Remove daemon, improve tests, add tests, fix bugs

build.gradle

@@ -63,8 +63,7 @@ dependencies {
     compile group: 'commons-cli', name: 'commons-cli', version: '1.2'
     compile group: 'org.apache.commons', name: 'commons-text', version: '1.1'
     compile 'com.google.guava:guava:23.0'
-    // compile 'com.github.eilslabs:RoddyToolLib:master-SNAPSHOT'
-    compile 'com.github.theroddywms:RoddyToolLib:2.0.0'
+    compile 'com.github.theroddywms:RoddyToolLib:2.1.0'
 }
 
 task writePom {

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-5.1.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.8-all.zip

gradlew

@@ -28,7 +28,7 @@ APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+DEFAULT_JVM_OPTS='"-Xmx64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"

gradlew.bat

@@ -14,7 +14,7 @@ set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
 @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
+set DEFAULT_JVM_OPTS="-Xmx64m"
 
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome

src/main/groovy/de/dkfz/roddy/execution/jobs/BatchEuphoriaJobManager.groovy

@@ -35,7 +35,7 @@ abstract class BatchEuphoriaJobManager<C extends Command> {
 
     protected boolean queryOnlyStartedJobs
 
-    protected final Duration maxAgeOfJobsForQueries
+    protected final Duration maxTrackingTimeForFinishedJobs
 
     protected String userIDForQueries
 
@@ -85,7 +85,7 @@ abstract class BatchEuphoriaJobManager<C extends Command> {
 
         this.isTrackingOfUserJobsEnabled = parms.userIdForJobQueries as boolean
         this.queryOnlyStartedJobs = parms.trackOnlyStartedJobs
-        this.maxAgeOfJobsForQueries = parms.maxAgeOfJobsForJobQueries
+        this.maxTrackingTimeForFinishedJobs = parms.maxTrackingTimeForFinishedJobs
         this.userIDForQueries = parms.userIdForJobQueries
 
         this.userEmail = parms.userEmail

src/main/groovy/de/dkfz/roddy/execution/jobs/GenericJobInfo.groovy

@@ -23,7 +23,7 @@ class GenericJobInfo {
     ResourceSet askedResources
     ResourceSet usedResources
     String jobName
-    File tool
+    String command
     BEJobID jobID
 
     /** The date-time the job entered the queue. */
@@ -81,9 +81,9 @@ class GenericJobInfo {
     ZonedDateTime timeOfCalculation
 
 
-    GenericJobInfo(String jobName, File tool, BEJobID jobID, Map<String, String> parameters, List<String> parentJobIDs) {
+    GenericJobInfo(String jobName, String command, BEJobID jobID, Map<String, String> parameters, List<String> parentJobIDs) {
         this.jobName = jobName
-        this.tool = tool
+        this.command = command
         this.jobID = jobID
         this.parameters = parameters
         this.parentJobIDs = parentJobIDs

src/main/groovy/de/dkfz/roddy/execution/jobs/JobManagerOptions.groovy

@@ -23,7 +23,7 @@ class JobManagerOptions {
 
     String userIdForJobQueries
 
-    Duration maxAgeOfJobsForJobQueries
+    Duration maxTrackingTimeForFinishedJobs
 
     boolean trackOnlyStartedJobs
 
@@ -91,7 +91,7 @@ class JobManagerOptionsBuilder {
     JobManagerOptionsBuilder() {
         trackOnlyStartedJobs = false
         updateInterval = Duration.ofMinutes(5)
-        maxAgeOfJobsForJobQueries = Duration.ofDays(14)
+        maxTrackingTimeForFinishedJobs = Duration.ofDays(14)
         createDaemon = false
         requestMemoryIsEnabled = true
         requestWalltimeIsEnabled = true

src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFCommandParser.groovy

@@ -9,9 +9,8 @@ import de.dkfz.roddy.tools.BufferValue
 import de.dkfz.roddy.tools.ComplexLine
 import de.dkfz.roddy.tools.TimeUnit
 import groovy.transform.CompileStatic
-import static de.dkfz.roddy.StringConstants.SPLIT_COLON
-import static de.dkfz.roddy.StringConstants.SPLIT_COMMA
-import static de.dkfz.roddy.StringConstants.SPLIT_EQUALS
+
+import static de.dkfz.roddy.StringConstants.*
 
