Merge pull request #2 from nextflow-io/picocli

Picocli

build.gradle

@@ -140,6 +140,7 @@ dependencies {
     compile("ch.grengine:grengine:1.2.1") { exclude group: 'org.codehaus.groovy', module: 'groovy-all' }
     compile "commons-lang:commons-lang:2.6"
     compile "com.beust:jcommander:1.35"
+    compile('info.picocli:picocli:2.2.1')
     compile("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
     compile('org.iq80.leveldb:leveldb:0.7')
     compile('org.eclipse.jgit:org.eclipse.jgit:4.8.0.201706111038-r')

src/main/groovy/nextflow/Session.groovy

@@ -364,9 +364,12 @@ class Session implements ISession {
         Boolean isEnabled = config.navigate('report.enabled') as Boolean
         if( isEnabled ) {
             String fileName = config.navigate('report.file')
+            def maxTasks = config.navigate('report.maxTasks', ReportObserver.DEF_MAX_TASKS) as int
             if( !fileName ) fileName = ReportObserver.DEF_FILE_NAME
             def report = (fileName as Path).complete()
             def observer = new ReportObserver(report)
+            observer.maxTasks = maxTasks
+
             result << observer
         }
     }

src/main/groovy/nextflow/cli/CliOptions.groovy

@@ -19,65 +19,79 @@
  */
 
 package nextflow.cli
-
 import com.beust.jcommander.DynamicParameter
 import com.beust.jcommander.Parameter
+import picocli.CommandLine
+
 /**
  * Main application command line options
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
+@CommandLine.Command
 class CliOptions {
 
     /**
      * The packages to debug
      */
     @Parameter(hidden = true, names='-debug')
+    @CommandLine.Option(hidden = true, names=['--debug'])
     List<String> debug
 
     @Parameter(names=['-log'], description = 'Set nextflow log file path')
+    @CommandLine.Option(names=['--log'])
     String logFile
 
     @Parameter(names=['-c','-config'], description = 'Add the specified file to configuration set')
+    @CommandLine.Option(names=['-c','--config'])
     List<String> userConfig
 
     @Parameter(names=['-C'], description = 'Use the specified configuration file(s) overriding any defaults')
+    @CommandLine.Option(names=['-C'])
     List<String> config
 
     /**
      * the packages to trace
      */
     @Parameter(names='-trace', hidden = true)
+    @CommandLine.Option(names=['--trace'])
     List<String> trace
 
     /**
      * Enable syslog appender
      */
     @Parameter(names = ['-syslog'], description = 'Send logs to syslog server (eg. localhost:514)' )
+    @CommandLine.Option(names=['--syslog'])
     String syslog
 
     /**
      * Print out the version number and exit
      */
     @Parameter(names = ['-v','-version'], description = 'Print the program version')
+    @CommandLine.Option(names=['-v','--version'])
     boolean version
 
     /**
      * Print out the 'help' and exit
      */
     @Parameter(names = ['-h'], description = 'Print this help', help = true)
+    @CommandLine.Option(names=['-h','--help'])
     boolean help
 
     @Parameter(names = ['-q','-quiet'], description = 'Do not print information messages' )
+    @CommandLine.Option(names=['-q','--quite'])
     boolean quiet
 
     @Parameter(names = ['-bg'], description = 'Execute nextflow in background', arity = 0)
+    @CommandLine.Option(names=['--bg'], arity='0')
     boolean background
 
     @DynamicParameter(names = ['-D'], description = 'Set JVM properties' )
+    @CommandLine.Option(names=['-D'])
     Map<String,String> jvmOpts = [:]
 
     @Parameter(names = ['-self-update'], description = 'Update nextflow to the latest version', arity = 0, hidden = true)
+    @CommandLine.Option(names=['-u','--self-update'], arity = '0', hidden = true)
     boolean selfUpdate
 
 }

src/main/groovy/nextflow/cli/CmdClean.groovy

@@ -35,6 +35,7 @@ import nextflow.exception.AbortOperationException
 import nextflow.file.FileHelper
 import nextflow.trace.TraceRecord
 import nextflow.util.HistoryFile.Record
+import picocli.CommandLine
 
 /**
  * Implements cache clean up command
@@ -44,6 +45,7 @@ import nextflow.util.HistoryFile.Record
 @Slf4j
 @CompileStatic
 @Parameters(commandDescription = "Clean up project cache and work directories")
+@CommandLine.Command
 class CmdClean extends CmdBase implements CacheBase {
 
     static final public NAME = 'clean'

