Additional Resources
- These external sites provide additional useful information for exploring AD targets.
+ These external sites provide additional information about therapeutic targets for AD and related dementias.
= 10
- if (event.field === 'sm_druggability_display_value'
- || event.field === 'safety_rating_display_value'
- || event.field === 'ab_modality_display_value') {
- let nA = parseInt(a.split(':')[0], 10);
- let nB = parseInt(b.split(':')[0], 10);
-
- nA = !isNaN(nA) ? nA : 999 * event.order;
- nB = !isNaN(nB) ? nB : 999 * event.order;
-
- result = nA < nB ? -1 : nA > nB ? 1 : 0;
- } else {
- result = a.localeCompare(b);
- }
+ result = a.localeCompare(b);
} else {
result = a < b ? -1 : a > b ? 1 : 0;
}
diff --git a/src/app/models/AdditionalResource.ts b/src/app/models/ResourceCard.ts
similarity index 69%
rename from src/app/models/AdditionalResource.ts
rename to src/app/models/ResourceCard.ts
index 35d2aa82..f6f76cab 100644
--- a/src/app/models/AdditionalResource.ts
+++ b/src/app/models/ResourceCard.ts
@@ -1,4 +1,4 @@
-export interface AdditionalResource {
+export interface ResourceCard {
title: string;
description: string;
linkText: string;
diff --git a/src/app/models/genes.ts b/src/app/models/genes.ts
index 6f8e5939..7f11a466 100644
--- a/src/app/models/genes.ts
+++ b/src/app/models/genes.ts
@@ -23,7 +23,6 @@ export interface TargetNomination {
input_data: string;
validation_study_details: string;
initial_nomination: number;
- //
team_data?: Team;
}
@@ -41,7 +40,7 @@ export interface Druggability {
sm_druggability_bucket: number;
safety_bucket: number;
abability_bucket: number;
- pharos_class: string;
+ pharos_class?: string[];
// classification should really be named sm_druggability_bucket_definition
classification: string;
safety_bucket_definition: string;
@@ -55,6 +54,7 @@ export interface Gene {
summary: string;
hgnc_symbol: string;
alias: string[];
+ uniprotkb_accessions: string[];
is_igap: boolean;
is_eqtl: boolean;
is_any_rna_changed_in_ad_brain: boolean;
@@ -63,7 +63,7 @@ export interface Gene {
protein_brain_change_studied: boolean;
target_nominations: TargetNomination[] | null;
median_expression: MedianExpression[];
- druggability: Druggability[];
+ druggability: Druggability;
total_nominations: number | null;
is_adi: boolean;
is_tep: boolean;
@@ -84,10 +84,7 @@ export interface Gene {
similar_genes_network?: SimilarGenesNetwork;
// Similar table (not in mongo document)
- ab_modality_display_value?: string;
- safety_rating_display_value?: string;
- sm_druggability_display_value?: string;
- pharos_class_display_value?: string;
+ pharos_class_display_value?: string[];
is_any_rna_changed_in_ad_brain_display_value?: string;
is_any_protein_changed_in_ad_brain_display_value?: string;
nominated_target_display_value?: boolean;
diff --git a/src/app/models/index.ts b/src/app/models/index.ts
index 06fdfa87..3c411cf3 100644
--- a/src/app/models/index.ts
+++ b/src/app/models/index.ts
@@ -15,4 +15,4 @@ export * from './charts';
export * from './scores';
export * from './GCTColumn';
export * from './biodomains';
-export * from './AdditionalResource';
\ No newline at end of file
+export * from './ResourceCard';
\ No newline at end of file
diff --git a/src/app/testing/gene-mocks.ts b/src/app/testing/gene-mocks.ts
index c26bdea0..0edc07b0 100644
--- a/src/app/testing/gene-mocks.ts
+++ b/src/app/testing/gene-mocks.ts
@@ -28,6 +28,7 @@ export const geneMock1: Gene = {
'Moesin (for membrane-organizing extension spike protein) is a member of the ERM family which includes ezrin and radixin. ERM proteins appear to function as cross-linkers between plasma membranes and actin-based cytoskeletons. Moesin is localized to filopodia and other membranous protrusions that are important for cell-cell recognition and signaling and for cell movement. [provided by RefSeq, Jul 2008].',
hgnc_symbol: 'MSN',
alias: ['HEL70', 'IMD50'],
+ uniprotkb_accessions: [],
is_igap: false,
is_eqtl: false,
is_any_rna_changed_in_ad_brain: true,
@@ -204,20 +205,18 @@ export const geneMock1: Gene = {
tissue: 'STG',
},
],
- druggability: [
- {
- sm_druggability_bucket: 3,