 /**
  * Used to convert commands from cli to e.g. GenericJobInfo
@@ -53,11 +52,11 @@ class LSFCommandParser {
 
         if (!commandString.startsWith("bsub")) return  // It is obviously not a PBS call
 
-        String[] splitted = line.splitBy(" ").findAll { it }
+        Collection<String> splitted = line.splitBy(" ").findAll { it }
         script = splitted[-1]
         jobName = "not readable"
 
-        for (int i = 0; i < splitted.length - 1; i++) {
+        for (int i = 0; i < splitted.size() - 1; i++) {
             String option = splitted[i]
             if (!option.startsWith("-")) continue // It is not an option but a parameter or a text (e.g. bsub, script)
 
@@ -124,7 +123,7 @@ class LSFCommandParser {
     }
 
     GenericJobInfo toGenericJobInfo() {
-        GenericJobInfo jInfo = new GenericJobInfo(jobName, new File(script), jobID, parameters, dependencies)
+        GenericJobInfo jInfo = new GenericJobInfo(jobName, script, jobID, parameters, dependencies)
         ResourceSet askedResources = new ResourceSet(null, memory ? new BufferValue(memory as Integer, bufferUnit) : null,
                 cores ? cores as Integer : null, nodes ? nodes as Integer : null, walltime ? new TimeUnit(walltime) : null,
                 null, null, null)

src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManager.groovy

@@ -56,12 +56,24 @@ class LSFJobManager extends AbstractLSFJobManager {
         return date
     }
 
+    /**
+     * Important here is, that LSF puts " L" or other status codes at the end of some dates, e.g. FINISH_DATE
+     * Thus said, " L" does not apply for all dates reported by LSF! This method just removes the last two characters
+     * of the time string.
+     */
+    static String stripAwayStatusInfo(String time) {
+        if (time)
+            return time[0..-3]
+        return null
+    }
+
     @Override
     Map<BEJobID, GenericJobInfo> queryExtendedJobStateById(List<BEJobID> jobIds) {
         Map<BEJobID, GenericJobInfo> queriedExtendedStates = [:]
         for (BEJobID id : jobIds) {
-            Map<String, Object> jobDetails = runBjobs([id], true).get(id)
-            queriedExtendedStates.put(id, convertJobDetailsMapToGenericJobInfoobject(jobDetails))
+            Map<String, String> jobDetails = runBjobs([id], true)[id]
+            if (jobDetails) // Ignore filtered / nonexistent ids
+                queriedExtendedStates.put(id, convertJobDetailsMapToGenericJobInfoObject(jobDetails))
         }
         return queriedExtendedStates
     }
@@ -102,7 +114,7 @@ class LSFJobManager extends AbstractLSFJobManager {
 
     }
 
-    Map<BEJobID, Map<String, Object>> runBjobs(List<BEJobID> jobIDs, boolean extended) {
+    Map<BEJobID, Map<String, String>> runBjobs(List<BEJobID> jobIDs, boolean extended) {
         StringBuilder queryCommand = new StringBuilder(extended ? LSF_COMMAND_QUERY_EXTENDED_STATES : LSF_COMMAND_QUERY_STATES)
 
         // user argument must be passed before the job IDs
@@ -121,12 +133,12 @@ class LSFJobManager extends AbstractLSFJobManager {
             throw new BEException(error)
         }
 
-        Map<BEJobID, Map<String, Object>> result = convertBJobsJsonOutputToResultMap(resultLines.join("\n"))
-        return filterJobMapByAge(result, maxAgeOfJobsForQueries)
+        Map<BEJobID, Map<String, String>> result = convertBJobsJsonOutputToResultMap(resultLines.join("\n"))
+        return filterJobMapByAge(result, maxTrackingTimeForFinishedJobs)
     }
 
