Add manifest contributors and license

Signed-off-by: Ben Sherman <[email protected]>
nextflow-io · Nov 5, 2024 · f2c9416 · f2c9416
1 parent 4594477
commit f2c9416
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Showing 4 changed files with 40 additions and 26 deletions.
diff --git a/plugins/nf-prov/build.gradle b/plugins/nf-prov/build.gradle
@@ -56,21 +56,18 @@ sourceSets {
 
 dependencies {
     // This dependency is exported to consumers, that is to say found on their compile classpath.
-    compileOnly 'io.nextflow:nextflow:23.04.0'
+    compileOnly 'io.nextflow:nextflow:24.10.0'
     compileOnly 'org.slf4j:slf4j-api:1.7.10'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
-    // add here plugins depepencies
+    compileOnly 'org.pf4j:pf4j:3.12.0'
 
     // test configuration
-    testImplementation "org.codehaus.groovy:groovy:3.0.8"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.8"
-    testImplementation 'io.nextflow:nextflow:23.04.0'
-    testImplementation ("org.codehaus.groovy:groovy-test:3.0.8") { exclude group: 'org.codehaus.groovy' }
+    testImplementation 'io.nextflow:nextflow:24.10.0'
+    testImplementation ("org.codehaus.groovy:groovy-test:4.0.23") { exclude group: 'org.codehaus.groovy' }
     testImplementation ("cglib:cglib-nodep:3.3.0")
-    testImplementation ("org.objenesis:objenesis:3.1")
-    testImplementation ("org.spockframework:spock-core:2.0-M3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('org.spockframework:spock-junit4:2.0-M3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('com.google.jimfs:jimfs:1.1')
+    testImplementation ("org.objenesis:objenesis:3.2")
+    testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
+    testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
+    testImplementation ('com.google.jimfs:jimfs:1.2')
 
     // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
     modules {

diff --git a/plugins/nf-prov/src/main/nextflow/prov/BcoRenderer.groovy b/plugins/nf-prov/src/main/nextflow/prov/BcoRenderer.groovy
@@ -24,10 +24,13 @@ import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import nextflow.Session
 import nextflow.SysEnv
+import nextflow.config.Manifest
 import nextflow.processor.TaskRun
 import nextflow.script.WorkflowMetadata
 import nextflow.util.CacheHelper
 
+import static nextflow.config.Manifest.ContributionType
+
 /**
  * Renderer for the BioCompute Object (BCO) format.
  *
@@ -64,7 +67,7 @@ class BcoRenderer implements Renderer {
         final nextflowMeta = metadata.nextflow
 
         final dateCreated = DateTimeFormatter.ISO_OFFSET_DATE_TIME.format(metadata.start)
-        final authors = (manifest.author ?: '').tokenize(',')*.trim()
+        final contributors = getContributors(manifest)
         final nextflowVersion = nextflowMeta.version.toString()
         final params = session.config.params as Map
 
@@ -88,15 +91,13 @@ class BcoRenderer implements Renderer {
                 "name": manifest.name ?: "",
                 "version": manifest.version ?: "",
                 "review": review,
+                "derived_from": derived_from,
                 "obsolete_after": obsolete_after,
                 "embargo": embargo,
                 "created": dateCreated,
                 "modified": dateCreated,
-                "contributors": authors.collect( name -> [
-                    "contribution": ["authoredBy"],
-                    "name": name
-                ] ),
-                "license": ""
+                "contributors": contributors,
+                "license": manifest.license
             ],
             "usability_domain": usability,
             "extension_domain": [],
@@ -191,4 +192,20 @@ class BcoRenderer implements Renderer {
         path.text = JsonOutput.prettyPrint(JsonOutput.toJson(bco))
     }
 
+    private List getContributors(Manifest manifest) {
+        manifest.contributors.collect { c -> [
+            "name": c.name,
+            "affiliation": c.affiliation,
+            "email": c.email,
+            "contribution": c.contribution.collect { ct -> CONTRIBUTION_TYPES[ct] },
+            "orcid": c.orcid
+        ] }
+    }
+
+    private static Map<ContributionType, String> CONTRIBUTION_TYPES = [
+        (ContributionType.AUTHOR) : "authoredBy",
+        (ContributionType.MAINTAINER) : "curatedBy",
+        (ContributionType.CONTRIBUTOR) : "curatedBy",
+    ]
+
 }
diff --git a/plugins/nf-prov/src/main/nextflow/prov/DagRenderer.groovy b/plugins/nf-prov/src/main/nextflow/prov/DagRenderer.groovy
@@ -64,8 +64,8 @@ class DagRenderer implements Renderer {
     }
 
     private Map<TaskRun,Vertex> getVertices(Set<TaskRun> tasks) {
-        def result = [:]
-        for( def task : tasks ) {
+        Map<TaskRun,Vertex> result = [:]
+        for( final task : tasks ) {
             final inputs = task.getInputFilesMap()
             final outputs = ProvHelper.getTaskOutputs(task)
 
@@ -154,7 +154,7 @@ class DagRenderer implements Renderer {
         }
 
         // render task outputs
-        final outputs = [:] as Map<Path,String>
+        Map<Path,String> outputs = [:]
 
         dag.vertices.each { task, vertex ->
             vertex.outputs.each { path ->
@@ -184,11 +184,11 @@ class DagRenderer implements Renderer {
      * @param vertices
      */
     private Map getTaskTree(Map<TaskRun,Vertex> vertices) {
-        def taskTree = [:]
+        final taskTree = [:]
 
-        for( def entry : vertices ) {
-            def task = entry.key
-            def vertex = entry.value
+        for( final entry : vertices ) {
+            final task = entry.key
+            final vertex = entry.value
 
             // infer subgraph keys from fully qualified process name
             final result = getSubgraphKeys(task.processor.name)
@@ -200,7 +200,7 @@ class DagRenderer implements Renderer {
 
             // navigate to given subgraph
             def subgraph = taskTree
-            for( def key : keys ) {
+            for( final key : keys ) {
                 if( key !in subgraph )
                     subgraph[key] = [:]
                 subgraph = subgraph[key]

diff --git a/plugins/nf-prov/src/resources/META-INF/MANIFEST.MF b/plugins/nf-prov/src/resources/META-INF/MANIFEST.MF
@@ -3,4 +3,4 @@ Plugin-Id: nf-prov
 Plugin-Version: 1.2.4
 Plugin-Class: nextflow.prov.ProvPlugin
 Plugin-Provider: nextflow
-Plugin-Requires: >=23.04.0
+Plugin-Requires: >=24.10.0