Add CID H2 plugin

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

@@ -26,7 +26,10 @@ import nextflow.config.ConfigBuilder
 import nextflow.config.ConfigMap
 import nextflow.exception.AbortOperationException
 import nextflow.plugin.Plugins
+import org.pf4j.ExtensionPoint
+
 /**
+ * CID command line interface
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
@@ -36,7 +39,7 @@ class CmdCid extends CmdBase implements UsageAware {
 
     private static final String NAME = 'cid'
 
-    interface CidOperation {
+    interface CidCommand extends ExtensionPoint {
         void log(ConfigMap config)
         void show(ConfigMap config, List<String> args)
         void lineage(ConfigMap config, List<String> args)
@@ -51,7 +54,7 @@ class CmdCid extends CmdBase implements UsageAware {
 
     private List<SubCmd> commands = new ArrayList<>()
 
-    private CidOperation operations
+    private CidCommand operation
 
     private ConfigMap config
 
@@ -81,9 +84,11 @@ class CmdCid extends CmdBase implements UsageAware {
             .setOptions(launcher.options)
             .setBaseDir(Paths.get('.'))
             .build()
+        // init plugins
+        Plugins.load(config)
         // load the command operations
-        this.operations = ServiceLoader.load(CidOperation.class).findFirst().orElse(null)
-        if( !operations )
+        this.operation = Plugins.getExtension(CidCommand)
+        if( !operation )
             throw new IllegalStateException("Unable to load CID plugin")
         // consume the first argument
         getCmd(args).apply(args.drop(1))
@@ -157,7 +162,7 @@ class CmdCid extends CmdBase implements UsageAware {
                 usage()
                 return
             }
-            operations.log(config)
+            operation.log(config)
         }
 
         @Override
@@ -186,7 +191,7 @@ class CmdCid extends CmdBase implements UsageAware {
                 return
             }
 
-            operations.show(config, args)
+            operation.show(config, args)
         }
 
         @Override
@@ -213,7 +218,7 @@ class CmdCid extends CmdBase implements UsageAware {
                 return
             }
 
-            operations.lineage(config, args)
+            operation.lineage(config, args)
         }
 
         @Override

modules/nextflow/src/test/groovy/nextflow/cli/CmdCidTest.groovy

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2024, Seqera Labs
+ * Copyright 2013-2025, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,6 +12,7 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
+ *
  */
 
 package nextflow.cli
@@ -20,6 +21,7 @@ import groovy.json.JsonOutput
 
 import java.nio.file.Files
 
+import nextflow.SysEnv
 import nextflow.dag.MermaidHtmlRenderer
 import nextflow.data.cid.CidHistoryRecord
 import nextflow.data.cid.CidStoreFactory
@@ -36,9 +38,15 @@ import test.OutputCapture
  */
 class CmdCidTest extends Specification {
 
+    def setup() {
+        // clear the environment to avoid the local env pollute the test env
+        SysEnv.push([:])
+    }
+
     def cleanup() {
         Plugins.stop()
         CidStoreFactory.reset()
+        SysEnv.pop()
     }
 
     def setupSpec() {

modules/nf-cid/src/main/nextflow/data/cid/CidStore.groovy

@@ -17,23 +17,21 @@
 
 package nextflow.data.cid
 
-import java.nio.file.Path
 
 import groovy.transform.CompileStatic
 import nextflow.data.config.DataConfig
-
 /**
  * Interface for the CID store
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @CompileStatic
-interface CidStore {
+interface CidStore extends Closeable {
 
     /**
      * Open the CID store.
      * @param config Configuration to open the CID store.
      */
-    void open(DataConfig config)
+    CidStore open(DataConfig config)
 
     /**
      * Save a CID entry in the store for in a given key.
@@ -49,12 +47,6 @@ interface CidStore {
      */
     Object load(String key)
 
