Put CLI v1 code back into original command classes

Signed-off-by: Ben Sherman <[email protected]>

launch-v1.sh

@@ -14,4 +14,4 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
-MAIN_CLASS="nextflow.cli.v1.Launcher" ./launch.sh "$@"
+MAIN_CLASS="nextflow.cli.Launcher" ./launch.sh "$@"

launch.sh

@@ -57,7 +57,7 @@ fi
 declare -a args=()
 DEBUG=''
 COLUMNS=${COLUMNS:-`tput cols 2> /dev/tty`}
-MAIN_CLASS=${MAIN_CLASS:-'nextflow.cli.v1.Launcher'}
+MAIN_CLASS=${MAIN_CLASS:-'nextflow.cli.Launcher'}
 JAVA_VER="$($JAVA_BIN -version 2>&1)"
 if [ $? -ne 0 ]; then
     echo "${JAVA_VER:-Failed to launch the Java virtual machine}"

modules/nextflow/build.gradle

@@ -65,7 +65,7 @@ test {
 }
 
 application {
-    mainClass = 'nextflow.cli.v1.Launcher'
+    mainClass = 'nextflow.cli.Launcher'
 }
 
 run{

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

@@ -28,7 +28,7 @@ import nextflow.util.HistoryFile
 import static nextflow.util.HistoryFile.Record
 
 /**
- * Common cache operations shared by {@link LogImpl} and {@link CleanImpl}
+ * Common cache operations shared by {@link CmdLog} and {@link CmdClean}
  *
  * @author Paolo Di Tommaso <[email protected]>
  */

modules/nextflow/src/main/groovy/nextflow/cli/v1/AbstractCmd.groovy → modules/nextflow/src/main/groovy/nextflow/cli/CmdBase.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.cli.v1
+package nextflow.cli
 
 import com.beust.jcommander.Parameter
 import groovy.transform.CompileStatic
@@ -25,7 +25,7 @@ import groovy.transform.CompileStatic
  * @author Paolo Di Tommaso <[email protected]>
  */
 @CompileStatic
-abstract class AbstractCmd implements Runnable {
+abstract class CmdBase implements Runnable {
 
     private Launcher launcher
 

modules/nextflow/src/main/groovy/nextflow/cli/CleanImpl.groovy → modules/nextflow/src/main/groovy/nextflow/cli/CmdClean.groovy

@@ -15,7 +15,6 @@
  */
 
 package nextflow.cli
-
 import java.nio.file.FileVisitResult
 import java.nio.file.FileVisitor
 import java.nio.file.Files
@@ -24,6 +23,8 @@ import java.nio.file.Path
 import java.nio.file.Paths
 import java.nio.file.attribute.BasicFileAttributes
 
+import com.beust.jcommander.Parameter
+import com.beust.jcommander.Parameters
 import com.google.common.hash.HashCode
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
@@ -39,14 +40,14 @@ import nextflow.trace.TraceRecord
 import nextflow.util.HistoryFile.Record
 
 /**
- * CLI `clean` sub-command
+ * Implements cache clean up command
  *
  * @author Paolo Di Tommaso <[email protected]>
  * @author Lorenz Gerber <[email protected]>
  */
 @Slf4j
 @CompileStatic
-class CleanImpl implements CacheBase {
+class CmdClean implements CacheBase {
 
     interface Options {
         String getAfter()
@@ -61,14 +62,56 @@ class CleanImpl implements CacheBase {
         ILauncherOptions getLauncherOptions()
     }
 
+    @Parameters(commandDescription = 'Clean up project cache and work directories')
+    static class V1 extends CmdBase implements Options {
+
+        @Parameter(names=['-q', '-quiet'], description = 'Do not print names of files removed', arity = 0)
+        boolean quiet
+
+        @Parameter(names=['-f', '-force'], description = 'Force clean command', arity = 0)
+        boolean force
+
+        @Parameter(names=['-n', '-dry-run'], description = 'Print names of file to be removed without deleting them' , arity = 0)
+        boolean dryRun
+
+        @Parameter(names='-after', description = 'Clean up runs executed after the specified one')
+        String after
+
+        @Parameter(names='-before', description = 'Clean up runs executed before the specified one')
+        String before
+
+        @Parameter(names='-but', description = 'Clean up all runs except the specified one')
+        String but
+
+        @Parameter(names=['-k', '-keep-logs'], description = 'Removes only temporary files but retains execution log entries and metadata')
+        boolean keepLogs
+
+        @Parameter
+        List<String> args
+
+        @Override
+        ILauncherOptions getLauncherOptions() {
+            launcher.options
+        }
+
+        @Override
+        String getName() { 'clean' }
+
+        @Override
+        void run() {
+            new CmdClean(this).run()
+        }
+
+    }
+
     @Delegate
     private Options options
 
     private CacheDB currentCacheDb
 
     private Map<HashCode, Short> dryHash = new HashMap<>()
 
-    CleanImpl(Options options) {
+    CmdClean(Options options) {
         this.options = options
     }
 

