adding remaining api methods via openapi

Sage-Bionetworks · Oct 6, 2024 · f23c33d · f23c33d
1 parent 4c9a8fc
commit f23c33d
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Showing 75 changed files with 2,299 additions and 234 deletions.
diff --git a/apps/agora/api/src/components/biodomains.ts b/apps/agora/api/src/components/biodomains.ts
@@ -3,8 +3,8 @@
 // -------------------------------------------------------------------------- //
 import { Request, Response, NextFunction } from 'express';
 import { cache, setHeaders } from '../helpers';
-import { AllBioDomainsCollection, BioDomains, BioDomainsCollection } from '../models';
-import { BioDomainInfo } from '../../app/models';
+import { AllBioDomainsCollection, BioDomainsCollection } from '../models';
+import { BioDomains, BioDomainInfo } from '@sagebionetworks/agora/api-client-angular';
 
 // -------------------------------------------------------------------------- //
 // Functions

diff --git a/apps/agora/api/src/components/comparison.ts b/apps/agora/api/src/components/comparison.ts
@@ -12,16 +12,19 @@ import {
   Gene,
   GCTGene,
   GCTGeneNominations,
-  RnaDifferentialExpression,
   RnaDifferentialExpressionCollection,
-  ProteinDifferentialExpression,
   ProteomicsLFQCollection,
   ProteomicsTMTCollection,
-  Team,
   ProteomicsSRMCollection,
 } from '../models';
-import { BioDomains, TargetNomination, Scores } from '../../app/models';
-
+import {
+  BioDomains,
+  ProteinDifferentialExpression,
+  RnaDifferentialExpression,
+  TargetNomination,
+  Team,
+} from '@sagebionetworks/agora/api-client-angular';
+import { Scores } from 'libs/agora/models';
 // -------------------------------------------------------------------------- //
 // Functions
 // -------------------------------------------------------------------------- //

diff --git a/apps/agora/api/src/components/distribution.ts b/apps/agora/api/src/components/distribution.ts
@@ -12,14 +12,21 @@ import {
   ProteomicDistributionCollection,
   OverallScoresDistributionCollection,
 } from '../models';
+import {
+  RnaDistribution,
+  Distribution,
+  OverallScores,
+  OverallScoresDistribution,
+  ProteomicsDistribution,
+} from '@sagebionetworks/agora/api-client-angular';
 
 // -------------------------------------------------------------------------- //
 // Functions
 // -------------------------------------------------------------------------- //
 
 export async function getRnaDistribution() {
   const cacheKey = 'rna-distribution';
-  let result = cache.get(cacheKey);
+  let result: RnaDistribution[] | undefined = cache.get(cacheKey);
 
   if (result) {
     return result;
@@ -33,7 +40,7 @@ export async function getRnaDistribution() {
 
 export async function getProteomicDistribution(type: string) {
   const cacheKey = 'proteomics-' + type + '-distribution';
-  let result = cache.get(cacheKey);
+  let result: ProteomicsDistribution[] | undefined = cache.get(cacheKey);
 
   if (result) {
     return result;
@@ -47,7 +54,7 @@ export async function getProteomicDistribution(type: string) {
 
 export async function getOverallScoresDistribution() {
   const cacheKey = 'overall-scores-distribution';
-  let result: any = cache.get(cacheKey);
+  let result: OverallScoresDistribution[] | undefined = cache.get(cacheKey);
 
   if (result) {
     return result;
@@ -66,7 +73,7 @@ export async function getOverallScoresDistribution() {
 
 export async function getDistribution() {
   const cacheKey = 'distribution';
-  let result: any = cache.get(cacheKey);
+  let result: Distribution | undefined = cache.get(cacheKey);
 
   if (result) {
     return result;

diff --git a/apps/agora/api/src/components/experimental-validation.ts b/apps/agora/api/src/components/experimental-validation.ts
@@ -2,7 +2,8 @@
 // Internal
 // -------------------------------------------------------------------------- //
 import { cache } from '../helpers';
-import { ExperimentalValidation, ExperimentalValidationCollection } from '../models';
+import { ExperimentalValidationCollection } from '../models';
+import { ExperimentalValidation } from 'libs/agora/models';
 
