Load schemas before calling print_deps

Small modifications to other tests:
1. `baseCommand: true` is invalid CWL, and unrelated to the scandep bugs
   that are being tested
2. for the content_types test, choose a different URL to avoid
   "429 Client Error: Too Many Requests for url"

Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>

Author: kinow

cwltool/main.py

@@ -1093,10 +1093,6 @@ 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,
@@ -1112,6 +1108,10 @@ def main(
                 print(print_pack(loadingContext, uri), file=stdout)
                 return 0
 
+            if args.print_deps:
+                printdeps(workflowobj, loadingContext.loader, stdout, args.relative_deps, uri)
+                return 0
+
             if args.provenance and runtimeContext.research_obj:
                 # Can't really be combined with args.pack at same time
                 packed_workflow(runtimeContext.research_obj, print_pack(loadingContext, uri))

tests/test_content_type.py

@@ -7,7 +7,7 @@ def test_content_types(caplog: LogCaptureFixture) -> None:
     for _ in ("js_output.cwl", "js_output_workflow.cwl"):
         commands = [
             "https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/main/v1.0/v1.0/test-cwl-out2.cwl",
-            "https://github.com/common-workflow-language/common-workflow-language/blob/main/v1.0/v1.0/empty.json",
+            "https://www.cnn.com",
         ]
         error_code, _, stderr = get_main_output(commands)
 

tests/test_examples.py

@@ -575,6 +575,27 @@ 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:
+    """Test for issue 1765.
+
+    An external workflow step passed the validation, but failed to print-deps.
+    """
+    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: list[CWLObjectType] = [
         {"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

tests/wf/trick_defaults.cwl

@@ -13,4 +13,4 @@ inputs:
       class: Directory
       location: indir1
 outputs: []
-baseCommand: true
+baseCommand: []

tests/wf/trick_defaults2.cwl

@@ -11,4 +11,4 @@ inputs:
         - class: Directory
           location: indir1
 outputs: []
-baseCommand: true
+baseCommand: []