Merge branch 'cBioPortal:master' into 10299-genetable-version

docs/Donate.md

@@ -0,0 +1,21 @@
+## The cBioPortal Foundation
+
+The mission of cBioPortal Foundation is to support the development and adoption of the cBioPortal for Cancer Genomics, open-source software for the interactive exploration of multidimensional cancer genomics data sets. The cBioPortal aims to significantly lower the barriers between complex genomic data and cancer researchers by providing rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects, and by doing so, empower researchers to translate these rich data sets into biologic insights and clinical applications.
+
+The cBioPortal Foundation will help further the mission of cBioPortal by supporting hackathons, user meetings, internships and other activities. 
+
+## Contribute to cBioPortal Foundation
+
+**TAX-DEDUCTIBLE CONTRIBUTIONS**
+
+**Grants or distributions accepted from:**  
+Individuals • Corporations • Donor-Advised Funds • Foundations  
+Retirement Accounts • Charitable Trusts
+
+**Donate any asset with established or appraisable value, such as:**  
+Stocks • Bonds • Real Estate • Collectibles • Art  
+Cryptocurrency • Privately Held Business Interests  
+
+[Asset & Large Contributions](https://lohas.org/client/cbioportal-foundation/#donation_form)
+
+[Online Donations](https://abqwvktl.donorsupport.co/page/FUNFLDNZDHK)

docs/SUMMARY.md

@@ -73,4 +73,4 @@
   * [Release Procedure](development/Release-Procedure.md)
   * [Deployment Procedure](development/Deployment-Procedure.md)
   * [This documentation site](development/Documentation-site.md)
-
+* [Donate](Donate.md)

docs/deployment/deploy-without-docker/Import-the-Seed-Database.md

@@ -17,23 +17,23 @@ After download, the files can be unzipped by entering the following command:
 1. Import the database schema (/db-scripts/src/main/resources/cgds.sql):
 
     ```
-    mysql --user=cbio_user --password=somepassword cbioportal < cgds.sql
+    mysql --user=cbio --password=P@ssword1 cbioportal < cgds.sql
     ```
 
     Note that this may currently fail when using the default character encoding on MySQL 8.0 (`utf8mb4`); this is why MySQL 5.7 (which uses `latin1`) is recommended.
 
 2. Import the main part of the seed database:
 
     ```
-    mysql --user=cbio_user --password=somepassword cbioportal < seed-cbioportal_RefGenome_vX.Y.Z.sql
+    mysql --user=cbio --password=P@ssword1 cbioportal < seed-cbioportal_RefGenome_vX.Y.Z.sql
     ```
 
     **Important:** Replace `seed-cbioportal_RefGenome_vX.Y.Z.sql` with the downloaded version of the seed database, such as `seed-cbioportal_hg19_v2.3.1.sql` or `seed-cbioportal_mm10_v2.3.1.sql`.
 
 3. (Human only) Import the Protein Data Bank (PDB) part of the seed database. This will enable the visualization of PDB structures in the mutation tab. Loading this file takes more time than loading the previous files, and is optional for users that do not require PDB structures.
 
     ```
-    mysql --user=cbio_user --password=somepassword cbioportal < seed-cbioportal_hg19_vX.Y.Z_only-pdb.sql
+    mysql --user=cbio --password=P@ssword1 cbioportal < seed-cbioportal_hg19_vX.Y.Z_only-pdb.sql
     ```
     **Important:** Replace `seed-cbioportal_hg19_vX.Y.Z_only-pdb.sql` with the downloaded version of the PDB database, such as `seed-cbioportal_hg19_v2.3.1_only-pdb.sql`.
 

pom.xml

@@ -12,7 +12,7 @@
 
 	<groupId>org.cbioportal</groupId>
 	<artifactId>cbioportal</artifactId>
-	<version>6.0.22-SNAPSHOT</version>
+	<version>6.0.23-SNAPSHOT</version>
 
 	<description>cBioPortal for Cancer Genomics</description>
 
@@ -27,7 +27,7 @@
 		<!--        TODO replace with version of cbioportal frontend with compatible
         login url-->
 		<frontend.groupId>com.github.cbioportal</frontend.groupId>
-		<frontend.version>v6.0.21</frontend.version>
+		<frontend.version>v6.0.22</frontend.version>
 
         <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
 		<db.version>2.13.1</db.version>

src/main/java/org/cbioportal/WebAppConfig.java

@@ -37,7 +37,7 @@ public void addViewControllers(ViewControllerRegistry registry) {
 		registry.addRedirectViewController("/installations", "https://installationmap.netlify.app/");
 		registry.addRedirectViewController("/tutorials", "https://docs.cbioportal.org/user-guide/overview/#tutorial-slides");
 		registry.addRedirectViewController("/oql", "https://docs.cbioportal.org/user-guide/oql/");
-        registry.addRedirectViewController("/faq", "https://docs.cbioportal.org/user-guide/faq/");
+        registry.addRedirectViewController("/donate", "https://docs.cbioportal.org/donate/");
 
 		List<String> endpoints = List.of(
 			"/results/*",

src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java

@@ -181,6 +181,7 @@ public enum FrontendProperty {
         skin_patient_view_structural_variant_table_columns_show_on_init("skin.patient_view.structural_variant_table.columns.show_on_init", null),
         skin_results_view_tables_default_sort_column("skin.results_view.tables.default_sort_column", null),
         skin_survival_plot_clinical_event_types_show_on_init("skin.survival_plot.clinical_event_types.show_on_init", null),
+        skin_show_donate_button("skin.show_donate_button", "false"),
 
         skin_patient_view_tables_default_sort_column("skin.patient_view.tables.default_sort_column", null),
         enable_treatment_groups("enable_treatment_groups", null),

src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java

@@ -153,6 +153,9 @@ public List<GeneMolecularData> getMolecularDataInMultipleMolecularProfiles(List<
 
         Map<String, MolecularProfileSamples> commaSeparatedSampleIdsOfMolecularProfilesMap =  molecularDataRepository
                 .commaSeparatedSampleIdsOfMolecularProfilesMap(distinctMolecularProfileIds);
+        if (commaSeparatedSampleIdsOfMolecularProfilesMap.size() == 0) {
+            return molecularDataList;
+        }
 
         Map<String, Map<Integer, Integer>> internalSampleIdsMap = new HashMap<>();
         List<Integer> allInternalSampleIds = new ArrayList<>();

src/main/resources/webapp/config_service.jsp

@@ -84,6 +84,7 @@
             "skin.show_tutorials_tab",
             "skin.show_web_api_tab",
             "skin.show_tweet_button",
+            "skin.show_donate_button",
             "skin.patientview.filter_genes_profiled_all_samples",
             "skin.patientview.show_mskcc_slide_viewer",
             "skin.home_page.show_unauthorized_studies",