 // -------------------------------------------------------------------------- //
 // Functions

diff --git a/apps/agora/api/src/components/metabolomics.ts b/apps/agora/api/src/components/metabolomics.ts
@@ -2,7 +2,8 @@
 // Internal
 // -------------------------------------------------------------------------- //
 import { cache } from '../helpers';
-import { Metabolomics, MetabolomicsCollection } from '../models';
+import { MetabolomicsCollection } from '../models';
+import { Metabolomics } from 'libs/agora/models';
 
 // -------------------------------------------------------------------------- //
 // Functions

diff --git a/apps/agora/api/src/components/neuropathologic-correlations.ts b/apps/agora/api/src/components/neuropathologic-correlations.ts
@@ -2,7 +2,8 @@
 // Internal
 // -------------------------------------------------------------------------- //
 import { cache } from '../helpers';
-import { NeuropathologicCorrelation, NeuropathologicCorrelationCollection } from '../models';
+import { NeuropathologicCorrelationCollection } from '../models';
+import { NeuropathologicCorrelation } from 'libs/agora/models';
 
 // -------------------------------------------------------------------------- //
 // Functions

diff --git a/apps/agora/api/src/components/overall-scores.ts b/apps/agora/api/src/components/overall-scores.ts
@@ -2,7 +2,8 @@
 // Internal
 // -------------------------------------------------------------------------- //
 import { cache } from '../helpers';
-import { OverallScores, OverallScoresCollection } from '../models';
+import { OverallScoresCollection } from '../models';
+import { OverallScores } from 'libs/agora/models';
 
 // -------------------------------------------------------------------------- //
 // Functions

diff --git a/apps/agora/api/src/components/proteomics.ts b/apps/agora/api/src/components/proteomics.ts
@@ -3,11 +3,11 @@
 // -------------------------------------------------------------------------- //
 import { cache } from '../helpers';
 import {
-  ProteinDifferentialExpression,
   ProteomicsLFQCollection,
   ProteomicsSRMCollection,
   ProteomicsTMTCollection,
 } from '../models';
+import { ProteinDifferentialExpression } from 'libs/agora/models';
 
 // -------------------------------------------------------------------------- //
 // Functions

diff --git a/apps/agora/api/src/components/rna.ts b/apps/agora/api/src/components/rna.ts
@@ -2,9 +2,8 @@
 // Internal
 // -------------------------------------------------------------------------- //
 import { cache } from '../helpers';
-
-import { RnaDifferentialExpression, RnaDifferentialExpressionCollection } from '../models';
-
+import { RnaDifferentialExpressionCollection } from '../models';
+import { RnaDifferentialExpression } from 'libs/agora/models';
 // -------------------------------------------------------------------------- //
 // Functions
 // -------------------------------------------------------------------------- //

diff --git a/apps/agora/api/src/components/scores.ts b/apps/agora/api/src/components/scores.ts
@@ -2,7 +2,8 @@
 // Internal
 // -------------------------------------------------------------------------- //
 import { cache } from '../helpers';
-import { Scores, ScoresCollection } from '../models';
+import { ScoresCollection } from '../models';
+import { Scores } from 'libs/agora/models';
 
 // -------------------------------------------------------------------------- //
 // Functions

diff --git a/apps/agora/api/src/models/biodomains.ts b/apps/agora/api/src/models/biodomains.ts
@@ -1,17 +1,6 @@
-// -------------------------------------------------------------------------- //
-// External
-// -------------------------------------------------------------------------- //
 import { Schema, model } from 'mongoose';
+import { BioDomains, BioDomain, BioDomainInfo } from '@sagebionetworks/agora/api-client-angular';
 
-// -------------------------------------------------------------------------- //
-// Internal
-// -------------------------------------------------------------------------- //
-import { BioDomains, BioDomain, BioDomainInfo } from '../../app/models';
-export { BioDomains, BioDomain } from '../../app/models';
-
-// -------------------------------------------------------------------------- //
-// Schemas
-// -------------------------------------------------------------------------- //
 const BioDomainSchema = new Schema<BioDomain>({
   biodomain: { type: String, required: true },
   go_terms: { type: [String], required: true },

diff --git a/apps/agora/api/src/models/comparison.ts b/apps/agora/api/src/models/comparison.ts
@@ -2,4 +2,8 @@
 // Internal
 // -------------------------------------------------------------------------- //
 
