Merge branch 'master' into feat/GPE-1202

jenkins-dcp.planx-pla.net/manifest.json

@@ -278,7 +278,8 @@
     "useryaml_s3path": "s3://cdis-gen3-users/qa/user.yaml",
     "dispatcher_job_num": "5",
     "netpolicy": "on",
-    "tier_access_level" : "libre"
+    "tier_access_level" : "libre",
+    "es7": true
   },
   "ssjdispatcher": {
     "job_images": {

qa-brh.planx-pla.net/manifests/hatchery/hatchery.json

@@ -201,7 +201,7 @@
       "nextflow": {
         "enabled": true,
         "job-image-whitelist": [
-          "*"
+          "143731057154.dkr.ecr.us-east-1.amazonaws.com/nextflow-approved/{{username}}:*"
         ],
         "s3-bucket-whitelist": [
           "ngi-igenomes"

qa-covid19.planx-pla.net/manifests/hatchery/jupyter-covid19-restricted-download.yaml

@@ -1,7 +1,7 @@
 version: '3'
 services:
    webapp:
-      image: "quay.io/cdis/jupyter-notebook:covid19-jupyter-covid19-restrict-download"
+      image: "quay.io/cdis/jupyter-notebook:covid19-master"
       volumes:
          - ${DATA_VOLUME}:/data
          - ${USER_VOLUME}:/home/jovyan/pd

qa-heal.planx-pla.net/manifests/hatchery/hatchery.json

@@ -2,12 +2,8 @@
   "user-namespace": "jupyter-pods-qa-heal",
   "sub-dir": "/lw-workspace",
   "user-volume-size": "10Gi",
-  "gen3-license-user-maps-dynamodb-table": "gen3-license-user-maps",
-  "gen3-license-type": "STATA-HEAL",
-  "gen3-license-max-ids": 6,
-  "gen3-g3auto-name": "stata-workspace-gen3-license-g3auto",
-  "gen3-g3auto-key": "stata_license.txt",
-  "gen3-license-file-path": "stata.lic",
+  "license-user-maps-dynamodb-table": "gen3-license-user-maps",
+  "license-user-maps-global-secondary-index": "activeUsersIndex",
   "sidecar": {
     "cpu-limit": "1.0",
     "memory-limit": "256Mi",
@@ -109,6 +105,15 @@
       "env": {
         "FRAME_ANCESTORS": "https://qa-heal.planx-pla.net"
       },
+      "license": {
+        "enabled": true,
+        "license-type": "STATA-HEAL",
+        "max-license-ids": 6,
+        "g3auto-name": "stata-workspace-gen3-license-g3auto",
+        "g3auto-key": "stata_license.txt",
+        "file-path": "stata.lic",
+        "workspace-flavor": "gen3-licensed"
+      },
       "args": [
         "--NotebookApp.base_url=/lw-workspace/proxy/",
         "--NotebookApp.password=''",

