Cleanup

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

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

@@ -0,0 +1,137 @@
+/*
+ * Copyright 2020-2022, 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.cli
+
+import com.beust.jcommander.DynamicParameter
+import com.beust.jcommander.Parameter
+import groovy.util.logging.Slf4j
+import nextflow.exception.AbortOperationException
+import org.fusesource.jansi.Ansi
+
+/**
+ * Interface for top-level CLI options.
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@Slf4j
+trait CliOptions {
+
+    abstract Boolean getAnsiLogCli()
+
+    abstract boolean isBackground()
+
+    abstract List<String> getConfig()
+
+    abstract List<String> getDebug()
+
+    abstract boolean getIgnoreConfigIncludes()
+
+    abstract String getLogFile()
+
+    abstract boolean isQuiet()
+
+    abstract String getSyslog()
+
+    abstract List<String> getTrace()
+
+    abstract List<String> getUserConfig()
+
+    abstract void setAnsiLog(boolean value)
+
+    abstract void setBackground(boolean value)
+
+    static class V1 implements CliOptions {
+
+        Boolean ansiLogCli
+
+        void setAnsiLog(boolean value) { ansiLogCli = value }
+
+        @Parameter(names = ['-bg'], arity = 0, description = 'Execute nextflow in background')
+        boolean background
+
+        @Parameter(names = ['-C'], description = 'Use the specified configuration file(s) overriding any defaults')
+        List<String> config
+
+        @Parameter(names = ['-c','-config'], description = 'Add the specified file to configuration set')
+        List<String> userConfig
+
+        @Parameter(names = ['-config-ignore-includes'], description = 'Disable the parsing of config includes')
+        boolean ignoreConfigIncludes
+
+        @DynamicParameter(names = ['-D'], description = 'Set JVM properties' )
+        Map<String,String> jvmOpts = [:]
+
+        @Parameter(names = ['-debug'], hidden = true)
+        List<String> debug
+
+        @Parameter(names = ['-d','-dockerize'], arity = 0, description = 'Launch nextflow via Docker (experimental)')
+        boolean dockerize
+
+        @Parameter(names = ['-h'], description = 'Print this help', help = true)
+        boolean help
+
+        @Parameter(names = ['-log'], description = 'Set nextflow log file path')
+        String logFile
+
+        @Parameter(names = ['-q','-quiet'], description = 'Do not print information messages' )
+        boolean quiet
+
+        @Parameter(names = ['-self-update'], arity = 0, description = 'Update nextflow to the latest version', hidden = true)
+        boolean selfUpdate
+
+        @Parameter(names = ['-syslog'], description = 'Send logs to syslog server (eg. localhost:514)' )
+        String syslog
+
+        @Parameter(names = ['-trace'], description = 'Enable trace level logging for the specified package name - multiple packages can be provided separating them with a comma e.g. \'-trace nextflow,io.seqera\'')
+        List<String> trace
+
+        @Parameter(names = ['-v'], description = 'Print the program version')
+        boolean version
+
+        @Parameter(names = ['-version'], description = 'Print the program version (full)')
+        boolean fullVersion
+
+    }
+
+    boolean getAnsiLog() {
+        if( ansiLogCli && quiet )
+            throw new AbortOperationException("Command line options `quiet` and `ansi-log` cannot be used together")
+
+        if( ansiLogCli != null )
+            return ansiLogCli
+
+        if( background )
+            return ansiLogCli = false
+
+        if( quiet )
+            return ansiLogCli = false
+
+        final env = System.getenv('NXF_ANSI_LOG')
+        if( env ) try {
+            return Boolean.parseBoolean(env)
+        }
+        catch (Exception e) {
+            log.warn "Invalid boolean value for variable NXF_ANSI_LOG: $env -- it must be 'true' or 'false'"
+        }
+        return Ansi.isEnabled()
+    }
+
+    boolean hasAnsiLogFlag() {
+        ansiLogCli==true || System.getenv('NXF_ANSI_LOG')=='true'
+    }
+
+}

