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AG-1425 updating variables and comments for clarity, fixing plural bu…
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…g for protein header label
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@sagely1
sagely1 committed May 9, 2024
1 parent 9f19393 commit abae471
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14 changes: 7 additions & 7 deletions src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html
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Original file line number Diff line number Diff line change
Expand Up @@ -284,20 +284,20 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
</p-table>

<div
*ngIf="pinnedGenes.length > 0"
*ngIf="pinnedItems.length > 0"
class="table-divider table-divider-1"
>
<div class="table-divider-inner">
<div id="pinned-genes-header">
<span *ngIf="category === 'RNA - Differential Expression'">
Pinned Genes ({{ pinnedGenes.length }}/50)
Pinned Genes ({{ pinnedItems.length }}/50)
</span>
<div *ngIf="category === 'Protein - Differential Expression'">
<div>
Pinned Genes ({{ uniquePinnedGenesCount }}/50)&nbsp;&nbsp;&nbsp;
</div>
<div id="pinned-proteins">
{{ pinnedGenes.length }} Proteins
{{ pinnedItems.length }} Protein<ng-container *ngIf="pinnedItems.length > 1">s</ng-container>
</div>
</div>
</div>
Expand All @@ -314,7 +314,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
</div>
<p-table
#pinnedTable
[value]="pinnedGenes"
[value]="pinnedItems"
[customSort]="true"
(sortFunction)="sortCallback($event)"
breakpoint="0"
Expand Down Expand Up @@ -425,7 +425,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
</div>
<div
*ngIf="
!searchTerm && !hasSelectedFilters() && pinnedGenes.length > 0
!searchTerm && !hasSelectedFilters() && pinnedItems.length > 0
"
class="table-divider"
>
Expand Down Expand Up @@ -573,8 +573,8 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
<gene-comparison-tool-pinned-genes-modal
#pinnedGenesModal
(onChange)="onPinnedGenesModalChange($event)"
[pinnedGenes]="pinnedGenes"
[pendingPinnedGenes]="pendingPinnedGenes"
[pinnedGenes]="pinnedItems"
[pendingPinnedGenes]="pendingPinnedItems"
[maxPinnedGenes]="maxPinnedGenes"
></gene-comparison-tool-pinned-genes-modal>
</div>
Expand Down
10 changes: 5 additions & 5 deletions ...app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ describe('Component: GeneComparisonToolComponent', () => {
fixture.detectChanges();

expect(component.genes).toEqual([comparisonGeneMock1, comparisonGeneMock2]);
expect(component.pinnedGenes).toEqual([comparisonGeneMock1]);
expect(component.pinnedItems).toEqual([comparisonGeneMock1]);
flush();
}));

Expand Down Expand Up @@ -190,15 +190,15 @@ describe('Component: GeneComparisonToolComponent', () => {

component.clearPinnedGenes();
fixture.detectChanges();
expect(component.pinnedGenes.length).toEqual(0);
expect(component.pinnedItems.length).toEqual(0);

component.onPinGeneClick(comparisonGeneMock1);
fixture.detectChanges();
expect(component.pinnedGenes.length).toEqual(1);
expect(component.pinnedItems.length).toEqual(1);

component.onUnPinGeneClick(comparisonGeneMock1, true);
fixture.detectChanges();
expect(component.pinnedGenes.length).toEqual(0);
expect(component.pinnedItems.length).toEqual(0);
});

it('should clear pinned genes', fakeAsync(() => {
Expand All @@ -207,7 +207,7 @@ describe('Component: GeneComparisonToolComponent', () => {

component.clearPinnedGenes();
fixture.detectChanges();
expect(component.pinnedGenes.length).toEqual(0);
expect(component.pinnedItems.length).toEqual(0);
flush();
}));

Expand Down
113 changes: 58 additions & 55 deletions src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -100,10 +100,10 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
lastPinnedCategory = '';
lastPinnedSubCategory = '';

pinnedGenes: GCTGene[] = [];
pinnedItems: GCTGene[] = [];
uniquePinnedGenesCount = 0;
pinnedGenesCache: GCTGene[] = [];
pendingPinnedGenes: GCTGene[] = [];
pinnedItemsCache: GCTGene[] = [];
pendingPinnedItems: GCTGene[] = [];
maxPinnedGenes = 50;

