SUT genome-nexus

jdk_8_maven/cs/rest-gui/genome-nexus/.circleci/config.yml

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+# Use the latest 2.1 version of CircleCI pipeline process engine.
+# See: https://circleci.com/docs/2.0/configuration-reference
+version: 2.1
+
+# Define a job to be invoked later in a workflow.
+# See: https://circleci.com/docs/2.0/configuration-reference/#jobs
+jobs:
+  # Below is the definition of your job to build and test your app, you can rename and customize it as you want.
+  build:
+    # These next lines define a Docker executor: https://circleci.com/docs/2.0/executor-types/
+    # You can specify an image from Dockerhub or use one of our Convenience Images from CircleCI's Developer Hub.
+    # Be sure to update the Docker image tag below to openjdk version of your application.
+    # A list of available CircleCI Docker Convenience Images are available here: https://circleci.com/developer/images/image/cimg/openjdk
+    docker:
+      - image: cimg/openjdk:11.0
+    # Add steps to the job
+    # See: https://circleci.com/docs/2.0/configuration-reference/#steps
+    steps:
+      # Checkout the code as the first step.
+      - checkout
+      # Use mvn clean and package as the standard maven build phase
+      - run:
+          name: Build
+          command: mvn -DskipTests clean install
+      # Then run your tests!
+      - run:
+          name: Test
+          command: mvn test
+
+# Invoke jobs via workflows
+# See: https://circleci.com/docs/2.0/configuration-reference/#workflows
+workflows:
+  sample: # This is the name of the workflow, feel free to change it to better match your workflow.
+    # Inside the workflow, you define the jobs you want to run.
+    jobs:
+      - build

jdk_8_maven/cs/rest-gui/genome-nexus/.dockerignore

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+notebooks/*
+docs/*

jdk_8_maven/cs/rest-gui/genome-nexus/.editorconfig

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+# The EditorConfig project consists of a file format for defining coding styles
+# and a collection of text editor plugins that enable editors to read the file format
+# and adhere to defined styles.
+
+# EditorConfig files are read top to bottom and the closest EditorConfig files are read last.
+# Properties from matching EditorConfig sections are applied in the order they were read,
+# so properties in closer files take precedence.
+
+# Please only specify the formats you want to apply through out the project in this file.
+# Otherwise, please create new config file in your directory where you want to apply these styles.
+
+# More details about EditorConfig: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+# 4 space indentation
+indent_style = space
+indent_size = 4
+# Unix-style newlines with a newline ending every file
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+# Formats for markdown files only
+[*.md]
+trim_trailing_whitespace = false
+
+# Formats for HTML files only
+[**.html]
+insert_final_newline = false

jdk_8_maven/cs/rest-gui/genome-nexus/.env

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+REF_ENSEMBL_VERSION=ensembl92_grch37
+VEP_ASSEMBLY=GRCh37
+VEP_CACHE=/opt/vep/.vep/
+SPECIES=homo_sapiens

jdk_8_maven/cs/rest-gui/genome-nexus/.gitbook.yaml

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+root: ./docs/
+
+structure:
+  readme: README.md
+  summary: SUMMARY.md 

jdk_8_maven/cs/rest-gui/genome-nexus/.github/release-drafter.yml

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+name-template: 'v$NEXT_PATCH_VERSION'
+tag-template: 'v$NEXT_PATCH_VERSION'
+categories:
+  - title: '🧬 Features'
+    labels:
+      - 'feature'
+      - 'cl-feature'
+  - title: '✨ Enhancements'
+    labels:
+      - 'enhancement'
+      - 'cl-enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+      - 'cl-bug'
+  - title: '🏎 Performance Tweaks'
+    labels:
+      - 'performance'
+      - 'cl-performance'
+  - title: '🎨 Style Tweaks'
+    labels:
+      - 'style tweak'
+      - 'cl-style-tweak'
+  - title: '⚙️ REST API Changes'
+    labels:
+      - 'api'
+  - title: '⚙️ Changes to handle external APIs'
+    labels:
+      - 'external api'
+      - 'cl-external-api'
+  - title: '🗄 Database Migration'
+    labels:
+      - 'includes db changes'
+      - 'migration'
+      - 'cl-db-migration'
+  - title: '⚠️ Deprecation'
+    labels:
+      - 'deprecation'
+      - 'cl-deprecation'
+  - title: '📘 Documentation'
+    labels:
+      - 'documentation'
+      - 'cl-documentation'
+  - title: '🧹 Cleanup & Refactoring 🔧'
+    labels:
+      - 'cleanup'
+      - 'refactoring'
+      - 'cl-refactoring'
+  - title: '👷‍♀️ Testing, Configuration & Deployment'
+    labels:
+      - 'devops'
+      - 'test'
+      - 'cl-test'
+      - 'cl-devops'
+  - title: '🧰 Maintenance'
+    labels:
+      - 'chore'
+      - 'dependencies'
+      - 'cl-chore'
+  - title: '📐 Prototype (Internal Use)'
+    labels:
+      - 'cl-prototype'
+exclude-labels:
+  - 'skip-changelog'
+  - 'cl-skip-changelog'
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+template: |
+  ## Changes
+  $CHANGES
+  
+  ## 🕵️‍♀️ Full commit logs
+  
+  - https://github.com/genome-nexus/genome-nexus/compare/$PREVIOUS_TAG...v$NEXT_PATCH_VERSION

