Merge branch 'master' into dependabot/npm_and_yarn/ssh2-and-node-ssh-…

…1.11.0
uc-cdis · Jul 22, 2024 · bd9ba93 · bd9ba93
2 parents 062713a + e3c44d1
commit bd9ba93
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diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -0,0 +1,31 @@
+name: Lint
+
+on: [push]
+
+jobs:
+  lint:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Use Node.js 16
+      uses: actions/setup-node@v1
+      with:
+        node-version: 16
+
+    - name: Cache node modules
+      uses: actions/cache@v2
+      with:
+        path: ~/.npm
+        key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
+        restore-keys: |
+          ${{ runner.os }}-node-
+
+    - name: Install dependencies
+      run: npm install
+
+    - name: Run eslintdiff
+      run: npm run eslintdiff
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/Yelp/detect-secrets.git
-    rev: v1.0.3
+    rev: v1.4.0
     hooks:
     - id: detect-secrets
       args: ['--baseline', '.secrets.baseline']

diff --git a/.secrets.baseline b/.secrets.baseline
@@ -1,5 +1,5 @@
 {
-  "version": "1.0.3",
+  "version": "1.4.0",
   "plugins_used": [
     {
       "name": "ArtifactoryDetector"
@@ -80,6 +80,12 @@
     {
       "path": "detect_secrets.filters.heuristic.is_likely_id_string"
     },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
     {
       "path": "detect_secrets.filters.heuristic.is_potential_uuid"
     },
@@ -89,6 +95,9 @@
     {
       "path": "detect_secrets.filters.heuristic.is_sequential_string"
     },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
     {
       "path": "detect_secrets.filters.heuristic.is_templated_secret"
     },
@@ -100,24 +109,6 @@
     }
   ],
   "results": {
-    "README.md": [
-      {
-        "type": "Secret Keyword",
-        "filename": "README.md",
-        "hashed_secret": "398ec9c29cf195ff9202bd85b75002adc88832c3",
-        "is_verified": false,
-        "line_number": 154
-      }
-    ],
-    "getAccessToken.sh": [
-      {
-        "type": "Secret Keyword",
-        "filename": "getAccessToken.sh",
-        "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f",
-        "is_verified": false,
-        "line_number": 21
-      }
-    ],
     "load-testing/grafana/grafana-provisioning/datasources/datasource.yml": [
       {
         "type": "Secret Keyword",
@@ -136,15 +127,6 @@
         "line_number": 66
       }
     ],
-    "load-testing/sample-descriptors/load-test-metadata-service-create-and-query-sample.json": [
-      {
-        "type": "Secret Keyword",
-        "filename": "load-testing/sample-descriptors/load-test-metadata-service-create-and-query-sample.json",
-        "hashed_secret": "dd29ecf524b030a65261e3059c48ab9e1ecb2585",
-        "is_verified": false,
-        "line_number": 22
-      }
-    ],
     "services/portal/studyViewer/studyViewerProps.js": [
       {
         "type": "Base64 High Entropy String",
@@ -313,22 +295,22 @@
         "line_number": 24
       }
     ],
-    "suites/apis/presignedUrlTest.js": [
+    "suites/apis/oidcClientTest.js": [
       {
         "type": "Hex High Entropy String",
-        "filename": "suites/apis/presignedUrlTest.js",
+        "filename": "suites/apis/oidcClientTest.js",
         "hashed_secret": "62bd0c4d3a6b445b13212d23500a7f0916757c3e",
         "is_verified": false,
-        "line_number": 13
+        "line_number": 97
       }
     ],
-    "suites/apis/rasIntegrationTest.js": [
+    "suites/apis/presignedUrlTest.js": [
       {
-        "type": "Secret Keyword",
-        "filename": "suites/apis/rasIntegrationTest.js",
-        "hashed_secret": "f44217a81173869e08671753c52553646ff5d95b",
+        "type": "Hex High Entropy String",
+        "filename": "suites/apis/presignedUrlTest.js",
+        "hashed_secret": "62bd0c4d3a6b445b13212d23500a7f0916757c3e",
         "is_verified": false,
-        "line_number": 10
+        "line_number": 13
       }
     ],
     "suites/batch/GoogleBucketManifestGenerationTest.js": [
@@ -363,6 +345,15 @@
         "line_number": 32
       }
     ],
+    "suites/coremetadata/testPlan.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "suites/coremetadata/testPlan.md",
+        "hashed_secret": "c9705c520825a1682dac6283066f577c950844bf",
+        "is_verified": false,
+        "line_number": 25
+      }
+    ],
     "suites/google/googleDataAccessTest.js": [
       {
         "type": "Hex High Entropy String",
@@ -379,6 +370,15 @@
         "line_number": 62
       }
     ],
+    "suites/google/googleServiceAccountKeyTest.js": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "suites/google/googleServiceAccountKeyTest.js",
+        "hashed_secret": "5e7cb7af2f82537bd0716cb4e821ffe25064af6f",
+        "is_verified": false,
+        "line_number": 193
+      }
+    ],
     "suites/portal/indexingPageTest.js": [
       {
         "type": "Hex High Entropy String",
@@ -388,13 +388,13 @@
         "line_number": 18
       }
     ],
-    "suites/portal/rasAuthN.js": [
+    "suites/pre-release/dcf/3.googleCredentialsTest.js": [
       {
-        "type": "Secret Keyword",
-        "filename": "suites/portal/rasAuthN.js",
-        "hashed_secret": "f44217a81173869e08671753c52553646ff5d95b",
+        "type": "Hex High Entropy String",
+        "filename": "suites/pre-release/dcf/3.googleCredentialsTest.js",
+        "hashed_secret": "1ffff910318085530fb395f27ec73a52084f0685",
         "is_verified": false,
-        "line_number": 11
+        "line_number": 119
       }
     ],
     "utils/user.js": [
@@ -407,5 +407,5 @@
       }
     ]
   },
-  "generated_at": "2022-11-22T23:02:57Z"
+  "generated_at": "2023-05-01T21:15:31Z"
 }
diff --git a/.travis.yml b/.travis.yml
diff --git a/suites/gen3-client/gen3clientTest.js → ...ived/suites/gen3-client/gen3clientTest.js b/suites/gen3-client/gen3clientTest.js → ...ived/suites/gen3-client/gen3clientTest.js
@@ -1,7 +1,7 @@
 Feature('Gen3-dataclient');
 
