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Include WorkflowMetadata in lineage records #6069

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37 changes: 35 additions & 2 deletions modules/nf-lineage/src/main/nextflow/lineage/LinObserver.groovy
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Expand Up @@ -16,7 +16,11 @@

package nextflow.lineage

import nextflow.NextflowMeta
import nextflow.extension.FilesEx
import nextflow.lineage.exception.OutputRelativePathException
import nextflow.script.FusionMetadata
import nextflow.script.WaveMetadata

import static nextflow.lineage.fs.LinPath.*

Expand Down Expand Up @@ -71,6 +75,11 @@ import nextflow.util.TestOnly
@Slf4j
@CompileStatic
class LinObserver implements TraceObserverV2 {
private static List<String> workflowMetadataPropertiesToRemove = [
"sessionId", "name", //Already in workflowRun
"scriptFile", "scriptName", "scriptId", "repository", "commitId", "revision", "projectName", "manifest", //Already in workflow
"stats", "success" // End
]
Comment on lines +78 to +82
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I think it would be preferable to keep as much as possible aligned to WorkflowMeta structure, in the same way as it's done in the tower client

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

Line 620 in 5bfe1c1

result.workflow = workflow

we could consider removing repeated values in the parent object

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@jorgee jorgee May 14, 2025 •
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Not sure if I get your comment.

If I am not wrong, in TowerClient, the workflow is a plain map that contains everything that is in WorkflowMetadata, removing stats and adding other properties like the resolved config and params.

If we do the same and include everything as property of the WorkflowRun class, it will be very difficult to maintain, so I prefer to keep it inside the metadata property (or rename it to another name). If a new parameter is added in the WorkflowMetadata, it will also be added to the 'metadata' without any model update.

A small difference is the sessionId and name that are properties in WorkflowRun and they were also in the WorkflowMetadata map. I do not see a problem with keeping it in metadata and removing it from WorkflowRun. We can also add the resolved config if you think it is better.

The big difference is in the workflow and params. I think they are the parts that mainly describe the WorkflowRun, and, in the TowerClient, they are spread in a set of properties. In workflow, we already included the information that is in scriptFile, scriptName, scriptId, repository, commitId. I have just added other info (revision, projectName and manifest) that I think they are describing the workflow more than the execution. In fact, I think the workflow description could have a separate record, and LID and just have a reference in the WorkflowRun.

private static Map<Class<? extends BaseParam>, String> taskParamToValue = [
(StdOutParam) : "stdout",
(StdInParam) : "stdin",
Expand Down Expand Up @@ -155,15 +164,19 @@ class LinObserver implements TraceObserverV2 {
final workflow = new Workflow(
collectScriptDataPaths(normalizer),
session.workflowMetadata.repository,
session.workflowMetadata.commitId
session.workflowMetadata.commitId,
session.workflowMetadata.revision,
session.workflowMetadata.projectName,
session.workflowMetadata.manifest?.toMap()
)
// create the workflow run main object
final value = new WorkflowRun(
workflow,
session.uniqueId.toString(),
session.runName,
getNormalizedParams(session.params, normalizer),
SecretHelper.hideSecrets(session.config.deepClone()) as Map
SecretHelper.hideSecrets(session.config.deepClone()) as Map,
addOtherMetadata()
)
final executionHash = CacheHelper.hasher(value).hash().toString()
store.save(executionHash, value)
Expand Down Expand Up @@ -473,4 +486,24 @@ class LinObserver implements TraceObserverV2 {
}
return paths
}

