DO NOT MERGE: Migrate CWL parsing from cwltool to cwl-utils #58

GlassOfWhiskey · 2023-01-31T10:07:47Z

This commit replaces the cwltool parser with the faster auto-generated parser included in cwl-utils.

codecov-commenter · 2023-01-31T17:57:15Z

Codecov Report

Attention: 38 lines in your changes are missing coverage. Please review.

Comparison is base (33da6e6) 65.93% compared to head (1ca11fd) 64.96%.
Report is 1 commits behind head on master.

Files	Patch %	Lines
streamflow/cwl/translator.py	86.49%	20 Missing and 17 partials ⚠️
streamflow/cwl/utils.py	50.00%	1 Missing ⚠️

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #58      +/-   ##
==========================================
- Coverage   65.93%   64.96%   -0.98%     
==========================================
  Files          82       82              
  Lines       10234    10303      +69     
  Branches     2419     2442      +23     
==========================================
- Hits         6748     6693      -55     
- Misses       3052     3167     +115     
- Partials      434      443       +9

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

streamflow/cwl/translator.py

-            current_context["requirements"][requirement["class"]] = requirement
+        for hint in cwl_element.hints or []:
+            if not isinstance(hint, MutableMapping):
+                current_context["hints"][hint.class_] = hint


streamflow/cwl/translator.py

+            if not isinstance(hint, MutableMapping):
+                current_context["hints"][hint.class_] = hint
+        for requirement in cwl_element.requirements or []:
+            current_context["requirements"][requirement.class_] = requirement


streamflow/cwl/translator.py

+                    )
+                else:
+                    for requirement in self.cwl_inputs[req_string]:
+                        current_context["requirements"][


streamflow/cwl/translator.py

        ),
        context: MutableMapping[str, Any],
        name_prefix: str,
        cwl_name_prefix: str,
    ):
+        context["elements"][cwl_element.id] = cwl_element


streamflow/cwl/translator.py

+            cwl_utils.parser.utils.static_checker(cwl_element)
+        except ValidationException as ve:
+            raise WorkflowDefinitionException from ve
+        context["elements"][cwl_element.id] = cwl_element


streamflow/cwl/translator.py

        context: MutableMapping[str, Any],
        name_prefix: str,
        cwl_name_prefix: str,
    ):
        # Process content
+        context["elements"][cwl_element.id] = cwl_element


streamflow/cwl/translator.py

-            context["requirements"][requirement["class"]] = requirement
+        for hint in cwl_element.hints or []:
+            if not isinstance(hint, MutableMapping):
+                context["hints"][hint.class_] = hint


streamflow/cwl/translator.py

+            if not isinstance(hint, MutableMapping):
+                context["hints"][hint.class_] = hint
+        for requirement in cwl_element.requirements or []:
+            context["requirements"][requirement.class_] = requirement


This commit replaces the cwltool parser with the faster auto-generated parser included in cwl-utils.

GlassOfWhiskey force-pushed the feature/cwl-utils branch 4 times, most recently from e38eb72 to 461df47 Compare January 31, 2023 17:47

GlassOfWhiskey force-pushed the feature/cwl-utils branch 2 times, most recently from a656498 to 025ba47 Compare February 1, 2023 20:00

GlassOfWhiskey changed the title ~~Migrate CWL parsing from cwltool to cwl-utils~~ DO NOT MERGE: Migrate CWL parsing from cwltool to cwl-utils Feb 1, 2023

GlassOfWhiskey force-pushed the feature/cwl-utils branch 9 times, most recently from dd2d48d to 2502ef0 Compare February 12, 2023 15:28

GlassOfWhiskey force-pushed the feature/cwl-utils branch from 2502ef0 to 8ce2b7c Compare February 17, 2023 15:15

GlassOfWhiskey force-pushed the feature/cwl-utils branch 6 times, most recently from 0899281 to 2eadb6d Compare March 4, 2023 15:49

GlassOfWhiskey force-pushed the master branch 2 times, most recently from 2a84f23 to fe6fd4a Compare March 13, 2023 13:44

GlassOfWhiskey force-pushed the feature/cwl-utils branch 3 times, most recently from 32083a0 to 8acb8ad Compare June 18, 2023 19:26

GlassOfWhiskey force-pushed the feature/cwl-utils branch from 8acb8ad to 28acb03 Compare November 3, 2023 08:23

GlassOfWhiskey force-pushed the feature/cwl-utils branch 2 times, most recently from db57c6b to e7c7f32 Compare November 3, 2023 08:46

github-advanced-security bot found potential problems Nov 3, 2023

View reviewed changes

GlassOfWhiskey force-pushed the feature/cwl-utils branch 3 times, most recently from 0a1b138 to 087edd1 Compare November 15, 2023 23:39

GlassOfWhiskey force-pushed the feature/cwl-utils branch 4 times, most recently from d95f92b to dc7094f Compare December 3, 2023 23:38

GlassOfWhiskey added 2 commits December 9, 2023 00:23

Migrate CWL parsing from cwltool to cwl-utils

f668914

This commit replaces the cwltool parser with the faster auto-generated parser included in cwl-utils.

Moved type to type_ for CWL objects

c35088b

GlassOfWhiskey force-pushed the feature/cwl-utils branch 10 times, most recently from 0a8efe0 to 1d892f8 Compare December 9, 2023 15:09

Substitute getattr with class-aware functions

1ca11fd

GlassOfWhiskey force-pushed the feature/cwl-utils branch from 1d892f8 to 1ca11fd Compare December 9, 2023 15:19

GlassOfWhiskey force-pushed the master branch from d1735c2 to e9bb106 Compare February 7, 2024 14:27

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

DO NOT MERGE: Migrate CWL parsing from cwltool to cwl-utils #58

DO NOT MERGE: Migrate CWL parsing from cwltool to cwl-utils #58

GlassOfWhiskey commented Jan 31, 2023

codecov-commenter commented Jan 31, 2023 •

edited

DO NOT MERGE: Migrate CWL parsing from cwltool to cwl-utils #58

Are you sure you want to change the base?

DO NOT MERGE: Migrate CWL parsing from cwltool to cwl-utils #58

Conversation

GlassOfWhiskey commented Jan 31, 2023

codecov-commenter commented Jan 31, 2023 • edited

Codecov Report

codecov-commenter commented Jan 31, 2023 •

edited