Load schemas before calling print_deps

Author: kinow

cwltool/main.py

@@ -1113,12 +1113,6 @@ def main(
 
             loadingContext, workflowobj, uri = fetch_document(uri, loadingContext)
 
-            if args.print_deps and loadingContext.loader:
-                printdeps(
-                    workflowobj, loadingContext.loader, stdout, args.relative_deps, uri
-                )
-                return 0
-
             loadingContext, uri = resolve_and_validate_document(
                 loadingContext,
                 workflowobj,
@@ -1127,6 +1121,12 @@ def main(
                 skip_schemas=args.skip_schemas,
             )
 
+            if args.print_deps and loadingContext.loader:
+                printdeps(
+                    workflowobj, loadingContext.loader, stdout, args.relative_deps, uri
+                )
+                return 0
+
             if loadingContext.loader is None:
                 raise Exception("Impossible code path.")
             processobj, metadata = loadingContext.loader.resolve_ref(uri)

tests/test_examples.py

@@ -586,6 +586,25 @@ def test_scandeps_defaults_with_secondaryfiles() -> None:
     ].endswith(os.path.join("tests", "wf", "indir1"))
 
 
+def test_issue_1765_print_deps_with_workflows_having_namespace_location_steps() -> None:
+    stream = StringIO()
+
+    main(
+        [
+            "--print-deps",
+            "--relative-deps=primary",
+            "--debug",
+            get_data(
+                "tests/wf/print_deps_with_workflows_having_namespace_location_steps.cwl"
+            ),
+        ],
+        stdout=stream,
+    )
+    assert json.loads(stream.getvalue())["secondaryFiles"][0]["secondaryFiles"][0][
+        "location"
+    ].endswith("EDAM_1.18.owl")
+
+
 def test_dedupe() -> None:
     not_deduped = [
         {"class": "File", "location": "file:///example/a"},

tests/wf/print_deps_with_workflows_having_namespace_location_steps.cwl

@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+# From:
+# - https://github.com/common-workflow-language/cwltool/issues/1765
+# - https://github.com/pvanheus/lukasa/blob/99e827e0125cf07621253ae081199298adf7227b/protein_evidence_mapping.cwl
+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+  contigs_fasta:
+    label: "Genomic contigs (FASTA)"
+    type: File
+    format: edam:format_1929
+outputs:
+  out:
+    type: File
+    outputSource:
+      samtools_index_contigs/sequences_with_index
+
+steps:
+  samtools_index_contigs:
+    # This step is from an external file. print_deps failed here, with a validation
+    # error message, even though --validate passed.
+    run: bio-cwl-tools:samtools/samtools_faidx.cwl
+    in:
+      sequences: contigs_fasta
+    out:
+      - sequences_with_index
+$namespaces:
+  edam: http://edamontology.org/
+  bio-cwl-tools: https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/
+$schemas:
+  - http://edamontology.org/EDAM_1.18.owl