Add support for timezoned timestamp to metadata

modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy

@@ -18,6 +18,7 @@ package nextflow.script
 
 import java.nio.file.Path
 import java.nio.file.Paths
+import java.time.OffsetDateTime
 
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
@@ -78,13 +79,17 @@ class WorkflowMetadata {
 
     /**
      * Timestamp at workflow execution start
+     *
+     * Use OffDateTime instead of Date -- See https://stackoverflow.com/a/32443004/395921
      */
-    Date start
+    OffsetDateTime start
 
     /**
      * Timestamp at workflow execution complete
+     *
+     * Use OffDateTime instead of Date -- See https://stackoverflow.com/a/32443004/395921
      */
-    Date complete
+    OffsetDateTime complete
 
     /**
      * Time elapsed to complete workflow execution
@@ -217,7 +222,8 @@ class WorkflowMetadata {
         this.commitId = scriptFile?.commitId
         this.revision = scriptFile?.revision
         this.projectDir = scriptFile?.localPath
-        this.start = new Date()
+        this.projectName = scriptFile?.projectName ?: scriptName
+        this.start = OffsetDateTime.now()
         this.container = session.fetchContainers()
         this.commandLine = session.commandLine
         this.nextflow = NextflowMeta.instance
@@ -364,8 +370,8 @@ class WorkflowMetadata {
      */
     @PackageScope
     void invokeOnComplete() {
-        this.complete = new Date()
-        this.duration = Duration.of( complete.time - start.time )
+        this.complete = OffsetDateTime.now()
+        this.duration = Duration.between( start, complete )
         this.success = !(session.aborted || session.cancelled)
 
         setErrorAttributes()

modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html

@@ -137,7 +137,7 @@ <h4>Workflow execution completed unsuccessfully!</h4>
       <dl>
         <dt>Run times</dt>
         <dd>
-          <span id="workflow_start">${workflow.start}</span> - <span id="workflow_complete">${workflow.complete}</span>
+          <span id="workflow_start">${workflow.start.format('dd-MMM-yyyy HH:mm:ss')}</span> - <span id="workflow_complete">${workflow.complete.format('dd-MMM-yyyy HH:mm:ss')}</span>
           (<span id="completed_fromnow"></span>duration: <strong>${workflow.duration}</strong>)
         </dd>
 

modules/nextflow/src/test/groovy/nextflow/NextflowMetaTest.groovy

@@ -30,7 +30,7 @@ class NextflowMetaTest extends Specification {
         map.version == '10.12.0'
         map.build == 123
         map.preview.dsl == 2
-        dateToString(map.timestamp) == Const.APP_TIMESTAMP_UTC
+        dateToString((Date)map.timestamp) == Const.APP_TIMESTAMP_UTC
 
     }
 }

modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy

@@ -16,10 +16,9 @@
 
 package nextflow.script
 
-import spock.lang.Specification
-
 import java.nio.file.Files
 import java.nio.file.Paths
+import java.time.OffsetDateTime
 
 import nextflow.Const
 import nextflow.Session
@@ -28,8 +27,8 @@ import nextflow.trace.TraceRecord
 import nextflow.util.Duration
 import nextflow.util.VersionNumber
 import org.eclipse.jgit.api.Git
+import spock.lang.Specification
 import test.TestHelper
-
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -39,7 +38,7 @@ class WorkflowMetadataTest extends Specification {
     def 'should populate workflow object' () {
 
         given:
-        final begin = new Date()
+        final begin = OffsetDateTime.now()
         def dir = Files.createTempDirectory('test')
         /*
          * create the github repository
@@ -99,7 +98,7 @@ class WorkflowMetadataTest extends Specification {
         metadata.projectDir == dir
         metadata.projectName == 'nextflow-io/rnaseq-nf'
         metadata.start >= begin
-        metadata.start <= new Date()
+        metadata.start <= OffsetDateTime.now()
         metadata.complete == null
         metadata.commandLine == 'nextflow run -this -that'
         metadata.nextflow.version == new VersionNumber(Const.APP_VER)
@@ -120,8 +119,8 @@ class WorkflowMetadataTest extends Specification {
         metadata.invokeOnComplete()
         then:
         metadata.complete > metadata.start
-        metadata.complete <= new Date()
-        metadata.duration == new Duration( metadata.complete.time - metadata.start.time )
+        metadata.complete <= OffsetDateTime.now()
+        metadata.duration == Duration.between(metadata.start, metadata.complete)
         handlerInvoked == metadata.commandLine
 