/* ----------------------------------------------------------------------- */
Expand Down Expand Up @@ -240,53 +240,56 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
getGeneProperty(gene: GCTGene, property: string) {
return property.split('.').reduce((o: any, i: any) => o[i], gene);
}

initData(genes: GCTGene[]) {
// hide brain region columns initially
this.brainRegionsColumns.forEach(c => c.visible = false);

const pinnedGenes: GCTGene[] = [];

const currentPinnedGenesCache = this.pinnedGenesCache;

let previousPins: (string | undefined)[] = [];
getUid(item: GCTGene) {
// rna is just the ensembl gene id
// protein is a combination of ensembl gene id and uniprotid
if (this.category === 'RNA - Differential Expression')
return item.ensembl_gene_id;
else
return item.ensembl_gene_id + item.uniprotid;
}

getPreviousPins() {
if (this.currentCategoriesMatchLastPinnedCategories()) {
// no need to load from cache if it was last pinned from the current page
// previousPins = this.getUrlParam('pinned', true);
previousPins = currentPinnedGenesCache.map((g: GCTGene) => g.uid);
// load from cache since it has been previously cached
return this.pinnedItemsCache.map((g: GCTGene) => g.uid);
} else {
// if it is the initial load, the categories will not match since the last pinned categories
// will be empty strings. In this case we want to check the url to see if this was a shared url
// with pinned genes/proteins.

// since the last pinned category is blank, we don't need to check the subcategory
// if the last pinned category is blank, then this means this is the initial load
// note: we only need to check the category for blank but subcategory will also be blank
// In this scenario, we check the url to see if this was a shared url with pinned genes/proteins
if (this.lastPinnedCategory === '') {
// check the url for pinned genes/proteins
previousPins = this.getUrlParam('pinned', true);
this.setLastPinnedCategories();
return this.getUrlParam('pinned', true);
} else {
// categories don't match, so grab it from the cache
if (this.category === 'RNA - Differential Expression') {
previousPins = currentPinnedGenesCache
.map((g: GCTGene) => g.uid?.substring(0, 15));
return this.pinnedItemsCache.map((g: GCTGene) => g.ensembl_gene_id);
} else {
previousPins = currentPinnedGenesCache.map((g: GCTGene) => g.uid);
return this.pinnedItemsCache.map((g: GCTGene) => g.uid);
}
}
}

}

initData(genes: GCTGene[]) {
// hide brain region columns initially
this.brainRegionsColumns.forEach(c => c.visible = false);

const pinnedGenes: GCTGene[] = [];

// load the previous pins and format previousPins to match the current category
const previousPins = this.getPreviousPins();

genes.forEach((gene: GCTGene) => {
gene.uid = gene.ensembl_gene_id;
gene.uid = this.getUid(gene);
gene.search_array = [
gene.ensembl_gene_id.toLowerCase(),
gene.hgnc_symbol.toLowerCase(),
];

if (this.category === 'Protein - Differential Expression') {
// for this category, the uid will be ensg + uniprotid
gene.uid += gene.uniprotid;

gene.search_array.push(gene.uniprotid?.toLowerCase() || '');

// if there is a match on uid or ensembl_gene_id, add it to pinnedGenes
Expand Down Expand Up @@ -356,16 +359,16 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
'Protein - Differential Expression' === this.category &&
this.uniquePinnedGenesCount > this.maxPinnedGenes
) {
this.pendingPinnedGenes = pinnedGenes;
this.pendingPinnedItems = pinnedGenes;
this.pinnedGenesModal.show();
} else {
this.pinnedGenes = [];
this.pendingPinnedGenes = [];
this.pinnedItems = [];
this.pendingPinnedItems = [];
this.uniquePinnedGenesCount = this.getCountOfUniqueGenes();
this.pinGenes(pinnedGenes);
}
} else {
this.pinnedGenes = [];
this.pinnedItems = [];
}

this.genes = genes;
Expand Down Expand Up @@ -659,16 +662,16 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
}

setPinnedGenesCache(genes: GCTGene[]) {
this.pinnedGenesCache = genes;
this.pinnedItemsCache = genes;
}

clearPinnedGenesCache() {
this.pinnedGenesCache = [];
this.pinnedItemsCache = [];
this.uniquePinnedGenesCount = this.getCountOfUniqueGenes();
}

refreshPinnedGenes() {
this.setPinnedGenesCache(this.pinnedGenes);
this.setPinnedGenesCache(this.pinnedItems);
this.filter();
this.updateUrl();
}
Expand All @@ -684,11 +687,11 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
}

pinGene(gene: GCTGene, refresh = true) {
const index = this.pinnedGenes.findIndex(
const index = this.pinnedItems.findIndex(
(g: GCTGene) => g.uid === gene.uid
);
if (this.category === 'RNA - Differential Expression') {
if (index > -1 || this.pinnedGenes.length >= this.maxPinnedGenes)
if (index > -1 || this.pinnedItems.length >= this.maxPinnedGenes)
return;
} else {
// the same unique id exists, so don't allow it to be added
Expand All @@ -698,7 +701,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
// border condition: if we are at the max allowable pinned genes
// check if the pinned genes list has a gene with the ensembl id,
// in which case the protein can be added
const ensemblIndex = this.pinnedGenes.findIndex(
const ensemblIndex = this.pinnedItems.findIndex(
(g: GCTGene) => g.ensembl_gene_id === gene.ensembl_gene_id
);
if (ensemblIndex < 0) {
Expand All @@ -708,7 +711,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
}
}

this.pinnedGenes.push(gene);
this.pinnedItems.push(gene);

if (refresh) {
this.clearPinnedGenesCache();
Expand All @@ -720,7 +723,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
// this method is used for protein views since there can be multiple pinned proteins
// that have the same ensg value but different uniprotids
// so this will return the count of genes with unique ensgs
const uids = this.pinnedGenes.map(g => g.ensembl_gene_id);
const uids = this.pinnedItems.map(g => g.ensembl_gene_id);
const uniqueUids = new Set(uids);
return uniqueUids.size;
}
Expand Down Expand Up @@ -752,7 +755,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
}

pinGenes(genes: GCTGene[]) {
const remaining = this.maxPinnedGenes - this.pinnedGenes.length;
const remaining = this.maxPinnedGenes - this.pinnedItems.length;

if (remaining < 1) {
return;
Expand Down Expand Up @@ -793,7 +796,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
}

ensgExistsInProteins(ensemblGeneId: string) {
const ensemblIndex = this.pinnedGenes.findIndex(
const ensemblIndex = this.pinnedItems.findIndex(
(g: GCTGene) => g.ensembl_gene_id === ensemblGeneId
);
if (ensemblIndex < 0) {
Expand Down Expand Up @@ -837,15 +840,15 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
onUnPinGeneClick(gene: GCTGene, refresh = true) {
this.setLastPinnedCategories();

const index = this.pinnedGenes.findIndex(
const index = this.pinnedItems.findIndex(
(g: GCTGene) => g.uid === gene.uid
);

if (index === -1) {
return;
}

this.pinnedGenes.splice(index, 1);
this.pinnedItems.splice(index, 1);

if (refresh) {
this.clearPinnedGenesCache();
Expand All @@ -862,22 +865,22 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
}

clearPinnedGenes() {
this.pinnedGenes = [];
this.pinnedItems = [];
this.clearPinnedGenesCache();
this.refreshPinnedGenes();
}

getPinnedEnsemblGeneIds() {
return this.pinnedGenes.map((g: GCTGene) => g.ensembl_gene_id);
return this.pinnedItems.map((g: GCTGene) => g.ensembl_gene_id);
}

getPinnedUniProtIds() {
return this.pinnedGenes.map((g: GCTGene) => g.uniprotid);
return this.pinnedItems.map((g: GCTGene) => g.uniprotid);
}

getPinDisabledStatus() {
if (this.category === 'RNA - Differential Expression')
return this.pinnedGenes.length >= this.maxPinnedGenes;
return this.pinnedItems.length >= this.maxPinnedGenes;
else {
// default to showing pin all button for protein view
return false;
Expand All @@ -904,13 +907,13 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {

onPinnedGenesModalChange(response: boolean) {
if (response) {
this.pinnedGenes = [];
this.pinGenes(this.pendingPinnedGenes);
this.pinnedItems = [];
this.pinGenes(this.pendingPinnedItems);
} else {
this.category = this.categories[0].value;
this.onCategoryChange();
}
this.pendingPinnedGenes = [];
this.pendingPinnedItems = [];
}

/* ----------------------------------------------------------------------- */
Expand Down Expand Up @@ -945,8 +948,8 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
params['sortOrder'] = this.sortOrder;
}

if (this.pinnedGenes.length > 0) {
params['pinned'] = this.pinnedGenes.map(
if (this.pinnedItems.length > 0) {
params['pinned'] = this.pinnedItems.map(
(g: GCTGene) => g.uid
);
params['pinned'].sort();
Expand Down Expand Up @@ -1167,7 +1170,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
];
const data: any[][] = [];

this.pinnedGenes.forEach((g: GCTGene) => {
this.pinnedItems.forEach((g: GCTGene) => {
const baseRow = [
g.ensembl_gene_id,
g.hgnc_symbol,
Expand Down

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