Merge pull request #17 from bcgsc/release/v5.1.1

Release/v5.1.1
bcgsc · Jul 7, 2021 · aef05b2 · aef05b2
2 parents 78f5a57 + b788752
commit aef05b2
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diff --git a/README.md b/README.md
@@ -2,6 +2,8 @@
 
 ![build](https://github.com/bcgsc/pori_graphkb_loader/workflows/build/badge.svg?branch=master) ![Docker Image Version (latest semver)](https://img.shields.io/docker/v/bcgsc/pori-graphkb-loader?label=docker%20image) ![node versions](https://img.shields.io/badge/node-10%20%7C%2012%20%7C%2014-blue)
 
+This repository is part of the [platform for oncogenomic reporting and interpretation](https://github.com/bcgsc/pori).
+
 This package is used to import content from a variety of sources into GraphKB using the API.
 
 - [Loaders](#loaders)

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "@bcgsc-pori/graphkb-loader",
   "main": "src/index.js",
-  "version": "5.1.0",
+  "version": "5.2.0",
   "repository": {
     "type": "git",
     "url": "https://github.com/bcgsc/pori_graphkb_loader.git"

diff --git a/src/civic/index.js b/src/civic/index.js
@@ -112,12 +112,20 @@ const validateEvidenceSpec = ajv.compile({
 
 
 /**
- * Convert the CIViC relevance types to GraphKB terms
+ * Extract the appropriate GraphKB relevance term from a CIViC evidence record
  */
-const getRelevance = async ({ rawRecord, conn }) => {
-    const translateRelevance = ({ evidenceType, clinicalSignificance, evidenceDirection }) => {
-        switch (evidenceType) { // eslint-disable-line default-case
-            case 'Predictive': {
+const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificance) => {
+    switch (evidenceType) { // eslint-disable-line default-case
+        case 'Predictive': {
+            if (evidenceDirection === 'Does Not Support') {
+                switch (clinicalSignificance) { // eslint-disable-line default-case
+                    case 'Sensitivity':
+
+                    case 'Sensitivity/Response': {
+                        return 'no response';
+                    }
+                }
+            } else if (evidenceDirection === 'Supports') {
                 switch (clinicalSignificance) { // eslint-disable-line default-case
                     case 'Sensitivity':
                     case 'Adverse Response':
@@ -129,61 +137,66 @@ const getRelevance = async ({ rawRecord, conn }) => {
 
                     case 'Sensitivity/Response': { return 'sensitivity'; }
                 }
-                break;
             }
+            break;
+        }
 
-            case 'Functional': {
-                return clinicalSignificance.toLowerCase();
-            }
+        case 'Functional': {
+            return clinicalSignificance.toLowerCase();
+        }
 
-            case 'Diagnostic': {
-                switch (clinicalSignificance) { // eslint-disable-line default-case
-                    case 'Positive': { return 'favours diagnosis'; }
+        case 'Diagnostic': {
+            switch (clinicalSignificance) { // eslint-disable-line default-case
+                case 'Positive': { return 'favours diagnosis'; }
 
-                    case 'Negative': { return 'opposes diagnosis'; }
-                }
-                break;
+                case 'Negative': { return 'opposes diagnosis'; }
             }
+            break;
+        }
 
-            case 'Prognostic': {
-                switch (clinicalSignificance) { // eslint-disable-line default-case
-                    case 'Negative':
+        case 'Prognostic': {
+            switch (clinicalSignificance) { // eslint-disable-line default-case
+                case 'Negative':
 
-                    case 'Poor Outcome': {
-                        return 'unfavourable prognosis';
-                    }
-                    case 'Positive':
+                case 'Poor Outcome': {
+                    return 'unfavourable prognosis';
+                }
+                case 'Positive':
 
-                    case 'Better Outcome': {
-                        return 'favourable prognosis';
-                    }
+                case 'Better Outcome': {
+                    return 'favourable prognosis';
                 }
-                break;
             }
+            break;
+        }
 
