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Remove duplicate logging #57

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merged 2 commits into from
Jan 21, 2025
+23 −13
Merged

Remove duplicate logging #57

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9b67309
fix(src/cpg_flow/stage.py): removed duplicate logging
nevoodoo Jan 21, 2025
306ea7a
chore: update badges.yaml with test results and coverage
cpg-software-ci-bot Jan 21, 2025
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19 changes: 15 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,13 @@
[![semantic-release: conventional commits](https://img.shields.io/badge/semantic--release-conventional%20commits-Æ1A7DBD?logo=semantic-release&color=1E7FBF)](https://github.com/semantic-release/semantic-release)
[![GitHub license](https://img.shields.io/github/license/populationgenomics/cpg-flow.svg)](https://github.com/populationgenomics/cpg-flow/blob/main/LICENSE)

![Tests](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2FSET-362-abbreviate-multicohort-name%2Fdocs%2Fbadges.yaml&query=%24.test-badge.status&label=Tests&color=%24.test-badge.color)
![Coverage](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2FSET-362-abbreviate-multicohort-name%2Fdocs%2Fbadges.yaml&query=%24.coverage-badge.status&label=Coverage&color=%24.coverage-badge.color)
<<<<<<< Updated upstream
![Tests](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2Fremove-duplicate-logging%2Fdocs%2Fbadges.yaml&query=%24.test-badge.status&label=Tests&color=%24.test-badge.color)
![Coverage](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2Fremove-duplicate-logging%2Fdocs%2Fbadges.yaml&query=%24.coverage-badge.status&label=Coverage&color=%24.coverage-badge.color)
=======
![Tests](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2Fremove-duplicate-logging%2Fdocs%2Fbadges.yaml&query=%24.test-badge.status&label=Tests&color=%24.test-badge.color)
![Coverage](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2Fremove-duplicate-logging%2Fdocs%2Fbadges.yaml&query=%24.coverage-badge.status&label=Coverage&color=%24.coverage-badge.color)
>>>>>>> Stashed changes

[![Technical Debt](https://sonarqube.populationgenomics.org.au/api/project_badges/measure?project=populationgenomics_cpg-flow&metric=sqale_index&token=sqb_bd2c5ce00628492c0af714f727ef6f8e939d235c)](https://sonarqube.populationgenomics.org.au/dashboard?id=populationgenomics_cpg-flow)
[![Duplicated Lines (%)](https://sonarqube.populationgenomics.org.au/api/project_badges/measure?project=populationgenomics_cpg-flow&metric=duplicated_lines_density&token=sqb_bd2c5ce00628492c0af714f727ef6f8e939d235c)](https://sonarqube.populationgenomics.org.au/dashboard?id=populationgenomics_cpg-flow)
Expand Down Expand Up @@ -160,9 +165,15 @@ Ensure you have the necessary permissions and are authenticated with Google Clou

#### Unit Tests

![Tests](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2FSET-362-abbreviate-multicohort-name%2Fdocs%2Fbadges.yaml&query=%24.test-badge.status&label=Tests&color=%24.test-badge.color)
<<<<<<< Updated upstream
![Tests](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2Fremove-duplicate-logging%2Fdocs%2Fbadges.yaml&query=%24.test-badge.status&label=Tests&color=%24.test-badge.color)

![Coverage](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2FSET-362-abbreviate-multicohort-name%2Fdocs%2Fbadges.yaml&query=%24.coverage-badge.status&label=Coverage&color=%24.coverage-badge.color)
![Coverage](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2Fremove-duplicate-logging%2Fdocs%2Fbadges.yaml&query=%24.coverage-badge.status&label=Coverage&color=%24.coverage-badge.color)
=======
![Tests](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2Fremove-duplicate-logging%2Fdocs%2Fbadges.yaml&query=%24.test-badge.status&label=Tests&color=%24.test-badge.color)

![Coverage](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpopulationgenomics%2Fcpg-flow%2Frefs%2Fheads%2Fremove-duplicate-logging%2Fdocs%2Fbadges.yaml&query=%24.coverage-badge.status&label=Coverage&color=%24.coverage-badge.color)
>>>>>>> Stashed changes


#### E2E Test
Expand Down
2 changes: 1 addition & 1 deletion docs/badges.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@ test-badge:
status: 43 / 43 passed
color: green
coverage-badge:
status: 79.84%
status: 79.82%
color: orange
9 changes: 4 additions & 5 deletions src/cpg_flow/stage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -241,7 +241,9 @@ def _get(
f'decorator? Available: {self._outputs_by_target_by_stage}',
)
if not self._outputs_by_target_by_stage[stage.__name__].get(target.target_id):
LOGGER.error(f'Available: {self._outputs_by_target_by_stage[stage.__name__]}, trying to find {target.target_id}')
LOGGER.error(
f'Available: {self._outputs_by_target_by_stage[stage.__name__]}, trying to find {target.target_id}',
)
raise StageInputNotFoundError(
f'Not found output for {target} from stage {stage.__name__}, required for stage {self.stage.name}',
)
Expand Down Expand Up @@ -857,9 +859,8 @@ def queue_for_multicohort(
"""
output_by_target: dict[str, StageOutput | None] = dict()
# iterate directly over the datasets in this multicohort
for dataset_i, dataset in enumerate(multicohort.get_datasets()):
for dataset in multicohort.get_datasets():
action = self._get_action(dataset)
LOGGER.info(f'{self.name}: #{dataset_i + 1}/{dataset} [{action.name}]')
output_by_target[dataset.target_id] = self._queue_jobs_with_checks(
dataset,
action,
Expand Down Expand Up @@ -894,7 +895,6 @@ def queue_for_multicohort(
output_by_target: dict[str, StageOutput | None] = dict()
for cohort in multicohort.get_cohorts():
action = self._get_action(cohort)
LOGGER.info(f'{self.name}: {cohort} [{action.name}]')
output_by_target[cohort.target_id] = self._queue_jobs_with_checks(
cohort,
action,
Expand Down Expand Up @@ -932,7 +932,6 @@ def queue_for_multicohort(
"""
output_by_target: dict[str, StageOutput | None] = dict()
action = self._get_action(multicohort)
LOGGER.info(f'{self.name}: {multicohort} [{action.name}]')
output_by_target[multicohort.target_id] = self._queue_jobs_with_checks(
multicohort,
action,
Expand Down
6 changes: 3 additions & 3 deletions uv.lock
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