Remove unused properties from data model

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

modules/nf-lineage/src/main/nextflow/lineage/LinObserver.groovy

@@ -228,7 +228,6 @@ class LinObserver implements TraceObserver {
             normalizer.normalizePath(task.getCondaEnv()),
             normalizer.normalizePath(task.getSpackEnv()),
             task.config?.getArchitecture()?.toString(),
-            task.processor.getTaskGlobalVars(task),
             task.processor.getTaskBinEntries(task.source).collect { Path p -> new DataPath(
                 normalizer.normalizePath(p.normalize()),
                 Checksum.ofNextflow(p) )

modules/nf-lineage/src/main/nextflow/lineage/LinPropertyValidator.groovy

@@ -20,6 +20,7 @@ import groovy.transform.CompileStatic
 import nextflow.lineage.model.Annotation
 import nextflow.lineage.model.Checksum
 import nextflow.lineage.model.DataPath
+import nextflow.lineage.model.FileOutput
 import nextflow.lineage.model.Parameter
 import nextflow.lineage.model.TaskRun
 import nextflow.lineage.model.Workflow
@@ -37,8 +38,8 @@ class LinPropertyValidator {
     private static final List<Class> LIN_MODEL_CLASSES = [
         Annotation,
         Checksum,
-        DataOutput,
         DataPath,
+        FileOutput,
         Parameter,
         TaskRun,
         Workflow,

modules/nf-lineage/src/main/nextflow/lineage/model/TaskRun.groovy

@@ -64,10 +64,6 @@ class TaskRun implements LinSerializable {
      * Architecture defined in the Spack environment used for the task run
      */
     String architecture
-    /**
-     * Global variables defined in the task run
-     */
-    Map globalVars
     /**
      * Binaries used in the task run
      */
@@ -76,8 +72,4 @@ class TaskRun implements LinSerializable {
      * Workflow launch associated to the task run
      */
     String workflowLaunch
-    /**
-     * Annotations attached to the task run
-     */
-    List<Annotation> annotations
 }

modules/nf-lineage/src/main/nextflow/lineage/model/WorkflowLaunch.groovy

@@ -48,8 +48,4 @@ class WorkflowLaunch implements LinSerializable {
      * Resolved Configuration
      */
     Map config
-    /**
-     * Annotations attached to the workflow run
-     */
-    List<Annotation> annotations
 }

modules/nf-lineage/src/main/nextflow/lineage/model/WorkflowRun.groovy

@@ -42,8 +42,4 @@ class WorkflowRun implements LinSerializable {
      * Workflow output
      */
     List<Parameter> output
-    /**
-     * Annotations attached to the workflow outputs
-     */
-    List<Annotation> annotations
 }

modules/nf-lineage/src/test/nextflow/lineage/LinObserverTest.groovy

@@ -240,7 +240,6 @@ class LinObserverTest extends Specification {
         Files.createDirectories(taskWd)
         and:
         def processor = Mock(TaskProcessor){
-            getTaskGlobalVars(_) >> [:]
             getTaskBinEntries(_) >> []
         }
 
@@ -298,7 +297,7 @@ class LinObserverTest extends Specification {
                 new Parameter("path", "file1", ['lid://78567890/file1.txt']),
                 new Parameter("path", "file2", [[path: normalizer.normalizePath(file), checksum: [value:fileHash, algorithm: "nextflow", mode:  "standard"]]]),
                 new Parameter("val", "id", "value")
-            ], null, null, null, null, [:], [], "lid://hash", null)
+            ], null, null, null, null, [], "lid://hash")
         def dataOutput1 = new FileOutput(outFile1.toString(), new Checksum(fileHash1, "nextflow", "standard"),
             "lid://1234567890", "lid://hash", "lid://1234567890", attrs1.size(), LinUtils.toDate(attrs1.creationTime()), LinUtils.toDate(attrs1.lastModifiedTime()) )
         def dataOutput2 = new FileOutput(outFile2.toString(), new Checksum(fileHash2, "nextflow", "standard"),

modules/nf-lineage/src/test/nextflow/lineage/cli/LinCommandImplTest.groovy

@@ -185,15 +185,15 @@ class LinCommandImplTest extends Specification{
              new Parameter("path","reads", ["lid://45678/output.txt"] ),
              new Parameter("path","input", [new DataPath("path/to/file",new Checksum("45372qe","nextflow","standard"))])
             ],
-            null, null, null, null, [:],[], null)
+            null, null, null, null, [], null)
         lidFile3.text = encoder.encode(entry)
         entry  = new FileOutput("path/to/file",new Checksum("45372qe","nextflow","standard"),
             "lid://45678", "lid://45678", null, 1234, time, time, null)
         lidFile4.text = encoder.encode(entry)
         entry = new TaskRun("u345-2346-1stw2", "bar",
             new Checksum("abfs2556","nextflow","standard"),
             'this is a script',
-            null,null, null, null, null, [:],[], null)
+            null,null, null, null, null, [], null)
         lidFile5.text = encoder.encode(entry)
         final network = """flowchart BT
     lid://12345/file.bam@{shape: document, label: "lid://12345/file.bam"}

modules/nf-lineage/src/test/nextflow/lineage/serde/LinEncoderTest.groovy

@@ -108,7 +108,7 @@ class LinEncoderTest extends Specification{
         def taskRun = new TaskRun(
             uniqueId.toString(),"name", new Checksum("78910", "nextflow", "standard"), 'this is a script',
             [new Parameter("String", "param1", "value1")], "container:version", "conda", "spack", "amd64",
-            [a: "A", b: "B"], [new DataPath("path/to/file", new Checksum("78910", "nextflow", "standard"))]
+            [new DataPath("path/to/file", new Checksum("78910", "nextflow", "standard"))]
         )
         when:
         def encoded = encoder.encode(taskRun)
@@ -126,7 +126,6 @@ class LinEncoderTest extends Specification{
         result.conda == "conda"
         result.spack == "spack"
         result.architecture == "amd64"
-        result.globalVars == [a: "A", b: "B"]
         result.binEntries.size() == 1
         result.binEntries.get(0).path == "path/to/file"
         result.binEntries.get(0).checksum.value == "78910"
@@ -141,7 +140,7 @@ class LinEncoderTest extends Specification{
         def encoded = encoder.encode(wfResults)
         def object = encoder.decode(encoded)
         then:
-        encoded == '{"type":"WorkflowRun","createdAt":null,"launch":"lid://1234","output":null,"annotations":null}'
+        encoded == '{"type":"WorkflowRun","createdAt":null,"launch":"lid://1234","output":null}'
         def result = object as WorkflowRun
         result.createdAt == null