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..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) 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`. diff --git a/pom.xml b/pom.xml index 48fed442e59..41ea357868c 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.cbioportal cbioportal - 6.0.22-SNAPSHOT + 6.0.23-SNAPSHOT cBioPortal for Cancer Genomics @@ -27,7 +27,7 @@ com.github.cbioportal - v6.0.21 + v6.0.22 2.13.1 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/*", 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), 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<>(); 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",