 const chai = require('chai');
-const { interactive, ifInteractive } = require('../../utils/interactive.js');
+const { interactive, ifInteractive } = require('../../../utils/interactive.js');
 
 const { expect } = chai;
 const hostname = process.env.HOSTNAME;

diff --git a/suites/google/googleServiceAccountKeyTest.js → ...tes/google/googleServiceAccountKeyTest.js b/suites/google/googleServiceAccountKeyTest.js → ...tes/google/googleServiceAccountKeyTest.js
@@ -190,7 +190,7 @@ Scenario('Test no data access anymore after SA key is deleted @reqGoogle', async
 
 
 Scenario('Delete SA creds that do not exist @reqGoogle', async ({ fence, users }) => {
-  const fakeKeyId = '64a48da067f4a4f053e6197bf2b134df7d0abcde';
+  const fakeKeyId = '64a48da067f4a4f053e6197bf2b134df7d0abcde';  // pragma: allowlist secret
   const deleteRes = await fence.do.deleteTempGoogleCreds(
     fakeKeyId,
     users.user0.accessTokenHeader,

diff --git a/...google/googleServiceAccountRemovalTest.js → ...google/googleServiceAccountRemovalTest.js b/...google/googleServiceAccountRemovalTest.js → ...google/googleServiceAccountRemovalTest.js
diff --git a/suites/google/googleServiceAccountTest.js → ...suites/google/googleServiceAccountTest.js b/suites/google/googleServiceAccountTest.js → ...suites/google/googleServiceAccountTest.js
diff --git a/suites/portal/GWASUITest.js → archived/suites/portal/GWASUITest.js b/suites/portal/GWASUITest.js → archived/suites/portal/GWASUITest.js
@@ -1,11 +1,11 @@
 /* eslint-disable codeceptjs/no-skipped-tests */
 Feature('GWAS UI @requires-portal @requires-argo-wrapper @requires-cohort-middleware');
 
