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Pva/cdisc feedback part 4 #323

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merged 8 commits into from
Dec 16, 2024
Merged

Pva/cdisc feedback part 4 #323

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a5cba61
fix export
peter-va Dec 9, 2024
7f3f4a6
small formatting
peter-va Dec 9, 2024
47f8cb7
change source checking in grouper
peter-va Dec 9, 2024
09eb414
Merge branch 'develop' into pva/CDISC-feedback-part-4
bcarlsenca Dec 11, 2024
db8e410
Another round of review and cleanup
bcarlsenca Dec 12, 2024
a95f027
Merge branch 'develop' into pva/CDISC-feedback-part-4
bcarlsenca Dec 12, 2024
b3a450e
small export fixes
peter-va Dec 13, 2024
28c9e4c
add changes for grouper subsets
peter-va Dec 13, 2024
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18 changes: 7 additions & 11 deletions web/frontend/src/app/component/subset-details/subset-details.component.html
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Original file line number Diff line number Diff line change
Expand Up @@ -219,28 +219,24 @@
</tr>
</ng-template>
<ng-template pTemplate="body" let-value let-i="rowIndex">
<tr [ngStyle]="{ 'background-color': i === 0 && !selectedSubset.isCdiscGrouper() ? 'lightblue' : 'transparent' }">
<tr [ngStyle]="{ 'background-color': i === 0 && selectedSubset.isCdiscCodeList() ? 'lightblue' : 'transparent' }">
<td class="w-10">
<a [routerLink]="[urlBase, terminology, value.code]" target="_top">
<!-- <i class="fa fa-external-link"
style="margin-left:0.2em;"></i> -->
{{ value.code }}
</a>
<span *ngIf="subsetCodes[value.code] && !selectedSubset.code === value.code"
><br />( <a [routerLink]="['/subset', terminology, value.code]" target="_top">view subset</a>)
<a [routerLink]="[urlBase, terminology, value.code]" target="_top">{{ value.code }}</a>
<span *ngIf="subsetCodes[value.code]"
><br />(<a [routerLink]="['/subset', terminology, value.code]" target="_top">view subset</a>)
</span>
</td>
<td class="w-10">
<span> {{ getCdiscCodelistCode() }}</span>
<span> {{ getCdiscCodelistCode() }}</span>
</td>
<td class="w-10">
<span *ngFor="let prop of value.properties">
<span *ngIf="prop.type == 'Extensible_List'">{{ prop.value }}</span>
</span>
</td>
<td class="w-20">{{ getCodelistName(value) }}</td>
<td class="w-20">{{ getCdiscCodelistName(value) }}</td>
<td class="w-10">{{ getCdiscSubmissionValue(value) }}</td>
<td class="w-20">
<td class="w-15">
<span *ngFor="let syn of value.getSynonymNames(cdiscSubsetSource, 'SY'); last as isLast">
<span
>{{ syn }} <span *ngIf="!isLast"><br /></span>
Expand Down
170 changes: 77 additions & 93 deletions web/frontend/src/app/component/subset-details/subset-details.component.ts
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,6 @@ export class SubsetDetailsComponent implements OnInit {
subsets: Array<Concept>;
avoidLazyLoading = true;
loading: boolean;
synonymSources: any;
termAutoSearch: string;
textSuggestions: string[] = [];
subsetFormat: string;
Expand Down Expand Up @@ -77,17 +76,13 @@ export class SubsetDetailsComponent implements OnInit {
this.subsets.push(new Concept(c, this.configService));
});
}
const synonymMap = new Array<Map<string, string>>();
this.subsetCodes = {};
this.subsetCodes[this.selectedSubset?.code] = 1;
this.subsets.forEach((c) => {
if (c && c['synonyms'].length > 0) {
synonymMap.push(this.getSynonymSources(c['synonyms']));
}
if (c && c['inverseAssociations'].length > 0 && c['inverseAssociations'].find((assoc) => assoc.type == 'Concept_In_Subset')) {
if (c && c.isSubset()) {
this.subsetCodes[c.code] = 1;
}
});
this.synonymSources = synonymMap;
this.termAutoSearch = '';

