - "archiveRetentionTime": { - "type": "date", - "description": "Day when the dataset's future fate will be evaluated again, e.g. to decide if the dataset can be deleted from archive." - }, - "isExported": { - "type": "boolean", - "description": "Flag is true if data was exported to another location" - }, - "exportedTo": { - "type": "string", - "description": "Location of the export destination" + "name": "DatasetLifecycle", + "description": "For each dataset there exists exactly one dataset lifecycle document which describes the current status of the dataset during its lifetime with respect to the storage handling systems", + "base": "Ownable", + "idInjection": false, + "strict": true, + "indexes": { + "datasetId_index": { + "keys": { + "datasetId": 1 + } + } }, - "dateOfPublishing": { - "type": "date", - "description": "Day when dataset is supposed to become public according to data policy" - } - }, - "validations": [], - "relations": { - "dataset": { - "type": "belongsTo", - "model": "Dataset", - "foreignKey": "", - "required": true - } - }, - "acls": [ - { - "accessType": "*", - "principalType": "ROLE", - "principalId": "$everyone", - "permission": "DENY" + "options": { + "validateUpsert": true + }, + "replaceOnPUT": false, + "mixins": { + "TimeStamp": { + "createdAt": "createdAt", + "updatedAt": "updatedAt", + "required": false, + "validateUpsert": true, + "silenceWarnings": false + } }, - { - "accessType": "*", - "principalType": "ROLE", - "principalId": "admin", - "permission": "ALLOW" + "properties": { + "id": { + "type": "string", + "id": true, + "required": true, + "description": "ID of status information. This must be the ID of the associated dataset" + }, + "archivable": { + "type": "boolean", + "description": "Flag which is true, if dataset is available to be archived and no archive job for this dataset exists yet" + }, + "retrievable": { + "type": "boolean", + "description": "Flag which is true, if dataset is stored on archive system and is ready to be retrieved" + }, + "dateOfDiskPurging": { + "type": "date", + "description": "Day when dataset will be removed from disk, assuming that is already stored on tape." + }, + "archiveRetentionTime": { + "type": "date", + "description": "Day when the dataset's future fate will be evaluated again, e.g. to decide if the dataset can be deleted from archive." + }, + "dateOfPublishing": { + "type": "date", + "description": "Day when dataset is supposed to become public according to data policy" + }, + "isOnDisk": { + "type": "boolean", + "description": "Flag which is true, if full dataset is available on disk. Warning: will be obsoleted in coming versions" + }, + "isOnTape": { + "type": "boolean", + "description": "Flag which is true, if full dataset has been stored to tape. Warning: will be obsoleted in coming versions" + }, + "archiveStatusMessage": { + "type": "string", + "description": "Current status of Dataset with respect to storage on disk/tape. Warning: will be obsoleted in coming versions" + }, + "retrieveStatusMessage": { + "type": "string", + "description": "Latest message for this dataset concerning retrieve from archive system. Warning: will be obsoleted in coming versions" + }, + "lastUpdateMessage": { + "type": "string", + "description": "Latest status update / transition message for this dataset. Warning: will be obsoleted in coming versions" + }, + "archiveReturnMessage": { + "type": "string", + "description": "Detailed status or error message returned by archive system when treating this dataset. Warning: will be obsoleted in coming versions" + }, + "dateOfLastMessage": { + "type": "date", + "description": "Time when last status message was sent. Format according to chapter 5.6 internet date/time format in RFC 3339. This will be filled automatically if not provided. Local times without timezone/offset info are automatically transformed to UTC using the timezone of the API server. Warning: will be obsoleted in coming versions" + }, + "isExported": { + "type": "boolean", + "description": "Flag is true if data was exported to another location. Warning: will be obsoleted in coming versions" + }, + "exportedTo": { + "type": "string", + "description": "Location of the export destination. Warning: will be obsoleted in coming versions" + } }, - { - "accessType": "*", - "principalType": "ROLE", - "principalId": "ingestor", - "permission": "ALLOW" + "validations": [], + "relations": { + "dataset": { + "type": "belongsTo", + "model": "Dataset", + "foreignKey": "", + "required": true + }, + "messageHistory": { + "type": "embedsMany", + "model": "Message", + "property": "messageHistory", + "options": { + "validate": false, + "forceId": false, + "persistent": true + } + } }, - { - "accessType": "*", - "principalType": "ROLE", - "principalId": "archivemanager", - "permission": "ALLOW" - } - ], - "methods":{ - "reset": { - "accepts": [{ - "arg": "datasetId", - "type": "string" - }, - { - "arg": "options", - "type": "object", - "http": "optionsFromRequest" - }], - "returns": { - "root": true - }, - "description": "Delete datablocks of dataset and reset status message.", - "http": { - "path": "/resetArchiveStatus", - "verb": "put" + "acls": [{ + "accessType": "*", + "principalType": "ROLE", + "principalId": "$everyone", + "permission": "DENY" + }, + { + "accessType": "*", + "principalType": "ROLE", + "principalId": "admin", + "permission": "ALLOW" + }, + { + "accessType": "*", + "principalType": "ROLE", + "principalId": "ingestor", + "permission": "ALLOW" + }, + { + "accessType": "*", + "principalType": "ROLE", + "principalId": "archivemanager", + "permission": "ALLOW" + } + ], + "methods": { + "reset": { + "accepts": [{ + "arg": "datasetId", + "type": "string" + }, + { + "arg": "options", + "type": "object", + "http": "optionsFromRequest" + } + ], + "returns": { + "root": true + }, + "description": "Delete datablocks of dataset and reset status message.", + "http": { + "path": "/resetArchiveStatus", + "verb": "put" } } } diff --git a/common/models/job.js b/common/models/job.js index 5807c7d9..b6c05178 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -76,11 +76,36 @@ module.exports = function (Job) { }); } }); + } else { + next() } } else { - console.log('Updated %s matching %j', ctx.Model.pluralModelName, - ctx.where); - next(); + if ('smtpSettings' in config && 'smtpMessage' in config) { + let transporter = nodemailer.createTransport(config.smtpSettings); + transporter.verify(function (error, success) { + if (error) { + console.log(error); + next(); + } else { + console.log('Server is ready to take our messages'); + var message = Object.assign({}, config.smtpMessage); + message['to'] = ctx.instance.emailJobInitiator; + message['subject'] += ' Job Finished with status '+ ctx.instance.jobStatusMessage; + let text = 'Hello, \n\n Your Job with id is now finished. \n\n The resulting job description is.\n\n'+JSON.stringify(ctx.instance, null, 4); + message['text'] = text; + transporter.sendMail(message, function (err, info) { + if (err) { + console.log(err); + } else { + console.log('Email sent'); + } + next(); + }); + } + }); + } else { + next() + } } }); }; diff --git a/common/models/job.json b/common/models/job.json index f99e9a87..99f93c68 100644 --- a/common/models/job.json +++ b/common/models/job.json @@ -54,22 +54,33 @@ "type": "string", "description": "Defines current status of job lifecycle" }, + "datasetList": { + "type": "object", + "required": true, + "description": "Array of objects with keys: pid, files. The value for the pid key defines the dataset ID, the value for the files key is an array of file names. This array is either an empty array, implying that all files within the dataset are selected or an explicit list of dataset-relative file paths, which should be selected" + }, "archiveReturnMessage": { "type": "string", - "description": "Detailed status or error message returned by archive system at archive job creation time. If One Job request triggers many archive requests, e.g. when archiving multiple datasets in one job, then this message contains the result of the last dataset handled" + "description": "Detailed status or error message returned by archive system at archive job creation time. If One Job request triggers many archive requests, e.g. when archiving multiple datasets in one job, then this message contains the result of the last dataset handled. Warning: to be obsoleted" }, "dateOfLastMessage": { "type": "date", - "description": "Time when last status message was sent. Format according to chapter 5.6 internet date/time format in RFC 3339. This will be filled automatically if not provided" - }, - "datasetList": { - "type": "object", - "required": true, - "description": "Array of objects with keys: pid, files. The value for the pid key defines the dataset ID, the value for the files key is an array of file names. This array is either an empty array, implying that all files within the dataset are selected or an explicit list of dataset-relative file paths, which should be selected" + "description": "Time when last status message was sent. Format according to chapter 5.6 internet date/time format in RFC 3339. This will be filled automatically if not provided. Warning: to be obsoleted." } }, "validations": [], - "relations": {}, + "relations": { + "messageHistory": { + "type": "embedsMany", + "model": "Message", + "property": "messageHistory", + "options": { + "validate": false, + "forceId": false, + "persistent": true + } + } + }, "acls": [], "methods": {} } diff --git a/common/models/message.js b/common/models/message.js new file mode 100644 index 00000000..a0f88c8a --- /dev/null +++ b/common/models/message.js @@ -0,0 +1,5 @@ +'use strict'; + +module.exports = function(Message) { + +}; diff --git a/common/models/message.json b/common/models/message.json new file mode 100644 index 00000000..684800ae --- /dev/null +++ b/common/models/message.json @@ -0,0 +1,49 @@ +{ + "name": "Message", + "description": "Embedded information used inside DatasetLifecycle or Job to keep track of history.", + "base": "PersistedModel", + "idInjection": true, + "strict": true, + "options": { + "validateUpsert": true + }, + "properties": { + "id": { + "type": "string", + "id": "true", + "required": true, + "description": "id currently needed by limitation in embedsmanny" + }, + "shortMessage": { + "type": "string", + "required": true, + "index": true, + "description": "Short description of message, like datasetArchiveSuccesful" + }, + "sender": { + "type": "string", + "required": true, + "index": true, + "description": "User or role who triggered the message" + }, + "when": { + "type": "Date", + "index": true, + "default": "$now", + "description": "Time when message was received. Will be filled automatically by the server, format according to chapter 5.6 internet date/time format in RFC 3339." + }, + "comment": { + "type": "Object", + "description": "Additional information relevant for this message" + } + }, + "validations": [], + "relations": {}, + "acls": [{ + "accessType": "*", + "principalType": "ROLE", + "principalId": "$everyone", + "permission": "ALLOW" + }], + "methods": {} +} diff --git a/package.json b/package.json index 5b67488d..b5adf880 100644 --- a/package.json +++ b/package.json @@ -1,53 +1,51 @@ { - "name": "dacat-api", - "version": "2.8.1", - "main": "server/server.js", - "engines": { - "node": ">=4" - }, - "scripts": { - "lint": "eslint common/models", - "start": "node .", - "posttests": "npm run lint && nsp check", - "test": "./node_modules/mocha/bin/mocha --timeout=10000 --reporter spec --exit 2>/dev/null" - }, - "dependencies": { - "compression": "^1.0.3", - "cors": "^2.5.2", - "helmet": "^3.10.0", - "loopback-boot": "^2.6.5", - "serve-favicon": "2.5.0", - "strong-error-handler": "3.1.0", - "loopback-component-explorer": "^6.0.0", - "loopback": "^3.19.0", - "loopback-component-model-diagram": "^0.4.2", - "loopback-component-mq": "^2.2.5", - "loopback-component-passport": "^3.4.1", - "loopback-component-visualizer": "^1.2.1", - "loopback-connector-kafka": "^0.2.1", - "loopback-connector-mongodb": "^3.3.0", - "loopback-ds-timestamp-mixin": "^3.4.1", - "moment": "^2.20.1", - "moment-timezone": "^0.5.14", - "nodemailer": "^4.3.1", - "passport-ldapauth": "^2.0.0", - "passport-local": "^1.0.0", - "passport-openidconnect": "^0.0.2", - "uuid": "^3.2.1" - }, - "devDependencies": { - "eslint": "^5.3.0", - "eslint-config-loopback": "^11.0.0", - "@mean-expert/loopback-sdk-builder": "^2.1.0", - "chai": "^4.1.2", - "chai-http": "^4.0.0", - "mocha": "^5.2.0", - "supertest": "^3.0.0" - }, - "repository": { - "type": "", - "url": "" - }, - "license": "GPL-3.0", - "description": "dacat-api" + "name": "dacat-api", + "version": "2.8.0", + "main": "server/server.js", + "scripts": { + "lint": "eslint common/models", + "start": "node .", + "posttests": "npm run lint && nsp check", + "test": "./node_modules/mocha/bin/mocha --timeout=10000 --reporter spec --exit 2>/dev/null" + }, + "dependencies": { + "compression": "1.7.1", + "cors": "2.8.4", + "helmet": "3.9.0", + "loopback": "3.16.2", + "loopback-boot": "2.27.0", + "loopback-component-explorer": "5.2.0", + "loopback-component-model-diagram": "0.3.0", + "loopback-component-mq": "^2.2.5", + "loopback-component-passport": "3.4.1", + "loopback-component-visualizer": "1.2.1", + "loopback-connector-kafka": "^0.2.1", + "loopback-connector-mongodb": "3.3.0", + "loopback-ds-timestamp-mixin": "^3.4.1", + "moment": "^2.20.1", + "moment-timezone": "^0.5.14", + "nodemailer": "^4.3.1", + "passport-ldapauth": "2.0.0", + "passport-local": "1.0.0", + "passport-openidconnect": "0.0.2", + "serve-favicon": "2.4.5", + "strong-error-handler": "2.3.0", + "uuid": "^3.2.1" + }, + "devDependencies": { + "@mean-expert/loopback-sdk-builder": "2.1.0", + "chai": "^4.1.2", + "chai-http": "^3.0.0", + "eslint": "4.10.0", + "eslint-config-loopback": "8.0.0", + "mocha": "^4.1.0", + "nsp": "2.8.1", + "supertest": "^3.0.0" + }, + "repository": { + "type": "", + "url": "" + }, + "license": "GPL-3.0", + "description": "dacat-api" } diff --git a/server/model-config.json b/server/model-config.json index 591888ea..ae5abd8b 100644 --- a/server/model-config.json +++ b/server/model-config.json @@ -1,118 +1,122 @@ { - "_meta": { - "sources": [ - "loopback/common/models", - "loopback/server/models", - "../common/models", - "./models", - "./node_modules/loopback-component-passport/lib/models" - ], - "mixins": [ - "loopback/common/mixins", - "loopback/server/mixins", - "../node_modules/loopback-component-mq/lib/mixins", - "../node_modules/loopback-ds-timestamp-mixin", - "../common/mixins", - "./mixins" - ] - }, - "User": { - "dataSource": "mongo" - }, - "AccessToken": { - "dataSource": "mongo", - "public": false - }, - "ACL": { - "dataSource": "mongo", - "public": false - }, - "RoleMapping": { - "dataSource": "mongo", - "public": false - }, - "Role": { - "dataSource": "mongo", - "public": false - }, - "Dataset": { - "dataSource": "mongo", - "public": true - }, - "RawDataset": { - "dataSource": "mongo", - "public": true - }, - "DerivedDataset": { - "dataSource": "mongo", - "public": true - }, - "Sample": { - "dataSource": "mongo", - "public": true - }, - "Proposal": { - "dataSource": "mongo", - "public": true - }, - "PublishedData": { - "dataSource": "mongo", - "public": true - }, - "Datafile": { - "dataSource": "transient", - "public": false - }, - "DatasetLifecycle": { - "dataSource": "mongo", - "public": true - }, - "Datablock": { - "dataSource": "mongo", - "public": true - }, - "MeasurementPeriod": { - "dataSource": "transient", - "public": false - }, - "AccessUser": { - "dataSource": "mongo", - "public": true - }, - "AccessGroup": { - "dataSource": "mongo", - "public": true - }, - "UserCredential": { - "dataSource": "mongo", - "public": true - }, - "UserIdentity": { - "dataSource": "mongo", - "public": true - }, - "ApplicationCredential": { - "dataSource": "mongo", - "public": true - }, - "Ownable": { - "dataSource": "mongo", - "public": false - }, - "Policy": { - "dataSource": "mongo", - "public": true - }, - "Job": { - "dataSource": "mongo", - "public": true - }, - "DatasetAttachment": { - "dataSource": "mongo", - "public": true - }, - "OrigDatablock": { - "dataSource": "mongo", - "public": true - } + "_meta": { + "sources": [ + "loopback/common/models", + "loopback/server/models", + "../common/models", + "./models", + "./node_modules/loopback-component-passport/lib/models" + ], + "mixins": [ + "loopback/common/mixins", + "loopback/server/mixins", + "../node_modules/loopback-component-mq/lib/mixins", + "../node_modules/loopback-ds-timestamp-mixin", + "../common/mixins", + "./mixins" + ] + }, + "User": { + "dataSource": "mongo" + }, + "AccessToken": { + "dataSource": "mongo", + "public": false + }, + "ACL": { + "dataSource": "mongo", + "public": false + }, + "RoleMapping": { + "dataSource": "mongo", + "public": false + }, + "Role": { + "dataSource": "mongo", + "public": false + }, + "Dataset": { + "dataSource": "mongo", + "public": true + }, + "RawDataset": { + "dataSource": "mongo", + "public": true + }, + "DerivedDataset": { + "dataSource": "mongo", + "public": true + }, + "Sample": { + "dataSource": "mongo", + "public": true + }, + "Proposal": { + "dataSource": "mongo", + "public": true + }, + "PublishedData": { + "dataSource": "mongo", + "public": true + }, + "Datafile": { + "dataSource": "transient", + "public": false + }, + "DatasetLifecycle": { + "dataSource": "mongo", + "public": true + }, + "Datablock": { + "dataSource": "mongo", + "public": true + }, + "MeasurementPeriod": { + "dataSource": "transient", + "public": false + }, + "AccessUser": { + "dataSource": "mongo", + "public": true + }, + "AccessGroup": { + "dataSource": "mongo", + "public": true + }, + "UserCredential": { + "dataSource": "mongo", + "public": true + }, + "UserIdentity": { + "dataSource": "mongo", + "public": true + }, + "ApplicationCredential": { + "dataSource": "mongo", + "public": true + }, + "Ownable": { + "dataSource": "mongo", + "public": false + }, + "Policy": { + "dataSource": "mongo", + "public": true + }, + "Job": { + "dataSource": "mongo", + "public": true + }, + "DatasetAttachment": { + "dataSource": "mongo", + "public": true + }, + "OrigDatablock": { + "dataSource": "mongo", + "public": true + }, + "Message": { + "dataSource": "transient", + "public": false + } } diff --git a/test/Job.js b/test/Job.js new file mode 100644 index 00000000..686bf6bb --- /dev/null +++ b/test/Job.js @@ -0,0 +1,413 @@ +/* jshint node:true */ +/* jshint esversion:6 */ +'use strict'; + +// process.env.NODE_ENV = 'test'; + +var chai = require('chai'); +var chaiHttp = require('chai-http'); +var request = require('supertest'); +var app = require('../server/server'); +var should = chai.should(); +var utils = require('./LoginUtils'); + +var accessTokenIngestor = null; +var accessTokenArchiveManager = null; +var accessTokenUser = null; + +var pid = null; +var pid2 = null; +var idDatasetLifecycle = null; +var idDatasetLifecycle2 = null; + +var testraw = { + "principalInvestigator": "bertram.astor@grumble.com", + "endTime": "2011-09-14T06:31:25.000Z", + "creationLocation": "/SU/XQX/RAMJET", + "dataFormat": "Upchuck pre 2017", + "scientificMetadata": { + "beamlineParameters": { + "Monostripe": "Ru/C", + "Ring current": { + "v": 0.402246, + "u": "A" + }, + "Beam energy": { + "v": 22595, + "u": "eV" + } + }, + "detectorParameters": { + "Objective": 20, + "Scintillator": "LAG 20um", + "Exposure time": { + "v": 0.4, + "u": "s" + } + }, + "scanParameters": { + "Number of projections": 1801, + "Rot Y min position": { + "v": 0, + "u": "deg" + }, + "Inner scan flag": 0, + "File Prefix": "817b_B2_", + "Sample In": { + "v": 0, + "u": "m" + }, + "Sample folder": "/ramjet/817b_B2_", + "Number of darks": 10, + "Rot Y max position": { + "v": 180, + "u": "deg" + }, + "Angular step": { + "v": 0.1, + "u": "deg" + }, + "Number of flats": 120, + "Sample Out": { + "v": -0.005, + "u": "m" + }, + "Flat frequency": 0, + "Number of inter-flats": 0 + } + }, + "owner": "Bertram Astor", + "ownerEmail": "bertram.astor@grumble.com", + "orcidOfOwner": "unknown", + "contactEmail": "bertram.astor@grumble.com", + "sourceFolder": "/iramjet/tif/", + "size": 0, + "creationTime": "2011-09-14T06:08:25.000Z", + "description": "The ultimate test", + "doi": "not yet defined", + "isPublished": false, + "ownerGroup": "p10029", + "accessGroups": [], + "proposalId": "10.540.16635/20110123", + "keywords": ["sls", "protein"] +} + +var testDatasetLifecycle = { + "id": "", // must be set to the id of the dataset, + "isOnDisk": true, + "isOnTape": false, + "archiveStatusMessage": "datasetCreated", + "retrieveStatusMessage": "", + "isExported": false +} + + +describe('Test DatasetLifecycle and the relation to Datasets', () => { + before((done) => { + utils.getToken(app, { + 'username': 'ingestor', + 'password': 'aman' + }, + (tokenVal) => { + accessTokenIngestor = tokenVal; + }); + utils.getToken(app, { + 'username': 'archiveManager', + 'password': 'aman' + }, + (tokenVal) => { + accessTokenArchiveManager = tokenVal; + done(); + }); + }); + + it('adds a new raw dataset', function(done) { + request(app) + .post('/api/v2/RawDatasets?access_token=' + accessTokenIngestor) + .send(testraw) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + res.body.should.have.property('owner').and.be.string; + res.body.should.have.property('type').and.equal('raw'); + res.body.should.have.property('pid').and.be.string; + // store link to this dataset in datablocks + testDatasetLifecycle.id = res.body['pid'] + testDatasetLifecycle.datasetId = res.body['pid'] + pid = encodeURIComponent(res.body['pid']); + done(); + }); + }); + + it('adds a new DatasetLifecycle', function(done) { + request(app) + .post('/api/v2/DatasetLifecycles?access_token=' + accessTokenIngestor) + .send(testDatasetLifecycle) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + idDatasetLifecycle = encodeURIComponent(res.body['id']); + done(); + }); + }); + + it('adds another new raw dataset', function(done) { + // modify owner + testraw.ownerGroup = "p12345" + request(app) + .post('/api/v2/RawDatasets?access_token=' + accessTokenIngestor) + .send(testraw) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + res.body.should.have.property('owner').and.be.string; + res.body.should.have.property('type').and.equal('raw'); + res.body.should.have.property('pid').and.be.string; + // store link to this dataset in datablocks + testDatasetLifecycle.id = res.body['pid'] + testDatasetLifecycle.datasetId = res.body['pid'] + pid2 = encodeURIComponent(res.body['pid']); + done(); + }); + }); + + it('adds a corresponding new DatasetLifecycle', function(done) { + testDatasetLifecycle.archiveStatusMessage = "some other message" + request(app) + .post('/api/v2/DatasetLifecycles?access_token=' + accessTokenIngestor) + .send(testDatasetLifecycle) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + idDatasetLifecycle2 = encodeURIComponent(res.body['id']); + done(); + }); + }); + + // TODO add test for raw and derived dataset queries as well + + it('Should return datasets with complex join query fulfilled', function(done) { + var fields = { + "ownerGroup": ["p12345", "p10029"], + "text": "\"ultimate test\"", + "creationTime": { + "begin": "2011-09-13", + "end": "2011-09-15" + }, + "archiveStatusMessage": "datasetCreated", + "keywords": ["energy", "protein"] + } + + request(app) + .get('/api/v2/Datasets/fullquery?fields=' + encodeURIComponent(JSON.stringify(fields)) + '&access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + res.body.should.be.an('array').that.is.not.empty; + res.body[0]['datasetlifecycle'].should.have.property('archiveStatusMessage').and.equal("datasetCreated"); + done(); + }); + }); + + it('Should return datasets with ordered results', function(done) { + var fields = { + "ownerGroup": ["p12345", "p10029"] + } + var limits = { + order: "creationTime:desc", + skip: 0 + } + + request(app) + .get('/api/v2/Datasets/fullquery?fields=' + encodeURIComponent(JSON.stringify(fields)) + '&limits=' + encodeURIComponent(JSON.stringify(limits)) + '&access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + res.body.should.be.instanceof(Array); + done(); + }); + }); + + + it('Should return no datasets, because number of hits exhausted', function(done) { + var fields = { + ownerGroup: ["p12345"], + archiveStatusMessage: "datasetCreated" + } + var limits = { + skip: 10 + } + + request(app) + .get('/api/v2/Datasets/fullquery?fields=' + encodeURIComponent(JSON.stringify(fields)) + '&limits=' + encodeURIComponent(JSON.stringify(limits)) + '&access_token=' + accessTokenIngestor) + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + res.body.should.be.an('array').that.is.empty; + done(); + }); + }); + + it('Should return facets with complex join query fulfilled', function(done) { + var fields = { + "ownerGroup": ["p12345", "p10029"], + "text": "\"ultimate test\"", + "creationTime": { + "begin": "2011-09-13", + "end": "2011-09-15" + }, + "keywords": ["energy", "protein"] + } + var facets=["type","creationTime","creationLocation","ownerGroup","keywords"] + request(app) + .get('/api/v2/Datasets/fullfacet?fields=' + encodeURIComponent(JSON.stringify(fields)) + '&facets=' + encodeURIComponent(JSON.stringify(facets))+ '&access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + + it('Should update archive status message from archiveManager account', function(done) { + request(app) + .patch('/api/v2/DatasetLifecycles/' + pid + '?access_token=' + accessTokenArchiveManager) + .send({ + "archiveStatusMessage": "dataArchivedOnTape" + }) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + res.body.should.have.property('archiveStatusMessage').and.equal("dataArchivedOnTape"); + done(); + }); + + }); + + + it('Should fetch the datasetLifefycle belonging to the new dataset', function(done) { + request(app) + .get('/api/v2/Datasets/' + pid + '/datasetlifecycle?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + res.body.should.be.instanceof(Object); + done(); + }); + }); + + it('Should update a single field in DatasetLifecycle via PUT command', function(done) { + request(app) + .put('/api/v2/DatasetLifecycles/' + pid + '?access_token=' + accessTokenArchiveManager) + .send({ + "archiveStatusMessage": "someDummyMessage" + }) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + res.body.archiveStatusMessage.should.be.equal('someDummyMessage'); + done(); + }); + }); + + it('Should reset the DatasetLifecycle status and delete Datablocks', function(done) { + request(app) + .put('/api/v2/DatasetLifecycles/resetArchiveStatus?access_token=' + accessTokenArchiveManager) + .send({ + datasetId: testDatasetLifecycle.id + }) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + it('should delete the DatasetLifecycle', function(done) { + request(app) + .delete('/api/v2/DatasetLifecycles/' + idDatasetLifecycle + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + it('should delete the other DatasetLifecycle', function(done) { + request(app) + .delete('/api/v2/DatasetLifecycles/' + idDatasetLifecycle2 + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + + it('should delete the newly created dataset', function(done) { + request(app) + .delete('/api/v2/Datasets/' + pid + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + it('should delete the newly created dataset', function(done) { + request(app) + .delete('/api/v2/Datasets/' + pid2 + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + +}); From de4ae9912647758c09692ae7ddcf700cced008c9 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 6 Sep 2018 20:44:02 +0200 Subject: [PATCH 049/147] Testcase for new messageHistory for both Datasetlifecycle and Job added --- common/models/dataset-lifecycle.json | 2 +- common/models/job.json | 2 +- common/models/measurement-period.json | 2 +- common/models/message.json | 15 +- test/Job.js | 413 -------------------------- test/MessageHistory.js | 300 +++++++++++++++++++ 6 files changed, 309 insertions(+), 425 deletions(-) delete mode 100644 test/Job.js create mode 100644 test/MessageHistory.js diff --git a/common/models/dataset-lifecycle.json b/common/models/dataset-lifecycle.json index c035f470..7816b867 100644 --- a/common/models/dataset-lifecycle.json +++ b/common/models/dataset-lifecycle.json @@ -99,7 +99,7 @@ "messageHistory": { "type": "embedsMany", "model": "Message", - "property": "messageHistory", + "property": "MessageHistory", "options": { "validate": false, "forceId": false, diff --git a/common/models/job.json b/common/models/job.json index 99f93c68..2507a79e 100644 --- a/common/models/job.json +++ b/common/models/job.json @@ -73,7 +73,7 @@ "messageHistory": { "type": "embedsMany", "model": "Message", - "property": "messageHistory", + "property": "MessageHistory", "options": { "validate": false, "forceId": false, diff --git a/common/models/measurement-period.json b/common/models/measurement-period.json index 3e12b1ca..d8ddfdf4 100644 --- a/common/models/measurement-period.json +++ b/common/models/measurement-period.json @@ -12,7 +12,7 @@ "type": "string", "id": "true", "required": true, - "description": "id currently needed by limitation in embedsmanny" + "description": "id currently needed by limitation in embedsmany" }, "instrument": { "type": "string", diff --git a/common/models/message.json b/common/models/message.json index 684800ae..3c758a69 100644 --- a/common/models/message.json +++ b/common/models/message.json @@ -1,7 +1,7 @@ { "name": "Message", "description": "Embedded information used inside DatasetLifecycle or Job to keep track of history.", - "base": "PersistedModel", + "base": "Model", "idInjection": true, "strict": true, "options": { @@ -11,30 +11,27 @@ "id": { "type": "string", "id": "true", - "required": true, - "description": "id currently needed by limitation in embedsmanny" + "defaultFn": "uuid", + "description": "id currently needed by limitation in embedsmany" }, "shortMessage": { "type": "string", "required": true, - "index": true, "description": "Short description of message, like datasetArchiveSuccesful" }, "sender": { "type": "string", "required": true, - "index": true, - "description": "User or role who triggered the message" + "description": "Email of user or role who triggered the message" }, "when": { "type": "Date", - "index": true, "default": "$now", "description": "Time when message was received. Will be filled automatically by the server, format according to chapter 5.6 internet date/time format in RFC 3339." }, - "comment": { + "payload": { "type": "Object", - "description": "Additional information relevant for this message" + "description": "Additional information relevant for this message. Please note this is an object" } }, "validations": [], diff --git a/test/Job.js b/test/Job.js deleted file mode 100644 index 686bf6bb..00000000 --- a/test/Job.js +++ /dev/null @@ -1,413 +0,0 @@ -/* jshint node:true */ -/* jshint esversion:6 */ -'use strict'; - -// process.env.NODE_ENV = 'test'; - -var chai = require('chai'); -var chaiHttp = require('chai-http'); -var request = require('supertest'); -var app = require('../server/server'); -var should = chai.should(); -var utils = require('./LoginUtils'); - -var accessTokenIngestor = null; -var accessTokenArchiveManager = null; -var accessTokenUser = null; - -var pid = null; -var pid2 = null; -var idDatasetLifecycle = null; -var idDatasetLifecycle2 = null; - -var testraw = { - "principalInvestigator": "bertram.astor@grumble.com", - "endTime": "2011-09-14T06:31:25.000Z", - "creationLocation": "/SU/XQX/RAMJET", - "dataFormat": "Upchuck pre 2017", - "scientificMetadata": { - "beamlineParameters": { - "Monostripe": "Ru/C", - "Ring current": { - "v": 0.402246, - "u": "A" - }, - "Beam energy": { - "v": 22595, - "u": "eV" - } - }, - "detectorParameters": { - "Objective": 20, - "Scintillator": "LAG 20um", - "Exposure time": { - "v": 0.4, - "u": "s" - } - }, - "scanParameters": { - "Number of projections": 1801, - "Rot Y min position": { - "v": 0, - "u": "deg" - }, - "Inner scan flag": 0, - "File Prefix": "817b_B2_", - "Sample In": { - "v": 0, - "u": "m" - }, - "Sample folder": "/ramjet/817b_B2_", - "Number of darks": 10, - "Rot Y max position": { - "v": 180, - "u": "deg" - }, - "Angular step": { - "v": 0.1, - "u": "deg" - }, - "Number of flats": 120, - "Sample Out": { - "v": -0.005, - "u": "m" - }, - "Flat frequency": 0, - "Number of inter-flats": 0 - } - }, - "owner": "Bertram Astor", - "ownerEmail": "bertram.astor@grumble.com", - "orcidOfOwner": "unknown", - "contactEmail": "bertram.astor@grumble.com", - "sourceFolder": "/iramjet/tif/", - "size": 0, - "creationTime": "2011-09-14T06:08:25.000Z", - "description": "The ultimate test", - "doi": "not yet defined", - "isPublished": false, - "ownerGroup": "p10029", - "accessGroups": [], - "proposalId": "10.540.16635/20110123", - "keywords": ["sls", "protein"] -} - -var testDatasetLifecycle = { - "id": "", // must be set to the id of the dataset, - "isOnDisk": true, - "isOnTape": false, - "archiveStatusMessage": "datasetCreated", - "retrieveStatusMessage": "", - "isExported": false -} - - -describe('Test DatasetLifecycle and the relation to Datasets', () => { - before((done) => { - utils.getToken(app, { - 'username': 'ingestor', - 'password': 'aman' - }, - (tokenVal) => { - accessTokenIngestor = tokenVal; - }); - utils.getToken(app, { - 'username': 'archiveManager', - 'password': 'aman' - }, - (tokenVal) => { - accessTokenArchiveManager = tokenVal; - done(); - }); - }); - - it('adds a new raw dataset', function(done) { - request(app) - .post('/api/v2/RawDatasets?access_token=' + accessTokenIngestor) - .send(testraw) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end(function(err, res) { - if (err) - return done(err); - res.body.should.have.property('owner').and.be.string; - res.body.should.have.property('type').and.equal('raw'); - res.body.should.have.property('pid').and.be.string; - // store link to this dataset in datablocks - testDatasetLifecycle.id = res.body['pid'] - testDatasetLifecycle.datasetId = res.body['pid'] - pid = encodeURIComponent(res.body['pid']); - done(); - }); - }); - - it('adds a new DatasetLifecycle', function(done) { - request(app) - .post('/api/v2/DatasetLifecycles?access_token=' + accessTokenIngestor) - .send(testDatasetLifecycle) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end(function(err, res) { - if (err) - return done(err); - idDatasetLifecycle = encodeURIComponent(res.body['id']); - done(); - }); - }); - - it('adds another new raw dataset', function(done) { - // modify owner - testraw.ownerGroup = "p12345" - request(app) - .post('/api/v2/RawDatasets?access_token=' + accessTokenIngestor) - .send(testraw) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end(function(err, res) { - if (err) - return done(err); - res.body.should.have.property('owner').and.be.string; - res.body.should.have.property('type').and.equal('raw'); - res.body.should.have.property('pid').and.be.string; - // store link to this dataset in datablocks - testDatasetLifecycle.id = res.body['pid'] - testDatasetLifecycle.datasetId = res.body['pid'] - pid2 = encodeURIComponent(res.body['pid']); - done(); - }); - }); - - it('adds a corresponding new DatasetLifecycle', function(done) { - testDatasetLifecycle.archiveStatusMessage = "some other message" - request(app) - .post('/api/v2/DatasetLifecycles?access_token=' + accessTokenIngestor) - .send(testDatasetLifecycle) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end(function(err, res) { - if (err) - return done(err); - idDatasetLifecycle2 = encodeURIComponent(res.body['id']); - done(); - }); - }); - - // TODO add test for raw and derived dataset queries as well - - it('Should return datasets with complex join query fulfilled', function(done) { - var fields = { - "ownerGroup": ["p12345", "p10029"], - "text": "\"ultimate test\"", - "creationTime": { - "begin": "2011-09-13", - "end": "2011-09-15" - }, - "archiveStatusMessage": "datasetCreated", - "keywords": ["energy", "protein"] - } - - request(app) - .get('/api/v2/Datasets/fullquery?fields=' + encodeURIComponent(JSON.stringify(fields)) + '&access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - res.body.should.be.an('array').that.is.not.empty; - res.body[0]['datasetlifecycle'].should.have.property('archiveStatusMessage').and.equal("datasetCreated"); - done(); - }); - }); - - it('Should