Merge branch 'master' into issue-10652-Java-Formatter

.github/workflows/integration-test.yml

@@ -10,15 +10,9 @@ jobs:
       PORTAL_INFO_DIR: /home/runner/work/cbioportal/cbioportal/portalInfo
     steps:
       - name: 'Checkout cbioportal repo'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           path: ./cbioportal
-      - name: 'Install python requirements'
-        working-directory: ./cbioportal
-        run: |
-          sudo apt-get install python3-setuptools && \
-          pip3 install -U wheel && \
-          pip3 install -r ./requirements.txt
       - name: 'Set up JDK 21'
         uses: oracle-actions/setup-java@v1
         with:

dev/README.md

@@ -40,7 +40,7 @@ spring.security.oauth2.client.provider.keycloak.issuer-uri=http://localhost:8084
 spring.security.oauth2.client.provider.keycloak.user-name-attribute=email
 ```
 
-4. Set the following in _portal.properties_:
+4. Set the following in _application.properties_:
 
 ```properties
 persistence.cache_type=no-cache
@@ -55,4 +55,4 @@ spring.datasource.driver-class-name=com.mysql.jdbc.Driver
 
 4. Start cBioPortal application on port 8080. The login credentials are `testuser:P@assword1`.
 
-⚠️ Warning: Do not use this directly for production use as it takes several shortcuts to get a quick keycloak instance up.
+⚠️ Warning: Do not use this directly for production use as it takes several shortcuts to get a quick keycloak instance up.

docs/404.md

@@ -32,7 +32,8 @@ window.redirectMap = {
     "2.2-authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak":"deployment/authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak",
     "2.2-authorization-and-authentication/authenticating-users-via-tokens":"deployment/authorization-and-authentication/authenticating-users-via-tokens",
     "2.3-customization/customizing-your-instance-of-cbioportal":"deployment/customization/customizing-your-instance-of-cbioportal",
-    "2.3-customization/portal.properties-reference":"deployment/customization/portal.properties-reference",
+    "2.3-customization/portal.properties-reference":"deployment/customization/application.properties-reference/",
+    "deployment/customization/portal.properties-reference":"deployment/customization/application.properties-reference/",
     "2.3-customization/caching":"deployment/customization/caching",
     "2.3-customization/layout":"deployment/customization/studyview/#how-does-the-study-view-organize-the-charts",
     "2.3-customization/priority":"deployment/customization/studyview/#study-view-customization-with-priority-data",

docs/News.md

@@ -1,3 +1,18 @@
+## Mar 5, 2024
+*   **Local Installations Feature**: Make representation of custom driver annotation configurable:
+    ![image](https://github.com/cBioPortal/cbioportal/assets/1334004/f67fd82f-1789-4427-9ca1-f17fc70c1a09)
+
+## Feb 7, 2024
+* **New feature**: The _Datasets Page_ now lists what studies have samples profiled for Structural Variants:
+
+    ![image](https://github.com/cBioPortal/cbioportal/assets/1334004/0e4e73e4-d9d8-417d-912c-710163480905)
+
+* **New Major Release**: **v6.0.0** includes a major repackaging of the backend software to improve the development experience. The backend has been upgraded to use Java Spring Boot v3.1.4. The CORE and MAF modules have been moved to new repositories. All other modules have been compacted into a single source repository. We have also updated the JVM to 21 and many libraries have been updated to address security and performance issues. See more information in the [v6.0.0 release notes](https://github.com/cBioPortal/cbioportal/releases/tag/v6.0.0).
+
+* **Local Installations Feature**: When mutational signature data is loaded, show COSMIC reference signatures on the _Patient View_:
+
+    ![image](https://github.com/cBioPortal/cbioportal/assets/1334004/10f73baa-d28c-4bb7-ad62-4751bd7f61cd)
+
 ## Dec 29, 2023
 *   **Added data** consisting of 5,120 samples from 13 studies:
 	* [Endometrial Cancer (MSK, Cancer Discovery 2023)](https://www.cbioportal.org/study/summary?id=ucec_ancestry_cds_msk_2023) *1882 samples*
@@ -16,6 +31,38 @@
 
 *   **Gene Tables Update:** Updated tables of genes (main and alias), based on [Oct 1, 2023 HGNC release](http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/). See seedDB release notes [here](https://github.com/cBioPortal/datahub/tree/master/seedDB#latest-seed-database-schema-2131) for details.
 