// getting the subs
Expand All @@ -102,12 +97,12 @@ export class SubsetDetailsComponent implements OnInit {
// CHECK FOR CDISC
else if (ContSource.some((entry) => entry.value.startsWith('CDISC') || entry.value.startsWith('MRCT-Ctr'))) {
this.subsetFormat = 'CDISC';
// For subsets there will be only one contributing source value, take the first
this.cdiscSubsetSource = ContSource[0].value;
if (!this.titleDesc) {
this.titleDesc = this.getSynonymNames(this.selectedSubset, 'CDISC', 'PT')[0];
}
if(!this.selectedSubset?.isCdiscGrouper())
// If this is a codelist, add the "blue" row at the top of the table
if (this.selectedSubset?.isCdiscCodeList()) {
this.subsets.unshift(this.selectedSubset);
}
} else if (ContSource.length === 1) {
this.subsetFormat = ContSource[0].value;
} else {
Expand Down Expand Up @@ -149,52 +144,28 @@ export class SubsetDetailsComponent implements OnInit {
.then((nodes) => {
this.hitsFound = nodes['total'];
this.subsets = new Array<Concept>();
if(!this.selectedSubset?.isCdiscGrouper())
if (this.selectedSubset?.isCdiscCodeList()) {
this.subsets.unshift(this.selectedSubset);
}
if (nodes['concepts']) {
nodes['concepts'].forEach((c) => {
this.subsets.push(new Concept(c, this.configService));
});
}

const synonymMap = new Array<Map<string, string>>();
this.subsetCodes = {};
this.subsetCodes[this.selectedSubset?.code] = 1;
this.subsets.forEach((c) => {
synonymMap.push(this.getSynonymSources(c['synonyms']));
if (c.inverseAssociations?.find((assoc) => assoc.type == 'Concept_In_Subset')) {
if (c && c.isSubset()) {
this.subsetCodes[c.code] = 1;
}
});
this.synonymSources = synonymMap;
});
this.fromRecord = fromRecord;
this.pageSize = event.rows;
}
}

// get synonym sources for a concept
getSynonymSources(synonyms) {
const synonymSourceMap = new Map<string, string>();
synonyms.forEach((synonym) => {
if (synonym['source'] === undefined) {
if (!synonymSourceMap.has('No Source')) {
synonymSourceMap.set('No Source', synonym['name']);
} else {
const key = synonymSourceMap.get('No Source') + ', ' + synonym['name'];
synonymSourceMap.set('No Source', key);
}
} else {
if (!synonymSourceMap.has(synonym['source'])) {
synonymSourceMap.set(synonym['source'], synonym['name']);
} else {
const key = synonymSourceMap.get(synonym['source']) + ', ' + synonym['name'];
synonymSourceMap.set(synonym['source'], key);
}
}
});
return synonymSourceMap;
}

// search for a concept
search(event, columnName = null) {
if (this.lastSearch !== event.query) {
Expand Down Expand Up @@ -228,21 +199,20 @@ export class SubsetDetailsComponent implements OnInit {
this.hitsFound = nodes['total'];
if (this.hitsFound > 0) {
this.subsets = new Array<Concept>();
if(!this.selectedSubset?.isCdiscGrouper())
if (this.selectedSubset?.isCdiscCodeList()) {
this.subsets.unshift(this.selectedSubset);
}
nodes['concepts'].forEach((c) => {
this.subsets.push(new Concept(c, this.configService));
});

const synonymMap = new Array<Map<string, string>>();
this.subsetCodes = {};
this.subsetCodes[this.selectedSubset?.code] = 1;
this.subsets.forEach((c) => {
synonymMap.push(this.getSynonymSources(c['synonyms']));
if (c.inverseAssociations?.find((assoc) => assoc.type == 'Concept_In_Subset')) {
if (c.isSubset()) {
this.subsetCodes[c.code] = 1;
}
});
this.synonymSources = synonymMap;
} else {
this.subsets = null;
}
Expand All @@ -266,8 +236,8 @@ export class SubsetDetailsComponent implements OnInit {
const pages = Math.ceil(Math.min(exportMax, this.hitsFound) / exportPageSize);
const pageList = Array.from(Array(pages).keys());

if (this.subsetFormat === 'CDISC') {
subsetText += this.exportCodeFormatter(this.selectedSubset, true);
if (this.subsetFormat === 'CDISC' && !this.selectedSubset.isCdiscGrouper()) {
subsetText += this.exportCodeFormatter(this.selectedSubset);
}
for (const page of pageList) {
await this.subsetDetailService
Expand All @@ -290,7 +260,7 @@ export class SubsetDetailsComponent implements OnInit {
}

