Update test cases for TcsExecutor.

Signed-off-by: Satoshi OHSHIMA <[email protected]>

Author: exthnet

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

@@ -52,13 +52,6 @@ class TcsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
 
         result << '-N' << modName(getJobNameFor(task))
 
-        result << '-j' << ''
-        result << '-S' << ''
-		if( !task.workDir ) {
-			result << '-o' << (task.isArray() ? '/dev/null' : quote(task.workDir.resolve(TaskRun.CMD_LOG)))
-		}
-		//result << '-o' << (task.isArray() ? '/dev/null' : quote(task.workDir.resolve(TaskRun.CMD_LOG)))
-
         // max task duration
         if( task.config.getTime() ) {
             final duration = task.config.getTime()
@@ -92,9 +85,16 @@ class TcsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
      * @return A list representing the submit command line
      */
     List<String> getSubmitCommandLine(TaskRun task, Path scriptFile ) {
-        return pipeLauncherScript()
-                ? List.of('pjsub')
-                : List.of('pjsub', scriptFile.getName())
+		if( task instanceof TaskArrayRun ){
+			final arraySize = task.getArraySize()
+			return pipeLauncherScript()
+			? List.of('pjsub', '--bulk --sparam ', "0-${arraySize - 1}".toString())
+			: List.of('pjsub', scriptFile.getName())
+		}else{
+			return pipeLauncherScript()
+			? List.of('pjsub')
+			: List.of('pjsub', scriptFile.getName())
+		}
 /*        [ 'pjsub', '-N', modName(getJobNameFor(task)), scriptFile.getName() ] */
     }
 
@@ -123,10 +123,7 @@ class TcsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
 
     @Override
     protected List<String> queueStatusCommand(Object queue) {
-        //String cmd = 'pjstat | grep -v JOB_ID'
-        //if( queue ) cmd += ' ' + queue
-        //return ['bash','-c', "set -o pipefail; $cmd | { grep -E '(Job Id:|job_state =)' || true; }".toString()]
-		final result = ['pjstat2', '-E']
+		final result = ['pjstat', '-E']
 		return result
     }
 
@@ -141,28 +138,7 @@ class TcsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
             'HLD': QueueStatus.HOLD,    // holding
             'ERR': QueueStatus.ERROR,   // error
     ]
-/*
-    protected QueueStatus decode(String status) {
-        DECODE_STATUS.get(status)
-    }
-	*/
-/*
-    @Override
-    protected Map<String, QueueStatus> parseQueueStatus(String text) {
-        final result = new LinkedHashMap<String, QueueStatus>()
-        text.eachLine { String line ->
-            def cols = line.split(/\s+/)
-            if( cols.size() > 1 ) {
-                result.put( cols[0], STATUS_MAP.get(cols[3]) )
-            }
-            else {
-                log.debug "[TCS] invalid status line: `$line`"
-            }
-        }
 
-        return result
-    }
-*/
     @Override
     protected Map<String, QueueStatus> parseQueueStatus(String text) {
         final result = new LinkedHashMap<String, QueueStatus>()

modules/nextflow/src/test/groovy/nextflow/executor/TcsExecutorTest.groovy

@@ -28,7 +28,7 @@ import spock.lang.Unroll
 
 /**
  *
- * @author Satoshi Ohshima <[email protected]>
+ * @author Satoshi Ohshima <[email protected]>
  */
 
 class TcsExecutorTest extends Specification {
@@ -86,20 +86,60 @@ class TcsExecutorTest extends Specification {
         task.workDir = Paths.get('/work/path')
         task.name = 'the task name'
 