-    /**
-     * Get the CID store location path.
-     * @return CID store location path.
-     */
-    Path getPath()
-
     /**
      * Get the {@link CidHistoryLog} object associated to the CidStore.
      * @return {@link CidHistoryLog} object

modules/nf-cid/src/main/nextflow/data/cid/CidStoreFactory.groovy

@@ -38,13 +38,16 @@ abstract class CidStoreFactory implements ExtensionPoint {
 
     private static boolean initialized
 
+    protected abstract boolean canOpen(DataConfig config)
+
     protected abstract CidStore newInstance(DataConfig config)
 
      static CidStore create(DataConfig config){
-        final all = Plugins.getPriorityExtensions(CidStoreFactory)
-        if( !all )
+         final factory = Plugins
+             .getPriorityExtensions(CidStoreFactory)
+             .find( f-> f.canOpen(config))
+         if( !factory )
             throw new IllegalStateException("Unable to find Nextflow CID store factory")
-        final factory = all.first()
         log.debug "Using Nextflow CID store factory: ${factory.getClass().getName()}"
         return factory.newInstance(config)
     }

modules/nf-cid/src/main/nextflow/data/cid/DefaultCidStore.groovy

@@ -17,6 +17,7 @@
 
 package nextflow.data.cid
 
+import nextflow.file.FileHelper
 import nextflow.util.TestOnly
 
 import java.nio.file.Files
@@ -39,17 +40,25 @@ class DefaultCidStore implements CidStore {
     private static String HISTORY_FILE_NAME =".history"
     private static final String METADATA_FILE = '.data.json'
     private static final String METADATA_PATH = '.meta'
+
     private Path metaLocation
     private Path location
     private CidHistoryLog historyLog
 
-    void open(DataConfig config) {
-        location = config.store.location
-        metaLocation = config.store.location.resolve(METADATA_PATH)
+    DefaultCidStore open(DataConfig config) {
+        location = toLocationPath(config.store.location)
+        metaLocation = location.resolve(METADATA_PATH)
         if( !Files.exists(metaLocation) && !Files.createDirectories(metaLocation) ) {
             throw new AbortOperationException("Unable to create CID store directory: $metaLocation")
         }
-        historyLog = new CidHistoryFile(config.store.logLocation ?: metaLocation.resolve(HISTORY_FILE_NAME))
+        historyLog = new CidHistoryFile(metaLocation.resolve(HISTORY_FILE_NAME))
+        return this
+    }
+
+    protected Path toLocationPath(String location) {
+        return location
+            ? FileHelper.toCanonicalPath(location)
+            : Path.of('.').toAbsolutePath().normalize().resolve('data')
     }
 
     @Override
@@ -70,13 +79,20 @@ class DefaultCidStore implements CidStore {
         return null
     }
 
-    @Override
-    Path getPath(){ location }
+    Path getLocation(){
+        return location
+    }
 
     @TestOnly
-    Path getMetadataPath() {metaLocation}
+    Path getMetadataPath() {
+        return metaLocation
+    }
 
     @Override
-    CidHistoryLog getHistoryLog(){ historyLog }
+    CidHistoryLog getHistoryLog(){
+        return historyLog
+    }
 
+    @Override
+    void close() { }
 }

modules/nf-cid/src/main/nextflow/data/cid/DefaultCidStoreFactory.groovy

@@ -16,6 +16,8 @@
  */
 package nextflow.data.cid
 
+import java.util.regex.Pattern
+
 import groovy.transform.CompileStatic
 import nextflow.data.config.DataConfig
 import nextflow.plugin.Priority
@@ -29,11 +31,22 @@ import nextflow.plugin.Priority
 @Priority(0)
 class DefaultCidStoreFactory extends CidStoreFactory {
 
