From 5c89dbcb09d51e6b0d81d8a026bec04ef8d3bc4e Mon Sep 17 00:00:00 2001 From: Bryan Lai <56288120+gblaih@users.noreply.github.com> Date: Fri, 13 Dec 2024 10:53:32 -0500 Subject: [PATCH 1/9] fix issue with full data download failing with pie chart (#11239) Co-authored-by: Bryan Lai --- .../org/cbioportal/service/impl/MolecularDataServiceImpl.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java b/src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java index 57be74b44d3..40f60c0dbff 100644 --- a/src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java +++ b/src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java @@ -153,6 +153,9 @@ public List getMolecularDataInMultipleMolecularProfiles(List< Map commaSeparatedSampleIdsOfMolecularProfilesMap = molecularDataRepository .commaSeparatedSampleIdsOfMolecularProfilesMap(distinctMolecularProfileIds); + if (commaSeparatedSampleIdsOfMolecularProfilesMap.size() == 0) { + return molecularDataList; + } Map> internalSampleIdsMap = new HashMap<>(); List allInternalSampleIds = new ArrayList<>(); From 31fa62f688503a19e7794da5c3d2a93f424beaf3 Mon Sep 17 00:00:00 2001 From: Ino de Bruijn Date: Fri, 13 Dec 2024 13:41:26 -0500 Subject: [PATCH 2/9] add donate page to docs (#11282) * add donate page to docs * Update Donate.md --------- Co-authored-by: JJ Gao --- docs/Donate.md | 21 +++++++++++++++++++++ docs/SUMMARY.md | 2 +- 2 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 docs/Donate.md diff --git a/docs/Donate.md b/docs/Donate.md new file mode 100644 index 00000000000..ac356130fda --- /dev/null +++ b/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) diff --git a/docs/SUMMARY.md b/docs/SUMMARY.md index 68b1cd52e5d..e6b115126dc 100644 --- a/docs/SUMMARY.md +++ b/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] From 079b532a22e5431de63050b1580b423cf5810361 Mon Sep 17 00:00:00 2001 From: alisman Date: Fri, 13 Dec 2024 13:56:27 -0500 Subject: [PATCH 3/9] Add redirect to donate page (#11283) --- src/main/java/org/cbioportal/WebAppConfig.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/cbioportal/WebAppConfig.java b/src/main/java/org/cbioportal/WebAppConfig.java index 2ea3e019d65..0105465e96b 100644 --- a/src/main/java/org/cbioportal/WebAppConfig.java +++ b/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 endpoints = List.of( "/results/*", From 31b05a914c6a9443a1006f39f8e1cb36e8906630 Mon Sep 17 00:00:00 2001 From: Ino de Bruijn Date: Fri, 13 Dec 2024 13:59:45 -0500 Subject: [PATCH 4/9] fix donate TOC link in retype --- docs/SUMMARY.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/SUMMARY.md b/docs/SUMMARY.md index e6b115126dc..2424d9dbe4d 100644 --- a/docs/SUMMARY.md +++ b/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] +* [Donate](Donate.md) From 8018c7d32dad5a299b75c66ed7d2b0049f8969a9 Mon Sep 17 00:00:00 2001 From: alisman Date: Fri, 13 Dec 2024 14:00:05 -0500 Subject: [PATCH 5/9] Add property for donate button configuration (#11284) --- .../org/cbioportal/service/FrontendPropertiesServiceImpl.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java b/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java index eb2c94c43a2..429f3346a77 100644 --- a/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java +++ b/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), From 2834b0bbb55b7b4828931a5d89c952f06ff3e4e2 Mon Sep 17 00:00:00 2001 From: VenkateshVishwas <149477255+VenkateshVishwas@users.noreply.github.com> Date: Sat, 14 Dec 2024 00:32:15 +0530 Subject: [PATCH 6/9] Fix seed database commands in docs (#11279) --- .../deploy-without-docker/Import-the-Seed-Database.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/deployment/deploy-without-docker/Import-the-Seed-Database.md b/docs/deployment/deploy-without-docker/Import-the-Seed-Database.md index fdab0c8463e..74a5e8ac676 100644 --- a/docs/deployment/deploy-without-docker/Import-the-Seed-Database.md +++ b/docs/deployment/deploy-without-docker/Import-the-Seed-Database.md @@ -17,7 +17,7 @@ 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. @@ -25,7 +25,7 @@ After download, the files can be unzipped by entering the following command: 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`. @@ -33,7 +33,7 @@ After download, the files can be unzipped by entering the following command: 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`. From cee4161154e64889e6473c0087265a62775cffe7 Mon Sep 17 00:00:00 2001 From: Ino de Bruijn Date: Fri, 13 Dec 2024 14:27:07 -0500 Subject: [PATCH 7/9] add show_donate button to config_service.jsp Seems like we still use this standalone frontend mode --- src/main/resources/webapp/config_service.jsp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/resources/webapp/config_service.jsp b/src/main/resources/webapp/config_service.jsp index 0bdce370781..3a4f8af440d 100644 --- a/src/main/resources/webapp/config_service.jsp +++ b/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", From 6c49b108d2397abc09e9cfb73c6f7ed340b070b1 Mon Sep 17 00:00:00 2001 From: Zain Nasir <49543216+zainasir@users.noreply.github.com> Date: Fri, 13 Dec 2024 16:21:08 -0500 Subject: [PATCH 8/9] Frontend v6.0.22 --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 60b345655a3..8d23208e228 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.cbioportal cbioportal - 6.0.22-SNAPSHOT + 6.0.22 cBioPortal for Cancer Genomics @@ -27,7 +27,7 @@ com.github.cbioportal - v6.0.21 + v6.0.22 2.13.1 From 711a61d7f3d67a106f4266010506657040300f01 Mon Sep 17 00:00:00 2001 From: Zain Nasir <49543216+zainasir@users.noreply.github.com> Date: Fri, 13 Dec 2024 16:28:30 -0500 Subject: [PATCH 9/9] Prepare for v6.0.23 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 8d23208e228..2dd05f792ae 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.cbioportal cbioportal - 6.0.22 + 6.0.23-SNAPSHOT cBioPortal for Cancer Genomics