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

@@ -25,6 +25,8 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.exception.AbortOperationException
 import nextflow.scm.AssetManager
+import picocli.CommandLine
+
 /**
  * CLI sub-command clone
  *
@@ -33,6 +35,7 @@ import nextflow.scm.AssetManager
 @Slf4j
 @CompileStatic
 @Parameters(commandDescription = "Clone a project into a folder")
+@CommandLine.Command
 class CmdClone extends CmdBase implements HubOptions {
 
     static final public NAME = 'clone'

src/main/groovy/nextflow/cli/CmdCloud.groovy

@@ -43,6 +43,8 @@ import nextflow.exception.AbortOperationException
 import nextflow.ui.TableBuilder
 import nextflow.ui.TextLabel
 import nextflow.util.SysHelper
+import picocli.CommandLine
+
 /**
  * Implements the `cloud` command
  *
@@ -51,6 +53,7 @@ import nextflow.util.SysHelper
 @Slf4j
 //@CompileStatic -- Don't use. It causes a weird exception: CmdCloud$LaunchMaster cannot be cast to nextflow.cli.CmdCloud
 @Parameters(commandDescription = "Manage Nextflow clusters in the cloud")
+@CommandLine.Command
 class CmdCloud extends CmdBase implements UsageAware {
 
     interface SubCmd {

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

@@ -29,7 +29,8 @@ import groovy.util.logging.Slf4j
 import nextflow.config.ConfigBuilder
 import nextflow.exception.AbortOperationException
 import nextflow.scm.AssetManager
-import org.codehaus.groovy.runtime.InvokerHelper
+import nextflow.util.ConfigHelper
+import picocli.CommandLine
 
 /**
  *  Prints the pipeline configuration
@@ -39,6 +40,7 @@ import org.codehaus.groovy.runtime.InvokerHelper
 @Slf4j
 @CompileStatic
 @Parameters(commandDescription = "Print a project configuration")
+@CommandLine.Command
 class CmdConfig extends CmdBase {
 
     static final public NAME = 'config'
@@ -81,8 +83,7 @@ class CmdConfig extends CmdBase {
                 .setOptions(launcher.options)
                 .setBaseDir(base.complete())
                 .setCmdConfig(this)
-                .build()
-                .toConfigObject()
+                .configObject()
 
         if( printProperties ) {
             printProperties(config, stdout)
@@ -103,57 +104,7 @@ class CmdConfig extends CmdBase {
      * @param output The stream where output the formatted configuration notation
      */
     protected void printCanonical(ConfigObject config, OutputStream output) {
-        def writer = new PrintWriter(output)
-        canonicalFormat(writer,config,0)
-        writer.flush()
-    }
-
-    private static final String TAB = '   '
-
-    private void canonicalFormat(Writer writer, ConfigObject object, int level) {
-
-        final keys = object.keySet().sort()
-
-        // remove all empty config objects
-        final itr = keys.iterator()
-        while( itr.hasNext() ) {
-            final key = itr.next()
-            final value = object.get(key)
-            if( value instanceof ConfigObject && value.size()==0 ) {
-                itr.remove()
-            }
-        }
-
-        for( int i=0; i<keys.size(); i++) {
-            final key = keys[i]
-            final value = object.get(key)
-            if( value instanceof ConfigObject ) {
-                // add an extra new-line to separate simple values from a config object
-                if( level==0 && i>0 ) {
-                    writer.write('\n')
-                }
-
-                writer.write(TAB*level)
-                writer.write(key.toString())
-                writer.write(' {\n')
-                canonicalFormat(writer, value, level+1)
-                writer.write(TAB*level)
-                writer.write('}\n')
-
-            }
-            else {
-                // add a new-line to separate simple values from a previous config object
-                if( level==0 && i>0 && object.get(keys[i-1]) instanceof ConfigObject) {
-                    writer.write('\n')
-                }
-
-                writer.write(TAB*level)
-                writer.write(key.toString())
-                writer.write(' = ')
-                writer.write( InvokerHelper.inspect(value) )
-                writer.write('\n')
-            }
-        }
+        output << ConfigHelper.toCanonicalString(config)
     }
 
     /**
@@ -163,9 +114,7 @@ class CmdConfig extends CmdBase {
      * @param output The stream where output the formatted configuration notation
      */
     protected void printProperties(ConfigObject config, OutputStream output) {
-        def writer = new PrintWriter(output)
-        writer.write( propertiesFormat(new OrderedProperties(config.toProperties())) )
-        writer.flush()
+        output << ConfigHelper.toPropertiesString(config)
     }
 