-            case 'Predisposing': {
-                if (['Positive', null, 'null'].includes(clinicalSignificance)) {
-                    return 'Predisposing';
-                } if (clinicalSignificance.includes('Pathogenic')) {
-                    return clinicalSignificance;
-                } if (clinicalSignificance === 'Uncertain Significance') {
-                    return 'likely predisposing';
-                }
-                break;
+        case 'Predisposing': {
+            if (['Positive', null, 'null'].includes(clinicalSignificance)) {
+                return 'predisposing';
+            } if (clinicalSignificance.includes('Pathogenic')) {
+                return clinicalSignificance.toLowerCase();
+            } if (clinicalSignificance === 'Uncertain Significance') {
+                return 'likely predisposing';
             }
+            break;
         }
+    }
 
-        throw new Error(
-            `unable to process relevance (${JSON.stringify({ clinicalSignificance, evidenceDirection, evidenceType })})`,
-        );
-    };
+    throw new Error(
+        `unable to process relevance (${JSON.stringify({ clinicalSignificance, evidenceDirection, evidenceType })})`,
+    );
+};
 
+/**
+ * Convert the CIViC relevance types to GraphKB terms
+ */
+const getRelevance = async ({ rawRecord, conn }) => {
     // translate the type to a GraphKB vocabulary term
-    let relevance = translateRelevance({
-        clinicalSignificance: rawRecord.clinical_significance,
-        evidenceDirection: rawRecord.evidence_direction,
-        evidenceType: rawRecord.evidence_type,
-    }).toLowerCase();
+    let relevance = translateRelevance(
+        rawRecord.evidence_type,
+        rawRecord.evidence_direction,
+        rawRecord.clinical_significance,
+    ).toLowerCase();
 
     if (RELEVANCE_CACHE[relevance] === undefined) {
         relevance = await conn.getVocabularyTerm(relevance);
@@ -572,7 +585,6 @@ const downloadEvidenceRecords = async (baseUrl) => {
 
         if (
             record.clinical_significance === 'N/A'
-            || record.evidence_direction === 'Does Not Support'
             || (record.clinical_significance === null && record.evidence_type === 'Predictive')
         ) {
             counts.skip++;
@@ -682,6 +694,7 @@ const upload = async (opt) => {
 
         const oneToOne = mappedCount === 1 && preupload.size === 1;
 
+        // upload all GraphKB statements for this CIViC Evidence Item
         for (const record of recordList) {
             for (const variant of record.variants) {
                 for (const drugs of record.drugs) {
@@ -738,5 +751,6 @@ const upload = async (opt) => {
 module.exports = {
     SOURCE_DEFN,
     specs: { validateEvidenceSpec },
+    translateRelevance,
     upload,
 };
diff --git a/src/civic/variant.js b/src/civic/variant.js
@@ -133,6 +133,7 @@ const normalizeVariantRecord = ({
             type: name.replace(/-/g, ' '),
         }];
     } if (match = /^t\(([^;()]+);([^;()]+)\)\(([^;()]+);([^;()]+)\)$/i.exec(name)) {
+        // convert translocation syntax
         const [, chr1, chr2, pos1, pos2] = match;
         return [{
             positional: true,
@@ -141,6 +142,7 @@ const normalizeVariantRecord = ({
             variant: `translocation(${pos1}, ${pos2})`,
         }];
     } if (match = /^(p\.)?([a-z*]\d+\S*)\s+\((c\.[^)]+)\)$/i.exec(name)) {
+        // split combined protein + cds notation
         let [, , protein, cds] = match;
 
         // correct deprecated cds syntac
@@ -152,7 +154,7 @@ const normalizeVariantRecord = ({
             }
         }
         return [{
-            inferredBy: [
+            inferredBy: [ // keep the cds variant as a link to the protein variant
                 {
                     positional: true,
                     reference1: { ...referenceGene },
@@ -183,7 +185,10 @@ const normalizeVariantRecord = ({
         let rest = { type: 'fusion' };
 
         if (tail) {
-            if (match = /^[a-z](\d+);[a-z](\d+)$/.exec(tail || '')) {
+            if (match = /^e(\d+)-e(\d+)$/.exec(tail || '')) {
+                const [, exon1, exon2] = match;
+                rest = { positional: true, variant: `fusion(e.${exon1},e.${exon2})` };
+            } else if (match = /^[a-z](\d+);[a-z](\d+)$/.exec(tail || '')) {
                 const [, exon1, exon2] = match;
                 rest = { positional: true, variant: `fusion(e.${exon1},e.${exon2})` };
             } else {