- safety_bucket: 4,
- abability_bucket: 3,
- pharos_class: 'Tbio',
- classification:
- 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
- safety_bucket_definition:
- 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
- abability_bucket_definition:
- 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
- },
- ],
+ druggability: {
+ sm_druggability_bucket: 3,
+ safety_bucket: 4,
+ abability_bucket: 3,
+ pharos_class: ['Tbio'],
+ classification:
+ 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+ safety_bucket_definition:
+ 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+ abability_bucket_definition:
+ 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+ },
total_nominations: 5,
rna_differential_expression: [
{
@@ -2986,6 +2985,7 @@ export const geneMock2: Gene = {
'PLEC1b',
'PLTN',
],
+ uniprotkb_accessions: [],
is_igap: false,
is_eqtl: true,
is_any_rna_changed_in_ad_brain: true,
@@ -3127,20 +3127,18 @@ export const geneMock2: Gene = {
tissue: 'STG',
},
],
- druggability: [
- {
- sm_druggability_bucket: 3,
- safety_bucket: 4,
- abability_bucket: 3,
- pharos_class: 'Tbio',
- classification:
- 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
- safety_bucket_definition:
- 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
- abability_bucket_definition:
- 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
- },
- ],
+ druggability: {
+ sm_druggability_bucket: 3,
+ safety_bucket: 4,
+ abability_bucket: 3,
+ pharos_class: ['Tbio'],
+ classification:
+ 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+ safety_bucket_definition:
+ 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+ abability_bucket_definition:
+ 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+ },
total_nominations: 3,
is_adi: false,
is_tep: true,
@@ -3164,6 +3162,7 @@ export const geneMock3: Gene = {
'p59Hck',
'p61Hck',
],
+ uniprotkb_accessions: [],
is_igap: false,
is_eqtl: true,
is_any_rna_changed_in_ad_brain: true,
@@ -3254,20 +3253,18 @@ export const geneMock3: Gene = {
tissue: 'STG',
},
],
- druggability: [
- {
- sm_druggability_bucket: 3,
- safety_bucket: 4,
- abability_bucket: 3,
- pharos_class: 'Tbio',
- classification:
- 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
- safety_bucket_definition:
- 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
- abability_bucket_definition:
- 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
- },
- ],
+ druggability: {
+ sm_druggability_bucket: 3,
+ safety_bucket: 4,
+ abability_bucket: 3,
+ pharos_class: ['Tbio'],
+ classification:
+ 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+ safety_bucket_definition:
+ 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+ abability_bucket_definition:
+ 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+ },
total_nominations: null,
is_adi: false,
is_tep: true,
@@ -3372,6 +3369,7 @@ export const nominatedGeneMock1: Gene = {
summary: '',
hgnc_symbol: 'MSN',
alias: [],
+ uniprotkb_accessions: [],
is_igap: false,
is_eqtl: false,
is_any_rna_changed_in_ad_brain: false,
@@ -3437,20 +3435,18 @@ export const nominatedGeneMock1: Gene = {
},
],
median_expression: [],
- druggability: [
- {
- sm_druggability_bucket: 3,
- safety_bucket: 4,
- abability_bucket: 3,
- pharos_class: 'Tbio',
- classification:
- 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
- safety_bucket_definition:
- 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
- abability_bucket_definition:
- 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
- },
- ],
+ druggability: {
+ sm_druggability_bucket: 3,
+ safety_bucket: 4,
+ abability_bucket: 3,
+ pharos_class: ['Tbio'],
+ classification:
+ 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+ safety_bucket_definition:
+ 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+ abability_bucket_definition:
+ 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+ },
total_nominations: 4,
is_adi: false,
is_tep: false,
@@ -3469,6 +3465,7 @@ export const noHGNCgeneMock: Gene = {
summary: '',
hgnc_symbol: '',
alias: [],
+ uniprotkb_accessions: [],
is_igap: false,
is_eqtl: false,
is_any_rna_changed_in_ad_brain: false,
