Revert "Merge branch 'master' of https://github.com/cBioPortal/cbiopo…

…rtal"

This reverts commit 9ca165d, reversing
changes made to 14df8ca.

CONTRIBUTING.md

@@ -146,8 +146,9 @@ New features:
 ### Devops
 New features:
 
-- Does the configuration style follow the config guidelines? That is compile.
-- Runtime (Spring) goes in `application.properties`. Default values should be in `GlobalProperties.java`.
+- Does the configuration style follow the config guidelines? That is compile
+  (Maven) config goes in the appriopriate `pom.xml` (root, `scripts/`, `portal/`, `core/`).
+  Runtime (Spring) goes in `portal.properties`. Default values should be in `GlobalProperties.java`.
 - Non-stable configuration should be done through war overlays.
 - Is the configuration tested as part of the CI tests? It's not a necessity but be
   aware that untested configuration will be tough to maintain.

README.md

@@ -26,9 +26,11 @@ If you want to run the cBioPortal web app from the command line please follow th
 docker compose -f docker-compose.yml -f open-ports.yml up
 ```
 This should open the ports. Now we are ready to run the cBioPortal web app locally. You can compile the backend code with:
-
 ```
-
+export JAVA_HOME=/Library/Java/JavaVirtualMachines/temurin-11.jdk/Contents/Home/ && mvn -DskipTests clean install
+```
+Note: change `JAVA_HOME` to point to a JDK 11 version. If everything compiles correctly you can then run the app like this:
+```
 java -Xms2g -Xmx4g \
      -Dauthenticate=noauthsessionservice \
      -Dsession.service.url=http://localhost:5000/api/sessions/my_portal/ \
@@ -45,7 +47,6 @@ java -Xms2g -Xmx4g \
      -cp "$PWD:$PWD/BOOT-INF/lib/*" \
      org.cbioportal.PortalApplication
 ```
-
 The app should now show up at http://localhost:8080.
 
 #### Deploy your development image inside Docker Compose
@@ -85,7 +86,6 @@ You can then use a JAVA IDE to connect to that port. E.g. in [VSCode](https://co
 ```
 
 ## 🌳 Branch Information
-
 | | main branch | upcoming release branch | later release candidate branch |
 | --- | --- | --- | --- |
 | Branch name | [`master`](https://github.com/cBioPortal/cbioportal/tree/master) |  -- |  [`rc`](https://github.com/cBioPortal/cbioportal/tree/rc) |

docker/web-and-data/docker-entrypoint.sh

@@ -64,7 +64,7 @@ check_db_connection() {
         echo "----------------------------------------------------------------------------------------------------------------"
         echo "-- Connection error:"
         echo "-- You try to connect to the database using the deprecated 'db.host', 'db.portal_db_name' and 'db.use_ssl' properties."
-        echo "-- Please remove these properties and use the 'db.connection_string' property instead. See https://docs.cbioportal.org/deployment/customization/application.properties-reference/"
+        echo "-- Please remove these properties and use the 'db.connection_string' property instead. See https://docs.cbioportal.org/deployment/customization/portal.properties-reference/"
         echo "-- for assistance on building a valid connection string."
         echo "------------------------------------------------------------f---------------------------------------------------"
         exit 1
@@ -128,7 +128,7 @@ _main() {
         echo "Running Migrate DB Script"
         # Custom logic to handle the case when "org.cbioportal.PortalApplication" is present
         # Parse database config. Use command line parameters (e.g. -Ddb.host) if
-        # available, otherwise use application.properties
+        # available, otherwise use portal.properties
         if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then
             echo "Using database config:"
             parse_db_params_from_config_and_command_line $@

docs/Architecture-Overview.md

@@ -74,7 +74,7 @@ relevance of variants (or biomarker alterations) in cancer. For information on
 how to deploy this service yourself see:
 https://github.com/griffithlab/civic-server. It is also possible to disable
 showing CIVIC in cBioPortal by setting `show.civic=false` in the
-`application.properties` (See [application.properties reference](/deployment/customization/application.properties-Reference.md#civic-integration)).
+`portal.properties` (See [portal.properties reference](/deployment/customization/portal.properties-Reference.md#civic-integration)).
 
