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Remove hard-coded sample logic #1516 #1535

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merged 8 commits into from
Jan 17, 2024
Merged

Remove hard-coded sample logic #1516 #1535

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06e3f44
Remove hard-coded sample name on backend #1516
jacobtylerwalls Jan 12, 2024
ab628ad
Remove hard-coded sample name on frontend #1516
jacobtylerwalls Jan 12, 2024
9b81e96
Standardize sampleOf and analysisAreaOf #1516
jacobtylerwalls Jan 12, 2024
c7fb668
Localize two more strings #1516
jacobtylerwalls Jan 12, 2024
78a7339
Remove more hardcoded sample logic #1516
jacobtylerwalls Jan 12, 2024
a5e8865
Remove hardcoded sample substrings #1516
jacobtylerwalls Jan 12, 2024
4046d16
Add handling for no label re #1516
jacobtylerwalls Jan 15, 2024
e44d9b2
Merge branch 'localization' into 1516-sample-logic
jacobtylerwalls Jan 17, 2024
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16 changes: 9 additions & 7 deletions arches_for_science/media/js/views/components/annotation-summary.js
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Original file line number Diff line number Diff line change
Expand Up @@ -69,22 +69,24 @@ define([
return feature.properties;
},
onEachFeature: function(feature, layer) {
const classificationConcepts = Object.freeze({
// Concept IDs, not values
"a2588fa8-5ae6-4770-a473-dec0c05fb175": 'Analysis Area',
"2703e524-b5ea-4548-bea7-7ce354e4e05a": 'Sample Area',
"9db724b9-b3c7-4761-9a50-673d64a15bd8": 'Sample',
});
if (feature.properties.active === false){
var popup = L.popup({
closeButton: false,
maxWidth: 250
})
.setContent(popupHtml)
.on('add', function() {
// hope that translator has not adjusted the location of the bracket.
const titleArray = feature.properties.name.split('[');
const title = titleArray[0].trim();
// TODO(i18n) samples
const type = titleArray[1].startsWith('Analysis Area') ? 'Analysis Area':
titleArray[1].startsWith('Sample Area') ? 'Sample Area':
'Part';
const parent = titleArray[1].startsWith('Analysis Area') ? titleArray[1].replace('Analysis Area of ', '').replace(']',''):
titleArray[1].startsWith('Sample Area') ? titleArray[1].replace('Sample Area of ','').replace(']',''):
titleArray[1].replace(']','');
const type = classificationConcepts[feature.properties.classificationConceptId];
const parent = feature.properties.parentPhysicalThingName;
const description = (
arches.translations.existingAnnotation
.replace('{title}', title)
Expand Down
6 changes: 3 additions & 3 deletions ...a/js/views/components/workflows/analysis-areas-workflow/analysis-areas-annotation-step.js
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Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ define([
this.areaNameFromTileData = (tileData) => {
const nameValue = tileData[self.partIdentifierAssignmentLabelNodeId];
const baseName = self.getStrValue(nameValue) || "";
return `${baseName} [${arches.translations.analysisArea} ${arches.translations.of} ${self.physicalThingName()}]`;
return arches.translations.analysisAreaOf.replace('{analysisName}', baseName).replace('{physicalThingName}', self.physicalThingName());
};
this.areaName = ko.computed(function(){
if (self.selectedAnalysisAreaInstance()){
Expand Down Expand Up @@ -410,7 +410,6 @@ define([
parentPhysicalThingTileData: koMapping.toJSON(parentPhysicalThing.data),
parentPhysicalThingTileId: parentPhysicalThing.tileid,
transactionId: params.form.workflowId,
analysisAreaName: self.areaName()
};

self.savingTile(true);
Expand Down Expand Up @@ -504,12 +503,12 @@ define([

const data = {
parentPhysicalThingResourceid: self.physicalThingResourceId,
parentPhysicalThingName: self.physicalThingName(),
collectionResourceid: params.projectSet,
partIdentifierAssignmentTileData: koMapping.toJSON(self.selectedAnalysisAreaInstance().data),
partIdentifierAssignmentTileId: self.selectedAnalysisAreaInstance().tileid,
partIdentifierAssignmentResourceId: self.selectedAnalysisAreaInstance().resourceinstance_id,
transactionId: params.form.workflowId,
analysisAreaName: self.areaName(),
};

