Upgrade from Apache Commons Lang 2.6 to Commons Lang3 3.18.0 (#6511)

This commit migrates the codebase from the legacy commons-lang library
to commons-lang3. Key changes include:

- Updated dependency in build.gradle files from commons-lang:2.6 to
  commons-lang3:3.18.0
- Updated all import statements from org.apache.commons.lang to
  org.apache.commons.lang3
- Replaced StringEscapeUtils.escapeJavaScript() with escapeEcmaScript()
  in TimelineObserver (method renamed in lang3)
- Replaced StrBuilder with standard Java StringBuilder in ConfigParser
  (StrBuilder moved to commons-text library)

All modules compile successfully with the new dependency.

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

modules/nextflow/build.gradle

@@ -38,7 +38,7 @@ dependencies {
     api "ch.qos.logback:logback-core:1.5.20"
     api "org.codehaus.gpars:gpars:1.2.1"
     api("ch.artecat.grengine:grengine:3.0.2") { exclude group: 'org.codehaus.groovy' }
-    api "commons-lang:commons-lang:2.6"
+    api "org.apache.commons:commons-lang3:3.18.0"
     api "commons-codec:commons-codec:1.15"
     api "commons-io:commons-io:2.15.1"
     api "com.beust:jcommander:1.35"

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -89,7 +89,7 @@ import nextflow.util.SysHelper
 import nextflow.util.ThreadPoolManager
 import nextflow.util.Threads
 import nextflow.util.VersionNumber
-import org.apache.commons.lang.exception.ExceptionUtils
+import org.apache.commons.lang3.exception.ExceptionUtils
 import sun.misc.Signal
 import sun.misc.SignalHandler
 /**

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

@@ -49,7 +49,7 @@ import nextflow.secret.SecretsLoader
 import nextflow.util.CustomPoolFactory
 import nextflow.util.Duration
 import nextflow.util.HistoryFile
-import org.apache.commons.lang.StringUtils
+import org.apache.commons.lang3.StringUtils
 import org.fusesource.jansi.AnsiConsole
 import org.yaml.snakeyaml.Yaml
 /**

modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy

@@ -29,7 +29,7 @@ import nextflow.processor.TaskRun
 import nextflow.util.Duration
 import nextflow.util.Escape
 import nextflow.util.Throttle
-import org.apache.commons.lang.StringUtils
+import org.apache.commons.lang3.StringUtils
 /**
  * Generic task processor executing a task through a grid facility
  *

modules/nextflow/src/main/groovy/nextflow/script/parser/v1/ScriptLoaderV1.groovy

@@ -36,7 +36,7 @@ import nextflow.script.ScriptLoader
 import nextflow.script.ScriptMeta
 import nextflow.util.Duration
 import nextflow.util.MemoryUnit
-import org.apache.commons.lang.StringUtils
+import org.apache.commons.lang3.StringUtils
 import org.codehaus.groovy.control.CompilationFailedException
 import org.codehaus.groovy.control.CompilerConfiguration
 import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer

modules/nextflow/src/main/groovy/nextflow/trace/TimelineObserver.groovy

@@ -31,7 +31,7 @@ import nextflow.trace.config.TimelineConfig
 import nextflow.trace.event.TaskEvent
 import nextflow.util.Duration
 import nextflow.util.TestOnly
-import org.apache.commons.lang.StringEscapeUtils
+import org.apache.commons.lang3.StringEscapeUtils
 /**
  * Render pipeline timeline processes execution
  *
@@ -195,7 +195,7 @@ class TimelineObserver implements TraceObserverV2 {
         final indent = "    ";
 
         template << indent << indent << '{'
-        template << "\"label\": \"${StringEscapeUtils.escapeJavaScript(name)}\", "
+        template << "\"label\": \"${StringEscapeUtils.escapeEcmaScript(name)}\", "
         template << "\"cached\": ${record.cached}, "
         template << "\"index\": $index, "
         template << "\"times\": ["
@@ -204,7 +204,7 @@ class TimelineObserver implements TraceObserverV2 {
             template << "{\"starting_time\": $submit, \"ending_time\": $start}"
 
             if( start && realtime ) {
-                final label = StringEscapeUtils.escapeJavaScript(labelString(record))
+                final label = StringEscapeUtils.escapeEcmaScript(labelString(record))
                 final ending = start+realtime
                 template << ", {\"starting_time\": $start, \"ending_time\": $ending, \"label\": \"$label\"}"
 

modules/nextflow/src/main/groovy/nextflow/util/ClusterConfig.groovy

@@ -18,7 +18,7 @@ package nextflow.util
 
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
-import org.apache.commons.lang.StringUtils
+import org.apache.commons.lang3.StringUtils
 /**
  * Helper class retrieve cluster configuration properties
  */

modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy

@@ -72,7 +72,7 @@ import nextflow.script.FunctionDef
 import nextflow.script.ScriptMeta
 import nextflow.script.WorkflowBinding
 import nextflow.script.WorkflowDef
-import org.apache.commons.lang.exception.ExceptionUtils
+import org.apache.commons.lang3.exception.ExceptionUtils
 import org.slf4j.Logger
 import org.slf4j.LoggerFactory
 import org.slf4j.Marker

modules/nf-commons/build.gradle

@@ -29,7 +29,7 @@ dependencies {
     api "ch.qos.logback:logback-classic:1.5.20"
     api "org.apache.groovy:groovy:4.0.29"
     api "org.apache.groovy:groovy-nio:4.0.29"
-    api "commons-lang:commons-lang:2.6"
+    api "org.apache.commons:commons-lang3:3.18.0"
     api 'com.google.guava:guava:33.0.0-jre'
     api 'org.pf4j:pf4j:3.12.0'
     api 'org.pf4j:pf4j-update:2.3.0'

modules/nf-commons/src/main/nextflow/Global.groovy

@@ -24,8 +24,8 @@ import nextflow.util.Duration
 import nextflow.util.IniFile
 import nextflow.util.MemoryUnit
 import nextflow.util.TestOnly
-import org.apache.commons.lang.StringUtils
-import org.apache.commons.lang.exception.ExceptionUtils
+import org.apache.commons.lang3.StringUtils
+import org.apache.commons.lang3.exception.ExceptionUtils
 /**
  * Hold global variables
  *