+## Dec 5, 2023
+* **New feature**: Filter by data types on the homepage:
+
+    ![image](https://github.com/cBioPortal/cbioportal/assets/1334004/cf6d5486-bfd7-4f69-add0-442dbb4d354a)
+* **New feature**: Change colors of tracks in Oncoprint:
+
+    <img src="https://github.com/cBioPortal/cbioportal/assets/1334004/301b0efb-3063-44db-bc4c-86973e7c566a" width="700" />
+
+* **New feature**: Show alteration frequencies per group in OncoPrint. [Example: RTK-RAS alterations in Smokers vs Never Smokers Lung Cancer Cases in MSK-IMPACT Clinical Sequencing Cohort](https://bit.ly/3PwKsDJ)
+
+    <img src="https://github.com/cBioPortal/cbioportal/assets/1334004/f2a9576e-c06d-447a-8eac-f0292bd1f935" width="700" />
+
+## Oct 17, 2023
+* **New feature**: Survival charts with landmark events and hazard ratios. [Example: TP53 in Lung Cancer Cases in MSK-IMPACT Clinical Sequencing Cohort](https://bit.ly/48QktxS)
+
+    <img src="https://github.com/cBioPortal/cbioportal/assets/1334004/dc97c3ae-ebd7-4cd3-bb76-165517c9d2ba" width="700" />
+
+## Oct 3, 2023
+* **New feature**: New Structural Variants Tab on _Results View_. [Example: TMPRSS2 Structural Variants in MSK-IMPACT Clinical Sequencing Cohort](https://bit.ly/49FDhRk)
+
+    <img src="https://github.com/cBioPortal/cbioportal/assets/1334004/141e2817-3300-4af2-a845-005403d75e74" width="700" />
+
+## Sep 5, 2023
+* **New feature**:  Add gene-specific CNA charts to show all levels of copy number alterations (including gain and hetloss) on _Study View_:
+
+    <img src="https://github.com/cBioPortal/cbioportal/assets/1334004/873401ad-cbcf-4b07-9b80-8487af5abb18" width="700" />
+
+## Aug 30, 2023
+* **Enhancement**: Exclude a patient from your selection directly from the _Patient View_:
+
+    ![image](https://github.com/cBioPortal/cbioportal/assets/1334004/501fe998-8408-48e3-a183-e27ab3ff3f28)
+
 ## Aug 21, 2023
 *   **Added data** consisting of 4,488 samples from 7 studies:
 	* [Lung Adenocarcinoma Met Organotropism (MSK, Cancer Cell 2023)](https://www.cbioportal.org/study/summary?id=luad_mskcc_2023_met_organotropism) *2653 samples*
@@ -26,6 +73,7 @@
     * [Bladder Cancer (Columbia University/MSK, Cell 2018)](https://www.cbioportal.org/study/summary?id=bladder_columbia_msk_2018) *130 samples*
     * [Myoepithelial Carcinomas of Soft Tissue (WCM, CSH Molecular Case Studies 2022)](https://www.cbioportal.org/study/summary?id=stmyec_wcm_2022) *12 samples*
 
+
 *   **Gene Tables Update:** Updated tables of genes (main and alias), based on [Apr 1, 2023 HGNC release](http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/). See seedDB release notes [here](https://github.com/cBioPortal/datahub/tree/master/seedDB#latest-seed-database) for details.
 
 ## Aug 1, 2023
@@ -39,12 +87,23 @@
 
     Several users pointed out that using a one-sided test was incorrect for these comparisons. Please see discussions [here](https://github.com/cBioPortal/cbioportal/issues/9943) for more information.
 
