extend validation to the inputs of the top level proces

Author: mr-c

cwltool/context.py

@@ -2,6 +2,7 @@
 import copy
 import os
 import shutil
+import sys
 import tempfile
 import threading
 from typing import (
@@ -197,6 +198,8 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
         self.mpi_config: MpiConfig = MpiConfig()
         self.default_stdout: Optional[Union[IO[bytes], TextIO]] = None
         self.default_stderr: Optional[Union[IO[bytes], TextIO]] = None
+        self.validate_only: bool = False
+        self.validate_stdout: Union[IO[bytes], TextIO, IO[str]] = sys.stdout
         super().__init__(kwargs)
         if self.tmp_outdir_prefix == "":
             self.tmp_outdir_prefix = self.tmpdir_prefix

cwltool/executors.py

@@ -143,6 +143,8 @@ def check_for_abstract_op(tool: CWLObjectType) -> None:
                 process.requirements.append(req)
 
         self.run_jobs(process, job_order_object, logger, runtime_context)
+        if runtime_context.validate_only is True:
+            return (None, "ValidationSuccess")
 
         if self.final_output and self.final_output[0] is not None and finaloutdir is not None:
             self.final_output[0] = relocateOutputs(
@@ -238,6 +240,16 @@ def run_jobs(
                             process_run_id = prov_obj.record_process_start(process, job)
                             runtime_context = runtime_context.copy()
                         runtime_context.process_run_id = process_run_id
+                    if runtime_context.validate_only is True:
+                        if isinstance(job, WorkflowJob):
+                            name = job.tool.lc.filename
+                        else:
+                            name = getattr(job, "name", str(job))
+                        print(
+                            f"{name} is valid CWL. No errors detected in the inputs.",
+                            file=runtime_context.validate_stdout,
+                        )
+                        return
                     job.run(runtime_context)
                 else:
                     logger.error("Workflow cannot make any more progress.")

cwltool/main.py

@@ -1134,7 +1134,7 @@ def main(
                 make_template(tool, stdout)
                 return 0
 
-            if args.validate:
+            if len(args.job_order) == 0 and args.validate:
                 print(f"{args.workflow} is valid CWL.", file=stdout)
                 return 0
 
@@ -1294,10 +1294,14 @@ def main(
                     use_biocontainers=args.beta_use_biocontainers,
                     container_image_cache_path=args.beta_dependencies_directory,
                 )
+            runtimeContext.validate_only = args.validate
+            runtimeContext.validate_stdout = stdout
 
             (out, status) = real_executor(
                 tool, initialized_job_order_object, runtimeContext, logger=_logger
             )
+            if runtimeContext.validate_only is True:
+                return 0
 
             if out is not None:
                 if runtimeContext.research_obj is not None:

tests/test_validate.py

@@ -1,5 +1,5 @@
 """Tests --validation."""
-
+import re
 
 from .util import get_data, get_main_output
 
@@ -14,3 +14,41 @@ def test_validate_graph_with_no_default() -> None:
     assert "packed_no_main.cwl#cat is valid CWL" in stdout
     assert "packed_no_main.cwl#collision is valid CWL" in stdout
     assert "tests/wf/packed_no_main.cwl is valid CWL" in stdout
+
+
+def test_validate_with_valid_input_object() -> None:
+    """Ensure that --validate with a valid input object."""
+    exit_code, stdout, stderr = get_main_output(
+        [
+            "--validate",
+            get_data("tests/wf/1st-workflow.cwl"),
+            "--inp",
+            get_data("tests/wf/1st-workflow.cwl"),
+            "--ex",
+            "FOO",
+        ]
+    )
+    assert exit_code == 0
+    assert "tests/wf/1st-workflow.cwl is valid CWL. No errors detected in the inputs." in stdout
+
+
+def test_validate_with_invalid_input_object() -> None:
+    """Ensure that --validate with an invalid input object."""
+    exit_code, stdout, stderr = get_main_output(
+        [
+            "--validate",
+            get_data("tests/wf/1st-workflow.cwl"),
+            get_data("tests/wf/1st-workflow_bad_inputs.yml"),
+        ]
+    )
+    assert exit_code == 1
+    stderr = re.sub(r"\s\s+", " ", stderr)
+    assert "Invalid job input record" in stderr
+    assert (
+        "tests/wf/1st-workflow_bad_inputs.yml:2:1: * the 'ex' field is not "
+        "valid because the value is not string" in stderr
+    )
+    assert (
+        "tests/wf/1st-workflow_bad_inputs.yml:1:1: * the 'inp' field is not "
+        "valid because is not a dict. Expected a File object." in stderr
+    )

tests/wf/1st-workflow_bad_inputs.yml

@@ -0,0 +1,4 @@
+inp: 42
+ex:
+  class: File
+  path: 1st-workflow.cwl