filter features by type

shashankbrgowda · Oct 21, 2024 · 89398ea · 89398ea
2 parents c6bfa7a + 7cc023b
commit 89398ea
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Showing 39 changed files with 445 additions and 324 deletions.
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -15,7 +15,7 @@ on:
 
 jobs:
   build:
-    name: Build and upload
+    name: Build or fetch and upload
     runs-on: ubuntu-latest
     steps:
       - name: Check out
@@ -26,10 +26,23 @@ jobs:
           node-version: 18
           cache: yarn
       - name: Install
+        if: inputs.environment == 'staging'
         run: yarn --immutable
       - name: Build plugin
+        if: inputs.environment == 'staging'
         run: yarn build
         working-directory: packages/jbrowse-plugin-apollo
+      - name: Fetch plugin
+        if: inputs.environment == 'prod'
+        working-directory: packages/jbrowse-plugin-apollo
+        run: |
+          mkdir --parents dist
+          cd dist/
+          wget --output-document=- --quiet https://registry.npmjs.org/@apollo-annotation/jbrowse-plugin-apollo/ > jpa.json
+          LATEST_VERSION=$(jq --raw-output '."dist-tags".latest' jpa.json)
+          TARBALL=$(jq --raw-output ".versions.\"${LATEST_VERSION}\".dist.tarball" jpa.json)
+          wget --output-document=- --quiet ${TARBALL} | \
+            tar --extract --gzip --file=- --strip=2 package/dist/jbrowse-plugin-apollo.umd.development.js package/dist/jbrowse-plugin-apollo.umd.production.min.js
       - name: Upload built plugin files
         uses: actions/upload-artifact@v4
         with:
@@ -101,4 +114,4 @@ jobs:
         run: |
           docker --context staging compose down
           docker --context staging compose pull
-          docker --context staging compose up --build --detach
+          docker --context staging compose up --build --detach --wait --wait-timeout 120
diff --git a/.github/workflows/reload_demo_data.yml b/.github/workflows/reload_demo_data.yml
@@ -46,50 +46,66 @@ jobs:
             HostName ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }}
             User ec2-user
             IdentityFile ~/.ssh/staging
+            ServerAliveInterval 60
+            ServerAliveCountMax 10
           END
           ssh-keyscan -H ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} >> ~/.ssh/known_hosts
-      - name: Test ssh
+      - name: Create Docker context
         run: |
-          xid=`date +"%Y-%m-%dT%H-%M-%S"`
-          cat <<'EOF' > cleanup_apollo.$xid.sh
-          set -e
-          set -u
-          set -o pipefail
-          set -x
-
-          demoDataDir=${{ '${HOME}' }}/dario/demoData
-          rm -rf $demoDataDir
-          mkdir -p $demoDataDir
-          cd $demoDataDir
-
-          wormbase='https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS19/species'
-          curl -O -s -L $wormbase/schistosoma_haematobium/TD2_PRJEB44434/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz
-          curl -O -s -L $wormbase/schistosoma_mansoni/PRJEA36577/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz
-          curl -O -s -L $wormbase/schistosoma_haematobium/TD2_PRJEB44434/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3.gz
-          curl -O -s -L $wormbase/schistosoma_mansoni/PRJEA36577/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3.gz
-          gunzip *.gz
-
-          cd ${{ '${HOME}' }}/Apollo3/packages/apollo-cli
-
-          export APOLLO_PROFILE=auto
-          function apollo () {
-            yarn node bin/run.js "$@"
+          docker context create staging \
+            --docker host=ssh://staging \
+            --description "Staging server"
+      - name: Load data
+        run: |
+          docker pull ghcr.io/gmod/apollo-cli:${{ vars.DOCKER_TAG }}
+          function apollo() {
+            docker \
+              --context staging \
+              run \
+              --rm \
+              --interactive \
+              --add-host host.docker.internal=host-gateway \
+              --volume /home/ec2-user/.config/apollo-cli:/root/.config/apollo-cli \
+              --volume /home/ec2-user/data:/data \
+              --env APOLLO_PROFILE=auto \
+              ghcr.io/gmod/apollo-cli:${{ vars.DOCKER_TAG }} \
+              "$@"
           }
 
-          apollo config address http://localhost
+          set -x
+          apollo config address http://host.docker.internal/apollo
           apollo config accessType root
           apollo config rootCredentials.username ${{ secrets.ROOT_USER_NAME }}
           apollo config rootCredentials.password ${{ secrets.ROOT_USER_PASSWORD }}
-          apollo login
+          apollo login --force
+
+          apollo jbrowse set-config /data/config.json
+
+          apollo assembly get | apollo assembly delete --verbose --assembly -
+          apollo file get | apollo file delete
 
-          apollo assembly get | apollo assembly delete -v -a -
+          apollo assembly \
+            add-from-fasta \
+            /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz \
+            --fai /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz.fai \
+            --gzi /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz.gzi \
+            --assembly 'Schistosoma haematobium' \
+            --not-editable
 
-          apollo assembly add-from-fasta $demoDataDir/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa -a schistosoma_haematobium -f
-          apollo assembly add-from-fasta $demoDataDir/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa -a schistosoma_mansoni -f
+          apollo assembly \
+            add-from-fasta \
+            /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz \
+            --fai /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz.fai \
+            --gzi /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz.gzi \
+            --assembly 'Schistosoma mansoni' \
+            --not-editable
 
-          apollo feature import -i $demoDataDir/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3 -a schistosoma_haematobium -d
-          apollo feature import -i $demoDataDir/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3 -a schistosoma_mansoni -d
-          EOF
+          apollo feature \
+            import \
+            --input-file /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.genes.gff3 \
+            --assembly 'Schistosoma haematobium'
 
-          rsync -av cleanup_apollo.$xid.sh staging:dario/
-          ssh staging -f "bash dario/cleanup_apollo.$xid.sh > dario/cleanup_apollo.$xid.out 2> dario/cleanup_apollo.$xid.err"
+          apollo feature \
+            import \
+            --input-file /data/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.genes.gff3 \
+            --assembly 'Schistosoma mansoni'
diff --git a/package.json b/package.json
@@ -8,6 +8,7 @@
   "scripts": {
     "lint": "cross-env NODE_OPTIONS='--max-old-space-size=4096' yarn eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts,.jsx,.tsx .",
     "build:shared": "yarn workspace @apollo-annotation/shared run build",
+    "release": "tsx scripts/makeGitTag.ts",
     "start:shared": "yarn workspace @apollo-annotation/shared run start",
     "start:server": "yarn workspace @apollo-annotation/collaboration-server run start",
     "start:plugin": "yarn workspace @apollo-annotation/jbrowse-plugin-apollo run start",
@@ -18,6 +19,7 @@
   "devDependencies": {
     "@types/cross-spawn": "^6.0.6",
     "@types/node": "^18.14.2",
+    "@types/semver": "^7",
     "@types/yargs": "^17.0.32",
     "@typescript-eslint/eslint-plugin": "^7.16.0",
     "@typescript-eslint/parser": "^7.16.0",
@@ -44,6 +46,8 @@
     "prettier": "^3.3.2",
     "prettier-plugin-packagejson": "^2.5.2",
     "react": "^18.2.0",
+    "semver": "^7.6.3",
+    "tslib": "^2.3.1",
     "tsx": "^4.6.2",
     "typescript": "^5.5.3",
     "yargs": "^17.7.2"