 

modules/nextflow/src/test/groovy/nextflow/script/WorkflowNotifierTest.groovy

@@ -17,6 +17,9 @@
 package nextflow.script
 
 import java.nio.file.Paths
+import java.time.Instant
+import java.time.OffsetDateTime
+import java.time.ZoneId
 
 import nextflow.NextflowMeta
 import nextflow.mail.Attachment
@@ -38,14 +41,14 @@ class WorkflowNotifierTest extends Specification {
         given:
         def work = TestHelper.createInMemTempDir()
         def sessionId = UUID.randomUUID()
-        def now = new Date(1513285947928)
-        def end = new Date( now.time + 150_000 )
+        def now = OffsetDateTime.ofInstant(Instant.ofEpochMilli(1513285947928), ZoneId.systemDefault())
+        def end = now.plusSeconds(150)
         def meta = new WorkflowMetadata(
                 runName: 'foo_bartali',
                 exitStatus: 0,
                 start: now,
                 complete: end,
-                duration: Duration.of( end.time - now.time ),
+                duration: Duration.between( now, end ),
                 commandLine: 'nextflow run big-workflow',
                 launchDir: Paths.get('/launch/dir'),
                 workDir: work,
@@ -163,16 +166,16 @@ class WorkflowNotifierTest extends Specification {
 
         given:
         def sessionId = UUID.randomUUID()
-        def now = new Date(1513285947928)
-        def end = new Date( now.time + 150_000 )
+        def now = OffsetDateTime.ofInstant(Instant.ofEpochMilli(1513285947928), ZoneId.systemDefault())
+        def end = now.plusSeconds(150)
         def workDir = TestHelper.createInMemTempDir()
 
         def meta = new WorkflowMetadata(
                 runName: 'foo_bartali',
                 exitStatus: 0,
                 start: now,
                 complete: end,
-                duration: Duration.of( end.time - now.time ),
+                duration: Duration.between( now, end ),
                 commandLine: 'nextflow run big-workflow',
                 launchDir: Paths.get('/launch/dir'),
                 workDir: workDir,

modules/nextflow/src/test/groovy/nextflow/trace/ReportObserverTest.groovy

@@ -15,9 +15,10 @@
  */
 
 package nextflow.trace
+
 import java.nio.file.Files
 import java.nio.file.Paths
-import java.util.concurrent.Executors
+import java.time.OffsetDateTime
 
 import groovy.json.JsonSlurper
 import nextflow.NextflowMeta
@@ -115,6 +116,8 @@ class ReportObserverTest extends Specification {
         given:
         def workDir = TestHelper.createInMemTempDir()
         def workflow = new WorkflowMetadata(
+                start: OffsetDateTime.now(),
+                complete: OffsetDateTime.now(),
                 workDir: workDir,
                 stats: new WorkflowStats(),
                 nextflow: new NextflowMeta('0.27.9', 3232, '2017-12-12')

modules/nf-commons/src/main/nextflow/extension/Bolts.groovy

@@ -20,6 +20,8 @@ import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 import java.text.DateFormat
 import java.text.SimpleDateFormat
+import java.time.OffsetDateTime
+import java.time.format.DateTimeFormatter
 import java.util.concurrent.locks.Lock
 import java.util.regex.Pattern
 
@@ -83,6 +85,10 @@ class Bolts {
         getLocalDateFormat(format ?: DATETIME_FORMAT, zone).get().format(self)
     }
 
+    static String format(OffsetDateTime self, String format) {
+        return self.format(DateTimeFormatter.ofPattern(format))
+    }
+
     /**
      * Format a {@link Date} object
      *

modules/nf-commons/src/main/nextflow/util/Duration.groovy

@@ -16,6 +16,7 @@
 
 package nextflow.util
 
+import java.time.temporal.Temporal
 import java.util.concurrent.TimeUnit
 
 import groovy.transform.CompileStatic
@@ -210,6 +211,10 @@ class Duration implements Comparable<Duration>, Serializable, Cloneable {
         }
     }
 
+    static Duration between( Temporal start, Temporal end ) {
+        new Duration(java.time.Duration.between(start, end).toMillis())
+    }
+
     long toMillis() {
         durationInMillis
     }

modules/nf-commons/src/test/nextflow/extension/BoltsTest.groovy

@@ -16,6 +16,10 @@
 
 package nextflow.extension
 
+import java.time.Instant
+import java.time.OffsetDateTime
+import java.time.ZoneId
+
 import spock.lang.Specification
 import spock.lang.Unroll
 
@@ -54,6 +58,19 @@ class BoltsTest extends Specification {
 
     }
 
+    def 'should format offset datetime' () {
+        given:
+        def now = OffsetDateTime.ofInstant(Instant.ofEpochMilli(1513285947928), ZoneId.of('CET'))
+        expect:
+        now.format(FMT) == EXPECTED
+
+        where:
+        FMT                     | EXPECTED
+        'dd-MM-yyyy HH:mm'      | '14-12-2017 22:12'
+        'dd-MMM-yyyy HH:mm:ss'  | '14-Dec-2017 22:12:27'
+
+    }
+
     def testTrimDotZero() {
 
         expect:

modules/nf-commons/src/test/nextflow/util/DurationTest.groovy

@@ -16,6 +16,8 @@
 
 package nextflow.util
 
+import java.time.Instant
+
 import spock.lang.Specification
 
 /**
@@ -181,4 +183,15 @@ class DurationTest extends Specification {
     }
 
 
+    def 'should validate duration between' () {
+
+        given:
+        def start = Instant.now()
+        def end = start.plusMillis(1000)
+
+        expect:
+        Duration.between(start, end) == Duration.of('1sec')
+    }
+
+
 }