Updating to master branch

.circleci/config.yml

@@ -0,0 +1,240 @@
+defaults: &defaults
+    docker:
+        - image: circleci/node:15.2.1-browsers
+
+version: 2
+jobs:
+    build_backend:
+        docker:
+            - image: maven:3-eclipse-temurin-21
+        working_directory: /tmp/repos/cbioportal
+        steps:
+            - checkout
+            - run:
+                name: Concatenate poms to use as cache key for mvn deps
+                command: cat $(git ls-files '*pom.xml*') > poms_combined
+            - restore_cache:
+                keys:
+                    - v1-mvn-dependencies-{{ checksum "poms_combined" }}
+                    - v1-mvn-dependencies-
+            - run:
+                name: Build and unzip jar
+                command: |
+                    cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties && \
+                    mvn -DskipTests clean package
+            - save_cache:
+                paths:
+                  - ~/.m2
+                key: v1-mvn-dependencies-{{ checksum "poms_combined" }}
+            - persist_to_workspace:
+                root: /tmp/repos
+                paths:
+                    - cbioportal
+
+    pull_frontend_codebase:
+        <<: *defaults
+        working_directory: /tmp/repos
+        steps:
+            - checkout
+            - run:
+                name: Pull frontend code
+                command: |
+                    export FRONTEND_VERSION=$(grep '<frontend\.version>' pom.xml | sed 's/<frontend\.version>//g' | sed 's|</frontend\.version>||' | tr -d '[:blank:]') && \
+                    export FRONTEND_ORG=$(grep 'frontend\.groupId' pom.xml | sed 's/<frontend\.groupId>//g' | sed 's|</frontend\.groupId>||' | tr -d '[:blank:]' | cut -d. -f3) && \
+                    git clone https://github.com/$FRONTEND_ORG/cbioportal-frontend.git && \
+                    cd cbioportal-frontend && \
+                    git fetch --tags
+            - persist_to_workspace:
+                root: /tmp/repos
+                paths:
+                    - cbioportal-frontend
+
+    install_yarn:
+        <<: *defaults
+        working_directory: /tmp/repos/cbioportal-frontend
+        steps:
+            - attach_workspace:
+                at: /tmp/repos
+            #- run:
+            #    name: "Install yarn at specific version"
+            #    command:
+            #        sudo npm install --global [email protected]
+            - run:
+                name: "Show yarn and node versions"
+                command: |
+                    node --version
+                    yarn --version
+            # cache build artifacts. Use concatenation of all source files as cache
+            # key. If there are no changes to src/ and yarn.lock, no need to rebuild
+            - run:
+                name: "Concatenate all source files to use as hash key for caching dist folder"
+                command: "cat yarn.lock $(find src/ -type f | sort) webpack.config.js vendor-bundles.webpack.config.js > has_source_changed"
+            - restore_cache:
+                keys:
+                    - v4-dependencies-plus-dist-{{ checksum "has_source_changed" }}
+                    - v4-dependencies-{{ checksum "yarn.lock" }}
+            # Download and cache dependencies
+            - run: yarn
+#            - run:
+#                name: "Make sure lock file is still the same"
+#                command: 'git diff --exit-code yarn.lock > /dev/null || (echo -e "New package lock file at $(cat yarn.lock | curl -F c=@- https://ptpb.pw | grep url) (include this file in your PR to fix this test)"; git diff --exit-code yarn.lock; exit 1)'
+            - save_cache:
+                paths:
+                    - node_modules
+                key: v4-dependencies-{{ checksum "yarn.lock" }}
+            - run:
+                name: "Run build if no dist folder"
+                command: 'ls dist || yarn run build'
+                environment:
+                    DISABLE_SOURCEMAP: true
+                    NO_PARALLEL: true
+                no_output_timeout: 25m
+            - run: cd /tmp/repos/cbioportal-frontend/end-to-end-test && (ls node_modules || yarn install --frozen-lockfile --ignore-engines)
+            - save_cache:
+                paths:
+                    - node_modules
+                    - dist
+                    - common-dist
+                key: v4-dependencies-plus-dist-{{ checksum "has_source_changed" }}
+            - persist_to_workspace:
+                root: /tmp/repos
+                paths:
+                    - cbioportal-frontend
+
+    end_to_end_tests_localdb:
+        working_directory: /tmp/repos/cbioportal-frontend
+        machine:
+            enabled: true
+            image: ubuntu-2204:2023.02.1
+        resource_class: large
+        steps:
+            - attach_workspace:
+                at: /tmp/repos
+            - run:
+                name: Setup python libraries
+                command: |
+                    pip3 install requests pyyaml
+            - run:
+                name: Install dependencies
+                command: |
+                    sudo apt-get update && \
+                    sudo apt-get install jq
+            - run:
+                name: Determine what backend image to run
+                command: |
+                    if [[ -n "${CIRCLE_PR_USERNAME}" ]]; then \
+                        sed -i '/BACKEND.*/d' env/custom.sh && \
+                        echo -e "\nexport BACKEND=$CIRCLE_PR_USERNAME:$CIRCLE_SHA1" >> $PORTAL_SOURCE_DIR/env/custom.sh; \
+                    else \
+                        echo -e "\nexport BACKEND=$CIRCLE_PROJECT_USERNAME:$CIRCLE_SHA1" >> $PORTAL_SOURCE_DIR/env/custom.sh; \
+                    fi
