GenomicInterpretations hook

bento-platform · Oct 18, 2023 · 0a1afed · 0a1afed
1 parent 0a8b281
commit 0a1afed
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Showing 2 changed files with 65 additions and 11 deletions.
diff --git a/src/components/explorer/IndividualVariants.js b/src/components/explorer/IndividualVariants.js
@@ -7,7 +7,7 @@ import { Button, Descriptions, Empty } from "antd";
 
 import { individualPropTypesShape } from "../../propTypes";
 import { setIgvPosition } from "../../modules/explorer/actions";
-import { useDeduplicatedIndividualBiosamples } from "./utils";
+import { useDeduplicatedIndividualBiosamples, useIndividualInterpretations, useIndividualVariantInterpretations } from "./utils";
 import "./explorer.css";
 
 // TODO: Only show variants from the relevant dataset, if specified;
@@ -62,19 +62,31 @@ SampleVariants.propTypes = {
 };
 
 const IndividualVariants = ({individual, tracksUrl}) => {
-    const biosamples = useDeduplicatedIndividualBiosamples(individual);
+    // const biosamples = useDeduplicatedIndividualBiosamples(individual);
+    const interpretations = useIndividualVariantInterpretations(individual);
 
     const variantsMapped = useMemo(
-        () => Object.fromEntries(biosamples.map((biosample) => [
-            biosample.id,
-            (biosample.variants ?? []).map((v) => ({
-                id: v.hgvsAllele?.id,
-                hgvs: v.hgvsAllele?.hgvs,
-                geneContext: v.extra_properties?.gene_context ?? "",
-            })),
-        ])),
-        [biosamples],
+        () => Object.fromEntries(
+                interpretations.map(i => i.diagnosis)
+                    .flatMap(d => d.genomic_interpretations)
+                    .filter(gi => gi.hasOwnProperty("variant_interpretation"))
+                    .map(gi => [gi.subject_or_biosample_id, gi])
+        ),
+        [interpretations]
     );
+    console.log(variantsMapped);
+
+    // const variantsMapped = useMemo(
+    //     () => Object.fromEntries(biosamples.map((biosample) => [
+    //         biosample.id,
+    //         (biosample.variants ?? []).map((v) => ({
+    //             id: v.hgvsAllele?.id,
+    //             hgvs: v.hgvsAllele?.hgvs,
+    //             geneContext: v.extra_properties?.gene_context ?? "",
+    //         })),
+    //     ])),
+    //     [biosamples],
+    // );
 
     return (
       <div className="variantDescriptions">

diff --git a/src/components/explorer/utils.js b/src/components/explorer/utils.js
@@ -14,6 +14,48 @@ export const useDeduplicatedIndividualBiosamples = (individual) =>
         [individual],
     );
 
+export const useIndividualInterpretations = (individual, withDiagnosis = false) =>
+    useMemo(
+        () => Object.values(
+            Object.fromEntries(
+                (individual?.phenopackets ?? [])
+                    .flatMap(p => p.interpretations)
+                    .filter(i => withDiagnosis ? i.hasOwnProperty("diagnosis") : true)
+                    .map(i => [i.id, i]),
+            ),
+        ),
+        [individual],
+    );
+
+/**
+ * Returns the Interpretations that contain the call
+ * @param {array} interpretations Array of Phenopacket Interpretation
+ * @param {string} call "gene_descriptor" or "variant_interpretation"
+ * @returns Interpretations with call
+ */
+export const useGenomicInterpretations = (interpretations, call) =>
+    useMemo(
+        () => Object.values(
+            Object.fromEntries(
+                interpretations
+                    .filter(interp => interp.hasOwnProperty("diagnosis"))
+                    .filter(interp => interp.diagnosis.hasOwnProperty("genomic_interpretations") 
+                                        && interp.diagnosis.genomic_interpretations.length)
+                    .filter(interp => interp.diagnosis.genomic_interpretations.some(i => i.hasOwnProperty(call)))
+                    .map(interp => [interp.id, interp]),
+            ),
+        ),
+    );
+
+export const useIndividualVariantInterpretations = (individual) => {
+    const interpretations = useIndividualInterpretations(individual);
+    return useGenomicInterpretations(interpretations, "variant_interpretation");
+};
+
+export const useIndividualGeneInterpretations = (individual) => {
+    const interpretations = useIndividualInterpretations(individual);
+    return useGenomicInterpretations(interpretations, "gene_descriptor");
+}
 
 export const useDatasetResources = (datasetIDOrDatasetIDs) => {
     const dispatch = useDispatch();