return datasets with ordered results', function(done) { - var fields = { - "ownerGroup": ["p12345", "p10029"] - } - var limits = { - order: "creationTime:desc", - skip: 0 - } - - request(app) - .get('/api/v2/Datasets/fullquery?fields=' + encodeURIComponent(JSON.stringify(fields)) + '&limits=' + encodeURIComponent(JSON.stringify(limits)) + '&access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - res.body.should.be.instanceof(Array); - done(); - }); - }); - - - it('Should return no datasets, because number of hits exhausted', function(done) { - var fields = { - ownerGroup: ["p12345"], - archiveStatusMessage: "datasetCreated" - } - var limits = { - skip: 10 - } - - request(app) - .get('/api/v2/Datasets/fullquery?fields=' + encodeURIComponent(JSON.stringify(fields)) + '&limits=' + encodeURIComponent(JSON.stringify(limits)) + '&access_token=' + accessTokenIngestor) - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - res.body.should.be.an('array').that.is.empty; - done(); - }); - }); - - it('Should return facets with complex join query fulfilled', function(done) { - var fields = { - "ownerGroup": ["p12345", "p10029"], - "text": "\"ultimate test\"", - "creationTime": { - "begin": "2011-09-13", - "end": "2011-09-15" - }, - "keywords": ["energy", "protein"] - } - var facets=["type","creationTime","creationLocation","ownerGroup","keywords"] - request(app) - .get('/api/v2/Datasets/fullfacet?fields=' + encodeURIComponent(JSON.stringify(fields)) + '&facets=' + encodeURIComponent(JSON.stringify(facets))+ '&access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - - - it('Should update archive status message from archiveManager account', function(done) { - request(app) - .patch('/api/v2/DatasetLifecycles/' + pid + '?access_token=' + accessTokenArchiveManager) - .send({ - "archiveStatusMessage": "dataArchivedOnTape" - }) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - res.body.should.have.property('archiveStatusMessage').and.equal("dataArchivedOnTape"); - done(); - }); - - }); - - - it('Should fetch the datasetLifefycle belonging to the new dataset', function(done) { - request(app) - .get('/api/v2/Datasets/' + pid + '/datasetlifecycle?access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - res.body.should.be.instanceof(Object); - done(); - }); - }); - - it('Should update a single field in DatasetLifecycle via PUT command', function(done) { - request(app) - .put('/api/v2/DatasetLifecycles/' + pid + '?access_token=' + accessTokenArchiveManager) - .send({ - "archiveStatusMessage": "someDummyMessage" - }) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - res.body.archiveStatusMessage.should.be.equal('someDummyMessage'); - done(); - }); - }); - - it('Should reset the DatasetLifecycle status and delete Datablocks', function(done) { - request(app) - .put('/api/v2/DatasetLifecycles/resetArchiveStatus?access_token=' + accessTokenArchiveManager) - .send({ - datasetId: testDatasetLifecycle.id - }) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - - it('should delete the DatasetLifecycle', function(done) { - request(app) - .delete('/api/v2/DatasetLifecycles/' + idDatasetLifecycle + '?access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - - it('should delete the other DatasetLifecycle', function(done) { - request(app) - .delete('/api/v2/DatasetLifecycles/' + idDatasetLifecycle2 + '?access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - - - it('should delete the newly created dataset', function(done) { - request(app) - .delete('/api/v2/Datasets/' + pid + '?access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - - it('should delete the newly created dataset', function(done) { - request(app) - .delete('/api/v2/Datasets/' + pid2 + '?access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - - -}); diff --git a/test/MessageHistory.js b/test/MessageHistory.js new file mode 100644 index 00000000..420186b4 --- /dev/null +++ b/test/MessageHistory.js @@ -0,0 +1,300 @@ +/* jshint node:true */ +/* jshint esversion:6 */ +'use strict'; + +// process.env.NODE_ENV = 'test'; + +var chai = require('chai'); +var chaiHttp = require('chai-http'); +var request = require('supertest'); +var app = require('../server/server'); +var should = chai.should(); +var utils = require('./LoginUtils'); + +var accessTokenIngestor = null; +var accessTokenArchiveManager = null; +var accessTokenUser = null; + +var pid = null; +var pid2 = null; +var idDatasetLifecycle = null; +var idDatasetLifecycle2 = null; +var idJob = null + +var testraw = { + "principalInvestigator": "bertram.astor@grumble.com", + "endTime": "2011-09-14T06:31:25.000Z", + "creationLocation": "/SU/XQX/RAMJET", + "dataFormat": "Upchuck pre 2017", + "scientificMetadata": { + "beamlineParameters": { + "Monostripe": "Ru/C", + "Ring current": { + "v": 0.402246, + "u": "A" + }, + "Beam energy": { + "v": 22595, + "u": "eV" + } + }, + "detectorParameters": { + "Objective": 20, + "Scintillator": "LAG 20um", + "Exposure time": { + "v": 0.4, + "u": "s" + } + }, + "scanParameters": { + "Number of projections": 1801, + "Rot Y min position": { + "v": 0, + "u": "deg" + }, + "Inner scan flag": 0, + "File Prefix": "817b_B2_", + "Sample In": { + "v": 0, + "u": "m" + }, + "Sample folder": "/ramjet/817b_B2_", + "Number of darks": 10, + "Rot Y max position": { + "v": 180, + "u": "deg" + }, + "Angular step": { + "v": 0.1, + "u": "deg" + }, + "Number of flats": 120, + "Sample Out": { + "v": -0.005, + "u": "m" + }, + "Flat frequency": 0, + "Number of inter-flats": 0 + } + }, + "owner": "Bertram Astor", + "ownerEmail": "bertram.astor@grumble.com", + "orcidOfOwner": "unknown", + "contactEmail": "bertram.astor@grumble.com", + "sourceFolder": "/iramjet/tif/", + "size": 0, + "creationTime": "2011-09-14T06:08:25.000Z", + "description": "The ultimate test", + "doi": "not yet defined", + "isPublished": false, + "ownerGroup": "p10029", + "accessGroups": [], + "proposalId": "10.540.16635/20110123", + "keywords": ["sls", "protein"] +} + +var testDatasetLifecycle = { + "id": "", // must be set to the id of the dataset, + // the following 4 fields become obsolete in future + "isOnDisk": true, + "isOnTape": false, + "archiveStatusMessage": "datasetCreated", + "retrieveStatusMessage": "", + "isExported": false, + "archivable": true, + "retrievable": false, + "MessageHistory": [{ + "shortMessage": "datasetCreated", + "sender": "stephan.egli@psi.ch", + "payload": { + "text": "Nothing special to report" + } + }] +} + +var testjob = { + "emailJobInitiator": "scicatarchivemanger@psi.ch", + "type": "retrieve", + "jobStatusMessage": "jobForwarded", + "datasetList": [{ + "pid": "20.500.11935/93128a6e-6c0c-48aa-bd3d-34b8fafc29ff", + "files": [] + }, + { + "pid": "20.500.11935/c26ab160-3725-459c-a4fd-a8c88d0ff170", + "files": [] + }, + ], + "archiveReturnMessage": "will move to messageList", + "MessageHistory": [] +} + + + +// TODO do I need to pass id explicitly ? +var newMessage = { + "shortMessage": "JustAnExample", + "sender": "stephan.egli@psi.ch", + "payload": { + "text": "whatever" + } +} + +describe('Test DatasetLifecycle and the relation to Datasets', () => { + before((done) => { + utils.getToken(app, { + 'username': 'ingestor', + 'password': 'aman' + }, + (tokenVal) => { + accessTokenIngestor = tokenVal; + }); + utils.getToken(app, { + 'username': 'archiveManager', + 'password': 'aman' + }, + (tokenVal) => { + accessTokenArchiveManager = tokenVal; + done(); + }); + }); + + it('adds a new raw dataset', function(done) { + request(app) + .post('/api/v2/RawDatasets?access_token=' + accessTokenIngestor) + .send(testraw) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + res.body.should.have.property('owner').and.be.string; + res.body.should.have.property('type').and.equal('raw'); + res.body.should.have.property('pid').and.be.string; + // store link to this dataset in datablocks + testDatasetLifecycle.id = res.body['pid'] + testDatasetLifecycle.datasetId = res.body['pid'] + pid = encodeURIComponent(res.body['pid']); + done(); + }); + }); + + it('adds a new DatasetLifecycle including messageHistory', function(done) { + request(app) + .post('/api/v2/DatasetLifecycles?access_token=' + accessTokenIngestor) + .send(testDatasetLifecycle) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + idDatasetLifecycle = encodeURIComponent(res.body['id']); + done(); + }); + }); + + it('Adds a new message to Datasetlifecycle MessageHistory', function(done) { + request(app) + .post('/api/v2/DatasetLifecycles/' + idDatasetLifecycle + '/messageHistory?access_token=' + accessTokenIngestor) + .send(newMessage) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + done(); + }); + }); + + it('Check if message was added', function(done) { + request(app) + .get('/api/v2/DatasetLifecycles/' + idDatasetLifecycle + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + // console.log("Lifecycle with new message:", res.body) + done(); + }); + }); + + + it('Adds a new job request', function(done) { + request(app) + .post('/api/v2/Jobs?access_token=' + accessTokenIngestor) + .send(testjob) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + res.body.should.have.property('type').and.be.string; + idJob = res.body['id'] + console.log("Jobid:",idJob) + done(); + }); + }); + + it('Adds a new message to Jobs MessageHistory', function(done) { + request(app) + .post('/api/v2/DatasetLifecycles/' + idDatasetLifecycle + '/messageHistory?access_token=' + accessTokenIngestor) + .send(newMessage) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + console.log(res.body) + done(); + }); + }); + + +it('should delete the Job', function(done) { + request(app) + .delete('/api/v2/Jobs/' + idJob+ '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); +}); + + it('should delete the DatasetLifecycle', function(done) { + request(app) + .delete('/api/v2/DatasetLifecycles/' + idDatasetLifecycle + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + + + it('should delete the newly created dataset', function(done) { + request(app) + .delete('/api/v2/Datasets/' + pid + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); + +}); From 5436cee607b7260a3e71055832a4a081cd8ffe39 Mon Sep 17 00:00:00 2001 From: egli Date: Sun, 9 Sep 2018 17:20:18 +0200 Subject: [PATCH 050/147] Correct package handling for docker deployment --- Dockerfile | 2 +- package-lock.json | 1296 +++++++++++++-------------------------------- package.json | 100 ++-- 3 files changed, 417 insertions(+), 981 deletions(-) diff --git a/Dockerfile b/Dockerfile index b08803c3..04688404 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,7 +10,7 @@ RUN addgroup mygroup && adduser -D -G mygroup myuser && mkdir -p /usr/src/app && # Prepare app directory WORKDIR /usr/src/app -COPY package.json /usr/src/app/ +COPY package*.json ./ USER myuser # Install our packages diff --git a/package-lock.json b/package-lock.json index e635fba0..c1a1de21 100644 --- a/package-lock.json +++ b/package-lock.json @@ -4,6 +4,34 @@ "lockfileVersion": 1, "requires": true, "dependencies": { + "@babel/code-frame": { + "version": "7.0.0", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.0.0.tgz", + "integrity": "sha512-OfC2uemaknXr87bdLUkWog7nYuliM9Ij5HUcajsVcMCpQrcLmtxRbVFTIqmcSkSeYRBFBRxs2FiUqFJDLdiebA==", + "dev": true, + "requires": { + "@babel/highlight": "7.0.0" + } + }, + "@babel/highlight": { + "version": "7.0.0", + "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.0.0.tgz", + "integrity": "sha512-UFMC4ZeFC48Tpvj7C8UgLvtkaUuovQX+5xNWrsIoMG8o2z+XFKjKaN9iVmS84dPwVN00W4wPmqvYoZF3EGAsfw==", + "dev": true, + "requires": { + "chalk": "2.4.1", + "esutils": "2.0.2", + "js-tokens": "4.0.0" + }, + "dependencies": { + "js-tokens": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/js-tokens/-/js-tokens-4.0.0.tgz", + "integrity": "sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ==", + "dev": true + } + } + }, "@kyleshockey/object-assign-deep": { "version": "0.4.2", "resolved": "https://registry.npmjs.org/@kyleshockey/object-assign-deep/-/object-assign-deep-0.4.2.tgz", @@ -72,6 +100,12 @@ "@types/node": "7.0.65" } }, + "@types/chai": { + "version": "4.1.4", + "resolved": "https://registry.npmjs.org/@types/chai/-/chai-4.1.4.tgz", + "integrity": "sha512-h6+VEw2Vr3ORiFCyyJmcho2zALnUq9cvdB/IO8Xs9itrJVCenC7o26A6+m7D0ihTTr65eS259H5/Ghl/VjYs6g==", + "dev": true + }, "@types/connect": { "version": "3.4.32", "resolved": "https://registry.npmjs.org/@types/connect/-/connect-3.4.32.tgz", @@ -80,6 +114,12 @@ "@types/node": "7.0.65" } }, + "@types/cookiejar": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/@types/cookiejar/-/cookiejar-2.1.0.tgz", + "integrity": "sha512-EIjmpvnHj+T4nMcKwHwxZKUfDmphIKJc2qnEMhSoOvr1lYEQpuRKRz8orWr//krYIIArS/KGGLfL2YGVUYXmIA==", + "dev": true + }, "@types/events": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/@types/events/-/events-1.2.0.tgz", @@ -146,6 +186,16 @@ "@types/mime": "2.0.0" } }, + "@types/superagent": { + "version": "3.8.4", + "resolved": "https://registry.npmjs.org/@types/superagent/-/superagent-3.8.4.tgz", + "integrity": "sha512-Dnh0Iw6NO55z1beXvlsvUrfk4cd9eL2nuTmUk+rAhSVCk10PGGFbqCCTwbau9D0d2W3DITiXl4z8VCqppGkMPQ==", + "dev": true, + "requires": { + "@types/cookiejar": "2.1.0", + "@types/node": "7.0.65" + } + }, "JSONStream": { "version": "1.3.3", "resolved": "https://registry.npmjs.org/JSONStream/-/JSONStream-1.3.3.tgz", @@ -534,12 +584,6 @@ "concat-map": "0.0.1" } }, - "browser-stdout": { - "version": "1.3.0", - "resolved": "https://registry.npmjs.org/browser-stdout/-/browser-stdout-1.3.0.tgz", - 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a/package.json +++ b/package.json @@ -1,51 +1,53 @@ { - "name": "dacat-api", - "version": "2.8.0", - "main": "server/server.js", - "scripts": { - "lint": "eslint common/models", - "start": "node .", - "posttests": "npm run lint && nsp check", - "test": "./node_modules/mocha/bin/mocha --timeout=10000 --reporter spec --exit 2>/dev/null" - }, - "dependencies": { - "compression": "1.7.1", - "cors": "2.8.4", - "helmet": "3.9.0", - "loopback": "3.16.2", - "loopback-boot": "2.27.0", - "loopback-component-explorer": "5.2.0", - "loopback-component-model-diagram": "0.3.0", - "loopback-component-mq": "^2.2.5", - "loopback-component-passport": "3.4.1", - "loopback-component-visualizer": "1.2.1", - "loopback-connector-kafka": "^0.2.1", - "loopback-connector-mongodb": "3.3.0", - "loopback-ds-timestamp-mixin": "^3.4.1", - "moment": "^2.20.1", - "moment-timezone": "^0.5.14", - "nodemailer": "^4.3.1", - "passport-ldapauth": "2.0.0", - "passport-local": "1.0.0", - "passport-openidconnect": "0.0.2", - "serve-favicon": "2.4.5", - "strong-error-handler": "2.3.0", - "uuid": "^3.2.1" - }, - "devDependencies": { - "@mean-expert/loopback-sdk-builder": "2.1.0", - "chai": "^4.1.2", - "chai-http": "^3.0.0", - "eslint": "4.10.0", - "eslint-config-loopback": "8.0.0", - "mocha": "^4.1.0", - "nsp": "2.8.1", - "supertest": "^3.0.0" - }, - "repository": { - "type": "", - "url": "" - }, - "license": "GPL-3.0", - "description": "dacat-api" + "name": "dacat-api", + "version": "2.8.1", + "main": "server/server.js", + "engines": { + "node": ">=4" + }, + "scripts": { + "lint": "eslint common/models", + "start": "node .", + "posttests": "npm run lint && nsp check", + "test": "./node_modules/mocha/bin/mocha --timeout=10000 --reporter spec --exit 2>/dev/null" + }, + "dependencies": { + "compression": "^1.0.3", + "cors": "^2.5.2", + "helmet": "^3.10.0", + "loopback-boot": "^2.6.5", + "serve-favicon": "2.5.0", + "strong-error-handler": "3.1.0", + "loopback-component-explorer": "^6.0.0", + "loopback": "^3.19.0", + "loopback-component-model-diagram": "^0.4.2", + "loopback-component-mq": "^2.2.5", + "loopback-component-passport": "^3.4.1", + "loopback-component-visualizer": "^1.2.1", + "loopback-connector-kafka": "^0.2.1", + "loopback-connector-mongodb": "^3.3.0", + "loopback-ds-timestamp-mixin": "^3.4.1", + "moment": "^2.20.1", + "moment-timezone": "^0.5.14", + "nodemailer": "^4.3.1", + "passport-ldapauth": "^2.0.0", + "passport-local": "^1.0.0", + "passport-openidconnect": "^0.0.2", + "uuid": "^3.2.1" + }, + "devDependencies": { + "eslint": "^5.3.0", + "eslint-config-loopback": "^11.0.0", + "@mean-expert/loopback-sdk-builder": "^2.1.0", + "chai": "^4.1.2", + "chai-http": "^4.0.0", + "mocha": "^5.2.0", + "supertest": "^3.0.0" + }, + "repository": { + "type": "", + "url": "" + }, + "license": "GPL-3.0", + "description": "dacat-api" } From fa9642fbbc5a3c64ad0bb97bda64d550a3294c6a Mon Sep 17 00:00:00 2001 From: egli Date: Sun, 9 Sep 2018 18:21:09 +0200 Subject: [PATCH 051/147] Add support for datasets whose files are stored on decentral storage units --- common/models/dataset-lifecycle.json | 4 ++++ common/models/dataset.json | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/common/models/dataset-lifecycle.json b/common/models/dataset-lifecycle.json index 7816b867..aeb2c18d 100644 --- a/common/models/dataset-lifecycle.json +++ b/common/models/dataset-lifecycle.json @@ -51,6 +51,10 @@ "type": "date", "description": "Day when dataset is supposed to become public according to data policy" }, + "isOnCentralDisk": { + "type": "boolean", + "description": "Flag which is true, if full dataset is available on central fileserver. If false data needs to be copied from decentral storage place to a cache server before the ingest. This information needs to be transferred to the archive system at archive time" + }, "isOnDisk": { "type": "boolean", "description": "Flag which is true, if full dataset is available on disk. Warning: will be obsoleted in coming versions" diff --git a/common/models/dataset.json b/common/models/dataset.json index 637fd515..5a721bb6 100644 --- a/common/models/dataset.json +++ b/common/models/dataset.json @@ -134,7 +134,7 @@ "permission": "ALLOW" }, { - "accessType": "READ", + "accessType": "*", "principalType": "ROLE", "principalId": "$authenticated", "permission": "ALLOW" From 804b6a5534fd6e28db4e6e5a03e8adef8303e87f Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 10 Sep 2018 11:20:47 +0200 Subject: [PATCH 052/147] Update ESS pid prefix --- CI/ESS/envfiles/config.ess.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CI/ESS/envfiles/config.ess.js b/CI/ESS/envfiles/config.ess.js index 73f72c5b..86201675 100644 --- a/CI/ESS/envfiles/config.ess.js +++ b/CI/ESS/envfiles/config.ess.js @@ -4,7 +4,7 @@ module.exports = { restApiRoot: '/api' + (version > 0 ? '/v' + version : ''), host: process.env.HOST || '0.0.0.0', port: process.env.PORT || 3000, - pidPrefix: '10.17199', + pidPrefix: '20.500.12269', policyPublicationShiftInYears: 3, policyRetentionShiftInYears: 10, site: 'ESS', From 79847fdb76717ea06a07311d56d603ce4059df04 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Tue, 11 Sep 2018 10:13:20 +0200 Subject: [PATCH 053/147] add data description --- common/models/published-data.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/common/models/published-data.json b/common/models/published-data.json index ef5d0714..76587422 100644 --- a/common/models/published-data.json +++ b/common/models/published-data.json @@ -52,6 +52,11 @@ "required": true, "description": "Abstract text for published datasets" }, + "dataDescription": { + "type": "string", + "required": true, + "description": "Link to description of how to re-use data" + }, "thumbnail": { "type": "string", "required": true, From bf2ce01727b39e0acd2fa8f3621619f370e11a43 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 12 Sep 2018 16:04:48 +0200 Subject: [PATCH 054/147] Issue #41 work in progress --- common/models/job.js | 179 ++++++++++++++++++++++++---------------- common/models/policy.js | 4 +- 2 files changed, 112 insertions(+), 71 deletions(-) diff --git a/common/models/job.js b/common/models/job.js index 5807c7d9..d56868b9 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -6,81 +6,122 @@ var nodemailer = require('nodemailer'); var config = require('../../server/config.local'); var app = require('../../server/server'); -module.exports = function (Job) { +module.exports = function(Job) { - // Attach job submission to Kafka - if ('queue' in config && config.queue === 'kafka') { - // var options = { - // connectionString: 'localhost:2181/' - // }; - var dataSource = new DataSource('kafka', options); - Job.attachTo(dataSource); - } - Job.observe('before save', (ctx, next) => { - if (ctx.instance) { - // auto fill dataOfLastMessage - var now = new Date(); - if (!ctx.instance.dateOfLastMessage) { - ctx.instance.dateOfLastMessage = now.toISOString(); - } - // make some consistency checks: - // - ensure that all wanted datasets exist already - // - TODO: for archive jobs all datasetslifecycle should be in an "archiveable" state - // TODO ensure that job is created by user who has read access to all datasets in case of retrieve JOBS - var Dataset = app.models.Dataset; - // create array of all pids - // console.log("Verifying datasets:",ctx.options) - const idList=ctx.instance.datasetList.map(x => x.pid) - Dataset.find({where: {pid: {inq: idList}}}, ctx.options, function (err, p){ - console.log("JOBS:lengths",err,p.length,idList.length,p) - if (err || (p.length != idList.length)){ - var e = new Error(); - e.statusCode = 400; - e.message = 'At least one of the datasets could not be found'; - next(e); + // Attach job submission to Kafka + if ('queue' in config && config.queue === 'kafka') { + // var options = { + // connectionString: 'localhost:2181/' + // }; + var dataSource = new DataSource('kafka', options); + Job.attachTo(dataSource); + } + Job.observe('before save', (ctx, next) => { + if (ctx.instance) { + // auto fill dataOfLastMessage + var now = new Date(); + if (!ctx.instance.dateOfLastMessage) { + ctx.instance.dateOfLastMessage = now.toISOString(); + } + + + + // make some consistency checks: + // - ensure that all wanted datasets exist already + // - TODO: for archive jobs all datasetslifecycle should be in an "archiveable" state + // TODO ensure that job is created by user who has read access to all datasets in case of retrieve JOBS + var Dataset = app.models.Dataset; + + // create array of all pids + // console.log("Verifying datasets:",ctx.options) + const idList = ctx.instance.datasetList.map(x => x.pid); + //test for missing datasets + Dataset.find({ + where: { + //inq loopback operator + pid: { + inq: idList + } + } + }, ctx.options, function(err, p) { + console.log("JOBS:lengths", err, p.length, idList.length, p) + if (err || (p.length != idList.length)) { + var e = new Error(); + e.statusCode = 400; + e.message = 'At least one of the datasets could not be found'; + next(e); + } + }); + + console.log("Here!!!!!!!!!!!!!!!"); + //test for datasets already archived + /*var Lifecycle = app.models.DatasetLifecycle; + Lifecycle.find({ + where: { + archivable: false, + datasetId: { + inq: idList + } + } + }, ctx.options, function(err, p) { + console.log("LifeCycle: ", p, idList); + if (p.length > 0) { + var e = new Error(); + e.statusCode = 400; + e.message = 'At least one of the datasets is already archived'; + next(e); + } + else { + next(); + } + });*/ + console.log("......: ", ctx.instance); + //find the relevant lifecycle entries and update their archivable property } else { - next(); + next(); } + + + }); - } else { - next(); - } - }); - Job.observe('after save', (ctx, next) => { - if (ctx.instance && ctx.isNewInstance) { - if ('queue' in config && config.queue === 'rabbitmq') { - Job.publishJob(ctx.instance, "jobqueue") - console.log('Saved Job %s#%s and published to message broker', ctx.Model.modelName, ctx.instance.id); - } - if ('smtpSettings' in config && 'smtpMessage' in config) { - let transporter = nodemailer.createTransport(config.smtpSettings); - transporter.verify(function (error, success) { - if (error) { - console.log(error); - next(); - } else { - console.log('Server is ready to take our messages'); - var message = Object.assign({}, config.smtpMessage); - message['to'] = ctx.instance.emailJobInitiator; - message['subject'] += ' Job Submitted Successfully'; - let text = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n'+JSON.stringify(ctx.instance, null, 4); - message['text'] = text; - transporter.sendMail(message, function (err, info) { - if (err) { - console.log(err); + + + + Job.observe('after save', (ctx, next) => { + if (ctx.instance && ctx.isNewInstance) { + if ('queue' in config && config.queue === 'rabbitmq') { + Job.publishJob(ctx.instance, "jobqueue") + console.log('Saved Job %s#%s and published to message broker', ctx.Model.modelName, ctx.instance.id); + } + if ('smtpSettings' in config && 'smtpMessage' in config) { + let transporter = nodemailer.createTransport(config.smtpSettings); + transporter.verify(function(error, success) { + if (error) { + console.log(error); + next(); } else { - console.log('Email sent'); + console.log('Server is ready to take our messages'); + var message = Object.assign({}, config.smtpMessage); + message['to'] = ctx.instance.emailJobInitiator; + message['subject'] += ' Job Submitted Successfully'; + let text = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n' + JSON.stringify(ctx.instance, null, 4); + message['text'] = text; + transporter.sendMail(message, function(err, info) { + if (err) { + console.log(err); + } else { + console.log('Email sent'); + } + next(); + }); } - next(); }); } - }); - } - } else { - console.log('Updated %s matching %j', ctx.Model.pluralModelName, - ctx.where); - next(); - } - }); -}; + } else { + console.log('Updated %s matching %j', ctx.Model.pluralModelName, + ctx.where); + next(); + } + }); + }; diff --git a/common/models/policy.js b/common/models/policy.js index 3ab1a585..f27a8eb3 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -27,8 +27,8 @@ module.exports = function(Policy) { } }, function(err, instance) { var email = instance.profile.email; - //console.log("email:", email); - //console.log("manager: ", ctx.currentInstance.manager); + console.log("email:", email); + console.log("manager: ", ctx.currentInstance.manager); if (!ctx.currentInstance.manager.includes(email)) { var e = new Error('Access Not Allowed - policy manager action'); e.statusCode = 401; From b0b6a0a7e4b5e5355f4c2ce43b57ff72aca8953d Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 24 Oct 2018 14:51:03 +0200 Subject: [PATCH 055/147] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 646db569..57d4f14b 100644 --- a/README.md +++ b/README.md @@ -109,8 +109,9 @@ NOTE: An example of kafka has been set in `Job.js` The data model is defined inside the common/models directory according to the rules defined by the Loopback API framework The data model is visualized in form of an -[Model UML diagram](http://localhost:3000/modeldiagram) or -[Model Visualizer](http://localhost:3000/visualize) +Model UML diagram which can be seen at /modeldiagram or + +Model Visualizer which can be seen at /visualize # Data Catalog API From c332bb9681a424efd9ee1f14e97be761e76ee204 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 24 Oct 2018 14:52:35 +0200 Subject: [PATCH 056/147] Add files via upload --- CI/ESS/scicatmodeldiagram.png | Bin 0 -> 260654 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 CI/ESS/scicatmodeldiagram.png diff --git a/CI/ESS/scicatmodeldiagram.png b/CI/ESS/scicatmodeldiagram.png new file mode 100644 index 0000000000000000000000000000000000000000..99d676de720038f4fc75d7caa28472280bc07f3a GIT binary patch literal 260654 zcmb??byU<**X{t$&>`JO3)0;<1|5RZ-QC?KAsx~+Dxq|DBV7YX4_$+FH(adu{l5F( zUF-f93(ml>&vW*9_Othi`S3(CHq0;-RsFU(8rZZG$8w^fjrY^g8EPLJtqEfo>wQ&Uk0eeVHZh0aZU z@B3c4zBp7_3aPKk&4DC*%}Ji0>MkqH{G1uv)>sti>+Iob{XW2T_D5%9?bn)$FOeU7 zV

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zeMFq|*Oi&Yp7c;bl6#WFGU@Z^%PgUhUil`gc>@&53PX$A)A zAFQqDl#a@&`w9or-}rOhF1yrQz`M1!;Z<4$BYywoq+6=h2>qk4?m?UQnfR zZ9A=Pa5|Cu#(>ua8?31FEX*Wc!+P`dZr8Ml{nQJ~cjFP1}={>jHmw`}PI>;17(r8gKQ)#cx_(kLiT% z&FASAYF&fsh)VLqqKHnQ95)!h;c@}b%*76fs1TY)voR;0JMuz}ek)T}iE@s0co<_i za10ovBJ!pk%ZIh^$QJVM35+%<=Y=A4^79`x9Ghv2SbY3?GkRT|FFcavzM_{g>n{C| zAZ)}ydpACytVyx!SXdO+CCVR+Ur>t;6q+7g_(V<)yx;&GEj2QS{Xx^e(rvEw|4BRS zAQ1XLnbY3?@t4Tb?FjRoOaQ(Cfp@9J*)K8@Bxv?$101^SkVBtuA+r+3(c3S-zxn_7 b%fB7{8}#WD%9S Date: Wed, 24 Oct 2018 14:55:09 +0200 Subject: [PATCH 057/147] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 57d4f14b..7145f9d1 100644 --- a/README.md +++ b/README.md @@ -110,6 +110,7 @@ The data model is defined inside the common/models directory according to the ru The data model is visualized in form of an Model UML diagram which can be seen at /modeldiagram or +![model diagram](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/scicatmodeldiagram.png) Model Visualizer which can be seen at /visualize From 875d0349697a13c2542e31e3e91e3be33bcb3f88 Mon Sep 17 00:00:00 2001 From: Thomas A Caswell Date: Wed, 24 Oct 2018 10:42:26 -0400 Subject: [PATCH 058/147] Point install instructions at public repo Cloning from the PSI gitlab requires authentication. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7145f9d1..1343a32c 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ The needed database will be created automatically when the API server starts. Fo ## Get code ``` -git clone https://gitlab.psi.ch/MELANIE/catamel.git +git clone https://github.com/SciCatProject/catamel.git cd catamel npm install ``` From f87995b05697004a4db1220d7fc4a4b5165e7b29 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 25 Oct 2018 10:01:21 +0200 Subject: [PATCH 059/147] Correct filenames, add mongo install, add config Add config.local.js --- README.md | 50 ++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 48 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1343a32c..06f654c8 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,12 @@ You need to setup a MongoDB server. E.g. on a Redhat Linux System the following yum install mongodb-org-server ``` +On MacOS +``` +brew install mongodb +``` + + The needed database will be created automatically when the API server starts. Follow this [description](https://docs.mongodb.com/manual/tutorial/enable-authentication/) to enable authenticated access to the Mongo DB. ## Get code @@ -23,10 +29,10 @@ npm install ``` ## adjust Configuration -Add a datasources.local.json file inside server directory with connection data to your mongodb instance +Add a `datasources.json` file inside server directory with connection data to your mongodb instance ``` -server/datasources.local.json e.g. +server/datasources.json e.g. { "mongo": { "host": "mongodbprod.my.site", @@ -35,6 +41,46 @@ server/datasources.local.json e.g. } } +``` +## Add local config file +Add a file `config.local.js` inside server directory. You can add you own PID prefix (e.g. from Handle.net), site name (e.g. ESS) and facilities ('beamline1', 'beamline2', etc) +``` +var p = require('../package.json'); +var version = p.version.split('.').shift(); +module.exports = { + restApiRoot: '/api' + (version > 0 ? '/v' + version : ''), + host: process.env.HOST || '0.0.0.0', + port: process.env.PORT || 3000, + pidPrefix: '', + policyPublicationShiftInYears: 3, + policyRetentionShiftInYears: 10, + site: '', + facilities: [], + datasetStatusMessages: { + datasetCreated: "Dataset created", + datasetOndisk: "Stored on primary disk and on archive disk", + datasetOnDiskAndTape: "Stored on primary disk and on tape", + datasetOnTape: "Stored only in archive", + datasetRetrieved: "Retrieved to target disk", + datasetDeleted: "Deleted from archive and disk" + }, + datasetTransitionMessages: { + scheduleArchive: "Scheduled for archiving", + schedulePurgeFromDisk: "Scheduled for purging from primary disk", + scheduleRetrieve: "Scheduled for retrieval", + scheduleDelete: "Scheduled for removal from archive" + }, + jobMessages: { + jobSubmitted: "Submitted for immediate execution", + jobSubmittedDelayed: "Submitted for delayed execution", + jobForwarded: "Forwarded to archive system", + jobStarted: "Execution started", + jobInProgress: "Finished by %i percent", + jobSuccess: "Succesfully finished", + jobError: "Finished with errors", + jobCancel: "Cancelled" + } +}; ``` ## Email Notifications From 52e6dcd0a47022e037b6161251b0bab5c309eac4 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 25 Oct 2018 10:19:05 +0200 Subject: [PATCH 060/147] Update README.md --- README.md | 24 ++++++++++++++++++++++-- 1 file changed, 22 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 06f654c8..819d4f10 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ npm install ``` ## adjust Configuration -Add a `datasources.json` file inside server directory with connection data to your mongodb instance +Add a `datasources.json` file inside the `server` directory with connection data to your mongodb instance ``` server/datasources.json e.g. @@ -42,8 +42,28 @@ server/datasources.json e.g. } ``` + +## Add providers.json +Add a file `providers.json` inside the `server` directory. + +``` +{ + "local": { + "provider": "local", + "module": "passport-local", + "usernameField": "username", + "passwordField": "password", + "authPath": "/auth/local", + "successRedirect": "/auth/account", + "failureRedirect": "/local", + "failureFlash": true + } +} +``` + + ## Add local config file -Add a file `config.local.js` inside server directory. You can add you own PID prefix (e.g. from Handle.net), site name (e.g. ESS) and facilities ('beamline1', 'beamline2', etc) +Add a file `config.local.js` inside the `server` directory. You can add your own PID prefix (e.g. from Handle.net), site name (e.g. ESS) and facilities ('beamline1', 'beamline2', etc) ``` var p = require('../package.json'); var version = p.version.split('.').shift(); From 29559dfae5b5ffac30f6031601bdbf264ef8dac5 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 25 Oct 2018 10:22:55 +0200 Subject: [PATCH 061/147] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 819d4f10..79d1386d 100644 --- a/README.md +++ b/README.md @@ -28,8 +28,8 @@ cd catamel npm install ``` -## adjust Configuration -Add a `datasources.json` file inside the `server` directory with connection data to your mongodb instance +## Configure database source +Add a `datasources.json` file inside the `server` directory with connection data to your mongodb instance. If using a local mongodb installation, running on port 27017, e.g. you can change the `"host"` property to read `"host":"localhost:27017"` ``` server/datasources.json e.g. From 7c4ceaf487eab4e6b63f84aba071774739865b1b Mon Sep 17 00:00:00 2001 From: Hannes Petri Date: Thu, 25 Oct 2018 12:31:55 -0400 Subject: [PATCH 062/147] Validates uniqueness of pid for all dataset models --- common/models/dataset.js | 2 ++ common/models/derived-dataset.js | 2 ++ common/models/raw-dataset.js | 1 + 3 files changed, 5 insertions(+) diff --git a/common/models/dataset.js b/common/models/dataset.js index fad151ae..fecb7b80 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -13,6 +13,8 @@ module.exports = function(Dataset) { var app = require('../../server/server'); // make sure that all times are UTC + Dataset.validatesUniquenessOf('pid'); + // put Dataset.beforeRemote('replaceOrCreate', function(ctx, instance, next) { utils.updateTimesToUTC(['creationTime'], ctx.args.data); diff --git a/common/models/derived-dataset.js b/common/models/derived-dataset.js index 0e017b50..f10a3457 100644 --- a/common/models/derived-dataset.js +++ b/common/models/derived-dataset.js @@ -3,6 +3,8 @@ module.exports = function (Deriveddataset) { var utils = require('./utils'); + Deriveddataset.validatesUniquenessOf('pid'); + // filter on dataset type (raw, derived etc) Deriveddataset.observe('access', function (ctx, next) { var typeCondition = { diff --git a/common/models/raw-dataset.js b/common/models/raw-dataset.js index 80437a42..9a94a596 100644 --- a/common/models/raw-dataset.js +++ b/common/models/raw-dataset.js @@ -2,6 +2,7 @@ var utils = require('./utils'); module.exports = function(Rawdataset) { + Rawdataset.validatesUniquenessOf('pid'); // filter on dataset type (raw, derived etc) Rawdataset.observe('access', function(ctx, next) { From 4d37efd43408e1bd5c25abc0ca0e4b8de6b58bd4 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 29 Oct 2018 14:41:50 +0100 Subject: [PATCH 063/147] added