17054 custom name

cwltool/extensions-v1.1.yml

@@ -64,3 +64,22 @@ $graph:
         The number of MPI processes to start. If you give a string,
         this will be evaluated as a CWL Expression and it must
         evaluate to an integer.
+
+- name: JobName
+  type: record
+  inVocab: false
+  extends: cwl:ProcessRequirement
+  doc: |
+    Provide a string or expression for naming the runtime workflow step in logs or user interface.
+  fields:
+    - name: class
+      type: string
+      doc: "Always 'JobName'"
+      jsonldPredicate:
+        "_id": "@type"
+        "_type": "@vocab"
+    - name: jobname
+      type: [string, cwl:Expression]
+      doc: |
+        A string or expression returning a string with the preferred name for the job.
+        If it is an expression, it is evaluated after the input object has been completely determined.

cwltool/main.py

@@ -664,12 +664,14 @@ def setup_schema(
         use_custom_schema("v1.2.0-dev1", "http://commonwl.org/cwltool", ext11)
         use_custom_schema("v1.2.0-dev2", "http://commonwl.org/cwltool", ext11)
         use_custom_schema("v1.2.0-dev3", "http://commonwl.org/cwltool", ext11)
+        use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext11)
     else:
         use_standard_schema("v1.0")
         use_standard_schema("v1.1")
         use_standard_schema("v1.2.0-dev1")
         use_standard_schema("v1.2.0-dev2")
         use_standard_schema("v1.2.0-dev3")
+        use_standard_schema("v1.2")
 
 
 class ProvLogFormatter(logging.Formatter):

cwltool/process.py

@@ -119,6 +119,7 @@ def filter(self, record: logging.LogRecord) -> bool:
     "http://commonwl.org/cwltool#NetworkAccess",
     "http://commonwl.org/cwltool#LoadListingRequirement",
     "http://commonwl.org/cwltool#InplaceUpdateRequirement",
+    "http://commonwl.org/cwltool#StepName",
 ]
 
 cwl_files = (

cwltool/workflow_job.py

@@ -69,7 +69,17 @@ def job(
     ) -> JobsGeneratorType:
         runtimeContext = runtimeContext.copy()
         runtimeContext.part_of = self.name
-        runtimeContext.name = shortname(self.id)
+
+        jobnameReq, is_required = self.step.get_requirement(
+            "http://commonwl.org/cwltool#JobName"
+        )
+        if jobnameReq is not None:
+            vfinputs = {shortname(k): v for k, v in joborder.items()}
+            runtimeContext.name = expression.do_eval(
+                jobnameReq["jobname"], vfinputs, self.step.requirements, None, None, {}
+            )
+        else:
+            runtimeContext.name = shortname(self.id)
 
         _logger.info("[%s] start", self.name)
 

tests/echo_no_output.cwl

@@ -0,0 +1,9 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  text:
+    type: string
+    inputBinding: {}
+outputs: []
+baseCommand: echo

tests/scatter-echo-wf.cwl

@@ -0,0 +1,26 @@
+#!/usr/bin/env cwl-runner
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"
+cwlVersion: v1.1
+class: Workflow
+requirements:
+  ScatterFeatureRequirement: {}
+  InlineJavascriptRequirement: {}
+  StepInputExpressionRequirement: {}
+
+inputs:
+  texts:
+    type: string[]
+
+outputs: []
+
+steps:
+  echo:
+    run: echo_no_output.cwl
+    scatter: text
+    hints:
+      cwltool:JobName:
+        jobname: $("test_" + inputs.text.split('.')[0])
+    in:
+      text: texts
+    out: []

tests/scatter-echo-wf.yml

@@ -0,0 +1 @@
+texts: ["a.vcf", "b.vcf", "c.vcf"]

tests/test_ext.py

@@ -295,3 +295,23 @@ def test_warn_large_inputs() -> None:
         )
     finally:
         cwltool.process.FILE_COUNT_WARNING = was
+
+
+def test_jobname() -> None:
+    """Test JobName requirement."""
+    stream = StringIO()
+
+    main(
+        [
+            "--enable-ext",
+            get_data("tests/scatter-echo-wf.cwl"),
+            get_data("tests/scatter-echo-wf.yml"),
+        ],
+        stderr=stream,
+    )
+
+    assert (
+        "test_a" in stream.getvalue()
+        and "test_b" in stream.getvalue()
+        and "test_c" in stream.getvalue()
+    )