From 68022a09d76a8d1f8d6ff23904c0407f177e5e21 Mon Sep 17 00:00:00 2001
From: felmer <franz-josef.elmer@id.ethz.ch>
Date: Mon, 24 Apr 2023 09:04:40 +0200
Subject: [PATCH] SSDM-13120: Bug fixed: Semantic Annotations did shown up on
sample creation view. Also remove doubled property annotations when not
overload by property assignments.
---
.../eln-lims/html/js/server/ServerFacade.js | 24 +++--------
.../js/views/SampleForm/SampleFormView.js | 42 +++++++++++++++----
2 files changed, 40 insertions(+), 26 deletions(-)
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
index 44e7799baaa..5861601681c 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
@@ -643,6 +643,11 @@ function ServerFacade(openbisServer) {
var entityTypePermId = new EntityTypePermId(sampleType, EntityKind.SAMPLE);
var sampleTypeFetchOptions = new SampleTypeFetchOptions();
sampleTypeFetchOptions.withPropertyAssignments().withPropertyType();
+ if (profile.showSemanticAnnotations != false) {
+ sampleTypeFetchOptions.withSemanticAnnotations();
+ sampleTypeFetchOptions.withPropertyAssignments().withSemanticAnnotations();
+ sampleTypeFetchOptions.withPropertyAssignments().withPropertyType().withSemanticAnnotations();
+ }
mainController.openbisV3.getSampleTypes(entityTypePermId, sampleTypeFetchOptions).done(function(sampleTypesByIds) {
callback(sampleTypesByIds[entityTypePermId]);
}).fail(function(error) {
@@ -2409,18 +2414,6 @@ function ServerFacade(openbisServer) {
v1Sample["experimentIdentifierOrNull"] = (v3Sample.experiment)?v3Sample.experiment.identifier.identifier:null;
v1Sample["experimentTypeCode"] = v3Sample.experiment && v3Sample.experiment.type ? v3Sample.experiment.type.code : null;
v1Sample["sampleTypeCode"] = (v3Sample.type)?v3Sample.type.code:null;
- v1Sample["semanticAnnotations"] = (v3Sample.type)?v3Sample.type.semanticAnnotations:null;
- if (v3Sample.type && v3Sample.type.propertyAssignments) {
- v1Sample["propertyTypesSemanticAnnotations"] = {}
- v3Sample.type.propertyAssignments.forEach(function(assignment) {
- var propertyType = assignment.getPropertyType();
- var annotations = [].concat(assignment.getSemanticAnnotations());
- if (propertyType && propertyType.getSemanticAnnotations()) {
- annotations = annotations.concat(propertyType.getSemanticAnnotations());
- }
- v1Sample["propertyTypesSemanticAnnotations"][propertyType.getCode()] = annotations;
- });
- }
v1Sample["properties"] = v3Sample.properties;
v1Sample["registrationDetails"] = {};
@@ -2754,11 +2747,6 @@ function ServerFacade(openbisServer) {
var fetchOptions = new SampleFetchOptions();
fetchOptions.withSpace();
fetchOptions.withType();
- if (fechOptions["withSemanticAnnotations"] && profile.showSemanticAnnotations != false) {
- fetchOptions.withType().withSemanticAnnotations();
- fetchOptions.withType().withPropertyAssignments().withSemanticAnnotations();
- fetchOptions.withType().withPropertyAssignments().withPropertyType().withSemanticAnnotations();
- }
fetchOptions.withRegistrator();
fetchOptions.withModifier();
fetchOptions.withProject();
@@ -2819,7 +2807,6 @@ function ServerFacade(openbisServer) {
"samplePermId" : samplePermId,
"withProperties" : true,
"withParents" : true,
- "withSemanticAnnotations" : true,
"withChildren" : true
}, callbackFunction);
}
@@ -2916,7 +2903,6 @@ function ServerFacade(openbisServer) {
"withProperties" : true,
"withParents" : true,
"withChildren" : true,
- "withSemanticAnnotations" : true,
"sampleIdentifier" : sampleIdentifier
}, function(samples) {
samples.forEach(function(sample) {
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
index e7a9d22e87d..1218fe7c8f0 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
@@ -675,14 +675,11 @@ function SampleFormView(sampleFormController, sampleFormModel) {
$legend.remove();