-const GWASTasks = require('../../services/portal/GWAS/GWASTasks.js');
-const GWASProps = require('../../services/portal/GWAS/GWASProps.js');
-const GWASQuestions = require('../../services/portal/GWAS/GWASQuestions.js');
+const GWASTasks = require('../../../services/portal/GWAS/GWASTasks.js');
+const GWASProps = require('../../../services/portal/GWAS/GWASProps.js');
+const GWASQuestions = require('../../../services/portal/GWAS/GWASQuestions.js');
 
-Scenario('GWAS submit workflow through Case Control GWAS @GWASUI', async ({
+Scenario('GWAS submit workflow through Case Control GWAS', async ({
   I, home, users,
 }) => {
   I.useWebDriverTo('set window size', async ({ browser }) => {
@@ -51,7 +51,7 @@ Scenario('GWAS submit workflow through Case Control GWAS @GWASUI', async ({
   I.saveScreenshot('GWAS_page_check_job_status_Complete_1.png');
 });
 
-Scenario('GWAS submit workflow through Quantitative Phenotype GWAS @GWASUI', async ({
+Scenario('GWAS submit workflow through Quantitative Phenotype GWAS', async ({
   I, home, users,
 }) => {
   I.useWebDriverTo('set window size', async ({ browser }) => {
@@ -94,7 +94,7 @@ Scenario('GWAS submit workflow through Quantitative Phenotype GWAS @GWASUI', asy
   I.saveScreenshot('GWAS_page_check_job_status_Complete_2.png');
 });
 
-Scenario('GWAS previous button and next button @GWASUI', async ({
+Scenario('GWAS previous button and next button', async ({
   I, home, users,
 }) => {
   home.do.goToHomepage();
@@ -125,7 +125,7 @@ Scenario('GWAS previous button and next button @GWASUI', async ({
   I.seeElement(GWASProps.SelectConceptTitle);
 });
 
-Scenario('Select different GWAS Type @GWASUI', async ({
+Scenario('Select different GWAS Type', async ({
   I, home, users,
 }) => {
   home.do.goToHomepage();
@@ -156,7 +156,7 @@ Scenario('Select different GWAS Type @GWASUI', async ({
   I.seeElement(GWASProps.SelectedRadio);
 });
 
-Scenario('Unauthorize to workflow @GWASUI', async ({
+Scenario('Unauthorize to workflow', async ({
   I, home, users,
 }) => {
   home.do.goToHomepage();

diff --git a/.../dcf/2.serviceAccountsRegistrationTest.js → .../dcf/2.serviceAccountsRegistrationTest.js b/.../dcf/2.serviceAccountsRegistrationTest.js → .../dcf/2.serviceAccountsRegistrationTest.js
diff --git a/codecept.conf.js b/codecept.conf.js
@@ -71,7 +71,6 @@ exports.config = {
     indexd: './services/apis/indexd/indexdService.js',
     drs: './services/apis/drs/drsService.js',
     peregrine: './services/apis/peregrine/peregrineService.js',
-    pidgin: './services/apis/pidgin/pidginService.js',
     fence: './services/apis/fence/fenceService.js',
     dataClient: './services/apis/dataClient/dataClientService.js',
     etl: './services/apis/etl/etlService.js',
@@ -81,9 +80,11 @@ exports.config = {
     auditService: './services/apis/auditService/auditService.js',
     nondbgap: './services/apis/nondbgapUsersync/nonDbgapService.js',
     ras: './services/apis/rasDrs/rasService.js',
+    requestor: './services/apis/requestor/requestorService.js',
 