+        // 1min job
         when:
 		task.index = 21
         task.config = new TaskConfig()
 		task.config.time = '00:10:00'
         then:
         executor.getHeaders(task) == '''
-		        #PJM -N nf-the_task_name
-				#PJM -j
-				#PJM -S
-				#PJM -L elapse=00:10:00
+                #PJM -N nf-the_task_name
+                #PJM -L elapse=00:10:00
+                #PJM -o /work/path/.command.log
+                #PJM -j
+                #PJM -S
+                '''
+                .stripIndent().leftTrim()
+
+        // 1hour job
+        when:
+		task.index = 22
+        task.config = new TaskConfig()
+		task.config.time = '01:00:00'
+        task.name = '1hour job'
+        then:
+        executor.getHeaders(task) == '''
+                #PJM -N nf-1hour_job
+                #PJM -L elapse=01:00:00
+                #PJM -o /work/path/.command.log
+                #PJM -j
+                #PJM -S
+                '''
+                .stripIndent().leftTrim()
+
+        // job array (bulk job)
+        when: 'with job array (bulk job)'
+		task.config = new TaskConfig()
+		task.workDir = Paths.get('/work/path')
+		task.name = 'array job'
+        def taskArray = Mock(TaskArrayRun) {
+            config >> new TaskConfig()
+            name >> task.name
+            getArraySize() >> 5
+            workDir >> task.workDir
+        }
+		taskArray.config.time = '01:00:00'
+
+        then:
+        executor.getHeaders(taskArray) == '''
+                #PJM -N nf-array_job
+                #PJM -L elapse=01:00:00
+                #PJM -j
+                #PJM -S
                 '''
                 .stripIndent().leftTrim()
     }
-/*
+
     def testWorkDirWithBlanks() {
 
         setup:
@@ -122,16 +162,15 @@ class TcsExecutorTest extends Specification {
 		task.config.time = '00:10:00'
         then:
         executor.getHeaders(task) == '''
-		        #PJM -N nf-the_task_name
-				#PJM -j
-				#PJM -S
-				#PJM -L elapse=00:10:00
+                #PJM -N nf-the_task_name
+                #PJM -L elapse=00:10:00
                 #PJM -o "/work/some\\ data/path/.command.log"
+                #PJM -j
+                #PJM -S
                 '''
                 .stripIndent().leftTrim()
 
     }
-*/
 
     def testQstatCommand() {
 
@@ -169,12 +208,9 @@ class TcsExecutorTest extends Specification {
 
     def testQueueStatusCommand() {
         when:
-        def usr = System.getProperty('user.name')
         def exec = [:] as TcsExecutor
         then:
-        usr
-        exec.queueStatusCommand(null) == ['pjstat2', '-E']
-        //exec.queueStatusCommand('long') == ['pjstat2','-E']
+        exec.queueStatusCommand(null) == ['pjstat', '-E']
     }
 
     def 'should get array (bulk) index name and start' () {
@@ -197,39 +233,7 @@ class TcsExecutorTest extends Specification {
         JOB_ID      | TASK_INDEX    | EXPECTED
         '1234'      | 1             | '1234[1]'
         '123456'    | 2             | '123456[2]'
-/*
-        JOB_ID      JOB_NAME  MD  STATUS  USER        RSCGROUP     START_DATE             ELAPSE    NODE  CORE  GPU  POINT
-        3209914     bulk1.sh  BU  RUN     ku40000105  a-batch-low  -                      -            -     1    -      -
-        3209914[1]  bulk1.sh  BU  RUN     ku40000105  a-batch-low  2025/06/13 17:53:43    00:00:01     -     1    -      1
-*/
     }
 
-/* There is no project option in TCS. (on Genkai and Flow) */
-/*
-    @Unroll
-    def 'should set tcs account' () {
-        given:
-        // task
-        def task = new TaskRun()
-        task.workDir = Paths.get('/work/dir')
-        task.processor = Mock(TaskProcessor)
-        task.processor.getSession() >> Mock(Session)
-        task.config = Mock(TaskConfig)
-        and:
-        def executor = Spy(TcsExecutor)
-        executor.getJobNameFor(_) >> 'foo'
-        executor.getName() >> 'tcs'
-        executor.getSession() >> Mock(Session) { getExecConfigProp('tcs', 'account',null)>>ACCOUNT }
-
-        when:
-        def result = executor.getDirectives(task, [])
-        then:
-        result == EXPECTED
-
-        where:
-        ACCOUNT             | EXPECTED
-        null                | ['-N', 'foo', '-o', '/work/dir/.command.log', '-j']
-        'project-123'       | ['-N', 'foo', '-o', '/work/dir/.command.log', '-j']
-    }
-	*/
 }
+