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Merge pull request #100 from EBISPOT/develop
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‎.gitignore‎

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/target/
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/log/
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/.idea/

‎.gitlab-ci.yml‎

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image: docker:latest
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services:
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- docker:dind
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stages:
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- build-frontend
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- build-artefact
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- build-container
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- build-frontend-release
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- build-artefact-release
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- build-container-release
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- deploy-sandbox
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- deploy-fallback
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- deploy-live
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variables:
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DOCKER_DRIVER: overlay2
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DOCKER_TLS_CERTDIR: ""
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REGISTRY_IMAGE: ebispot/ontotools-curation-service
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SERVICE_NAME: ontotools-curation-service
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build-front:
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image: node:10.15.3
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stage: build-frontend
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script:
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- npm -v
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- node -v
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- cd frontend
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- rm -rf node_modules
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- npm install
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- CI=false npm run build:sandbox
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artifacts:
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paths:
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- frontend/build/*
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only:
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- develop
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maven-build:
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image: maven:3-jdk-12
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stage: build-artefact
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script:
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- mkdir src/main/webapp
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- mv frontend/build/* src/main/webapp/
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- ls -lah src/main/webapp
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- mvn clean package spring-boot:repackage -DskipTests=true
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dependencies:
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- build-front
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artifacts:
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paths:
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- target/*.war
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only:
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- develop
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build-container:
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stage: build-container
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script:
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- echo "$DOCKER_HUB_PASSWORD" > dhpw.txt
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- docker login -u "${DOCKER_HUB_USER}" --password-stdin < dhpw.txt
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- docker build --cache-from $REGISTRY_IMAGE:latest -t $REGISTRY_IMAGE:$CI_COMMIT_SHA .
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- docker push $REGISTRY_IMAGE:$CI_COMMIT_SHA
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only:
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- develop
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build-front-release:
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image: node:10.15.3
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stage: build-frontend-release
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script:
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- npm -v
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- node -v
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- cd frontend
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- rm -rf node_modules
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- npm install
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- CI=false npm run build:prod
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artifacts:
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paths:
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- frontend/build/*
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only:
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- tags
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maven-build-release:
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image: maven:3-jdk-12
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stage: build-artefact-release
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script:
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- mkdir src/main/webapp
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- mv frontend/build/* src/main/webapp/
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- ls -lah src/main/webapp
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- mvn clean package spring-boot:repackage -DskipTests=true
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dependencies:
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- build-front-release
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artifacts:
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paths:
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- target/*.war
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only:
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- tags
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build-release:
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variables:
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GIT_STRATEGY: none
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stage: build-container-release
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script:
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- echo "$DOCKER_HUB_PASSWORD" > dhpw.txt
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- docker login -u "${DOCKER_HUB_USER}" --password-stdin < dhpw.txt
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- docker pull $REGISTRY_IMAGE:$CI_COMMIT_SHA
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- docker tag $REGISTRY_IMAGE:$CI_COMMIT_SHA $REGISTRY_IMAGE:latest
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- docker tag $REGISTRY_IMAGE:$CI_COMMIT_SHA $REGISTRY_IMAGE:$CI_COMMIT_TAG
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- docker push $REGISTRY_IMAGE:latest
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- docker push $REGISTRY_IMAGE:$CI_COMMIT_TAG
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only:
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- tags
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deploy-sandbox:
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image: dtzar/helm-kubectl:2.13.1
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stage: deploy-sandbox
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script:
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- echo "Deploy to sandbox server"
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- mkdir -p /root/.kube
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- echo ${SANBOX_KUBECONF} | base64 -d > /root/.kube/config
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- helm init --stable-repo-url https://charts.helm.sh/stable
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- helm delete --purge ontotools-curation-service || true
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- helm install --name ontotools-curation-service --set k8Namespace=ontotools,image.repository=$REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA,image.env.secretsName=ontotools-secrets,image.env.secretsKey=db-pwd ./k8chart/ --wait
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environment:
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name: sandbox
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when: manual
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only:
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- develop
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deploy-fallback:
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image: dtzar/helm-kubectl:2.13.1
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stage: deploy-fallback
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script:
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- echo "Deploy to Production fallback server"
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- mkdir -p /root/.kube
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- echo ${PFALLBACK_KUBECONFIG} | base64 -d > /root/.kube/config
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- helm init --stable-repo-url https://charts.helm.sh/stable
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- helm delete --purge ontotools-curation-service || true
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- helm install --name ontotools-curation-service --set k8Namespace=ontotools,replicaCount=1,image.env.envName=prod,image.repository=$REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA,image.env.dbUser=ontotoolscurator,image.env.secretsName=ontotools-secrets,image.env.secretsKey=db-pwd ./k8chart/ --wait
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environment:
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name: prod
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when: manual
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only:
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- tags
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deploy-live:
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image: dtzar/helm-kubectl:2.13.1
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stage: deploy-live
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script:
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- echo "Deploy to Production server"
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- mkdir -p /root/.kube
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- echo ${PLIVE_KUBECONFIG} | base64 -d > /root/.kube/config
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- helm init --stable-repo-url https://charts.helm.sh/stable
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- helm delete --purge ontotools-curation-service || true
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- helm install --name ontotools-curation-service --set k8Namespace=ontotools,replicaCount=1,image.env.envName=prod,image.repository=$REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA,image.env.dbUser=ontotoolscurator,image.env.secretsName=ontotools-secrets,image.env.secretsKey=db-pwd ./k8chart/ --wait
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environment:
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name: prod
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when: manual
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only:
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- tags