     // Pages
     home: './services/portal/home/homeService.js',
+    gwas: './services/portal/GWAS/GWASService.js',
     indexing: './services/portal/indexing/indexingService.js',
     login: './services/portal/login/loginService.js',
     explorer: './services/portal/explorer/explorerService.js',
@@ -93,6 +94,7 @@ exports.config = {
     discovery: './services/portal/discovery/discoveryService.js',
     workspace: './services/portal/workspace/workspaceService.js',
     gen3ffLandingPage: './services/portal/gen3ffLandingPage/gen3ffLandingPageService.js',
+    studyRegistration: './services/portal/studyRegistration/studyRegistrationService.js',
   },
   mocha: {
     reporterOptions: {
@@ -124,7 +126,11 @@ exports.config = {
     steps: './suites/bdd/**/*.js',
   },
   plugins: {
-    allure: {},
+    allure: {
+      enabled: true,
+      require: "allure-codeceptjs",
+      outputDir: "output",
+    },
     tryTo: {
       enabled: true,
     },

diff --git a/docs/howto/authentication_file_phs001194.txt b/docs/howto/authentication_file_phs001194.txt
@@ -0,0 +1,2 @@
+user name, login, authority, role, email, phone, status, phsid, permission set, created, updated, expires, downloader for, downloader for names, downloader for emails
+cdis.autotest@gmail.com,cdis.autotest@gmail.com,eRA,Downloader,cdis.autotest@gmail.com,"+(111) 1111111",active,"phs001194","General Research Use",2022-12-09 14:29:32.580,2022-12-10 12:49:58.870,2023-12-09 00:00:00.000,ME,ME ME,cdis.autotest@gmail.com
diff --git a/docs/howto/cascading-auth-config.md b/docs/howto/cascading-auth-config.md
@@ -0,0 +1,28 @@
+# Configuring Cascading Authorization for dbGaP Sync Tests
+
+1. Add the `authentication_file_phs001194.txt` in this directory to the SFTP Server used by the integration test environments. 
+2. Update the integration test environments' fence-config.yaml to include the `parent_to_child_studies_mapping` for the dbGaP.info configuration for the SFTP Server in Step 1.
+3. Run `gen3 kube-setup-fence` so the changes to the fence-config.yaml changes are applied to the cluster.
+
+fence-config.yaml example: 
+
+```
+dbGaP:
+  - info:
+      host: 'sftp.server.example.not-a-real-server.amazonaws.com'
+      username: 'jenkins-dcp'
+      password: ''
+      port: 22
+      proxy: 'cloud-proxy.internal.io'
+      proxy_user: 'sftpuser'
+      encrypted: false
+    study_to_resource_namespaces:
+        '_default': ['/']
+    allow_non_dbGaP_whitelist: true
+    allowed_whitelist_patterns: ['authentication_file_PROJECT-(\d*).(csv|txt)', 'authentication_file_NCI-(\d*).(csv|txt)']  
+    protocol: 'sftp'
+    decrypt_key: <redacted>
+    parse_consent_code: false
+    parent_to_child_studies_mapping:
+      'phs001194': ['phs000571']
+```
diff --git a/docs/testplans/GWAS/GWAS++_test_plan.md b/docs/testplans/GWAS/GWAS++_test_plan.md
@@ -1,4 +1,4 @@
-# GWAS++ Test Plan
+# GWAS app Test Plan
 
 ## Overview
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		user name, login, authority, role, email, phone, status, phsid, permission set, created, updated, expires, downloader for, downloader for names, downloader for emails
		cdis.autotest@gmail.com,cdis.autotest@gmail.com,eRA,Downloader,cdis.autotest@gmail.com,"+(111) 1111111",active,"phs001194","General Research Use",2022-12-09 14:29:32.580,2022-12-10 12:49:58.870,2023-12-09 00:00:00.000,ME,ME ME,cdis.autotest@gmail.com