Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [ci…

… skip]



Signed-off-by: Jordi Deu-Pons <jordi@jordeu.net>

plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy

@@ -17,6 +17,8 @@
 
 package io.seqera.tower.plugin
 
+import nextflow.exception.AbortOperationException
+
 import java.nio.file.FileAlreadyExistsException
 import java.nio.file.Path
 import java.time.temporal.ChronoUnit
@@ -130,26 +132,41 @@ class TowerArchiver {
     }
 
     void archiveLogs() {
-        archiveFile(env.get('NXF_OUT_FILE'))
-        archiveFile(env.get('NXF_LOG_FILE'))
-        archiveFile(env.get('NXF_TML_FILE'))
-        archiveFile(env.get('TOWER_CONFIG_FILE'))
-        archiveFile(env.get('TOWER_REPORTS_FILE'))
+        // Nextflow log file are expected to be found at the working directory
+        // when running from Tower launcher the cache command, if needed, has
+        // copied them before starting the archive process
+
+        final work = env.get('NXF_WORK') ?: env.get('NXF_TEST_WORK')
+        if( !work ) {
+            log.error("Missing target work dir - Tower archive cannot be performed")
+            return
+        }
+        if( !work.startsWith('/') ) {
+            log.error("Invalid NXF_WORK work directory - it must start with a slash character - offending value: '${work}'")
+            return
+        }
+
+        final base = Path.of(work)
+        archiveFile(base, env.get('NXF_OUT_FILE'))
+        archiveFile(base, env.get('NXF_LOG_FILE'))
+        archiveFile(base, env.get('NXF_TML_FILE'))
+        archiveFile(base, env.get('TOWER_CONFIG_FILE'))
+        archiveFile(base, env.get('TOWER_REPORTS_FILE'))
     }
 
     void archiveTaskLogs(String workDir) {
         final base = Path.of(workDir)
-        archiveFile(base.resolve('.command.out'))
-        archiveFile(base.resolve('.command.err'))
-        archiveFile(base.resolve('.command.log'))
-        archiveFile(base.resolve('.command.run'))
-        archiveFile(base.resolve('.command.sh'))
-        archiveFile(base.resolve('.exitcode'))
+        archiveFile(base, '.command.out')
+        archiveFile(base, '.command.err')
+        archiveFile(base, '.command.log')
+        archiveFile(base, '.command.run')
+        archiveFile(base, '.command.sh')
+        archiveFile(base, '.exitcode')
     }
 
-    protected void archiveFile(String name) {
+    protected void archiveFile(Path base, String name) {
         if( name )
-            archiveFile(Path.of(name).toAbsolutePath())
+            archiveFile(base.resolve(name))
     }
 
     protected void archiveFile(Path source) {

plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerArchiverTest.groovy

@@ -17,6 +17,7 @@
 
 package io.seqera.tower.plugin
 
+import java.nio.file.Files
 import java.nio.file.Path
 import java.util.concurrent.Executors
 
@@ -125,4 +126,28 @@ class TowerArchiverTest extends Specification {
         target.exists()
     }
 
+    def 'should archive Nextflow log file' () {
+        given:
+        def workDir = Files.createTempDirectory('workdir')
+        def targetDir = Files.createTempDirectory('target')
+        def nextflowLog = workDir.resolve('nextflow.log'); nextflowLog.text = 'nextflow logs'
+        def targetLog = targetDir.resolve('nextflow.log')
+        and:
+        def sess = Mock(Session) { getConfig() >> [:] }
+        def exec = Executors.newSingleThreadExecutor()
+        def archiver = new TowerArchiver(workDir,targetDir, sess, ['NXF_WORK': workDir.toString(), 'NXF_LOG_FILE': 'nextflow.log'])
+
+        when:
+        archiver.archiveLogs()
+        sleep 100 // <-- sleep a bit to allow the task to enter in the exec pool
+        exec.shutdown()
+
+        then:
+        targetLog.exists()
+
+        cleanup:
+        workDir?.deleteDir()
+        targetDir?.deleteDir()
+    }
+
 }