Accomodates refactored service

tair · Feb 19, 2020 · aeb9166 · aeb9166
1 parent aae859e
commit aeb9166
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Showing 2 changed files with 19 additions and 33 deletions.
diff --git a/src/services/v1_service/service.ts b/src/services/v1_service/service.ts
@@ -1,28 +1,10 @@
-import {readFileSync} from "fs";
-import {resolve} from "path";
 import {Errors, GET, Path, QueryParam, Return, ContextResponse} from "typescript-rest";
+import {AnnotationStatus, Aspect, makeAnnotationIndex} from "../../utils/ingest";
 import {queryAnnotated, QueryOption, Segment, Strategy} from "../../queries/queries";
-import {
-  AnnotationStatus,
-  Aspect,
-  ingestData,
-  makeAnnotationIndex,
-  StructuredData,
-  UnstructuredText
-} from "../../utils/ingest";
 import {annotationsToGAF, genesToCSV} from '../../utils/exporters';
+import { getDataset } from '../../utils/data_fetcher';
 import express from "express";
 
-// TODO use data fetcher rather than files.
-console.log("Begin reading data");
-const genesText = readFileSync(process.env["GENES_FILE"] || resolve("src/assets/gene-types.txt")).toString();
-const annotationsText = readFileSync(process.env["ANNOTATIONS_FILE"] || 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;
-console.log("Finished parsing data");
-
 type Format = "gaf" | "gene-csv" | "json";
 
 type QueryStatus = "EXP" | "OTHER" | "UNKNOWN" | "UNANNOTATED";
@@ -69,6 +51,8 @@ export class V1Service {
       query = {tag: "QueryWith", strategy, segments};
     }
 
+    const dataset = getDataset();
+
     // TODO include unannotated genes
     const [queriedGenes, queriedAnnotations] = queryAnnotated(dataset, query);
 
@@ -97,6 +81,7 @@ export class V1Service {
   @Path("/wgs_segments")
   @GET
   get_wgs() {
+    const dataset = getDataset();
     const totalGeneCount = Object.keys(dataset.genes.index).length;
 
     const result = Object.entries(dataset.annotations.index)

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()) => {