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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
/*
* Copyright 2013-2024, 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 java.lang.management.ManagementFactory
import java.nio.file.spi.FileSystemProvider
import com.beust.jcommander.Parameter
import com.beust.jcommander.Parameters
import com.sun.management.OperatingSystemMXBean
import groovy.json.JsonOutput
import groovy.transform.CompileStatic
import groovy.util.logging.Slf4j
import nextflow.BuildInfo
import nextflow.exception.AbortOperationException
import nextflow.plugin.DefaultPlugins
import nextflow.plugin.Plugins
import nextflow.scm.AssetManager
import nextflow.util.MemoryUnit
import nextflow.util.Threads
import org.yaml.snakeyaml.Yaml
/**
* CLI sub-command INFO
*
* @author Paolo Di Tommaso
*/
@Slf4j
@CompileStatic
@Parameters(commandDescription = "Print project and system runtime information")
class CmdInfo extends CmdBase {
static final public NAME = 'info'
private PrintStream out = System.out
@Parameter(description = 'project name')
List args
@Parameter(names='-d',description = 'Show detailed information', arity = 0)
boolean detailed
@Parameter(names='-dd', hidden = true, arity = 0)
boolean moreDetailed
@Parameter(names='-o', description = 'Output format, either: text (default), json, yaml')
String format
@Parameter(names=['-u','-check-updates'], description = 'Check for remote updates')
boolean checkForUpdates
@Override
final String getName() { NAME }
@Override
void run() {
int level = moreDetailed ? 2 : ( detailed ? 1 : 0 )
if( !args ) {
println getInfo(level)
return
}
Plugins.init()
final manager = new AssetManager(args[0])
if( !manager.isLocal() )
throw new AbortOperationException("Unknown project `${args[0]}`")
if( !format || format == 'text' ) {
printText(manager,level)
return
}
def map = createMap(manager)
if( format == 'json' ) {
printJson(map)
}
else if( format == 'yaml' ) {
printYaml(map)
}
else
throw new AbortOperationException("Unknown output format: $format");
}
protected printText(AssetManager manager, int level) {
final manifest = manager.getManifest()
out.println " project name: ${manager.project}"
out.println " repository : ${manager.repositoryUrl}"
out.println " local path : ${manager.localPath}"
out.println " main script : ${manager.mainScriptName}"
if( manager.homePage && manager.homePage != manager.repositoryUrl )
out.println " home page : ${manager.homePage}"
if( manifest.description )
out.println " description : ${manifest.description}"
if( manifest.author )
out.println " author : ${manifest.author}"
def revs = manager.getRevisions(level)
if( revs.size() == 1 )
out.println " revision : ${revs[0]}"
else {
out.println " revisions : "
revs.each { out.println " $it" }
}
if( !checkForUpdates )
return
def updates = manager.getUpdates(level)
if( updates ) {
if( updates.size() == 1 && revs.size() == 1 )
out.println " updates : ${updates[0]}"
else {
out.println " updates : "
updates.each { out.println " $it" }
}
}
out.flush()
}
protected Map createMap(AssetManager manager) {
def result = [:]
result.projectName = manager.project
result.repository = manager.repositoryUrl
result.localPath = manager.localPath?.toString()
result.manifest = manager.manifest.toMap()
result.revisions = manager.getBranchesAndTags(checkForUpdates)
return result
}
protected printJson(Map map) {
out.println JsonOutput.prettyPrint(JsonOutput.toJson(map))
out.flush()
}
protected printYaml(Map map) {
out.println new Yaml().dump(map).toString()
out.flush()
}
final static private BLANK = ' '
final static private NEWLINE = '\n'
static String status(boolean detailed = false) {
getInfo( detailed ? 1 : 0, true )
}
static private String totMem(OperatingSystemMXBean os) {
try {
new MemoryUnit(os.totalPhysicalMemorySize).toString()
}
catch (Throwable t) {
log.debug "Unable to fetch totalPhysicalMemorySize - ${t.message ?: t}"
return '-'
}
}
static private String freeMem(OperatingSystemMXBean os) {
try {
return new MemoryUnit(os.freePhysicalMemorySize).toString()
}
catch (Throwable t) {
log.debug "Unable to fetch freePhysicalMemorySize - ${t.message ?: t}"