-    static Map<BEJobID, Map<String, Object>> convertBJobsJsonOutputToResultMap(String rawJson) {
-        Map<BEJobID, Map<String, Object>> result = [:]
+    static Map<BEJobID, Map<String, String>> convertBJobsJsonOutputToResultMap(String rawJson) {
+        Map<BEJobID, Map<String, String>> result = [:]
 
         if (!rawJson)
             return result
@@ -135,7 +147,7 @@ class LSFJobManager extends AbstractLSFJobManager {
         List records = (List) parsedJson["RECORDS"]
         for (record in records) {
             BEJobID jobID = new BEJobID(record["JOBID"] as String)
-            result[jobID] = record as Map<String, Object>
+            result[jobID] = record as Map<String, String>
         }
 
         result
@@ -150,17 +162,16 @@ class LSFJobManager extends AbstractLSFJobManager {
      * @return The map of records where too old entries are filtered out.
      */
     @CompileStatic
-    static Map<BEJobID, Map<String, Object>> filterJobMapByAge(
-            Map<BEJobID, Map<String, Object>> records,
+    static Map<BEJobID, Map<String, String>> filterJobMapByAge(
+            Map<BEJobID, Map<String, String>> records,
             Duration maxJobKeepDuration
     ) {
         records.findAll { def k, def record ->
             String finishTime = record["FINISH_TIME"]
             boolean youngEnough = true
             if (finishTime) {
-                String timeString = "${finishTime[0..-3]}"
                 withCaughtAndLoggedException {
-                    ZonedDateTime _finishTime = parseTime(timeString)
+                    ZonedDateTime _finishTime = parseTime(stripAwayStatusInfo(finishTime))
                     Duration timeSpan = Duration.between(_finishTime.toLocalDateTime(), LocalDateTime.now())
                     if (dateTimeHelper.durationExceeds(timeSpan, maxJobKeepDuration))
                         youngEnough = false
@@ -173,82 +184,95 @@ class LSFJobManager extends AbstractLSFJobManager {
     /**
      * Used by @getJobDetails to set JobInfo
      */
-    GenericJobInfo convertJobDetailsMapToGenericJobInfoobject(Map<String, Object> jobResult) {
+    GenericJobInfo convertJobDetailsMapToGenericJobInfoObject(Map<String, String> _jobResult) {
+        // Remove empty entries first to keep the output clean (use null, where the value is null or empty.)
+        Map<String, String> jobResult = _jobResult.findAll { String k, String v -> v }
 
         GenericJobInfo jobInfo
         BEJobID jobID
+        String JOBID = jobResult["JOBID"]
         try {
-            jobID = new BEJobID(jobResult["JOBID"] as String)
+            jobID = new BEJobID(JOBID)
         } catch (Exception exp) {
-            throw new BEException("Job ID '${jobResult["JOBID"]}' could not be transformed to BEJobID ")
+            throw new BEException("Job ID '${JOBID}' could not be transformed to BEJobID ")
         }
 
