Merge pull request #11816 from cBioPortal/master

Merge master into rc-7.0-clickhouse-only

Author: dippindots

.github/workflows/dockerimage.yml

@@ -28,6 +28,7 @@ jobs:
           # The latest tag will also be generated on tag event with a valid semver tag
           tags: |
             type=ref,event=branch
+            type=ref,event=tag
             type=semver,pattern={{version}}
 
       - name: Login to DockerHub
@@ -75,6 +76,7 @@ jobs:
               suffix=-web-shenandoah
             tags: |
               type=ref,event=branch
+              type=ref,event=tag
               type=semver,pattern={{version}}
 
         - name: Login to DockerHub

docs/Create-And-Publish-Virtual-Study.md

@@ -2,6 +2,8 @@
 
 A [Virtual Study](./user-guide/faq.md#what-is-a-virtual-study) defines a subset or a combination of samples from one or more studies in the system.
 
+A [Virtual Study](./user-guide/faq.md#what-is-a-virtual-study) is a custom study made up of samples from one or more existing studies. By default, a virtual study appears only under **My Virtual Studies** for its author. When it is published to the `/api/public_virtual_studies` endpoint, it becomes a **public virtual study** that is visible to all users on the landing page and can be used as a shared, reusable cohort. Publishing works for both static virtual studies (saved cohorts) and dynamic virtual studies whose contents are recomputed from filters on each load.
+
 *Note*: To publish or un-publish a virtual study, your cBioPortal instance must be configured with  `session.endpoint.publisher-api-key` in the `application.properties`.
 
 ## Create Virtual Study
@@ -23,28 +25,53 @@ You can always find the ID of the virtual study from the URL of the page that op
 
 ## Publish Virtual Study
 
-To publish a virtual study, you need to supply the publisher API key in the `X-PUBLISHER-API-KEY` header.
+Publishing requires the publisher API key in the `X-PUBLISHER-API-KEY` header and can now happen in two different ways:
+
+1. **Create in the UI, then publish by hash ID.** This is the original workflow where you first create a virtual study through the interface (the ID in the study URL is a MongoDB hash), and then publish that specific study.
+2. **Create and publish with a custom ID.** This RFC96 addition lets you publish a public virtual study in a single request by providing its definition (constraints/filters) and the desired ID. The ID must be unique and is typically a human-readable string so permissions can be managed up front.
+
+### Publish an existing virtual study
+
+After creating the study in the UI and copying its ID (hash), publish it via:
 
-Here is a curl command to publish a virtual study:
 ```shell
 curl \
   -X POST \
   -H 'X-PUBLISHER-API-KEY: <session.endpoint.publisher-api-key>' \
   -v 'http://<cbioportal_host>/api/public_virtual_studies/<virtual_study_id>'
 ```
-The published virtual study will appear under the `Public Virtual Studies` section (next to the `My Virtual Studies` section) on the landing page for all users of cBioPortal.
 
-While publishing, you can specify the PubMed ID (`pmid`) and `typeOfCancerId` of the virtual study using the following command:
+You can set optional metadata while publishing:
+
 ```shell
 curl \
   -X POST \
   -H 'X-PUBLISHER-API-KEY: <session.endpoint.publisher-api-key>' \
   -v 'http://<cbioportal_host>/api/public_virtual_studies/<virtual_study_id>?pmid=<pmid>&typeOfCancerId=<code>'
 ```
 
-The type of cancer code should match the known types of cancers in the cBioPortal database.
-If the type of cancer is specified, the published virtual study will appear under the respective cancer section on the landing page.
-Specifying the `pmid` enables a link to the PubMed page of the study.
+The `typeOfCancerId` must match an existing cancer type so it shows up in that category on the landing page; `pmid` links the public study to PubMed.
+
+### Create and publish with a custom ID
+
+To publish a new public virtual study in one go, call the same endpoint but supply:
+
+- `/<custom_id>` path segment with the ID you want to assign
+- `Content-Type: application/json`
+- A request body containing the virtual study definition (filters/constraints)
+
+Example:
+
+```shell
+curl \
+  -X POST \
+  -H 'X-PUBLISHER-API-KEY: <session.endpoint.publisher-api-key>' \
+  -H 'Content-Type: application/json' \
+  -v 'http://<cbioportal_host>/api/public_virtual_studies/<custom_id>' \
+  --data-raw @virtual_study_definition.json
+```
+
+The JSON payload should follow the format returned by the `/api/session/virtual_study` endpoint (fields such as `name`, `description`, `studyViewFilter`, and `studies`). If the ID already exists you will receive a `409 Conflict`. When the request succeeds, the virtual study is immediately available to all users under the `Public Virtual Studies` section, optionally enriched with `pmid` and `typeOfCancerId` query parameters the same way as above.
 