+    private static Pattern SCHEME = ~/^([a-zA-Z][a-zA-Z\d+\-.]*):/
+    private static List SUPPORTED_SCHEMES = ['file', 's3', 'gs', 'az']
+
+    @Override
+    boolean canOpen(DataConfig config) {
+        final loc = config.store.location
+        if( !loc ) {
+            return true
+        }
+        final matcher = SCHEME.matcher(loc)
+        return matcher.find() ? matcher.group(1) in SUPPORTED_SCHEMES : true
+    }
+
     @Override
     protected CidStore newInstance(DataConfig config) {
-        final cidStore = new DefaultCidStore()
-        cidStore.open(config)
-        return cidStore
+        return new DefaultCidStore() .open(config)
     }
 
 }

modules/nf-cid/src/main/nextflow/data/cid/operation/CidOperationImpl.groovy → modules/nf-cid/src/main/nextflow/data/cid/cli/CidCommandImpl.groovy

@@ -15,7 +15,7 @@
  *
  */
 
-package nextflow.data.cid.operation
+package nextflow.data.cid.cli
 
 import static nextflow.data.cid.fs.CidPath.*
 
@@ -34,11 +34,12 @@ import nextflow.data.cid.CidStoreFactory
 import nextflow.data.cid.model.DataType
 import nextflow.ui.TableBuilder
 /**
+ * Implements CID command line operations
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @CompileStatic
-class CidOperationImpl implements CmdCid.CidOperation {
+class CidCommandImpl implements CmdCid.CidCommand {
 
     @Canonical
     static class Edge {

modules/nf-cid/src/main/nextflow/data/config/DataConfig.groovy

@@ -20,7 +20,6 @@ package nextflow.data.config
 import groovy.transform.CompileStatic
 import nextflow.Global
 import nextflow.Session
-import nextflow.util.TestOnly
 
 /**
  * Model workflow data config

modules/nf-cid/src/main/nextflow/data/config/DataStoreOpts.groovy

@@ -17,10 +17,6 @@
 
 package nextflow.data.config
 
-import nextflow.file.FileHelper
-
-import java.nio.file.Path
-
 import groovy.transform.CompileStatic
 /**
  * Model data store options
@@ -30,14 +26,10 @@ import groovy.transform.CompileStatic
 @CompileStatic
 class DataStoreOpts {
 
-    final Path location
-    final Path logLocation
+    final String location
 
     DataStoreOpts(Map opts) {
-        this.location = opts.location
-            ? FileHelper.toCanonicalPath(opts.location as String)
-            : Path.of('.').toAbsolutePath().normalize().resolve('data')
-        this.logLocation = opts.logLocation ? FileHelper.toCanonicalPath(opts.logLocation as String) : null
+        this.location = opts.location as String
     }
 
 }

modules/nf-cid/src/resources/META-INF/extensions.idx

@@ -16,4 +16,4 @@
 
 nextflow.data.cid.DefaultCidStoreFactory
 nextflow.data.cid.CidObserverFactory
-
+nextflow.data.cid.cli.CidCommandImpl

modules/nf-cid/src/test/nextflow/data/cid/DefaultCidStoreFactoryTest.groovy

@@ -0,0 +1,50 @@
+/*
+ * Copyright 2013-2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.data.cid
+
+import nextflow.data.config.DataConfig
+import spock.lang.Specification
+import spock.lang.Unroll
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class DefaultCidStoreFactoryTest extends Specification {
+
+    @Unroll
+    def 'should validate can open' () {
+        given:
+        def factory = new DefaultCidStoreFactory()
+        def config = new DataConfig(CONFIG)
+
+        expect:
+        factory.canOpen(config) == EXPECTED
+
+        where:
+        EXPECTED    | CONFIG
+        true        | [:]
+        true        | [store:[location:'/some/path']]
+        true        | [store:[location:'some/rel/path']]
+        true        | [store:[location:'file:/this/that']]
+        true        | [store:[location:'s3://some/path']]
+        false       | [store:[location:'http://some/path']]
+        false       | [store:[location:'jdbc:foo']]
+    }
+
+}