Add support for fusion tags (#3609) [ci fast]

nextflow-io · Feb 8, 2023 · 8385ec2 · 8385ec2
1 parent 85b6e7d
commit 8385ec2
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Showing 6 changed files with 17 additions and 7 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
@@ -96,6 +96,7 @@ class FusionScriptLauncher extends BashWrapperBuilder {
             final work = toContainerMount(remoteWorkDir).toString()
             final result = new LinkedHashMap(10)
             result.FUSION_WORK = work
+            result.FUSION_TAGS="[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)"
             // foreign env
             final provider = new FusionEnvProvider()
             result.putAll(provider.getEnvironment(scheme))

diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/GridTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/GridTaskHandlerTest.groovy
@@ -123,7 +123,7 @@ class GridTaskHandlerTest extends Specification {
         result == '''\
                 #!/bin/bash
                 #$ directive=one
-                docker run -i -e "FUSION_WORK=/fusion/http/foo.com/some/dir" ubuntu:latest /usr/bin/fusion bash '/fusion/http/foo.com/some/dir/.command.run'
+                docker run -i -e "FUSION_WORK=/fusion/http/foo.com/some/dir" -e "FUSION_TAGS=[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)" ubuntu:latest /usr/bin/fusion bash '/fusion/http/foo.com/some/dir/.command.run'
                 '''.stripIndent(true)
     }
 

diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionScriptLauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionScriptLauncherTest.groovy
@@ -67,7 +67,10 @@ class FusionScriptLauncherTest extends Specification {
                 remoteWorkDir: XPath.get('http://foo/work'))
 
         expect:
-        fusion.fusionEnv() == [FUSION_WORK: '/fusion/http/foo/work']
+        fusion.fusionEnv() == [
+                FUSION_WORK: '/fusion/http/foo/work',
+                FUSION_TAGS: "[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)"
+        ]
     }
 
     def 'should get header script' () {

diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/local/LocalTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/local/LocalTaskHandlerTest.groovy
@@ -73,7 +73,7 @@ class LocalTaskHandlerTest extends Specification {
         then:
         handler.fusionEnabled() >> true
         and:
-        builder.command() == ['sh','-c','docker run -i -e "FUSION_WORK=/fusion/http/some/work/dir" --rm --privileged ubuntu:latest /usr/bin/fusion bash \'/fusion/http/some/work/dir/.command.run\'']
+        builder.command() == ['sh','-c','docker run -i -e "FUSION_WORK=/fusion/http/some/work/dir" -e "FUSION_TAGS=[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)" --rm --privileged ubuntu:latest /usr/bin/fusion bash \'/fusion/http/some/work/dir/.command.run\'']
         builder.directory() == null
         builder.redirectErrorStream()
         builder.redirectOutput().file()

diff --git a/plugins/nf-amazon/src/test/nextflow/executor/FusionScriptLauncherS3Test.groovy b/plugins/nf-amazon/src/test/nextflow/executor/FusionScriptLauncherS3Test.groovy
@@ -59,7 +59,9 @@ class FusionScriptLauncherS3Test extends Specification {
 
         expect:
         fusion.fusionEnv() == [AWS_S3_ENDPOINT: 'http://foo.com',
-                               FUSION_WORK: '/fusion/s3/foo/work']
+                               FUSION_WORK: '/fusion/s3/foo/work',
+                               FUSION_TAGS: "[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)"
+                                ]
 
         cleanup:
         SysEnv.pop()
@@ -79,7 +81,9 @@ class FusionScriptLauncherS3Test extends Specification {
         expect:
         fusion.fusionEnv() == [AWS_ACCESS_KEY_ID: 'xxx',
                                AWS_SECRET_ACCESS_KEY: 'zzz',
-                               FUSION_WORK: '/fusion/s3/foo/work']
+                               FUSION_WORK: '/fusion/s3/foo/work',
+                               FUSION_TAGS: "[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)"
+        ]
 
         cleanup:
         Global.config = null
@@ -102,7 +106,9 @@ class FusionScriptLauncherS3Test extends Specification {
         fusion.fusionEnv() == [AWS_ACCESS_KEY_ID: 'k1',
                                AWS_SECRET_ACCESS_KEY: 's1',
                                AWS_S3_ENDPOINT: 'http://minio.com',
-                               FUSION_WORK: '/fusion/s3/foo/work']
+                               FUSION_WORK: '/fusion/s3/foo/work',
+                               FUSION_TAGS: "[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)"
+        ]
 
         cleanup:
         Global.config = null

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -206,7 +206,7 @@ class WaveClient {
                     return sendRequest0(request, attempt+1)
                 }
                 else
-                    throw new UnauthorizedException("Unauthorised [401] - Verify you have provided a valid access token")
+                    throw new UnauthorizedException("Unauthorized [401] - Verify you have provided a valid access token")
             }
             else
                 throw new BadResponseException("Wave invalid response: [${resp.statusCode()}] ${resp.body()}")