 ## Un-publish Virtual Study
 
@@ -58,4 +85,4 @@ curl \
   -X DELETE \
   -H 'X-PUBLISHER-API-KEY: <session.endpoint.publisher-api-key>' \
   -v 'http://<cbioportal_host>/api/public_virtual_studies/<virtual_study_id>'
-```
+```

docs/Data-Loading-Maintaining-Studies.md

@@ -6,6 +6,8 @@ This script can also be used to delete studies.
 - [Requirements](#requirements)
 - [Importing a study without validation](#importing-a-study-without-validation)
 - [Deleting a study](#deleting-a-study)
+- [Deleting patients](#deleting-patients)
+- [Deleting samples](#deleting-samples)
 
 ## Requirements
 This script requires `$PORTAL_HOME` to point to the folder containing your
@@ -58,3 +60,27 @@ You can also remove multiple studies at once by passing the Cancer Study Ids sep
 ./cbioportalImporter.py -c remove-study -id study1_id,study2_id,study3_id
 ```
 Where `study1_id`, `study2_id` and `study3_id` are the Cancer Study IDs of the studies you would like to remove.
+
+## Deleting patients
+To remove patients (and their associated samples and data) from one or more studies, run:
+```
+./cbioportalImporter.py remove-patients --study_ids <study_ids> --patient_ids <patient_ids>
+```
+Where `study_ids` is a comma-separated list of Cancer Study IDs to search and `patient_ids` is a comma-separated list of patient identifiers to delete.
+
+For example:
+```
+./cbioportalImporter.py remove-patients --study_ids study1_id --patient_ids patientA,patientB
+```
+
+## Deleting samples
+To remove specific samples from one or more studies, run:
+```
+./cbioportalImporter.py remove-samples --study_ids <study_ids> --sample_ids <sample_ids>
+```
+Where `study_ids` is a comma-separated list of Cancer Study IDs to search and `sample_ids` is a comma-separated list of sample identifiers to delete.
+
+For example:
+```
+./cbioportalImporter.py remove-samples --study_ids study1_id,study2_id --sample_ids sampleX,sampleY
+```

docs/News.md

@@ -1,3 +1,19 @@
+## Oct 31, 2025
+*   **Added data** consisting of 9,749 samples from 13 studies:
+    * [Mixed Tumors - MiMSI Cohort (MSK, Nat Commun 2024)](https://www.cbioportal.org/study/summary?id=pancan_mimsi_msk_2024) *5033 samples*
+    * [Cancer Cell Line Encyclopedia (Broad, Nat Rev Cancer 2025)](https://www.cbioportal.org/study/summary?id=ccle_broad_2025) *1970 samples*
+    * [Colorectal Cancer- ChangKang Project (SYSUCC, Nat Commun 2022)](https://www.cbioportal.org/study/summary?id=crc_sysucc_2022) *1015 samples*
+	* [Cancer Cell Line Encyclopedia (Genentech, Nat biotech 2014)](https://www.cbioportal.org/study/summary?id=ccle_genentech_2014) *675 samples*
+    * [Bladder Urothelial Carcinoma SWOG S1314 Trial (MSK, JCO Precis Oncol 2024)](https://www.cbioportal.org/study/summary?id=blca_msk_2024) *184 samples*
+    * [Pediatric solid tumor PDXs (UTHSA, Nat Commun 2023)](https://www.cbioportal.org/study/summary?id=pancan_pdx_uthsa_2023) *136 samples*
+    * [Solitary Fibrous Tumors (SYSUCC, Nat Commun 2023)](https://www.cbioportal.org/study/summary?id=sft_sysucc_2023) *131 samples*
+    * [Melanoma (MSK, Cell 2017) - iAtlas Harmonized](https://www.cbioportal.org/study/summary?id=mel_iatlas_riaz_nivolumab_2017) *107 samples*
+    * [Lung Adenocarcinoma (CAS, Cell 2020)](https://www.cbioportal.org/study/summary?id=luad_cas_2020) *103 samples*
+    * [Hereditary SDHB-Mutant Pheochromocytomas and Paragangliomas (A5 Consortium, Nature 2025)](https://www.cbioportal.org/study/summary?id=hnsc_a5consortium_2025) *94 samples*
+    * [Triple Negative Breast Cancer (DLDCCC, Cancer Discov 2022)](https://www.cbioportal.org/study/summary?id=brca_dldccc_2022) *75 samples*
+    * [Colorectal Adenocarcinoma (DFCI/Orion, BioRxiv 2024)](https://www.cbioportal.org/study/summary?id=crc_orion_2024) *74 samples*
+    * [Schwannoma (Children's Tumor Foundation, Acta Neuropathologica 2020)](https://www.cbioportal.org/study/summary?id=schw_ctf_synodos_2025) *52 samples*
+
 ## May 06, 2025
 *   **Added data** consisting of 4,571 samples from 10 studies:
     * [Pancreatic Adenocarcinoma (MSK, Nat Med 2024)](https://www.cbioportal.org/study/summary?id=pdac_msk_2024) *2336 samples*

docs/deployment/customization/security.properties-Reference.md

@@ -1,6 +1,6 @@
 # Security Properties
 
-The following are the properties for configuring authentication and authorization in the application. The cBioPortal application mainly uses Spring Security for auth configuration; see also [Spring Security](./../authorization-and-authentication/authorization-and-authentication/Spring-Security.md) docs.
+The following are the properties for configuring authentication and authorization in the application. The cBioPortal application mainly uses Spring Security for auth configuration; see also [Spring Security](./../authorization-and-authentication/Spring-Security.md) docs.
 
 ## Authentication Configuration
 

src/main/resources/mappers/export/GeneticProfileDataMapper.xml

@@ -32,8 +32,7 @@
             <result property="type" column="GENE_TYPE"/>
         </association>
     </resultMap>
-    <select id="getData" resultMap="GeneticProfileDataResultMap"
-            resultSetType="FORWARD_ONLY">
+    <select id="getData" resultMap="GeneticProfileDataResultMap" resultSetType="FORWARD_ONLY" resultOrdered="true">
         SELECT
             ga.VALUES,
             ga.GENETIC_ENTITY_ID,