emabrgoPeriod --- common/models/policy.js | 4 ++-- common/models/policy.json | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/common/models/policy.js b/common/models/policy.js index f27a8eb3..3ab1a585 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -27,8 +27,8 @@ module.exports = function(Policy) { } }, function(err, instance) { var email = instance.profile.email; - console.log("email:", email); - console.log("manager: ", ctx.currentInstance.manager); + //console.log("email:", email); + //console.log("manager: ", ctx.currentInstance.manager); if (!ctx.currentInstance.manager.includes(email)) { var e = new Error('Access Not Allowed - policy manager action'); e.statusCode = 401; diff --git a/common/models/policy.json b/common/models/policy.json index e2bc4319..6a203988 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -48,6 +48,11 @@ "retrieveEmailsToBeNotified": { "type": ["string"], "description": "Array of additional email addresses that should be notified up a retrieval job creation" + }, + "embargoPeriod": { + "type": "number", + "description": "Number of years after dataset creation before the dataset becomes public", + "default": 3 } }, "validations": [], From 3238bea162e5b27176e4dfb309f110db7e4ebeda Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 29 Oct 2018 17:04:47 +0100 Subject: [PATCH 064/147] user correct email in job notification --- common/models/job.js | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/common/models/job.js b/common/models/job.js index d56868b9..7956a854 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -23,8 +23,7 @@ module.exports = function(Job) { if (!ctx.instance.dateOfLastMessage) { ctx.instance.dateOfLastMessage = now.toISOString(); } - - + console.log("ctx.instance.emailJobInitiator: ", ctx.instance.emailJobInitiator); // make some consistency checks: // - ensure that all wanted datasets exist already @@ -53,7 +52,6 @@ module.exports = function(Job) { } }); - console.log("Here!!!!!!!!!!!!!!!"); //test for datasets already archived /*var Lifecycle = app.models.DatasetLifecycle; Lifecycle.find({ @@ -75,7 +73,6 @@ module.exports = function(Job) { next(); } });*/ - console.log("......: ", ctx.instance); //find the relevant lifecycle entries and update their archivable property } else { next(); @@ -90,6 +87,19 @@ module.exports = function(Job) { Job.observe('after save', (ctx, next) => { if (ctx.instance && ctx.isNewInstance) { + // replace email with that from userIdentity + var initEmail = ""; + var UserIdentity = app.models.UserIdentity; + var userId = ctx.options.accessToken.userId; + //PersistedModel Static Method call + UserIdentity.findOne({ + //json filter + where: { + userId: userId + } + }, function(err, instance) { + initEmail = instance.profile.email; + }); if ('queue' in config && config.queue === 'rabbitmq') { Job.publishJob(ctx.instance, "jobqueue") console.log('Saved Job %s#%s and published to message broker', ctx.Model.modelName, ctx.instance.id); @@ -103,7 +113,7 @@ module.exports = function(Job) { } else { console.log('Server is ready to take our messages'); var message = Object.assign({}, config.smtpMessage); - message['to'] = ctx.instance.emailJobInitiator; + message['to'] = initEmail; message['subject'] += ' Job Submitted Successfully'; let text = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n' + JSON.stringify(ctx.instance, null, 4); message['text'] = text; From 456dcc58724970be0f6b5e208d399a1377925ed8 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 29 Oct 2018 18:51:26 +0100 Subject: [PATCH 065/147] merge --- common/models/job.js | 245 ++++++++++++++++++++++--------------------- 1 file changed, 127 insertions(+), 118 deletions(-) diff --git a/common/models/job.js b/common/models/job.js index 7956a854..6284788f 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -6,132 +6,141 @@ var nodemailer = require('nodemailer'); var config = require('../../server/config.local'); var app = require('../../server/server'); -module.exports = function(Job) { +module.exports = function (Job) { - // Attach job submission to Kafka - if ('queue' in config && config.queue === 'kafka') { - // var options = { - // connectionString: 'localhost:2181/' - // }; - var dataSource = new DataSource('kafka', options); - Job.attachTo(dataSource); - } - Job.observe('before save', (ctx, next) => { - if (ctx.instance) { - // auto fill dataOfLastMessage - var now = new Date(); - if (!ctx.instance.dateOfLastMessage) { - ctx.instance.dateOfLastMessage = now.toISOString(); - } - console.log("ctx.instance.emailJobInitiator: ", ctx.instance.emailJobInitiator); - - // make some consistency checks: - // - ensure that all wanted datasets exist already - // - TODO: for archive jobs all datasetslifecycle should be in an "archiveable" state - // TODO ensure that job is created by user who has read access to all datasets in case of retrieve JOBS - var Dataset = app.models.Dataset; - - // create array of all pids - // console.log("Verifying datasets:",ctx.options) - const idList = ctx.instance.datasetList.map(x => x.pid); - //test for missing datasets - Dataset.find({ - where: { - //inq loopback operator - pid: { - inq: idList - } - } - }, ctx.options, function(err, p) { - console.log("JOBS:lengths", err, p.length, idList.length, p) - if (err || (p.length != idList.length)) { - var e = new Error(); - e.statusCode = 400; - e.message = 'At least one of the datasets could not be found'; - next(e); - } - }); - - //test for datasets already archived - /*var Lifecycle = app.models.DatasetLifecycle; - Lifecycle.find({ - where: { - archivable: false, - datasetId: { - inq: idList - } - } - }, ctx.options, function(err, p) { - console.log("LifeCycle: ", p, idList); - if (p.length > 0) { - var e = new Error(); - e.statusCode = 400; - e.message = 'At least one of the datasets is already archived'; - next(e); - } - else { - next(); - } - });*/ - //find the relevant lifecycle entries and update their archivable property + // Attach job submission to Kafka + if ('queue' in config && config.queue === 'kafka') { + // var options = { + // connectionString: 'localhost:2181/' + // }; + var dataSource = new DataSource('kafka', options); + Job.attachTo(dataSource); + } + Job.observe('before save', (ctx, next) => { + if (ctx.instance) { + // auto fill dataOfLastMessage + var now = new Date(); + if (!ctx.instance.dateOfLastMessage) { + ctx.instance.dateOfLastMessage = now.toISOString(); + } + // make some consistency checks: + // - ensure that all wanted datasets exist already + // - TODO: for archive jobs all datasetslifecycle should be in an "archiveable" state + // TODO ensure that job is created by user who has read access to all datasets in case of retrieve JOBS + var Dataset = app.models.Dataset; + // create array of all pids + // console.log("Verifying datasets:",ctx.options) + const idList=ctx.instance.datasetList.map(x => x.pid) + Dataset.find({where: {pid: {inq: idList}}}, ctx.options, function (err, p){ + console.log("JOBS:lengths",err,p.length,idList.length,p) + if (err || (p.length != idList.length)){ + var e = new Error(); + e.statusCode = 400; + e.message = 'At least one of the datasets could not be found'; + next(e); } else { - next(); + next(); } - - - }); + //test for datasets already archived + /*var Lifecycle = app.models.DatasetLifecycle; + Lifecycle.find({ + where: { + archivable: false, + datasetId: { + inq: idList + } + } + }, ctx.options, function(err, p) { + console.log("LifeCycle: ", p, idList); + if (p.length > 0) { + var e = new Error(); + e.statusCode = 400; + e.message = 'At least one of the datasets is already archived'; + next(e); + } + else { + next(); + } + });*/ + } else { + next(); + } + }); + Job.observe('after save', (ctx, next) => { + // replace email with that from userIdentity + var initEmail = ""; + var UserIdentity = app.models.UserIdentity; + var userId = ctx.options.accessToken.userId; + //PersistedModel Static Method call + UserIdentity.findOne({ + //json filter + where: { + userId: userId + } + }, function(err, instance) { + initEmail = instance.profile.email; + }); + if (ctx.instance && ctx.isNewInstance) { - - - Job.observe('after save', (ctx, next) => { - if (ctx.instance && ctx.isNewInstance) { - // replace email with that from userIdentity - var initEmail = ""; - var UserIdentity = app.models.UserIdentity; - var userId = ctx.options.accessToken.userId; - //PersistedModel Static Method call - UserIdentity.findOne({ - //json filter - where: { - userId: userId - } - }, function(err, instance) { - initEmail = instance.profile.email; - }); - if ('queue' in config && config.queue === 'rabbitmq') { - Job.publishJob(ctx.instance, "jobqueue") - console.log('Saved Job %s#%s and published to message broker', ctx.Model.modelName, ctx.instance.id); + if ('queue' in config && config.queue === 'rabbitmq') { + Job.publishJob(ctx.instance, "jobqueue") + console.log('Saved Job %s#%s and published to message broker', ctx.Model.modelName, ctx.instance.id); + } + if ('smtpSettings' in config && 'smtpMessage' in config) { + let transporter = nodemailer.createTransport(config.smtpSettings); + transporter.verify(function (error, success) { + if (error) { + console.log(error); + next(); + } else { + console.log('Server is ready to take our messages'); + var message = Object.assign({}, config.smtpMessage); + message['to'] = initEmail; + message['subject'] += ' Job Submitted Successfully'; + let text = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n'+JSON.stringify(ctx.instance, null, 4); + message['text'] = text; + transporter.sendMail(message, function (err, info) { + if (err) { + console.log(err); + } else { + console.log('Email sent'); + } + next(); + }); } - if ('smtpSettings' in config && 'smtpMessage' in config) { - let transporter = nodemailer.createTransport(config.smtpSettings); - transporter.verify(function(error, success) { - if (error) { - console.log(error); - next(); + }); + } else { + next() + } + } else { + if ('smtpSettings' in config && 'smtpMessage' in config) { + let transporter = nodemailer.createTransport(config.smtpSettings); + transporter.verify(function (error, success) { + if (error) { + console.log(error); + next(); + } else { + console.log('Server is ready to take our messages'); + var message = Object.assign({}, config.smtpMessage); + message['to'] = initEmail; + message['subject'] += ' Job Finished with status '+ ctx.instance.jobStatusMessage; + let text = 'Hello, \n\n Your Job with id is now finished. \n\n The resulting job description is.\n\n'+JSON.stringify(ctx.instance, null, 4); + message['text'] = text; + transporter.sendMail(message, function (err, info) { + if (err) { + console.log(err); } else { - console.log('Server is ready to take our messages'); - var message = Object.assign({}, config.smtpMessage); - message['to'] = initEmail; - message['subject'] += ' Job Submitted Successfully'; - let text = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n' + JSON.stringify(ctx.instance, null, 4); - message['text'] = text; - transporter.sendMail(message, function(err, info) { - if (err) { - console.log(err); - } else { - console.log('Email sent'); - } - next(); - }); + console.log('Email sent'); } + next(); }); } - } else { - console.log('Updated %s matching %j', ctx.Model.pluralModelName, - ctx.where); - next(); - } - }); - }; + }); + } else { + next() + } + } + }); +}; From 9ddc3476f7182e2ad776a3d9202104d96c889d04 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 29 Oct 2018 19:08:02 +0100 Subject: [PATCH 066/147] Update policy.json --- common/models/policy.json | 4 ---- 1 file changed, 4 deletions(-) diff --git a/common/models/policy.json b/common/models/policy.json index 6a203988..105ce8ee 100644 --- a/common/models/policy.json +++ b/common/models/policy.json @@ -17,10 +17,6 @@ "description": "Defines the level of redundancy in storage to minimize loss of data. Allowed values are low, medium, high. Low could e.g. mean one tape copy only, medium could mean two tape copies and high two geo-redundant tape copies", "default": "low" }, - "autoArchive": { - "type": "boolean", - "description": "automatically archive dataset" - }, "autoArchive": { "type": "boolean", "description": "Flag to indicate that a dataset should be automatically archived after ingest. If false then archive delay is ignored", From 97c98a76911234af060213ebfd535ba0a4467929 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 31 Oct 2018 12:26:26 +0100 Subject: [PATCH 067/147] moved email resolve into before save --- common/models/job.js | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/common/models/job.js b/common/models/job.js index 6284788f..6e3010c4 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -17,6 +17,21 @@ module.exports = function (Job) { Job.attachTo(dataSource); } Job.observe('before save', (ctx, next) => { + // replace email with that from userIdentity + var UserIdentity = app.models.UserIdentity; + var userId = ctx.options.accessToken.userId; + //PersistedModel Static Method call + UserIdentity.findOne({ + //json filter + where: { + userId: userId + } + }, function(err, instance) { + if(!!instance) + { + ctx.instance.emailJobInitiator = instance.profile.email; + } + }); if (ctx.instance) { // auto fill dataOfLastMessage var now = new Date(); @@ -69,19 +84,6 @@ module.exports = function (Job) { }); Job.observe('after save', (ctx, next) => { - // replace email with that from userIdentity - var initEmail = ""; - var UserIdentity = app.models.UserIdentity; - var userId = ctx.options.accessToken.userId; - //PersistedModel Static Method call - UserIdentity.findOne({ - //json filter - where: { - userId: userId - } - }, function(err, instance) { - initEmail = instance.profile.email; - }); if (ctx.instance && ctx.isNewInstance) { if ('queue' in config && config.queue === 'rabbitmq') { @@ -97,7 +99,7 @@ module.exports = function (Job) { } else { console.log('Server is ready to take our messages'); var message = Object.assign({}, config.smtpMessage); - message['to'] = initEmail; + message['to'] = ctx.instance.emailJobInitiator; message['subject'] += ' Job Submitted Successfully'; let text = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n'+JSON.stringify(ctx.instance, null, 4); message['text'] = text; @@ -124,7 +126,7 @@ module.exports = function (Job) { } else { console.log('Server is ready to take our messages'); var message = Object.assign({}, config.smtpMessage); - message['to'] = initEmail; + message['to'] = ctx.instance.emailJobInitiator; message['subject'] += ' Job Finished with status '+ ctx.instance.jobStatusMessage; let text = 'Hello, \n\n Your Job with id is now finished. \n\n The resulting job description is.\n\n'+JSON.stringify(ctx.instance, null, 4); message['text'] = text; From 55e2a3cf01367d132dff45b9074b5eba5328fdc8 Mon Sep 17 00:00:00 2001 From: egli Date: Sat, 3 Nov 2018 17:34:44 +0100 Subject: [PATCH 068/147] Send emails only at start and end of job, enhanced subject infos --- common/models/job.js | 50 ++++++++++++++++++++++++-------------------- 1 file changed, 27 insertions(+), 23 deletions(-) diff --git a/common/models/job.js b/common/models/job.js index 6e3010c4..54dea608 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -100,7 +100,7 @@ module.exports = function (Job) { console.log('Server is ready to take our messages'); var message = Object.assign({}, config.smtpMessage); message['to'] = ctx.instance.emailJobInitiator; - message['subject'] += ' Job Submitted Successfully'; + message['subject'] += ' ' + ctx.instance.type + ' job submitted successfully'; let text = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n'+JSON.stringify(ctx.instance, null, 4); message['text'] = text; transporter.sendMail(message, function (err, info) { @@ -117,29 +117,33 @@ module.exports = function (Job) { next() } } else { - if ('smtpSettings' in config && 'smtpMessage' in config) { - let transporter = nodemailer.createTransport(config.smtpSettings); - transporter.verify(function (error, success) { - if (error) { - console.log(error); - next(); - } else { - console.log('Server is ready to take our messages'); - var message = Object.assign({}, config.smtpMessage); - message['to'] = ctx.instance.emailJobInitiator; - message['subject'] += ' Job Finished with status '+ ctx.instance.jobStatusMessage; - let text = 'Hello, \n\n Your Job with id is now finished. \n\n The resulting job description is.\n\n'+JSON.stringify(ctx.instance, null, 4); - message['text'] = text; - transporter.sendMail(message, function (err, info) { - if (err) { - console.log(err); - } else { - console.log('Email sent'); - } + if ('smtpSettings' in config && 'smtpMessage' in config) { + if (ctx.instance.jobStatusMessage.startsWith("finish")) { + let transporter = nodemailer.createTransport(config.smtpSettings); + transporter.verify(function(error, success) { + if (error) { + console.log(error); next(); - }); - } - }); + } else { + console.log('Server is ready to send message to ', ctx.instance.emailJobInitiator); + var message = Object.assign({}, config.smtpMessage); + message['to'] = ctx.instance.emailJobInitiator; + message['subject'] += ' '+ctx.instance.type + ' job from ' + ctx.instance.creationTime.toISOString().replace(/T/, ' ').replace(/\..+/, '') + ' (UTC) finished with status ' + ctx.instance.jobStatusMessage; + let text = 'Hello, \n\n Your Job from ' + ctx.instance.creationTime + ' is now finished. \n\n The resulting job description is.\n\n' + JSON.stringify(ctx.instance, null, 4); + message['text'] = text; + transporter.sendMail(message, function(err, info) { + if (err) { + console.log(err); + } else { + console.log('Email sent'); + } + next(); + }); + } + }); + } else { + next() + } } else { next() } From 1bc52bf122b6a6d2367fd180e54617282dd6ba54 Mon Sep 17 00:00:00 2001 From: egli Date: Sun, 11 Nov 2018 15:45:40 +0100 Subject: [PATCH 069/147] Boot code for role creation now handled asynchronously, test cases protected against already existing entries in DB --- server/boot/common_utils.js | 16 ++++++----- server/boot/createRoles.js | 26 ++++++++++------- test/Datablock.js | 57 +++++++++++++++++++++++++++++++------ test/Proposal.js | 40 ++++++++++++++++++++++++-- 4 files changed, 110 insertions(+), 29 deletions(-) diff --git a/server/boot/common_utils.js b/server/boot/common_utils.js index 5b1a8b15..e04cd8cc 100644 --- a/server/boot/common_utils.js +++ b/server/boot/common_utils.js @@ -1,7 +1,7 @@ //no need for callback since it is not used -exports.connectRole = function(app, roleName, user) { +exports.connectRole = function(app, roleName, user, cb) { var Role = app.models.Role; var RoleMapping = app.models.RoleMapping; RoleMapping.settings.strictObjectIDCoercion = true; @@ -11,35 +11,37 @@ exports.connectRole = function(app, roleName, user) { name: roleName } }, function(err, role) { - if (err) throw err; + if (err) return cb(err); if (role.length == 0) { Role.create({ name: roleName }, function(err, role) { - if (err) throw err; + if (err) return cb(err); console.log('Created role:', role); - mapRole(RoleMapping, role, user); + mapRole(RoleMapping, role, user,cb); }); }else if (role.length === 1) { - mapRole(RoleMapping, role[0], user); + mapRole(RoleMapping, role[0], user,cb); } }); }; -function mapRole(RoleMapping, role, user) { +function mapRole(RoleMapping, role, user, cb) { //check mapping exists first, maybe also look at user id? RoleMapping.find({ where: { roleId: role.id } }, function(err, maps) { + if(err) return cb(err) if(maps.length === 0) { role.principals.create({ principalType: RoleMapping.USER, principalId: user.id }, function(err, principal) { - if (err) throw err; + if (err) return cb(err); console.log('Assigned user %s to role %s', user.username, role.name); + cb(null) }); } }); diff --git a/server/boot/createRoles.js b/server/boot/createRoles.js index 7c24f992..c5c99357 100644 --- a/server/boot/createRoles.js +++ b/server/boot/createRoles.js @@ -1,12 +1,14 @@ var utils = require('./common_utils'); var fs = require('fs'); -module.exports = function(app) { +module.exports = function(app,cb) { // define roles // note: role names are all lowercase , corresponding accounts camelcase // - createRole = function(account) { + + + createRole = function(account,cb) { var User = app.models.User; @@ -16,7 +18,7 @@ module.exports = function(app) { } }, function(err, users) { if (err) { - throw err; + return cb(err); } else if (users.length === 0) { // check for password file for this role path='server/'+account; @@ -32,8 +34,9 @@ module.exports = function(app) { }, function(err, user) { if (err) { console.log("User create:"+err+" "+user) + return cb(err) } else { - utils.connectRole(app, account.toLowerCase(), user); + utils.connectRole(app, account.toLowerCase(), user, cb); } }); } else { @@ -46,22 +49,23 @@ module.exports = function(app) { }, function(err, user) { if (err) { console.log("User create:"+err+" "+user) + return cb(err) } else { - utils.connectRole(app, account.toLowerCase(), user); + utils.connectRole(app, account.toLowerCase(), user, cb); } }); } } else { console.log('Found ' + account + ' user:', users[0].username); //create the role if not yet there - utils.connectRole(app, account.toLowerCase(), users[0]); + utils.connectRole(app, account.toLowerCase(), users[0], cb); } }); }; - createRole('admin'); - createRole('archiveManager'); - createRole('ingestor'); - createRole('proposalIngestor'); - createRole('userGroupIngestor') + createRole('admin',cb); + createRole('archiveManager',cb); + createRole('ingestor',cb); + createRole('proposalIngestor',cb); + createRole('userGroupIngestor',cb) }; diff --git a/test/Datablock.js b/test/Datablock.js index ad98faf7..9e77bdea 100644 --- a/test/Datablock.js +++ b/test/Datablock.js @@ -200,14 +200,17 @@ describe('Test Datablocks and OrigDatablocks and their relation to Datasets', () }, (tokenVal) => { accessTokenIngestor = tokenVal; - }); - utils.getToken(app, { - 'username': 'archiveManager', - 'password': 'aman' - }, - (tokenVal) => { - accessTokenArchiveManager = tokenVal; - done(); + utils.getToken(app, { + 'username': 'archiveManager', + 'password': 'aman' + }, + (tokenVal) => { + accessTokenArchiveManager = tokenVal; + console.log("============ Both accessToken received") + console.log("Tokens:", accessTokenIngestor, accessTokenArchiveManager) + done(); + }); + }); }); @@ -249,6 +252,42 @@ describe('Test Datablocks and OrigDatablocks and their relation to Datasets', () }); }); + // the following two function definition prepare for + // multi-delete actions to finish + async function deleteDatablock(item) { + await request(app) + .delete('/api/v2/Datablocks/' + item.id + '?access_token=' + accessTokenArchiveManager) + .set('Accept', 'application/json') + .expect(200) + } + + async function processArray(array) { + for (const item of array) { + await deleteDatablock(item) + } + // console.log("==== Finishing all deletes") + } + + it('remove potentially existing datablocks to guarantee uniqueness', function(done) { + let filter = '{"where": {"archiveId": {"inq": ["someOtherId", "' + testdataBlock.archiveId + '"]}}}' + // console.log("Filter expression before encoding:",filter) + let url = '/api/v2/Datablocks?filter=' + encodeURIComponent(filter) + '&access_token=' + accessTokenArchiveManager + // console.log("============= url of query: ", url) + request(app) + .get(url) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + // console.log(" ==================== Found existing datablocks:", res.body) + // now remove all these entries + processArray(res.body) + done() + }); + }); + it('adds a new datablock', function(done) { request(app) .post('/api/v2/Datablocks?access_token=' + accessTokenArchiveManager) @@ -295,7 +334,7 @@ describe('Test Datablocks and OrigDatablocks and their relation to Datasets', () }); it('adds a second datablock for same dataset', function(done) { - testdataBlock.archiveId = "oneCopyBig/p10029/raw/2018/01/23/20.500.11935/07e8a14c-f496-42fe-b4b4-9ff410616xxx_1_2018-01-23-03-11-34.tar", + testdataBlock.archiveId = "someOtherId", request(app) .post('/api/v2/Datablocks?access_token=' + accessTokenArchiveManager) .send(testdataBlock) diff --git a/test/Proposal.js b/test/Proposal.js index 972420c4..4bf1386e 100644 --- a/test/Proposal.js +++ b/test/Proposal.js @@ -14,7 +14,7 @@ var utils = require('./LoginUtils'); var accessToken = null, proposalId = null; -var testdataset = { +var testproposal = { "proposalId": "20170266", "email": "proposer%40uni.edu", "title": "A test proposal", @@ -35,10 +35,46 @@ describe('Simple Proposal tests', () => { }); }); + // the following two function definition prepare for + // multi-delete actions to finish + async function deleteProposal(item) { + await request(app) + .delete('/api/v2/Proposals/' + item.proposalId + '?access_token=' + accessToken) + .set('Accept', 'application/json') + .expect(200) + } + + async function processArray(array) { + for (const item of array) { + await deleteProposal(item) + } + // console.log("==== Finishing all deletes") + } + + it('remove potentially existing proposals to guarantee uniqueness', function(done) { + let filter = '{"where": {"proposalId": "' + testproposal.proposalId + '"}}' + // console.log("Filter expression before encoding:",filter) + let url = '/api/v2/Proposals?filter=' + encodeURIComponent(filter) + '&access_token=' + accessToken + // console.log("============= url of query: ", url) + request(app) + .get(url) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + //console.log(" ==================== Found existing proposals:", res.body) + // now remove all these entries + processArray(res.body) + done() + }); + }); + it('adds a new proposal', function(done) { request(app) .post('/api/v2/Proposals?access_token=' + accessToken) - .send(testdataset) + .send(testproposal) .set('Accept', 'application/json') .expect(200) .expect('Content-Type', /json/) From b8c5908b07d5e0b626c6a234e5ecf4f24f0c1d06 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 12 Nov 2018 12:58:09 +0100 Subject: [PATCH 070/147] Issue #86 generate default policy record for A groups --- common/models/dataset.js | 7 ++++++- common/models/policy.js | 21 +++++++++++++++++++-- 2 files changed, 25 insertions(+), 3 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index fecb7b80..becb5c2c 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -33,7 +33,7 @@ module.exports = function(Dataset) { next(); }); - // auto add pid + // auto add pid, add a policy record Dataset.observe('before save', (ctx, next) => { if (ctx.instance) { if (ctx.isNewInstance) { @@ -44,6 +44,10 @@ module.exports = function(Dataset) { } ctx.instance.version = p.version; ctx.instance.type = 'base'; + + // add a policy record now (A Groups). Check that one doesnt already exist + var Policy = app.models.Policy; + Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail); } next(); }); @@ -381,5 +385,6 @@ module.exports = function(Dataset) { }); }; + Dataset.getPolicies = function(ctx, cb) {} }; diff --git a/common/models/policy.js b/common/models/policy.js index 3ab1a585..3eb799f5 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -33,8 +33,7 @@ module.exports = function(Policy) { var e = new Error('Access Not Allowed - policy manager action'); e.statusCode = 401; next(e); - } - else next(); + } else next(); }); } else { //is an full update/insert/delete @@ -42,4 +41,22 @@ module.exports = function(Policy) { next(); } }); + + Policy.addDefault = function(ownerGroup, ownerEmail) { + // TODO: move the deault definition somewhere more sensible + var defaultPolicy = Object(); + defaultPolicy.ownerGroup = ownerGroup; //mandatory + defaultPolicy.manager = ownerEmail.split(","); //mandatory + defaultPolicy.tapeRedundancy = "low"; + defaultPolicy.autoArchive = false; + defaultPolicy.autoArchiveDelay = 7; + defaultPolicy.archiveEmailNotification = true; + defaultPolicy.retrieveEmailNotification = true; + defaultPolicy.tapeRedundancy = "low"; + defaultPolicy.embargoPeriod = 3; + //filter must be an object + var filter = JSON.parse('{"where": {"ownerGroup":"' + ownerGroup + '"}}'); + console.log("default policy: " + JSON.stringify(defaultPolicy)); + Policy.findOrCreate(filter, defaultPolicy); + }; }; From 1fe06798b1e16581e6463c4a59a0bce6198c63e7 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 12 Nov 2018 13:00:30 +0100 Subject: [PATCH 071/147] remove unwanted function def --- common/models/dataset.js | 1 - 1 file changed, 1 deletion(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index becb5c2c..fa9866f4 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -385,6 +385,5 @@ module.exports = function(Dataset) { }); }; - Dataset.getPolicies = function(ctx, cb) {} }; From 6da2e7942e37441baefdf9672ce24079deeca9a0 Mon Sep 17 00:00:00 2001 From: egli Date: Tue, 13 Nov 2018 08:47:33 +0100 Subject: [PATCH 072/147] Corrected API endpoint which is used for travis tests --- CI/ESS/envfiles/settings.sample.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CI/ESS/envfiles/settings.sample.json b/CI/ESS/envfiles/settings.sample.json index 48a24eed..6ae373b6 100644 --- a/CI/ESS/envfiles/settings.sample.json +++ b/CI/ESS/envfiles/settings.sample.json @@ -5,7 +5,7 @@ "admin": { "username": "ingestor", "password": "aman", - "login": "User/login" + "login": "api/v2/Users/login" }, "user": { "username": "admin", From 47bc22fb0e9cccd8aa153c158750c4c6e8c16965 Mon Sep 17 00:00:00 2001 From: egli Date: Tue, 13 Nov 2018 12:18:26 +0100 Subject: [PATCH 073/147] Corrected asynch behaviour of boot scripts --- server/boot/common_utils.js | 9 +- server/boot/createRoles.js | 28 +++--- test/SITES_PSI/FEATURE_NAME.js | 168 --------------------------------- test/SITES_PSI/Ownable.js | 144 ---------------------------- 4 files changed, 22 insertions(+), 327 deletions(-) delete mode 100644 test/SITES_PSI/FEATURE_NAME.js delete mode 100644 test/SITES_PSI/Ownable.js diff --git a/server/boot/common_utils.js b/server/boot/common_utils.js index e04cd8cc..805ae24d 100644 --- a/server/boot/common_utils.js +++ b/server/boot/common_utils.js @@ -17,16 +17,17 @@ exports.connectRole = function(app, roleName, user, cb) { name: roleName }, function(err, role) { if (err) return cb(err); - console.log('Created role:', role); - mapRole(RoleMapping, role, user,cb); + mapRole(RoleMapping, role, user, cb); }); }else if (role.length === 1) { mapRole(RoleMapping, role[0], user,cb); + } else { + return cb(err) } }); }; -function mapRole(RoleMapping, role, user, cb) { +function mapRole(RoleMapping, role, user,cb) { //check mapping exists first, maybe also look at user id? RoleMapping.find({ where: { @@ -43,6 +44,8 @@ function mapRole(RoleMapping, role, user, cb) { console.log('Assigned user %s to role %s', user.username, role.name); cb(null) }); + } else { + cb(null) } }); } diff --git a/server/boot/createRoles.js b/server/boot/createRoles.js index c5c99357..938ae14d 100644 --- a/server/boot/createRoles.js +++ b/server/boot/createRoles.js @@ -1,14 +1,14 @@ var utils = require('./common_utils'); var fs = require('fs'); -module.exports = function(app,cb) { +module.exports = function(app, cb) { // define roles // note: role names are all lowercase , corresponding accounts camelcase // - createRole = function(account,cb) { + createRole = function(account, cb) { var User = app.models.User; @@ -21,8 +21,8 @@ module.exports = function(app,cb) { return cb(err); } else if (users.length === 0) { // check for password file for this role - path='server/'+account; - console.log("creating account "+account); + path = 'server/' + account; + console.log("creating account " + account); if (fs.existsSync(path)) { var data = fs.readFileSync(path, 'utf8').split('\n')[0].split(" "); User.create({ @@ -33,7 +33,7 @@ module.exports = function(app,cb) { emailVerified: true }, function(err, user) { if (err) { - console.log("User create:"+err+" "+user) + console.log("User create:" + err + " " + user) return cb(err) } else { utils.connectRole(app, account.toLowerCase(), user, cb); @@ -48,7 +48,7 @@ module.exports = function(app,cb) { emailVerified: true }, function(err, user) { if (err) { - console.log("User create:"+err+" "+user) + console.log("User create:" + err + " " + user) return cb(err) } else { utils.connectRole(app, account.toLowerCase(), user, cb); @@ -63,9 +63,13 @@ module.exports = function(app,cb) { }); }; - createRole('admin',cb); - createRole('archiveManager',cb); - createRole('ingestor',cb); - createRole('proposalIngestor',cb); - createRole('userGroupIngestor',cb) -}; + createRole('admin', function() { + createRole('archiveManager', function() { + createRole('ingestor', function() { + createRole('proposalIngestor', function() { + createRole('userGroupIngestor', cb) + }) + }) + }) + }) +} diff --git a/test/SITES_PSI/FEATURE_NAME.js b/test/SITES_PSI/FEATURE_NAME.js deleted file mode 100644 index 5347bf96..00000000 --- a/test/SITES_PSI/FEATURE_NAME.js +++ /dev/null @@ -1,168 +0,0 @@ -/* jshint node:true */ -/* jshint esversion:6 */ -'use strict'; - -// process.env.NODE_ENV = 'test'; - -var chai = require('chai'); -var chaiHttp = require('chai-http'); -var request = require('supertest'); -var app = require('../../server/server'); -var should = chai.should(); -var utils = require('../LoginUtils'); - -var accessToken = null, - pid = null; - -var testraw = { - "principalInvestigator": "bertram.astor@grumble.com", - "endTime": "2011-09-14T06:31:25.000Z", - "creationLocation": "/SU/XQX/RAMJET", - "dataFormat": "Upchuck pre 2017", - "scientificMetadata": { - "beamlineParameters": { - "Monostripe": "Ru/C", - "Ring current": { - "v": 0.402246, - "u": "A" - }, - "Beam energy": { - "v": 22595, - "u": "eV" - } - }, - "detectorParameters": { - "Objective": 20, - "Scintillator": "LAG 20um", - "Exposure time": { - "v": 0.4, - "u": "s" - } - }, - "scanParameters": { - "Number of projections": 1801, - "Rot Y min position": { - "v": 0, - "u": "deg" - }, - "Inner scan flag": 0, - "File Prefix": "817b_B2_", - "Sample In": { - "v": 0, - "u": "m" - }, - "Sample folder": "/ramjet/817b_B2_", - "Number of darks": 10, - "Rot Y max position": { - "v": 180, - "u": "deg" - }, - "Angular step": { - "v": 0.1, - "u": "deg" - }, - "Number of flats": 120, - "Sample Out": { - "v": -0.005, - "u": "m" - }, - "Flat frequency": 0, - "Number of inter-flats": 0 - } -}, - "owner": "Bertram Astor", - "ownerEmail": "bertram.astor@grumble.com", - "orcidOfOwner": "unknown", - "contactEmail": "bertram.astor@grumble.com", - "sourceFolder": "/iramjet/tif/", - "size": 0, - "creationTime": "2011-09-14T06:08:25.000Z", - "type": "raw", - "description": "None", - "classification": "AV=medium,CO=low", - "license": "CC BY-SA 4.0", - "version": "2.5.0", - "doi": "not yet defined", - "isPublished": false, - "ownerGroup": "p13388", - "accessGroups": [], - "createdAt": "2017-11-01T18:02:49.825Z", - "updatedAt": "2017-11-01T18:03:04.673Z", - "proposalId": "10.540.16635/20110123" -} - - -describe('Feature that does X when Y', () => { - beforeEach((done) => { - utils.getToken(app, {'username': 'ingestor', 'password': 'aman'}, - (tokenVal) => { - accessToken = tokenVal; - done(); - }); - }); - describe('POST /api/v2/RawDatasets', function () { - it('adds a new dataset', function (done) { - request(app) - .post('/api/v2/RawDatasets?access_token=' + accessToken) - .send(testraw) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end(function (err, res) { - if (err) - return done(err); - res.body.should.have.property('owner').and.be.string; - res.body.should.have.property('pid').and.be.string; - pid = encodeURIComponent(res.body['pid']); - done(); - }); - }); - }); - - describe('get one rawdataset', function () { - it('should fetch one dataset', function (done) { - request(app) - .get('/api/v2/RawDatasets/' + pid + '?access_token=' + accessToken) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - }); - - describe('delete a RawDataset', function () { - it('should delete a rawdataset', function (done) { - request(app) - .delete('/api/v2/RawDatasets/' + pid + '?access_token=' + accessToken) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - }); - - - describe('Get All RawDatasets', function () { - it('should fetch all raw datasets', function (done) { - request(app) - .get('/api/v2/RawDatasets?filter=%7B%22limit%22%3A2%7D&access_token=' + accessToken) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - res.body.should.be.instanceof(Array); - done(); - }); - }); - }); -}); diff --git a/test/SITES_PSI/Ownable.js b/test/SITES_PSI/Ownable.js deleted file mode 100644 index d1cbeac2..00000000 --- a/test/SITES_PSI/Ownable.js +++ /dev/null @@ -1,144 +0,0 @@ -/* jshint node:true */ -/* jshint esversion:6 */ -'use strict'; - -// process.env.NODE_ENV = 'test'; -var config = require('../config/settings') -var chai = require('chai'); -var chaiHttp = require('chai-http'); -var request = require('supertest'); -var app = require('../../server/server'); -var should = chai.should(); -var utils = require('../LoginUtils'); - -var accessToken = null, - pid = null; - -var testraw = { - "principalInvestigator": "bertram.astor@grumble.com", - "endTime": "2011-09-14T06:31:25.000Z", - "creationLocation": "/SU/XQX/RAMJET", - "dataFormat": "Upchuck pre 2017", - "scientificMetadata": { - "beamlineParameters": { - "Monostripe": "Ru/C", - "Ring current": { - "v": 0.402246, - "u": "A" - }, - "Beam energy": { - "v": 22595, - "u": "eV" - } - }, - "detectorParameters": { - "Objective": 20, - "Scintillator": "LAG 20um", - "Exposure time": { - "v": 0.4, - "u": "s" - } - }, - "scanParameters": { - "Number of projections": 1801, - "Rot Y min position": { - "v": 0, - "u": "deg" - }, - "Inner scan flag": 0, - "File Prefix": "817b_B2_", - "Sample In": { - "v": 0, - "u": "m" - }, - "Sample folder": "/ramjet/817b_B2_", - "Number of darks": 10, - "Rot Y max position": { - "v": 180, - "u": "deg" - }, - "Angular step": { - "v": 0.1, - "u": "deg" - }, - "Number of flats": 120, - "Sample Out": { - "v": -0.005, - "u": "m" - }, - "Flat frequency": 0, - "Number of inter-flats": 0 - } - }, - "owner": "Bertram Astor", - "ownerEmail": "bertram.astor@grumble.com", - "orcidOfOwner": "unknown", - "contactEmail": "bertram.astor@grumble.com", - "sourceFolder": "/iramjet/tif/", - "size": 0, - "creationTime": "2011-09-14T06:08:25.000Z", - "description": "None", - "doi": "not yet defined", - "isPublished": false, - "ownerGroup": "p10021", - "accessGroups": [], - "proposalId": "10.540.16635/20110123" -} - - -describe('TestCreation', () => { - before((done) => { - utils.getTokenAD(app, { - 'username': config.users.user.username, - 'password': config.users.user.password - }, - (tokenVal) => { - accessToken = tokenVal; - done(); - }); - }); - it('adds a new raw dataset', function(done) { - request(app) - .post('/api/v2/RawDatasets?access_token=' + accessToken) - .send(testraw) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end(function(err, res) { - if (err) - return done(err); - res.body.should.have.property('owner').and.be.string; - res.body.should.have.property('type').and.equal('raw'); - res.body.should.have.property('pid').and.be.string; - pid = encodeURIComponent(res.body['pid']); - done(); - }); - }); - - - it('should fetch this raw dataset', function(done) { - request(app) - .get('/api/v2/RawDatasets/' + pid + '?access_token=' + accessToken) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); - }); - - it('should not delete this raw dataset', function(done) { - request(app) - .delete('/api/v2/RawDatasets/' + pid + '?access_token=' + accessToken) - .set('Accept', 'application/json') - .expect(401) - .expect('Content-Type', /json/) - .end((err, res) => { - res.body.should.have.property('error'); - done(); - }); - }); - -}); From 3c87584047a877f0d4626dfb187b973f27ed7cba Mon Sep 17 00:00:00 2001 From: egli Date: Tue, 13 Nov 2018 17:01:45 +0100 Subject: [PATCH 074/147] Ensure that boot process is finished before tests start --- CI/ESS/wait.sh | 4 +--- server/boot/createRoles.js | 7 +++++-- test/CheckDifferentDatasetTypes.js | 11 ++++++++++- test/Datablock.js | 7 ++++++- test/Dataset.js | 6 +++++- test/DatasetLifecycle.js | 5 ++++- test/DerivedDataset.js | 5 ++++- test/MessageHistory.js | 6 +++++- test/Policy.js | 6 ++++-- test/Proposal.js | 6 +++++- test/RawDataset.js | 5 ++++- test/ResetDataset.js | 6 +++++- test/Users.js | 8 ++++++-- test/test.js | 7 +++++-- test/testGenerator.js | 5 ++++- 15 files changed, 73 insertions(+), 21 deletions(-) diff --git a/CI/ESS/wait.sh b/CI/ESS/wait.sh index 5bcda799..cd02ee90 100755 --- a/CI/ESS/wait.sh +++ b/CI/ESS/wait.sh @@ -1,4 +1,2 @@ #!