private Map addOtherMetadata() {
try {
def metadata = session.workflowMetadata.toMap()
.collectEntries { it.value instanceof Path ? [it.key, FilesEx.toUriString(it.value as Path) ] : [it.key, it.value] }
metadata.removeAll {it.key.toString() in workflowMetadataPropertiesToRemove }
if( metadata.containsKey("nextflow") )
metadata["nextflow"] = (metadata["nextflow"] as NextflowMeta).toJsonMap()
if( metadata.containsKey("configFiles") )
metadata["configFiles"] = (metadata["configFiles"] as List<Path>).collect {FilesEx.toUriString(it)}
if( metadata.containsKey( "wave") )
metadata["wave"] = (metadata["wave"] as WaveMetadata).enabled
if( metadata.containsKey( "fusion") )
metadata["fusion"] = (metadata["fusion"] as FusionMetadata).enabled
return metadata
}catch( Throwable e){
log.debug("Error creating metadata", e)
return [:]
}
}
}
12 changes: 12 additions & 0 deletions modules/nf-lineage/src/main/nextflow/lineage/model/v1beta1/Workflow.groovy
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Expand Up @@ -41,4 +41,16 @@ class Workflow implements LinSerializable {
* Workflow commit identifier
*/
String commitId
/**
* Workflow revision
*/
String revision
/**
* Project name
*/
String projectName
/**
* Workflow Manifest
*/
Map manifest
}
5 changes: 5 additions & 0 deletions modules/nf-lineage/src/main/nextflow/lineage/model/v1beta1/WorkflowRun.groovy
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Expand Up @@ -48,4 +48,9 @@ class WorkflowRun implements LinSerializable {
* Resolved Configuration
*/
Map config
/**
* Raw metadata
*/
Map metadata

}
34 changes: 26 additions & 8 deletions modules/nf-lineage/src/test/nextflow/lineage/LinObserverTest.groovy
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Expand Up @@ -17,6 +17,7 @@

package nextflow.lineage

import nextflow.extension.FilesEx
import nextflow.lineage.exception.OutputRelativePathException

import java.nio.file.Files
Expand Down Expand Up @@ -165,14 +166,31 @@ class LinObserverTest extends Specification {
def store = new DefaultLinStore();
def uniqueId = UUID.randomUUID()
def scriptFile = folder.resolve("main.nf")
def map = [
repository: "https://nextflow.io/nf-test/",
commitId: "123456",
scriptId: "78910",
scriptFile: scriptFile,
projectDir: folder.resolve("projectDir"),
revision: "main",
projectName: "nextflow.io/nf-test",
workDir: folder.resolve("workDir")
]
def metadata = Mock(WorkflowMetadata){
getRepository() >> "https://nextflow.io/nf-test/"
getCommitId() >> "123456"
getScriptId() >> "78910"
getScriptFile() >> scriptFile
getProjectDir() >> folder.resolve("projectDir")
getWorkDir() >> folder.resolve("workDir")
getRepository() >> map.repository
getCommitId() >> map.commitId
getScriptId() >> map.scriptId
getScriptFile() >> map.scriptFile
getProjectDir() >> map.projectDir
getRevision() >> map.revision
getProjectName() >> map.projectName
getWorkDir() >> map.workDir
toMap() >> map
}
def expectedMap = [
projectDir: FilesEx.toUriString(map.projectDir),
workDir: FilesEx.toUriString(map.workDir)
]
def session = Mock(Session) {
getConfig() >> config
getUniqueId() >> uniqueId
Expand All @@ -183,8 +201,8 @@ class LinObserverTest extends Specification {
store.open(LineageConfig.create(session))
def observer = new LinObserver(session, store)
def mainScript = new DataPath("file://${scriptFile.toString()}", new Checksum("78910", "nextflow", "standard"))
def workflow = new Workflow([mainScript],"https://nextflow.io/nf-test/", "123456" )
def workflowRun = new WorkflowRun(workflow, uniqueId.toString(), "test_run", [], config)
def workflow = new Workflow([mainScript], map.repository, map.commitId, map.revision, map.projectName )
def workflowRun = new WorkflowRun(workflow, uniqueId.toString(), "test_run", [], config, expectedMap)
when:
observer.onFlowCreate(session)
observer.onFlowBegin()
Expand Down