+## Jul 18, 2023
+* **New Feature**: Add mutations table and two-sided exact p-value to comparison. [Example: AR mutations in Primary vs Metastatic Prostate Cancer samples in MSK-IMPACT Clinical Sequencing Cohort](https://www.cbioportal.org/comparison/mutations?sessionId=5cf89323e4b0ab413787436c&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D&selectedGene=AR)
+
+    <img src="https://github.com/cBioPortal/cbioportal/assets/1334004/da0cd1ef-b9b4-49f0-a9d3-42cff0204dc2" width="700" />
+
+
 ## May 2, 2023
 *   **New Feature**: The mutations tab now shows variant annotations from the [repository of Variant with Unexpected Effects (reVUE)](https://www.cancerrevue.org/).
+
     <img src="https://user-images.githubusercontent.com/16869603/234271379-6a0876ea-8477-426e-a0e4-5e0b0b66aef9.gif" width="700" />
 
+## Apr 25, 2023
+*   **Local Installations Feature**: When custom driver annotations for structural variants are loaded, one can now filter by them in both the Oncoprint and the _Study View_. 
+
 ## Apr 11, 2023
 *   **New Feature**: Disable autocommit and manually commit filters in study view. Manually commit filters can improve cBioPortal performance when query large dataset.
+
     <img src="https://user-images.githubusercontent.com/3323006/221857599-1eb6e9a5-55c7-4fb5-bc14-283699be0990.png" width="700" />
     <img src="https://user-images.githubusercontent.com/3323006/221858244-bf359850-79b5-4f9c-8008-6b5271721854.png" width="700" />
 
@@ -61,21 +120,23 @@
 
 ## Apr 4, 2023
 *   **New Feature**: Allow numeric data type for custom data charts.
+
     <img src="https://user-images.githubusercontent.com/33220871/222459360-9c251f7f-1005-442f-811d-dd1ee1103161.png" width="700" />
     <img src="https://user-images.githubusercontent.com/33220871/222460439-ac7007c8-059a-4ecc-816c-90752adff444.png" width="700" />
 
     This also allows to have numerical custom data after we query based on genes (custom data 2 in the image):
+
     <img src="https://user-images.githubusercontent.com/33220871/223729410-03a094f4-7671-453f-b8b8-f7bc10b61c7c.png" width="700" />
     <img src="https://user-images.githubusercontent.com/33220871/223729522-fd9e19e2-6218-40d4-b9fb-f253c4faa858.png" width="700" />
 
 ## Jan 10, 2023
-*   **New Feature**: New Pathways tab on the Group Comparison view. 
-    [Example: Primary vs Metastasis samples in MSK-IMPACT Clinical Sequencing Cohort](https://www.cbioportal.org/comparison/pathways?comparisonId=61791fa92e3200072db9b64e&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D)
+*   **New Feature**: New Pathways tab on the Group Comparison view. [Example: Primary vs Metastasis samples in MSK-IMPACT Clinical Sequencing Cohort](https://www.cbioportal.org/comparison/pathways?comparisonId=61791fa92e3200072db9b64e&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D)
+
     <img src="https://user-images.githubusercontent.com/15748980/235750129-661682f7-6593-4b7e-8873-ebba70eeae32.png" width="700" />
 
 ## Dec 13, 2022
-*   **New Feature**: New Mutations tab on the Group Comparison view.
-    [Example: Primary vs Metastasis samples in MSK-IMPACT Clinical Sequencing Cohort](https://www.cbioportal.org/comparison/mutations?comparisonId=61791fa92e3200072db9b64e&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D)
+*   **New Feature**: New Mutations tab on the Group Comparison view. [Example: Primary vs Metastasis samples in MSK-IMPACT Clinical Sequencing Cohort](https://www.cbioportal.org/comparison/mutations?comparisonId=61791fa92e3200072db9b64e&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D)
+
     <img src="https://user-images.githubusercontent.com/15748980/235748831-78652ccd-b3ab-496f-9626-74ceb8c7230d.png" width="700" />
 
 ## Oct 12, 2022
@@ -92,7 +153,8 @@
 	* [Urothelial Carcinoma (BCAN/HCRN 2022)](http://www.cbioportal.org/study/summary?id=blca_bcan_hcrn_2022) *203 samples*
 