@@ -3539,20 +3536,18 @@ export const noHGNCgeneMock: Gene = {
},
],
median_expression: [],
- druggability: [
- {
- sm_druggability_bucket: 3,
- safety_bucket: 4,
- abability_bucket: 3,
- pharos_class: 'Tbio',
- classification:
- 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
- safety_bucket_definition:
- 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
- abability_bucket_definition:
- 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
- },
- ],
+ druggability: {
+ sm_druggability_bucket: 3,
+ safety_bucket: 4,
+ abability_bucket: 3,
+ pharos_class: ['Tbio'],
+ classification:
+ 'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+ safety_bucket_definition:
+ 'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+ abability_bucket_definition:
+ 'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+ },
total_nominations: 4,
is_adi: false,
is_tep: false,
diff --git a/src/server/api.ts b/src/server/api.ts
index b37be822..fc47c37c 100644
--- a/src/server/api.ts
+++ b/src/server/api.ts
@@ -38,30 +38,37 @@ const database = { url: '' };
doc && ('doc => ' + util.inspect(doc)), '\n');
}); */
-console.log(process.env);
-console.log(process.env.MONGODB_HOST);
-console.log(process.env.MONGODB_PORT);
-
// Set the database url
if (
process.env.MONGODB_HOST &&
process.env.MONGODB_PORT &&
process.env.APP_ENV
) {
- const results = awsParamStore.getParametersSync(
- [
- '/agora-' + process.env.APP_ENV + '/MongodbUsername',
- '/agora-' + process.env.APP_ENV + '/MongodbPassword',
- ],
- { region: 'us-east-1' }
- );
+ let dbUser: string | undefined;
+ let dbPass: string | undefined;
+ if (process.env.APP_ENV === 'e2e') {
+ dbUser = process.env.DB_USER;
+ dbPass = process.env.DB_PASS;
+ } else {
+ const results = awsParamStore.getParametersSync(
+ [
+ '/agora-' + process.env.APP_ENV + '/MongodbUsername',
+ '/agora-' + process.env.APP_ENV + '/MongodbPassword',
+ ],
+ { region: 'us-east-1' }
+ );
+ if (results && results.Parameters) {
+ dbUser = results.Parameters[1]['Value'];
+ dbPass = results.Parameters[0]['Value'];
+ }
+ }
- if (results && results.Parameters) {
+ if (dbUser && dbPass) {
database.url =
'mongodb://' +
- results.Parameters[1]['Value'] +
+ dbUser +
':' +
- results.Parameters[0]['Value'] +
+ dbPass +
'@' +
process.env.MONGODB_HOST +
':' +
diff --git a/src/server/models/genes.ts b/src/server/models/genes.ts
index a4fe82b2..e714e078 100644
--- a/src/server/models/genes.ts
+++ b/src/server/models/genes.ts
@@ -53,7 +53,7 @@ const DruggabilitySchema = new Schema({
sm_druggability_bucket: { type: Number, required: true },
safety_bucket: { type: Number, required: true },
abability_bucket: { type: Number, required: true },
- pharos_class: { type: String, required: true },
+ pharos_class: { type: [String], required: true },
classification: { type: String, required: true },
safety_bucket_definition: { type: String, required: true },
abability_bucket_definition: { type: String, required: true },
@@ -67,6 +67,7 @@ const GeneSchema = new Schema(
summary: { type: String, required: true },
hgnc_symbol: { type: String, required: true },
alias: [{ type: String, required: true }],
+ uniprotkb_accessions: [{ type: String, required: true }],
is_igap: { type: Boolean, required: true },
is_eqtl: { type: Boolean, required: true },
is_any_rna_changed_in_ad_brain: { type: Boolean, required: true },
@@ -75,7 +76,7 @@ const GeneSchema = new Schema(
protein_brain_change_studied: { type: Boolean, required: true },
target_nominations: { type: [TargetNominationSchema], required: true },
median_expression: { type: [MedianExpressionSchema], required: true },
- druggability: { type: [DruggabilitySchema], required: true },
+ druggability: { type: DruggabilitySchema, required: true },
total_nominations: { type: Number, required: true },
ensembl_info: { type: EnsemblInfoSchema, required: true }
},
diff --git a/tests/nominated-targets.spec.ts b/tests/nominated-targets.spec.ts
index d350f668..757c8a80 100644
--- a/tests/nominated-targets.spec.ts
+++ b/tests/nominated-targets.spec.ts
@@ -9,57 +9,4 @@ test.describe('specific viewport block', () => {
// Expect a title "to contain" a substring.
