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Commit 804fc0c8 authored by Raphaël Flores's avatar Raphaël Flores
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Configure CI/CD for FAIDARE cards

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2 merge requests!129Configure CI/CD for FAIDARE cards,!82Epic/merge faidare dd
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.gitlab-ci.yml
+ 95
− 121
View file @ 804fc0c8
......@@ -18,8 +18,8 @@ image: registry.forgemia.inra.fr/urgi-is/docker-rare/docker-browsers:latest
variables:
GRADLE_OPTS: "-Dorg.gradle.daemon=false"
GRADLE_USER_HOME: $CI_PROJECT_DIR/.gradle
APP_NAME: faidare
JAR_PATH: "backend/build/libs/${APP_NAME}.jar"
SERVICE_NAME: faidare-cards
JAR_PATH: "backend/build/libs/faidare.jar"
GIT_DEPTH: 0
IMAGE_TAG: $CI_COMMIT_REF_SLUG
ELASTIC_VERSION: "7.13.2"
......@@ -34,33 +34,31 @@ cache:
# PRE-BUILD
build-loader-docker-image:
image: registry.forgemia.inra.fr/urgi-is/docker-rare/docker-git:latest
stage: pre-build
services:
- docker:20.10.6-dind
script:
# build the image
- docker build -t registry.forgemia.inra.fr/urgi-is/docker-rare/faidare-loader:${IMAGE_TAG} .
- docker build -t registry.forgemia.inra.fr/urgi-is/docker-rare/faidare-loader:latest .
# Login before pushing the image
- docker login registry.forgemia.inra.fr -u $CONTAINER_REGISTRY_USERNAME -p $CONTAINER_REGISTRY_TOKEN
# push the built image
- docker push registry.forgemia.inra.fr/urgi-is/docker-rare/faidare-loader:${IMAGE_TAG}
# only push latest tag on master branch
- if [ "master" == "${CI_COMMIT_REF_SLUG}" ] ; then docker push registry.forgemia.inra.fr/urgi-is/docker-rare/faidare-loader:latest ; fi;
only:
changes:
- Dockerfile
- scripts/*
- backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/*_mapping.json
- backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json
- .gitlab-ci.yml
allow_failure: true
image: registry.forgemia.inra.fr/urgi-is/docker-rare/docker-git:latest
stage: pre-build
services:
- docker:20.10.6-dind
script:
# build the image
- docker build -t registry.forgemia.inra.fr/urgi-is/docker-rare/faidare-loader:${IMAGE_TAG} .
- docker build -t registry.forgemia.inra.fr/urgi-is/docker-rare/faidare-loader:latest .
# Login before pushing the image
- docker login registry.forgemia.inra.fr -u $CONTAINER_REGISTRY_USERNAME -p $CONTAINER_REGISTRY_TOKEN
# push the built image
- docker push registry.forgemia.inra.fr/urgi-is/docker-rare/faidare-loader:${IMAGE_TAG}
# only push latest tag on master branch
- if [ "${CI_DEFAULT_BRANCH}" == "${CI_COMMIT_REF_SLUG}" ] ; then docker push registry.forgemia.inra.fr/urgi-is/docker-rare/faidare-loader:latest ; fi;
rules:
- changes:
- Dockerfile
- scripts/*
- backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/*_mapping.json
- backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json
- .gitlab-ci.yml
- if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
allow_failure: true
# TESTS
test-and-sonarqube:
stage: test
tags:
......@@ -84,6 +82,7 @@ test-and-sonarqube:
GRADLE_OPTS: "-Dorg.gradle.daemon=true"
SONAR_USER_HOME: "${CI_PROJECT_DIR}/.sonar" # Defines the location of the analysis task cache
GIT_DEPTH: "0" # Tells git to fetch all the branches of the project, required by the analysis task
ES_JAVA_OPTS: "-Xms2g -Xmx2g"
cache:
key: "${CI_COMMIT_REF_NAME}"
policy: pull-push
......@@ -95,28 +94,16 @@ test-and-sonarqube:
# disable sonarqube because it apparently needs node, but I don't know why, and it can't find it anymore now that
# there is no frontend project anymore, and it takes sooooo much time to complete anyway for results that nobody
# will ever look
# - find /tmp/node/*/bin -name node -exec ln -s {} /tmp/node/node \;
# - export PATH="/tmp/node/:$PATH"
# - ./gradlew -s sonarqube -x test --parallel
- ./gradlew -s sonarqube -x test --parallel
artifacts:
reports:
junit:
- ./backend/build/test-results/test/TEST-*.xml
only:
refs:
- merge_requests
test-and-sonarqube-master:
extends: test-and-sonarqube
only:
refs:
- master
rules:
- if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
interruptible: true
# BUILD
build:
tags:
- openstack
......@@ -132,9 +119,18 @@ build:
paths:
- "$JAR_PATH"
expire_in: 1 week
rules:
- if: $CI_COMMIT_MESSAGE =~ /SKIP_DEPLOY/i
when: never
- if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
interruptible: true
.restart-config-server: &restart_config_server
restart-config-server-openstack:
tags:
- openstack
variables:
SERVER_IP: ${SERVER_IP_OPENSTACK_DEV}
SERVER_USER: ${SERVER_USER_OPENSTACK}
stage: build
script:
- eval $(ssh-agent -s)
......@@ -143,28 +139,17 @@ build:
- ssh ${SERVER_USER}@${SERVER_IP} "sudo systemctl restart bootapp@config-server"
- eval $(ssh-agent -k)
allow_failure: true
restart-config-server-proxmox:
variables:
SERVER_IP: ${SERVER_IP_PROXMOX}
SERVER_USER: ${SERVER_USER_PROXMOX}
<<: *restart_config_server
restart-config-server-openstack:
tags:
- openstack
variables:
SERVER_IP: ${SERVER_IP_OPENSTACK_DEV}
SERVER_USER: ${SERVER_USER_OPENSTACK}
<<: *restart_config_server
rules:
- if: $CI_COMMIT_MESSAGE =~ /SKIP_DEPLOY/i
when: never
- if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
# DEPLOY
.deploy-to-vm: &deploy_to_vm
.deploy-to-vm:
# Hidden job which serves as template for executed jobs below.
# See https://docs.gitlab.com/ee/ci/yaml/#anchors
tags:
- openstack
retry: 2
script:
## SSH initialization
......@@ -172,21 +157,19 @@ restart-config-server-openstack:
- ssh-add <(echo "${SSH_PRIVATE_KEY}")
- ssh -o StrictHostKeyChecking=no ${SERVER_USER}@${SERVER_IP} 'echo "Successfully connected on $(hostname)"'
# Copy jar
- scp ./backend/build/libs/${APP_NAME}.jar ${SERVER_USER}@${SERVER_IP}:/tmp/${APP_NAME}-${ENV}.jar
- ssh ${SERVER_USER}@${SERVER_IP} "sudo mv /tmp/${APP_NAME}-${ENV}.jar /opt/bootapp/${APP_NAME}-${ENV}.jar ; sudo chown -R bootapp:bootapp /opt/bootapp/"
# Restarting service with the updated jar and the according Spring profiles enabled
- ssh ${SERVER_USER}@${SERVER_IP} "sudo systemctl restart bootapp@${APP_NAME}-${ENV}"
- scp ${JAR_PATH} ${SERVER_USER}@${SERVER_IP}:/tmp/${SERVICE_NAME}-${ENV}.jar
- ssh ${SERVER_USER}@${SERVER_IP} "sudo mv /tmp/${SERVICE_NAME}-${ENV}.jar /opt/bootapp/ ; sudo chown -R bootapp:bootapp /opt/bootapp/ ; sudo systemctl restart bootapp@${SERVICE_NAME}-${ENV}"
- eval $(ssh-agent -k)
- echo "Deploy done. Application should be available at http://${SERVER_IP}:${APP_PORT}/${CONTEXT_PATH}"
only:
changes:
rules:
- changes:
- .gitlab-ci.yml
- backend/src/**/*
allow_failure: false
interruptible: false
needs: ["build"]
deploy-to-beta:
tags:
- openstack
stage: deploy-beta
extends: .deploy-to-vm
variables:
......@@ -194,78 +177,69 @@ deploy-to-beta:
SERVER_IP: ${SERVER_IP_OPENSTACK_DEV}
APP_PORT: ${BETA_FAIDARE_PORT}
ENV: beta
CONTEXT_PATH: faidare-beta
except:
refs:
- master
only:
refs:
- branches
when: always
CONTEXT_PATH: faidare
rules:
- if: $CI_COMMIT_MESSAGE =~ /SKIP_DEPLOY/i
when: never
- if: $CI_PIPELINE_SOURCE == "merge_request_event"
when: always
deploy-to-staging:
tags:
- openstack
deploy-to-staging-public:
stage: deploy-staging