$.ajax({
Expand Down Expand Up @@ -812,6 +811,7 @@ define([
})
.then(function(json) {
json.features.forEach(function(feature) {
// TODO(i18n) slug or name?
feature.properties.graphName = "Physical Thing";
if (self.sampleLocationTileIds.includes(feature.properties.tileId)) {
feature.properties.type = 'sample_location';
Expand Down
24 changes: 17 additions & 7 deletions .../media/js/views/components/workflows/analysis-areas-workflow/analysis-areas-final-step.js
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,9 @@ define([
'arches',
'views/components/workflows/summary-step',
'templates/views/components/workflows/analysis-areas-workflow/analysis-areas-final-step.htm',
'utils/label-based-graph-utils',
'views/components/annotation-summary',
], function(ko, _, uuid, arches, SummaryStep, analysisAreasFinalStepTemplate) {
], function(ko, _, uuid, arches, SummaryStep, analysisAreasFinalStepTemplate, labelBasedGraphUtils) {

function viewModel(params) {
var self = this;
Expand Down Expand Up @@ -97,12 +98,21 @@ define([
annotator: annotation.annotator,
});
} else {
annotation.annotationJson.features.map(feature => {
feature.properties.color = '#999999';
feature.properties.fillColor = '#999999';
feature.properties.tileId = annotation.tileId;
feature.properties.name = annotation.annotationName;
feature.properties.active = false;
// TODO: fetch in parallel
fetch(self.urls.api_resources(annotation.resourceId) + '?format=json&compact=false&v=beta')
.then(response => response.json())
.then(data => {
annotation.annotationJson.features.map(feature => {
feature.properties.color = '#999999';
feature.properties.fillColor = '#999999';
feature.properties.tileId = annotation.tileId;
feature.properties.name = annotation.annotationName;
feature.properties.active = false;
feature.properties.classificationConceptId = data.resource.type.concept_details[0].concept_id;
feature.properties.parentPhysicalThingName = labelBasedGraphUtils.getPropByNodeId(
data.resource, 'f8d5fe4c-b31d-11e9-9625-a4d18cec433a', '@display_value'
);
});
});
}
});
Expand Down
7 changes: 2 additions & 5 deletions ...or_science/media/js/views/components/workflows/create-project-workflow/add-things-step.js
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Original file line number Diff line number Diff line change
Expand Up @@ -94,9 +94,6 @@ define([
analysis: '31d97bdd-f10f-4a26-958c-69cb5ab69af1',
};
this.physicalThingTypeNodeId = '8ddfe3ab-b31d-11e9-aff0-a4d18cec433a';
// TODO(i18n) samples
const sampleSubstring = '[Sample'; // for "[Sample of ..." and "[Sample Area of ..."
const regionSubstring = '[Region';

