Updates branch to master changes

tair · Feb 4, 2020 · 23bd352 · 23bd352
1 parent fc71dcb
commit 23bd352
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Showing 2 changed files with 19 additions and 35 deletions.
diff --git a/src/services/v1_service/service.ts b/src/services/v1_service/service.ts
@@ -1,24 +1,7 @@
-import {readFileSync} from "fs";
-import {resolve} from "path";
 import {Errors, GET, Path, QueryParam} from "typescript-rest";
-import {
-  AnnotationStatus,
-  Aspect,
-  ingestData,
-  makeAnnotationIndex, StructuredData,
-  UnstructuredText
-} from "../../utils/ingest";
+import {AnnotationStatus, Aspect, makeAnnotationIndex} from "../../utils/ingest";
 import {queryAnnotated, QueryOption, Segment, Strategy} from "../../queries/queries";
-
-// TODO use data fetcher rather than files.
-console.log("Begin reading data");
-const genesText = readFileSync(resolve("src/assets/gene-types.txt")).toString();
-const annotationsText = readFileSync(resolve("src/assets/gene_association.tair")).toString();
-const unstructuredText: UnstructuredText = { genesText, annotationsText };
-const maybeDataset = ingestData(unstructuredText);
-if (!maybeDataset) throw new Error("failed to parse data");
-const dataset: StructuredData = maybeDataset;
-console.log("Finished parsing data");
+import {getDataset} from "../../utils/data_fetcher";
 
 @Path("/api/v1")
 export class V1Service {
@@ -55,17 +38,17 @@ export class V1Service {
         }
 
         // TODO include unannotated genes
-        const [queriedGenes, queriedAnnotations] = queryAnnotated(dataset, query);
+        const [queriedGenes, queriedAnnotations] = queryAnnotated(getDataset(), query);
 
         return {annotatedGenes: queriedGenes, annotations: queriedAnnotations, unannotatedGenes: []};
     }
 
     @Path("/wgs_segments")
     @GET
     get_wgs() {
-      const totalGeneCount = Object.keys(dataset.geneIndex).length;
+      const totalGeneCount = Object.keys(getDataset().geneIndex).length;
 
-      const result = Object.entries(dataset.annotations.index)
+      const result = Object.entries(getDataset().annotations.index)
         .reduce((acc, [aspect, {all, known: {all: known_all, exp, other }, unknown}]) => {
           acc[aspect].all = all.size;
           acc[aspect].known.all = known_all.size;

diff --git a/src/utils/data_fetcher.ts b/src/utils/data_fetcher.ts
@@ -1,14 +1,10 @@
-import {GeneMap, IAnnotation, GroupedAnnotations, IGene, readData} from "./ingest";
+import {readFileSync} from "fs";
+import {resolve} from "path";
+import {ingestData, StructuredData, UnstructuredText} from "../utils/ingest";
 
-let mostRecentGeneMap: GeneMap;
-let mostRecentAnnotations: IAnnotation[];
-let mostRecentGroupedAnnotations: GroupedAnnotations<Set<IGene>>;
+let mostRecentDataset: StructuredData;
 
-export const getGeneMap = (): GeneMap => { return mostRecentGeneMap; };
-
-export const getAnnotations = (): IAnnotation[] => { return mostRecentAnnotations; };
-
-export const getGroupedAnnotations = (): GroupedAnnotations<Set<IGene>> => { return mostRecentGroupedAnnotations; };
+export const getDataset = (): StructuredData => { return mostRecentDataset; };
 
 export const downloadData = (dataUrl: string = "http://current.geneontology.org/annotations/tair.gaf.gz") => {
     const { execSync } = require("child_process");
@@ -17,10 +13,15 @@ export const downloadData = (dataUrl: string = "http://current.geneontology.org/
 
 export const updateData = () => {
     downloadData();
-    const { geneMap, annotations, groupedAnnotations } = readData();
-    mostRecentGeneMap = geneMap;
-    mostRecentAnnotations = annotations;
-    mostRecentGroupedAnnotations = groupedAnnotations;
+    console.log("Begin reading data");
+    const genesText = readFileSync(resolve("src/assets/gene-types.txt")).toString();
+    const annotationsText = readFileSync(resolve("src/assets/tair.gaf")).toString();
+    const unstructuredText: UnstructuredText = { genesText, annotationsText };
+    const maybeDataset = ingestData(unstructuredText);
+    if (!maybeDataset) throw new Error("failed to parse data");
+    const dataset: StructuredData = maybeDataset;
+    mostRecentDataset = dataset;
+    console.log("Finished parsing data");
 };
 
 export const startPeriodicallyCalling = (fn: (...args: any[]) => void, interval: number = (1000 * 60 * 60 * 24), startDate: Date = getTomorrowMorning()) => {