 ### Genome Nexus
 [Genome Nexus](https://www.genomenexus.org) is a comprehensive one-stop

docs/File-Formats.md

@@ -47,7 +47,7 @@ This file contains metadata about the cancer study. The file contains the follow
 7. **groups (Optional)**: When using an authenticating cBioPortal, lists the user-groups that are allowed access to this study. Multiple groups are separated with a semicolon ";". The study will be invisible to users not in _at least one_ of the listed groups, as if it wasn't loaded at all. e.g., "PUBLIC;GDAC;SU2C-PI3K". see [User-Authorization](/deployment/authorization-and-authentication/User-Authorization.md) for more information on groups
 8. **add_global_case_list (Optional)**: set to 'true' if you would like the "All samples" case list to be generated automatically for you. See also [Case lists](#case-lists).
 9. **tags_file (Optional)**: the file name containing custom study tags for the [study tags](#study-tags-file).
-10. **reference_genome (Optional)**: the study reference genome (e.g. `hg19`, `hg38`). Without specifying this property, the study will be assigned to the reference genome specified in `application.properties` (property `ucsc.build`).
+10. **reference_genome (Optional)**: the study reference genome (e.g. `hg19`, `hg38`). Without specifying this property, the study will be assigned to the reference genome specified in `portal.properties` (property `ucsc.build`).
 
 ### Example  
 An example meta_study.txt file would be:
@@ -403,7 +403,7 @@ All genes referenced in the custom driver annotation file must be present in the
 
 The `cbp_driver` column flags the mutation as either driver or passenger. In cBioPortal, passenger mutations are also known as variants of unknown significance (VUS). The `cbp_driver_tiers` column assigns an annotation tier to the mutation, such as "Driver", "Highly actionable" or "Potential drug target". When a tier is selected, mutations with that annotation are highlighted as driver. Both types of custom annotations contain a second column with the suffix `_annotation`, to add a description. This is displayed in the tooltip that appears when hovering over the sample's custom annotation icon in the OncoPrint view.
 
-You can learn more about configuring these annotations in the [application.properties documentation](/deployment/customization/application.properties-Reference.md#custom-annotation-of-driver-and-passenger-mutations). When properly configured, the customized annotations appear in the "Mutation Color" menu of the OncoPrint view: \
+You can learn more about configuring these annotations in the [portal.properties documentation](/deployment/customization/portal.properties-Reference.md#custom-annotation-of-driver-and-passenger-mutations). When properly configured, the customized annotations appear in the "Mutation Color" menu of the OncoPrint view: \
 ![schreenshot mutation color menu](images/screenshot-mutation-color-menu.png) 
 
 ### Example
@@ -769,7 +769,7 @@ It is possible to manually add columns for defining custom driver annotations. T
 
 The `cbp_driver` column flags the mutation as either driver or passenger. In cBioPortal, passenger mutations are also known as variants of unknown significance (VUS). The `cbp_driver_tiers` column assigns an annotation tier to the mutation, such as "Driver", "Highly actionable" or "Potential drug target". When a tier is selected, mutations with that annotation are highlighted as driver. Both types of custom annotations contain a second column with the suffix `_annotation`, to add a description. This is displayed in the tooltip that appears when hovering over the sample's custom annotation icon in the OncoPrint view.
 
-You can learn more about configuring these annotations in the [application.properties documentation](/deployment/customization/application.properties-Reference.md#custom-annotation-of-driver-and-passenger-mutations). When properly configured, the customized annotations appear in the "Mutation Color" menu of the OncoPrint view: \
+You can learn more about configuring these annotations in the [portal.properties documentation](/deployment/customization/portal.properties-Reference.md#custom-annotation-of-driver-and-passenger-mutations). When properly configured, the customized annotations appear in the "Mutation Color" menu of the OncoPrint view: \
 ![schreenshot mutation color menu](/images/screenshot-mutation-color-menu.png) 
 