‎Dockerfile‎

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# Import base image
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FROM openjdk:15-buster
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RUN apt-get update
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RUN apt-get install -y --no-install-recommends less
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# Create log file directory and set permission
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RUN groupadd -r ontotools-curation-service && useradd -r --create-home -g ontotools-curation-service ontotools-curation-service
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RUN if [ ! -d /var/log/ontotools/ ];then mkdir /var/log/ontotools/;fi
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RUN chown -R ontotools-curation-service:ontotools-curation-service /var/log/ontotools
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# Move project artifact
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ADD target/ontotools-curation-service-*.war /home/ontotools-curation-service/
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USER ontotools-curation-service
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# Launch application server
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ENTRYPOINT exec $JAVA_HOME/bin/java $XMX $XMS -jar -Dspring.profiles.active=$ENVIRONMENT /home/ontotools-curation-service/ontotools-curation-service-*.war

‎README.md‎

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# Future Curation App
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# Onto-tools Curation App
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## Requirements to build and run locally
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* Local MongoDB instance running on port `27017`
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* Some test credentials and data added to the DB (if authentication is turned on) - see https://github.com/EBISPOT/ontotools-curator/wiki/Test-data
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* Alternatively:
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* Add at least one `super` user in the DB in the `users` collection:
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```
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{
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"name": "Super user",
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"email": "[email protected]",
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"superUser": true
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}
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```
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* Set `ontotools-curation.auth.enabled` to `false` in the `dev` profile in `application.yml`
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### Build package
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* Run `mvn clean install -Dspring.profiles.active=dev`
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* Alternatively, introduce in a new profile in `application.yml` and use it as active when building
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* At least one active profile has to be specified when building the package
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### Build docker container
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* Run the `build.sh` script under `scripts`
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### Run locally
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* `java -jar -Dspring.profiles.active=dev target/ontotools-curation-service-*.jar`

‎frontend/.env‎

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REACT_APP_AAPURL="https://api.aai.ebi.ac.uk"
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REACT_APP_APIURL="http://localhost:8080/ontotools/curation/api"
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PUBLIC_URL=""
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‎frontend/.env.prod‎

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REACT_APP_AAPURL="https://api.aai.ebi.ac.uk"
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REACT_APP_APIURL="/curator"
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PUBLIC_URL="/curator"
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‎frontend/.env.sandbox‎

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REACT_APP_AAPURL="https://api.aai.ebi.ac.uk"
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REACT_APP_APIURL="/curator"
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PUBLIC_URL="/curator"
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‎frontend/.gitignore‎

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# See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
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# dependencies
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/node_modules
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/.pnp
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.pnp.js
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# testing
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/coverage
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# production
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/build
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# misc
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.DS_Store
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.env.local
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.env.development.local
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.env.test.local
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.env.production.local
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npm-debug.log*
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yarn-debug.log*
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yarn-error.log*

‎frontend/README.md‎

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# Getting Started with Create React App
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This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
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## Available Scripts
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In the project directory, you can run:
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### `yarn start`
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Runs the app in the development mode.\
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Open [http://localhost:3000](http://localhost:3000) to view it in the browser.
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The page will reload if you make edits.\
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You will also see any lint errors in the console.
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### `yarn test`
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Launches the test runner in the interactive watch mode.\
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See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.
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### `yarn build`
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Builds the app for production to the `build` folder.\
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It correctly bundles React in production mode and optimizes the build for the best performance.
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The build is minified and the filenames include the hashes.\
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Your app is ready to be deployed!
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See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
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### `yarn eject`
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**Note: this is a one-way operation. Once you `eject`, you can’t go back!**
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If you aren’t satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.
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Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you’re on your own.
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You don’t have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn’t feel obligated to use this feature. However we understand that this tool wouldn’t be useful if you couldn’t customize it when you are ready for it.
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## Learn More
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You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).
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To learn React, check out the [React documentation](https://reactjs.org/).

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