Added parsers for CWL input files (#199)

This commit adds support for parsing CWL input files with autogenerated Schema SALAD parsers, in order to obtain a coherent representation of CWL object between processfile and jobfile.
common-workflow-language · Dec 1, 2023 · 8e4ed82 · 8e4ed82
1 parent f2ac3ea
commit 8e4ed82
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Showing 18 changed files with 33,440 additions and 8,025 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -10,7 +10,9 @@ include cwl_utils/cwlNodeEngineJSConsole.js
 include cwl_utils/cwlNodeEngineWithContext.js
 include testdata/*.cwl
 include testdata/*.yaml
+include testdata/*.yml
 include testdata/*.input
+include testdata/*.json
 include testdata/*.ttl
 include testdata/*.owl
 include testdata/*.js

diff --git a/create_cwl_from_objects.py b/create_cwl_from_objects.py
@@ -9,11 +9,11 @@
 
 def main() -> None:
     """Generate a CWL object to match "cat-tool.cwl"."""
-    inputs = [cwl.CommandInputParameter(id="file1", type="File")]
+    inputs = [cwl.CommandInputParameter(id="file1", type_="File")]
     outputs = [
         cwl.CommandOutputParameter(
             id="output",
-            type="File",
+            type_="File",
             outputBinding=cwl.CommandOutputBinding(glob="output"),
         )
     ]

diff --git a/cwl_utils/cwl_v1_0_expression_refactor.py b/cwl_utils/cwl_v1_0_expression_refactor.py
diff --git a/cwl_utils/cwl_v1_1_expression_refactor.py b/cwl_utils/cwl_v1_1_expression_refactor.py
diff --git a/cwl_utils/cwl_v1_2_expression_refactor.py b/cwl_utils/cwl_v1_2_expression_refactor.py