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Updated get_project_info() #147

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merged 1 commit into from
Jul 11, 2024
Merged

Updated get_project_info() #147

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6 changes: 5 additions & 1 deletion sequence_processing_pipeline/Pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -723,10 +723,14 @@ def get_project_info(self, short_names=False):
for res in bioinformatics.to_dict('records'):
p_name, q_id = self._parse_project_name(res['Sample_Project'],
short_names)

# parsed SampleSheet() objects should now contain only
# boolean values in contains_replicates column.

contains_replicates = False

if 'contains_replicates' in res:
if res['contains_replicates'] == 'True':
if res['contains_replicates'] is True:
contains_replicates = True

results.append({'project_name': p_name,
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11 changes: 11 additions & 0 deletions sequence_processing_pipeline/tests/test_Pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1558,6 +1558,17 @@ def test_get_project_info(self):

self.assertEqual(sorted(obs_project_names), sorted(exp_project_names))

pipeline = Pipeline(self.good_config_file, self.good_run_id,
self.good_sheet_w_replicates, None,
self.output_file_path, self.qiita_id,
Pipeline.METAGENOMIC_PTYPE)

obs_proj_info = pipeline.get_project_info()

# assert value is boolean type True, even though the method no longer
# silently converts string values to bool.
self.assertTrue(obs_proj_info[0]['contains_replicates'])

def test_configuration_profiles(self):
pipeline = Pipeline(self.good_config_file, self.good_run_id,
self.good_sample_sheet_path, None,
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