{{ gene.hgnc_symbol || gene.ensembl_gene_id }}
-
+
({{ gene.uniprotid }})
{{ gene.hgnc_symbol || gene.ensembl_gene_id }}
-
+
({{ gene.uniprotid }})
diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts
index faba1600..ace93c52 100644
--- a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts
+++ b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts
@@ -14,6 +14,8 @@ import { MessageService, SortEvent } from 'primeng/api';
import { Table } from 'primeng/table';
import { Checkbox } from 'primeng/checkbox';
+import * as helpers from './gene-comparison-tool.helpers';
+
import {
GeneComparisonToolComponent,
GeneComparisonToolDetailsPanelComponent,
@@ -24,7 +26,7 @@ import {
import { ApiService, HelperService } from '../../../../core/services';
import { GeneService } from '../../../../features/genes/services';
import { routes } from '../../../../app.routing';
-import { comparisonGeneMock1, comparisonGeneMock2 } from '../../../../testing';
+import { comparisonGeneEmptyHGNCMock, comparisonGeneMock1, comparisonGeneMock2 } from '../../../../testing';
const DEFAULT_SIGNIFICANCE_THRESHOLD = 0.05;
@@ -506,5 +508,15 @@ describe('Component: GeneComparisonToolComponent', () => {
expectSignificanceThresholdIsApplied(newValue);
}));
+
+ it('should have a label for SRM popup', () => {
+ const label = helpers.getGeneLabelForSRM(comparisonGeneMock1);
+ const expected = 'MSN - ENSG00000147065';
+ expect(label).toBe(expected);
+
+ const label2 = helpers.getGeneLabelForSRM(comparisonGeneEmptyHGNCMock);
+ const expected2 = 'ENSG00000147065';
+ expect(label2).toBe(expected2);
+ });
});
});
diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.helpers.ts b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.helpers.ts
index 2f3b544f..467c07a3 100644
--- a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.helpers.ts
+++ b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.helpers.ts
@@ -68,6 +68,12 @@ export function getGeneLabelForProteinDifferentialExpression(gene: GCTGene) {
gene.ensembl_gene_id;
}
+export function getGeneLabelForSRM(gene: GCTGene) {
+ let label = gene.hgnc_symbol ? `${ gene.hgnc_symbol } - ` : '';
+ label += gene.ensembl_gene_id;
+ return label;
+}
+
export function getScore(columnName: string, gene: GCTGene) {
columnName = columnName.toUpperCase();
if (columnName === 'RISK SCORE')
@@ -140,17 +146,13 @@ export const getDetailsPanelData = function (
};
if (category === 'Protein - Differential Expression') {
- data.label = getGeneLabelForProteinDifferentialExpression(gene);
+ if (subCategory === 'SRM') {
+ data.label = getGeneLabelForSRM(gene);
+ } else {
+ data.label = getGeneLabelForProteinDifferentialExpression(gene);
+ }
data.heading = 'Differential Protein Expression (' + tissue.name + ')';
data.allTissueLink = false;
-
- // if ('TMT' === subCategory) {
- // data.min = -35;
- // data.max = 35;
- // } else {
- // data.min = -4;
- // data.max = 4;
- // }
} else {
data.label = getGeneLabel(gene);
data.heading = 'Differential RNA Expression (' + tissue.name + ')';
diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.variables.ts b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.variables.ts
index 26c90db2..62eaf5ae 100644
--- a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.variables.ts
+++ b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.variables.ts
@@ -32,13 +32,17 @@ export const subCategories: { [key: string]: GCTSelectOption[] } = {
],
'Protein - Differential Expression': [
{
- label: 'Label-free Quantification (LFQ)',
- value: 'LFQ',
+ label: 'Targeted Selected Reaction Monitoring (SRM)',
+ value: 'SRM',
},
{
- label: 'Tandem Mass Tag (TMT)',
+ label: 'Genome-wide Tandem Mass Tag (TMT)',
value: 'TMT',
},
+ {
+ label: 'Genome-wide Label-free Quantification (LFQ)',
+ value: 'LFQ',
+ },
],
};
diff --git a/src/app/testing/gene-comparison-tool-mocks.ts b/src/app/testing/gene-comparison-tool-mocks.ts
index 4266f4b5..a3b6de95 100644
--- a/src/app/testing/gene-comparison-tool-mocks.ts
+++ b/src/app/testing/gene-comparison-tool-mocks.ts
@@ -173,6 +173,92 @@ export const comparisonGeneMock2: GCTGene = {
multi_omics_score: 1.3
};
+export const comparisonGeneEmptyHGNCMock: GCTGene = {
+ ensembl_gene_id: 'ENSG00000147065',
+ hgnc_symbol: '',
+ tissues: [
+ {
+ name: 'ACC',
+ logfc: -0.0144678061734664,
+ adj_p_val: 0.893263674388766,
+ ci_l: -0.133332670728704,
+ ci_r: 0.104397058381771,
+ },
+ {
+ name: 'CBE',
+ logfc: -0.0751554371582435,
+ adj_p_val: 0.530889774959758,
+ ci_l: -0.247449816301241,
+ ci_r: 0.0971389419847545,
+ },
+ {
+ name: 'DLPFC',
+ logfc: 0.0349940606540153,
+ adj_p_val: 0.604655110745068,
+ ci_l: -0.0564780903179806,
+ ci_r: 0.126466211626011,
+ },
+ {
+ name: 'FP',
+ logfc: 0.235992067764791,
+ adj_p_val: 0.0293685880983672,
+ ci_l: 0.0813918568317721,
+ ci_r: 0.390592278697809,
+ },
+ {
+ name: 'IFG',
+ logfc: 0.393613393602616,
+ adj_p_val: 0.0000468370819411619,
+ ci_l: 0.236604395922642,
+ ci_r: 0.550622391282589,
+ },
+ {
+ name: 'PCC',
+ logfc: 0.0870992749746771,
+ adj_p_val: 0.275931011190809,
+ ci_l: -0.0292845799777793,
+ ci_r: 0.203483129927133,
+ },
+ {
+ name: 'PHG',
+ logfc: 0.6626818751507,
+ adj_p_val: 9.688467425132421e-14,
+ ci_l: 0.506746460875332,
+ ci_r: 0.818617289426068,
+ },
+ {
+ name: 'STG',
+ logfc: 0.421363564302165,
+ adj_p_val: 0.0000165742209158385,
+ ci_l: 0.26315969917125,
+ ci_r: 0.57956742943308,
+ },
+ {
+ name: 'TCX',
+ logfc: 0.450452869099202,
+ adj_p_val: 0.00000476005829762979,
+ ci_l: 0.275315930793305,
+ ci_r: 0.625589807405099,
+ },
+ ],
+ nominations: {
+ count: 4,
+ year: 2018,
+ teams: ['Chang Lab', 'Emory', 'MSSM', 'MSSM'],
+ studies: ['ROSMAP', 'Kronos', 'MSBB', 'ACT', 'BLSA', 'Banner'],
+ inputs: ['Genetics', 'RNA', 'Protein'],
+ programs: ['Community Contributed', 'AMP-AD'],
+ validations: [
+ 'validation studies ongoing',
+ 'not prioritized for experimental validation',
+ ],
+ },
+ associations: [3, 4],
+ target_risk_score: 3.1,
+ genetics_score: 2.2,
+ multi_omics_score: 3.3
+};
+
export const gctDetailsPanelDataMock: GCTDetailsPanelData = {
label: 'label',
heading: 'heading',
diff --git a/src/server/api.ts b/src/server/api.ts
index 468f58f7..b37be822 100644
--- a/src/server/api.ts
+++ b/src/server/api.ts
@@ -38,23 +38,9 @@ const database = { url: '' };
doc && ('doc => ' + util.inspect(doc)), '\n');
}); */
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
console.log(process.env);
console.log(process.env.MONGODB_HOST);
console.log(process.env.MONGODB_PORT);
-console.log('DONE!');
-console.log('DONE!');
-console.log('DONE!');
-console.log('DONE!');
-console.log('DONE!');
-console.log('DONE!');
// Set the database url
if (
diff --git a/src/server/components/comparison.ts b/src/server/components/comparison.ts
index bd147698..e3e4f995 100644
--- a/src/server/components/comparison.ts
+++ b/src/server/components/comparison.ts
@@ -18,6 +18,7 @@ import {
ProteomicsLFQCollection,
ProteomicsTMTCollection,
Team,
+ ProteomicsSRMCollection,
} from '../models';
import { BioDomains, TargetNomination, Scores } from '../../app/models';
@@ -208,11 +209,19 @@ export async function getProteinComparisonGenes(method: string) {
.lean()
.sort({ hgnc_symbol: 1, tissue: 1 })
.exec();
- } else {
+ } else if ('LFQ' === method) {
items = await ProteomicsLFQCollection.find()
.lean()
.sort({ hgnc_symbol: 1, tissue: 1 })
.exec();
+ } else if ('SRM' === method) {
+ items = await ProteomicsSRMCollection.find()
+ .lean()
+ .sort({ hgnc_symbol: 1, tissue: 1 })
+ .exec();
+ } else {
+ // TODO capture corner scenarios
+ throw 'unknown method selected: ' + method;
}
if (items) {
diff --git a/tests/gene-comparison-tool.spec.ts b/tests/gene-comparison-tool.spec.ts
new file mode 100644
index 00000000..f203600a
--- /dev/null
+++ b/tests/gene-comparison-tool.spec.ts
@@ -0,0 +1,30 @@
+import { test, expect } from '@playwright/test';
+
+test.describe('specific viewport block', () => {
+ test.slow();
+ test.use({ viewport: { width: 1600, height: 1200 } });
+
+ test('has title', async ({ page }) => {
+ await page.goto('/genes/comparison?category=Protein+-+Differential+Expression');
+
+ // wait for page to load (i.e. spinner to disappear)
+ await expect(page.locator('div:nth-child(4) > div > .spinner'))
+ .not.toBeVisible({ timeout: 250000});
+
+ // Expect a title "to contain" a substring.
+ await expect(page).toHaveTitle('Gene Comparison | Visual comparison tool for AD genes');
+ });
+
+ test('sub-category is SRM by default', async ({ page }) => {
+ // set category for Protein - Differential Expression
+ await page.goto('/genes/comparison?category=Protein+-+Differential+Expression');
+
+ // wait for page to load (i.e. spinner to disappear)
+ await expect(page.locator('div:nth-child(4) > div > .spinner'))
+ .not.toBeVisible({ timeout: 150000});
+
+ // expect sub-category dropdown to be SRM
+ const dropdown = page.locator('#subCategory');
+ await expect(dropdown).toHaveText('Targeted Selected Reaction Monitoring (SRM)');
+ });
+});