await expect(page).toHaveTitle('Nominated Targets | Candidate genes for AD treatment or prevention');
});
-
- test('has correct sort on druggability columns', async ({ page }) => {
- await page.goto('/genes/nominated-targets');
-
- await expect(page.locator('table')).toBeVisible();
-
- await page.locator('#pr_id_3 span').click();
-
- await page.getByLabel('Nominations').click();
- await page.getByLabel('Year First Nominated').click();
- await page.getByLabel('Nominating Teams').click();
- await page.getByLabel('Cohort Study').click();
- await page.getByLabel('Small Molecule Druggability').click();
- await page.getByLabel('Safety Rating').click();
- await page.getByLabel('Antibody Modality').click();
-
- // sort forward on small molecule druggability
- await page.getByRole('cell', { name: 'Small Molecule Druggability' }).click();
-
- const row = page.locator('table tr:nth-child(2)');
- let cell = row.getByRole('cell').nth(1);
- await expect(cell).not.toContainText('No Value');
-
- // sort reverse on small molecule druggability
- await page.getByRole('cell', { name: 'Small Molecule Druggability' }).click();
-
- cell = row.getByRole('cell').nth(1);
- await expect(cell).not.toContainText('No Value');
-
- // sort forward on safety rating
- await page.getByRole('cell', { name: 'Safety Rating' }).click();
-
- cell = row.getByRole('cell').nth(2);
- await expect(cell).not.toContainText('No Value');
-
- // sort reverse on safety rating
- await page.getByRole('cell', { name: 'Safety Rating' }).click();
-
- cell = row.getByRole('cell').nth(2);
- await expect(cell).not.toContainText('No Value');
-
- // sort forward on antibody modality
- await page.getByRole('cell', { name: 'Antibody Modality' }).click();
-
- cell = row.getByRole('cell').nth(3);
- await expect(cell).not.toContainText('No Value');
-
- // sort reverse on antibody modality
- await page.getByRole('cell', { name: 'Antibody Modality' }).click();
-
- cell = row.getByRole('cell').nth(3);
- await expect(cell).not.toContainText('No Value');
- });
});
\ No newline at end of file
diff --git a/tests/similar-genes.spec.ts b/tests/similar-genes.spec.ts
index c0292a09..4796e075 100644
--- a/tests/similar-genes.spec.ts
+++ b/tests/similar-genes.spec.ts
@@ -20,12 +20,5 @@ test.describe('specific viewport block', () => {
const cell = await page.getByRole('row').nth(1).getByRole('cell').nth(1).innerText();
expect(cell).not.toBe('');
-
-
- // sort reverse on small molecule druggability
- await page.getByRole('cell', { name: 'Nominated Target' }).click();
-
- const cell2 = await page.getByRole('row').nth(1).getByRole('cell').nth(1).innerText();
- expect(cell2).not.toBe('');
});
});
\ No newline at end of file