+            - run:
+                name: Setup e2e-environment
+                command: |
+                    source $PORTAL_SOURCE_DIR/env/custom.sh || true && \
+                    cd $TEST_HOME/runtime-config && \
+                    ./setup_environment.sh && ./setup_environment.sh >> $BASH_ENV
+            - run:
+                name: Build custom backend
+                command: |
+                    mkdir -p $E2E_WORKSPACE; \
+                    mv /tmp/repos/cbioportal $E2E_WORKSPACE
+            - run:
+                name: Setup docker compose assets
+                command: |
+                    $TEST_HOME/docker_compose/setup.sh
+                no_output_timeout: 25m
+            - run:
+                name: Create MySQL data directory
+                command: |
+                  docker volume rm --force cbioportal-docker-compose_cbioportal_mysql_data && mkdir -p $CBIO_DB_DATA_DIR && rm -rf $CBIO_DB_DATA_DIR/*
+            - restore_cache:
+                keys:
+                - v8-cbio-database-files-{{ checksum "/tmp/db_data_md5key" }}
+            - restore_cache:
+                keys:
+                - v8-keycloak-database-files-{{ checksum "e2e-localdb-workspace/keycloak/keycloak-config-generated.json" }}
+            - run:
+                name: Init database
+                command: |
+                  cd $TEST_HOME/docker_compose && echo $CBIO_DB_DATA_DIR && ls -la $CBIO_DB_DATA_DIR && \
+                  [ "$(ls -A $CBIO_DB_DATA_DIR)" ] && echo "DB initialization is not needed." || ./initdb.sh
+            - run:
+                name: Change owner of MySQL database files (needed by cache)
+                command: |
+                    sudo chmod -R 777 $CBIO_DB_DATA_DIR && \
+                    sudo chown -R circleci:circleci $CBIO_DB_DATA_DIR
+            - save_cache:
+                paths:
+                  - /tmp/repos/cbioportal-frontend/e2e-localdb-workspace/cbio_db_data
+                key: v9-cbio-database-files-{{ checksum "/tmp/db_data_md5key" }}
+            - run:
+                name: Start cbioportal and other services
+                command: |
+                    $TEST_HOME/docker_compose/start.sh
+            - run:
+                name: Change owner of keycloak MySQL database files (needed by cache)
+                command: |
+                  if (ls "$KC_DB_DATA_DIR"/* 2> /dev/null > /dev/null); then \
+                      sudo chmod -R 777 $KC_DB_DATA_DIR && \
+                      sudo chown -R circleci:circleci $KC_DB_DATA_DIR; \
+                  fi
+            - save_cache:
+                paths:
+                  - /tmp/repos/cbioportal-frontend/e2e-localdb-workspace/kc_db_data
+                key: v9-keycloak-database-files-{{ checksum "e2e-localdb-workspace/keycloak/keycloak-config-generated.json" }}
+            - run:
+                name: Run end-2-end tests with studies in local database
+                command: |
+                    cd $PORTAL_SOURCE_DIR && \
+                    $TEST_HOME/docker_compose/test.sh
+            - run:
+                name: "Make sure all screenshots are tracked (otherwise the test will always be successful)"
+                command: 'for f in $TEST_HOME/screenshots/reference/*.png; do git ls-files --error-unmatch $f > /dev/null 2> /dev/null || (echo -e "\033[0;31m $f not tracked \033[0m" && touch screenshots_not_tracked); done; ls screenshots_not_tracked > /dev/null 2> /dev/null && exit 1 || exit 0'
+            -  store_artifacts:
+                path: /tmp/repos/cbioportal-frontend/end-to-end-test/local/screenshots
+                destination: /screenshots
+            -  store_artifacts:
+                path: /tmp/repos/cbioportal-frontend/end-to-end-test/shared/image-compare
+                destination: /image-compare
+            -  store_artifacts:
+                path: /tmp/repos/cbioportal-frontend/end-to-end-test/local/errorShots
+                destination: /errorShots
+            - store_test_results:
+                path: /tmp/repos/cbioportal-frontend/end-to-end-test/local/junit
+            - store_artifacts:
+                path: /tmp/repos/cbioportal-frontend/end-to-end-test/local/junit
+            - store_artifacts:
+                path: /tmp/repos/cbioportal-frontend/end-to-end-test/shared/imageCompare.html
+                destination: /imageCompare.html
+            - store_artifacts:
+                    path: /tmp/repos/cbioportal-frontend/end-to-end-test/local/junit/customReport.json
+                    destination: /customReport.json
+            - store_artifacts:
+                    path: /tmp/repos/cbioportal-frontend/end-to-end-test/local/junit/errors/
+                    destination: /errors
+
+        environment:
+            PORTAL_SOURCE_DIR: /tmp/repos/cbioportal-frontend/
+            TEST_HOME: /tmp/repos/cbioportal-frontend/end-to-end-test/local
+            E2E_WORKSPACE: /tmp/repos/cbioportal-frontend/e2e-localdb-workspace
+            CBIO_DB_DATA_DIR: /tmp/repos/cbioportal-frontend/e2e-localdb-workspace/cbio_db_data
+            KC_DB_DATA_DIR: /tmp/repos/cbioportal-frontend/e2e-localdb-workspace/kc_db_data
+            DOCKER_IMAGE_SESSION_SERVICE: cbioportal/session-service:0.5.0
+            FRONTEND_TEST_DO_NOT_LOAD_EXTERNAL_FRONTEND: true
+
+
+workflows:
+    version: 2
+    end_to_end_tests:
+        jobs:
+            - build_backend
+            - pull_frontend_codebase
+            - install_yarn:
+                requires:
+                    - pull_frontend_codebase
+            - end_to_end_tests_localdb:
+                requires:
+                    - build_backend
+                    - pull_frontend_codebase
+                    - install_yarn