// format the export file
exportCodeFormatter(concept: Concept, firstCDISC = false) {
exportCodeFormatter(concept: Concept) {
let rowText = '';
if (this.subsetFormat === 'NCIt') {
rowText += concept.code + '\t';
Expand Down Expand Up @@ -323,11 +293,11 @@ export class SubsetDetailsComponent implements OnInit {
const extensible = concept.properties.filter((prop) => prop.type == 'Extensible_List')[0]?.value;
rowText += (extensible ? extensible : '') + '\t';
// codelist name
rowText += this.getCodelistName(concept) + '\t';
rowText += this.getCdiscCodelistName(new Concept(concept, this.configService)) + '\t';
// cdisc submission value
rowText += this.getCdiscSubmissionValue(concept) + '\t';
rowText += this.getCdiscSubmissionValue(new Concept(concept, this.configService)) + '\t';
// cdisc synonyms
rowText += '"' + this.getSynonymNames(concept, 'CDISC', 'SY').join('\n') + '"' + '\t';
rowText += '"' + this.getSynonymNames(concept, this.cdiscSubsetSource, 'SY').join('\n') + '"' + '\t';
// cdisc definition
rowText += concept.definitions.filter((def) => def.source.startsWith('CDISC') || def.source.startsWith('MRCT-Ctr'))[0]?.definition + '\t';
// NCIt pref term
Expand Down Expand Up @@ -404,72 +374,87 @@ export class SubsetDetailsComponent implements OnInit {
}

getCdiscCodelistCode() {
if(this.selectedSubset.isCdiscGrouper()) {
return null;
if (this.selectedSubset.isCdiscGrouper()) {
return '';
} else {
return this.selectedSubset.code;
}
}

// Uses this.submissionValueCode to determine the submission value column for CDISC display
getCdiscSubmissionValue(concept: Concept): string {
if(concept.isCdiscGrouper()) {
return null;
// Groupers do not have a submission value
if (concept.isCdiscGrouper()) {
return '';
}

// Codelists have a submission value matching CDISC or MRCTPT
if (concept.isCdiscCodeList()) {
return concept.getCdiscPtName();
}

// if selected subset is a grouper, no value
if (this.selectedSubset.isCdiscGrouper()) {
return '';
}
// Kim's algorithm

// assumption: codelist only has one contributing source
// Otherwise our concept is just a regular value

// CDISC Submission Value algorithm

// ASSUMPTION: codelist only has one contributing source
var subsetContSource = this.selectedSubset.properties?.find((item) => item.type === 'Contributing_Source')?.value;
if(!subsetContSource) {
return "Unable to find submission value because codelist lacks contributing source";
if (!subsetContSource) {
return 'Unable to find submission value because codelist lacks contributing source';
}
// Find the matching contributing source PT
// ASSUMPTION: there will be at least 1
const cdiscSynonyms = concept.synonyms.filter((syn) => syn.source === subsetContSource && syn.termType === 'PT');
if (cdiscSynonyms.length == 0) {
return 'Unable to find submission value for ' + subsetContSource + '/PT';
}
const cdiscSynonyms = concept.synonyms.filter(
(syn) =>
syn.source === subsetContSource &&
syn.type === "FULL_SYN" &&
syn.termType === "PT"
);

