Move PluginExecAware to nextflow module

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

…y/nextflow/cli/PluginAbstractExec.groovy …low/plugin/cli/PluginAbstractExec.groovymodules/nf-cli-v1/src/main/groovy/nextflow/cli/PluginAbstractExec.groovy renamed to modules/nextflow/src/main/groovy/nextflow/plugin/cli/PluginAbstractExec.groovy modules/nf-cli-v1/src/main/groovy/nextflow/cli/PluginAbstractExec.groovy renamed to modules/nextflow/src/main/groovy/nextflow/plugin/cli/PluginAbstractExec.groovy

@@ -15,16 +15,15 @@
  *
  */
 
-package nextflow.cli
-
-import java.nio.file.Paths
+package nextflow.plugin.cli
 
 import groovy.transform.CompileStatic
 import nextflow.Session
-import nextflow.config.ConfigCmdAdapter
+import nextflow.SysEnv
 import nextflow.exception.AbortOperationException
 import org.slf4j.Logger
 import org.slf4j.LoggerFactory
+
 import static PluginExecAware.CMD_SEP
 
 /**
@@ -38,23 +37,13 @@ trait PluginAbstractExec implements PluginExecAware {
     private static Logger log = LoggerFactory.getLogger(PluginAbstractExec)
 
     private Session session
-    private Launcher launcher
 
     Session getSession() { session }
 
-    Launcher getLauncher() { launcher }
-
     abstract List<String> getCommands()
 
     @Override
-    final int exec(Launcher launcher1, String pluginId, String cmd, List<String> args) {
-        this.launcher = launcher1
-        // create the config
-        final config = new ConfigCmdAdapter()
-                .setOptions(launcher1.options)
-                .setBaseDir(Paths.get('.'))
-                .build()
-
+    final int exec(String pluginId, String cmd, List<String> args) {
         if( !cmd || cmd !in getCommands() ) {
             def msg = cmd ? "Invalid command '$pluginId:$cmd' - usage: nextflow plugin ${pluginId}${CMD_SEP}<command>" : "Usage: nextflow plugin ${pluginId}${CMD_SEP}<command>"
             msg += "\nAvailable commands:"
@@ -64,7 +53,8 @@ trait PluginAbstractExec implements PluginExecAware {
         }
 
         // create the session object
-        this.session = new Session(config)
+        this.session = new Session(getConfig())
+
         // invoke the command
         try {
             exec(cmd, args)
@@ -78,7 +68,16 @@ trait PluginAbstractExec implements PluginExecAware {
         return 0
     }
 
-    abstract int exec(String cmd, List<String> args)
+    private Map getConfig() {
+        final result = [
+            workDir: SysEnv.get('NXF_WORK') ?: 'work'
+        ]
+        final cloudCachePath = SysEnv.get('NXF_CLOUDCACHE_PATH')
+        if( cloudCachePath )
+            result.cloudcache = [ enabled: true, path: cloudCachePath ]
+        return result
+    }
 
+    abstract int exec(String cmd, List<String> args)
 
 }

…oovy/nextflow/cli/PluginExecAware.groovy …xtflow/plugin/cli/PluginExecAware.groovymodules/nf-cli-v1/src/main/groovy/nextflow/cli/PluginExecAware.groovy renamed to modules/nextflow/src/main/groovy/nextflow/plugin/cli/PluginExecAware.groovy modules/nf-cli-v1/src/main/groovy/nextflow/cli/PluginExecAware.groovy renamed to modules/nextflow/src/main/groovy/nextflow/plugin/cli/PluginExecAware.groovy

@@ -15,7 +15,7 @@
  *
  */
 
-package nextflow.cli
+package nextflow.plugin.cli
 
 /**
  * Define the interface for plugin commands
@@ -26,6 +26,6 @@ interface PluginExecAware {
 
     static final String CMD_SEP = ':'
 
-    int exec(Launcher launcher, String pluginId, String cmd, List<String> args)
+    int exec(String pluginId, String cmd, List<String> args)
 
