pkg-test fail

quiltdata · Sep 5, 2023 · c07fafb · c07fafb
1 parent f166844
commit c07fafb
Show file tree

Hide file tree

Showing 4 changed files with 71 additions and 9 deletions.
diff --git a/.github/workflows/pkg-test.yml b/.github/workflows/pkg-test.yml
@@ -0,0 +1,61 @@
+name: Test
+
+on:
+  # Trigger at every push. Action will also be visible from Pull Requests to master
+  push: # Comment this line to trigger action only on pull-requests (not recommended if you don't pay for GH Actions)
+  pull_request:
+    branches: [master]
+
+permissions: read-all
+
+jobs:
+  build:
+    name: Test
+    permissions:
+      contents: read
+      id-token: write
+      issues: write
+      pull-requests: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        java_version: [19]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    # Git Checkout
+    - name: Checkout Code
+      uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # v4
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        fetch-depth: 0
+
+    - name: Configure AWS Credentials
+      uses: aws-actions/configure-aws-credentials@v3
+      with:
+        role-to-assume: arn:aws:iam::712023778557:role/GitHub-Testing-NF-Quilt
+        aws-region: us-east-1
+
+    - name: Setup Java ${{matrix.java_version}}
+      uses: actions/setup-java@v3
+      with:
+        java-version: ${{matrix.java_version}}
+        distribution: 'temurin'
+        architecture: x64
+        cache: gradle
+
+    - name: Setup Gradle
+      uses: gradle/gradle-build-action@v2
+
+    - name: Run Package Tests
+      run: make pkg-test
+
+    - name: Archive production artifacts
+      if: ${{ success() }} || ${{ failure() }}
+      uses: actions/upload-artifact@v3
+      with:
+        name: nf-quilt-pkg-test
+        path: |
+          /home/runner/work/nf-quilt/nf-quilt/plugins/nf-quilt/build/reports/tests/test/
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -230,8 +230,9 @@ ${meta['workflow']['stats']['processes']}
         return template.toString()
     }
 
-    List<Path> match(String glob) throws IOException {
-        Path folder = pkg.install()
+    List<Path> match(String glob, boolean shouldInstall = false) throws IOException {
+        log.debug("QuiltProduct.match[$shouldInstall]: $glob")
+        Path folder = shouldInstall ? pkg.install() : pkg.packageDest()
         FileSystem fs = FileSystems.getDefault()
         PathMatcher pathMatcher = fs.getPathMatcher("glob:${glob}")
         List<Path> matches = []

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -137,17 +137,17 @@ class QuiltPackage {
         return namespace
     }
 
-    String resolveHash() {
+    String resolveHash(Namespace namespace) {
         if (hash == 'latest' || hash == null || hash == 'null') {
-            Namespace namespace = packageNamespace()
             return namespace.getHash('latest')
         }
         return hash
     }
 
     Manifest packageManifest() {
         Namespace namespace = packageNamespace()
-        Manifest manifest = namespace.getManifest(resolveHash())
+        String newHash = resolveHash(namespace)
+        Manifest manifest = namespace.getManifest(newHash)
         return manifest
     }
 
@@ -204,7 +204,6 @@ class QuiltPackage {
         try {
             log.info("installing $packageName from $bucket...")
             Manifest manifest = packageManifest()
-
             manifest.install(dest)
             log.info('done')
             installed = true

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
@@ -272,12 +272,13 @@ class QuiltFileSystemProvider extends FileSystemProvider {
                 attributesCache = [:] // reset cache
                 notifyFilePublish(qPath)
             } else {
+                // log.debug("\tEnsure installed: $installedPath")
                 // ensure QuiltPackage installed
-                QuiltPackage pkg = qPath.pkg()
-                pkg.install()
+                qPath.pkg().install()
+                log.debug("\tReading from: $installedPath")
             }
-            //log.debug("\tOpening channel to: $installedPath")
             FileChannel channel = FileChannel.open(installedPath, options)
+            log.debug("FileChannel.open: ${channel}")
             return channel
         }
         catch (java.nio.file.NoSuchFileException e) {