test_status_lists #67
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| name: test_status_lists | |
| on: workflow_dispatch | |
| env: | |
| RELEASE: ${{ github.ref_name }} | |
| DOCKERVERSION: develop | |
| jobs: | |
| run_test: | |
| runs-on: [self-hosted, runner3] | |
| steps: | |
| - name: Get dockers | |
| run: | | |
| docker pull genomehubs/genomehubs:$DOCKERVERSION | |
| docker run --rm genomehubs/genomehubs sh -c 'echo $CONTAINER_VERSION' | |
| - uses: actions/checkout@v3 | |
| with: | |
| persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. | |
| fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. | |
| - name: Check es health | |
| run: curl -s "es1:9200/_cat/health" | |
| - name: Delete indices for this branch/$RELEASE | |
| run: | | |
| curl -s -X DELETE "es1:9200/*--$RELEASE" | |
| - name: Restore and rename snapshot to current branch | |
| run: | | |
| curl -s -X POST "es1:9200/_snapshot/dev/initassembly/_restore?wait_for_completion=true&pretty" \ | |
| -H 'Content-Type: application/json' \ | |
| -d' { | |
| "ignore_unavailable": true, | |
| "include_global_state": false, | |
| "include_aliases": false, | |
| "rename_pattern" : "--goat--202.*", | |
| "rename_replacement" : "--goat--${{ env.RELEASE }}" | |
| }' | |
| - name: Add ES index.mapping.nested_objects.limit 1000000 | |
| run: | | |
| curl -s -X PUT "es1:9200/taxon--ncbi--goat--${RELEASE}/_settings" \ | |
| -H 'Content-Type: application/json' \ | |
| -d '{ "index.mapping.nested_objects.limit" : 1000000 }' | |
| - name: update config.yaml version | |
| run: | | |
| perl -i -plne 's/^(\s*version:) .*/$1 ${{ env.RELEASE }}/' sources/goat.yaml | |
| - name: genomehubs index taxon status_lists | |
| run: | | |
| docker run --rm --network=host \ | |
| -v `pwd`/sources:/genomehubs/sources \ | |
| genomehubs/genomehubs:$DOCKERVERSION bash -c \ | |
| "genomehubs index \ | |
| --es-host es1:9200 \ | |
| --taxonomy-source ncbi \ | |
| --config-file sources/goat.yaml \ | |
| --taxon-dir sources/status_lists \ | |
| --taxon-lookup any --taxon-spellcheck" | |
| - name: genomehubs index taxon genomesizekaryotype | |
| run: | | |
| docker run --rm --network=host \ | |
| -v `pwd`/sources:/genomehubs/sources \ | |
| genomehubs/genomehubs:$DOCKERVERSION bash -c \ | |
| "genomehubs index \ | |
| --es-host es1:9200 \ | |
| --taxonomy-source ncbi \ | |
| --config-file sources/goat.yaml \ | |
| --taxon-dir sources/genomesize_karyotype \ | |
| --taxon-lookup any --taxon-spellcheck" | |
| - name: genomehubs index taxon assembly-data-taxon | |
| run: | | |
| docker run --rm --network=host \ | |
| -v `pwd`/sources:/genomehubs/sources \ | |
| genomehubs/genomehubs:$DOCKERVERSION bash -c \ | |
| "genomehubs index \ | |
| --es-host es1:9200 \ | |
| --taxonomy-source ncbi \ | |
| --config-file sources/goat.yaml \ | |
| --taxon-dir sources/assembly-data-taxon" | |
| - name: genomehubs fill | |
| run: | | |
| docker run --rm --network=host \ | |
| -v `pwd`/sources:/genomehubs/sources \ | |
| genomehubs/genomehubs:$DOCKERVERSION bash -c \ | |
| "genomehubs fill \ | |
| --es-host es1:9200 \ | |
| --taxonomy-source ncbi \ | |
| --config-file sources/goat.yaml \ | |
| --traverse-root 2759 \ | |
| --traverse-infer-both" | |
| - name: restart dockers | |
| run: | | |
| mkdir -p /volumes/docker/logs/$RELEASE | |
| docker pull genomehubs/genomehubs-api:$DOCKERVERSION | |
| docker rm -f goat-api | |
| docker run -d \ | |
| --restart=always \ | |
| --net net-es \ | |
| -p 3010:3000 \ | |
| --user $UID:$GROUPS \ | |
| -e GH_ORIGINS="http://172.27.18.167:8010 http://172.27.18.167 null http://localhost:8010" \ | |
| -e GH_HUBNAME=goat -e GH_HUBPATH="/genomehubs/resources/" \ | |
| -e GH_NODE=http://es1:9200 \ | |
| -e GH_RELEASE=$RELEASE \ | |
| -e GH_SOURCE=https://github.com/genomehubs/goat-data/tree/$RELEASE \ | |
| -e GH_ACCESS_LOG=/genomehubs/logs/access.log \ | |
| -e GH_API_URL=https://172.27.18.167:3010/api/v2 \ | |
| -e GH_ERROR_LOG=/genomehubs/logs/error.log \ | |
| -v /volumes/docker/logs/$RELEASE:/genomehubs/logs \ | |
| -v /volumes/docker/resources:/genomehubs/resources \ | |
| --name goat-api \ | |
| genomehubs/genomehubs-api:$DOCKERVERSION | |
| docker pull genomehubs/goat:$DOCKERVERSION | |
| docker rm -f goat-ui | |
| docker run -d --restart always \ | |
| --net net-es \ | |
| -p 8010:8880 \ | |
| --user $UID:$GROUPS \ | |
| -e GH_CLIENT_PORT=8880 \ | |
| -e GH_API_URL=http://172.27.18.167:3010/api/v2 \ | |
| -e GH_SUGGESTED_TERM=Canidae \ | |
| -e GH_BASENAME=/ \ | |
| -e GH_SITENAME=GoaT \ | |
| -e GH_ARCHIVE=latest \ | |
| --name goat-ui \ | |
| genomehubs/goat:$DOCKERVERSION |