extends: .deploy-to-vm
variables:
SERVER_USER: ${SERVER_USER_OPENSTACK}
SERVER_IP: ${SERVER_IP_OPENSTACK_DEV}
APP_PORT: ${STAGING_FAIDARE_PORT}
ENV: staging
CONTEXT_PATH: faidare-staging
only:
refs:
- branches
except:
refs:
- master
when: manual
APP_PORT: ${STAGING_PUBLIC_FAIDARE_PORT}
ENV: staging-public
CONTEXT_PATH: faidare
rules:
- if: $CI_COMMIT_MESSAGE =~ /SKIP_DEPLOY/i
when: never
- if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when: manual
deploy-to-int:
tags:
- proxmox
stage: deploy-production
deploy-to-staging-private:
stage: deploy-staging
extends: .deploy-to-vm
variables:
SERVER_USER: ${SERVER_USER_PROXMOX}
SERVER_IP: ${SERVER_IP_PROXMOX}
APP_PORT: ${INT_FAIDARE_PORT}
ENV: int
CONTEXT_PATH: faidare-int
only:
refs:
- master
when: manual
SERVER_USER: ${SERVER_USER_OPENSTACK}
SERVER_IP: ${SERVER_IP_OPENSTACK_DEV}
APP_PORT: ${STAGING_PRIVATE_FAIDARE_PORT}
ENV: staging-private
CONTEXT_PATH: faidare-private
rules:
- if: $CI_COMMIT_MESSAGE =~ /SKIP_DEPLOY/i
when: never
- if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when: manual
deploy-to-prod-public:
tags:
- proxmox
stage: deploy-production
extends: .deploy-to-vm
variables:
SERVER_USER: ${SERVER_USER_PROXMOX}
SERVER_IP: ${SERVER_IP_PROXMOX}
SERVER_USER: ${SERVER_USER_OPENSTACK}
SERVER_IP: ${SERVER_IP_OPENSTACK_PROD}
APP_PORT: ${PROD_PUBLIC_FAIDARE_PORT}
ENV: prod-public
CONTEXT_PATH: faidare
only:
refs:
- master
when: manual
rules:
- if: $CI_COMMIT_MESSAGE =~ /SKIP_DEPLOY/i
when: never
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when: manual
deploy-to-prod-private:
tags:
- proxmox
stage: deploy-production
extends: .deploy-to-vm
variables:
SERVER_USER: ${SERVER_USER_PROXMOX}
SERVER_IP: ${SERVER_IP_PROXMOX}
SERVER_USER: ${SERVER_USER_OPENSTACK}
SERVER_IP: ${SERVER_IP_OPENSTACK_PROD}
APP_PORT: ${PROD_PRIVATE_FAIDARE_PORT}
ENV: prod-private
CONTEXT_PATH: faidare-private
only:
refs:
- master
when: manual
rules:
- if: $CI_COMMIT_MESSAGE =~ /SKIP_DEPLOY/i
when: never
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when: manual
ABOUT.md
+ 4
− 4
View file @ 804fc0c8
......@@ -3,11 +3,11 @@
The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.
It is based on the [Breeding API (BrAPI)](https://brapi.org/) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface.
It also provides a standard interface that can be accessed programatically through [web services](https://urgi.versailles.inra.fr/faidare/swagger-ui.html).
It also provides a standard interface that can be accessed programatically through [web services](https://urgi.versailles.inrae.fr/faidare/swagger-ui.html).
It is an extension of the generic [Data-Discovery portal](https://forgemia.inra.fr/urgi-is/data-discovery), a web portal that allows finding any type of data across several databases through a lightweight keyword based search.
FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.
FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.
It has been developed by [INRA-URGI](http://urgi.versailles.inra.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
It has been developed by [INRAE-URGI](http://urgi.versailles.inrae.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
If you want to join the FAIDARE federation, please read the "Join us" section and [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
If you want to join the FAIDARE federation, please read the "Join us" section and [contact us](mailto:urgi-contact@inrae.fr?subject=%5BFAIDARE%5D).
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