/usr/bin/env bash - -sleep 20 -npm test +npm run test diff --git a/server/boot/createRoles.js b/server/boot/createRoles.js index 938ae14d..4ec031ab 100644 --- a/server/boot/createRoles.js +++ b/server/boot/createRoles.js @@ -56,7 +56,7 @@ module.exports = function(app, cb) { }); } } else { - console.log('Found ' + account + ' user:', users[0].username); + console.log('Found ' + account + ' user:', users[0].username, new Date()); //create the role if not yet there utils.connectRole(app, account.toLowerCase(), users[0], cb); } @@ -67,7 +67,10 @@ module.exports = function(app, cb) { createRole('archiveManager', function() { createRole('ingestor', function() { createRole('proposalIngestor', function() { - createRole('userGroupIngestor', cb) + createRole('userGroupIngestor', function(){ + console.log("Last role mapped, now wait a bit ",new Date()) + setTimeout(cb,20000) + }) }) }) }) diff --git a/test/CheckDifferentDatasetTypes.js b/test/CheckDifferentDatasetTypes.js index 76e0979d..b2d42874 100644 --- a/test/CheckDifferentDatasetTypes.js +++ b/test/CheckDifferentDatasetTypes.js @@ -7,7 +7,7 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); + var should = chai.should(); var utils = require('./LoginUtils'); @@ -145,6 +145,14 @@ var derivedCountDataset = 0; var pid = null; var pidraw = null; var pidderived = null; +var app; + +// Make sure thet the boot code, which is executed via the require statement +// is finished before any test is run + +before( function(){ + app = require('../server/server') +}); describe('Check different dataset types and their inheritance', () => { before((done) => { @@ -154,6 +162,7 @@ describe('Check different dataset types and their inheritance', () => { }, (tokenVal) => { accessToken = tokenVal; + // app(done) done(); }); }); diff --git a/test/Datablock.js b/test/Datablock.js index 9e77bdea..581efb5d 100644 --- a/test/Datablock.js +++ b/test/Datablock.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -20,6 +19,7 @@ var idDatablock = null; var idOrigDatablock = null; var idDatablock2 = null; + var testraw = { "principalInvestigator": "bertram.astor@grumble.com", "endTime": "2011-09-14T06:31:25.000Z", @@ -191,6 +191,11 @@ var testorigDataBlock = { ] } +var app + +before( function(){ + app = require('../server/server') +}); describe('Test Datablocks and OrigDatablocks and their relation to Datasets', () => { before((done) => { diff --git a/test/Dataset.js b/test/Dataset.js index a7b14862..d3f4e1aa 100644 --- a/test/Dataset.js +++ b/test/Dataset.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -32,6 +31,11 @@ var testdataset = { "accessGroups": [] } +var app +before( function(){ + app = require('../server/server') +}); + describe('Simple Dataset tests', () => { before((done) => { utils.getToken(app, { diff --git a/test/DatasetLifecycle.js b/test/DatasetLifecycle.js index 686bf6bb..6c6a4330 100644 --- a/test/DatasetLifecycle.js +++ b/test/DatasetLifecycle.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -101,6 +100,10 @@ var testDatasetLifecycle = { "isExported": false } +var app +before( function(){ + app = require('../server/server') +}); describe('Test DatasetLifecycle and the relation to Datasets', () => { before((done) => { diff --git a/test/DerivedDataset.js b/test/DerivedDataset.js index d30e3d9c..610a037b 100644 --- a/test/DerivedDataset.js +++ b/test/DerivedDataset.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -41,6 +40,10 @@ var testderived = { "ownerGroup": "p34123" } +var app +before( function(){ + app = require('../server/server') +}); describe('DerivedDatasets', () => { before((done) => { diff --git a/test/MessageHistory.js b/test/MessageHistory.js index 420186b4..b8cbfad8 100644 --- a/test/MessageHistory.js +++ b/test/MessageHistory.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -140,6 +139,11 @@ var newMessage = { } } +var app +before( function(){ + app = require('../server/server') +}); + describe('Test DatasetLifecycle and the relation to Datasets', () => { before((done) => { utils.getToken(app, { diff --git a/test/Policy.js b/test/Policy.js index 38c32e42..897a25d5 100644 --- a/test/Policy.js +++ b/test/Policy.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -35,7 +34,10 @@ var testdataset = { ] } - +var app +before( function(){ + app = require('../server/server') +}); describe('Simple Policy tests', () => { before((done) => { diff --git a/test/Proposal.js b/test/Proposal.js index 4bf1386e..afbf4b48 100644 --- a/test/Proposal.js +++ b/test/Proposal.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -23,6 +22,11 @@ var testproposal = { } +var app +before( function(){ + app = require('../server/server') +}); + describe('Simple Proposal tests', () => { before((done) => { utils.getToken(app, { diff --git a/test/RawDataset.js b/test/RawDataset.js index f353aa8b..4fd7e67f 100644 --- a/test/RawDataset.js +++ b/test/RawDataset.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -85,6 +84,10 @@ var testraw = { "proposalId": "10.540.16635/20110123" } +var app +before( function(){ + app = require('../server/server') +}); describe('RawDatasets', () => { before((done) => { diff --git a/test/ResetDataset.js b/test/ResetDataset.js index c5462f1e..11a5f8e2 100644 --- a/test/ResetDataset.js +++ b/test/ResetDataset.js @@ -7,7 +7,6 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var should = chai.should(); var utils = require('./LoginUtils'); @@ -161,6 +160,11 @@ var testDatasetLifecycle = { var foundId1 = null; var foundId2 = null; +var app +before( function(){ + app = require('../server/server') +}); + describe('Create Dataset and its Datablocks DatasetLifecycle, then reset Datablocks and Datasetlifecycle status', () => { before((done) => { utils.getToken(app, { diff --git a/test/Users.js b/test/Users.js index 7eac1bb6..b9e3b5e7 100644 --- a/test/Users.js +++ b/test/Users.js @@ -7,12 +7,16 @@ var chai = require('chai'); var chaiHttp = require('chai-http'); var request = require('supertest'); -var app = require('../server/server'); var utils = require('./LoginUtils'); var should = chai.should(); var accessToken = null; +var app +before( function(){ + app = require('../server/server') +}); + describe('Login with functional accounts', () => { it('Ingestor login fails with incorrect credentials', function(done) { @@ -28,7 +32,7 @@ describe('Login with functional accounts', () => { .end((err, res) => { res.body.should.have.property('error'); done(); - }); + }); }); diff --git a/test/test.js b/test/test.js index f173edc6..b1dbec4b 100644 --- a/test/test.js +++ b/test/test.js @@ -3,9 +3,12 @@ var loopbackApiTesting = require('./testGenerator'); var tests = require('./config/tests.json'); var config = require('./config/settings.json'); var server = require('../server/server.js'); - + +// This codes initializes the "generated" mocha tests. +// Note that these tests run using a local http server on port 3000 + loopbackApiTesting.run(tests, server, config, function(err) { if (err) { console.log(err); } -}); \ No newline at end of file +}); diff --git a/test/testGenerator.js b/test/testGenerator.js index 317835e0..c0dd8188 100644 --- a/test/testGenerator.js +++ b/test/testGenerator.js @@ -4,6 +4,8 @@ var supertest = require('supertest'); var async = require('async'); +// Code to generate simple mocha tests via configuration files + module.exports = { run: function (conf, app, settings, callback) { var server; @@ -15,6 +17,7 @@ module.exports = { if (app) { before(function (done) { + console.log("Starting local webserver:",new Date()) server = app.listen(done); }); @@ -41,7 +44,7 @@ module.exports = { const withData = c.body || false; const isWithAuthentication = c.authenticate || false; - + var authenticationDescription = (isWithAuthentication) ? 'authenticated' : 'unauthenticated'; From 213a16be3e44ecf22c525aa7b1c9083359138b01 Mon Sep 17 00:00:00 2001 From: egli Date: Tue, 13 Nov 2018 17:15:46 +0100 Subject: [PATCH 075/147] Add delay again for mongo to come up --- CI/ESS/wait.sh | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CI/ESS/wait.sh b/CI/ESS/wait.sh index cd02ee90..5bcda799 100755 --- a/CI/ESS/wait.sh +++ b/CI/ESS/wait.sh @@ -1,2 +1,4 @@ #!/usr/bin/env bash -npm run test + +sleep 20 +npm test From b243fc24e6879b8c62132c513299e6590ab9a684 Mon Sep 17 00:00:00 2001 From: egli Date: Wed, 14 Nov 2018 08:05:36 +0100 Subject: [PATCH 076/147] Add further delay for mongo to come up --- CI/ESS/wait.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CI/ESS/wait.sh b/CI/ESS/wait.sh index 5bcda799..c6c5dca2 100755 --- a/CI/ESS/wait.sh +++ b/CI/ESS/wait.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash -sleep 20 -npm test +sleep 120 +npm run test From afbe6fe9c16b95ec0af844f905c45f167930dc54 Mon Sep 17 00:00:00 2001 From: egli Date: Wed, 14 Nov 2018 17:16:40 +0100 Subject: [PATCH 077/147] Added delay to allow for boot to settle in tests, bugfix for ResetDataset --- server/boot/createRoles.js | 6 +++--- test/CheckDifferentDatasetTypes.js | 13 +++++++++---- test/ResetDataset.js | 29 ++++++++++++++++++----------- 3 files changed, 30 insertions(+), 18 deletions(-) diff --git a/server/boot/createRoles.js b/server/boot/createRoles.js index 4ec031ab..aa3a45fe 100644 --- a/server/boot/createRoles.js +++ b/server/boot/createRoles.js @@ -1,7 +1,7 @@ var utils = require('./common_utils'); var fs = require('fs'); -module.exports = function(app, cb) { +module.exports = function(app, cb2) { // define roles // note: role names are all lowercase , corresponding accounts camelcase @@ -68,8 +68,8 @@ module.exports = function(app, cb) { createRole('ingestor', function() { createRole('proposalIngestor', function() { createRole('userGroupIngestor', function(){ - console.log("Last role mapped, now wait a bit ",new Date()) - setTimeout(cb,20000) + console.log("Last role mapped, finished booting ",new Date()) + cb2(null) }) }) }) diff --git a/test/CheckDifferentDatasetTypes.js b/test/CheckDifferentDatasetTypes.js index b2d42874..5fc00515 100644 --- a/test/CheckDifferentDatasetTypes.js +++ b/test/CheckDifferentDatasetTypes.js @@ -12,6 +12,7 @@ var should = chai.should(); var utils = require('./LoginUtils'); var accessToken = null; +var boot = require('loopback-boot'); // TODO // add tests for normal users (non functional accounts) @@ -149,10 +150,14 @@ var app; // Make sure thet the boot code, which is executed via the require statement // is finished before any test is run - -before( function(){ - app = require('../server/server') -}); +// since there is no callback or this available I simply have to wait here +// This wait should be added to the first test running + +before(function(done) { + app = require('../server/server'); + console.log("Waiting for 15 seconds for boot tasks to finish: ",new Date()) + setTimeout(done,15000) + }); describe('Check different dataset types and their inheritance', () => { before((done) => { diff --git a/test/ResetDataset.js b/test/ResetDataset.js index 11a5f8e2..9ca31db0 100644 --- a/test/ResetDataset.js +++ b/test/ResetDataset.js @@ -161,7 +161,7 @@ var foundId1 = null; var foundId2 = null; var app -before( function(){ +before(function() { app = require('../server/server') }); @@ -208,6 +208,7 @@ describe('Create Dataset and its Datablocks DatasetLifecycle, then reset Datablo .expect(200) .expect('Content-Type', /json/) .end((err, res) => { + console.log("Result of looking for first id:", res.body) if (err) return done(err); foundId2 = res.body[0] ? res.body[0].id : null @@ -215,8 +216,8 @@ describe('Create Dataset and its Datablocks DatasetLifecycle, then reset Datablo }); }); - if (foundId1) { - it('should delete existing Datablocks with specific archiveId', function(done) { + it('should delete existing Datablocks with specific archiveId', function(done) { + if (foundId1) { request(app) .delete('/api/v2/Datablocks/' + foundId1 + '?access_token=' + accessTokenArchiveManager) .set('Accept', 'application/json') @@ -225,14 +226,17 @@ describe('Create Dataset and its Datablocks DatasetLifecycle, then reset Datablo .end((err, res) => { if (err) return done(err); - // console.log("Deleted datablock:", res.body) + console.log("Deleted datablock:", res.body) done(); }); - }); - } + } else { + done() + } + }); + - if (foundId2) { - it('should delete existing Datablocks with 2nd specific archiveId', function(done) { + it('should delete existing Datablocks with 2nd specific archiveId', function(done) { + if (foundId2) { request(app) .delete('/api/v2/Datablocks/' + foundId2 + '?access_token=' + accessTokenArchiveManager) .set('Accept', 'application/json') @@ -241,11 +245,14 @@ describe('Create Dataset and its Datablocks DatasetLifecycle, then reset Datablo .end((err, res) => { if (err) return done(err); - // console.log("Deleted datablock:", res.body) + console.log("Deleted datablock:", res.body) done(); }); - }); - } + } else { + done() + } + }); + it('adds a new raw dataset', function(done) { request(app) From c1b984bf4e4068e92245c1f57292c563050b5462 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 08:00:57 +0100 Subject: [PATCH 078/147] Reduced wait time to be compatible with timeout settings --- test/CheckDifferentDatasetTypes.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/CheckDifferentDatasetTypes.js b/test/CheckDifferentDatasetTypes.js index 5fc00515..1a3cb9c0 100644 --- a/test/CheckDifferentDatasetTypes.js +++ b/test/CheckDifferentDatasetTypes.js @@ -155,8 +155,8 @@ var app; before(function(done) { app = require('../server/server'); - console.log("Waiting for 15 seconds for boot tasks to finish: ",new Date()) - setTimeout(done,15000) + console.log("Waiting for 5 seconds for boot tasks to finish: ",new Date()) + setTimeout(done,5000) }); describe('Check different dataset types and their inheritance', () => { From 7d2bbc2b7ff7187943ca45dd0c6586bb25d55f09 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 09:07:57 +0100 Subject: [PATCH 079/147] Added auto creation of text index at boot time --- CI/ESS/wait.sh | 4 +-- server/boot/0-script.js | 75 +++++++++++++++++++++++------------------ test/Datablock.js | 2 -- 3 files changed, 45 insertions(+), 36 deletions(-) diff --git a/CI/ESS/wait.sh b/CI/ESS/wait.sh index c6c5dca2..87056c40 100755 --- a/CI/ESS/wait.sh +++ b/CI/ESS/wait.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash - -sleep 120 +# wait for mongo container to come up +sleep 15 npm run test diff --git a/server/boot/0-script.js b/server/boot/0-script.js index 985fa3bd..d24721b4 100644 --- a/server/boot/0-script.js +++ b/server/boot/0-script.js @@ -1,38 +1,49 @@ module.exports = function(app) { - var dataSource = app.datasources.mongo; - console.log("Datasource host %s, database %s", dataSource.connector.settings.host, dataSource.connector.settings.database) - dataSource.isActual(function(err, actual) { - // console.log("Database actual:", actual) - // if (!actual) { - dataSource.autoupdate(function(err, result) { - if (err) { - console.log("Database Autoupdate error: %s", err) - } else { - console.log("Database Autoupdate result: %s", result) + var dataSource = app.datasources.mongo; + console.log("Datasource host %s, database %s", dataSource.connector.settings.host, dataSource.connector.settings.database) + dataSource.isActual(function(err, actual) { + // console.log("Database actual:", actual) + // if (!actual) { + dataSource.autoupdate(function(err, result) { + if (err) { + console.log("Database Autoupdate error: %s", err) + } else { + console.log("Database Autoupdate result: %s", result) - } - }); - //} - }); + } + }); + //} + }); - var loopback = require('loopback'); - var DataModel = loopback.PersistedModel; + var loopback = require('loopback'); + var DataModel = loopback.PersistedModel; - console.log("Adding ACLS for UserIdentity") + console.log("Adding ACLS for UserIdentity") - DataModel.extend('UserIdentity', null, { - acls: [{ - principalType: 'ROLE', - principalId: '$everyone', - permission: 'DENY' - }, - { - accessType: 'READ', - principalType: 'ROLE', - principalId: '$authenticated', - permission: 'ALLOW' - } - ] - }); -}; + DataModel.extend('UserIdentity', null, { + acls: [{ + principalType: 'ROLE', + principalId: '$everyone', + permission: 'DENY' + }, + { + accessType: 'READ', + principalType: 'ROLE', + principalId: '$authenticated', + permission: 'ALLOW' + } + ] + }); + dataSource.connector.connect(function(err, db) { + db.collection('Dataset').createIndex({ + "$**": "text" + }, function(err) { + if (!err) { + console.log("Text Index on dataset created succesfully") + } else { + console.log(err); + } + }); + }); +}; diff --git a/test/Datablock.js b/test/Datablock.js index 581efb5d..b8b80a5a 100644 --- a/test/Datablock.js +++ b/test/Datablock.js @@ -211,8 +211,6 @@ describe('Test Datablocks and OrigDatablocks and their relation to Datasets', () }, (tokenVal) => { accessTokenArchiveManager = tokenVal; - console.log("============ Both accessToken received") - console.log("Tokens:", accessTokenIngestor, accessTokenArchiveManager) done(); }); From 6e6c5667b01f389fa51d439017caadc8f434be1f Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 09:38:22 +0100 Subject: [PATCH 080/147] Corrected testcase for MessageHistory expecting the wrong dataset ids --- common/models/job.js | 4 ++-- test/MessageHistory.js | 15 ++++++--------- 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/common/models/job.js b/common/models/job.js index 54dea608..f38dd5d9 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -33,7 +33,7 @@ module.exports = function (Job) { } }); if (ctx.instance) { - // auto fill dataOfLastMessage + // auto fill dateOfLastMessage var now = new Date(); if (!ctx.instance.dateOfLastMessage) { ctx.instance.dateOfLastMessage = now.toISOString(); @@ -47,7 +47,7 @@ module.exports = function (Job) { // console.log("Verifying datasets:",ctx.options) const idList=ctx.instance.datasetList.map(x => x.pid) Dataset.find({where: {pid: {inq: idList}}}, ctx.options, function (err, p){ - console.log("JOBS:lengths",err,p.length,idList.length,p) + //console.log("JOBS:lengths",err,p.length,idList.length,p) if (err || (p.length != idList.length)){ var e = new Error(); e.statusCode = 400; diff --git a/test/MessageHistory.js b/test/MessageHistory.js index b8cbfad8..c46ff68f 100644 --- a/test/MessageHistory.js +++ b/test/MessageHistory.js @@ -116,14 +116,9 @@ var testjob = { "type": "retrieve", "jobStatusMessage": "jobForwarded", "datasetList": [{ - "pid": "20.500.11935/93128a6e-6c0c-48aa-bd3d-34b8fafc29ff", + "pid": "dummy", "files": [] - }, - { - "pid": "20.500.11935/c26ab160-3725-459c-a4fd-a8c88d0ff170", - "files": [] - }, - ], + }], "archiveReturnMessage": "will move to messageList", "MessageHistory": [] } @@ -177,8 +172,10 @@ describe('Test DatasetLifecycle and the relation to Datasets', () => { res.body.should.have.property('type').and.equal('raw'); res.body.should.have.property('pid').and.be.string; // store link to this dataset in datablocks - testDatasetLifecycle.id = res.body['pid'] - testDatasetLifecycle.datasetId = res.body['pid'] + var pidtest=res.body['pid'] + testDatasetLifecycle.id = pidtest + testDatasetLifecycle.datasetId = pidtest + testjob.datasetList[0].pid= pidtest pid = encodeURIComponent(res.body['pid']); done(); }); From 11f2926595e0acc1c022fa2380dc12d3549c53b1 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 11:01:08 +0100 Subject: [PATCH 081/147] Fill in users in ldap as part of docker-compose --- CI/ESS/envfiles/settings.sample.json | 4 +- CI/ESS/ldif_files/addAll.sh | 7 ++ CI/ESS/ldif_files/people.ldif | 69 ++++++++++++++ docker-compose.yaml | 129 ++++++++------------------- 4 files changed, 115 insertions(+), 94 deletions(-) create mode 100644 CI/ESS/ldif_files/addAll.sh create mode 100644 CI/ESS/ldif_files/people.ldif diff --git a/CI/ESS/envfiles/settings.sample.json b/CI/ESS/envfiles/settings.sample.json index 6ae373b6..1dc78e4f 100644 --- a/CI/ESS/envfiles/settings.sample.json +++ b/CI/ESS/envfiles/settings.sample.json @@ -8,8 +8,8 @@ "login": "api/v2/Users/login" }, "user": { - "username": "admin", - "password": "admin", + "username": "zach", + "password": "pass", "login": "auth/msad" } } diff --git a/CI/ESS/ldif_files/addAll.sh b/CI/ESS/ldif_files/addAll.sh new file mode 100644 index 00000000..2e67db1d --- /dev/null +++ b/CI/ESS/ldif_files/addAll.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash +echo "sleep for 5, waiting for ldap" +sleep 5 +ldapsearch -v -h openldap -x -D "cn=admin,dc=example,dc=org" -w admin -b "dc=example,dc=org" -s sub +echo "adding to ldap" +ldapadd -v -h openldap -c -D "cn=admin,dc=example,dc=org" -w admin -f /ldif_files/people.ldif +echo "done adding to ldap" diff --git a/CI/ESS/ldif_files/people.ldif b/CI/ESS/ldif_files/people.ldif new file mode 100644 index 00000000..6f601daf --- /dev/null +++ b/CI/ESS/ldif_files/people.ldif @@ -0,0 +1,69 @@ +# --- OUs ------------------------------------- + +dn: ou=Groups,dc=example,dc=org +objectClass: organizationalunit +objectClass: top +ou: Groups + +dn: ou=People,dc=example,dc=org +objectClass: organizationalunit +objectClass: top +ou: People + + +# --- People ---------------------------------- + +dn: cn=marpontes,ou=People,dc=example,dc=org +objectClass: person +objectClass: inetOrgPerson +objectClass: organizationalPerson +objectClass: top +cn: marpontes +userpassword: pass +givenname: Marcello +sn: Pontes +mail: marcello@oncase.com.br +uid: 1001 + +dn: cn=zach,ou=People,dc=example,dc=org +objectClass: person +objectClass: inetOrgPerson +objectClass: organizationalPerson +objectClass: top +cn: zach +userpassword: pass +givenname: Zachary +sn: Zeus +mail: zach@oncase.com.br +uid: 1002 + +dn: cn=leonardo,ou=People,dc=example,dc=org +objectClass: person +objectClass: inetOrgPerson +objectClass: organizationalPerson +objectClass: top +cn: leonardo +userpassword: pass +givenname: Leonardo +sn: Luiz +mail: zach@oncase.com.br +uid: 1003 + + +# --- Groups ---------------------------------- + +dn: cn=Administrator,ou=Groups,dc=example,dc=org +objectClass: groupofuniquenames +objectClass: top +ou: Groups +cn: Administrator +uniquemember: cn=marpontes, ou=People, dc=example,dc=org + +dn: cn=Developers,ou=Groups,dc=example,dc=org +objectClass: groupofuniquenames +objectClass: top +ou: Groups +cn: Administrator +uniquemember: cn=marpontes, ou=People, dc=example,dc=org +uniquemember: cn=zach, ou=People, dc=example,dc=org +uniquemember: cn=leonardo, ou=People, dc=example,dc=org diff --git a/docker-compose.yaml b/docker-compose.yaml index c70d57bd..d6f5d6f6 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -2,111 +2,56 @@ version: "3" services: mongodb: image: 'bitnami/mongodb:latest' - labels: - kompose.service.type: nodeport ports: - "27017:27017" volumes: - 'mongodb_data:/bitnami' - - catamel: - build: + build: context: . - dockerfile: CI/ESS/Dockerfile.test + dockerfile: CI/ESS/Dockerfile.unittests image: garethcmurphy/catamel ports: - '3000:3000' - - '3001:3001' - depends_on: + depends_on: - mongodb + - openldap-seed links: - mongodb - openldap - + - openldap-seed openldap: - image: osixia/openldap:1.2.0 - container_name: openldap - environment: - LDAP_LOG_LEVEL: "256" - LDAP_ORGANISATION: "Example Inc." - LDAP_DOMAIN: "example.org" - LDAP_BASE_DN: "" - LDAP_ADMIN_PASSWORD: "admin" - LDAP_CONFIG_PASSWORD: "config" - LDAP_READONLY_USER: "true" - LDAP_READONLY_USER_USERNAME: "readonly" - LDAP_READONLY_USER_PASSWORD: "readonly" - LDAP_RFC2307BIS_SCHEMA: "false" - LDAP_BACKEND: "mdb" - LDAP_TLS: "true" - LDAP_TLS_CRT_FILENAME: "ldap.crt" - LDAP_TLS_KEY_FILENAME: "ldap.key" - LDAP_TLS_CA_CRT_FILENAME: "ca.crt" - LDAP_TLS_ENFORCE: "false" - LDAP_TLS_CIPHER_SUITE: "SECURE256:-VERS-SSL3.0" - LDAP_TLS_PROTOCOL_MIN: "3.1" - LDAP_TLS_VERIFY_CLIENT: "demand" - LDAP_REPLICATION: "false" - #LDAP_REPLICATION_CONFIG_SYNCPROV: "binddn="cn=admin,cn=config" bindmethod=simple credentials=$LDAP_CONFIG_PASSWORD searchbase="cn=config" type=refreshAndPersist retry="60 +" timeout=1 starttls=critical" - #LDAP_REPLICATION_DB_SYNCPROV: "binddn="cn=admin,$LDAP_BASE_DN" bindmethod=simple credentials=$LDAP_ADMIN_PASSWORD searchbase="$LDAP_BASE_DN" type=refreshAndPersist interval=00:00:00:10 retry="60 +" timeout=1 starttls=critical" - #LDAP_REPLICATION_HOSTS: "#PYTHON2BASH:['ldap://ldap.example.org','ldap://ldap2.example.org']" - KEEP_EXISTING_CONFIG: "false" - LDAP_REMOVE_CONFIG_AFTER_SETUP: "true" - LDAP_SSL_HELPER_PREFIX: "ldap" - tty: true - stdin_open: true - volumes: - - /var/lib/ldap - - /etc/ldap/slapd.d - - /container/service/slapd/assets/certs/ - ports: + image: osixia/openldap + container_name: openldap + hostname: openldap + environment: + LDAP_ORGANISATION: "LDAP Catamel Auth" + LDAP_SSL_HELPER_PREFIX: "ldap" + LDAP_TLS_VERIFY_CLIENT: "never" + LDAP_LOG_LEVEL: 256 + LDAP_ADMIN_PASSWORD: "admin" + ports: - "389:389" - - "636:636" - domainname: "example.org" # important: same as hostname - hostname: "example.org" -# -# zookeeper: -# image: wurstmeister/zookeeper -# ports: -# - "2181:2181" -# -# kafka: -# image: wurstmeister/kafka -# depends_on: -# - zookeeper -# ports: -# - "9092:9092" -# environment: -# KAFKA_ADVERTISED_HOST_NAME: "kafka" -# KAFKA_ADVERTISED_PORT: "9092" -# KAFKA_CREATE_TOPICS: "test:1:1" -# KAFKA_ZOOKEEPER_CONNECT: zookeeper:2181 -# consumer: -# image: wurstmeister/kafka -# depends_on: -# - kafka -# command: [ "sh", "-c", "sleep 10 && $$KAFKA_HOME/bin/kafka-console-consumer.sh --topic=test --zookeeper=zookeeper:2181" ] -# producer: -# image: wurstmeister/kafka -# depends_on: -# - kafka -# command: [ "sh", "-c", "sleep 15 && echo 'hello kafka' | $$KAFKA_HOME/bin/kafka-console-producer.sh --topic=test --broker-list=kafka:9092" ] -# -# nodered: -# build: nodered -# ports: -# - "1880:1880" -# -# myshell: -# build: -# context: myshell -# image: garethcmurphy/myshell -# depends_on: -# - mongodb -# - local-rabbit-rabbitmq.dev - - + openldap-seed: + image: osixia/openldap + volumes: + - ./CI/ESS/ldif_files:/ldif_files + links: + - openldap + entrypoint: sh -c '/ldif_files/addAll.sh' + openldap-admin: + image: osixia/phpldapadmin + container_name: openldap-admin + hostname: openldap-admin + environment: + PHPLDAPADMIN_HTTPS=false: + PHPLDAPADMIN_LDAP_HOSTS: "openldap" + ports: + - "8080:80" + links: + - "openldap:openldap" + depends_on: + - openldap volumes: - mongodb_data: - driver: local + mongodb_data: + driver: local From 6354637fda21c15c35b5ce5685f6bb338c7583d1 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 11:09:54 +0100 Subject: [PATCH 082/147] Added missing Dockerfile --- CI/ESS/Dockerfile.unittests | 38 +++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 CI/ESS/Dockerfile.unittests diff --git a/CI/ESS/Dockerfile.unittests b/CI/ESS/Dockerfile.unittests new file mode 100644 index 00000000..f2c28b65 --- /dev/null +++ b/CI/ESS/Dockerfile.unittests @@ -0,0 +1,38 @@ +# gives a docker image below 200 MB +FROM node:9 + +ENV http_proxy "http://192.168.1.1:8123" +ENV https_proxy $http_proxy +ENV no_proxy "localhost, 127.0.0.1" +RUN npm config set proxy $http_proxy +RUN npm config set https-proxy $http_proxy +RUN npm config set registry http://registry.npmjs.org/ +RUN npm config set strict-ssl false + + +RUN apt-get update && apt-get install -y --no-install-recommends mongodb-clients vim ldap-utils + +ENV PORT 3000 +EXPOSE 3000 + +WORKDIR /usr/src/app +COPY package.json /usr/src/app/ +# Install our packages +RUN npm install + + +# Copy the rest of our application, node_modules is ignored via .dockerignore +COPY . /usr/src/app +COPY CI/ESS/envfiles/config.ess.js /usr/src/app/server/config.local.js +COPY CI/ESS/envfiles/middleware.json /usr/src/app/server/ +RUN touch /usr/src/app/test/config/providers.json +COPY CI/ESS/envfiles/providers.unittests.json /usr/src/app/server/providers.json +COPY CI/ESS/envfiles/datasources.json /usr/src/app/server/ +COPY CI/ESS/envfiles/component-config.json /usr/src/app/server/ +RUN touch /usr/src/app/test/config/settings.json +COPY CI/ESS/envfiles/settings.sample.json /usr/src/app/test/config/settings.json +COPY CI/ESS/wait.sh /usr/src/app/ +# no longer needed COPY CI/ESS/createIndex.js /usr/src/app/ + +# Start the app +CMD ["./wait.sh"] From 4c9885ea66b9bf70dc64757ec95f8878d8735220 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 11:40:20 +0100 Subject: [PATCH 083/147] Use non-proxy Dockerfile for travis tests --- CI/ESS/Dockerfile.test | 6 ++++-- docker-compose.yaml | 4 ++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/CI/ESS/Dockerfile.test b/CI/ESS/Dockerfile.test index ca7f93a3..43128df0 100644 --- a/CI/ESS/Dockerfile.test +++ b/CI/ESS/Dockerfile.test @@ -1,19 +1,21 @@ FROM node:9 +RUN apt-get update && apt-get install -y --no-install-recommends mongodb-clients ldap-utils vim + ENV PORT 3000 EXPOSE 3000 WORKDIR /usr/src/app COPY package.json /usr/src/app/ # Install our packages -RUN npm install +RUN npm install # Copy the rest of our application, node_modules is ignored via .dockerignore COPY . /usr/src/app COPY CI/ESS/envfiles/config.ess.js /usr/src/app/server/config.local.js COPY CI/ESS/envfiles/middleware.json /usr/src/app/server/ -COPY CI/ESS/envfiles/providers.json /usr/src/app/server/ +COPY CI/ESS/envfiles/providers.unittests.json /usr/src/app/server/providers.json COPY CI/ESS/envfiles/datasources.json /usr/src/app/server/ COPY CI/ESS/envfiles/component-config.json /usr/src/app/server/ COPY CI/ESS/envfiles/settings.sample.json /usr/src/app/test/config/settings.json diff --git a/docker-compose.yaml b/docker-compose.yaml index d6f5d6f6..a2889432 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -9,7 +9,7 @@ services: catamel: build: context: . - dockerfile: CI/ESS/Dockerfile.unittests + dockerfile: CI/ESS/Dockerfile.test image: garethcmurphy/catamel ports: - '3000:3000' @@ -30,7 +30,7 @@ services: LDAP_TLS_VERIFY_CLIENT: "never" LDAP_LOG_LEVEL: 256 LDAP_ADMIN_PASSWORD: "admin" - ports: + ports:CI/ESS/envfiles/settings.sample.json - "389:389" openldap-seed: image: osixia/openldap From 6a3107e8cf0ab0d2d3e00f5a1062faf6d13bf817 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 11:44:52 +0100 Subject: [PATCH 084/147] Typo in yaml file --- CI/ESS/envfiles/providers.unittests.json | 34 ++++++++++++++++++++++++ docker-compose.yaml | 2 +- 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 CI/ESS/envfiles/providers.unittests.json diff --git a/CI/ESS/envfiles/providers.unittests.json b/CI/ESS/envfiles/providers.unittests.json new file mode 100644 index 00000000..1e206710 --- /dev/null +++ b/CI/ESS/envfiles/providers.unittests.json @@ -0,0 +1,34 @@ +{ + "local": { + "provider": "local", + "module": "passport-local", + "usernameField": "username", + "passwordField": "password", + "authPath": "/auth/local", + "successRedirect": "/auth/account", + "failureRedirect": "/local", + "failureFlash": true + }, + "ldap": { + "provider": "ldap", + "authScheme": "ldap", + "module": "passport-ldapauth", + "authPath": "/auth/msad", + "successRedirect": "/auth/account", + "failureRedirect": "/msad", + "session": true, + "json": true, + "failureFlash": true, + "profileAttributesFromLDAP": { + "displayName": "displayName", + "email": "mail" + }, + "server": { + "url": "ldap://openldap:389", + "bindDn": "cn=admin,dc=example,dc=org", + "bindCredentials": "admin", + "searchBase": "dc=example,dc=org", + "searchFilter": "(cn={{username}})" + } + } +} diff --git a/docker-compose.yaml b/docker-compose.yaml index a2889432..a71a537d 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -30,7 +30,7 @@ services: LDAP_TLS_VERIFY_CLIENT: "never" LDAP_LOG_LEVEL: 256 LDAP_ADMIN_PASSWORD: "admin" - ports:CI/ESS/envfiles/settings.sample.json + ports: - "389:389" openldap-seed: image: osixia/openldap From 8e8631397dfbca06803fd54ab58944d5cbab3de9 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 11:59:16 +0100 Subject: [PATCH 085/147] Make addAll.sh script executable --- CI/ESS/ldif_files/addAll.sh | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 CI/ESS/ldif_files/addAll.sh diff --git a/CI/ESS/ldif_files/addAll.sh b/CI/ESS/ldif_files/addAll.sh old mode 100644 new mode 100755 From e2dc9cb72a4d86451b0b912fe26cbd84938d36d0 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 13:11:01 +0100 Subject: [PATCH 086/147] Adjusted travis configuration to new ldap init --- .travis.