 ### Adding your own mutation annotation columns

docs/Hardware-Requirements.md

@@ -22,4 +22,4 @@ Another possible consideration is caching. The portal can cache responses to
 requests so that repeated database queries are avoided. On the public cBioPortal
 deployment we enable this cache and allocate 1GB of additional RAM and 4GB of
 additional disk space for caching. For directions on configuring caching, see
-[Ehcache Settings](/deployment/customization/application.properties-Reference.md#cache-settings)
+[Ehcache Settings](/deployment/customization/portal.properties-Reference.md#cache-settings)

docs/Import-Gene-Panels.md

@@ -30,7 +30,7 @@ cd <cbioportal_source_folder>/core/src/main/scripts
 ```
 
 After loading gene panels into the database, please restart Tomcat or call the `/api/cache` endpoint with a `DELETE` http-request
-(see [here](/deployment/customization/application.properties-Reference.md#cache-settings) for more information) so that the
+(see [here](/deployment/customization/portal.properties-Reference.md#cache-settings) for more information) so that the
 validator can retrieve gene panel information from the cBioPortal API. 
 
 #### Update existing gene panel

docs/Import-Gene-Sets.md

@@ -31,7 +31,7 @@ Note: This removes existing gene set, gene set hierarchy and gene set genetic pr
 ```
 
 4. Restart Tomcat if you have it running or call the `/api/cache` endpoint with a `DELETE` http-request
-   (see [here](/deployment/customization/application.properties-Reference.md#evict-caches-with-the-apicache-endpoint) for more information).
+   (see [here](/deployment/customization/portal.properties-Reference.md#evict-caches-with-the-apicache-endpoint) for more information).
 
 
 5. Import study (replace argument after `-u` with local cBioPortal and `-html` with preferred location for html report):

docs/Import-Study-Using-Docker.md

@@ -1,7 +1,7 @@
 # Import Study Using Docker
 
 :warning: Every time you add/remove/overwrite a study please restart tomcat (or the Docker container), or 
-call the `/api/cache` endpoint with a `DELETE` http-request (see [here](/deployment/customization/application.properties-Reference.md#evict-caches-with-the-apicache-endpoint) for more information).
+call the `/api/cache` endpoint with a `DELETE` http-request (see [here](/deployment/customization/portal.properties-Reference.md#evict-caches-with-the-apicache-endpoint) for more information).
 
 ## Adding a Study
 

docs/MSK-Maintenance.md

@@ -61,10 +61,10 @@ 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-cron/git-repos/cbioportal/src/main/resources/application.properties`
+        - `vi /data/portal-cron/git-repos/cbioportal/src/main/resources/portal.properties`
     - Move to directory
         - `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/application.properties --sql db-scripts/src/main/resources/migration.sql`
+        - `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
     - Access database and verify the DB scheme is updated

docs/SUMMARY.md

@@ -33,9 +33,8 @@
     * [Authenticating and Authorizing Users via Keycloak](deployment/authorization-and-authentication/Authenticating-and-Authorizing-Users-via-keycloak.md)
     * [Authenticating Users via Tokens](deployment/authorization-and-authentication/Authenticating-Users-via-Tokens.md)
   * [Customization]()
-    * [Customizing your cBioPortal Instance via application.properties](deployment/customization/Customizing-your-instance-of-cBioPortal.md)
-    * [More application.properties Settings](deployment/customization/application.properties-Reference.md)
-    * [Security Properties Settings](deployment/customization/security.properties-Reference.md)
+    * [Customizing your cBioPortal Instance via portal.properties](deployment/customization/Customizing-your-instance-of-cBioPortal.md)
+    * [More portal.properties Settings](deployment/customization/portal.properties-Reference.md)
     * [Configuring Caching Behavior](deployment/customization/Caching.md)
     * [How does the study view organize the charts](deployment/customization/Studyview.md)
     * [Utilize priority setting from database to visualize charts](deployment/customization/Studyview.md)

docs/Support-multiple-reference-genomes.md.BK

@@ -11,7 +11,7 @@ and migrate your database schema to the latest version. The migrartion script by
 if your study is profiled by a reference geome other than a default genome value listed in your portal properties file.
 
 **Important Note**
-* Add the following default values to your application.properties file. Those default genome values will be used by the validation script when importing a new study.
+* Add the following default values to your portal.properties file. Those default genome values will be used by the validation script when importing a new study.
 ```# species and genomic information
    species=human
    ncbi.build=GRCh37

docs/Updating-gene-and-gene_alias-tables.md

@@ -41,7 +41,7 @@ ALTER TABLE `geneset` AUTO_INCREMENT = 1;
 ```
 
 4- Restart cBioPortal (restart webserver)  or call the `/api/cache` endpoint with a `DELETE` http-request
-(see [here](/deployment/customization/application.properties-Reference.md#evict-caches-with-the-apicache-endpoint) for more information)
+(see [here](/deployment/customization/portal.properties-Reference.md#evict-caches-with-the-apicache-endpoint) for more information)
 to clean-up any cached gene lists.
 
