Merge branch 'master' into connection-string-python

.github/workflows/label-check.yml

@@ -8,6 +8,9 @@ on:
     types:
       - opened
       - synchronize
+      - reopened
+      - labeled
+      - unlabeled
 
 jobs:
   label-check:

docs/MSK-Maintenance.md

@@ -14,22 +14,22 @@ In the database migration process, we are going to have two main steps: building
     - Take the cbioportal hash and new genome nexus annotation pipeline hash (from above) and propagate to pipelines POM; also update db version if db migration is part of change
     - Login to pipelines server
     - Sets general env variables needed for building
-        - Run `sh /data/portal-con/scripts/automation-environment.sh`
+        - Run `sh /data/portal-cron/scripts/automation-environment.sh`
     - Specific to cbioportal build, looks for properties and xml files off of $PORTAL_HOME
         - Run `export PORTAL_HOME=/data/portal-cron/git-repos/cbioportal`
     - Make sure the local cbioportal codebase is on the correct git hash at `/data/portal-cron/git-repos/cbioportal`
     - Specify importer to be build
-        - Copy importer properties to `/data/portal-con-git-repos/cbioportal/src/main/resources` (e.g. triage `/data/portal-cron/git-repos/pipelines-configuration/properties/import-triage/*`)
+        - Copy importer properties to `/data/portal-cron/git-repos/cbioportal/src/main/resources` (e.g. triage `/data/portal-cron/git-repos/pipelines-configuration/properties/import-triage/*`)
     - Navigate to pipelines folder
-        - `cd /data/portal-con/git-repos/pipelines`
+        - `cd /data/portal-cron/git-repos/pipelines`
     - Build importer
         - mvn clean install -DskipTests
 - Build multiple importers
     - Take the cbioportal hash and add it to genome nexus annotation pipeline POM -> push to fork
     - Take the cbioportal hash and new genome nexus annotation pipeline hash (from above) and propagate to pipelines POM; also update db version if db migration is part of change
     - Login to pipelines server
     - Sets general env variables needed for building
-        - Run `sh /data/portal-con/scripts/automation-environment.sh`
+        - Run `sh /data/portal-cron/scripts/automation-environment.sh`
     - Specific to cbioportal build, looks for properties and xml files off of $PORTAL_HOME
         - Run `export PORTAL_HOME=/data/portal-cron/git-repos/cbioportal`
     - Make sure the local cbioportal codebase is on the correct git hash at `/data/portal-cron/git-repos/cbioportal`
@@ -61,9 +61,9 @@ Database needs to be updated one by one, we have four main databases: triage, pr
     - SSH into pipeline server
     - Checkout to the commit that contains the latest database scheme
     - Check if property sets up correctly to the right database (triage)
-        - `vi /data/portal-con-git-repos/cbioportal/src/main/resources/portal.properties`
+        - `vi /data/portal-cron/git-repos/cbioportal/src/main/resources/portal.properties`
     - Move to directory
-        - `cd /data/portal-con-git-repos/cbioportal`
+        - `cd /data/portal-cron/git-repos/cbioportal`
     - Run database migration using script:
         - `python3 core/src/main/scripts/migrate_db.py --properties-file src/main/resources/portal.properties --sql db-scripts/src/main/resources/migration.sql`
     - Monitor the DB migration process and look for possible errors

docs/News-Genie.md

@@ -1,4 +1,8 @@
 # Genie News
+## November 9, 2023
+*   **Public Release 14.1 of AACR Project GENIE:**
+    *  The public release 14.1 version of AACR GENIE has 10 samples retracted that were present in AACR GENIE 14.0-public. 
+    *  More detailed information can be found in the [AACR GENIE release notes](https://www.synapse.org/#!Synapse:syn52919317) and the data releases page from [Sage Bionetworks](https://www.synapse.org/#!Synapse:syn7222066/wiki/410924)
 ## September 20, 2023
 *   **Public Release 14.0 of AACR Project GENIE:**
      *   The first set of cancer genomic data aggregated through AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) was released to the global community in January 2017. The current release, GENIE 14.0-public now contains 183,000 sequenced samples from nearly 160,000 patients, making the AACR Project GENIE registry among the largest fully public cancer genomic data sets released to date.

docs/deployment/customization/Studyview.md

@@ -9,6 +9,7 @@ The layout of a chart is determined mainly based on priority. Higher priority wi
 In order to improve the layout, we added a layout algorithm layer. The study view page is using grid layout. All charts will be put into 2-dimensional systems. For example, pie chart, by default, takes 1 block and bar chart uses two blocks. All charts will be placed from left to right, top to bottom. In order to prevent misalignment, we promote small charts to fit into the space.
 
 For logged-in(authenticated) users, charts layout is saved to users profile i.e, whenever user tries to re-visits the same url, previously saved layout will be loaded.
+Please note for optimal performance, the portal will initially display 20 clinical charts by default. These charts are prioritized from high to low. Additional clinical charts are initially hidden but can be easily selected by users through the 'Add charts' dropdown menu.
 
 ## Study View Customization with Priority Data
 Example of study view in public portal: https://www.cbioportal.org/study?id=acc_tcga,lgg_tcga#summary