Merge pull request #54 from uc-cdis/fix/docker

chore(docker and babel): no compile at runtime

.gitignore

@@ -1,3 +1,8 @@
 .vscode
 node_modules/
 dist/
+*.swp
+*.log
+*.old
+*.bak
+

Dockerfile

@@ -13,17 +13,23 @@ RUN apt-get update \
     && apt-get install -y --no-install-recommends nodejs \
     && rm -rf /var/lib/apt/lists/*
 
-COPY . /guppy
+COPY . /guppy/
 WORKDIR /guppy
 
 RUN COMMIT=`git rev-parse HEAD` && echo "export const guppyCommit = \"${COMMIT}\";" >versions.js
 RUN VERSION=`git describe --always --tags` && echo "export const guppyVersion =\"${VERSION}\";" >>versions.js
 RUN /bin/rm -rf .git
 RUN /bin/rm -rf node_modules
 
+RUN useradd -d /guppy gen3 && chown -R gen3: /guppy
+# see https://superuser.com/questions/710253/allow-non-root-process-to-bind-to-port-80-and-443
+RUN setcap CAP_NET_BIND_SERVICE=+eip /usr/bin/node
+USER gen3
 RUN npm ci --unsafe-perm
+RUN npm run-script prepare
 
 EXPOSE 3000
+EXPOSE 80
 
-CMD npm start
+CMD node dist/server/server.js
 

Jenkinsfile

@@ -0,0 +1,6 @@
+#!groovy
+
+@Library('cdis-jenkins-lib@master') _
+
+testPipeline { 
+}

package.json

@@ -40,7 +40,7 @@
     "graphql-tools": "^4.0.4",
     "graphql-type-json": "^0.2.1",
     "isomorphic-fetch": "^2.2.1",
-    "lodash": "^4.17.11",
+    "lodash": "^4.17.15",
     "loglevel": "^1.6.1",
     "node-fetch": "^2.3.0",
     "prop-types": "^15.7.2",
@@ -53,12 +53,13 @@
     "@babel/plugin-transform-runtime": "^7.4.3",
     "@babel/preset-env": "^7.3.4",
     "@babel/preset-react": "^7.0.0",
-    "@storybook/addon-actions": "^5.0.1",
-    "@storybook/addon-links": "^5.0.1",
-    "@storybook/addons": "^5.0.1",
-    "@storybook/react": "^5.0.1",
+    "@storybook/addon-actions": "^5.1.1",
+    "@storybook/addon-links": "^5.1.1",
+    "@storybook/addons": "^5.1.1",
+    "@storybook/react": "^5.1.1",
     "babel-jest": "^24.7.1",
     "babel-loader": "^8.0.5",
+    "babel-preset-env": "^1.7.0",
     "eslint": "^5.16.0",
     "eslint-config-airbnb": "^17.1.0",
     "eslint-plugin-import": "^2.17.1",
@@ -67,6 +68,7 @@
     "jest": "^24.7.1",
     "nock": "^10.0.6",
     "nodemon": "^1.18.10",
+    "react-scripts": "^3.1.1",
     "react-table": "^6.9.2"
   }
 }

src/server/.babelrc

@@ -0,0 +1,11 @@
+{
+  "presets": [
+    ["env", {
+      "targets": {
+        "node": "current"
+      }
+    }]
+  ],
+  "sourceMaps": "inline",
+  "retainLines": true
+}

src/server/auth/authHelper.js

@@ -29,7 +29,7 @@ export class AuthHelper {
       log.debug('[AuthHelper] accessible resources: ', this._accessibleResourceList);
       log.debug('[AuthHelper] unaccessible resources: ', this._unaccessibleResourceList);
     } catch (err) {
-      log.error('[AuthHelper] error when initializing');
+      log.error('[AuthHelper] error when initializing', err);
     }
   }
 

src/server/es/aggs.js

@@ -530,7 +530,7 @@ export const textAggregation = async (
     resultSize = 0;
 
     result.aggregations[aggsName].buckets.forEach((item) => {
-      const resultObj = processResultsForNestedAgg (nestedAggFields, item, resultObj)
+      const resultObj = processResultsForNestedAgg (nestedAggFields, item, {})
       finalResults.push({
         key: item.key[field],
         count: item.doc_count,

stories/conf.js

@@ -39,7 +39,7 @@ export const tableConfig = [
 ];
 
 export const guppyConfig = {
-  path: 'http://localhost:3000',
+  path: 'http://localhost:80',
   type: 'subject',
   fileType: 'file',
 };