-export { GCTGene, GCTGeneTissue, GCTGeneNominations } from '../../app/models';
+export {
+  GCTGene,
+  GCTGeneTissue,
+  GCTGeneNominations,
+} from '@sagebionetworks/agora/api-client-angular';
diff --git a/apps/agora/api/src/models/dataversion.ts b/apps/agora/api/src/models/dataversion.ts
@@ -1,5 +1,5 @@
-import { Dataversion } from '@sagebionetworks/agora/api-client-angular';
 import { Schema, model } from 'mongoose';
+import { Dataversion } from '@sagebionetworks/agora/api-client-angular';
 
 const DataVersionSchema = new Schema<Dataversion>(
   {

diff --git a/apps/agora/api/src/models/distribution.ts b/apps/agora/api/src/models/distribution.ts
@@ -10,12 +10,7 @@ import {
   RnaDistribution,
   OverallScoresDistribution,
   ProteomicsDistribution,
-} from '../../app/models';
-export {
-  RnaDistribution,
-  OverallScoresDistribution,
-  ProteomicsDistribution,
-} from '../../app/models';
+} from '@sagebionetworks/agora/api-client-angular';
 
 // -------------------------------------------------------------------------- //
 // Schemas
@@ -34,14 +29,14 @@ const RnaDistributionSchema = new Schema<RnaDistribution>(
   { collection: 'rnaboxdistribution' },
 );
 
-const ProteomicDistributionSchema = new Schema(
+const ProteomicDistributionSchema = new Schema<ProteomicsDistribution>(
   {
     type: String,
   },
   { collection: 'proteomicsboxdistribution' },
 );
 
-const OverallScoresDistributionSchema = new Schema(
+const OverallScoresDistributionSchema = new Schema<OverallScoresDistribution>(
   {
     distribution: [{ type: Number, required: true }],
     bins: [[{ type: Number, required: true }]],

diff --git a/apps/agora/api/src/models/experimental-validation.ts b/apps/agora/api/src/models/experimental-validation.ts
@@ -1,17 +1,6 @@
-// -------------------------------------------------------------------------- //
-// External
-// -------------------------------------------------------------------------- //
 import { Schema, model } from 'mongoose';
+import { ExperimentalValidation } from '@sagebionetworks/agora/api-client-angular';
 
-// -------------------------------------------------------------------------- //
-// Internal
-// -------------------------------------------------------------------------- //
-import { ExperimentalValidation } from '../../app/models';
-export { ExperimentalValidation } from '../../app/models';
-
-// -------------------------------------------------------------------------- //
-// Schemas
-// -------------------------------------------------------------------------- //
 const ExperimentalValidationSchema = new Schema<ExperimentalValidation>(
   {
     _id: { type: String, required: true },

diff --git a/apps/agora/api/src/models/gene-links.ts b/apps/agora/api/src/models/gene-links.ts
@@ -1,17 +1,6 @@
-// -------------------------------------------------------------------------- //
-// External
-// -------------------------------------------------------------------------- //
 import { Schema, model } from 'mongoose';
+import { GeneNetworkLinks } from 'libs/agora/models';
 
-// -------------------------------------------------------------------------- //
-// Internal
-// -------------------------------------------------------------------------- //
-import { GeneNetworkLinks } from '../../app/models';
-export { GeneNetworkLinks } from '../../app/models';
-
-// -------------------------------------------------------------------------- //
-// Schemas
-// -------------------------------------------------------------------------- //
 const GeneLinkSchema = new Schema<GeneNetworkLinks>(
   {
     geneA_ensembl_gene_id: { type: String, required: true },
@@ -23,7 +12,4 @@ const GeneLinkSchema = new Schema<GeneNetworkLinks>(
   { collection: 'geneslinks' },
 );
 