-        List<String> dependIDs = ((String) jobResult["DEPENDENCY"]) ? ((String) jobResult["DEPENDENCY"]).tokenize(/&/).collect { it.find(/\d+/) } : null
-        jobInfo = new GenericJobInfo(jobResult["JOB_NAME"] as String ?: null, jobResult["COMMAND"] as String ? new File(jobResult["COMMAND"] as String) : null, jobID, null, dependIDs)
-
-        String queue = jobResult["QUEUE"] ?: null
-        Duration runTime = withCaughtAndLoggedException {
-            jobResult["RUN_TIME"] ? parseColonSeparatedHHMMSSDuration(jobResult["RUN_TIME"] as String) : null
-        }
+        List<String> dependIDs = jobResult["DEPENDENCY"]?.tokenize(/&/)?.collect { it.find(/\d+/) }
+        jobInfo = new GenericJobInfo(jobResult["JOB_NAME"], jobResult["COMMAND"], jobID, null, dependIDs)
+
+        /** Common */
+        jobInfo.user = jobResult["USER"]
+        jobInfo.userGroup = jobResult["USER_GROUP"]
+        jobInfo.description = jobResult["JOB_DESCRIPTION"]
+        jobInfo.projectName = jobResult["PROJ_NAME"]
+        jobInfo.jobGroup = jobResult["JOB_GROUP"]
+        jobInfo.priority = jobResult["JOB_PRIORITY"]
+        jobInfo.pidStr = jobResult["PIDS"]?.split(",")?.toList()
+        jobInfo.submissionHost = jobResult["FROM_HOST"]
+        jobInfo.executionHosts = jobResult["EXEC_HOST"]?.split(":")?.toList()
+
+        /** Resources */
+        String queue = jobResult["QUEUE"]
+        Duration runLimit = safelyParseColonSeparatedDuration(jobResult["RUNTIMELIMIT"])
+        Duration runTime = safelyParseColonSeparatedDuration(jobResult["RUN_TIME"])
+        BufferValue memory = safelyCastToBufferValue(jobResult["MAX_MEM"])
         BufferValue swap = withCaughtAndLoggedException {
-            jobResult["SWAP"] ? new BufferValue((jobResult["SWAP"] as String).find("\\d+"), BufferUnit.m) : null
-        }
-        BufferValue memory = withCaughtAndLoggedException {
-            String unit = (jobResult["MAX_MEM"] as String).find("[a-zA-Z]+")
-            BufferUnit bufferUnit
-            if (unit == "Gbytes")
-                bufferUnit = BufferUnit.g
-            else
-                bufferUnit = BufferUnit.m
-            jobResult["MAX_MEM"] ? new BufferValue((jobResult["MAX_MEM"] as String).find("([0-9]*[.])?[0-9]+"), bufferUnit) : null
-        }
-        Duration runLimit = withCaughtAndLoggedException {
-            jobResult["RUNTIMELIMIT"] ? parseColonSeparatedHHMMSSDuration(jobResult["RUNTIMELIMIT"] as String) : null
+            String SWAP = jobResult["SWAP"]
+            SWAP ? new BufferValue(SWAP.find("\\d+"), BufferUnit.m) : null
         }
-        Integer nodes = withCaughtAndLoggedException { jobResult["SLOTS"] ? jobResult["SLOTS"] as Integer : null }
-
-        ResourceSet usedResources = new ResourceSet(memory, null, nodes, runTime, null, queue, null)
-        jobInfo.setUsedResources(usedResources)
-
-        ResourceSet askedResources = new ResourceSet(null, null, null, runLimit, null, queue, null)
-        jobInfo.setAskedResources(askedResources)
-
-        jobInfo.setUser(jobResult["USER"] as String ?: null)
-        jobInfo.setDescription(jobResult["JOB_DESCRIPTION"] as String ?: null)
-        jobInfo.setProjectName(jobResult["PROJ_NAME"] as String ?: null)
-        jobInfo.setJobGroup(jobResult["JOB_GROUP"] as String ?: null)
-        jobInfo.setPriority(jobResult["JOB_PRIORITY"] as String ?: null)
-        jobInfo.setPidStr(jobResult["PIDS"] as String ? (jobResult["PIDS"] as String).split(",").toList() : null)
-        jobInfo.setJobState(parseJobState(jobResult["STAT"] as String))
-        jobInfo.setExitCode(jobInfo.jobState == JobState.COMPLETED_SUCCESSFUL ? 0 : (jobResult["EXIT_CODE"] ? Integer.valueOf(jobResult["EXIT_CODE"] as String) : null))
-        jobInfo.setSubmissionHost(jobResult["FROM_HOST"] as String ?: null)
-        jobInfo.setExecutionHosts(jobResult["EXEC_HOST"] as String ? (jobResult["EXEC_HOST"] as String).split(":").toList() : null)
+        Integer nodes = withCaughtAndLoggedException { jobResult["SLOTS"] as Integer }
+
+        jobInfo.usedResources = new ResourceSet(memory, null, nodes, runTime, null, queue, null)
+        jobInfo.askedResources = new ResourceSet(null, null, null, runLimit, null, queue, null)
+        jobInfo.resourceReq = jobResult["EFFECTIVE_RESREQ"]
+        jobInfo.runTime = runTime
+        jobInfo.cpuTime = safelyParseColonSeparatedDuration(jobResult["CPU_USED"])
+
+        /** Status info */
+        jobInfo.jobState = parseJobState(jobResult["STAT"])
+        jobInfo.exitCode = jobInfo.jobState == JobState.COMPLETED_SUCCESSFUL ? 0 : (jobResult["EXIT_CODE"] as Integer)
+        jobInfo.pendReason = jobResult["PEND_REASON"]
+
+        /** Directories and files */
+        jobInfo.cwd = jobResult["SUB_CWD"]
+        jobInfo.execCwd = jobResult["EXEC_CWD"]
+        jobInfo.logFile = getBjobsFile(jobResult["OUTPUT_FILE"], jobID, "out")
+        jobInfo.errorLogFile = getBjobsFile(jobResult["ERROR_FILE"], jobID, "err")
+        jobInfo.inputFile = jobResult["INPUT_FILE"] ? new File(jobResult["INPUT_FILE"]) : null
+        jobInfo.execHome = jobResult["EXEC_HOME"]
+
+        /** Timestamps */
+        jobInfo.submitTime = safelyParseTime(jobResult["SUBMIT_TIME"])
+        jobInfo.startTime = safelyParseTime(jobResult["START_TIME"])
+        jobInfo.endTime = safelyParseTime(stripAwayStatusInfo(jobResult["FINISH_TIME"]))
+
+        return jobInfo
+    }
+
+    Duration safelyParseColonSeparatedDuration(String value) {
         withCaughtAndLoggedException {
-            jobInfo.setCpuTime(jobResult["CPU_USED"] ? parseColonSeparatedHHMMSSDuration(jobResult["CPU_USED"] as String) : null)
+            value ? parseColonSeparatedHHMMSSDuration(value) : null
         }
-        jobInfo.setRunTime(runTime)
-        jobInfo.setUserGroup(jobResult["USER_GROUP"] as String ?: null)
-        jobInfo.setCwd(jobResult["SUB_CWD"] as String ?: null)
-        jobInfo.setPendReason(jobResult["PEND_REASON"] as String ?: null)
-        jobInfo.setExecCwd(jobResult["EXEC_CWD"] as String ?: null)
-        jobInfo.setLogFile(getBjobsFile(jobResult["OUTPUT_FILE"] as String, jobID, "out"))
-        jobInfo.setErrorLogFile(getBjobsFile(jobResult["ERROR_FILE"] as String, jobID, "err"))
-        jobInfo.setInputFile(jobResult["INPUT_FILE"] ? new File(jobResult["INPUT_FILE"] as String) : null)
-        jobInfo.setResourceReq(jobResult["EFFECTIVE_RESREQ"] as String ?: null)
-        jobInfo.setExecHome(jobResult["EXEC_HOME"] as String ?: null)
-
-        String submissionTime = jobResult["SUBMIT_TIME"]
-        String startTime = jobResult["START_TIME"]
-        String finishTime = jobResult["FINISH_TIME"]
-
-        if (submissionTime)
-            withCaughtAndLoggedException { jobInfo.setSubmitTime(parseTime(submissionTime)) }
-        if (startTime)
-            withCaughtAndLoggedException { jobInfo.setStartTime(parseTime(startTime as String)) }
-        if (finishTime)
-            withCaughtAndLoggedException { jobInfo.setEndTime(parseTime(finishTime[0..-3])) }
+    }
 
