install on readAttributes

quiltdata · Feb 6, 2024 · de88172 · de88172
1 parent c808d75
commit de88172
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy
@@ -29,6 +29,7 @@ import java.nio.file.attribute.BasicFileAttributes
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.quilt.jep.QuiltParser
+import nextflow.quilt.jep.QuiltPackage
 
 /**
  * Implements FileSystem interface for Quilt registries
@@ -63,7 +64,7 @@ final class QuiltFileSystem extends FileSystem implements Closeable {
     }
 
     void delete(QuiltPath path) {
-        //log.debug("QuiltFileSystem.delete: $path")
+        log.debug("QuiltFileSystem.delete: $path")
         path.deinstall()
     //throw new UnsupportedOperationException("Operation 'delete' is not supported by QuiltFileSystem")
     }
@@ -109,6 +110,11 @@ final class QuiltFileSystem extends FileSystem implements Closeable {
         log.debug("QuiltFileAttributes QuiltFileSystem.readAttributes($path)")
         Path installedPath = path.localPath()
         try {
+            QuiltPackage _pkg = path.pkg()
+            if (!_pkg.installed) {
+                log.debug("QuiltFileSystem.readAttributes: installing $_pkg")
+                _pkg.install()
+            }
             BasicFileAttributes attrs = Files.readAttributes(installedPath, BasicFileAttributes)
             return new QuiltFileAttributes(path, path.toString(), attrs)
         }

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
@@ -73,6 +73,7 @@ final class QuiltPath implements Path, Comparable {
         return sub_paths()
     }
 
+    // auto-install before using
     Path localPath() {
         Path pkgPath = pkg().packageDest()
         assert pkgPath
@@ -112,15 +113,15 @@ final class QuiltPath implements Path, Comparable {
 
     @Override
     Path getFileName() {
-        log.debug("getFileName[${this}]: paths=$paths")
+        log.debug('QuiltPath.getFileName')
         // if (isJustPackage()) { return this } // IF DIRECTORY
         QuiltPath filePath = new QuiltPath(filesystem, parsed.lastPath(), true)
         return filePath
     }
 
     @Override
     Path getParent() {
-        //log.debug("${this}.getParent: ${paths}`")
+        //log.debug("QuiltPath.getParent: ${paths}`")
         return new QuiltPath(filesystem, parsed.dropPath())
     }