Migrate CWL parsing from cwltool to cwl-utils #58
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #58 +/- ##
==========================================
+ Coverage 71.08% 71.11% +0.02%
==========================================
Files 88 88
Lines 11085 11131 +46
Branches 1912 1936 +24
==========================================
+ Hits 7880 7916 +36
- Misses 2753 2768 +15
+ Partials 452 447 -5 ☔ View full report in Codecov by Sentry. |
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This commit replaces the cwltool parser with the faster auto-generated parser included in cwl-utils.
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LanderOtto
approved these changes
Dec 6, 2024
streamflow/log_handler.py
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| @@ -122,5 +122,5 @@ def highlight(self, msg): | |||
| ) | |||
| defaultStreamHandler.setFormatter(formatter) | |||
| logger.addHandler(defaultStreamHandler) | |||
| logger.setLevel(logging.INFO) | |||
| logger.setLevel(logging.DEBUG) | |||
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Suggested change
| logger.setLevel(logging.DEBUG) | |
| logger.setLevel(logging.INFO) |
tests/test_build_wf.py
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| @@ -208,7 +208,7 @@ async def test_execute_step(context: StreamFlowContext): | |||
| port_target=None, | |||
| port_type="string", | |||
| cwl_element={}, | |||
| context={"hints": {}, "requirements": {}}, | |||
| context={"hints": {}, "requirements": {}, "version": "v1.2"}, | |||
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| context={"hints": {}, "requirements": {}, "version": "v1.2"}, | |
| context={"hints": {}, "requirements": {}, "version": CWL_VERSION}, |
from tests.utils.workflow import CWL_VERSION
tests/test_build_wf.py
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| @@ -350,7 +350,7 @@ async def test_workflow(context: StreamFlowContext): | |||
| port_target=None, | |||
| port_type="string", | |||
| cwl_element={}, | |||
| context={"hints": {}, "requirements": {}}, | |||
| context={"hints": {}, "requirements": {}, "version": "v1.2"}, | |||
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| context={"hints": {}, "requirements": {}, "version": "v1.2"}, | |
| context={"hints": {}, "requirements": {}, "version": CWL_VERSION}, |
tests/test_provenance.py
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| cwl_element=cwl_utils.parser.cwl_v1_2.CommandOutputParameter( | ||
| type_="string" | ||
| ), | ||
| context={"hints": {}, "requirements": {}, "version": "v1.2"}, |
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| context={"hints": {}, "requirements": {}, "version": "v1.2"}, | |
| context={"hints": {}, "requirements": {}, "version": CWL_VERSION}, |
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This commit replaces the
cwltoolparser with the faster auto-generated parser included incwl-utils. Starting from this commit,cwltoolis no more a StreamFlow requirement.