Merge pull request #32 from bcgsc/release/v6.0.0

Release/v6.0.0

.eslintrc.json

@@ -16,6 +16,8 @@
         "sort-keys-fix"
     ],
     "rules": {
+        "arrow-parens": "off",
+        "function-paren-newline": "off",
         "indent": [
             "error",
             4,
@@ -60,6 +62,7 @@
         ],
         "no-fallthrough": "off",
         "no-mixed-spaces-and-tabs": "error",
+        "no-multiple-empty-lines": "off",
         "no-multi-assign": "off",
         "no-param-reassign": "warn",
         "no-plusplus": "off",

.github/workflows/npm-test.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: [10, 12, 14]
+        node: ['12', '14']
     name: node-${{ matrix.node }}
     steps:
       - uses: actions/checkout@v2
@@ -19,6 +19,7 @@ jobs:
       - run: npm ci
       - run: npm run lint -- --quiet # errors only, no warnings
         name: eslint
+      - run: npm audit --production --audit-level high
       - run: npm run test
       - uses: EnricoMi/[email protected]
         with:

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:10
+FROM node:12
 WORKDIR /usr/src/app
 COPY package*.json ./
 RUN npm ci --only=production

README.md

@@ -1,6 +1,6 @@
 # GraphKB Loader
 
-![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)
+![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-12%20%7C%2014-blue)
 
 This repository is part of the [platform for oncogenomic reporting and interpretation](https://github.com/bcgsc/pori).
 

bin/load.js

@@ -26,14 +26,15 @@ const PMC4468049 = require('../src/PMC4468049');
 const PMC4232638 = require('../src/PMC4232638');
 const uberon = require('../src/uberon');
 const variants = require('../src/variants');
+const asco = require('../src/asco');
 
 const clinicaltrialsgov = require('../src/clinicaltrialsgov');
 
 const cosmicResistance = require('../src/cosmic/resistance');
 const cosmicFusions = require('../src/cosmic/fusions');
 
 const API_MODULES = {
-    civic, clinicaltrialsgov, dgidb, docm, fdaApprovals, oncotree,
+    asco, clinicaltrialsgov, dgidb, docm, fdaApprovals, oncotree,
 };
 
 const FILE_MODULES = {
@@ -65,6 +66,7 @@ const ALL_MODULES = {
     ...API_MODULES,
     ...FILE_MODULES,
     ...COSMIC_MODULES,
+    civic,
 };
 
 const parser = createOptionsMenu();
@@ -85,6 +87,19 @@ fileParser.add_argument('input', {
     help: 'path to the file/dir to be loaded',
     type: fileExists,
 });
+fileParser.add_argument('--ignoreCache', {
+    action: 'store_true',
+    default: false,
+    help: 'Load the full content, to not check for previously loaded records already in the GraphKB instance',
+});
+
+const civicParser = subparsers.add_parser('civic');
+civicParser.add_argument('--trustedCurators', {
+    default: [],
+    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: '+',
+});
+
 
 const cosmicParser = subparsers.add_parser('cosmic');
 cosmicParser.add_argument('module', {
@@ -100,29 +115,29 @@ cosmicParser.add_argument('classification', {
     type: fileExists,
 });
 
-const options = parser.parse_args();
+const { module: moduleName, input, ...options } = parser.parse_args();
 
 let loaderFunction;
 
-if (options.input) {
-    loaderFunction = ALL_MODULES[options.module].uploadFile;
+if (input) {
+    loaderFunction = ALL_MODULES[moduleName || 'civic'].uploadFile;
 } else {
-    loaderFunction = ALL_MODULES[options.module].upload;
+    loaderFunction = ALL_MODULES[moduleName || 'civic'].upload;
 }
 
-const loaderOptions = {};
+const loaderOptions = { ...options };
 
-if (options.input) {
-    if (options.module === 'clinicaltrialsgov') {
-        if (fs.lstatSync(options.input).isDirectory()) {
-            const files = fs.readdirSync(options.input)
-                .map(filename => path.join(options.input, filename));
+if (input) {
+    if (moduleName === 'clinicaltrialsgov') {
+        if (fs.lstatSync(input).isDirectory()) {
+            const files = fs.readdirSync(input)
+                .map(filename => path.join(input, filename));
             loaderOptions.files = files;
         } else {
-            loaderOptions.files = [options.input];
+            loaderOptions.files = [input];
         }
     } else {
-        loaderOptions.filename = options.input;
+        loaderOptions.filename = input;
 
         if (options.module === 'cosmic') {
             loaderOptions.mappingFilename = options.mappingFilename;