 5- To import gene data type the following commands when in the folder `<cbioportal_source_folder>/core/src/main/scripts`:

docs/Updating-your-cBioPortal-installation.md

@@ -12,11 +12,11 @@ DB schema version expected by Portal: yyy
 ```
 where `xxx` and `yyy` will be different version numbers. 
 
-If you get `DB version expected by Portal: 0` (i.e. you are building the new release from source), you need to  add a new property to your `application.properties` file which is needed for this check. 
+If you get `DB version expected by Portal: 0` (i.e. you are building the new release from source), you need to  add a new property to your `portal.properties` file which is needed for this check. 
 
 #### Step1
 
-In your `application.properties` file (e.g. `<your_cbioportal_dir>/src/main/resources/application.properties`) add the following property:
+In your `portal.properties` file (e.g. `<your_cbioportal_dir>/src/main/resources/portal.properties`) add the following property:
 ```
 # this is the *expected* DB version (expected by the code). Don't set it manually, it is filled by maven:
 db.version=${db.version}
@@ -28,7 +28,7 @@ Compile your code again. After restarting the webserver the page should now stat
 
 ## Running the migration script
 
-First, make sure you have the DB connection properties correctly set in your application.properties file (see [DB connection settings here](/deployment/customization/application.properties-Reference.md#database-settings)).
+First, make sure you have the DB connection properties correctly set in your portal.properties file (see [DB connection settings here](/deployment/customization/portal.properties-Reference.md#database-settings)).
 
 **Dependencies:** the migration script is a Python script that depends on the `mysqlclient` library. If necessary, you can install it with the following commands (example for Ubuntu):
 ```console
@@ -70,4 +70,4 @@ etc
 ```
 
 **Final step:** Restart your webserver or call the `/api/cache` endpoint with a `DELETE` http-request
-(see [here](/deployment/customization/application.properties-Reference.md#evict-caches-with-the-apicache-endpoint) for more information).
+(see [here](/deployment/customization/portal.properties-Reference.md#evict-caches-with-the-apicache-endpoint) for more information).

docs/Using-the-dataset-validator.md

@@ -776,7 +776,7 @@ cBioPortal is gradually introducing support for mouse. If you want to load mouse
 
 As an example, the command for the mouse example using the three parameters is given:
 ```
-./validateData.py -s ../../../test/scripts/test_data/study_es_0/ -P ../../../../../src/main/resources/application.properties -u http://localhost:8080 -v
+./validateData.py -s ../../../test/scripts/test_data/study_es_0/ -P ../../../../../src/main/resources/portal.properties -u http://localhost:8080 -v
 ```
 
 ## Running the validator for multiple studies

docs/deployment/authorization-and-authentication/Authenticating-Users-via-SAML.md

@@ -121,7 +121,7 @@ both keystore and secure-key. This seems to be an extra restriction by Tomcat.
 
 ## Modifying configuration
 
-Within application.properties, make sure that:
+Within portal.properties, make sure that:
 
     app.name=cbioportal
 
@@ -197,7 +197,7 @@ Next, please read the Wiki page on [User Authorization](User-Authorization.md),
 
 ## Configuring the Login.html Page (not applicable to most external IDPs)
 
-The login page is configurable via the `application.properties` properties `skin.authorization_message` and `skin.login.saml.registration_htm`. 
+The login page is configurable via the `portal.properties` properties `skin.authorization_message` and `skin.login.saml.registration_htm`. 
 For example in `skin.authorization_message` you can be set to something like this:
 
 ```

docs/deployment/authorization-and-authentication/Authenticating-Users-via-Tokens.md

@@ -37,7 +37,7 @@ A step-by-step guide to configure KeyCloak to provide OAuth2 client functionalit
 
 ### Modifying Configuration
 
-The following properties must be present in application.properties in order to allow direct access to the cBioPortal web service when login is required:
+The following properties must be present in portal.properties in order to allow direct access to the cBioPortal web service when login is required:
 
 **Property**: dat.method (required)