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

@@ -15,21 +15,21 @@
  */
 
 package nextflow.cli
-
+import com.beust.jcommander.Parameter
+import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.exception.AbortOperationException
 import nextflow.plugin.Plugins
 import nextflow.scm.AssetManager
-
 /**
- * CLI `clone` sub-command
+ * CLI sub-command clone
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
 @Slf4j
 @CompileStatic
-class CloneImpl {
+class CmdClone {
 
     interface Options extends IHubOptions {
         String getPipeline()
@@ -38,10 +38,39 @@ class CloneImpl {
         String getRevision()
     }
 
+    @Parameters(commandDescription = 'Clone a project into a folder')
+    static class V1 extends CmdBase implements Options, HubOptions {
+
+        @Parameter(required=true, description = 'name of the project to clone')
+        List<String> args
+
+        @Parameter(names='-r', description = 'Revision to clone - It can be a git branch, tag or revision number')
+        String revision
+
+        @Parameter(names=['-d','-deep'], description = 'Create a shallow clone of the specified depth')
+        Integer deep
+
+        @Override
+        String getPipeline() { args[0] }
+
+        @Override
+        String getTargetName() {
+            args.size() > 1 ? args[1] : null
+        }
+
+        @Override
+        String getName() { 'clone' }
+
+        @Override
+        void run() {
+            new CmdClone(this).run()
+        }
+    }
+
     @Delegate
     private Options options
 
-    CloneImpl(Options options) {
+    CmdClone(Options options) {
         this.options = options
     }
 

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

@@ -19,6 +19,8 @@ package nextflow.cli
 import java.nio.file.Path
 import java.nio.file.Paths
 
+import com.beust.jcommander.Parameter
+import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
@@ -27,15 +29,14 @@ import nextflow.exception.AbortOperationException
 import nextflow.plugin.Plugins
 import nextflow.scm.AssetManager
 import nextflow.util.ConfigHelper
-
 /**
- * CLI `config` sub-command
+ *  Prints the pipeline configuration
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
 @Slf4j
 @CompileStatic
-class ConfigImpl {
+class CmdConfig {
 
     interface Options {
         String getPipeline()
@@ -48,17 +49,58 @@ class ConfigImpl {
         ILauncherOptions getLauncherOptions()
     }
 
+    @Parameters(commandDescription = 'Print a project configuration')
+    static class V1 extends CmdBase implements Options {
+
+        @Parameter(description = 'project name')
+        List<String> args = []
+
+        @Parameter(names=['-a','-show-profiles'], description = 'Show all configuration profiles')
+        boolean showAllProfiles
+
+        @Parameter(names=['-profile'], description = 'Choose a configuration profile')
+        String profile
+
+        @Parameter(names = '-properties', description = 'Prints config using Java properties notation')
+        boolean printProperties
+
+        @Parameter(names = '-flat', description = 'Print config using flat notation')
+        boolean printFlatten
+
+        @Parameter(names = '-sort', description = 'Sort config attributes')
+        boolean sort
+
+        @Override
+        String getPipeline() {
+            args.size() > 0 ? args[0] : null
+        }
+
+        @Override
+        ILauncherOptions getLauncherOptions() {
+            launcher.options
+        }
+
+        @Override
+        String getName() { 'config' }
+
+        @Override
+        void run() {
+            new CmdConfig(this).run()
+        }
+
+    }
+
     private OutputStream stdout = System.out
 
     @Delegate
     private Options options
 
-    ConfigImpl(Options options) {
+    CmdConfig(Options options) {
         this.options = options
     }
 
     /* For testing purposes only */
-    ConfigImpl() {}
+    CmdConfig() {}
 
     void run() {
         Plugins.init()

modules/nextflow/src/main/groovy/nextflow/cli/ConsoleImpl.groovy → modules/nextflow/src/main/groovy/nextflow/cli/CmdConsole.groovy

@@ -16,26 +16,48 @@
 
 package nextflow.cli
 
+import com.beust.jcommander.Parameter
+import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
 import nextflow.plugin.Plugins
 import nextflow.ui.console.ConsoleExtension
 
 /**
- * CLI `console` sub-command
+ * Launch the Nextflow Console plugin
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
 @CompileStatic
-class ConsoleImpl {
+class CmdConsole {
 
     interface Options {
         String getScript()
     }
 
+    @Parameters(commandDescription = 'Launch Nextflow interactive console')
+    static class V1 extends CmdBase implements Options {
+
+        @Parameter(description = 'Nextflow console arguments')
+        List<String> args
+
+        @Override
+        String getScript() {
+            args.size() > 0 ? args[0] : null
+        }
+
+        @Override
+        String getName() { 'console' }
+
+        @Override
+        void run() {
+            new CmdConsole(this).run()
+        }
+    }
+
     @Delegate
     private Options options
 
-    ConsoleImpl(Options options) {
+    CmdConsole(Options options) {
         this.options = options
     }