From d7f45a2180f439bf8c97958acd1417cc0862f997 Mon Sep 17 00:00:00 2001
From: Timothy Geary <scourgemancer@users.noreply.github.com>
Date: Mon, 6 Apr 2020 17:52:04 -0400
Subject: [PATCH] Cleans up messy rebase

---
 src/services/v1.ts | 33 ++++++++++++++++++---------------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/src/services/v1.ts b/src/services/v1.ts
index 7bed13d..f9e0a33 100644
--- a/src/services/v1.ts
+++ b/src/services/v1.ts
@@ -1,9 +1,11 @@
 import {Errors, GET, Path, QueryParam, Return, ContextResponse} from "typescript-rest";
-import {AnnotationStatus, Aspect, makeAnnotationIndex} from "../ingest";
-import {QueryOption, Segment, Strategy} from "../queries";
+import {GeneProductTypeFilter, Query, queryDataset, QueryOption, Segment, Strategy} from "../queries";
+import {AnnotationStatus, Aspect, makeAnnotationIndex, StructuredData} from "../ingest";
 import {annotationsToGAF, genesToCSV, buildGenesMetadata, buildAnnotationMetadata} from '../export';
-import { getDataset } from '../data_fetcher';
 import express from "express";
+import { getDataset } from '../data_fetcher';
+
+const dataset: StructuredData = getDataset();
 
 type Format = "gaf" | "gene-csv" | "json";
 
@@ -63,15 +65,8 @@ export class V1Service {
       segments_meta.strategy = strategy;
     }
 
-    const dataset = getDataset();
-
-    // TODO include unannotated genes
-    const queriedDataset = queryAnnotated(dataset, query);
-
-    // TODO include unannotated genes
-    const format = validateFormat(maybeFormat);
-
-    const filters_meta = {filters: segments.map(f=>`${f.aspect}-${f.annotationStatus}`).join(", ")};
+    const query: Query = { filter, option: option };
+    const queriedDataset = queryDataset(dataset, query);
 
     switch (format) {
       case "gaf":
@@ -100,9 +95,17 @@ export class V1Service {
 
   @Path("/wgs_segments")
   @GET
-  get_wgs() {
-    const dataset = getDataset();
-    const totalGeneCount = Object.keys(dataset.genes.index).length;
+  get_wgs(
+    /**
+     * ?filter=""
+     * This filter describes which subset of Genes will be used for querying.
+     * The option for filter are "all" | "include_protein" | "exclude_pseudogene".
+     */
+    @QueryParam("filter") maybeFilter: string = "exclude_pseudogene",
+  ) {
+    const filter = validateFilter(maybeFilter);
+    const query: Query = { filter, option: {tag: "QueryGetAll"} };
+    let queryResult = queryDataset(dataset, query);
 
     const totalGeneCount = Object.keys(queryResult.genes.index).length;
     const result = Object.entries(queryResult.annotations.index)