// Check if there's exactly one unique synonym
var nci_ab = "";
var nci_ab = '';
if (cdiscSynonyms.length === 1) {
return cdiscSynonyms[0].name;
}
nci_ab = this.selectedSubset.synonyms.find(
(syn) =>
// no multiple MRCT
syn.source === "NCI" &&
syn.type === "FULL_SYN" &&
syn.termType === "AB"
)?.name;
if(nci_ab) {
const finalSynonym = cdiscSynonyms.find(
(syn) =>
syn.code === nci_ab
);
if(finalSynonym) {
return finalSynonym?.name;
} else {
return "Unable to find submission value (synonym that matches NCI source and AB term type)";
}
// Otherwise, find the NCI/AB of the codelist concept and find the CDISC/PT witha code matching the NCI/AB's name
nci_ab = this.selectedSubset.synonyms.find((syn) => syn.source === 'NCI' && syn.termType === 'AB')?.name;
if (nci_ab) {
const finalSynonym = cdiscSynonyms.find((syn) => syn.code === nci_ab);
if (finalSynonym) {
return finalSynonym.name;
}
// ASSUMPTION: there will be a final synonym
else {
return 'Unable to find submission value (synonym that matches NCI source and AB term type)';
}

}
return "Unable to find submission value";
return 'Unable to find submission value';
}

getCodelistName(value) {
if(!value.isSubset()) {
getCdiscCodelistName(concept: Concept) {
// For a regular entry in the table, the subset we are on is the codelist
if (!concept.isSubset()) {
if (this.selectedSubset.isCdiscGrouper()) {
return '';
}
return this.selectedSubset.name;

}

// If the subset we are on is a grouper
if (this.selectedSubset.isCdiscGrouper()) {
if(value.isCdiscGrouper()) {
return null;
} else {
return value.name;
// and the concept itself is a grouper, then don't show a name
if (concept.isCdiscGrouper()) {
return '';
}
// otherwise, the concept itself is a codelist entry, show its own name
else {
return concept.name;
}
} else {
return this.selectedSubset.name;
return this.selectedSubset.name;
}
}

Expand All @@ -480,5 +465,4 @@ export class SubsetDetailsComponent implements OnInit {
const desc = this.selectedSubset.properties.find((item) => item.type === 'Term_Browser_Value_Set_Description');
return this.selectedSubset.subsetLink !== undefined && desc !== undefined && !desc.value.includes(this.selectedSubset.subsetLink);
}

}
31 changes: 27 additions & 4 deletions web/frontend/src/app/model/concept.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -364,7 +364,7 @@ export class Concept {
}
}
}
return null;
return '';
}

// Get value from Concept_Status parameter
Expand Down Expand Up @@ -606,15 +606,38 @@ export class Concept {
}

isCdiscGrouper(): boolean {
return (this.code === "C61410" || ((this.name.startsWith("CDISC ") || this.name.startsWith("MRCT")) && !this.synonyms.some(syn => syn.source?.startsWith('CDISC') && syn.termType === 'SY'))) && this.inverseAssociations.some(invAssoc => invAssoc.type === "Concept_In_Subset");
// Only subsets can be groupers
if (!this.isSubset()) {
return false;
}

// CDISC subset without a CDISC/SY
return this.isCdiscSubset() && !this.hasCdiscSy();
}

isCdiscCodeList(): boolean {
return this.properties.some(prop => prop.type === "Publish_Value_Set" && prop.value === "true") && this.synonyms.some(syn => syn.source?.startsWith('CDISC') && syn.termType === 'SY');
// CDISC Subset with CDISC name a CDISC/SY
return this.isCdiscSubset() && this.hasCdiscSy();
}

hasCdiscSy(): boolean {
// source with CDISC* or MRCT* and termType = SY
return this.synonyms.some((syn) => syn.source && (syn.source.startsWith('CDISC') || syn.source.startsWith('MRCT-Ctr')) && syn.termType === 'SY');
}

getCdiscPtName(): string {
return this.synonyms?.find((syn) => syn.source && (syn.source.startsWith('CDISC') || syn.source.startsWith('MRCT-Ctr')) && syn.termType === 'PT')
?.name;
}

isCdiscSubset(): boolean {
// subset with a name starting with CDISC or MRCT
return this.code === 'C61410' || (this.isSubset() && (this.name.startsWith('CDISC ') || this.name.startsWith('MRCT-Ctr')));
}

isSubset(): boolean {
return this.inverseAssociations.some(invAssoc => invAssoc.type === "Concept_In_Subset");
// It's a subset if it has Publish_Value_Set=Yes
return this.properties.some((prop) => prop.type === 'Publish_Value_Set' && prop.value === 'Yes');
}

// Default string representation is the name
Expand Down
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