Merge branch 'develop' of https://github.com/bcgsc/pori_graphkb_loader into feat/external-deployment-merge-from-dev

Author: elewis2

bin/load.js

@@ -97,6 +97,16 @@ fileParser.add_argument('--ignoreCache', {
     default: false,
     help: 'Load the full content, to not check for previously loaded records already in the GraphKB instance',
 });
+fileParser.add_argument('--ignoreSynonyms', {
+    action: 'store_true',
+    default: false,
+    help: 'For NCIt loader only: ignore synonyms instead upload as alias records (overrides default behavior)',
+});
+fileParser.add_argument('--ignoreDeprecating', {
+    action: 'store_true',
+    default: false,
+    help: 'For NCIt loader only: ignore deprecation of old records (overrides default behavior)',
+});
 
 const civicParser = subparsers.add_parser('civic');
 civicParser.add_argument('--trustedCurators', {

data/evidenceLevels.json

@@ -135,12 +135,12 @@
         "biological": {
             "name": "biological"
         },
-        "cancer gene": {
-            "description": "Tumourigenesis gene that is neither oncogenic nor tumour suppressive",
+        "other cancer gene": {
+            "description": "Cancer gene that is neither oncogenic nor tumour suppressive",
             "links": [
                 {
                     "class": "SubClassOf",
-                    "target": "tumourigenesis"
+                    "target": "cancer gene"
                 }
             ]
         },
@@ -1395,7 +1395,7 @@
             "links": [
                 {
                     "class": "SubClassOf",
-                    "target": "tumourigenesis"
+                    "target": "cancer gene"
                 }
             ]
         },
@@ -2149,11 +2149,11 @@
             "links": [
                 {
                     "class": "SubClassOf",
-                    "target": "tumourigenesis"
+                    "target": "cancer gene"
                 }
             ]
         },
-        "tumourigenesis": {
+        "cancer gene": {
             "links": [
                 {
                     "class": "SubClassOf",