 ## Sep 6, 2022
-*   **Enhancement**: Oncoprint can now save clinical tracks after login
+*   **Enhancement**: Oncoprint can now save clinical tracks after login:
+
     <img src="https://user-images.githubusercontent.com/3323006/188828765-ded10947-7343-49dd-b605-50b58b67a388.png" width="700" />
 
 ## Aug 11, 2022
@@ -115,6 +177,7 @@
 
 ## May 31, 2022
 * **New Feature**: Added Quartiles, Median split and Generate bins options for bar charts on the study view page, where Generate bins allows user to define bin size and min value
+
     <img src="https://github.com/cBioPortal/cbioportal/assets/1334004/290e6d45-1c10-4a51-a823-24db27063486" width="700" />
 
 
@@ -200,6 +263,7 @@
     * [MSK MetTropism (MSK, Cell 2021)](https://www.cbioportal.org/study/summary?id=msk_met_2021) *25,775 samples*
     * [Cancer Therapy and Clonal Hematopoiesis (MSK, 2021)](https://www.cbioportal.org/study/summary?id=msk_ch_ped_2021) *657 samples*
 
+
 *   **Added TMB (nonsynonymous) scores** for all studies. [Example: new TMB field for study gbm_cptac_2021](https://www.cbioportal.org/study/clinicalData?id=gbm_cptac_2021)   
     (Details for the calculation can be found [HERE](https://github.com/cBioPortal/datahub-study-curation-tools/blob/master/tmb/calculate_tmb/Readme.md))   
     <img width="361" alt="Screen Shot 2022-01-04 at 11 39 20 PM" src="https://user-images.githubusercontent.com/5973438/148133673-a23506e9-7957-4581-99f0-820ca9548672.png">
@@ -340,6 +404,7 @@
     <img src="https://user-images.githubusercontent.com/1334004/104649378-9f1ac100-5682-11eb-91eb-4e0f024a4ded.png" width="700">
 
 *   **New Feature**: Display and compare generic assays, such as microbiome and treatment response, on the study view [Example: Prasinovirus microbiome signatures in TCGA](https://www.cbioportal.org/study?id=6000b6aae4b015b63e9d4d44)
+
     <img src="https://user-images.githubusercontent.com/1334004/104651211-54e70f00-5685-11eb-94f1-f20930793c28.png" width="700">
 
 *   **New Feature**: The Plots tab on _Results View_ now allows you to group alterations by Driver and VUS [Example: POLE driver mutations vs VUSs against mutation counts in TCGA Colorectal Adenocarcinoma](https://bit.ly/3ssY9Gu)

docs/deployment/deploy-without-docker/Build-from-Source.md

@@ -2,37 +2,10 @@
 
 ## Building with Maven
 
-While building, you must point the environment variable `PORTAL_HOME` to
-the root directory containing the portal source code.
-
-For example, run a command like the following if on macOS:
-```
-export PORTAL_HOME=/Users/ecerami/dev/cbioportal
-```
-
-To compile the cBioPortal source code, move into the source directory and
-run the following maven command:
+To compile the cBioPortal source code, move into the root directory and run the following maven command:
 
 ```
 mvn -DskipTests clean install
 ```
 
-After this command completes, you will find a `cbioportal.war` file suitable
-for Apache Tomcat deployment in `portal/target/`. It is not neccessary to
-install Tomcat yourself, since a command line runnable version of Tomcat is
-provided as a dependency in `portal/target/dependency/webapp-runner.jar`.
-
-However, if you will be deploying to a standalone Tomcat installation, and
-if you have configured Tomcat to use the Redisson client for user session
-management, you should expect a clash between the Redisson client being
-used for session management and the Redisson client which is embedded in
-the cbioportal.war file for the optional "redis" persitence layer caching
-mode. In this case, you should avoid using the "redis" option for the portal
-property `persistence.cache_type` and you should prevent the Redisson
-client from being packaged in cbioportal.war by building with this command
-instead:
-
-##### alternative for standalone tomcat deployments which use redis session management
-```
-mvn -Dexclude-redisson -DskipTests clean install
-```
+Note: cBioPortal 6.X requires Java 21