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 8464880b..92793833 100644 --- a/.travis.yml +++ b/.travis.yml @@ -35,9 +35,11 @@ before_install: # Setup your application stack. You may need to tweak these commands if you # doing out-of-the-ordinary docker-compose builds. - docker-compose build - - docker-compose up --abort-on-container-exit # You will want this for logging. If one of your containers does not build for # whatever reason it's best to report that now before your tests start # otherwise it can be really tricky to debug why tests are failing sometimes. - docker ps + +script: + - docker-compose run catamel ./wait.sh --verbose From b311744cdaa6bcb3d39a9d4a4aa98085da35fa8d Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 13:42:58 +0100 Subject: [PATCH 087/147] Removed wait for mongo to become ready --- CI/ESS/wait.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CI/ESS/wait.sh b/CI/ESS/wait.sh index 87056c40..cb5d0671 100755 --- a/CI/ESS/wait.sh +++ b/CI/ESS/wait.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash # wait for mongo container to come up -sleep 15 +# sleep 15 npm run test From 74b4b575c415e693db9697e1524e507d070c0fa2 Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 13:52:53 +0100 Subject: [PATCH 088/147] Allow for larger values of timeout --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index aad3c08c..faeb7b91 100644 --- a/package.json +++ b/package.json @@ -9,7 +9,7 @@ "lint": "eslint common/models", "start": "node .", "posttests": "npm run lint && nsp check", - "test": "./node_modules/mocha/bin/mocha --timeout=10000 --reporter spec --exit 2>/dev/null" + "test": "./node_modules/mocha/bin/mocha --timeout=30000 --reporter spec --exit 2>/dev/null" }, "dependencies": { "compression": "^1.0.3", From 512806a27ced758cc0623d9ba19536d008dbd8ff Mon Sep 17 00:00:00 2001 From: egli Date: Thu, 15 Nov 2018 13:58:26 +0100 Subject: [PATCH 089/147] Mongo still needs more time to come up... --- CI/ESS/wait.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CI/ESS/wait.sh b/CI/ESS/wait.sh index cb5d0671..87056c40 100755 --- a/CI/ESS/wait.sh +++ b/CI/ESS/wait.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash # wait for mongo container to come up -# sleep 15 +sleep 15 npm run test From cd750e694b485a7f91df1ff2d3397c0ed30298e5 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 15 Nov 2018 14:30:52 +0100 Subject: [PATCH 090/147] Add travis badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 79d1386d..aa4ed93e 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # SciCat Data Catalog Backend - +[![Build Status](https://travis-ci.org/SciCatProject/catamel.svg?branch=develop)](https://travis-ci.org/SciCatProject/catamel) [![Greenkeeper badge](https://badges.greenkeeper.io/SciCatProject/catamel.svg)](https://greenkeeper.io/) The data catalog backend is based on [NoSQL database MongoDB](https://www.mongodb.com/), [the Node based web application framework Express](http://expressjs.com/) and [the API framework Loopback](http://loopback.io/) technology stack (the "MEL" part of the "MELANIE" technology stack). It provides a REST based API which allows to store information about datasets and to allow to answer queries about the stored meta data for these datasets From 19ab27e7320b5468f8808ad1a772a7284356c0ed Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 15 Nov 2018 21:28:18 +0100 Subject: [PATCH 091/147] add latest packages --- package-lock.json | 3023 +++++++++++++++++---------------------------- package.json | 34 +- 2 files changed, 1180 insertions(+), 1877 deletions(-) diff --git a/package-lock.json b/package-lock.json index c1a1de21..78af0daa 100644 --- a/package-lock.json +++ b/package-lock.json @@ -10,7 +10,7 @@ "integrity": "sha512-OfC2uemaknXr87bdLUkWog7nYuliM9Ij5HUcajsVcMCpQrcLmtxRbVFTIqmcSkSeYRBFBRxs2FiUqFJDLdiebA==", "dev": true, "requires": { - "@babel/highlight": "7.0.0" + "@babel/highlight": "^7.0.0" } }, "@babel/highlight": { @@ -19,17 +19,9 @@ "integrity": "sha512-UFMC4ZeFC48Tpvj7C8UgLvtkaUuovQX+5xNWrsIoMG8o2z+XFKjKaN9iVmS84dPwVN00W4wPmqvYoZF3EGAsfw==", "dev": true, 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"integrity": "sha512-HxJdYWq1MTIQbJ3nw0cqssHoTNU267KlrDuGZ1WYlxDStUtKUhOaJmh112/TZmHxxUfuJqPXSOm7tDyas0OSIQ==", "requires": { - "isexe": "2.0.0" + "isexe": "^2.0.0" } }, "whistlepunk": { @@ -4762,11 +4063,11 @@ "requires": { "colors": "1.0.3", "debug": "2.2.0", - "lodash": "3.10.1", - "machina": "1.1.2", + "lodash": "3.x", + "machina": "1.x", "moment": "2.10.2", - "postal": "1.0.11", - "when": "3.7.8" + "postal": "1.x", + "when": "3.x" }, "dependencies": { "debug": { @@ -4787,7 +4088,7 @@ "resolved": "https://registry.npmjs.org/machina/-/machina-1.1.2.tgz", "integrity": "sha1-GMq+pfqet8AyQI6zCf6yr3qDckc=", "requires": { - "lodash": "3.10.1" + "lodash": "3.x" } }, "moment": { @@ -4805,7 +4106,7 @@ "resolved": "https://registry.npmjs.org/postal/-/postal-1.0.11.tgz", "integrity": "sha1-ejf/YCaGJthFzAM25X2QokU2l50=", "requires": { - "lodash": "4.17.10" + "lodash": "4.x" }, "dependencies": { "lodash": { @@ -4825,7 +4126,8 @@ "wordwrap": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-1.0.0.tgz", - "integrity": "sha1-J1hIEIkUVqQXHI0CJkQa3pDLyus=" + "integrity": "sha1-J1hIEIkUVqQXHI0CJkQa3pDLyus=", + "dev": true }, "wrappy": { "version": "1.0.2", @@ -4836,8 +4138,9 @@ "version": "0.2.1", "resolved": "https://registry.npmjs.org/write/-/write-0.2.1.tgz", "integrity": "sha1-X8A4KOJkzqP+kUVUdvejxWbLB1c=", + "dev": true, "requires": { - "mkdirp": "0.5.1" + "mkdirp": "^0.5.1" } }, "x-xss-protection": { @@ -4850,8 +4153,8 @@ "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.4.19.tgz", "integrity": "sha512-esZnJZJOiJR9wWKMyuvSE1y6Dq5LCuJanqhxslH2bxM6duahNZ+HMpCLhBQGZkbX6xRf8x1Y2eJlgt2q3qo49Q==", "requires": { - "sax": "1.2.4", - "xmlbuilder": "9.0.7" + "sax": ">=0.6.0", + "xmlbuilder": "~9.0.1" } }, "xmlbuilder": { @@ -4879,8 +4182,8 @@ "resolved": "https://registry.npmjs.org/yamljs/-/yamljs-0.3.0.tgz", "integrity": "sha512-C/FsVVhht4iPQYXOInoxUM/1ELSf9EsgKH34FofQOp6hwCPrW4vG4w5++TED3xRUo8gD7l0P1J1dLlDYzODsTQ==", "requires": { - "argparse": "1.0.10", - "glob": "7.1.2" + "argparse": "^1.0.7", + "glob": "^7.0.5" } } } diff --git a/package.json b/package.json index faeb7b91..5ff8e91e 100644 --- a/package.json +++ b/package.json @@ -12,37 +12,37 @@ "test": "./node_modules/mocha/bin/mocha --timeout=30000 --reporter spec --exit 2>/dev/null" }, "dependencies": { - "compression": "^1.0.3", - "cors": "^2.5.2", - "helmet": "^3.10.0", + "compression": "^1.7.3", + "cors": "^2.8.5", + "helmet": "^3.15.0", + "loopback": "^3.24.0", "loopback-boot": "^2.6.5", - "serve-favicon": "2.5.0", - "strong-error-handler": "3.2.0", - "loopback-component-explorer": "^6.0.0", - "loopback": "^3.19.0", + "loopback-component-explorer": "^6.3.1", "loopback-component-model-diagram": "^0.4.2", "loopback-component-mq": "^2.2.5", - "loopback-component-passport": "^3.4.1", + "loopback-component-passport": "^3.10.0", "loopback-component-visualizer": "^1.2.1", "loopback-connector-kafka": "^0.2.1", - "loopback-connector-mongodb": "^3.3.0", + "loopback-connector-mongodb": "^3.9.2", "loopback-ds-timestamp-mixin": "^3.4.1", "moment": "^2.20.1", - "moment-timezone": "^0.5.14", - "nodemailer": "^4.3.1", - "passport-ldapauth": "^2.0.0", + "moment-timezone": "^0.5.23", + "nodemailer": "^4.6.8", + "passport-ldapauth": "^2.1.0", "passport-local": "^1.0.0", "passport-openidconnect": "^0.0.2", - "uuid": "^3.2.1" + "serve-favicon": "2.5.0", + "strong-error-handler": "3.2.0", + "uuid": "^3.3.2" }, "devDependencies": { - "eslint": "^5.3.0", - "eslint-config-loopback": "^12.0.0", "@mean-expert/loopback-sdk-builder": "^2.1.0", - "chai": "^4.1.2", + "chai": "^4.2.0", "chai-http": "^4.0.0", + "eslint": "^5.9.0", + "eslint-config-loopback": "^12.0.0", "mocha": "^5.2.0", - "supertest": "^3.0.0" + "supertest": "^3.3.0" }, "repository": { "type": "", From 8f144d5e82c1c6e28df91a193fe20bb945fe7697 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 21 Nov 2018 13:56:11 +0100 Subject: [PATCH 092/147] add default robots.txt --- server/robots.txt | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 server/robots.txt diff --git a/server/robots.txt b/server/robots.txt new file mode 100644 index 00000000..eb053628 --- /dev/null +++ b/server/robots.txt @@ -0,0 +1,2 @@ +User-agent: * +Disallow: From 7674208c3ac71f993df1d0bfe2934c301fcfe573 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 21 Nov 2018 17:22:22 +0100 Subject: [PATCH 093/147] Issue #100 handle undefined ownerEmail --- common/models/policy.js | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/common/models/policy.js b/common/models/policy.js index 3eb799f5..a86644ef 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -45,8 +45,15 @@ module.exports = function(Policy) { Policy.addDefault = function(ownerGroup, ownerEmail) { // TODO: move the deault definition somewhere more sensible var defaultPolicy = Object(); - defaultPolicy.ownerGroup = ownerGroup; //mandatory - defaultPolicy.manager = ownerEmail.split(","); //mandatory + defaultPolicy.ownerGroup = ownerGroup; + if (config && !ownerEmail) + { + defaultPolicy.ownerEmail = config.defaultManager; + } + else + { + defaultPolicy.manager = ownerEmail.split(","); + } defaultPolicy.tapeRedundancy = "low"; defaultPolicy.autoArchive = false; defaultPolicy.autoArchiveDelay = 7; From 698deafe3d5ea041b253705c175b70017a5cbb0a Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Thu, 22 Nov 2018 11:33:12 +0100 Subject: [PATCH 094/147] add caption --- common/models/dataset-attachment.json | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/common/models/dataset-attachment.json b/common/models/dataset-attachment.json index 1d3bd2ee..345ce496 100644 --- a/common/models/dataset-attachment.json +++ b/common/models/dataset-attachment.json @@ -9,7 +9,7 @@ "collection": "DatasetAttachment" } }, - "description": "Small less than 16 MB attchments for datasets, envisaged for png/jpeg previews", + "description": "Small less than 16 MB attachments for datasets, envisaged for png/jpeg previews", "properties": { "thumbnail": { "type": "string", @@ -17,6 +17,11 @@ "description": "Contains a thumbnail preview in base64 encoded png format for a given dataset", "default": "retrieve" }, + "caption": { + "type": "string", + "description": "Contains a thumbnail preview in base64 encoded png format for a given dataset", + "default": "retrieve" + }, "creationTime": { "type": "date", "index": true, From 8702d2bf117a4b36ffcdf4f088114c949c41ea37 Mon Sep 17 00:00:00 2001 From: Hannes Petri Date: Thu, 22 Nov 2018 16:49:34 +0100 Subject: [PATCH 095/147] Made loopback-connector-kafka an optional dependency --- package-lock.json | 424 +++++++++++++++++++++++++++++++++++++++++++++- package.json | 4 +- 2 files changed, 422 insertions(+), 6 deletions(-) diff --git a/package-lock.json b/package-lock.json index 78af0daa..2254f54d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -197,6 +197,12 @@ "through": ">=2.2.7 <3" } }, + "abbrev": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/abbrev/-/abbrev-1.1.1.tgz", + "integrity": "sha512-nne9/IiQ/hzIhY6pdDnbBtz7DjPTKrY00P/zvPSm5pOFkl6xuGrGnXn/VtTNNfNtAfZ9/1RtehkszU9qcTii0Q==", + "optional": true + }, "accept-language": { "version": "3.0.18", "resolved": "https://registry.npmjs.org/accept-language/-/accept-language-3.0.18.tgz", @@ -281,6 +287,11 @@ } } }, + "ansi": { + "version": "0.3.1", + "resolved": "https://registry.npmjs.org/ansi/-/ansi-0.3.1.tgz", + "integrity": "sha1-DELU+xcWDVqa8eSEus4cZpIsGyE=" + }, "ansi-escapes": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-3.1.0.tgz", @@ -299,6 +310,16 @@ "integrity": "sha1-tDLdM1i2NM914eRmQ2gkBTPB3b4=", "dev": true }, + "are-we-there-yet": { + "version": "1.0.6", + "resolved": "https://registry.npmjs.org/are-we-there-yet/-/are-we-there-yet-1.0.6.tgz", + "integrity": "sha1-otKMkxAqpsyWJFomy5VN4G7FPww=", + "optional": true, + "requires": { + "delegates": "^1.0.0", + "readable-stream": "^2.0.0 || ^1.1.13" + } + }, "argparse": { "version": "1.0.10", "resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.10.tgz", @@ -312,6 +333,16 @@ "resolved": "https://registry.npmjs.org/array-flatten/-/array-flatten-1.1.1.tgz", "integrity": "sha1-ml9pkFGx5wczKPKgCJaLZOopVdI=" }, + "array-index": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/array-index/-/array-index-1.0.0.tgz", + "integrity": "sha1-7FanSe4QPk4Ix5C5w1PfFgVbl/k=", + "optional": true, + "requires": { + "debug": "^2.2.0", + "es6-symbol": "^3.0.2" + } + }, "asn1": { "version": "0.2.3", "resolved": "https://registry.npmjs.org/asn1/-/asn1-0.2.3.tgz", @@ -397,6 +428,22 @@ "resolved": "https://registry.npmjs.org/bcryptjs/-/bcryptjs-2.4.3.tgz", "integrity": "sha1-mrVie5PmBiH/fNrF2pczAn3x0Ms=" }, + "binary": { + "version": "0.3.0", + "resolved": "https://registry.npmjs.org/binary/-/binary-0.3.0.tgz", + "integrity": "sha1-n2BVO8XOjDOG87VTz/R0Yq3sqnk=", + 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@@ -2845,6 +3174,15 @@ "resolved": "https://registry.npmjs.org/nodemailer-stub-transport/-/nodemailer-stub-transport-1.1.0.tgz", "integrity": "sha1-EUIdLWa07m9AU1T5FMH0ZB6ySw0=" }, + "nopt": { + "version": "3.0.6", + "resolved": "https://registry.npmjs.org/nopt/-/nopt-3.0.6.tgz", + "integrity": "sha1-xkZdvwirzU2zWTF/eaxopkayj/k=", + "optional": true, + "requires": { + "abbrev": "1" + } + }, "npm-run-path": { "version": "2.0.2", "resolved": "https://registry.npmjs.org/npm-run-path/-/npm-run-path-2.0.2.tgz", @@ -2853,6 +3191,17 @@ "path-key": "^2.0.0" } }, + "npmlog": { + "version": "1.2.1", + "resolved": "https://registry.npmjs.org/npmlog/-/npmlog-1.2.1.tgz", + "integrity": "sha1-KOe+YZYJtT960d0wChDWTXFiaLY=", + "optional": true, + "requires": { + "ansi": "~0.3.0", + "are-we-there-yet": "~1.0.0", + "gauge": "~1.2.0" + } + }, "oauth": { "version": "0.9.15", "resolved": "https://registry.npmjs.org/oauth/-/oauth-0.9.15.tgz", @@ -2940,6 +3289,12 @@ "resolved": "https://registry.npmjs.org/options/-/options-0.0.6.tgz", "integrity": "sha1-7CLTEoBrtT5zF3Pnza788cZDEo8=" }, + "os-homedir": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/os-homedir/-/os-homedir-1.0.2.tgz", + "integrity": "sha1-/7xJiDNuDoM94MFox+8VISGqf7M=", + "optional": true + }, "os-locale": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/os-locale/-/os-locale-2.1.0.tgz", @@ -2953,8 +3308,17 @@ "os-tmpdir": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/os-tmpdir/-/os-tmpdir-1.0.2.tgz", - "integrity": "sha1-u+Z0BseaqFxc/sdm/lc0VV36EnQ=", - "dev": true + "integrity": "sha1-u+Z0BseaqFxc/sdm/lc0VV36EnQ=" + }, + "osenv": { + "version": "0.1.5", + "resolved": "https://registry.npmjs.org/osenv/-/osenv-0.1.5.tgz", + "integrity": "sha512-0CWcCECdMVc2Rw3U5w9ZjqX6ga6ubk1xDVKxtBQPK7wis/0F2r9T6k4ydGYhecl7YUBxBVxhL5oisPsNxAPe2g==", + "optional": true, + "requires": { + "os-homedir": "^1.0.0", + "os-tmpdir": "^1.0.0" + } }, "p-finally": { "version": "1.0.0", @@ -3010,6 +3374,15 @@ "resolved": "https://registry.npmjs.org/passport-strategy/-/passport-strategy-1.0.0.tgz", "integrity": "sha1-tVOaqPwiWj0a0XlHbd8ja0QPUuQ=" }, + "path-array": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/path-array/-/path-array-1.0.1.tgz", + "integrity": "sha1-fi8PNfB6IBUSK4aLfqwOssT+wnE=", + "optional": true, + "requires": { + "array-index": "^1.0.0" + } + }, "path-is-absolute": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/path-is-absolute/-/path-is-absolute-1.0.1.tgz", @@ -3276,11 +3649,16 @@ "signal-exit": "^3.0.2" } }, + "retry": { + "version": "0.6.1", + "resolved": "https://registry.npmjs.org/retry/-/retry-0.6.1.tgz", + "integrity": "sha1-/ckO7ZQ/3hG4k1VLjMY9DombqRg=", + "optional": true + }, "rimraf": { "version": "2.6.2", "resolved": "https://registry.npmjs.org/rimraf/-/rimraf-2.6.2.tgz", "integrity": "sha512-lreewLK/BlghmxtfH36YYVg1i8IAce4TI7oao75I1g245+6BctqTVQiBP3YUJ9C6DQOXJmkYR9X9fCLtCOJc5w==", - "dev": true, "requires": { "glob": "^7.0.5" } @@ -3436,6 +3814,12 @@ "nanoid": "^2.0.0" } }, + "sigmund": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/sigmund/-/sigmund-1.0.1.tgz", + "integrity": "sha1-P/IfGYytIXX587eBhT/ZTQ0ZtZA=", + "optional": true + }, "signal-exit": { "version": "3.0.2", "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.2.tgz", @@ -3459,6 +3843,25 @@ "nodemailer-shared": "1.1.0" } }, + "snappy": { + "version": "4.1.2", + "resolved": "https://registry.npmjs.org/snappy/-/snappy-4.1.2.tgz", + "integrity": "sha1-jN2cAIK5sF8VfsVv2RLBd0QBQps=", + "optional": true, + "requires": { + "bindings": "1.2.1", + "nan": "2.2.0", + "node-gyp": "3.2.1" + }, + "dependencies": { + "nan": { + "version": "2.2.0", + "resolved": "http://registry.npmjs.org/nan/-/nan-2.2.0.tgz", + "integrity": "sha1-d5wHE1YpUDz2p7fmqrMwSbPDhTw=", + "optional": true + } + } + }, "sparse-bitfield": { "version": "3.0.3", "resolved": "https://registry.npmjs.org/sparse-bitfield/-/sparse-bitfield-3.0.3.tgz", @@ -3802,6 +4205,17 @@ } } }, + "tar": { + "version": "2.2.1", + "resolved": "https://registry.npmjs.org/tar/-/tar-2.2.1.tgz", + "integrity": "sha1-jk0qJWwOIYXGsYrWlK7JaLg8sdE=", + "optional": true, + "requires": { + "block-stream": "*", + "fstream": "^1.0.2", + "inherits": "2" + } + }, "text-table": { "version": "0.2.0", "resolved": "https://registry.npmjs.org/text-table/-/text-table-0.2.0.tgz", diff --git a/package.json b/package.json index 5ff8e91e..9b703f08 100644 --- a/package.json +++ b/package.json @@ -22,7 +22,6 @@ "loopback-component-mq": "^2.2.5", "loopback-component-passport": "^3.10.0", "loopback-component-visualizer": "^1.2.1", - "loopback-connector-kafka": "^0.2.1", "loopback-connector-mongodb": "^3.9.2", "loopback-ds-timestamp-mixin": "^3.4.1", "moment": "^2.20.1", @@ -35,6 +34,9 @@ "strong-error-handler": "3.2.0", "uuid": "^3.3.2" }, + "optionalDependencies": { + "loopback-connector-kafka": "^0.2.1" + }, "devDependencies": { "@mean-expert/loopback-sdk-builder": "^2.1.0", "chai": "^4.2.0", From 19437fdbcdcc08a1644e4366e239451c4037642b Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 26 Nov 2018 14:22:28 +0100 Subject: [PATCH 096/147] Remove automatically setting type to base --- common/models/dataset.js | 1 - 1 file changed, 1 deletion(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index fa9866f4..8b52a1ab 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -43,7 +43,6 @@ module.exports = function(Dataset) { console.log(' unmodified pid:', ctx.instance.pid); } ctx.instance.version = p.version; - ctx.instance.type = 'base'; // add a policy record now (A Groups). Check that one doesnt already exist var Policy = app.models.Policy; From 25fd1e758ae64e3f5b926f46b46328628b23ce0c Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 26 Nov 2018 14:53:00 +0100 Subject: [PATCH 097/147] Update Dataset.js --- test/Dataset.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/Dataset.js b/test/Dataset.js index d3f4e1aa..be26927d 100644 --- a/test/Dataset.js +++ b/test/Dataset.js @@ -24,6 +24,7 @@ var testdataset = { "Cryo", "Calibration" ], "description": "None", + "type": "raw", "license": "CC BY-SA 4.0", "doi": "not yet defined", "isPublished": false, @@ -59,7 +60,7 @@ describe('Simple Dataset tests', () => { if (err) return done(err); res.body.should.have.property('version').and.be.string; - res.body.should.have.property('type').and.equal('base'); + res.body.should.have.property('type').and.equal('raw'); res.body.should.have.property('pid').and.be.string; pid = encodeURIComponent(res.body['pid']); done(); From ae4cf127f1f7586d1a97d67e36021af475378b3c Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 26 Nov 2018 14:55:51 +0100 Subject: [PATCH 098/147] Update tests.json --- test/config/tests.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/config/tests.json b/test/config/tests.json index c45a01e0..de3e1fe1 100644 --- a/test/config/tests.json +++ b/test/config/tests.json @@ -34,6 +34,7 @@ "Cryo", "Calibration" ], "description": "None", + "type": "raw", "license": "CC BY-SA 4.0", "doi": "not yet defined", "isPublished": false, @@ -42,7 +43,7 @@ }, "response": [ "res.body.should.have.property('version').and.be.string;", - "res.body.should.have.property('type').and.equal('base');", + "res.body.should.have.property('type').and.equal('raw');", "res.body.should.have.property('pid').and.be.string;" ] }, From 0a5404b43f556801a6268446c3a40843bae4f1da Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Mon, 26 Nov 2018 15:16:34 +0100 Subject: [PATCH 099/147] Update tests.json --- test/config/tests.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/config/tests.json b/test/config/tests.json index de3e1fe1..373286ab 100644 --- a/test/config/tests.json +++ b/test/config/tests.json @@ -63,6 +63,7 @@ "Cryo", "Calibration" ], "description": "None", + "type": "raw", "license": "CC BY-SA 4.0", "doi": "not yet defined", "isPublished": false, @@ -71,7 +72,7 @@ }, "response": [ "res.body.should.have.property('version').and.be.string;", - "res.body.should.have.property('type').and.equal('base');", + "res.body.should.have.property('type').and.equal('raw');", "res.body.should.have.property('pid').and.be.string;" ] }, From 4300a42171891962013c5151d671fe0258a8c1e0 Mon Sep 17 00:00:00 2001 From: egli Date: Tue, 27 Nov 2018 09:47:32 +0100 Subject: [PATCH 100/147] Archivable,Retrievable etc flags now also available directly inside Dataset --- common/models/dataset-lifecycle.js | 43 ++++++++++++++++++++++++++-- common/models/dataset-lifecycle.json | 8 ++++-- common/models/dataset.json | 12 ++++++++ test/DatasetLifecycle.js | 19 ++++++++++-- 4 files changed, 76 insertions(+), 6 deletions(-) diff --git a/common/models/dataset-lifecycle.js b/common/models/dataset-lifecycle.js index 0ec52c71..c6fc1da4 100644 --- a/common/models/dataset-lifecycle.js +++ b/common/models/dataset-lifecycle.js @@ -48,6 +48,45 @@ module.exports = function(Datasetlifecycle) { utils.addOwnerGroup(ctx, next) }) + // transfer status flags to linked dataset + Datasetlifecycle.observe('after save', (ctx, next) => { + var Dataset = app.models.Dataset + var instance = ctx.instance + if (!instance) { + instance = ctx.currentInstance + } + if (instance && (instance.datasetId !== undefined)) { + const datasetId = decodeURIComponent(instance.datasetId) + Dataset.findById(datasetId, null, ctx.options).then(datasetInstance => { + if (datasetInstance) { + // important to pass options here, otherwise context gets lost + datasetInstance.updateAttributes({ + archivable: instance.archivable, + retrievable: instance.retrievable, + publishable: instance.publishable + }, ctx.options, + function(err, datasetInstance) { + if (err) { + var error = new Error(); + error.statusCode = 403; + error.message = err; + next(error) + } else { + next() + } + }) + } else { + var error = new Error(); + error.statusCode = 404; + error.message = "DatasetLifecycle after save: No dataset found with pid " + datasetId + next(error) + } + }) + } else { + next() + } + }) + Datasetlifecycle.isValid = function(instance, next) { var ds = new Datasetlifecycle(instance) ds.isValid(function(valid) { @@ -87,12 +126,12 @@ module.exports = function(Datasetlifecycle) { } else { Dataset.findById(id, options, function(err, instance) { if (err) { - console.log("==== error finding dataset:",err) + console.log("==== error finding dataset:", err) next(err); } else { instance.updateAttributes({ packedSize: 0, - }, options, function(err,inst){ + }, options, function(err, inst) { next(); }); } diff --git a/common/models/dataset-lifecycle.json b/common/models/dataset-lifecycle.json index aeb2c18d..bcd29b82 100644 --- a/common/models/dataset-lifecycle.json +++ b/common/models/dataset-lifecycle.json @@ -33,11 +33,15 @@ }, "archivable": { "type": "boolean", - "description": "Flag which is true, if dataset is available to be archived and no archive job for this dataset exists yet" + "description": "Flag which is true, if dataset is available to be archived and no archive job for this dataset exists yet. Will be copied to Dataset for now and may become obsolete here eventually." }, "retrievable": { "type": "boolean", - "description": "Flag which is true, if dataset is stored on archive system and is ready to be retrieved" + "description": "Flag which is true, if dataset is stored on archive system and is ready to be retrieved. Will be copied to Dataset for now and may become obsolete here eventually." + }, + "publishable": { + "type": "boolean", + "description": "Flag which is true, if dataset can be published. Usually requires a longterm storage option on tape or similar. Will be copied to Dataset for now and may become obsolete here eventually." }, "dateOfDiskPurging": { "type": "date", diff --git a/common/models/dataset.json b/common/models/dataset.json index 5a721bb6..6622aa9f 100644 --- a/common/models/dataset.json +++ b/common/models/dataset.json @@ -102,6 +102,18 @@ "isPublished": { "type": "boolean", "description": "Flag is true when data are made publically available" + }, + "archivable":{ + "type": "boolean", + "description": "Copy of archivable flag from DatasetLifecycle" + }, + "retrievable":{ + "type": "boolean", + "description": "Copy of retrievable flag from DatasetLifecycle" + }, + "publishable":{ + "type": "boolean", + "description": "Copy of publishable flag from DatasetLifecycle" } }, "validations": [], diff --git a/test/DatasetLifecycle.js b/test/DatasetLifecycle.js index 6c6a4330..4c6d75b3 100644 --- a/test/DatasetLifecycle.js +++ b/test/DatasetLifecycle.js @@ -97,7 +97,10 @@ var testDatasetLifecycle = { "isOnTape": false, "archiveStatusMessage": "datasetCreated", "retrieveStatusMessage": "", - "isExported": false + "isExported": false, + "archivable":true, + "retrievable":true, + "publishable":false } var app @@ -156,7 +159,19 @@ describe('Test DatasetLifecycle and the relation to Datasets', () => { if (err) return done(err); idDatasetLifecycle = encodeURIComponent(res.body['id']); - done(); + request(app) + .get('/api/v2/Datasets/'+pid + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + res.body.should.have.property('archivable').and.equal(true); + res.body.should.have.property('retrievable').and.equal(true); + res.body.should.have.property('publishable').and.equal(false); + done(); + }); }); }); From bc5090c0c82a1cb7c516d4d3bc39a912258adbbe Mon Sep 17 00:00:00 2001 From: egli Date: Wed, 28 Nov 2018 09:10:38 +0100 Subject: [PATCH 101/147] Added datasetName field and updated swagger.json --- client/api/swagger.json | 2 +- common/models/dataset.json | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/client/api/swagger.json b/client/api/swagger.json index c3d16bbe..1c259a45 100644 --- a/client/api/swagger.json +++ b/client/api/swagger.json @@ -1 +1 @@ -{"swagger":"2.0","info":{"version":"2.6.3","title":"dacat-api"},"basePath":"/api/v2","paths":{"/Users/{id}/accessTokens/{fk}":{"get":{"tags":["User"],"summary":"Find a related item by id for accessTokens.","operationId":"User.prototype.__findById__accessTokens","parameters":[{"name":"id","in":"path","description":"User id","required":true,"type":"string","format":"JSON"},{"name":"fk","in":"path","description":"Foreign key for accessTokens","required":true,"type":"string","format":"JSON"}],"responses":{"200":{"description":"Request was successful","schema":{"$ref":"#/definitions/AccessToken"}}},"deprecated":false},"delete":{"tags":["User"],"summary":"Delete a related item by id for accessTokens.","operationId":"User.prototype.__destroyById__accessTokens","parameters":[{"name":"id","in":"path","description":"User id","required":true,"type":"string","format":"JSON"},{"name":"fk","in":"path","description":"Foreign key for accessTokens","required":true,"type":"string","format":"JSON"}],"responses":{"204":{"description":"Request was successful"}},"deprecated":false},"put":{"tags":["User"],"summary":"Update a related item by id for accessTokens.","operationId":"User.prototype.__updateById__accessTokens","parameters":[{"name":"id","in":"path","description":"User id","required":true,"type":"string","format":"JSON"},{"name":"fk","in":"path","description":"Foreign key for accessTokens","required":true,"type":"string","format":"JSON"},{"name":"data","in":"body","required":false,"schema":{"$ref":"#/definitions/AccessToken"}}],"responses":{"200":{"description":"Request was 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Please note this is an object","type":"object"}},"required":["id","shortMessage","sender"],"additionalProperties":false},"AccessUser":{"properties":{"sAMAccountName":{"type":"string"},"displayName":{"type":"string"},"description":{"type":"string"},"email":{"type":"string"},"memberOf":{"type":"array","items":{"type":"string"}}},"required":["sAMAccountName"],"additionalProperties":false},"AccessGroup":{"properties":{"sAMAccountName":{"type":"string"},"description":{"type":"string"},"member":{"type":"array","items":{"type":"string"}},"memberOf":{"type":"array","items":{"type":"string"}}},"required":["sAMAccountName"],"additionalProperties":false},"UserCredential":{"properties":{"provider":{"type":"string"},"authScheme":{"type":"string"},"externalId":{"type":"string"},"profile":{"type":"object"},"credentials":{"type":"object"},"created":{"type":"string","format":"date-time"},"modified":{"type":"string","format":"date-time"},"id":{"$ref":"#/definitions/ObjectID"},"userId":{"$ref":"#/definitions/ObjectID"}},"additionalProperties":false},"UserIdentity":{"properties":{"provider":{"type":"string"},"authScheme":{"type":"string"},"externalId":{"type":"string"},"profile":{"type":"object"},"credentials":{"type":"object"},"created":{"type":"string","format":"date-time"},"modified":{"type":"string","format":"date-time"},"id":{"$ref":"#/definitions/ObjectID"},"userId":{"$ref":"#/definitions/ObjectID"}},"additionalProperties":false},"ApplicationCredential":{"properties":{"provider":{"type":"string"},"authScheme":{"type":"string"},"credentials":{"type":"object"},"created":{"type":"string","format":"date-time"},"modified":{"type":"string","format":"date-time"},"id":{"$ref":"#/definitions/ObjectID"}},"required":["provider"],"additionalProperties":false},"Policy":{"description":"Definition of policy parameters relevant for the storgae lifecycle management of the datasets","properties":{"manager":{"description":"Defines the emails of users that can modify the policy parameters","type":"array","items":{"type":"string"}},"tapeRedundancy":{"default":"low","description":"Defines the level of redundancy in storage to minimize loss of data. Allowed values are low, medium, high. Low could e.g. mean one tape copy only, medium could mean two tape copies and high two geo-redundant tape copies","type":"string"},"autoArchive":{"default":true,"description":"Flag to indicate that a dataset should be automatically archived after ingest. If false then archive delay is ignored","type":"boolean"},"autoArchiveDelay":{"default":7,"description":"Number of days after dataset creation that (remaining) datasets are archived automatically","type":"number","format":"double"},"archiveEmailNotification":{"default":false,"description":"Flag is true when an email notification should be sent to archiveEmailsToBeNotified upon an archive job creation","type":"boolean"},"archiveEmailsToBeNotified":{"description":"Array of additional email addresses that should be notified up an archive job creation","type":"array","items":{"type":"string"}},"retrieveEmailNotification":{"default":false,"description":"Flag is true when an email notification should be sent to retrieveEmailsToBeNotified upon a retrieval job creation","type":"boolean"},"retrieveEmailsToBeNotified":{"description":"Array of additional email addresses that should be notified up a retrieval job creation","type":"array","items":{"type":"string"}},"embargoPeriod":{"default":3,"description":"Number of years after dataset creation before the dataset becomes public","type":"number","format":"double"},"ownerGroup":{"description":"Defines the group which owns the data, and therefore has unrestricted access to this data. Usually a pgroup like p12151","type":"string"},"accessGroups":{"description":"Optional additional groups which have read access to the data. Users which are member in one of the groups listed here are allowed to access this data. The special group 'public' makes data available to all users","type":"array","items":{"type":"string"}},"createdBy":{"description":"Functional or user account name who created this instance","type":"string"},"updatedBy":{"description":"Functional or user account name who last updated this instance","type":"string"},"id":{"$ref":"#/definitions/ObjectID"},"createdAt":{"type":"string","format":"date-time"},"updatedAt":{"type":"string","format":"date-time"}},"required":["ownerGroup"],"additionalProperties":false},"Job":{"description":"This collection keeps information about jobs to be excuted in external systems. In particular it keeps information about the jobs submitted for archiving or retrieving datasets stored inside an archive system. It can also be used to keep track of analysis jobs e.g. for automated analysis workflows.","properties":{"emailJobInitiator":{"description":"The email of the person initiating the job request","type":"string"},"type":{"default":"retrieve","description":"Type of job, e.g. archive, retrieve etc","type":"string"},"creationTime":{"description":"Time when job is created. Format according to chapter 5.6 internet date/time format in RFC 3339","type":"string","format":"date-time"},"executionTime":{"description":"Time when job should be executed. If not specified then the Job will be executed asap. Format according to chapter 5.6 internet date/time format in RFC 3339","type":"string","format":"date-time"},"jobParams":{"description":"Object of key-value pairs defining job input parameters, e.g. 