 }

modules/nf-cli-v1/src/main/groovy/nextflow/cli/CmdPlugin.groovy

@@ -17,8 +17,6 @@
 
 package nextflow.cli
 
-import static nextflow.cli.PluginExecAware.CMD_SEP
-
 import java.nio.file.Path
 
 import com.beust.jcommander.DynamicParameter
@@ -27,8 +25,11 @@ import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
 import nextflow.exception.AbortOperationException
 import nextflow.plugin.Plugins
+import nextflow.plugin.cli.PluginExecAware
 import nextflow.plugin.util.PluginRefactor
 import org.eclipse.jgit.api.Git
+
+import static nextflow.plugin.cli.PluginExecAware.CMD_SEP
 /**
  * Plugin manager command
  * 
@@ -89,7 +90,7 @@ class CmdPlugin extends CmdBase {
                     mapped << "$it.value".toString()
                 }
                 args.addAll(mapped)
-                final ret = plugin.exec(getLauncher(), target, cmd, args)
+                final ret = plugin.exec(target, cmd, args)
                 // use explicit exit to invoke the system shutdown hooks
                 System.exit(ret)
             }

modules/nf-cli-v1/src/main/groovy/nextflow/config/ConfigCmdAdapter.groovy

@@ -351,7 +351,7 @@ class ConfigCmdAdapter {
         if( cmdRun.libPath )
             config.libDir = cmdRun.libPath
 
-        else if ( !config.isSet('libDir') && env.get('NXF_LIB') )
+        else if ( !config.libDir && env.get('NXF_LIB') )
             config.libDir = env.get('NXF_LIB')
 
         // -- override 'process' parameters defined on the cmd line

plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy

@@ -20,7 +20,7 @@ package io.seqera.tower.plugin
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.SysEnv
-import nextflow.cli.PluginAbstractExec
+import nextflow.plugin.cli.PluginAbstractExec
 /**
  * Implements nextflow cache and restore commands
  *
@@ -60,10 +60,11 @@ class CacheCommand implements PluginAbstractExec {
     }
 
     protected void cacheRestore() {
-        if( !getSession().cloudCachePath ) {
+        final env = SysEnv.get()
+        if( !env.get('NXF_CLOUDCACHE_PATH') ) {
             log.debug "Running Nextflow cache restore"
             // legacy cache manager
-            new CacheManager(System.getenv()).restoreCacheFiles()
+            new CacheManager(env).restoreCacheFiles()
         }
         else {
             // this command is only kept for backward compatibility

plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerPlugin.groovy

@@ -20,7 +20,7 @@ package io.seqera.tower.plugin
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.plugin.BasePlugin
-import nextflow.cli.PluginExecAware
+import nextflow.plugin.cli.PluginExecAware
 import org.pf4j.PluginWrapper
 /**
  * Seqera Platform plugin
@@ -31,7 +31,8 @@ import org.pf4j.PluginWrapper
 @CompileStatic
 class TowerPlugin extends BasePlugin implements PluginExecAware {
 
-    @Delegate private CacheCommand delegate
+    @Delegate
+    private CacheCommand delegate
 
     TowerPlugin(PluginWrapper wrapper) {
         super(wrapper)

plugins/nf-wave/build.gradle

@@ -44,7 +44,7 @@ configurations {
 }
 
 dependencies {
-    compileOnly project(':nf-cli-v1')
+    compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.17'
     compileOnly 'org.pf4j:pf4j:3.12.0'
     compileOnly 'io.seqera:lib-trace:0.1.0'

plugins/nf-wave/src/main/io/seqera/wave/plugin/WavePlugin.groovy

@@ -18,8 +18,8 @@
 package io.seqera.wave.plugin
 
 import io.seqera.wave.plugin.cli.WaveCmdEntry
-import nextflow.cli.PluginExecAware
 import nextflow.plugin.BasePlugin
+import nextflow.plugin.cli.PluginExecAware
 import org.pf4j.PluginWrapper
 /**
  * Wave plugin entrypoint

plugins/nf-wave/src/main/io/seqera/wave/plugin/cli/WaveCmdEntry.groovy

@@ -26,9 +26,9 @@ import groovy.util.logging.Slf4j
 import io.seqera.wave.plugin.ContainerConfig
 import io.seqera.wave.plugin.packer.Packer
 import io.seqera.wave.plugin.util.BasicCliOpts
-import nextflow.cli.PluginAbstractExec
 import nextflow.exception.AbortOperationException
 import nextflow.io.BucketParser
+import nextflow.plugin.cli.PluginAbstractExec
 /**
  * Implements Wave CLI tool
  *