WIP: Use quiltcore to install packages

quiltdata · Jul 20, 2023 · 083e826 · 083e826
1 parent 6c8efb4
commit 083e826
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Showing 2 changed files with 45 additions and 9 deletions.
diff --git a/plugins/nf-quilt/build.gradle b/plugins/nf-quilt/build.gradle
@@ -59,6 +59,14 @@ ext{
 }
 
 dependencies {
+    // quiltcore
+    implementation files('/home/dima/src/quiltcore-java/lib/build/libs/lib.jar')
+
+    // quiltcore dependencies - why is this necessary???
+    implementation 'software.amazon.nio.s3:aws-java-nio-spi-for-s3:1.2.3'
+    implementation 'software.amazon.awssdk:s3:2.20.102'
+    implementation 'software.amazon.awssdk:s3-transfer-manager:2.20.102'
+
     // This dependency is exported to consumers, that is to say found on their compile classpath.
     compileOnly "io.nextflow:nextflow:$nextflowVersion"
     compileOnly 'org.slf4j:slf4j-api:2.0.7'

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -28,6 +28,14 @@ import java.nio.file.attribute.BasicFileAttributes
 import java.util.stream.Collectors
 import java.time.LocalDate
 
+import nextflow.file.FileHelper
+import nextflow.plugin.CustomPluginManager
+import nextflow.plugin.Plugins
+
+import com.quiltdata.quiltcore.Registry
+import com.quiltdata.quiltcore.Namespace
+import com.quiltdata.quiltcore.Manifest
+
 @Slf4j
 @CompileStatic
 class QuiltPackage {
@@ -45,6 +53,17 @@ class QuiltPackage {
     private boolean installed
     private String cmd = 'N/A'
 
+    // static {
+    //     Path path = Paths.get("nf-plugins")
+    //     Files.createDirectories(path)
+    //     Path root = path.toAbsolutePath().normalize()
+
+    //     CustomPluginManager manager = new CustomPluginManager(root)
+    //     manager.loadPlugins()
+
+    //     Plugins.init(root, "prod", manager)
+    // }
+
     static String today() {
         LocalDate date = LocalDate.now()
         return date.toString()
@@ -86,7 +105,7 @@ class QuiltPackage {
             log.debug("Installing `${pkg}` for.pkgKey $pkgKey")
             pkg.install()
         }
-        catch (Exception e) {
+        catch (IOException e) {
             log.warn("Package `${parsed.toUriString()}` does not yet exist")
         }
         return pkg
@@ -247,17 +266,26 @@ class QuiltPackage {
         }
     }
 
-    // usage: quilt3 install [-h] [--registry REGISTRY] [--top-hash TOP_HASH]
-    // [--dest DEST] [--dest-registry DEST_REGISTRY] [--path PATH] name
     Path install() {
-        int exitCode = call('install', packageName, key_registry(), key_hash(), key_dest())
-        if (exitCode != 0) {
-            log.error("`install.fail.exitCode` ${exitCode}: ${packageName}")
-            return null
-        }
+        log.info("installing $packageName ...")
+        // Path registryPath = Path.of(new URI("s3://${bucket}"))  // tries to use s3fs!
+        Path registryPath = FileHelper.asPath("s3://${bucket}")
+        log.info("registryPath: $registryPath")
+        Registry registry = new Registry(registryPath)
+        Namespace namespace = registry.getNamespace(packageName)
+        String resolvedHash = (hash == 'latest' || hash == null || hash == 'null') ? namespace.getHash('latest') : hash
+        log.info("hash: $hash -> $resolvedHash")
+        Manifest manifest = namespace.getManifest(resolvedHash)
+        Path dest = packageDest()
+        log.info("dest: $dest")
+
+        manifest.install(dest)
+        log.info("done")
+
         installed = true
         recursiveDeleteOnExit()
-        return packageDest()
+
+        return dest
     }
 
     // https://stackoverflow.com/questions/15022219