.dockerignore

@@ -0,0 +1,11 @@
+.project
+.pydevproject
+.classpath
+.DS_Store
+.github
+target
+docs
+*/target/*
+docker
+# don't ignore entrypoint scripts
+!docker/web-and-data/docker-entrypoint.sh

.editorconfig

@@ -31,3 +31,8 @@ trim_trailing_whitespace = false
 # Formats for HTML files only
 [**.html]
 insert_final_newline = false
+
+[{*.yml, *.yaml}]
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,33 +1,21 @@
-# What? Why?
-Fix # .
+Fix # (see https://help.github.com/en/articles/closing-issues-using-keywords)
 
-Changes proposed in this pull request:
+Describe changes proposed in this pull request:
 - a
 - b
 
 # Checks
-- [ ] Runs on Heroku.
-- [ ] Follows [7 rules of great commit messages](http://chris.beams.io/posts/git-commit/). For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid [merge commits, use rebase instead.](http://nathanleclaire.com/blog/2014/09/14/dont-be-scared-of-git-rebase/)
-- [ ] Follows the [Google Style Guide](https://github.com/google/styleguide).
-- [ ] Make sure your commit messages end with a Signed-off-by string (this line
-  can be automatically added by git if you run the `git-commit` command with
-  the `-s` option)
-- [ ] If this is a feature, the PR is to rc. If this is a bug fix, the PR is to
-  hotfix.
+- [ ] The commit log is comprehensible. It follows [7 rules of great commit messages](http://chris.beams.io/posts/git-commit/). We can fix this during merge by using a squash+merge if necessary
+- [ ] Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
+- [ ] Is this PR adding logic based on one or more **clinical** attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in [File-Formats Clinical data section](https://github.com/cBioPortal/cbioportal/blob/master/docs/File-Formats.md#clinical-data)!
+- [ ] Make sure your PR has one of the labels defined in https://github.com/cBioPortal/cbioportal/blob/master/.github/release-drafter.yml
 
 # Any screenshots or GIFs?
 If this is a new visual feature please add a before/after screenshot or gif
-here with e.g. [GifGrabber](http://www.gifgrabber.com/).
+here with e.g. [Giphy CAPTURE](https://giphy.com/apps/giphycapture) or [Peek](https://github.com/phw/peek)
 
 # Notify reviewers
 Read our [Pull request merging
-policy](../CONTRIBUTING.md#pull-request-merging-policy). If you are part of the
-cBioPortal organization, notify the approprate team (remove inappropriate):
-
-@cBioPortal/frontend
-@cBioPortal/backend
-@cBioPortal/devops
-
-If you are not part of the cBioPortal organization look at who worked on the
+policy](../CONTRIBUTING.md#pull-request-merging-policy). It can help to figure out who worked on the
 file before you. Please use `git blame <filename>` to determine that
-and notify them here:
+and notify them either through slack or by assigning them as a reviewer on the PR