-// -------------------------------------------------------------------------- //
-// Models
-// -------------------------------------------------------------------------- //
 export const GeneLinkCollection = model<GeneNetworkLinks>('GeneLinksCollection', GeneLinkSchema);
diff --git a/apps/agora/api/src/models/index.ts b/apps/agora/api/src/models/index.ts
@@ -1,5 +1,6 @@
-export * from './dataversion';
+export * from './biodomains';
 export * from './comparison';
+export * from './dataversion';
 export * from './distribution';
 export * from './experimental-validation';
 export * from './gene-links';
@@ -9,6 +10,5 @@ export * from './neuropathologic-correlations';
 export * from './overall-scores';
 export * from './proteomics';
 export * from './rna';
-export * from './teams';
 export * from './scores';
-export * from './biodomains';
+export * from './teams';
diff --git a/apps/agora/api/src/models/metabolomics.ts b/apps/agora/api/src/models/metabolomics.ts
@@ -6,8 +6,7 @@ import { Schema, model } from 'mongoose';
 // -------------------------------------------------------------------------- //
 // Internal
 // -------------------------------------------------------------------------- //
-import { Metabolomics } from '../../app/models';
-export { Metabolomics } from '../../app/models';
+import { Metabolomics } from 'libs/agora/models';
 
 // -------------------------------------------------------------------------- //
 // Schemas

diff --git a/apps/agora/api/src/models/neuropathologic-correlations.ts b/apps/agora/api/src/models/neuropathologic-correlations.ts
@@ -6,8 +6,7 @@ import { Schema, model } from 'mongoose';
 // -------------------------------------------------------------------------- //
 // Internal
 // -------------------------------------------------------------------------- //
-import { NeuropathologicCorrelation } from '../../app/models';
-export { NeuropathologicCorrelation } from '../../app/models';
+import { NeuropathologicCorrelation } from '@sagebionetworks/agora/api-client-angular';
 
 // -------------------------------------------------------------------------- //
 // Schemas

diff --git a/apps/agora/api/src/models/overall-scores.ts b/apps/agora/api/src/models/overall-scores.ts
@@ -6,8 +6,10 @@ import { Schema, model } from 'mongoose';
 // -------------------------------------------------------------------------- //
 // Internal
 // -------------------------------------------------------------------------- //
-import { OverallScores } from '../../app/models';
-export { OverallScores, OverallScoresDistribution } from '../../app/models';
+import {
+  OverallScores,
+  OverallScoresDistribution,
+} from '@sagebionetworks/agora/api-client-angular';
 
 // -------------------------------------------------------------------------- //
 // Schemas

diff --git a/apps/agora/api/src/models/proteomics.ts b/apps/agora/api/src/models/proteomics.ts
@@ -6,8 +6,7 @@ import { Schema, model } from 'mongoose';
 // -------------------------------------------------------------------------- //
 // Internal
 // -------------------------------------------------------------------------- //
-import { ProteinDifferentialExpression } from '../../app/models';
-export { ProteinDifferentialExpression } from '../../app/models';
+import { ProteinDifferentialExpression } from '@sagebionetworks/agora/api-client-angular';
 
 // -------------------------------------------------------------------------- //
 // Schemas

diff --git a/apps/agora/api/src/models/rna.ts b/apps/agora/api/src/models/rna.ts
@@ -6,8 +6,7 @@ import { Schema, model } from 'mongoose';
 // -------------------------------------------------------------------------- //
 // Internal
 // -------------------------------------------------------------------------- //
-import { RnaDifferentialExpression } from '../../app/models';
-export { RnaDifferentialExpression } from '../../app/models';
+import { RnaDifferentialExpression } from '@sagebionetworks/agora/api-client-angular';
 
 // -------------------------------------------------------------------------- //
 // Schemas

diff --git a/apps/agora/api/src/models/scores.ts b/apps/agora/api/src/models/scores.ts
@@ -6,8 +6,7 @@ import { Schema, model } from 'mongoose';
 // -------------------------------------------------------------------------- //
 // Internal
 // -------------------------------------------------------------------------- //
-import { Scores } from '../../app/models';
-export { Scores } from '../../app/models';
+import { Scores } from 'libs/agora/models';
 
 // -------------------------------------------------------------------------- //
 // Schemas