jdk_8_maven/cs/rest-gui/genome-nexus/.github/workflows/oncokb_test.yml

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+name: Test annotation endpoint with OncoKB
+
+on:
+  schedule:
+    - cron:  '1 0 * * *'
+
+jobs:
+  test-oncokb-endpoint:
+    runs-on: ubuntu-latest
+    steps:
+    - name: GET oncokb data
+      env:
+        ONCOKB_TOKEN: ${{ secrets.ONCOKB_TOKEN }}
+      run: |
+        curl -X GET --header 'Accept: application/json' 'https://www.genomenexus.org/annotation/17%3Ag.41242962_41242963insGA?token=$ONCOKB_TOKEN&fields=oncokb' -w ",http_code:%{http_code}" > curl_response.txt
+        SEARCH_HTTP_CODE="http_code:200"
+        SEARCH_ONCOKB="oncokb"
+        FILE="curl_response.txt"
+        if [ `grep -q "$SEARCH_HTTP_CODE" "$FILE"` -a `grep -q "$SEARCH_ONCOKB" "$FILE"` ]
+        then
+          echo "Request succeeded"
+          exit 0
+        else
+          echo "Request failed"
+          exit 1
+        fi
+

jdk_8_maven/cs/rest-gui/genome-nexus/.github/workflows/publish_docker_image.yml

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+name: Publish Docker Image on Tag
+on:
+  push:
+    tags: '*'
+jobs:
+  build_and_publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout git repo'
+        uses: actions/checkout@v1
+      - name: Publish Docker Image on Tag
+        uses: docker/build-push-action@v1
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+          repository: genomenexus/gn-spring-boot
+          tag_with_ref: true
+          push: ${{ startsWith(github.ref, 'refs/tags/') }}

jdk_8_maven/cs/rest-gui/genome-nexus/.github/workflows/release-management.yml

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+name: Release Management
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - master
+
+jobs:
+  update_draft_release:
+    runs-on: ubuntu-latest
+    steps:
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: toolmantim/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

jdk_8_maven/cs/rest-gui/genome-nexus/.github/workflows/test_docker_build.yml

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+name: Test Build of Docker image
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout git repo'
+        uses: actions/checkout@v1
+      - name: Build Docker image
+        uses: docker/[email protected]
+        with:
+          repository: genomenexus/gn-spring-boot
+          # don't push, since this is a test
+          push: false

jdk_8_maven/cs/rest-gui/genome-nexus/.gitignore

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+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+buildNumber.properties
+application.properties
+*.iml
+.idea/
+*.ipr
+*.iws
+*.DS_Store

jdk_8_maven/cs/rest-gui/genome-nexus/.travis.yml

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+language: java
+jdk:
+- openjdk8
+- openjdk13
+script:
+- mvn clean install
+after_success:
+- bash <(curl -s https://codecov.io/bash)

jdk_8_maven/cs/rest-gui/genome-nexus/Dockerfile

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+FROM maven:3.6-jdk-13
+RUN mkdir /genome-nexus
+ADD . /genome-nexus
+WORKDIR /genome-nexus
+RUN mvn -DskipTests clean install
+
+FROM openjdk:13-slim
+COPY --from=0 /genome-nexus/web/target/*.war /app.war
+CMD ["java", "-Dspring.data.mongodb.uri=${MONGODB_URI}", "-jar", "/app.war"]