'desinationPath' for retrieve jobs or 'tapeCopies' for archive jobs","type":"object"},"jobStatusMessage":{"description":"Defines current status of job lifecycle","type":"string"},"datasetList":{"description":"Array of objects with keys: pid, files. The value for the pid key defines the dataset ID, the value for the files key is an array of file names. This array is either an empty array, implying that all files within the dataset are selected or an explicit list of dataset-relative file paths, which should be selected","type":"object"},"archiveReturnMessage":{"description":"Detailed status or error message returned by archive system at archive job creation time. If One Job request triggers many archive requests, e.g. when archiving multiple datasets in one job, then this message contains the result of the last dataset handled. Warning: to be obsoleted","type":"string"},"dateOfLastMessage":{"description":"Time when last status message was sent. Format according to chapter 5.6 internet date/time format in RFC 3339. This will be filled automatically if not provided. Warning: to be obsoleted.","type":"string","format":"date-time"},"id":{"$ref":"#/definitions/ObjectID"},"createdAt":{"type":"string","format":"date-time"},"updatedAt":{"type":"string","format":"date-time"},"MessageHistory":{"type":"array","items":{"$ref":"#/definitions/Message"}}},"required":["emailJobInitiator","type","datasetList"],"additionalProperties":false},"ObjectID":{"type":"string","pattern":"^[a-fA-F\\d]{24}$"},"Datafile":{"description":"Embedded schema definition for which fields are required for each file","properties":{"path":{"description":"Relative path of the file within the dataset folder","type":"string"},"size":{"description":"Uncompressed file size in bytes","type":"number","format":"double"},"time":{"description":"Time of file creation on disk, format according to chapter 5.6 internet date/time format in RFC 3339. Local times without timezone/offset info are automatically transformed to UTC using the timezone of the API server","type":"string","format":"date-time"},"chk":{"description":"Checksum for the file, e.g. its sha-2 hashstring","type":"string"},"uid":{"description":"optional: user ID name as seen on filesystem","type":"string"},"gid":{"description":"optional: group ID name as seen on filesystem","type":"string"},"perm":{"description":"optional: Posix permission bits","type":"string"}},"required":["path"],"additionalProperties":false}}} \ No newline at end of file diff --git a/common/models/dataset.json b/common/models/dataset.json index 6622aa9f..e5c3c776 100644 --- a/common/models/dataset.json +++ b/common/models/dataset.json @@ -78,6 +78,10 @@ "type": "string", "description": "Free text explanation of contents of dataset" }, + "datasetName": { + "type": "string", + "description": "A name for the dataset, given by the creator to carry some semantic meaning. Useful for display purposes e.g. instead of displaying the pid" + }, "userTargetLocation": { "type": "string", "description": "User choosable absolute virtual path where datasets are stored. Mainly used as a help for the enduser at dataset retrieval time to find the proper dataset. Will be prepended by p-group" From 1a8d5b21dc4d657cf2ca0b27668f40196d3edfad Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 28 Nov 2018 10:22:56 +0100 Subject: [PATCH 102/147] change edit permissions --- common/models/dataset-attachment.json | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/common/models/dataset-attachment.json b/common/models/dataset-attachment.json index 345ce496..cb43cd23 100644 --- a/common/models/dataset-attachment.json +++ b/common/models/dataset-attachment.json @@ -37,6 +37,19 @@ "required": true } }, - "acls": [], + "acls": [ + { + "accessType": "*", + "principalType": "ROLE", + "principalId": "ingestor", + "permission": "ALLOW" + }, + { + "accessType": "*", + "principalType": "ROLE", + "principalId": "$everyone", + "permission": "DENY" + } + ], "methods": {} } From 12f11823456f33cd3e0f9644c1d9c274043ce851 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 28 Nov 2018 15:10:41 +0100 Subject: [PATCH 103/147] remove ESS docker image tag --- CI/ESS/Jenkinsfile | 1 + 1 file changed, 1 insertion(+) diff --git a/CI/ESS/Jenkinsfile b/CI/ESS/Jenkinsfile index 7f591845..9657ddc4 100644 --- a/CI/ESS/Jenkinsfile +++ b/CI/ESS/Jenkinsfile @@ -10,6 +10,7 @@ node('docker') { echo "Git image id : ${IMAGE_ID}" sh "docker push dacat/catamel:${IMAGE_ID}dev" sh "docker push dacat/catamel:latest" + sh "docker rmi dacat/catamel:${IMAGE_ID}dev" } } stage('SuperTest Catamel ') { From 14a64f661a19bcd6dde6d0b758cd344fddbca91e Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 5 Dec 2018 11:25:58 +0100 Subject: [PATCH 104/147] Issue #109 Issue #108 --- common/models/dataset-lifecycle.js | 65 ++++++++++++------------------ common/models/dataset.js | 61 +++++++++++++++++++++++++--- common/models/policy.js | 19 ++++----- 3 files changed, 92 insertions(+), 53 deletions(-) diff --git a/common/models/dataset-lifecycle.js b/common/models/dataset-lifecycle.js index c6fc1da4..5cc094c9 100644 --- a/common/models/dataset-lifecycle.js +++ b/common/models/dataset-lifecycle.js @@ -45,47 +45,34 @@ module.exports = function(Datasetlifecycle) { } } // add ownerGroup field from linked Datasets - utils.addOwnerGroup(ctx, next) + utils.addOwnerGroup(ctx, next); }) - // transfer status flags to linked dataset Datasetlifecycle.observe('after save', (ctx, next) => { - var Dataset = app.models.Dataset - var instance = ctx.instance - if (!instance) { - instance = ctx.currentInstance - } - if (instance && (instance.datasetId !== undefined)) { - const datasetId = decodeURIComponent(instance.datasetId) - Dataset.findById(datasetId, null, ctx.options).then(datasetInstance => { - if (datasetInstance) { - // important to pass options here, otherwise context gets lost - datasetInstance.updateAttributes({ - archivable: instance.archivable, - retrievable: instance.retrievable, - publishable: instance.publishable - }, ctx.options, - function(err, datasetInstance) { - if (err) { - var error = new Error(); - error.statusCode = 403; - error.message = err; - next(error) - } else { - next() - } - }) - } else { - var error = new Error(); - error.statusCode = 404; - error.message = "DatasetLifecycle after save: No dataset found with pid " + datasetId - next(error) + // TODO add here a hook to check the relevant policy record for "autoArchive" + // if this is "true" then create a new job instance to archive the dataset. + // do NOT override the CLI parameter for autoArchive... + + // if ingest CLI already auto archive return + /* var Policy = app.models.Policy; + Policy.findOne({ + where: { + ownerGroup: ctx.instance.ownerGroup + } + }, + function(err, policyInstance) { + if (!policyInstance || err) { + console.log("Error when looking for Policy of pgroup ", ctx.instance.ownerGroup, err) + } + else { + if (policyInstance && policyInstance.autoArchive ) { + // create auto archive job + + utils.createArchiveJob(policyInstance, ctx); + } } - }) - } else { - next() - } - }) + });*/ + }); Datasetlifecycle.isValid = function(instance, next) { var ds = new Datasetlifecycle(instance) @@ -126,12 +113,12 @@ module.exports = function(Datasetlifecycle) { } else { Dataset.findById(id, options, function(err, instance) { if (err) { - console.log("==== error finding dataset:", err) + console.log("==== error finding dataset:",err) next(err); } else { instance.updateAttributes({ packedSize: 0, - }, options, function(err, inst) { + }, options, function(err,inst){ next(); }); } diff --git a/common/models/dataset.js b/common/models/dataset.js index 8b52a1ab..4da6a5c5 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -33,7 +33,7 @@ module.exports = function(Dataset) { next(); }); - // auto add pid, add a policy record + // auto add pid Dataset.observe('before save', (ctx, next) => { if (ctx.instance) { if (ctx.isNewInstance) { @@ -43,12 +43,64 @@ module.exports = function(Dataset) { console.log(' unmodified pid:', ctx.instance.pid); } ctx.instance.version = p.version; + } - // add a policy record now (A Groups). Check that one doesnt already exist + // auto fill classification + if (ctx.instance) { + if (!ctx.instance.ownerGroup) { + next("No owner group defined"); + } var Policy = app.models.Policy; - Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail); + if (!ctx.instance.classification) { + // classification undefined + Policy.findOne({ + where: { + ownerGroup: ctx.instance.ownerGroup + } + }, + function(err, policyInstance) { + if (err) { + console.log("Error when looking for Policy of pgroup ", ctx.instance.ownerGroup, err); + next(err); + } else if (policyInstance) { + var classification = ""; + switch (policyInstance.tapeRedundancy) { + case "low": + classification = "IN=medium,AV=low,CO=low"; + break; + case "medium": + classification = "IN=medium,AV=medium,CO=low"; + break; + case "high": + classification = "IN=medium,AV=high,CO=low"; + break; + default: + classification = "IN=medium,AV=low,CO=low"; + } + ctx.instance.classification = classification; + next(); + } else { + // neither a policy or a classification exist + ctx.instance.classification = "N=medium,AV=low,CO=low"; + Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail, ""); + next(); + } + }); + } else { + // create policy from classification + var classification = ctx.instance.classification; + var tapeRedundancy = ""; + if (classification.includes("AV=low")) { + tapeRedundancy = "low"; + } else if (classification.includes("AV=medium")) { + tapeRedundancy = "medium"; + } else if (classification.includes("AV=high")) { + tapeRedundancy = "high"; + } + Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail, tapeRedundancy); + next(); + } } - next(); }); // clean up data connected to a dataset, e.g. if archiving failed @@ -384,5 +436,4 @@ module.exports = function(Dataset) { }); }; - }; diff --git a/common/models/policy.js b/common/models/policy.js index a86644ef..fedd3f2f 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -42,28 +42,29 @@ module.exports = function(Policy) { } }); - Policy.addDefault = function(ownerGroup, ownerEmail) { + Policy.addDefault = function(ownerGroup, ownerEmail, tapeRedundancy) { // TODO: move the deault definition somewhere more sensible var defaultPolicy = Object(); defaultPolicy.ownerGroup = ownerGroup; - if (config && !ownerEmail) - { + if (config && !ownerEmail) { defaultPolicy.ownerEmail = config.defaultManager; - } - else - { + } else { defaultPolicy.manager = ownerEmail.split(","); } - defaultPolicy.tapeRedundancy = "low"; + if (tapeRedundancy) { + defaultPolicy.tapeRedundancy = tapeRedundancy; + } else { + defaultPolicy.tapeRedundancy = "low"; // AV default low + } defaultPolicy.autoArchive = false; defaultPolicy.autoArchiveDelay = 7; defaultPolicy.archiveEmailNotification = true; defaultPolicy.retrieveEmailNotification = true; - defaultPolicy.tapeRedundancy = "low"; + defaultPolicy.archiveEmailsToBeNotified = defaultPolicy.manager; + defaultPolicy.retrieveEmailsToBeNotified = defaultPolicy.manager; defaultPolicy.embargoPeriod = 3; //filter must be an object var filter = JSON.parse('{"where": {"ownerGroup":"' + ownerGroup + '"}}'); - console.log("default policy: " + JSON.stringify(defaultPolicy)); Policy.findOrCreate(filter, defaultPolicy); }; }; From 7f014d7dff3eb656c6a081a9c4c6199b6a10bbbf Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 5 Dec 2018 11:37:45 +0100 Subject: [PATCH 105/147] undo unintended delete --- common/models/dataset-lifecycle.js | 65 ++++++++++++++++++------------ 1 file changed, 39 insertions(+), 26 deletions(-) diff --git a/common/models/dataset-lifecycle.js b/common/models/dataset-lifecycle.js index 5cc094c9..c6fc1da4 100644 --- a/common/models/dataset-lifecycle.js +++ b/common/models/dataset-lifecycle.js @@ -45,34 +45,47 @@ module.exports = function(Datasetlifecycle) { } } // add ownerGroup field from linked Datasets - utils.addOwnerGroup(ctx, next); + utils.addOwnerGroup(ctx, next) }) + // transfer status flags to linked dataset Datasetlifecycle.observe('after save', (ctx, next) => { - // TODO add here a hook to check the relevant policy record for "autoArchive" - // if this is "true" then create a new job instance to archive the dataset. - // do NOT override the CLI parameter for autoArchive... - - // if ingest CLI already auto archive return - /* var Policy = app.models.Policy; - Policy.findOne({ - where: { - ownerGroup: ctx.instance.ownerGroup - } - }, - function(err, policyInstance) { - if (!policyInstance || err) { - console.log("Error when looking for Policy of pgroup ", ctx.instance.ownerGroup, err) - } - else { - if (policyInstance && policyInstance.autoArchive ) { - // create auto archive job - - utils.createArchiveJob(policyInstance, ctx); - } + var Dataset = app.models.Dataset + var instance = ctx.instance + if (!instance) { + instance = ctx.currentInstance + } + if (instance && (instance.datasetId !== undefined)) { + const datasetId = decodeURIComponent(instance.datasetId) + Dataset.findById(datasetId, null, ctx.options).then(datasetInstance => { + if (datasetInstance) { + // important to pass options here, otherwise context gets lost + datasetInstance.updateAttributes({ + archivable: instance.archivable, + retrievable: instance.retrievable, + publishable: instance.publishable + }, ctx.options, + function(err, datasetInstance) { + if (err) { + var error = new Error(); + error.statusCode = 403; + error.message = err; + next(error) + } else { + next() + } + }) + } else { + var error = new Error(); + error.statusCode = 404; + error.message = "DatasetLifecycle after save: No dataset found with pid " + datasetId + next(error) } - });*/ - }); + }) + } else { + next() + } + }) Datasetlifecycle.isValid = function(instance, next) { var ds = new Datasetlifecycle(instance) @@ -113,12 +126,12 @@ module.exports = function(Datasetlifecycle) { } else { Dataset.findById(id, options, function(err, instance) { if (err) { - console.log("==== error finding dataset:",err) + console.log("==== error finding dataset:", err) next(err); } else { instance.updateAttributes({ packedSize: 0, - }, options, function(err,inst){ + }, options, function(err, inst) { next(); }); } From 9709a8b260aa7ac97af6943ed9b14d3b1ca85478 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 5 Dec 2018 12:58:50 +0100 Subject: [PATCH 106/147] unique policy per owner group --- common/models/policy.js | 2 ++ 1 file changed, 2 insertions(+) diff --git a/common/models/policy.js b/common/models/policy.js index fedd3f2f..119df667 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -67,4 +67,6 @@ module.exports = function(Policy) { var filter = JSON.parse('{"where": {"ownerGroup":"' + ownerGroup + '"}}'); Policy.findOrCreate(filter, defaultPolicy); }; + + Policy.validatesUniquenessOf('ownerGroup'); }; From 9eceb537947676892425a413e094a01a93be28dc Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 5 Dec 2018 13:15:42 +0100 Subject: [PATCH 107/147] add thumbnail endpoint --- common/models/dataset.js | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/common/models/dataset.js b/common/models/dataset.js index 8b52a1ab..b2990f3f 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -384,5 +384,25 @@ module.exports = function(Dataset) { }); }; + Dataset.thumbnail = function( id, cb) { + console.log("get thumbnail"); + const base64string ="data:image/gif;base64,R0lGODlhAQABAAAAACw="; + cb(null, base64string); + return base64string; + } + + Dataset.remoteMethod("thumbnail", { + accepts: [ + { + arg: "id", + type: "string", + required: true + } + ], + http: {path: "/:id/thumbnail", verb: "get"}, + returns: {arg: "base64string", type: "string"} + }); + + }; From e55101f6685b763764a22bea1f51ef3d6276811d Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 5 Dec 2018 13:31:32 +0100 Subject: [PATCH 108/147] add thumbnail endpoint --- common/models/dataset.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index b2990f3f..a31560fb 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -386,7 +386,7 @@ module.exports = function(Dataset) { Dataset.thumbnail = function( id, cb) { console.log("get thumbnail"); - const base64string ="data:image/gif;base64,R0lGODlhAQABAAAAACw="; + const base64string ="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; cb(null, base64string); return base64string; } From 35b336db97a1b4322e27bf9224e3904010711a02 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Thu, 6 Dec 2018 16:14:15 +0100 Subject: [PATCH 109/147] Issue #109 Issue #108fix callbacks --- common/models/dataset.js | 16 +++++++--------- common/models/policy.js | 7 ++++--- 2 files changed, 11 insertions(+), 12 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 4da6a5c5..e3015fd7 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -43,12 +43,11 @@ module.exports = function(Dataset) { console.log(' unmodified pid:', ctx.instance.pid); } ctx.instance.version = p.version; - } - // auto fill classification - if (ctx.instance) { + + // auto fill classification if (!ctx.instance.ownerGroup) { - next("No owner group defined"); + return next("No owner group defined"); } var Policy = app.models.Policy; if (!ctx.instance.classification) { @@ -60,8 +59,9 @@ module.exports = function(Dataset) { }, function(err, policyInstance) { if (err) { - console.log("Error when looking for Policy of pgroup ", ctx.instance.ownerGroup, err); - next(err); + var msg = "Error when looking for Policy of pgroup " + ctx.instance.ownerGroup + " " + err; + console.log(msg); + return next(msg); } else if (policyInstance) { var classification = ""; switch (policyInstance.tapeRedundancy) { @@ -78,12 +78,10 @@ module.exports = function(Dataset) { classification = "IN=medium,AV=low,CO=low"; } ctx.instance.classification = classification; - next(); } else { // neither a policy or a classification exist ctx.instance.classification = "N=medium,AV=low,CO=low"; Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail, ""); - next(); } }); } else { @@ -98,9 +96,9 @@ module.exports = function(Dataset) { tapeRedundancy = "high"; } Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail, tapeRedundancy); - next(); } } + return next(); }); // clean up data connected to a dataset, e.g. if archiving failed diff --git a/common/models/policy.js b/common/models/policy.js index 119df667..fd31fcb0 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -13,7 +13,6 @@ module.exports = function(Policy) { // for policy interactions // check logged in user email is a member of policy.manager Policy.observe('before save', (ctx, next) => { - if (ctx.currentInstance) { //is a partial update currentInstance rather than instance var UserIdentity = app.models.UserIdentity; @@ -48,11 +47,13 @@ module.exports = function(Policy) { defaultPolicy.ownerGroup = ownerGroup; if (config && !ownerEmail) { defaultPolicy.ownerEmail = config.defaultManager; - } else { + } else if (ownerEmail) { defaultPolicy.manager = ownerEmail.split(","); + } else { + defaultPolicy.manager = ""; } if (tapeRedundancy) { - defaultPolicy.tapeRedundancy = tapeRedundancy; + defaultPolicy.tapeRedundancy = tapeRedundancy; } else { defaultPolicy.tapeRedundancy = "low"; // AV default low } From 69037446c770af5b09ba57dd24b2d9248e07df1e Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Thu, 6 Dec 2018 16:35:22 +0100 Subject: [PATCH 110/147] Update dataset.js --- common/models/dataset.js | 1 - 1 file changed, 1 deletion(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index e3015fd7..cb91fafc 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -44,7 +44,6 @@ module.exports = function(Dataset) { } ctx.instance.version = p.version; - // auto fill classification if (!ctx.instance.ownerGroup) { return next("No owner group defined"); From 31b5019db3ddb103ae5e1775c12bd7c77a8fbe90 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 10 Dec 2018 15:14:44 +0100 Subject: [PATCH 111/147] Update dataset.js --- common/models/dataset.js | 1 + 1 file changed, 1 insertion(+) diff --git a/common/models/dataset.js b/common/models/dataset.js index cb91fafc..c9f1ca09 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -44,6 +44,7 @@ module.exports = function(Dataset) { } ctx.instance.version = p.version; + // auto fill classification if (!ctx.instance.ownerGroup) { return next("No owner group defined"); From b248c5573c0d96b7b7468f9bb2e560fb3e47a8a5 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Mon, 10 Dec 2018 16:19:15 +0100 Subject: [PATCH 112/147] Update package.json --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 9b703f08..51d8c138 100644 --- a/package.json +++ b/package.json @@ -9,7 +9,7 @@ "lint": "eslint common/models", "start": "node .", "posttests": "npm run lint && nsp check", - "test": "./node_modules/mocha/bin/mocha --timeout=30000 --reporter spec --exit 2>/dev/null" + "test": "./node_modules/mocha/bin/mocha --timeout=300000 --reporter spec --exit 2>/dev/null" }, "dependencies": { "compression": "^1.7.3", From d1a0caab3b326f1e70c36a15ef67d220882cef90 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 11:43:57 +0100 Subject: [PATCH 113/147] Update testGenerator.js --- test/testGenerator.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/testGenerator.js b/test/testGenerator.js index c0dd8188..59018ad4 100644 --- a/test/testGenerator.js +++ b/test/testGenerator.js @@ -42,7 +42,7 @@ module.exports = { const expect = c.expect; const url = settings.apiPrefix + route; const withData = c.body || false; - const isWithAuthentication = c.authenticate || false; + const isWithAuthentication = false; From 42114a0fe079af9f5455ca79c0c05ab51fa539df Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 11:55:35 +0100 Subject: [PATCH 114/147] Update testGenerator.js --- test/testGenerator.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/testGenerator.js b/test/testGenerator.js index 59018ad4..1095a37b 100644 --- a/test/testGenerator.js +++ b/test/testGenerator.js @@ -42,7 +42,7 @@ module.exports = { const expect = c.expect; const url = settings.apiPrefix + route; const withData = c.body || false; - const isWithAuthentication = false; + const isWithAuthentication = true; From 272ca6c13fa792b7398f6a9a86e3407aa8633a27 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 12:15:06 +0100 Subject: [PATCH 115/147] Update testGenerator.js --- test/testGenerator.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/testGenerator.js b/test/testGenerator.js index 1095a37b..c0dd8188 100644 --- a/test/testGenerator.js +++ b/test/testGenerator.js @@ -42,7 +42,7 @@ module.exports = { const expect = c.expect; const url = settings.apiPrefix + route; const withData = c.body || false; - const isWithAuthentication = true; + const isWithAuthentication = c.authenticate || false; From 08429c19e888bc5ab0280bf61e7d0e50178111be Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 12:55:17 +0100 Subject: [PATCH 116/147] Update tests.json --- test/config/tests.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/config/tests.json b/test/config/tests.json index 373286ab..fb9df6b9 100644 --- a/test/config/tests.json +++ b/test/config/tests.json @@ -80,7 +80,7 @@ "method": "GET", "route": "Datasets/fullfacet", "expect": 200, - "authenticate": "user", + "authenticate": "admin", "response": [ "res.body.should.be.instanceof(Object);", "res.body.should.be.instanceof(Array);" From 6835a37e30d5b40a3a236e4d7edb0dcade65b650 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 13:01:30 +0100 Subject: [PATCH 117/147] Update tests.json --- test/config/tests.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/config/tests.json b/test/config/tests.json index fb9df6b9..a3322d01 100644 --- a/test/config/tests.json +++ b/test/config/tests.json @@ -8,7 +8,7 @@ "method": "GET", "route": "Datasets?filter=%7B%22limit%22%3A10%7D", "expect": 200, - "authenticate": "user", + "authenticate": "admin", "response": [ "res.body.should.be.instanceof(Array);" ] From 700deef1ae69fd1a40e1e59713e762cdaa9ada99 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 13:22:20 +0100 Subject: [PATCH 118/147] Update tests.json --- test/config/tests.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/config/tests.json b/test/config/tests.json index a3322d01..64a3e316 100644 --- a/test/config/tests.json +++ b/test/config/tests.json @@ -51,7 +51,7 @@ "method": "POST", "route": "Datasets", "expect": 200, - "authenticate": "user", + "authenticate": "admin", "body": { "owner": "Bertram Astor", "ownerEmail": "bertram.astor@grumble.com", @@ -90,7 +90,7 @@ "method": "POST", "route": "Jobs", "expect": 400, - "authenticate": "user", + "authenticate": "admin", "body": { "emailJobInitiator": "scicatingestor@psi.ch", "type": "archive", From 5683bad7b2f08cd780b3259ddfe66338b1f12d6d Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 13:31:11 +0100 Subject: [PATCH 119/147] Update package.json --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 51d8c138..9b703f08 100644 --- a/package.json +++ b/package.json @@ -9,7 +9,7 @@ "lint": "eslint common/models", "start": "node .", "posttests": "npm run lint && nsp check", - "test": "./node_modules/mocha/bin/mocha --timeout=300000 --reporter spec --exit 2>/dev/null" + "test": "./node_modules/mocha/bin/mocha --timeout=30000 --reporter spec --exit 2>/dev/null" }, "dependencies": { "compression": "^1.7.3", From b9ea61d59c28932a7f08a919e3132410abdefac2 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 13:47:19 +0100 Subject: [PATCH 120/147] Update policy.js --- common/models/policy.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/policy.js b/common/models/policy.js index fd31fcb0..a08644cf 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -50,7 +50,7 @@ module.exports = function(Policy) { } else if (ownerEmail) { defaultPolicy.manager = ownerEmail.split(","); } else { - defaultPolicy.manager = ""; + defaultPolicy.manager = "scicatingestor@psi.ch"; } if (tapeRedundancy) { defaultPolicy.tapeRedundancy = tapeRedundancy; From 1ec7ae34e8e84192b2c263ca7da8276cb12f8522 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 13:56:23 +0100 Subject: [PATCH 121/147] Update dataset.js --- common/models/dataset.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index c9f1ca09..7e122b17 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -80,7 +80,7 @@ module.exports = function(Dataset) { ctx.instance.classification = classification; } else { // neither a policy or a classification exist - ctx.instance.classification = "N=medium,AV=low,CO=low"; + ctx.instance.classification = "IN=medium,AV=low,CO=low"; Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail, ""); } }); From 2cd091771e16f884630c13cc1fbe6406ab0e8947 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Tue, 11 Dec 2018 14:09:03 +0100 Subject: [PATCH 122/147] add endpoint --- .gitignore | 5 +++++ common/models/dataset.js | 2 +- server/boot/createRoles.js | 23 ++++++++++++----------- 3 files changed, 18 insertions(+), 12 deletions(-) diff --git a/.gitignore b/.gitignore index fc81ea6b..44fb6bff 100644 --- a/.gitignore +++ b/.gitignore @@ -23,6 +23,11 @@ coverage node_modules npm-debug.log server/pass +server/admin +server/ingestor +server/archiveManager +server/proposalIngestor +server/userGroupIngestor server/providers.json server/datasources.json CI/PSI/envfiles/* diff --git a/common/models/dataset.js b/common/models/dataset.js index a31560fb..fe7d5850 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -400,7 +400,7 @@ module.exports = function(Dataset) { } ], http: {path: "/:id/thumbnail", verb: "get"}, - returns: {arg: "base64string", type: "string"} + returns: {type: "string", root: true} }); diff --git a/server/boot/createRoles.js b/server/boot/createRoles.js index aa3a45fe..d4c7e5fd 100644 --- a/server/boot/createRoles.js +++ b/server/boot/createRoles.js @@ -1,14 +1,14 @@ var utils = require('./common_utils'); var fs = require('fs'); -module.exports = function(app, cb2) { +module.exports = function (app, cb2) { // define roles // note: role names are all lowercase , corresponding accounts camelcase // - createRole = function(account, cb) { + createRole = function (account, cb) { var User = app.models.User; @@ -16,7 +16,7 @@ module.exports = function(app, cb2) { where: { username: account } - }, function(err, users) { + }, function (err, users) { if (err) { return cb(err); } else if (users.length === 0) { @@ -25,13 +25,14 @@ module.exports = function(app, cb2) { console.log("creating account " + account); if (fs.existsSync(path)) { var data = fs.readFileSync(path, 'utf8').split('\n')[0].split(" "); + console.log("gm", data); User.create({ realm: 'localhost:3001', username: account, password: data[0], email: data[1], emailVerified: true - }, function(err, user) { + }, function (err, user) { if (err) { console.log("User create:" + err + " " + user) return cb(err) @@ -46,7 +47,7 @@ module.exports = function(app, cb2) { password: 'aman', email: account + '@change.com', emailVerified: true - }, function(err, user) { + }, function (err, user) { if (err) { console.log("User create:" + err + " " + user) return cb(err) @@ -63,12 +64,12 @@ module.exports = function(app, cb2) { }); }; - createRole('admin', function() { - createRole('archiveManager', function() { - createRole('ingestor', function() { - createRole('proposalIngestor', function() { - createRole('userGroupIngestor', function(){ - console.log("Last role mapped, finished booting ",new Date()) + createRole('admin', function () { + createRole('archiveManager', function () { + createRole('ingestor', function () { + createRole('proposalIngestor', function () { + createRole('userGroupIngestor', function () { + console.log("Last role mapped, finished booting ", new Date()) cb2(null) }) }) From 434ba9ec04142ee1f5ba6192bfbf2dceb76e8aa0 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Tue, 11 Dec 2018 14:15:20 +0100 Subject: [PATCH 123/147] add better description to caption --- .gitignore | 1 + common/models/dataset-attachment.json | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index fc81ea6b..0c712be7 100644 --- a/.gitignore +++ b/.gitignore @@ -23,6 +23,7 @@ coverage node_modules npm-debug.log server/pass +server/ingestor server/providers.json server/datasources.json CI/PSI/envfiles/* diff --git a/common/models/dataset-attachment.json b/common/models/dataset-attachment.json index cb43cd23..cfab59e0 100644 --- a/common/models/dataset-attachment.json +++ b/common/models/dataset-attachment.json @@ -19,7 +19,7 @@ }, "caption": { "type": "string", - "description": "Contains a thumbnail preview in base64 encoded png format for a given dataset", + "description": "Dataset attachment caption to show in catanie", "default": "retrieve" }, "creationTime": { From aab3f6fd0fffd9d859f75e0025d8b69c1981be28 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Tue, 11 Dec 2018 14:24:21 +0100 Subject: [PATCH 124/147] upgrade packages --- package-lock.json | 195 ++++++++++++++++++++++++++++++---------------- package.json | 8 +- 2 files changed, 132 insertions(+), 71 deletions(-) diff --git a/package-lock.json b/package-lock.json index 2254f54d..fc4ee05a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -139,7 +139,7 @@ }, "@types/ldapjs": { "version": "1.0.3", - "resolved": "https://registry.npmjs.org/@types/ldapjs/-/ldapjs-1.0.3.tgz", + "resolved": "http://registry.npmjs.org/@types/ldapjs/-/ldapjs-1.0.3.tgz", "integrity": "sha512-FSj24s1WsFEfOy8taIKp2DokSZfFkjWYZb88AS5eDj3WTocZ+4DnHjhzrXEs048WQ5mfOLJXMOAnc0kSnHh5Lw==", "requires": { "@types/events": "*", @@ -228,9 +228,9 @@ "dev": true }, "acorn-jsx": { - "version": "5.0.0", - "resolved": "https://registry.npmjs.org/acorn-jsx/-/acorn-jsx-5.0.0.tgz", - "integrity": "sha512-XkB50fn0MURDyww9+UYL3c1yLbOBz0ZFvrdYlGB8l+Ije1oSC75qAqrzSPjYQbdnQUzhlUGNKuesryAv0gxZOg==", + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/acorn-jsx/-/acorn-jsx-5.0.1.tgz", + "integrity": "sha512-HJ7CfNHrfJLlNTzIEUTj43LNWGkqpRLxm3YjAlcD0ACydk9XynzYsCBHxut+iqt+1aBXkx9UP/w/ZqMr13XIzg==", "dev": true }, "ajv": { @@ -294,7 +294,7 @@ }, "ansi-escapes": { "version": "3.1.0", - "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-3.1.0.tgz", + "resolved": "http://registry.npmjs.org/ansi-escapes/-/ansi-escapes-3.1.0.tgz", "integrity": "sha512-UgAb8H9D41AQnu/PbWlCofQVcnV4Gs2bBJi9eZPxfU/hgglFh3SMDMENRIqdr7H6XFnXdoknctFByVsCOotTVw==", "dev": true }, @@ -359,6 +359,12 @@ "integrity": "sha512-jgsaNduz+ndvGyFt3uSuWqvy4lCnIJiovtouQN5JZHOKCS2QuhEdbcQHFhVksz2N2U9hXJo8odG7ETyWlEeuDw==", "dev": true }, + "astral-regex": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/astral-regex/-/astral-regex-1.0.0.tgz", + "integrity": "sha512-+Ryf6g3BKoRc7jfp7ad8tM4TtMiaWvbF/1/sQcZPkkS7ag3D5nMBCe2UfOTONtAkaG0tO0ij3C5Lwmf1EiyjHg==", + "dev": true + }, "async": { "version": "2.6.1", "resolved": "https://registry.npmjs.org/async/-/async-2.6.1.tgz", @@ -594,7 +600,7 @@ }, "callsites": { "version": "0.2.0", - "resolved": "https://registry.npmjs.org/callsites/-/callsites-0.2.0.tgz", + "resolved": "http://registry.npmjs.org/callsites/-/callsites-0.2.0.tgz", "integrity": "sha1-r6uWJikQp/M8GaV3WCXGnzTjUMo=", "dev": true }, @@ -1204,9 +1210,9 @@ "integrity": "sha1-G2HAViGQqN/2rjuyzwIAyhMLhtQ=" }, "eslint": { - "version": "5.9.0", - "resolved": "https://registry.npmjs.org/eslint/-/eslint-5.9.0.tgz", - "integrity": "sha512-g4KWpPdqN0nth+goDNICNXGfJF7nNnepthp46CAlJoJtC5K/cLu3NgCM3AHu1CkJ5Hzt9V0Y0PBAO6Ay/gGb+w==", + "version": "5.10.0", + "resolved": "https://registry.npmjs.org/eslint/-/eslint-5.10.0.tgz", + "integrity": "sha512-HpqzC+BHULKlnPwWae9MaVZ5AXJKpkxCVXQHrFaRw3hbDj26V/9ArYM4Rr/SQ8pi6qUPLXSSXC4RBJlyq2Z2OQ==", "dev": true, "requires": { "@babel/code-frame": "^7.0.0", @@ -1218,7 +1224,7 @@ "eslint-scope": "^4.0.0", "eslint-utils": "^1.3.1", "eslint-visitor-keys": "^1.0.0", - "espree": "^4.0.0", + "espree": "^5.0.0", "esquery": "^1.0.1", "esutils": "^2.0.2", "file-entry-cache": "^2.0.0", @@ -1228,7 +1234,6 @@ "ignore": "^4.0.6", "imurmurhash": "^0.1.4", "inquirer": "^6.1.0", - "is-resolvable": "^1.1.0", "js-yaml": "^3.12.0", "json-stable-stringify-without-jsonify": "^1.0.1", "levn": "^0.3.0", @@ -1250,9 +1255,9 @@ }, "dependencies": { "ajv": { - "version": "6.5.5", - "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.5.5.tgz", - "integrity": "sha512-7q7gtRQDJSyuEHjuVgHoUa2VuemFiCMrfQc9Tc08XTAc4Zj/5U1buQJ0HU6i7fKjXU09SVgSmxa4sLvuvS8Iyg==", + "version": "6.6.1", + "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.6.1.tgz", + "integrity": "sha512-ZoJjft5B+EJBjUyu9C9Hc0OZyPZSSlOF+plzouTrg6UlA8f+e/n8NIgBFG/9tppJtpPWfthHakK7juJdNDODww==", "dev": true, "requires": { "fast-deep-equal": "^2.0.1", @@ -1310,18 +1315,18 @@ } }, "eslint-config-loopback": { - "version": "12.0.0", - "resolved": "https://registry.npmjs.org/eslint-config-loopback/-/eslint-config-loopback-12.0.0.tgz", - "integrity": "sha512-Pxz7ecK+/4ufJIMMtQ+XimQUP8qpM9IdVvIg78N17w6/PMBoFEeX1ef+ylb3c4BrAGcTzm+gb8VFtFW2JXoWKA==", + "version": "12.1.0", + "resolved": "https://registry.npmjs.org/eslint-config-loopback/-/eslint-config-loopback-12.1.0.tgz", + "integrity": "sha512-3YuzaOdfw5DwZuwmAZdFoBNpQDCDovyWITCY95gfyz9aYt5A8Zr95cEVfxcbTl3xQEyf/9wFUqEe8IbhrURkrA==", "dev": true, "requires": { - "eslint-plugin-mocha": "^4.11.0" + "eslint-plugin-mocha": "^5.2.0" } }, "eslint-plugin-mocha": { - "version": "4.12.1", - "resolved": "https://registry.npmjs.org/eslint-plugin-mocha/-/eslint-plugin-mocha-4.12.1.tgz", - "integrity": "sha512-hxWtYHvLA0p/PKymRfDYh9Mxt5dYkg2Goy1vZDarTEEYfELP9ksga7kKG1NUKSQy27C8Qjc7YrSWTLUhOEOksA==", + "version": "5.2.0", + "resolved": "https://registry.npmjs.org/eslint-plugin-mocha/-/eslint-plugin-mocha-5.2.0.tgz", + "integrity": "sha512-4VTX/qIoxUFRnXLNm6bEhEJyfGnGagmQzV4TWXKzkZgIYyP2FSubEdCjEFTyS/dGwSVRWCWGX7jO7BK8R0kppg==", "dev": true, "requires": { "ramda": "^0.25.0" @@ -1350,9 +1355,9 @@ "dev": true }, "espree": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/espree/-/espree-4.1.0.tgz", - "integrity": "sha512-I5BycZW6FCVIub93TeVY1s7vjhP9CY6cXCznIRfiig7nRviKZYdRnj/sHEWC6A7WE9RDWOFq9+7OsWSYz8qv2w==", + "version": "5.0.0", + "resolved": "https://registry.npmjs.org/espree/-/espree-5.0.0.tgz", + "integrity": "sha512-1MpUfwsdS9MMoN7ZXqAr9e9UKdVHDcvrJpyx7mm1WuQlx/ygErEQBzgi5Nh5qBHIoYweprhtMkTCb9GhcAIcsA==", "dev": true, "requires": { "acorn": "^6.0.2", @@ -1925,9 +1930,9 @@ "integrity": "sha1-Yzwsg+PaQqUC9SRmAiSA9CCCYd4=" }, "inquirer": { - "version": "6.2.0", - "resolved": "https://registry.npmjs.org/inquirer/-/inquirer-6.2.0.tgz", - "integrity": "sha512-QIEQG4YyQ2UYZGDC4srMZ7BjHOmNk1lR2JQj5UknBapklm6WHA+VVH7N+sUdX3A7NeCfGF8o4X1S3Ao7nAcIeg==", + "version": "6.2.1", + "resolved": "https://registry.npmjs.org/inquirer/-/inquirer-6.2.1.tgz", + "integrity": "sha512-088kl3DRT2dLU5riVMKKr1DlImd6X7smDhpXUCkJDCKvTEJeRiXh0G132HG9u5a+6Ylw9plFRY7RuTnwohYSpg==", "dev": true, "requires": { "ansi-escapes": "^3.0.0", @@ -1941,10 +1946,16 @@ "run-async": "^2.2.0", "rxjs": "^6.1.0", "string-width": "^2.1.0", - "strip-ansi": "^4.0.0", + "strip-ansi": "^5.0.0", "through": "^2.3.6" }, "dependencies": { + "ansi-regex": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.0.0.tgz", + "integrity": "sha512-iB5Dda8t/UqpPI/IjsejXu5jOGDrzn41wJyljwPH65VCIbk6+1BzFIMJGFwTNrYXT1CrD+B4l19U7awiQ8rk7w==", + "dev": true + }, "rxjs": { "version": "6.3.3", "resolved": "https://registry.npmjs.org/rxjs/-/rxjs-6.3.3.tgz", @@ -1953,6 +1964,15 @@ "requires": { "tslib": "^1.9.0" } + }, + "strip-ansi": { + "version": "5.0.0", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.0.0.tgz", + "integrity": "sha512-Uu7gQyZI7J7gn5qLn1Np3G9vcYGTVqB+lFTytnDJv83dd8T22aGH451P3jueT2/QemInJDfxHB5Tde5OzgG1Ow==", + "dev": true, + "requires": { + "ansi-regex": "^4.0.0" + } } } }, @@ -1983,12 +2003,6 @@ "integrity": "sha1-eaKp7OfwlugPNtKy87wWwf9L8/o=", "dev": true }, - "is-resolvable": { - "version": "1.1.0", - "resolved": 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"1.0.0", - "resolved": "https://registry.npmjs.org/slice-ansi/-/slice-ansi-1.0.0.tgz", - "integrity": "sha512-POqxBK6Lb3q6s047D/XsDVNPnF9Dl8JSaqe9h9lURl0OdNqy/ujDrOiIHtsqXMGbWWTIomRzAMaTyawAU//Reg==", + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/slice-ansi/-/slice-ansi-2.0.0.tgz", + "integrity": "sha512-4j2WTWjp3GsZ+AOagyzVbzp4vWGtZ0hEZ/gDY/uTvm6MTxUfTUIsnMIFb1bn8o0RuXiqUw15H1bue8f22Vw2oQ==", "dev": true, "requires": { + "ansi-styles": "^3.2.0", + "astral-regex": "^1.0.0", "is-fullwidth-code-point": "^2.0.0" + }, + "dependencies": { + "ansi-styles": { + "version": "3.2.1", + "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-3.2.1.tgz", + "integrity": "sha512-VT0ZI6kZRdTh8YyJw3SMbYm/u+NqfsAxEpWO0Pf9sq8/e94WxxOpPKx9FR1FlyCtOVDNOQ+8ntlqFxiRc+r5qA==", + "dev": true, + "requires": { + "color-convert": "^1.9.0" + } + } } }, "smtp-connection": { @@ -4168,21 +4223,21 @@ "dev": true }, "table": { - "version": "5.1.0", - "resolved": "https://registry.npmjs.org/table/-/table-5.1.0.tgz", - "integrity": "sha512-e542in22ZLhD/fOIuXs/8yDZ9W61ltF8daM88rkRNtgTIct+vI2fTnAyu/Db2TCfEcI8i7mjZz6meLq0nW7TYg==", + "version": "5.1.1", + "resolved": "https://registry.npmjs.org/table/-/table-5.1.1.tgz", + "integrity": "sha512-NUjapYb/qd4PeFW03HnAuOJ7OMcBkJlqeClWxeNlQ0lXGSb52oZXGzkO0/I0ARegQ2eUT1g2VDJH0eUxDRcHmw==", "dev": true, "requires": { - "ajv": "^6.5.3", - "lodash": "^4.17.10", - "slice-ansi": "1.0.0", + "ajv": "^6.6.1", + "lodash": "^4.17.11", + "slice-ansi": "2.0.0", "string-width": "^2.1.1" }, "dependencies": { "ajv": { - "version": "6.5.5", - "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.5.5.tgz", - "integrity": "sha512-7q7gtRQDJSyuEHjuVgHoUa2VuemFiCMrfQc9Tc08XTAc4Zj/5U1buQJ0HU6i7fKjXU09SVgSmxa4sLvuvS8Iyg==", + "version": "6.6.1", + "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.6.1.tgz", + "integrity": "sha512-ZoJjft5B+EJBjUyu9C9Hc0OZyPZSSlOF+plzouTrg6UlA8f+e/n8NIgBFG/9tppJtpPWfthHakK7juJdNDODww==", "dev": true, "requires": { "fast-deep-equal": "^2.0.1", @@ -4202,6 +4257,12 @@ "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-0.4.1.tgz", "integrity": "sha512-xbbCH5dCYU5T8LcEhhuh7HJ88HXuW3qsI3Y0zOZFKfZEHcpWiHU/Jxzk629Brsab/mMiHQti9wMP+845RPe3Vg==", "dev": true + }, + "lodash": { + "version": "4.17.11", + "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.11.tgz", + "integrity": "sha512-cQKh8igo5QUhZ7lg38DYWAxMvjSAKG0A8wGSVimP07SIUEK2UO+arSRKbRZWtelMtN5V0Hkwh5ryOto/SshYIg==", + "dev": true } } }, diff --git a/package.json b/package.json index 9b703f08..ad3e95db 100644 --- a/package.json +++ b/package.json @@ -26,8 +26,8 @@ "loopback-ds-timestamp-mixin": "^3.4.1", "moment": "^2.20.1", "moment-timezone": "^0.5.23", - "nodemailer": "^4.6.8", - "passport-ldapauth": "^2.1.0", + "nodemailer": "^4.7.0", + "passport-ldapauth": "^2.1.1", "passport-local": "^1.0.0", "passport-openidconnect": "^0.0.2", "serve-favicon": "2.5.0", @@ -41,8 +41,8 @@ "@mean-expert/loopback-sdk-builder": "^2.1.0", "chai": "^4.2.0", "chai-http": "^4.0.0", - "eslint": "^5.9.0", - "eslint-config-loopback": "^12.0.0", + "eslint": "^5.10.0", + "eslint-config-loopback": "^12.1.0", "mocha": "^5.2.0", "supertest": "^3.3.0" }, From c3a09c2412efa7968221942498c14f72dfc966f6 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 14:54:39 +0100 Subject: [PATCH 125/147] Update policy.js Minor change, using wrong property name --- common/models/policy.