this.value.subscribe(function(a) {
a.forEach(function(action) {
Expand Down Expand Up @@ -332,8 +329,8 @@ define([
return (
result.context_label.includes("Physical Thing") ||
result.context_label.includes("Search Term")
) && (self.includeSamples() || !result.text.includes(sampleSubstring))
&& (self.includeAnalysisAreas() || !result.text.includes(regionSubstring))
) && (self.includeSamples() || !result.text.includes(arches.translations.sample))
&& (self.includeAnalysisAreas() || !result.text.includes(arches.translations.analysisArea))
});
return {
"results": filteredResults
Expand Down
16 changes: 9 additions & 7 deletions ...or_science/media/js/views/components/workflows/project-report-workflow/add-annotations.js
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Original file line number Diff line number Diff line change
Expand Up @@ -225,15 +225,17 @@ define([
})
.setContent(popupHtml)
.on('add', function() {
const classificationConcepts = Object.freeze({
// Concept IDs, not values
"a2588fa8-5ae6-4770-a473-dec0c05fb175": 'Analysis Area',
"2703e524-b5ea-4548-bea7-7ce354e4e05a": 'Sample Area',
"9db724b9-b3c7-4761-9a50-673d64a15bd8": 'Sample',
});
// hope that translator has not adjusted the location of the bracket.
const titleArray = feature.properties.name.split('[');
const title = titleArray[0].trim();
// TODO(i18n) samples
const type = titleArray[1].startsWith('Analysis Area') ? 'Analysis Area':
titleArray[1].startsWith('Sample Area') ? 'Sample Area':
'Part';
const parent = titleArray[1].startsWith('Analysis Area') ? titleArray[1].replace('Analysis Area of ', '').replace(']',''):
titleArray[1].startsWith('Sample Area') ? titleArray[1].replace('Sample Area of ','').replace(']',''):
titleArray[1].replace(']','');
const type = classificationConcepts[feature.properties.classificationConceptId];
const parent = feature.properties.parentPhysicalThingName;
const description = (
arches.translations.existingAnnotation
.replace('{title}', title)
Expand Down
1 change: 0 additions & 1 deletion ...or_science/media/js/views/components/workflows/project-report-workflow/download-report.js
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,6 @@ define([
const reportDate = today.toLocaleDateString('en-US', options);
const physicalThingsDetailsArray = [...Object.values(physicalThingsDetails)];
const objectOfStudyDetailsArray = physicalThingsDetailsArray.filter(thing => physicalThingFromPreviousStep.includes(thing.resourceinstanceid));
// TODO(i18n) samples
const analysisAreas = physicalThingsDetailsArray.filter(physicalThing => physicalThing.resource?.type?.["@display_value"] == 'analysis areas');
const annotationScreenshots = screenshots?.map((screenshot) => {
const url = `${window.location.origin}/temp_file/${screenshot.fileId}`;
Expand Down
64 changes: 37 additions & 27 deletions ...ce/media/js/views/components/workflows/sample-taking-workflow/sample-taking-final-step.js
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Original file line number Diff line number Diff line change
Expand Up @@ -56,22 +56,24 @@ define([
return feature.properties;
},
onEachFeature: function(feature, layer) {
const classificationConcepts = Object.freeze({
// Concept IDs, not values
"a2588fa8-5ae6-4770-a473-dec0c05fb175": 'Analysis Area',
"2703e524-b5ea-4548-bea7-7ce354e4e05a": 'Sample Area',
"9db724b9-b3c7-4761-9a50-673d64a15bd8": 'Sample',
});
if (!feature.properties.active){
var popup = L.popup({
closeButton: false,
maxWidth: 250
})
.setContent(iiifPopup)
.on('add', function() {
// hope that translator has not adjusted the location of the bracket.
const titleArray = feature.properties.locationName.split('[');
const title = titleArray[0].trim();
// TODO(i18n) samples
const type = titleArray[1].startsWith('Analysis Area') ? 'Analysis Area':
titleArray[1].startsWith('Sample Area') ? 'Sample Area':
'Part';
const parent = titleArray[1].startsWith('Analysis Area') ? titleArray[1].replace('Analysis Area of ', '').replace(']',''):
titleArray[1].startsWith('Sample Area') ? titleArray[1].replace('Sample Area of ','').replace(']',''):
titleArray[1].replace(']','');
const type = classificationConcepts[feature.properties.classificationConceptId];
const parent = feature.properties.parentPhysicalThingName;
const description = (
arches.translations.existingAnnotation
.replace('{title}', title)
Expand Down Expand Up @@ -209,35 +211,43 @@ define([
const parentPhyiscalThingResourceId = self.getResourceValue(val.resource["Sampling Unit"][0], ['Sampling Area','Overall Object Sampled','resourceId']);
const parentPhyiscalThing = ko.observable();
self.getResourceData(parentPhyiscalThingResourceId, parentPhyiscalThing);
parentPhyiscalThing.subscribe(function(val){ // 2nd request
parentPhyiscalThing.subscribe(async function(val) { // 2nd request
const parts = self.getResourceValue(val.resource, ['Part Identifier Assignment']);
parts.forEach(function(part){
for (const part of parts) {
const locationName = self.getResourceValue(part,['Part Identifier Assignment_Physical Part of Object','@display_value']);
const tileId = self.getResourceValue(part,['@tile_id']);
const sampleAreaResourceId = self.getResourceValue(part,['Part Identifier Assignment_Physical Part of Object','resourceId']);
const partResourceId = self.getResourceValue(part,['Part Identifier Assignment_Physical Part of Object','resourceId']);
const partsAnnotationString = self.getResourceValue(part,['Part Identifier Assignment_Polygon Identifier','@display_value']);
if (partsAnnotationString) {
const locationAnnotation = JSON.parse(partsAnnotationString.replaceAll("'",'"'));
const canvas = locationAnnotation.features[0].properties.canvas;
locationAnnotation.features.forEach(function(feature){
feature.properties.active = false;
feature.properties.tileId = tileId;
feature.properties.locationName = locationName;
feature.properties.sampleAreaResourceId = sampleAreaResourceId;
});
if (canvas in partsAnnotationCollection) {
partsAnnotationCollection[canvas].push({
locationAnnotation: locationAnnotation,
sampleAreaResourceId: sampleAreaResourceId,
// TODO: fetch in parallel
await fetch(self.urls.api_resources(partResourceId) + '?format=json&compact=false&v=beta')
.then(response => response.json())
.then(data => {
locationAnnotation.features.forEach(function(feature) {
feature.properties.active = false;
feature.properties.tileId = tileId;
feature.properties.locationName = locationName;
// misnomer, could be analysis area
feature.properties.sampleAreaResourceId = partResourceId;
feature.properties.classificationConceptId = data.resource.type.concept_details[0].concept_id;
feature.properties.parentPhysicalThingName = parentPhyiscalThing().resource._label?.['@display_value'] ?? '';
});
} else {
partsAnnotationCollection[canvas] = [{
locationAnnotation: locationAnnotation,
sampleAreaResourceId: sampleAreaResourceId,
}];
}
if (canvas in partsAnnotationCollection) {
partsAnnotationCollection[canvas].push({
locationAnnotation: locationAnnotation,
sampleAreaResourceId: partResourceId,
});
} else {
partsAnnotationCollection[canvas] = [{
locationAnnotation: locationAnnotation,
sampleAreaResourceId: partResourceId,
}];
}
});
}
});
}

