Run data reloading directly on actions

This way we can get better results
GMOD · Oct 10, 2024 · 51f944e · 51f944e
1 parent a9a9b25
commit 51f944e
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Showing 2 changed files with 29 additions and 17 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:

diff --git a/.github/workflows/reload_demo_data.yml b/.github/workflows/reload_demo_data.yml
@@ -46,6 +46,8 @@ jobs:
             HostName ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }}
             User ec2-user
             IdentityFile ~/.ssh/staging
+            ServerAliveInterval 60
+            ServerAliveCountMax 10
           END
           ssh-keyscan -H ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} >> ~/.ssh/known_hosts
       - name: Create Docker context
@@ -55,11 +57,6 @@ jobs:
             --description "Staging server"
       - name: Load data
         run: |
-          set -e
-          set -u
-          set -o pipefail
-          set -x
-
           docker pull ghcr.io/gmod/apollo-cli:${{ vars.DOCKER_TAG }}
           function apollo() {
             docker \
@@ -75,6 +72,7 @@ jobs:
               "$@"
           }
 
+          set -x
           apollo config address http://host.docker.internal/apollo
           apollo config accessType root
           apollo config rootCredentials.username ${{ secrets.ROOT_USER_NAME }}
@@ -84,6 +82,15 @@ jobs:
           apollo assembly get | apollo assembly delete --verbose --assembly -
           apollo file get | apollo file delete
 
+
+          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 \
             /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz \
@@ -94,18 +101,10 @@ jobs:
 
           apollo feature \
             import \
-            --input-file /data/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.genes.gff3 \
-            --assembly 'Schistosoma mansoni'
-
-          apollo assembly \
-            add-from-fasta \
-            /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa \
-            --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
+            --input-file /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.genes.gff3 \
+            --assembly 'Schistosoma haematobium'
 
           apollo feature \
             import \
             --input-file /data/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.genes.gff3 \
-            --assembly 'Schistosoma haematobium'
+            --assembly 'Schistosoma mansoni'