jdk_8_maven/cs/rest-gui/genome-nexus/LICENSE

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+MIT License
+
+Copyright (c) Genome Nexus
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

jdk_8_maven/cs/rest-gui/genome-nexus/Procfile

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+web: SERVER_PORT=${PORT} java $JAVA_OPTS -Dspring.data.mongodb.uri=${MONGODB_URI} -jar web/target/web-*.jar

jdk_8_maven/cs/rest-gui/genome-nexus/README.md

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+# Genome Nexus 🧬
+
+Genome Nexus, a comprehensive one-stop resource for fast, automated and
+high-throughput annotation and interpretation of genetic variants in cancer.
+Genome Nexus integrates information from a variety of existing resources,
+including databases that convert DNA changes to protein changes, predict the
+functional effects of protein mutations, and contain information about mutation
+frequencies, gene function, variant effects, and clinical actionability.
+
+## Documentation 📖
+See the [docs](https://docs.genomenexus.org)
+
+## Run 💻
+
+### Alternative 1 - run genome-nexus, mongoDB and genome-nexus-vep in docker containers
+First, set environment variables for Ensembl Release, VEP Assembly, location of VEP Cache, and species (since a mouse instalation is supported). If these are not, the default values from `.env` will be set.
+
+The reference genome and Ensembl release must be consistent with a version in [genome-nexus-importer/data/](https://github.com/genome-nexus/genome-nexus-importer/tree/master/data).
+For example `grch37_ensembl92`, `grch38_ensembl92` or `grch38_ensembl95`:
+```
+export REF_ENSEMBL_VERSION=grch38_ensembl92
+```
+If you want to setup Genome Nexus for mouse, also set the `SPECIES` variable to 'mus_musculus'. Also see the [docs](https://github.com/genome-nexus/genome-nexus-importer/blob/master/docs/setup-genome-nexus-mouse.md) to create a mouse database.
+```bash
+export SPECIES=mus_musculus
+```
+
+If you would like to do local VEP annotations instead of using the public Ensembl API, please uncomment `# gn_vep.region.url=http://localhost:6060/vep/human/region/VARIANT` in your `application.properties`. This will require you to download the VEP cache files for the preferred Ensembl Release and Reference genome, see our documentation on [downloading the Genome Nexus VEP Cache](https://github.com/genome-nexus/genome-nexus-vep/blob/master/README.md#create-vep-cache). This will take several hours.
+```
+# Set local cache dir
+export VEP_CACHE=<local_vep_cache>
+
+# GRCh38 or GRCh37
+export VEP_ASSEMBLY=GRCh38
+```
+
+Run docker-compose to create images and containers:
+```
+docker-compose up --build -d
+```
+
+Run without recreating images:
+```
+docker-compose up -d
+```
+
+Run without Genome Nexus VEP:
+```
+# Start both the Web and DB (dependency of Web) containers
+docker-compose up -d web
+```
+
+Stop and remove containers:
+```
+docker-compose down
+```
+
+### Alternative 2 - run genome-nexus locally, but mongoDB in docker container
+```
+# the genomenexus/gn-mongo images comes with all the required tables imported
+# change latest to different version if necessary (only need to run this once)
+docker run --name=gn-mongo --restart=always -p 27017:27017 -d genomenexus/gn-mongo:latest 
+mvn  -DskipTests clean install
+java -jar web/target/web-*.war
+```
+
+### Alternative 3 - install mongoDB locally and run with local java
+Install mongoDB manually. Then follow instructions in
+[genome-nexus-importer](https://github.com/genome-nexus/genome-nexus-importer)
+to initialize the database.
+
+After that run this:
+```
+mvn clean install
+java -jar web/target/web-*.war
+```
+
+## Test Status 👷‍♀️
+
+| branch | master | rc |
+| --- | --- | --- |
+| status | [![Build Status](https://travis-ci.org/genome-nexus/genome-nexus.svg?branch=master)](https://travis-ci.org/genome-nexus/genome-nexus/branches) | [![Build Status](https://travis-ci.org/genome-nexus/genome-nexus.svg?branch=rc)](https://travis-ci.org/genome-nexus/genome-nexus/branches) |
+
+## Deploy 🚀
+
+[![Deploy](https://www.herokucdn.com/deploy/button.svg)](https://heroku.com/deploy)