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/common/models/policy.js b/common/models/policy.js index a08644cf..6e6f46e6 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -46,11 +46,11 @@ module.exports = function(Policy) { var defaultPolicy = Object(); defaultPolicy.ownerGroup = ownerGroup; if (config && !ownerEmail) { - defaultPolicy.ownerEmail = config.defaultManager; + defaultPolicy.manager = config.defaultManager; } else if (ownerEmail) { defaultPolicy.manager = ownerEmail.split(","); } else { - defaultPolicy.manager = "scicatingestor@psi.ch"; + defaultPolicy.manager = ""; } if (tapeRedundancy) { defaultPolicy.tapeRedundancy = tapeRedundancy; From 3db2809191b0a1eb253937480ac5efc9e34aa6ce Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 16:50:03 +0100 Subject: [PATCH 126/147] add png(s) to readme for policy --- CI/ESS/images/policy1.png | Bin 0 -> 29147 bytes CI/ESS/images/policy2.png | Bin 0 -> 75835 bytes 2 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 CI/ESS/images/policy1.png create mode 100644 CI/ESS/images/policy2.png diff --git a/CI/ESS/images/policy1.png b/CI/ESS/images/policy1.png new file mode 100644 index 0000000000000000000000000000000000000000..3f17ff0b52a32085135c3686410ade037b77ee4e GIT binary patch literal 29147 zcmeFYbx>Si*Ct95BzW*(jY|j;pm7fnAh<(t8h3XKF2OB$aCc}Nf_AV*8rR@K8g~K= z@AoFZ@0#2$Tpi5@Ko|nFq`M4$~K(j~>na;+%0K_(b2K;5*|3l_v^X(cp8T 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z6zw62zK`x%@QFp1#=N{r^Ptjcbm|A0(Q34G;tp1lsID_~Zf0%EGC|(s{#IVa6=7}n zn{Do7A4?r$Uhz}%cz5pQbOgL9%RB*GVrj3r{1ijkBi+TH>|MPT_l!K(SBSeh7{u7alPPBQqAtrM`V8*-D%uX)!9NBGwn#lL>0Myvpytg zFJV+DoH3y}!x<-J)&SEPD;^XWbW*no8(Vp|yXhvnVm-8)t6emQi*K6C_pAA~>-D%I zFi@7Si8k1K>Z3`ISk2HuN51K;Dlvj8FkBQ?JD0@09Hh2_o7WXpN|P_&2`Ai!mIq*T z7ppqA&iaYJs=cPdyO47( z7x$Fx?TTA`xwGYJmU3!^OV^0Y*z;Ug_OMgSXQy$rx7*65#X8PEW-tCC@f%=V7V$=B z=}JNA7Ug7r9mXm7K2e%=sQ4ml(z4V)7d6v9Df5Mg?sPu-VADI)$gh9t@hNKm&Y?K_ zogVW#%|&V#3Jaw}4%rV#D&`Q_glXe;oye|c5h6>((DH4192*TF#vzny$ptVK-Zm44q^V$wZvOS#?i z8@$23w~L6FXcZ@{L&T-l#u1&5FN+Uei=2Ray(1VrQ*++I8n7_$jsTJ9 zs3$F4?W_;hXG;0kYsY;=xjBzui?MO)c zrziT24;GlY$NmQbk%1im literal 0 HcmV?d00001 From 3934cc5f559526f6fcdd73eba9bc16bc920280b2 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 16:57:06 +0100 Subject: [PATCH 127/147] Update README.md --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index aa4ed93e..b434a833 100644 --- a/README.md +++ b/README.md @@ -204,3 +204,7 @@ The library is generated by the following command ## Authentication Users are authenticated by loopback built in user accounts and by accounts, which are connected via any of the passport supported strategies, in particular OpenID connected and a direct AD connection + +## Policy Configuration for Archiving and Retrieving + /images/policy1.png or +![model diagram](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/images/policy1.png) From 46dc2c5de2f093ff565e010706a974662281ee1a Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 16:57:54 +0100 Subject: [PATCH 128/147] Update README.md --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index b434a833..6028b7d4 100644 --- a/README.md +++ b/README.md @@ -206,5 +206,4 @@ The library is generated by the following command Users are authenticated by loopback built in user accounts and by accounts, which are connected via any of the passport supported strategies, in particular OpenID connected and a direct AD connection ## Policy Configuration for Archiving and Retrieving - /images/policy1.png or ![model diagram](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/images/policy1.png) From d89a672e68e4c80212731cc015f1899dc6716f5d Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 16:58:25 +0100 Subject: [PATCH 129/147] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6028b7d4..575db561 100644 --- a/README.md +++ b/README.md @@ -206,4 +206,4 @@ The library is generated by the following command Users are authenticated by loopback built in user accounts and by accounts, which are connected via any of the passport supported strategies, in particular OpenID connected and a direct AD connection ## Policy Configuration for Archiving and Retrieving -![model diagram](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/images/policy1.png) +![policy_table](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/images/policy1.png) From e983fd38a02aad6f613fe09bc01a8c0579a04e61 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 11 Dec 2018 17:00:24 +0100 Subject: [PATCH 130/147] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 575db561..f1595584 100644 --- a/README.md +++ b/README.md @@ -207,3 +207,4 @@ Users are authenticated by loopback built in user accounts and by accounts, whic ## Policy Configuration for Archiving and Retrieving ![policy_table](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/images/policy1.png) +![policy_edit](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/images/policy2.png) From ec40a5724ae96cc037a169185115bc1c3e609c88 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Tue, 11 Dec 2018 22:08:45 +0100 Subject: [PATCH 131/147] add to thumbnail --- common/models/dataset.js | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 1ea88b2a..ccaf2c85 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -435,8 +435,16 @@ module.exports = function(Dataset) { }; Dataset.thumbnail = function( id, cb) { - console.log("get thumbnail"); - const base64string ="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; + // console.log("get thumbnail"); + const base64string= Dataset.findById(id, options, function (err, da) { + const attach = da.datasetattachments; + let base64string ="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; + if (attach === undefined) { + } else { + base64string = attach[0].thumbnail; + } + return base64string; + }); cb(null, base64string); return base64string; } From 496f4fd6db533b2eeec513bee862f9efa23841f6 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Tue, 11 Dec 2018 22:10:50 +0100 Subject: [PATCH 132/147] add options to arg --- common/models/dataset.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index ccaf2c85..962c6091 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -434,7 +434,7 @@ module.exports = function(Dataset) { }); }; - Dataset.thumbnail = function( id, cb) { + Dataset.thumbnail = function( id, options, cb) { // console.log("get thumbnail"); const base64string= Dataset.findById(id, options, function (err, da) { const attach = da.datasetattachments; From ffcf463312de25bd0c09a7e15ffff0175ab8181c Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 12 Dec 2018 09:43:24 +0100 Subject: [PATCH 133/147] move screen dumps to catanie --- CI/ESS/images/policy1.png | Bin 29147 -> 0 bytes CI/ESS/images/policy2.png | Bin 75835 -> 0 bytes 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 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z=}JNA7Ug7r9mXm7K2e%=sQ4ml(z4V)7d6v9Df5Mg?sPu-VADI)$gh9t@hNKm&Y?K_ zogVW#%|&V#3Jaw}4%rV#D&`Q_glXe;oye|c5h6>((DH4192*TF#vzny$ptVK-Zm44q^V$wZvOS#?i z8@$23w~L6FXcZ@{L&T-l#u1&5FN+Uei=2Ray(1VrQ*++I8n7_$jsTJ9 zs3$F4?W_;hXG;0kYsY;=xjBzui?MO)c zrziT24;GlY$NmQbk%1im From d534dd623ca59176c8fb5d04eeedaea677b57cb5 Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 12 Dec 2018 09:57:13 +0100 Subject: [PATCH 134/147] Update README.md --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index f1595584..76e75413 100644 --- a/README.md +++ b/README.md @@ -205,6 +205,3 @@ The library is generated by the following command ## Authentication Users are authenticated by loopback built in user accounts and by accounts, which are connected via any of the passport supported strategies, in particular OpenID connected and a direct AD connection -## Policy Configuration for Archiving and Retrieving -![policy_table](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/images/policy1.png) -![policy_edit](https://github.com/SciCatProject/catamel/blob/develop/CI/ESS/images/policy2.png) From edf50eb3ad15c790e7e826dc32696b3e6bb50cc4 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 12 Dec 2018 10:19:15 +0100 Subject: [PATCH 135/147] update thumbnail --- common/models/dataset.js | 105 +- package-lock.json | 2166 +++++++++++++++++++++++++++++++++++++- package.json | 1 + 3 files changed, 2214 insertions(+), 58 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 962c6091..68818a8d 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -9,26 +9,26 @@ var dsr = require('./raw-dataset.json'); var dsd = require('./derived-dataset.json'); var own = require('./ownable.json'); -module.exports = function(Dataset) { +module.exports = function (Dataset) { var app = require('../../server/server'); // make sure that all times are UTC Dataset.validatesUniquenessOf('pid'); // put - Dataset.beforeRemote('replaceOrCreate', function(ctx, instance, next) { + Dataset.beforeRemote('replaceOrCreate', function (ctx, instance, next) { utils.updateTimesToUTC(['creationTime'], ctx.args.data); next(); }); // patch - Dataset.beforeRemote('patchOrCreate', function(ctx, instance, next) { + Dataset.beforeRemote('patchOrCreate', function (ctx, instance, next) { utils.updateTimesToUTC(['creationTime'], ctx.args.data); next(); }); // post - Dataset.beforeRemote('create', function(ctx, unused, next) { + Dataset.beforeRemote('create', function (ctx, unused, next) { utils.updateTimesToUTC(['creationTime'], ctx.args.data); next(); }); @@ -44,7 +44,7 @@ module.exports = function(Dataset) { } ctx.instance.version = p.version; - + // auto fill classification if (!ctx.instance.ownerGroup) { return next("No owner group defined"); @@ -53,11 +53,11 @@ module.exports = function(Dataset) { if (!ctx.instance.classification) { // classification undefined Policy.findOne({ - where: { - ownerGroup: ctx.instance.ownerGroup - } - }, - function(err, policyInstance) { + where: { + ownerGroup: ctx.instance.ownerGroup + } + }, + function (err, policyInstance) { if (err) { var msg = "Error when looking for Policy of pgroup " + ctx.instance.ownerGroup + " " + err; console.log(msg); @@ -104,11 +104,11 @@ module.exports = function(Dataset) { // clean up data connected to a dataset, e.g. if archiving failed // TODO obsolete this code, replaced by code in datasetLifecycle - Dataset.reset = function(id, options, next) { + Dataset.reset = function (id, options, next) { // console.log('resetting ' + id); var Datablock = app.models.Datablock; var DatasetLifecycle = app.models.DatasetLifecycle; - DatasetLifecycle.findById(id, options, function(err, l) { + DatasetLifecycle.findById(id, options, function (err, l) { if (err) { next(err); } else { @@ -121,12 +121,12 @@ module.exports = function(Dataset) { // console.log('Dataset Lifecycle reset'); Datablock.destroyAll({ datasetId: id, - }, options, function(err, b) { + }, options, function (err, b) { if (err) { next(err); } else { // console.log('Deleted blocks', b); - Dataset.findById(id, options, function(err, instance) { + Dataset.findById(id, options, function (err, instance) { if (err) { next(err); } else { @@ -148,15 +148,15 @@ module.exports = function(Dataset) { // add user Groups information of the logged in user to the fields object - Dataset.beforeRemote('facet', function(ctx, userDetails, next) { + Dataset.beforeRemote('facet', function (ctx, userDetails, next) { utils.handleOwnerGroups(ctx, next); }); - Dataset.beforeRemote('fullfacet', function(ctx, userDetails, next) { + Dataset.beforeRemote('fullfacet', function (ctx, userDetails, next) { utils.handleOwnerGroups(ctx, next); }); - Dataset.beforeRemote('fullquery', function(ctx, userDetails, next) { + Dataset.beforeRemote('fullquery', function (ctx, userDetails, next) { utils.handleOwnerGroups(ctx, next); }); @@ -202,7 +202,7 @@ module.exports = function(Dataset) { } } - Dataset.fullfacet = function(fields, facets = [], cb) { + Dataset.fullfacet = function (fields, facets = [], cb) { // keep the full aggregation pipeline definition let pipeline = [] let match = {} @@ -212,7 +212,7 @@ module.exports = function(Dataset) { // Since a match condition on usergroups is alway prepended at the start // this effectively yields the intersection handling of the two sets (ownerGroup condition and userGroups) - Object.keys(fields).map(function(key) { + Object.keys(fields).map(function (key) { if (facets.indexOf(key) < 0) { if (key === "text") { match["$or"] = [{ @@ -243,7 +243,7 @@ module.exports = function(Dataset) { // append all facet pipelines let facetObject = {}; - facets.forEach(function(facet) { + facets.forEach(function (facet) { if (facet in ds.properties) { facetObject[facet] = utils.createNewFacetPipeline(facet, ds.properties[facet].type, facetMatch); } else if (facet in dsr.properties) { @@ -267,11 +267,11 @@ module.exports = function(Dataset) { $facet: facetObject, }); // console.log("Resulting aggregate query:", JSON.stringify(pipeline, null, 4)); - Dataset.getDataSource().connector.connect(function(err, db) { + Dataset.getDataSource().connector.connect(function (err, db) { var collection = db.collection('Dataset'); var res = collection.aggregate(pipeline, - function(err, cursor) { - cursor.toArray(function(err, res) { + function (err, cursor) { + cursor.toArray(function (err, res) { if (err) { console.log("Facet err handling:", err); } @@ -289,13 +289,13 @@ module.exports = function(Dataset) { // - paging of results // - merging DatasetLifecycle Fields for fields not contained in Dataset - Dataset.fullquery = function(fields, limits, cb) { + Dataset.fullquery = function (fields, limits, cb) { // keep the full aggregation pipeline definition let pipeline = [] let match = {} let matchJoin = {} // construct match conditions from fields value, excluding facet material - Object.keys(fields).map(function(key) { + Object.keys(fields).map(function (key) { if (fields[key] && fields[key] !== 'null') { if (key === "text") { match["$or"] = [{ @@ -318,7 +318,7 @@ module.exports = function(Dataset) { // otherwise create intersection of userGroups and ownerGroup // this is needed here since no extra match step is done but all // filter conditions are applied in one match step - const intersect = fields['ownerGroup'].filter(function(n) { + const intersect = fields['ownerGroup'].filter(function (n) { return fields['userGroups'].indexOf(n) !== -1; }); match["ownerGroup"] = searchExpression('ownerGroup', intersect) @@ -374,7 +374,7 @@ module.exports = function(Dataset) { // input format: "creationTime:desc,creationLocation:asc" const sortExpr = {} const sortFields = limits.order.split(',') - sortFields.map(function(sortField) { + sortFields.map(function (sortField) { const parts = sortField.split(':') const dir = (parts[1] == 'desc') ? -1 : 1 sortExpr[parts[0]] = dir @@ -397,11 +397,11 @@ module.exports = function(Dataset) { } } // console.log("Resulting aggregate query:", JSON.stringify(pipeline, null, 4)); - Dataset.getDataSource().connector.connect(function(err, db) { + Dataset.getDataSource().connector.connect(function (err, db) { var collection = db.collection('Dataset'); var res = collection.aggregate(pipeline, - function(err, cursor) { - cursor.toArray(function(err, res) { + function (err, cursor) { + cursor.toArray(function (err, res) { if (err) { console.log("Facet err handling:", err); } @@ -418,9 +418,9 @@ module.exports = function(Dataset) { }); }; - Dataset.isValid = function(dataset, next) { + Dataset.isValid = function (dataset, next) { var ds = new Dataset(dataset); - ds.isValid(function(valid) { + ds.isValid(function (valid) { if (!valid) { next(null, { 'errors': ds.errors, @@ -434,19 +434,34 @@ module.exports = function(Dataset) { }); }; - Dataset.thumbnail = function( id, options, cb) { - // console.log("get thumbnail"); - const base64string= Dataset.findById(id, options, function (err, da) { - const attach = da.datasetattachments; - let base64string ="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; - if (attach === undefined) { + Dataset.thumbnail = function (id, callback) { + console.log("Entering thumbnail endpoint"); + var DatasetAttachment = app.models.DatasetAttachment; + let base64string = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; + const filter = { where: { datasetId: id } }; + DatasetAttachment.findOne(filter, function (err, instance) { + if (err) { + console.log("Error finding dataset attachment", err); + return callback(err) + }; + + let base64string2 = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; + if (instance && instance.__data) { + console.log("gm thumbnail found for", instance.__data.datasetId); + if (instance.__data.thumbnail === undefined) { + console.log("undefined gm, ", instance.__data.id); + } else { + console.log("thumbnail found for ", instance.__data.id); + base64string2 = instance.__data.thumbnail; + } } else { - base64string = attach[0].thumbnail; + console.log("no thumbnail found"); } - return base64string; - }); - cb(null, base64string); - return base64string; + + return base64string2; + }); + callback(null, base64string); + return base64string; } Dataset.remoteMethod("thumbnail", { @@ -457,8 +472,8 @@ module.exports = function(Dataset) { required: true } ], - http: {path: "/:id/thumbnail", verb: "get"}, - returns: {type: "string", root: true} + http: { path: "/:id/thumbnail", verb: "get" }, + returns: { type: "string", root: true } }); diff --git a/package-lock.json b/package-lock.json index 2254f54d..7ec169da 100644 --- a/package-lock.json +++ b/package-lock.json @@ -200,8 +200,7 @@ "abbrev": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/abbrev/-/abbrev-1.1.1.tgz", - "integrity": "sha512-nne9/IiQ/hzIhY6pdDnbBtz7DjPTKrY00P/zvPSm5pOFkl6xuGrGnXn/VtTNNfNtAfZ9/1RtehkszU9qcTii0Q==", - "optional": true + "integrity": "sha512-nne9/IiQ/hzIhY6pdDnbBtz7DjPTKrY00P/zvPSm5pOFkl6xuGrGnXn/VtTNNfNtAfZ9/1RtehkszU9qcTii0Q==" }, "accept-language": { "version": "3.0.18", @@ -292,6 +291,15 @@ "resolved": "https://registry.npmjs.org/ansi/-/ansi-0.3.1.tgz", "integrity": "sha1-DELU+xcWDVqa8eSEus4cZpIsGyE=" }, + "ansi-align": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/ansi-align/-/ansi-align-2.0.0.tgz", + "integrity": "sha1-w2rsy6VjuJzrVW82kPCx2eNUf38=", + "dev": true, + "requires": { + "string-width": "^2.0.0" + } + }, "ansi-escapes": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-3.1.0.tgz", @@ -310,6 +318,16 @@ "integrity": "sha1-tDLdM1i2NM914eRmQ2gkBTPB3b4=", "dev": true }, + "anymatch": { + "version": "2.0.0", + 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"https://registry.npmjs.org/xdg-basedir/-/xdg-basedir-3.0.0.tgz", + "integrity": "sha1-SWsswQnsqNus/i3HK2A8F8WHCtQ=", + "dev": true + }, "xml2js": { "version": "0.4.19", "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.4.19.tgz", diff --git a/package.json b/package.json index 9b703f08..09a5d43c 100644 --- a/package.json +++ b/package.json @@ -44,6 +44,7 @@ "eslint": "^5.9.0", "eslint-config-loopback": "^12.0.0", "mocha": "^5.2.0", + "nodemon": "^1.18.8", "supertest": "^3.3.0" }, "repository": { From a1979525baad54eceef6b256ee5186eb0c026957 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 12 Dec 2018 11:24:59 +0100 Subject: [PATCH 136/147] change to async --- common/models/dataset.js | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 68818a8d..59a14557 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -434,7 +434,7 @@ module.exports = function (Dataset) { }); }; - Dataset.thumbnail = function (id, callback) { + Dataset.thumbnail = async function(id) { console.log("Entering thumbnail endpoint"); var DatasetAttachment = app.models.DatasetAttachment; let base64string = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; @@ -457,10 +457,8 @@ module.exports = function (Dataset) { } else { console.log("no thumbnail found"); } - return base64string2; }); - callback(null, base64string); return base64string; } From 1d15abae2358efa7b993e827c1a3e8ae5d4272f3 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 12 Dec 2018 11:49:55 +0100 Subject: [PATCH 137/147] change to promises --- common/models/dataset.js | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 59a14557..c7233ed5 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -437,13 +437,8 @@ module.exports = function (Dataset) { Dataset.thumbnail = async function(id) { console.log("Entering thumbnail endpoint"); var DatasetAttachment = app.models.DatasetAttachment; - let base64string = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; const filter = { where: { datasetId: id } }; - DatasetAttachment.findOne(filter, function (err, instance) { - if (err) { - console.log("Error finding dataset attachment", err); - return callback(err) - }; + return DatasetAttachment.findOne(filter).then( instance => { let base64string2 = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; if (instance && instance.__data) { @@ -459,7 +454,6 @@ module.exports = function (Dataset) { } return base64string2; }); - return base64string; } Dataset.remoteMethod("thumbnail", { From 1cabd52ace84039d35cd0414f049636773f9480f Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 12 Dec 2018 12:03:11 +0100 Subject: [PATCH 138/147] remove all dbug print statements --- common/models/dataset.js | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index c7233ed5..9445d9d2 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -434,23 +434,20 @@ module.exports = function (Dataset) { }); }; - Dataset.thumbnail = async function(id) { - console.log("Entering thumbnail endpoint"); + Dataset.thumbnail = async function (id) { var DatasetAttachment = app.models.DatasetAttachment; const filter = { where: { datasetId: id } }; - return DatasetAttachment.findOne(filter).then( instance => { + return DatasetAttachment.findOne(filter).then(instance => { - let base64string2 = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; + const base64string_example = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; + let base64string2 = "" if (instance && instance.__data) { - console.log("gm thumbnail found for", instance.__data.datasetId); if (instance.__data.thumbnail === undefined) { - console.log("undefined gm, ", instance.__data.id); } else { - console.log("thumbnail found for ", instance.__data.id); base64string2 = instance.__data.thumbnail; } } else { - console.log("no thumbnail found"); + base64string2 = base64string_example; } return base64string2; }); From 55c4d8a7533557d8fe165777feecebd1e0f00145 Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 12 Dec 2018 12:15:05 +0100 Subject: [PATCH 139/147] change default to scicat --- common/models/dataset.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 9445d9d2..d04e65c5 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -439,7 +439,7 @@ module.exports = function (Dataset) { const filter = { where: { datasetId: id } }; return DatasetAttachment.findOne(filter).then(instance => { - const base64string_example = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAoAAAAKCAYAAACNMs+9AAAAFklEQVR42mP8v0DxPwMRgHFUIX0VAgD6BxuBmjKJqgAAAABJRU5ErkJggg=="; + const base64string_example = "data:image/png;base64,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"; let base64string2 = "" if (instance && instance.__data) { if (instance.__data.thumbnail === undefined) { From 2b8621df0b342dc68306f2a133739bfee2f5f88c Mon Sep 17 00:00:00 2001 From: Gareth Murphy Date: Wed, 12 Dec 2018 13:04:13 +0100 Subject: [PATCH 140/147] make smaller png --- common/models/dataset.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index d04e65c5..09285b9c 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -439,7 +439,7 @@ module.exports = function (Dataset) { const filter = { where: { datasetId: id } }; return DatasetAttachment.findOne(filter).then(instance => { - const base64string_example = "data:image/png;base64,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"; + const base64string_example = "data:image/png;base64,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"; let base64string2 = "" if (instance && instance.__data) { if (instance.__data.thumbnail === undefined) { From 4ec62aeabe98ec8badb66c678f42f8f3ca57916a Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Tue, 18 Dec 2018 16:25:46 +0100 Subject: [PATCH 141/147] Issue #135 endpoint wrapping update for policy --- common/models/policy.js | 32 +++++++++++++++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/common/models/policy.js b/common/models/policy.js index 6e6f46e6..96f33f18 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -25,7 +25,12 @@ module.exports = function(Policy) { userId: userId } }, function(err, instance) { - var email = instance.profile.email; + // need to handle functional user case + var email = ""; + if (!instance && Object.keys(ctx.options.authorizedRoles)[0]) { + return next(); + } + //console.log("email:", email); //console.log("manager: ", ctx.currentInstance.manager); if (!ctx.currentInstance.manager.includes(email)) { @@ -69,5 +74,30 @@ module.exports = function(Policy) { Policy.findOrCreate(filter, defaultPolicy); }; + Policy.updatewhere = async function(where, data) { + // where should look like {"or": [{"id":"5c0fe54ed8cc493d4b259989"},{"id": "5c110c90f1e2772bdb1dd868"}]} + return Policy.update(where, data); + } + + Policy.remoteMethod("updatewhere", { + accepts: [{ + arg: "where", + type: "object", + required: true + }, { + arg: "data", + type: "object", + required: true + }], + http: { + path: "/updatewhere", + verb: "post" + }, + returns: { + type: "string", + root: true + } + }); + Policy.validatesUniquenessOf('ownerGroup'); }; From a5a23958ebd0f097620d86851d8fc16618f146bd Mon Sep 17 00:00:00 2001 From: Luke Gorman Date: Wed, 19 Dec 2018 15:25:27 +0100 Subject: [PATCH 142/147] Issue #81 add sci meta to derived datasets model --- common/models/derived-dataset.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/common/models/derived-dataset.json b/common/models/derived-dataset.json index cf1c3c39..2cf9923a 100644 --- a/common/models/derived-dataset.json +++ b/common/models/derived-dataset.json @@ -38,6 +38,10 @@ "jobLogData": { "type": "string", "description": "The output job logfile. Keep the size of this log data well below 15 MB " + }, + "scientificMetadata": { + "type": "object", + "description": "JSON object containing the scientific meta data" } }, "validations": [], From c0e21a41931ffb46cdc087900229d54179d277d0 Mon Sep 17 00:00:00 2001 From: egli Date: Fri, 21 Dec 2018 11:55:28 +0100 Subject: [PATCH 143/147] Added default definition for datasetName --- common/models/dataset.js | 14 ++++++++++++++ common/models/dataset.json | 4 ++-- test/Dataset.js | 1 + 3 files changed, 17 insertions(+), 2 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 09285b9c..05931e1a 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -44,6 +44,20 @@ module.exports = function (Dataset) { } ctx.instance.version = p.version; + // sourceFolder handling + if(ctx.instance.sourceFolder){ + // remove trailing slashes + ctx.instance.sourceFolder = ctx.instance.sourceFolder.replace(/\/$/, ""); + // autofill datasetName + if (!ctx.instance.datasetName){ + var arr=ctx.instance.sourceFolder.split("/") + if(arr.length == 1){ + ctx.instance.datasetName=arr[0] + } else { + ctx.instance.datasetName=arr[arr.length-2]+"/"+arr[arr.length-1] + } + } + } // auto fill classification if (!ctx.instance.ownerGroup) { diff --git a/common/models/dataset.json b/common/models/dataset.json index e5c3c776..fb4a11cd 100644 --- a/common/models/dataset.json +++ b/common/models/dataset.json @@ -41,7 +41,7 @@ "type": "string", "required": true, "index": true, - "description": "Absolute file path on file server containing the files of this dataset, optionally including protocol and file server hostname, e.g. nfs://fileserver1.example.com/some/path/to/sourcefolder. In case of a single file dataset, e.g. HDF5 data it contains the path up to, but excluding the filename." + "description": "Absolute file path on file server containing the files of this dataset, optionally including protocol and file server hostname, e.g. nfs://fileserver1.example.com/some/path/to/sourcefolder. In case of a single file dataset, e.g. HDF5 data, it contains the path up to, but excluding the filename. Trailing slashes are removed." }, "size": { "type": "number", @@ -80,7 +80,7 @@ }, "datasetName": { "type": "string", - "description": "A name for the dataset, given by the creator to carry some semantic meaning. Useful for display purposes e.g. instead of displaying the pid" + "description": "A name for the dataset, given by the creator to carry some semantic meaning. Useful for display purposes e.g. instead of displaying the pid. Will be autofilled if missing using info from sourceFolder" }, "userTargetLocation": { "type": "string", diff --git a/test/Dataset.js b/test/Dataset.js index be26927d..7c805aa2 100644 --- a/test/Dataset.js +++ b/test/Dataset.js @@ -62,6 +62,7 @@ describe('Simple Dataset tests', () => { res.body.should.have.property('version').and.be.string; res.body.should.have.property('type').and.equal('raw'); res.body.should.have.property('pid').and.be.string; + res.body.should.have.property('datasetName').and.be.string; pid = encodeURIComponent(res.body['pid']); done(); }); From 3be076e51e9772b7afc3c0101cdb7ea862285827 Mon Sep 17 00:00:00 2001 From: egli Date: Fri, 21 Dec 2018 16:29:57 +0100 Subject: [PATCH 144/147] Bugfix for test cases: wrong asynch handling for tests with 2 different users --- test/DatasetLifecycle.js | 17 ++++++------ test/MessageHistory.js | 58 ++++++++++++++++++++-------------------- test/ResetDataset.js | 17 ++++++------ 3 files changed, 47 insertions(+), 45 deletions(-) diff --git a/test/DatasetLifecycle.js b/test/DatasetLifecycle.js index 4c6d75b3..d4f6fed9 100644 --- a/test/DatasetLifecycle.js +++ b/test/DatasetLifecycle.js @@ -116,17 +116,18 @@ describe('Test DatasetLifecycle and the relation to Datasets', () => { }, (tokenVal) => { accessTokenIngestor = tokenVal; - }); - utils.getToken(app, { - 'username': 'archiveManager', - 'password': 'aman' - }, - (tokenVal) => { - accessTokenArchiveManager = tokenVal; - done(); + utils.getToken(app, { + 'username': 'archiveManager', + 'password': 'aman' + }, + (tokenVal) => { + accessTokenArchiveManager = tokenVal; + done(); + }); }); }); + it('adds a new raw dataset', function(done) { request(app) .post('/api/v2/RawDatasets?access_token=' + accessTokenIngestor) diff --git a/test/MessageHistory.js b/test/MessageHistory.js index c46ff68f..5299deb9 100644 --- a/test/MessageHistory.js +++ b/test/MessageHistory.js @@ -116,9 +116,9 @@ var testjob = { "type": "retrieve", "jobStatusMessage": "jobForwarded", "datasetList": [{ - "pid": "dummy", - "files": [] - }], + "pid": "dummy", + "files": [] + }], "archiveReturnMessage": "will move to messageList", "MessageHistory": [] } @@ -135,11 +135,11 @@ var newMessage = { } var app -before( function(){ +before(function() { app = require('../server/server') }); -describe('Test DatasetLifecycle and the relation to Datasets', () => { +describe('Test MessageHistory in jobs', () => { before((done) => { utils.getToken(app, { 'username': 'ingestor', @@ -147,14 +147,14 @@ describe('Test DatasetLifecycle and the relation to Datasets', () => { }, (tokenVal) => { accessTokenIngestor = tokenVal; - }); - utils.getToken(app, { - 'username': 'archiveManager', - 'password': 'aman' - }, - (tokenVal) => { - accessTokenArchiveManager = tokenVal; - done(); + utils.getToken(app, { + 'username': 'archiveManager', + 'password': 'aman' + }, + (tokenVal) => { + accessTokenArchiveManager = tokenVal; + done(); + }); }); }); @@ -172,10 +172,10 @@ describe('Test DatasetLifecycle and the relation to Datasets', () => { res.body.should.have.property('type').and.equal('raw'); res.body.should.have.property('pid').and.be.string; // store link to this dataset in datablocks - var pidtest=res.body['pid'] + var pidtest = res.body['pid'] testDatasetLifecycle.id = pidtest testDatasetLifecycle.datasetId = pidtest - testjob.datasetList[0].pid= pidtest + testjob.datasetList[0].pid = pidtest pid = encodeURIComponent(res.body['pid']); done(); }); @@ -237,7 +237,7 @@ describe('Test DatasetLifecycle and the relation to Datasets', () => { return done(err); res.body.should.have.property('type').and.be.string; idJob = res.body['id'] - console.log("Jobid:",idJob) + console.log("Jobid:", idJob) done(); }); }); @@ -252,24 +252,24 @@ describe('Test DatasetLifecycle and the relation to Datasets', () => { .end(function(err, res) { if (err) return done(err); - console.log(res.body) + console.log(res.body) done(); }); }); -it('should delete the Job', function(done) { - request(app) - .delete('/api/v2/Jobs/' + idJob+ '?access_token=' + accessTokenIngestor) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .end((err, res) => { - if (err) - return done(err); - done(); - }); -}); + it('should delete the Job', function(done) { + request(app) + .delete('/api/v2/Jobs/' + idJob + '?access_token=' + accessTokenIngestor) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); it('should delete the DatasetLifecycle', function(done) { request(app) diff --git a/test/ResetDataset.js b/test/ResetDataset.js index 9ca31db0..78e53313 100644 --- a/test/ResetDataset.js +++ b/test/ResetDataset.js @@ -173,17 +173,18 @@ describe('Create Dataset and its Datablocks DatasetLifecycle, then reset Datablo }, (tokenVal) => { accessTokenIngestor = tokenVal; - }); - utils.getToken(app, { - 'username': 'archiveManager', - 'password': 'aman' - }, - (tokenVal) => { - accessTokenArchiveManager = tokenVal; - done(); + utils.getToken(app, { + 'username': 'archiveManager', + 'password': 