-        return jobInfo
+    ZonedDateTime safelyParseTime(String time) {
+        if (time)
+            return withCaughtAndLoggedException {
+                return parseTime(time)
+            }
+        return null
+    }
+
+    BufferValue safelyCastToBufferValue(String MAX_MEM) {
+        withCaughtAndLoggedException {
+            if (MAX_MEM) {
+                String bufferSize = MAX_MEM.find("([0-9]*[.])?[0-9]+")
+                String unit = MAX_MEM.find("[a-zA-Z]+")
+                BufferUnit bufferUnit = unit == "Gbytes" ? BufferUnit.g : BufferUnit.m
+                return new BufferValue(bufferSize, bufferUnit)
+            }
+            return null
+        }
     }
 
     private File getBjobsFile(String s, BEJobID jobID, String type) {

src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/rest/LSFRestJobManager.groovy

@@ -331,7 +331,7 @@ class LSFRestJobManager extends AbstractLSFJobManager {
      */
     private GenericJobInfo setJobInfoForJobDetails(NodeChild jobDetails) {
 
-        GenericJobInfo jobInfo = new GenericJobInfo(jobDetails.getProperty("jobName").toString(), new File(jobDetails.getProperty("command").toString()), new BEJobID(jobDetails.getProperty("jobId").toString()), null, null)
+        GenericJobInfo jobInfo = new GenericJobInfo(jobDetails.getProperty("jobName").toString(), jobDetails.getProperty("command").toString(), new BEJobID(jobDetails.getProperty("jobId").toString()), null, null)
 
         String queue = jobDetails.getProperty("queue").toString()
         BufferValue swap = jobDetails.getProperty("swap") ? withCaughtAndLoggedException { new BufferValue(jobDetails.getProperty("swap").toString(), BufferUnit.m) } : null