Fix JGit resources not being closed in CLI commands

modules/nextflow/src/main/groovy/nextflow/cli/CmdClone.groovy

@@ -52,25 +52,25 @@ class CmdClone extends CmdBase implements HubOptions {
         Plugins.init()
         // the pipeline name
         String pipeline = args[0]
-        final manager = new AssetManager(pipeline, this)
+        try (final manager = new AssetManager(pipeline, this)) {
+            // the target directory is the second parameter
+            // otherwise default the current pipeline name
+            def target = new File(args.size()> 1 ? args[1] : manager.getBaseName())
+            if( target.exists() ) {
+                if( target.isFile() )
+                    throw new AbortOperationException("A file with the same name already exists: $target")
+                if( !target.empty() )
+                    throw new AbortOperationException("Clone target directory must be empty: $target")
+            }
+            else if( !target.mkdirs() ) {
+                throw new AbortOperationException("Cannot create clone target directory: $target")
+            }
 
-        // the target directory is the second parameter
-        // otherwise default the current pipeline name
-        def target = new File(args.size()> 1 ? args[1] : manager.getBaseName())
-        if( target.exists() ) {
-            if( target.isFile() )
-                throw new AbortOperationException("A file with the same name already exists: $target")
-            if( !target.empty() )
-                throw new AbortOperationException("Clone target directory must be empty: $target")
+            manager.checkValidRemoteRepo()
+            print "Cloning ${manager.getProjectWithRevision()} ..."
+            manager.clone(target, revision, deep)
+            print "\r"
+            println "${manager.getProjectWithRevision()} cloned to: $target"
         }
-        else if( !target.mkdirs() ) {
-            throw new AbortOperationException("Cannot create clone target directory: $target")
-        }
-
-        manager.checkValidRemoteRepo()
-        print "Cloning ${manager.getProjectWithRevision()} ..."
-        manager.clone(target, revision, deep)
-        print "\r"
-        println "${manager.getProjectWithRevision()} cloned to: $target"
     }
 }

modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy

@@ -233,13 +233,13 @@ class CmdConfig extends CmdBase {
             return file.parent ?: Paths.get('/')
         }
 
-        final manager = new AssetManager(path, revision)
-        if( revision && manager.isUsingLegacyStrategy() ){
-            log.warn("The local asset for ${path} does not support multi-revision - 'revision' option is ignored\n" +
-                "Consider updating the project using 'nextflow pull ${path} -r $revision -migrate'")
+        try (final manager = new AssetManager(path, revision)) {
+            if( revision && manager.isUsingLegacyStrategy() ){
+                log.warn("The local asset for ${path} does not support multi-revision - 'revision' option is ignored\n" +
+                    "Consider updating the project using 'nextflow pull ${path} -r $revision -migrate'")
+            }
+            return manager.isLocal() ? manager.localPath.toPath() : manager.configFile?.parent
         }
-        manager.isLocal() ? manager.localPath.toPath() : manager.configFile?.parent
-
     }
 
 }

modules/nextflow/src/main/groovy/nextflow/cli/CmdDrop.groovy

@@ -50,6 +50,8 @@ class CmdDrop extends CmdBase {
     @Override
     void run() {
         Plugins.init()
-        new AssetManager(args[0]).drop(revision, force)
+        try (final manager = new AssetManager(args[0])) {
+            manager.drop(revision, force)
+        }
     }
 }

modules/nextflow/src/main/groovy/nextflow/cli/CmdInfo.groovy

@@ -75,25 +75,26 @@ class CmdInfo extends CmdBase {
         }
 
         Plugins.init()
-        final manager = new AssetManager(args[0])
-        if( manager.isNotInitialized() ) {
-            throw new AbortOperationException("Unknown project `${args[0]}`")
-        }
+        try (final manager = new AssetManager(args[0])) {
+            if( manager.isNotInitialized() ) {
+                throw new AbortOperationException("Unknown project `${args[0]}`")
+            }
 
-        if( !format || format == 'text' ) {
-            printText(manager,level)
-            return
-        }
+            if( !format || format == 'text' ) {
+                printText(manager,level)
+                return
+            }
 
-        def map = createMap(manager)
-        if( format == 'json' ) {
-            printJson(map)
-        }
-        else if( format == 'yaml' ) {
-            printYaml(map)
+            def map = createMap(manager)
+            if( format == 'json' ) {
+                printJson(map)
+            }
+            else if( format == 'yaml' ) {
+                printYaml(map)
+            }
+            else
+                throw new AbortOperationException("Unknown output format: $format");
         }
-        else
-            throw new AbortOperationException("Unknown output format: $format");
 