'aman' + }, + (tokenVal) => { + accessTokenArchiveManager = tokenVal; + done(); + }); }); }); + // first get existing datasets with the test archieId to allow to delete them From 576ca9254c98a3f5fd936cc514ce7a544145ce99 Mon Sep 17 00:00:00 2001 From: egli Date: Mon, 7 Jan 2019 13:55:52 +0100 Subject: [PATCH 145/147] New Jobs return error message when something wrong with archivable/retrievable bits --- common/models/dataset.js | 80 +++++----- common/models/job.js | 310 ++++++++++++++++++++++++--------------- common/models/policy.js | 9 +- common/models/utils.js | 105 ++----------- test/MessageHistory.js | 52 +++++-- 5 files changed, 296 insertions(+), 260 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 05931e1a..4efeecbe 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -45,38 +45,34 @@ module.exports = function (Dataset) { ctx.instance.version = p.version; // sourceFolder handling - if(ctx.instance.sourceFolder){ + if (ctx.instance.sourceFolder) { // remove trailing slashes ctx.instance.sourceFolder = ctx.instance.sourceFolder.replace(/\/$/, ""); // autofill datasetName - if (!ctx.instance.datasetName){ - var arr=ctx.instance.sourceFolder.split("/") - if(arr.length == 1){ - ctx.instance.datasetName=arr[0] + if (!ctx.instance.datasetName) { + var arr = ctx.instance.sourceFolder.split("/") + if (arr.length == 1) { + ctx.instance.datasetName = arr[0] } else { - ctx.instance.datasetName=arr[arr.length-2]+"/"+arr[arr.length-1] + ctx.instance.datasetName = arr[arr.length - 2] + "/" + arr[arr.length - 1] } } } - - // auto fill classification if (!ctx.instance.ownerGroup) { - return next("No owner group defined"); + next("No owner group defined"); } + + // auto fill classification and add policy if missing + var Policy = app.models.Policy; - if (!ctx.instance.classification) { - // classification undefined - Policy.findOne({ - where: { - ownerGroup: ctx.instance.ownerGroup - } - }, - function (err, policyInstance) { - if (err) { - var msg = "Error when looking for Policy of pgroup " + ctx.instance.ownerGroup + " " + err; - console.log(msg); - return next(msg); - } else if (policyInstance) { + Policy.findOne(function (err, policyInstance) { + if (err) { + var msg = "Error when looking for Policy of pgroup " + ctx.instance.ownerGroup + " " + err; + console.log(msg); + next(msg); + } else if (policyInstance) { + if (!ctx.instance.classification) { + // Case 1: classification undefined but policy defined:, define classification via policy var classification = ""; switch (policyInstance.tapeRedundancy) { case "low": @@ -92,27 +88,33 @@ module.exports = function (Dataset) { classification = "IN=medium,AV=low,CO=low"; } ctx.instance.classification = classification; - } else { - // neither a policy or a classification exist + } + // case 2: classification defined and policy defined: do nothing + return next() + } else { + let tapeRedundancy = "low" + if (!ctx.instance.classification) { + // case 3: neither a policy nor a classification exist: define default classification and create default policy ctx.instance.classification = "IN=medium,AV=low,CO=low"; - Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail, ""); + } else { + // case 4: classification exists but no policy: create policy from classification + var classification = ctx.instance.classification; + if (classification.includes("AV=low")) { + tapeRedundancy = "low"; + } else if (classification.includes("AV=medium")) { + tapeRedundancy = "medium"; + } else if (classification.includes("AV=high")) { + tapeRedundancy = "high"; + } } - }); - } else { - // create policy from classification - var classification = ctx.instance.classification; - var tapeRedundancy = ""; - if (classification.includes("AV=low")) { - tapeRedundancy = "low"; - } else if (classification.includes("AV=medium")) { - tapeRedundancy = "medium"; - } else if (classification.includes("AV=high")) { - tapeRedundancy = "high"; + Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail, tapeRedundancy, next); + } } - Policy.addDefault(ctx.instance.ownerGroup, ctx.instance.ownerEmail, tapeRedundancy); - } + ); + } else { + // no instance, continue + return next() } - return next(); }); // clean up data connected to a dataset, e.g. if archiving failed diff --git a/common/models/job.js b/common/models/job.js index f38dd5d9..9f283a12 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -6,6 +6,171 @@ var nodemailer = require('nodemailer'); var config = require('../../server/config.local'); var app = require('../../server/server'); + +function sendMail(to, subjectText, mailText, next) { + if ('smtpSettings' in config && 'smtpMessage' in config) { + let transporter = nodemailer.createTransport(config.smtpSettings); + transporter.verify(function (error, success) { + if (error) { + console.log(error); + next(); + } else { + console.log('Server is ready to send message to ', to); + var message = Object.assign({}, config.smtpMessage); + message['to'] = to; + message['subject'] += subjectText + message['text'] = mailText + transporter.sendMail(message, function (err, info) { + if (err) { + console.log(err); + } else { + console.log('Email sent'); + } + next(); + }); + } + }); + } else { + next() + } +} + +function publishJob(job, ctx, next) { + if ('queue' in config && config.queue === 'rabbitmq') { + job.publishJob(ctx.instance, "jobqueue") + console.log('Saved Job %s#%s and published to message broker', ctx.Model.modelName, ctx.instance.id); + } + + let subjectText = ' ' + ctx.instance.type + ' job submitted successfully'; + let mailText = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n' + JSON.stringify(ctx.instance, null, 4); + let to = ctx.instance.emailJobInitiator + sendMail(to, subjectText, mailText, next) +} + +function MarkDatasetsAsScheduled(job, ctx, idList, next) { + //console.log('Searching for datasetlifecycle with ids:', idList) + let DatasetLifecycle = app.models.DatasetLifecycle; + DatasetLifecycle.updateAll( + { + datasetId: { + inq: idList + } + }, + { + archivable: false, + retrievable: false, + archiveStatusMessage: "scheduledForArchiving" + } + , ctx.options, function (err, p) { + // console.log("============= DatasetLifecycle Result:", JSON.stringify(p)) + if (err) { + var e = new Error(); + e.statusCode = 400; + e.message = 'Can not find all needed DatasetLifecycle entries - no archive job sent:\n' + JSON.stringify(err) + next(e); + } else { + publishJob(job, ctx, next) + } + }); +} +// for archive jobs all datasets must be in state archivable +function TestArchiveJobs(job, ctx, idList, next) { + let Dataset = app.models.Dataset; + Dataset.find({ + where: { + archivable: false, + pid: { + inq: idList + } + } + }, ctx.options, function (err, p) { + //console.log("============= Archive Result:", JSON.stringify(p)) + if (p.length > 0) { + var e = new Error(); + e.statusCode = 400; + e.message = 'The following datasets are not in archivable state - no archive job sent:\n' + JSON.stringify(p) + next(e); + } else { + // mark all Datasets as in state scheduledForArchiving, archivable=false + MarkDatasetsAsScheduled(job, ctx, idList, next) + } + }); + +} + +// for retrieve jobs all datasets must be in state retrievable +// ownerGroup is tested implicitly via Ownable + +function TestRetrieveJobs(job, ctx, idList, next) { + let Dataset = app.models.Dataset; + Dataset.find({ + where: { + retrievable: true, + pid: { + inq: idList + } + } + }, ctx.options, function (err, p) { + // console.log("============= Retrieve Result:",JSON.stringify(p)) + if (err) { + return next(err) + } else if (p.length != idList.length) { + Dataset.find({ + where: { + retrievable: false, + pid: { + inq: idList + } + } + }, ctx.options, function (err2, pmiss) { + if (err2) { + return next(err2) + } else { + var e = new Error(); + e.statusCode = 400; + e.message = 'The following datasets are not in retrievable state - no retrieve job sent:\n' + JSON.stringify(pmiss) + return next(e); + } + }) + } else { + publishJob(job, ctx, next); + } + }); +} + +function TestAllDatasets(job, ctx, idList, next) { + //console.log(" ====== find datasets with id", idList) + let Dataset = app.models.Dataset; + Dataset.find({ + where: { + pid: { + inq: idList + } + } + }, ctx.options, function (err, p) { + let to = ctx.instance.emailJobInitiator + if (err || (p.length != idList.length)) { + var e = new Error(); + e.statusCode = 400; + e.message = 'At least one of the datasets could not be found - no Job sent'; + // TODO should I send an email here ? Only if triggered by autoarchive option ? + // subjectText = + // mailText= + // sendMail(to, subjectText, mailText, next) + return next(e) + } else { + //test if all datasets are in archivable state + if (ctx.instance.type == "archive") { + TestArchiveJobs(job, ctx, idList, next) + } else if (ctx.instance.type == "retrieve") { + TestRetrieveJobs(job, ctx, idList, next) + } else { + publishJob(job, ctx, next) + } + } + }); +} + module.exports = function (Job) { // Attach job submission to Kafka @@ -16,134 +181,49 @@ module.exports = function (Job) { var dataSource = new DataSource('kafka', options); Job.attachTo(dataSource); } + Job.observe('before save', (ctx, next) => { - // replace email with that from userIdentity - var UserIdentity = app.models.UserIdentity; - var userId = ctx.options.accessToken.userId; - //PersistedModel Static Method call - UserIdentity.findOne({ - //json filter - where: { - userId: userId - } - }, function(err, instance) { - if(!!instance) - { - ctx.instance.emailJobInitiator = instance.profile.email; - } - }); if (ctx.instance) { - // auto fill dateOfLastMessage - var now = new Date(); - if (!ctx.instance.dateOfLastMessage) { - ctx.instance.dateOfLastMessage = now.toISOString(); - } - // make some consistency checks: - // - ensure that all wanted datasets exist already - // - TODO: for archive jobs all datasetslifecycle should be in an "archiveable" state - // TODO ensure that job is created by user who has read access to all datasets in case of retrieve JOBS - var Dataset = app.models.Dataset; - // create array of all pids - // console.log("Verifying datasets:",ctx.options) - const idList=ctx.instance.datasetList.map(x => x.pid) - Dataset.find({where: {pid: {inq: idList}}}, ctx.options, function (err, p){ - //console.log("JOBS:lengths",err,p.length,idList.length,p) - if (err || (p.length != idList.length)){ - var e = new Error(); - e.statusCode = 400; - e.message = 'At least one of the datasets could not be found'; - next(e); - } else { - next(); - } - }); - //test for datasets already archived - /*var Lifecycle = app.models.DatasetLifecycle; - Lifecycle.find({ + + // replace email with that from userIdentity + var UserIdentity = app.models.UserIdentity; + var userId = ctx.options.accessToken.userId; + //PersistedModel Static Method call + UserIdentity.findOne({ + //json filter where: { - archivable: false, - datasetId: { - inq: idList - } + userId: userId } - }, ctx.options, function(err, p) { - console.log("LifeCycle: ", p, idList); - if (p.length > 0) { - var e = new Error(); - e.statusCode = 400; - e.message = 'At least one of the datasets is already archived'; - next(e); + }, function (err, u) { + if (!!u) { + ctx.instance.emailJobInitiator = u.profile.email; } - else { - next(); + // auto fill dateOfLastMessage + var now = new Date(); + if (!ctx.instance.dateOfLastMessage) { + ctx.instance.dateOfLastMessage = now.toISOString(); } - });*/ + next() + }) } else { - next(); + next() } }); Job.observe('after save', (ctx, next) => { if (ctx.instance && ctx.isNewInstance) { - - if ('queue' in config && config.queue === 'rabbitmq') { - Job.publishJob(ctx.instance, "jobqueue") - console.log('Saved Job %s#%s and published to message broker', ctx.Model.modelName, ctx.instance.id); - } - if ('smtpSettings' in config && 'smtpMessage' in config) { - let transporter = nodemailer.createTransport(config.smtpSettings); - transporter.verify(function (error, success) { - if (error) { - console.log(error); - next(); - } else { - console.log('Server is ready to take our messages'); - var message = Object.assign({}, config.smtpMessage); - message['to'] = ctx.instance.emailJobInitiator; - message['subject'] += ' ' + ctx.instance.type + ' job submitted successfully'; - let text = 'Hello, \n\n You created a job to ' + ctx.instance.type + ' datasets. Your job was received and will be completed as soon as possible. \n\n Many Thanks.\n\n'+JSON.stringify(ctx.instance, null, 4); - message['text'] = text; - transporter.sendMail(message, function (err, info) { - if (err) { - console.log(err); - } else { - console.log('Email sent'); - } - next(); - }); - } - }); - } else { - next() - } + // first create array of all pids + const idList = ctx.instance.datasetList.map(x => x.pid) + // this is a new job, make some consistency checks concerning the datasets + TestAllDatasets(Job, ctx, idList, next) } else { - if ('smtpSettings' in config && 'smtpMessage' in config) { - if (ctx.instance.jobStatusMessage.startsWith("finish")) { - let transporter = nodemailer.createTransport(config.smtpSettings); - transporter.verify(function(error, success) { - if (error) { - console.log(error); - next(); - } else { - console.log('Server is ready to send message to ', ctx.instance.emailJobInitiator); - var message = Object.assign({}, config.smtpMessage); - message['to'] = ctx.instance.emailJobInitiator; - message['subject'] += ' '+ctx.instance.type + ' job from ' + ctx.instance.creationTime.toISOString().replace(/T/, ' ').replace(/\..+/, '') + ' (UTC) finished with status ' + ctx.instance.jobStatusMessage; - let text = 'Hello, \n\n Your Job from ' + ctx.instance.creationTime + ' is now finished. \n\n The resulting job description is.\n\n' + JSON.stringify(ctx.instance, null, 4); - message['text'] = text; - transporter.sendMail(message, function(err, info) { - if (err) { - console.log(err); - } else { - console.log('Email sent'); - } - next(); - }); - } - }); - } else { - next() - } + // An existing job got some updates - check if you want to send an email + if (ctx.instance.jobStatusMessage.startsWith("finish")) { + // TODO add infos about which Datasets failed if this info is not yet in historyMessages of the Job + let subjectText = ' ' + ctx.instance.type + ' job from ' + ctx.instance.creationTime.toISOString().replace(/T/, ' ').replace(/\..+/, '') + ' (UTC) finished with status ' + ctx.instance.jobStatusMessage; + let mailText = 'Hello, \n\n Your Job from ' + ctx.instance.creationTime + ' is now finished. \n\n The resulting job description is.\n\n' + JSON.stringify(ctx.instance, null, 4); + let to = ctx.instance.emailJobInitiator + sendMail(to, subjectText, mailText, next) } else { next() } diff --git a/common/models/policy.js b/common/models/policy.js index 96f33f18..24a251b7 100644 --- a/common/models/policy.js +++ b/common/models/policy.js @@ -46,8 +46,8 @@ module.exports = function(Policy) { } }); - Policy.addDefault = function(ownerGroup, ownerEmail, tapeRedundancy) { - // TODO: move the deault definition somewhere more sensible + Policy.addDefault = function(ownerGroup, ownerEmail, tapeRedundancy, next) { + // TODO: move the default definition somewhere more sensible var defaultPolicy = Object(); defaultPolicy.ownerGroup = ownerGroup; if (config && !ownerEmail) { @@ -69,11 +69,10 @@ module.exports = function(Policy) { defaultPolicy.archiveEmailsToBeNotified = defaultPolicy.manager; defaultPolicy.retrieveEmailsToBeNotified = defaultPolicy.manager; defaultPolicy.embargoPeriod = 3; - //filter must be an object - var filter = JSON.parse('{"where": {"ownerGroup":"' + ownerGroup + '"}}'); - Policy.findOrCreate(filter, defaultPolicy); + Policy.findOrCreate(defaultPolicy, next); }; + // TODO: understand the following method Policy.updatewhere = async function(where, data) { // where should look like {"or": [{"id":"5c0fe54ed8cc493d4b259989"},{"id": "5c110c90f1e2772bdb1dd868"}]} return Policy.update(where, data); diff --git a/common/models/utils.js b/common/models/utils.js index fd1d3781..8ae4595f 100644 --- a/common/models/utils.js +++ b/common/models/utils.js @@ -12,7 +12,7 @@ var exports = module.exports = {}; // Note: Depending on the request PUT/POST etc either ctx.instance or ctx.currentInstance is set -exports.transferSizeToDataset = function(obj, sizeField, ctx, next) { +exports.transferSizeToDataset = function (obj, sizeField, ctx, next) { var instance = ctx.instance if (!instance) { instance = ctx.currentInstance @@ -31,7 +31,7 @@ exports.transferSizeToDataset = function(obj, sizeField, ctx, next) { } } obj.find(filter, ctx.options).then(instances => { - var total = instances.reduce(function(sum, value) { + var total = instances.reduce(function (sum, value) { return sum + value[sizeField] }, 0); @@ -40,9 +40,9 @@ exports.transferSizeToDataset = function(obj, sizeField, ctx, next) { if (instance) { // important to pass options here, otherwise context gets lost instance.updateAttributes({ - [sizeField]: total - }, ctx.options, - function(err, instance) { + [sizeField]: total + }, ctx.options, + function (err, instance) { if (err) { var error = new Error(); error.statusCode = 403; @@ -73,7 +73,7 @@ exports.transferSizeToDataset = function(obj, sizeField, ctx, next) { } // add ownerGroup field from linked Datasets -exports.addOwnerGroup = function(ctx, next) { +exports.addOwnerGroup = function (ctx, next) { var instance = ctx.instance if (!instance) { instance = ctx.currentInstance @@ -114,8 +114,8 @@ exports.addOwnerGroup = function(ctx, next) { // transform date strings in all fields with key dateKeys to updateTimesToUTC // do nothing if input values are already UTC -exports.updateTimesToUTC = function(dateKeys, instance) { - dateKeys.map(function(dateKey) { +exports.updateTimesToUTC = function (dateKeys, instance) { + dateKeys.map(function (dateKey) { if (instance[dateKey]) { // console.log("Updating old ", dateKey, instance[dateKey]) instance[dateKey] = moment.tz(instance[dateKey], moment.tz.guess()).format(); @@ -124,7 +124,7 @@ exports.updateTimesToUTC = function(dateKeys, instance) { }); } -exports.createNewFacetPipeline = function(name, type, query) { +exports.createNewFacetPipeline = function (name, type, query) { const pipeline = []; if (type.constructor === Array) { @@ -175,10 +175,10 @@ exports.createNewFacetPipeline = function(name, type, query) { // dito but for array of instances -exports.updateAllTimesToUTC = function(dateKeys, instances) { - dateKeys.map(function(dateKey) { +exports.updateAllTimesToUTC = function (dateKeys, instances) { + dateKeys.map(function (dateKey) { // console.log("Updating all time field %s to UTC for %s instances:", dateKey, instances.length) - instances.map(function(instance) { + instances.map(function (instance) { if (instance[dateKey]) { // console.log("Updating old ",dateKey,instance[dateKey]) instance[dateKey] = moment.tz(instance[dateKey], moment.tz.guess()).format() @@ -188,7 +188,7 @@ exports.updateAllTimesToUTC = function(dateKeys, instances) { }); } -exports.handleOwnerGroups = function(ctx, next) { +exports.handleOwnerGroups = function (ctx, next) { if (!ctx.args.fields) ctx.args.fields = {}; let userId = ctx.req.accessToken && ctx.req.accessToken.userId; @@ -203,7 +203,7 @@ exports.handleOwnerGroups = function(ctx, next) { next(e); } - User.findById(userId, function(err, user) { + User.findById(userId, function (err, user) { if (err) { next(err); } else if (user['username'].indexOf('.') === -1) { @@ -215,7 +215,7 @@ exports.handleOwnerGroups = function(ctx, next) { where: { userId: userId } - }, function(err, instance) { + }, function (err, instance) { console.log("UserIdentity Instance:", instance) if (instance && instance.profile) { var foundGroups = instance.profile.accessGroups; @@ -238,78 +238,3 @@ exports.handleOwnerGroups = function(ctx, next) { } }); } - - -exports.createArchiveJob = function(UserIdentity, Policy, Job, ctx) { - var instance = ctx.instance - if (!instance) { - instance = ctx.currentInstance - } - console.log("Instance:", JSON.stringify(instance)) - - const token = ctx.options && ctx.options.accessToken; - const userId = token && token.userId; - - console.log("options, userid:", ctx.options, userId) - //const user = userId ? 'user#' + userId : ''; - UserIdentity.findOne({ - where: { - userId: userId - } - }, function(err, user) { - console.log("UserIdentity Instance:", user) - // TODO: get it from User models - // TODO get proper emails in case of unctional accounts - // TODO remove console.log messages - // TODO add test cases - // TODO add creationTime (should not be needed any more) - var email - var login - if (user && user.profile) { - login = user.profile.login - email = user.profile.email - } else { - login = Object.keys(ctx.options.authorizedRoles)[0] - email = login - } - console.log("Email:", email) // check if a normal user or an internal ROLE - Policy.findOne({ - where: { - ownerGroup: instance.ownerGroup - } - }, function(err2, policyInstance) { - // get policy values for the instance.ownerGroups - if (err2) { - console.log("Error when looking for Policy of pgroup ", instance.ownerGroup, err2) - } else { - var jobParams = {} - jobParams.username = login - if (policyInstance) { - jobParams.autoArchive = (autoArchive in policyInstance) ? policyInstance.autoArchive : false - jobParams.tapeCopies = (tapeCopies in policyInstance) ? policyInstance.tapeCopies : "one" - } else { - console.log("No policy settings found for ownerGroup", instance.ownerGroup) - console.log("Assuming default values") - jobParams.autoArchive = false - jobParams.tapeCopies = "one" - } - var body = { - emailJobInitiator: email, - type: "archive", - jobParams: jobParams, - datasetList: [{ - pid: instance.datasetId, - files: [] - }] - } - console.log("Job body:", body) - if (jobParams.autoArchive) { - Job.create(body, function(err, jobmodel) { - console.log("Created Job:", err, jobmodel) - }) - } - } - - }) - }) -}; diff --git a/test/MessageHistory.js b/test/MessageHistory.js index 5299deb9..3d90e0c3 100644 --- a/test/MessageHistory.js +++ b/test/MessageHistory.js @@ -101,19 +101,21 @@ var testDatasetLifecycle = { "retrieveStatusMessage": "", "isExported": false, "archivable": true, - "retrievable": false, + "retrievable": true, "MessageHistory": [{ "shortMessage": "datasetCreated", - "sender": "stephan.egli@psi.ch", + "sender": "scicatarchivemanager@psi.ch", "payload": { "text": "Nothing special to report" } }] } -var testjob = { +//TODO test to retrieve datasets where you are NOT the owner + +var testArchiveJob = { "emailJobInitiator": "scicatarchivemanger@psi.ch", - "type": "retrieve", + "type": "archive", "jobStatusMessage": "jobForwarded", "datasetList": [{ "pid": "dummy", @@ -124,11 +126,21 @@ var testjob = { } +var testRetrieveJob = { + "emailJobInitiator": "scicatarchivemanger@psi.ch", + "type": "retrieve", + "jobStatusMessage": "jobForwarded", + "datasetList": [{ + "pid": "dummy", + "files": [] + }], + "archiveReturnMessage": "will move to messageList", + "MessageHistory": [] +} -// TODO do I need to pass id explicitly ? var newMessage = { "shortMessage": "JustAnExample", - "sender": "stephan.egli@psi.ch", + "sender": "ingestor", "payload": { "text": "whatever" } @@ -175,7 +187,8 @@ describe('Test MessageHistory in jobs', () => { var pidtest = res.body['pid'] testDatasetLifecycle.id = pidtest testDatasetLifecycle.datasetId = pidtest - testjob.datasetList[0].pid = pidtest + testArchiveJob.datasetList[0].pid = pidtest + testRetrieveJob.datasetList[0].pid = pidtest pid = encodeURIComponent(res.body['pid']); done(); }); @@ -225,10 +238,27 @@ describe('Test MessageHistory in jobs', () => { }); - it('Adds a new job request', function(done) { + it('Adds a new archive job request', function(done) { + request(app) + .post('/api/v2/Jobs?access_token=' + accessTokenIngestor) + .send(testArchiveJob) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function(err, res) { + if (err) + return done(err); + res.body.should.have.property('type').and.be.string; + idJob = res.body['id'] + //console.log("Jobid:", idJob) + done(); + }); + }); + + it('Adds a new retrieve job request', function(done) { request(app) .post('/api/v2/Jobs?access_token=' + accessTokenIngestor) - .send(testjob) + .send(testRetrieveJob) .set('Accept', 'application/json') .expect(200) .expect('Content-Type', /json/) @@ -237,7 +267,7 @@ describe('Test MessageHistory in jobs', () => { return done(err); res.body.should.have.property('type').and.be.string; idJob = res.body['id'] - console.log("Jobid:", idJob) + //console.log("Jobid:", idJob) done(); }); }); @@ -252,7 +282,7 @@ describe('Test MessageHistory in jobs', () => { .end(function(err, res) { if (err) return done(err); - console.log(res.body) + //console.log(res.body) done(); }); }); From 4caf8a554a5b67f7631c3f7c2f34a791dc9abae1 Mon Sep 17 00:00:00 2001 From: egli Date: Tue, 8 Jan 2019 14:44:18 +0100 Subject: [PATCH 146/147] Now the flags are explicitly transferred to dataset directly --- common/models/dataset-lifecycle.js | 3 ++- common/models/job.js | 39 ++++++++++++++++++++++-------- test/MessageHistory.js | 25 +++++++++++++------ test/config/tests.json | 2 +- 4 files changed, 49 insertions(+), 20 deletions(-) diff --git a/common/models/dataset-lifecycle.js b/common/models/dataset-lifecycle.js index c6fc1da4..f7706586 100644 --- a/common/models/dataset-lifecycle.js +++ b/common/models/dataset-lifecycle.js @@ -48,7 +48,8 @@ module.exports = function(Datasetlifecycle) { utils.addOwnerGroup(ctx, next) }) - // transfer status flags to linked dataset + // transfer status flags to linked dataset. + // Warning: when using the updateAll API endpoint the context is missing ! Datasetlifecycle.observe('after save', (ctx, next) => { var Dataset = app.models.Dataset var instance = ctx.instance diff --git a/common/models/job.js b/common/models/job.js index 9f283a12..76d1ec21 100644 --- a/common/models/job.js +++ b/common/models/job.js @@ -48,7 +48,7 @@ function publishJob(job, ctx, next) { } function MarkDatasetsAsScheduled(job, ctx, idList, next) { - //console.log('Searching for datasetlifecycle with ids:', idList) + let DatasetLifecycle = app.models.DatasetLifecycle; DatasetLifecycle.updateAll( { @@ -62,14 +62,35 @@ function MarkDatasetsAsScheduled(job, ctx, idList, next) { archiveStatusMessage: "scheduledForArchiving" } , ctx.options, function (err, p) { - // console.log("============= DatasetLifecycle Result:", JSON.stringify(p)) if (err) { var e = new Error(); - e.statusCode = 400; + e.statusCode = 404; e.message = 'Can not find all needed DatasetLifecycle entries - no archive job sent:\n' + JSON.stringify(err) next(e); } else { - publishJob(job, ctx, next) + // since updateAll does not send context and therefore the DatasetLifecycle updates are not copied over + // to Dataset one has to do the update here on Dataset in addition + let Dataset = app.models.Dataset; + Dataset.updateAll( + { + pid: { + inq: idList + } + }, + { + archivable: false, + retrievable: false + } + , ctx.options, function (err, p) { + if (err) { + var e = new Error(); + e.statusCode = 404; + e.message = 'Can not find all needed Dataset entries - no archive job sent:\n' + JSON.stringify(err) + next(e); + } else { + publishJob(job, ctx, next) + } + }); } }); } @@ -84,14 +105,14 @@ function TestArchiveJobs(job, ctx, idList, next) { } } }, ctx.options, function (err, p) { - //console.log("============= Archive Result:", JSON.stringify(p)) if (p.length > 0) { var e = new Error(); - e.statusCode = 400; + e.statusCode = 409; e.message = 'The following datasets are not in archivable state - no archive job sent:\n' + JSON.stringify(p) next(e); } else { // mark all Datasets as in state scheduledForArchiving, archivable=false + // console.log("mark datasets as to be archived: ctx.options,idlist",ctx.options,idList) MarkDatasetsAsScheduled(job, ctx, idList, next) } }); @@ -127,7 +148,7 @@ function TestRetrieveJobs(job, ctx, idList, next) { return next(err2) } else { var e = new Error(); - e.statusCode = 400; + e.statusCode = 409; e.message = 'The following datasets are not in retrievable state - no retrieve job sent:\n' + JSON.stringify(pmiss) return next(e); } @@ -139,7 +160,6 @@ function TestRetrieveJobs(job, ctx, idList, next) { } function TestAllDatasets(job, ctx, idList, next) { - //console.log(" ====== find datasets with id", idList) let Dataset = app.models.Dataset; Dataset.find({ where: { @@ -151,7 +171,7 @@ function TestAllDatasets(job, ctx, idList, next) { let to = ctx.instance.emailJobInitiator if (err || (p.length != idList.length)) { var e = new Error(); - e.statusCode = 400; + e.statusCode = 404; e.message = 'At least one of the datasets could not be found - no Job sent'; // TODO should I send an email here ? Only if triggered by autoarchive option ? // subjectText = @@ -184,7 +204,6 @@ module.exports = function (Job) { Job.observe('before save', (ctx, next) => { if (ctx.instance) { - // replace email with that from userIdentity var UserIdentity = app.models.UserIdentity; var userId = ctx.options.accessToken.userId; diff --git a/test/MessageHistory.js b/test/MessageHistory.js index 3d90e0c3..cff12d6d 100644 --- a/test/MessageHistory.js +++ b/test/MessageHistory.js @@ -255,19 +255,28 @@ describe('Test MessageHistory in jobs', () => { }); }); - it('Adds a new retrieve job request', function(done) { + it('Adds a new archive job request for same data which should fail', function(done) { + request(app) + .post('/api/v2/Jobs?access_token=' + accessTokenIngestor) + .send(testArchiveJob) + .set('Accept', 'application/json') + .expect(409) + .expect('Content-Type', /json/) + .end((err, res) => { + res.body.should.have.property('error'); + done(); + }); + }); + + it('Adds a new retrieve job request on same dataset, which should fail as well because not yet retrievable', function(done) { request(app) .post('/api/v2/Jobs?access_token=' + accessTokenIngestor) .send(testRetrieveJob) .set('Accept', 'application/json') - .expect(200) + .expect(409) .expect('Content-Type', /json/) - .end(function(err, res) { - if (err) - return done(err); - res.body.should.have.property('type').and.be.string; - idJob = res.body['id'] - //console.log("Jobid:", idJob) + .end((err, res) => { + res.body.should.have.property('error'); done(); }); }); diff --git a/test/config/tests.json b/test/config/tests.json index 64a3e316..518cf66a 100644 --- a/test/config/tests.json +++ b/test/config/tests.json @@ -89,7 +89,7 @@ { "method": "POST", "route": "Jobs", - "expect": 400, + "expect": 404, "authenticate": "admin", "body": { "emailJobInitiator": "scicatingestor@psi.ch", From 4b5ab89366e8075b860f4212d859d4a54379f8b0 Mon Sep 17 00:00:00 2001 From: egli Date: Tue, 8 Jan 2019 16:06:32 +0100 Subject: [PATCH 147/147] If no proposal is linked to rawdataset try to fill one by common ownership --- common/models/dataset.js | 4 +- common/models/raw-dataset.js | 17 +++++++- test/RawDataset.js | 76 ++++++++++++++++++++++++++++++------ 3 files changed, 81 insertions(+), 16 deletions(-) diff --git a/common/models/dataset.js b/common/models/dataset.js index 4efeecbe..b61d9152 100644 --- a/common/models/dataset.js +++ b/common/models/dataset.js @@ -38,9 +38,9 @@ module.exports = function (Dataset) { if (ctx.instance) { if (ctx.isNewInstance) { ctx.instance.pid = config.pidPrefix + '/' + ctx.instance.pid; - console.log(' new pid:', ctx.instance.pid); + console.log('New pid:', ctx.instance.pid); } else { - console.log(' unmodified pid:', ctx.instance.pid); + console.log('Unmodified pid:', ctx.instance.pid); } ctx.instance.version = p.version; diff --git a/common/models/raw-dataset.js b/common/models/raw-dataset.js index 9a94a596..aaf06e0f 100644 --- a/common/models/raw-dataset.js +++ b/common/models/raw-dataset.js @@ -2,6 +2,8 @@ var utils = require('./utils'); module.exports = function(Rawdataset) { + var app = require('../../server/server'); + Rawdataset.validatesUniquenessOf('pid'); // filter on dataset type (raw, derived etc) @@ -25,7 +27,20 @@ module.exports = function(Rawdataset) { if (ctx.instance) { ctx.instance.type = 'raw'; } - next(); + // check if proposal is linked, if not try to add one + if(!ctx.instance.proposalId){ + var Proposal = app.models.Proposal + const filter = { where: { ownerGroup: ctx.instance.ownerGroup } }; + Proposal.findOne(filter,ctx.options).then(instance => { + if(instance){ + console.log("Appended Proposal "+instance.proposalId+" to rawdataset "+ctx.instance.pid) + ctx.instance.proposalId=instance.proposalId + } + return next() + }) + } else { + return next() + } }); // put diff --git a/test/RawDataset.js b/test/RawDataset.js index 4fd7e67f..025a9654 100644 --- a/test/RawDataset.js +++ b/test/RawDataset.js @@ -10,8 +10,17 @@ var request = require('supertest'); var should = chai.should(); var utils = require('./LoginUtils'); -var accessToken = null, - pid = null; +var accessToken = null; +var pid = null; +var accessProposalToken = null; + +var testproposal = { + "proposalId": "someprefix/20170266", + "email": "proposer%40uni.edu", + "title": "A test proposal", + "abstract": "Abstract of test proposal", + "ownerGroup": "p10029" +} var testraw = { "principalInvestigator": "bertram.astor@grumble.com", @@ -80,12 +89,13 @@ var testraw = { "doi": "not yet defined", "isPublished": false, "ownerGroup": "p10029", - "accessGroups": [], - "proposalId": "10.540.16635/20110123" + "accessGroups": [] } var app -before( function(){ +var proposalId = null; + +before(function () { app = require('../server/server') }); @@ -97,17 +107,42 @@ describe('RawDatasets', () => { }, (tokenVal) => { accessToken = tokenVal; + utils.getToken(app, { + 'username': 'proposalIngestor', + 'password': 'aman' + }, + (tokenVal) => { + accessProposalToken = tokenVal; + done(); + }); + }); + }); + + it('adds a new proposal', function (done) { + request(app) + .post('/api/v2/Proposals?access_token=' + accessProposalToken) + .send(testproposal) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end(function (err, res) { + if (err) + return done(err); + res.body.should.have.property('ownerGroup').and.be.string; + res.body.should.have.property('proposalId').and.be.string; + proposalId = encodeURIComponent(res.body['proposalId']); done(); }); }); - it('adds a new raw dataset', function(done) { + + it('adds a new raw dataset', function (done) { request(app) .post('/api/v2/RawDatasets?access_token=' + accessToken) .send(testraw) .set('Accept', 'application/json') .expect(200) .expect('Content-Type', /json/) - .end(function(err, res) { + .end(function (err, res) { if (err) return done(err); res.body.should.have.property('owner').and.be.string; @@ -119,7 +154,7 @@ describe('RawDatasets', () => { }); - it('should fetch several raw datasets', function(done) { + it('should fetch several raw datasets', function (done) { request(app) .get('/api/v2/RawDatasets?filter=%7B%22limit%22%3A2%7D&access_token=' + accessToken) .set('Accept', 'application/json') @@ -133,7 +168,7 @@ describe('RawDatasets', () => { }); }); - it('should fetch this raw dataset', function(done) { + it('should fetch this raw dataset', function (done) { request(app) .get('/api/v2/RawDatasets/' + pid + '?access_token=' + accessToken) .set('Accept', 'application/json') @@ -146,7 +181,7 @@ describe('RawDatasets', () => { }); }); - it('should delete this raw dataset', function(done) { + it('should delete this raw dataset', function (done) { request(app) .delete('/api/v2/RawDatasets/' + pid + '?access_token=' + accessToken) .set('Accept', 'application/json') @@ -159,20 +194,35 @@ describe('RawDatasets', () => { }); }); - it('should contain an array of facets', function(done) { + + it('should contain an array of facets', function (done) { request(app) .get('/api/v2/RawDatasets/fullfacet?access_token=' + accessToken) .set('Accept', 'application/json') - .send({'ownerGroup': ['p11114']}) + .send({ + 'ownerGroup': ['p11114'] + }) .expect(200) .expect('Content-Type', /json/) .end((err, res) => { res.body.should.be.an('array'); - if(err) + if (err) done(err); done(); }); }); + it('should delete this proposal', function(done) { + request(app) + .delete('/api/v2/Proposals/' + proposalId + '?access_token=' + accessProposalToken) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .end((err, res) => { + if (err) + return done(err); + done(); + }); + }); });