// add the annotation of parts to the final object
self.annotationStatus = ko.observable();
Expand Down
10 changes: 7 additions & 3 deletions ...s/views/components/workflows/sample-taking-workflow/sample-taking-sample-location-step.js
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Original file line number Diff line number Diff line change
Expand Up @@ -164,11 +164,15 @@ define([
}
});

this.sampleNameFromTileData = (data) => {
const partIdentifierAssignmentLabelNodeId = '3e541cc6-859b-11ea-97eb-acde48001122';
const baseName = ko.unwrap(ko.unwrap(data[partIdentifierAssignmentLabelNodeId])?.[arches.activeLanguage]?.["value"]) || "";
return arches.translations.sampleOf.replace('{sampleName}', baseName).replace('{physicalThingName}', params.physicalThingName);
};

this.sampleName = ko.computed(function() {
var partIdentifierAssignmentLabelNodeId = '3e541cc6-859b-11ea-97eb-acde48001122';
if (self.selectedSampleLocationInstance()){
const baseName = ko.unwrap(ko.unwrap(self.selectedSampleLocationInstance().data[partIdentifierAssignmentLabelNodeId])?.[arches.activeLanguage]?.["value"]) || "";
return `${baseName} [Sample of ${params.physicalThingName}]`;
return self.sampleNameFromTileData(self.selectedSampleLocationInstance().data);
}
});

Expand Down
3 changes: 1 addition & 2 deletions ..._science/media/js/views/components/workflows/sample-taking-workflow/sampling-info-step.js
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,7 @@ define([
});

this.samplingDate.subscribe(function(val){
// TODO(i18n) samples
self.samplingName(["Sampling Activity of", self.physicalThingNameValue, val].join(' '));
self.samplingName(arches.translations.samplingActivityOf.replace('{physicalThingName}', self.physicalThingNameValue) + ' ' + val);
});

const selectPhysThingData = params.selectPhysThingData;
Expand Down
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