     /**
@@ -176,9 +125,7 @@ class CmdConfig extends CmdBase {
      * @param output The stream where output the formatted configuration notation
     */
     protected void printFlatten(ConfigObject config, OutputStream output) {
-        def writer = new PrintWriter(output, true)
-        writer.write( flattenFormat(config) )
-        writer.flush()
+        output << ConfigHelper.toFlattenString(config)
     }
 
     /**
@@ -192,30 +139,6 @@ class CmdConfig extends CmdBase {
         config.writeTo( writer )
     }
 
-    private String flattenFormat(ConfigObject config) {
-        final props = new Properties()
-        config.flatten(props)
-        final ordered = new OrderedProperties(props)
-        final result = new StringBuilder()
-        for( String name : ordered.keys() ) {
-            result << name << ' = ' << InvokerHelper.inspect(ordered.get(name))  << '\n'
-        }
-        result.toString()
-    }
-
-    private String propertiesFormat(Properties properties) {
-        def buffer = new ByteArrayOutputStream()
-        properties.store(buffer,null)
-        buffer.flush()
-
-        def result = new StringBuilder()
-        for( String line : buffer.toString().readLines() ) {
-            if(line.startsWith('#')) continue
-            result << line << '\n'
-        }
-        result.toString()
-    }
-
 
     Path getBaseDir(String path) {
 
@@ -232,24 +155,6 @@ class CmdConfig extends CmdBase {
 
     }
 
-    /**
-     * Extends the basic {@link Properties} to provide the ordered enumeration of keys
-     */
-    static class OrderedProperties extends Properties {
-
-        OrderedProperties() {}
 
-        OrderedProperties( Properties properties ) {
-            properties.each { key, value ->
-                this.put(key,value)
-            }
-        }
-
-        @Override
-        Enumeration<Object> keys() {
-            return new Vector<>(super.keySet().sort()).elements()
-        }
-
-    }
 
 }

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

@@ -26,6 +26,7 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.exception.AbortOperationException
 import nextflow.scm.AssetManager
+import picocli.CommandLine
 
 /**
  * CLI sub-command DROP
@@ -35,6 +36,7 @@ import nextflow.scm.AssetManager
 @Slf4j
 @CompileStatic
 @Parameters(commandDescription = "Delete the local copy of a project")
+@CommandLine.Command
 class CmdDrop extends CmdBase {
 
     static final public NAME = 'drop'

src/main/groovy/nextflow/cli/CmdFs.groovy

@@ -28,11 +28,14 @@ import nextflow.exception.AbortOperationException
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.file.FilePatternSplitter
+import picocli.CommandLine
+
 /**
  * Implements `fs` command
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
+@CommandLine.Command
 class CmdFs extends CmdBase implements UsageAware {
 
     static final public NAME = 'fs'

src/main/groovy/nextflow/cli/CmdHelp.groovy

@@ -22,13 +22,16 @@ package nextflow.cli
 import com.beust.jcommander.Parameter
 import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
+import picocli.CommandLine
+
 /**
  * CLI sub-command HELP
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @CompileStatic
 @Parameters(commandDescription = "Print the usage help for a command")
+@CommandLine.Command
 class CmdHelp extends CmdBase {
 
     static final public NAME = 'help'

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

@@ -30,25 +30,30 @@ import nextflow.Const
 import nextflow.exception.AbortOperationException
 import nextflow.scm.AssetManager
 import nextflow.util.MemoryUnit
-
+import picocli.CommandLine
+import picocli.CommandLine.Option
 /**
  * CLI sub-command INFO
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @CompileStatic
 @Parameters(commandDescription = "Print project and system runtime information")
+@CommandLine.Command
 class CmdInfo extends CmdBase {
 
     static final public NAME = 'info'
 
     @Parameter(description = 'project name')
+    @CommandLine.Parameters(description = 'Project name', arity = '0..1')
     List<String> args
 
     @Parameter(names='-d',description = 'Show detailed information', arity = 0)
+    @Option(names=['-d'], description = 'Show detailed information', arity = '0..1')
     boolean detailed
 
     @Parameter(names='-dd', hidden = true, arity = 0)
+    @Option(names=['-dd'], description = 'Show more detailed information', arity = '0..1')
     boolean moreDetailed
 
     @Override