     }
 

modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy

@@ -83,39 +83,41 @@ class CmdPull extends CmdBase implements HubOptions {
 
         for( String proj : list ) {
             if( all ) {
-                def branches = new AssetManager(proj).getBranchesAndTags(false).pulled as List<String>
-                branches.each { rev -> pullProjectRevision(proj, rev) }
+                try (def mgr = new AssetManager(proj)) {
+                    def branches = mgr.getBranchesAndTags(false).pulled as List<String>
+                    branches.each { rev -> pullProjectRevision(proj, rev) }
+                }
             } else {
                 pullProjectRevision(proj, revision)
             }
         }
     }
 
     private pullProjectRevision(String project, String revision) {
-        final manager = new AssetManager(project, this)
-
-        if( manager.isUsingLegacyStrategy() ) {
-            if( migrate ) {
-                log.info "Migrating ${project} revision ${revision} to multi-revision strategy"
-                manager.setStrategyType(AssetManager.RepositoryStrategyType.MULTI_REVISION)
-            } else {
-                log.warn "The local asset for ${project} does not support multi-revision - Pulling with legacy strategy\n" +
-                    "Consider updating the project ${project} using '-migrate' option"
+        try (final manager = new AssetManager(project, this)) {
+            if( manager.isUsingLegacyStrategy() ) {
+                if( migrate ) {
+                    log.info "Migrating ${project} revision ${revision} to multi-revision strategy"
+                    manager.setStrategyType(AssetManager.RepositoryStrategyType.MULTI_REVISION)
+                } else {
+                    log.warn "The local asset for ${project} does not support multi-revision - Pulling with legacy strategy\n" +
+                        "Consider updating the project ${project} using '-migrate' option"
+                }
             }
-        }
 
-        if( revision )
-            manager.setRevision(revision)
+            if( revision )
+                manager.setRevision(revision)
 
-        log.info "Checking ${manager.getProjectWithRevision()} ..."
+            log.info "Checking ${manager.getProjectWithRevision()} ..."
 
-        def result = manager.download(revision, deep)
-        manager.updateModules()
+            def result = manager.download(revision, deep)
+            manager.updateModules()
 
-        def scriptFile = manager.getScriptFile()
-        String message = !result ? " done" : " $result"
-        message += " - revision: ${scriptFile.revisionInfo}"
-        log.info message
+            def scriptFile = manager.getScriptFile()
+            String message = !result ? " done" : " $result"
+            message += " - revision: ${scriptFile.revisionInfo}"
+            log.info message
+        }
     }
 
 }

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -599,41 +599,42 @@ class CmdRun extends CmdBase implements HubOptions {
         /*
          * try to look for a pipeline in the repository
          */
-        def manager = new AssetManager(pipelineName, this)
-        if( revision )
-            manager.setRevision(revision)
-        def repo = manager.getProjectWithRevision()
-
-        boolean checkForUpdate = true
-        if( !manager.isRunnable() || latest ) {
-            if( offline )
-                throw new AbortOperationException("Unknown project `$repo` -- NOTE: automatic download from remote repositories is disabled")
-            log.info "Pulling $repo ..."
-            def result = manager.download(revision,deep)
-            if( result )
-                log.info " $result"
-            checkForUpdate = false
-        }
-        // Warn if using legacy
-        if( manager.isUsingLegacyStrategy() ){
-            log.warn1 "This Nextflow version supports a new Multi-revision strategy for managing the SCM repositories, " +
-                "but '${repo}' is single-revision legacy strategy - Please consider to update the repository with the 'nextflow pull -migrate' command."
-        }
-        // post download operations
-        try {
-            manager.checkout(revision)
-            manager.updateModules()
-            final scriptFile = manager.getScriptFile(mainScript)
-            if( checkForUpdate && !offline )
-                manager.checkRemoteStatus(scriptFile.revisionInfo)
-            // return the script file
-            return scriptFile
-        }
-        catch( AbortOperationException e ) {
-            throw e
-        }
-        catch( Exception e ) {
-            throw new AbortOperationException("Unknown error accessing project `$repo` -- Repository may be corrupted: ${manager.localPath}", e)
+        try (def manager = new AssetManager(pipelineName, this)) {
+            if( revision )
+                manager.setRevision(revision)
+            def repo = manager.getProjectWithRevision()
+
+            boolean checkForUpdate = true
+            if( !manager.isRunnable() || latest ) {
+                if( offline )
+                    throw new AbortOperationException("Unknown project `$repo` -- NOTE: automatic download from remote repositories is disabled")
+                log.info "Pulling $repo ..."
+                def result = manager.download(revision,deep)
+                if( result )
+                    log.info " $result"
+                checkForUpdate = false
+            }
+            // Warn if using legacy
+            if( manager.isUsingLegacyStrategy() ){
+                log.warn1 "This Nextflow version supports a new Multi-revision strategy for managing the SCM repositories, " +
+                    "but '${repo}' is single-revision legacy strategy - Please consider to update the repository with the 'nextflow pull -migrate' command."
+            }
+            // post download operations
+            try {
+                manager.checkout(revision)
+                manager.updateModules()
+                final scriptFile = manager.getScriptFile(mainScript)
+                if( checkForUpdate && !offline )
+                    manager.checkRemoteStatus(scriptFile.revisionInfo)
+                // return the script file
+                return scriptFile
+            }
+            catch( AbortOperationException e ) {
+                throw e
+            }
+            catch( Exception e ) {
+                throw new AbortOperationException("Unknown error accessing project `$repo` -- Repository may be corrupted: ${manager.localPath}", e)
+            }
         }
 