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

@@ -49,6 +49,8 @@ import nextflow.util.HistoryFile.Record
 @CompileStatic
 class CmdClean implements CacheBase {
 
+    static final public NAME = 'clean'
+
     interface Options {
         String getAfter()
         String getBefore()
@@ -59,7 +61,7 @@ class CmdClean implements CacheBase {
         boolean getQuiet()
         List<String> getArgs()
 
-        ILauncherOptions getLauncherOptions()
+        CliOptions getLauncherOptions()
     }
 
     @Parameters(commandDescription = 'Clean up project cache and work directories')
@@ -90,12 +92,12 @@ class CmdClean implements CacheBase {
         List<String> args
 
         @Override
-        ILauncherOptions getLauncherOptions() {
+        CliOptions getLauncherOptions() {
             launcher.options
         }
 
         @Override
-        String getName() { 'clean' }
+        String getName() { NAME }
 
         @Override
         void run() {

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

@@ -31,15 +31,17 @@ import nextflow.scm.AssetManager
 @CompileStatic
 class CmdClone {
 
-    interface Options extends IHubOptions {
+    static final public NAME = 'clone'
+
+    interface Options extends HubOptions {
         String getPipeline()
         String getTargetName()
         Integer getDeep()
         String getRevision()
     }
 
-    @Parameters(commandDescription = 'Clone a project into a folder')
-    static class V1 extends CmdBase implements Options, HubOptions {
+    @Parameters(commandDescription = "Clone a project into a folder")
+    static class V1 extends CmdBase implements Options, HubOptions.V1 {
 
         @Parameter(required=true, description = 'name of the project to clone')
         List<String> args
@@ -59,7 +61,7 @@ class CmdClone {
         }
 
         @Override
-        String getName() { 'clone' }
+        final String getName() { NAME }
 
         @Override
         void run() {

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

@@ -38,6 +38,8 @@ import nextflow.util.ConfigHelper
 @CompileStatic
 class CmdConfig {
 
+    static final public NAME = 'config'
+
     interface Options {
         String getPipeline()
         boolean getShowAllProfiles()
@@ -46,10 +48,10 @@ class CmdConfig {
         boolean getPrintFlatten()
         boolean getSort()
 
-        ILauncherOptions getLauncherOptions()
+        CliOptions getLauncherOptions()
     }
 
-    @Parameters(commandDescription = 'Print a project configuration')
+    @Parameters(commandDescription = "Print a project configuration")
     static class V1 extends CmdBase implements Options {
 
         @Parameter(description = 'project name')
@@ -76,12 +78,12 @@ class CmdConfig {
         }
 
         @Override
-        ILauncherOptions getLauncherOptions() {
+        CliOptions getLauncherOptions() {
             launcher.options
         }
 
         @Override
-        String getName() { 'config' }
+        String getName() { NAME }
 
         @Override
         void run() {

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

@@ -34,7 +34,7 @@ class CmdConsole {
         String getScript()
     }
 
-    @Parameters(commandDescription = 'Launch Nextflow interactive console')
+    @Parameters(commandDescription = "Launch Nextflow interactive console")
     static class V1 extends CmdBase implements Options {
 
         @Parameter(description = 'Nextflow console arguments')

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

@@ -33,12 +33,14 @@ import nextflow.scm.AssetManager
 @CompileStatic
 class CmdDrop {
 
+    static final public NAME = 'drop'
+
     interface Options {
         String getPipeline()
         boolean getForce()
     }
 
-    @Parameters(commandDescription = 'Delete the local copy of a project')
+    @Parameters(commandDescription = "Delete the local copy of a project")
     static class V1 extends CmdBase implements Options {
 
         @Parameter(required=true, description = 'name of the project to drop')
@@ -51,7 +53,7 @@ class CmdDrop {
         String getPipeline() { args[0] }
 
         @Override
-        String getName() { 'drop' }
+        final String getName() { NAME }
 
         @Override
         void run() {