}
- var showSemanticAnnotations = profile.showSemanticAnnotations;
var propertyGroupPropertiesOnForm = 0;
for(var j = 0; j < propertyTypeGroup.propertyTypes.length; j++) {
var propertyType = propertyTypeGroup.propertyTypes[j];
var propertyTypeV3 = profile.getPropertyTypeFromSampleTypeV3(this._sampleFormModel.sampleType, propertyType.code);
- if (this._sampleFormModel.sample.propertyTypesSemanticAnnotations) {
- var semanticAnnotations = this._renderPropertyTypeSemanticAnnotations(this._sampleFormModel.sample.propertyTypesSemanticAnnotations[propertyTypeV3.code]);
- }
+ var semanticAnnotations = this._renderPropertyTypeSemanticAnnotations(propertyType.code);
FormUtil.fixStringPropertiesForForm(propertyTypeV3, this._sampleFormModel.sample);
if(!propertyType.showInEditViews && (this._sampleFormModel.mode === FormMode.EDIT || this._sampleFormModel.mode === FormMode.CREATE) && propertyType.code !== "$XMLCOMMENTS") { //Skip
continue;
@@ -835,7 +832,8 @@ function SampleFormView(sampleFormController, sampleFormModel) {
return false;
}
- this._renderPropertyTypeSemanticAnnotations = function(annotations) {
+ this._renderPropertyTypeSemanticAnnotations = function(propertyTypeCode) {
+ var annotations = this._getAllSemanticAnnotations(propertyTypeCode);
if (annotations && annotations.length > 0) {
var $group = $("<div>", {class : "form-group"});
$group.append($("<label>", {class : "control-label"}).text("Semantic Annotations:"));
@@ -852,6 +850,36 @@ function SampleFormView(sampleFormController, sampleFormModel) {
return null;
}
+ this._getAllSemanticAnnotations = function(propertyTypeCode) {
+ // Using a dict because the same property type annotations appear for the assignments if not
+ // overloaded
+ var semanticAnnotations = {};
+ var propertyAssignment = this._getPropertyAssignment(propertyTypeCode);
+ if (propertyAssignment) {
+ [propertyAssignment.semanticAnnotations, propertyAssignment.propertyType.semanticAnnotations].forEach(function(annotations) {
+ if (annotations) {
+ annotations.forEach(function(annotation) {
+ semanticAnnotations[annotation.permId.permId] = annotation;
+ });
+ }
+ });
+ }
+ return Object.values(semanticAnnotations);
+ }
+
+ this._getPropertyAssignment = function(propertyTypeCode) {
+ if (this._sampleFormModel.sampleType && this._sampleFormModel.sampleType.propertyAssignments) {
+ var propertyAssignments = this._sampleFormModel.sampleType.propertyAssignments;
+ for (var i = 0; i < propertyAssignments.length; i++) {
+ var propertyAssignment = propertyAssignments[i];
+ if (propertyAssignment.propertyType.code === propertyTypeCode) {
+ return propertyAssignment;
+ }
+ }
+ }
+ return null;
+ }
+
this._createIdentificationInfoSection = function(hideShowOptionsModel, sampleType, entityPath) {
hideShowOptionsModel.push({
label : "Identification Info",
@@ -942,12 +970,12 @@ function SampleFormView(sampleFormController, sampleFormModel) {
}
this._appendSemanticAnnotions = function($fieldset) {
- if (this._sampleFormModel.sample.semanticAnnotations && this._sampleFormModel.sample.semanticAnnotations.length > 0) {
+ if (this._sampleFormModel.sampleType.semanticAnnotations && this._sampleFormModel.sampleType.semanticAnnotations.length > 0) {
var $group = $("<div>", {class : "form-group"});
$group.append($("<label>", {class : "control-label"}).text("Semantic Annotations:"));
var $controls = $("<div>", {class : "controls" });
var _this = this;
- this._sampleFormModel.sample.semanticAnnotations.forEach(function(annotation) {
+ this._sampleFormModel.sampleType.semanticAnnotations.forEach(function(annotation) {
$controls.append(_this._renderSemanticAnnotation(annotation.getDescriptorAccessionId(),
annotation.getDescriptorOntologyId(),
annotation.getDescriptorOntologyVersion()));
--
GitLab