qa-mickey.planx-pla.net/dashboard/Public/documentation/index.html

@@ -65,7 +65,7 @@ <h1>Table of Contents<a class="headerlink" href="#table-of-contents" title="Link
 <li><p><a class="reference internal" href="#troubleshooting-gwas-errors"><span class="xref myst"><strong>Troubleshooting GWAS Errors</strong></span></a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#data-dictionary"><span class="xref myst"><strong>Data Dictionary</strong></span></a></p></li>
+<li><p><a class="reference internal" href="#mvp-data-dictionary"><span class="xref myst"><strong>MVP Data Dictionary</strong></span></a></p></li>
 <li><p><a class="reference internal" href="#data-update-disclaimer"><span class="xref myst"><strong>Data Update Disclaimer</strong></span></a></p></li>
 </ul>
 </li>
@@ -110,9 +110,9 @@ <h2><strong>Apps</strong><a class="headerlink" href="#apps" title="Link to this
 <section id="ohdsi-atlas">
 <h2><strong>OHDSI Atlas</strong><a class="headerlink" href="#ohdsi-atlas" title="Link to this heading">¶</a></h2>
 <p>ATLAS is an open source software application developed as a part of <a class="reference external" href="https://www.ohdsi.org/">OHDSI</a> community intended to provide a unified interface to patient level data and analytics. Atlas software used to define cohorts, typically dichotomous variables, for analysis.</p>
-<p>ATLAS currently includes functionality for searching and navigating the vocabulary within the OMOP Common Data Model (CDM). Users may link to the <a class="reference internal" href="#data-dictionary"><span class="xref myst">Atlas Data Dictionary</span></a> to help with comprehension and curation of custon sets.  In addition to the search and navigation capabilities, it also provides features to curate and export custom sets of concept identifiers for use in cohort definitions. These will automatically populate on the Gen3 GWAS App.</p>
+<p>ATLAS currently includes functionality for searching and navigating the vocabulary within the OMOP Common Data Model (CDM). Users may link to the MVP Data Dictionary to help with comprehension and curation of custom sets. In addition to the search and navigation capabilities, it also provides features to curate and export custom sets of concept identifiers for use in cohort definitions. These will automatically populate on the Gen3 GWAS App.</p>
 <p>In general, ATLAS is an analytics platform that can be used to perform analyses across one or more observational databases which have been standardized to the OMOP Common Data Model V5 and can facilitate exchange of analysis designs with any other organizations across the OHDSI community.</p>
-<p>Tutorials for the ATLAS tool can be found <a class="reference external" href="https://github.com/OHDSI/Atlas/wiki">here</a> and the book about the OHDSI can be found <a class="reference external" href="https://ohdsi.github.io/TheBookOfOhdsi/">here</a>. These resources contain a lot of useful information, particularly you might find it useful to read about <a class="reference external" href="https://ohdsi.github.io/TheBookOfOhdsi/Cohorts.html#Cohorts">Cohort Definition</a>. It is highly advisable that you familiarize yourself with these resources before proceeding. Also, the OHDSI Atlas App includes a link to the <a class="reference internal" href="#data-dictionary"><span class="xref myst">Atlas Data Dictionary</span></a>.  We have also provided a brief step-by-step guide to creating dichotomous variables here:</p>
+<p>Tutorials for the ATLAS tool can be found <strong><a class="reference external" href="https://github.com/OHDSI/Atlas/wiki">here</a></strong> and also in the MVP data dictionary link.  The book about the OHDSI can be found <strong><a class="reference external" href="https://ohdsi.github.io/TheBookOfOhdsi/">here</a></strong>. These resources contain a lot of useful information, particularly you might find it useful to read about <a class="reference external" href="https://ohdsi.github.io/TheBookOfOhdsi/Cohorts.html#Cohorts">Cohort Definition</a>. It is highly advisable that you familiarize yourself with these resources before proceeding.</p>
 <section id="steps-to-generate-a-cohort">
 <h3><strong>Steps to Generate a Cohort</strong><a class="headerlink" href="#steps-to-generate-a-cohort" title="Link to this heading">¶</a></h3>
 <p><strong>Step 1 Create a Concept Set</strong></p>
@@ -290,10 +290,9 @@ <h4><strong>Step failed with an uncategorized error</strong><a class="headerlink
 </section>
 </section>
 </section>
-<section id="data-dictionary">
-<h2><strong>Data Dictionary</strong><a class="headerlink" href="#data-dictionary" title="Link to this heading">¶</a></h2>
-<p>The Data Dictionary connects users to the MVP data documentation which contains definitions, descriptions, and metadata for the variables and concepts available in the Atlas OHDSI and GWAS apps.  This is available as an App or as a link from the Atlas OHSDI page.   When selecting data dictionary from the Apps browser, the user will be directed to a static page and from there will select the data dictionary link.  Clicking on the Atlas Data Dictionary link will automatically launch a popup  explaining that the link takes the user away from VADC.  Clicking “OK” button will open the dictionary in a new tab of the user’s browser allowing
-toggling between the two sites.</p>
+<section id="mvp-data-dictionary">
+<h2><strong>MVP Data Dictionary</strong><a class="headerlink" href="#mvp-data-dictionary" title="Link to this heading">¶</a></h2>
+<p>The Data Dictionary App connects users to the static MVP data documentation which contains definitions, descriptions, and metadata for the variables and concepts available in the VADC Atlas OHDSI and GWAS apps. This is also available through a link from the VADC Atlas OHSDI page. When selecting data dictionary from the Apps browser, the user will be presented with a button.  This button directs the user to an outside tab.  Clicking on the MVP Data Dictionary button will automatically launch a popup explaining that the link takes the user away from VADC. Clicking the “OK” button will open the dictionary in a new tab of the user’s browser allowing toggling between the two sites. <strong>Please note- the site can only be accessible within the VA’s VPN.</strong></p>
 </section>
 <section id="data-update-disclaimer">
 <h2><strong>Data Update Disclaimer</strong><a class="headerlink" href="#data-update-disclaimer" title="Link to this heading">¶</a></h2>

qa-mickey.planx-pla.net/portal/gitops.json

@@ -112,9 +112,9 @@
       "needsTeamProject": true
     },
     {
-      "appId": "DataDictionary",
-      "title": "Data Dictionary",
-      "description": "Use this App to view a tabluar representation of the data dictionary",
+      "appId": "AtlasDataDictionary",
+      "title": "Atlas Data Dictionary",
+      "description": "Use this App to view a tabluar representation of the Atlas data dictionary",
       "image": "/src/img/analysis-icons/default-app.png",
       "needsTeamProject": false
     }