     }

modules/nextflow/src/main/groovy/nextflow/cli/CmdView.groovy

@@ -54,35 +54,35 @@ class CmdView extends CmdBase {
     @Override
     void run() {
         Plugins.init()
-        final manager = new AssetManager(args[0], revision)
-        if( !manager.isLocal() )
-            throw new AbortOperationException("Unknown project `${manager.getProjectWithRevision()}`")
-        if( revision && manager.isUsingLegacyStrategy()){
-            log.warn("The local asset ${args[0]} does not support multi-revision - 'revision' option is ignored\n" +
-                "Consider updating the asset using 'nextflow pull ${args[0]} -r $revision -migrate'")
-        }
-        if( all ) {
-            if( !quiet )
-                println "== content of path: ${manager.localPath}"
+        try (final manager = new AssetManager(args[0], revision)) {
+            if( !manager.isLocal() )
+                throw new AbortOperationException("Unknown project `${manager.getProjectWithRevision()}`")
+            if( revision && manager.isUsingLegacyStrategy()){
+                log.warn("The local asset ${args[0]} does not support multi-revision - 'revision' option is ignored\n" +
+                    "Consider updating the asset using 'nextflow pull ${args[0]} -r $revision -migrate'")
+            }
+            if( all ) {
+                if( !quiet )
+                    println "== content of path: ${manager.localPath}"
 
-            manager.localPath.eachFile { File it ->
-                println it.name
+                manager.localPath.eachFile { File it ->
+                    println it.name
+                }
             }
-        }
 
-        else {
-            /*
-             * prints the script main file
-             */
-            final script = manager.getMainScriptFile()
-            if( !script.exists() )
-                throw new AbortOperationException("Missing script file: '${script}'")
+            else {
+                /*
+                 * prints the script main file
+                 */
+                final script = manager.getMainScriptFile()
+                if( !script.exists() )
+                    throw new AbortOperationException("Missing script file: '${script}'")
 
-            if( !quiet )
-                println "== content of file: $script"
+                if( !quiet )
+                    println "== content of file: $script"
 
-            script.readLines().each { println it }
+                script.readLines().each { println it }
+            }
         }
-
     }
 }

modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy

@@ -58,7 +58,7 @@ import org.eclipse.jgit.merge.MergeStrategy
 
 @Slf4j
 @CompileStatic
-class AssetManager {
+class AssetManager implements Closeable {
 
     /**
      * The folder all pipelines scripts are installed
@@ -782,7 +782,7 @@ class AssetManager {
             clone.setBranch(revision)
         if( deep )
             clone.setDepth(deep)
-        clone.call()
+        clone.call().close()
     }
 
     /**

modules/nextflow/src/main/groovy/nextflow/scm/LegacyRepositoryStrategy.groovy

@@ -86,7 +86,7 @@ class LegacyRepositoryStrategy extends AbstractRepositoryStrategy {
                 .setCloneSubmodules(manifest.recurseSubmodules)
             if( deep )
                 clone.setDepth(deep)
-            clone.call()
+            clone.call().close()
 
             // git cli would automatically create a 'refs/remotes/origin/HEAD' symbolic ref pointing at the remote's
             // default branch. jgit doesn't do this, but since it automatically checked out the default branch on clone