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stages:

    - artifacts

variables:

  CI_REGISTRY_IMAGE: harbor.computational.bio.uni-giessen.de/psos/psot

  VERSIONLABELMETHOD: "OnlyIfThisCommitHasVersion" # options: "OnlyIfThisCommitHasVersion","LastVersionTagInGit"

  ADDITIONALTAGLIST: latest

  IMAGE_LABELS: >

    --label org.opencontainers.image.vendor=$CI_SERVER_URL/$GITLAB_USER_LOGIN

    --label org.opencontainers.image.authors=$CI_SERVER_URL/$GITLAB_USER_LOGIN

    --label org.opencontainers.image.revision=$CI_COMMIT_SHA

    --label org.opencontainers.image.source=$CI_PROJECT_URL

    --label org.opencontainers.image.documentation=$CI_PROJECT_URL

    --label org.opencontainers.image.licenses=$CI_PROJECT_URL

    --label org.opencontainers.image.url=$CI_PROJECT_URL

    --label vcs-url=$CI_PROJECT_URL

    --label com.gitlab.ci.user=$CI_SERVER_URL/$GITLAB_USER_LOGIN

    --label com.gitlab.ci.email=$GITLAB_USER_EMAIL

    --label com.gitlab.ci.tagorbranch=$CI_COMMIT_REF_NAME

    --label com.gitlab.ci.pipelineurl=$CI_PIPELINE_URL

    --label com.gitlab.ci.commiturl=$CI_PROJECT_URL/commit/$CI_COMMIT_SHA

    --label com.gitlab.ci.cijoburl=$CI_JOB_URL

    --label com.gitlab.ci.mrurl=$CI_PROJECT_URL/-/merge_requests/$CI_MERGE_REQUEST_ID

build-and-deploy-docker-image:

  stage: artifacts

  extends: .build-docker-image

get-latest-git-version:

  stage: .pre

  image:

    name: alpine/git

    entrypoint: [""]

  rules:

    - if: '$VERSIONLABELMETHOD == "LastVersionTagInGit"'

  script:

    - |

      echo "the google kaniko container does not have git and does not have a packge manager to install it"

      git clone https://github.com/GoogleContainerTools/kaniko.git

      cd kaniko

      echo "$(git describe --abbrev=0 --tags)" > ../VERSIONTAG.txt

      echo "VERSIONTAG.txt contains $(cat ../VERSIONTAG.txt)"

  artifacts:

    paths:

      - VERSIONTAG.txt

# taken from https://gitlab.com/guided-explorations/containers/kaniko-docker-build/-/blob/master/.gitlab-ci.yml

.build-docker-image:

  image:

    name: gcr.io/kaniko-project/executor:debug

    entrypoint: [""]

  script:

    - |

      echo "Building and shipping image to $CI_REGISTRY_IMAGE"

      #Build date for opencontainers

      BUILDDATE="'$(date '+%FT%T%z' | sed -E -n 's/(\+[0-9]{2})([0-9]{2})$/\1:\2/p')'" #rfc 3339 date

      IMAGE_LABELS="$IMAGE_LABELS --label org.opencontainers.image.created=$BUILDDATE --label build-date=$BUILDDATE"

      #Description for opencontainers

      BUILDTITLE=$(echo $CI_PROJECT_TITLE | tr " " "_")

      IMAGE_LABELS="$IMAGE_LABELS --label org.opencontainers.image.title=$BUILDTITLE --label org.opencontainers.image.description=$BUILDTITLE"

      #Add ref.name for opencontainers

      IMAGE_LABELS="$IMAGE_LABELS --label org.opencontainers.image.ref.name=$CI_REGISTRY_IMAGE:${CI_COMMIT_REF_NAME//\//_}"

      #Build Version Label and Tag from git tag, LastVersionTagInGit was placed by a previous job artifact

      if [[ "$VERSIONLABELMETHOD" == "LastVersionTagInGit" ]]; then VERSIONLABEL=$(cat VERSIONTAG.txt); fi

      if [[ "$VERSIONLABELMETHOD" == "OnlyIfThisCommitHasVersion" ]]; then VERSIONLABEL=$CI_COMMIT_TAG; fi

      if [[ ! -z "$VERSIONLABEL" ]]; then

        IMAGE_LABELS="$IMAGE_LABELS --label org.opencontainers.image.version=$VERSIONLABEL"

        ADDITIONALTAGLIST="$ADDITIONALTAGLIST $VERSIONLABEL"

      fi

      ADDITIONALTAGLIST="$ADDITIONALTAGLIST $CI_COMMIT_REF_NAME $CI_COMMIT_SHORT_SHA"

      if [[ "$CI_COMMIT_BRANCH" == "$CI_DEFAULT_BRANCH" ]]; then ADDITIONALTAGLIST="$ADDITIONALTAGLIST latest"; fi

      if [[ -n "$ADDITIONALTAGLIST" ]]; then

        for TAG in $ADDITIONALTAGLIST; do

          TAG=${TAG//\//_} # replace slashes with underscore in tag

          FORMATTEDTAGLIST="${FORMATTEDTAGLIST} --tag $CI_REGISTRY_IMAGE:$TAG ";

        done;

      fi

      if [[ -n "$ADDITIONALIMAGENAMES" ]]; then

        for TAG in $ADDITIONALIMAGENAMES; do

          FORMATTEDTAGLIST="${FORMATTEDTAGLIST} --tag $TAG ";

        done;

      fi

      #Reformat Docker tags to kaniko's --destination argument:

      FORMATTEDTAGLIST=$(echo "${FORMATTEDTAGLIST}" | sed s/\-\-tag/\-\-destination/g)

      mkdir -p /kaniko/.docker

      PROJECTDIR=$CI_PROJECT_DIR

      if [[ ! -z "$SUB_DIRECTORY" ]]; then

        PROJECTDIR=$CI_PROJECT_DIR/$SUB_DIRECTORY

      fi

      echo "{\"auths\":{\"$CI_REGISTRY\":{\"auth\":\"$(echo -n $CI_REGISTRY_USER:$CI_REGISTRY_PASSWORD | base64 | tr -d '\n')\"}}}" > /kaniko/.docker/config.json

      /kaniko/executor --context $PROJECTDIR --dockerfile $PROJECTDIR/Dockerfile $FORMATTEDTAGLIST $IMAGE_LABELS

FROM ubuntu:latest

FROM ubuntu:20.04

ENV DEBIAN_FRONTEND=noninteractive

ENV DEBIAN_FRONTEND=noninteractive \

    NXF_VERSION=21.10.6

RUN apt-get update && \

    apt-get install -y python3-pip python3-setuptools python3-sphinx docker.io openjdk-11-jdk-headless wget

RUN wget https://github.com/nextflow-io/nextflow/releases/download/v19.01.0/nextflow-19.01.0-all && \

    chmod +x nextflow-19.01.0-all && \

    mv nextflow-19.01.0-all /usr/local/bin/ && \

    ln -s /usr/local/bin/nextflow-19.01.0-all /usr/local/bin/nextflow

RUN wget https://github.com/nextflow-io/nextflow/releases/download/v${NXF_VERSION}/nextflow-${NXF_VERSION}-all && \

    chmod +x nextflow-${NXF_VERSION}-all && \

    mv nextflow-${NXF_VERSION}-all /usr/local/bin/ && \

    ln -s /usr/local/bin/nextflow-${NXF_VERSION}-all /usr/local/bin/nextflow

RUN pip3 install --upgrade git+https://git.computational.bio.uni-giessen.de/SOaAS/dbxref.git