return '-'
}
}
static private String totSwap(OperatingSystemMXBean os) {
try {
new MemoryUnit(os.totalSwapSpaceSize).toString()
}
catch (Throwable t) {
log.debug "Unable to fetch totalSwapSpaceSize - ${t.message ?: t}"
return '-'
}
}
static private String freeSwap(OperatingSystemMXBean os) {
try {
return new MemoryUnit(os.freeSwapSpaceSize).toString()
}
catch (Throwable t) {
log.debug "Unable to fetch freeSwapSpaceSize - ${t.message ?: t}"
return '-'
}
}
/**
* @return A string containing some system runtime information
*/
static String getInfo(int level, boolean printProc=false) {
def props = System.getProperties()
def result = new StringBuilder()
result << BLANK << "Version: ${BuildInfo.version} build ${BuildInfo.buildNum}" << NEWLINE
result << BLANK << "Created: ${BuildInfo.timestampUTC} ${BuildInfo.timestampDelta}" << NEWLINE
result << BLANK << "System: ${props['os.name']} ${props['os.version']}" << NEWLINE
result << BLANK << "Runtime: Groovy ${GroovySystem.getVersion()} on ${System.getProperty('java.vm.name')} ${props['java.runtime.version']}" << NEWLINE
result << BLANK << "Encoding: ${System.getProperty('file.encoding')} (${System.getProperty('sun.jnu.encoding')})" << NEWLINE
if( printProc ) {
final os = (OperatingSystemMXBean) ManagementFactory.getOperatingSystemMXBean()
result << BLANK << "Process: ${ManagementFactory.getRuntimeMXBean().getName()} " << getLocalAddress() << NEWLINE
result << BLANK << "CPUs: ${os.availableProcessors} - Mem: ${totMem(os)} (${freeMem(os)}) - Swap: ${totSwap(os)} (${freeSwap(os)})"
if( Threads.useVirtual() )
result << " - Virtual threads ON"
}
if( level == 0 )
return result.toString()
List capsule = []
List args = []
ManagementFactory
.getRuntimeMXBean()
.getInputArguments()
.each { String it ->
if( it.startsWith('-Dcapsule.'))
capsule << it.substring(2)
else
args << it
}
// file system
result << BLANK << "File systems: "
result << FileSystemProvider.installedProviders().collect { it.scheme }.join(', ')
result << NEWLINE
// plugins
result << BLANK << "Core plugins: "
result << DefaultPlugins.INSTANCE.toSortedString(', ')
result << NEWLINE
// JVM options
result << BLANK << "JVM opts:" << NEWLINE
for( String entry : args ) {
int p = entry.indexOf('=')
if( p!=-1 ) {
def key = entry.substring(0,p)
def value = entry.substring(p+1)
dump(key,value,2, result)
}
else {
dump(entry,null,2, result)
}
}
// Capsule options
dump("Capsule", capsule, 1, result)
// Env
result << BLANK << "Environment:" << NEWLINE
def entries = System.getenv().keySet().sort()
for( def key : entries ) {
if( key.startsWith('NXF_') || level>1 ) {
dump( key, System.getenv().get(key), 2, result )
}
}
// java properties
if( level>1 ) {
result << BLANK << "Properties:" << NEWLINE
entries = System.getProperties().keySet().sort()
for( String key : entries ) {
if( key == 'java.class.path' ) continue
dump( key, System.getProperties().get(key), 2, result )
}
}
// Class path
dump("Class-path" , System.getProperty('java.class.path'), 1, result)
// final string
return result.toString()
}
static private void dump(String key, def value, int indent, StringBuilder result) {
if( value instanceof String && value.count(':') && (key=~/.*PATH$/ || key=='PERL5LIB' || key.contains('.path') || key.contains('-path') || key.contains('.dir')) ) {
value = value.split(":") as Collection
}
else if( value?.class?.isArray() ) {
value = value as Collection
}
if ( value instanceof Collection ) {
blanks(indent, result)
result << key << (indent==1 ? ':' : '=')
for( String item : value ) {
result << NEWLINE
blanks(indent+1, result)
result << item
}
}
else if( value ) {
blanks(indent, result)
result << key << (indent==1 ? ':' : '=')
if( value == '\n' ) {
result << '\\n'
}
else if( value == '\r' ) {
result << '\\r'
}
else if( value == '\n\r' ) {
result << '\\n\\r'
}
else if( value == '\r\n' ) {
result << '\\r\\n'
}
else {
result << value
}
}
else if( key ) {
blanks(indent, result)
result << key
}
result << NEWLINE
}
static private blanks( int n, StringBuilder result ) {
for( int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy