Merge pull request #156 from bcgsc/release/v8.0.2

Release/v8.0.2

bin/load.js

@@ -1,6 +1,3 @@
-const fs = require('fs');
-const path = require('path');
-
 const { runLoader } = require('../src');
 const { createOptionsMenu, fileExists } = require('../src/cli');
 
@@ -36,7 +33,12 @@ const cosmicResistance = require('../src/cosmic/resistance');
 const cosmicFusions = require('../src/cosmic/fusions');
 
 const API_MODULES = {
-    asco, dgidb, docm, fdaApprovals, moa, oncotree,
+    asco,
+    dgidb,
+    docm,
+    fdaApprovals,
+    moa,
+    oncotree,
 };
 
 const FILE_MODULES = {
@@ -102,6 +104,11 @@ civicParser.add_argument('--trustedCurators', {
     help: 'CIViC User IDs of curators whose statements should be imported even if they have not yet been reviewed (evidence is submitted but not accepted)',
     nargs: '+',
 });
+civicParser.add_argument('--noUpdate', {
+    action: 'store_true',
+    default: false,
+    help: 'Will not check for updating content of existing GraphKB Statements',
+});
 
 const clinicaltrialsgovParser = subparsers.add_parser('clinicaltrialsgov');
 clinicaltrialsgovParser.add_argument('--days', {
@@ -132,14 +139,12 @@ let loaderFunction;
 if (input) {
     loaderFunction = ALL_MODULES[moduleName || subparser_name].uploadFile;
 } else {
-    debugger;
     loaderFunction = ALL_MODULES[moduleName || subparser_name].upload;
 }
 
 const loaderOptions = { ...options };
 
 if (input) {
-    debugger;
     loaderOptions.filename = input;
 }
 

package.json

@@ -1,7 +1,7 @@
 {
   "name": "@bcgsc-pori/graphkb-loader",
   "main": "src/index.js",
-  "version": "8.0.1",
+  "version": "8.0.2",
   "repository": {
     "type": "git",
     "url": "https://github.com/bcgsc/pori_graphkb_loader.git"

src/civic/disease.js

@@ -0,0 +1,41 @@
+const { orderPreferredOntologyTerms } = require('../graphkb');
+
+/**
+ * Given a CIViC EvidenceItem record with its disease property,
+ * returns the corresponding disease record from GraphKB
+ *
+ * @param {ApiConnection} conn graphkb API connector
+ * @param {object} param1
+ * @param {object} param1.rawRecord the EvidenceItem from CIViC
+ * @returns {object} the disease record from GraphKB
+ */
+const getDisease = async (conn, { rawRecord }) => {
+    let disease;
+
+    // Get corresponding GraphKB Disease by it's doid (disease ontology id)
+    if (rawRecord.disease) {
+        let diseaseQueryFilters = {};
+
+        if (rawRecord.disease.doid) {
+            diseaseQueryFilters = {
+                AND: [
+                    { sourceId: `doid:${rawRecord.disease.doid}` },
+                    { source: { filters: { name: 'disease ontology' }, target: 'Source' } },
+                ],
+            };
+        } else {
+            diseaseQueryFilters = { name: rawRecord.disease.name };
+        }
+
+        disease = await conn.getUniqueRecordBy({
+            filters: diseaseQueryFilters,
+            sort: orderPreferredOntologyTerms,
+            target: 'Disease',
+        });
+    }
+    return disease;
+};
+
+module.exports = {
+    getDisease,
+};