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TST: study associations endpoint test
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‎qiita_pet/test/rest/test_study_associations.py‎

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# -----------------------------------------------------------------------------
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# Copyright (c) 2014--, The Qiita Development Team.
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#
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# Distributed under the terms of the BSD 3-clause License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# -----------------------------------------------------------------------------
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from unittest import main
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from tornado.escape import json_decode
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from qiita_db.study import Study
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from qiita_pet.test.rest.test_base import RESTHandlerTestCase
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class StudyAssociationTests(RESTHandlerTestCase):
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def test_get_valid(self):
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IGNORE = IGNORE
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exp = {'study': 1,
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'prep_templates': [{'prep_id': 1,
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'prep_filepath': IGNORE,
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'prep_datatype': '18S',
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'prep_human_filtering': 'The greatest human filtering method',
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'prep_artifacts': [{'artifact_id': 1,
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'artifact_parent_ids': [1],
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'artifact_basal_id': 1,
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'artifact_processing_id': None,
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'artifact_processing_name': None,
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'artifact_processing_arguments': None,
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'artifact_filepaths': [{'artifact_filepath_id': 1,
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'artifact_filepath': IGNORE,
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'artifact_filepath_type': 'raw_forward_seqs'},
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{'artifact_filepath_id': 2,
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'artifact_filepath': IGNORE,
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'artifact_filepath_type': 'raw_barcodes'}]},
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{'artifact_id': 2,
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'artifact_parent_ids': None,
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'artifact_basal_id': 1,
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'artifact_processing_id': 1,
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'artifact_processing_name': 'Split libraries FASTQ',
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'artifact_processing_arguments': {'input_data': '1',
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'max_bad_run_length': '3',
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'min_per_read_length_fraction': '0.75',
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'sequence_max_n': '0',
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'rev_comp_barcode': 'False',
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'rev_comp_mapping_barcodes': 'False',
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'rev_comp': 'False',
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'phred_quality_threshold': '3',
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'barcode_type': 'golay_12',
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'max_barcode_errors': '1.5',
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'phred_offset': 'auto'},
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'artifact_filepaths': [{'artifact_filepath_id': 3,
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'artifact_filepath': IGNORE,
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'artifact_filepath_type': 'preprocessed_fasta'},
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{'artifact_filepath': IGNORE,
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'artifact_filepath_id': 4,
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'artifact_filepath_type': 'preprocessed_fastq'},
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{'artifact_filepath': IGNORE,
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'artifact_filepath_id': 5,
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'artifact_filepath_type': 'preprocessed_demux'}]},
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{'artifact_id': 3,
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'artifact_parent_ids': [1],
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'artifact_basal_id': 1,
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'artifact_processing_id': 1,
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'artifact_processing_name': 'Split libraries FASTQ',
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'artifact_processing_arguments': {'input_data': '1',
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'max_bad_run_length': '3',
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'min_per_read_length_fraction': '0.75',
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'sequence_max_n': '0',
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'rev_comp_barcode': 'False',
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'rev_comp_mapping_barcodes': 'False',
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'rev_comp': 'False',
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'phred_quality_threshold': '3',
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'barcode_type': 'golay_12',
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'max_barcode_errors': '1.5',
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'phred_offset': 'auto'},
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'artifact_filepaths': []},
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{'artifact_id': 4,
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'artifact_parent_ids': [2],
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'artifact_basal_id': 1,
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'artifact_processing_id': 3,
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'artifact_processing_name': 'Pick closed-reference OTUs',
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'artifact_processing_arguments': {'input_data': '2',
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'reference': '1',
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'sortmerna_e_value': '1',
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'sortmerna_max_pos': '10000',
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'similarity': '0.97',
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'sortmerna_coverage': '0.97',
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'threads': '1'},
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'artifact_filepaths': [{'artifact_filepath_id': 9,
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'artifact_filepath': IGNORE,
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'artifact_filepath_type': 'biom'}]},
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{'artifact_id': 5,
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'artifact_parent_ids': [2],
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'artifact_basal_id': 1,
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'artifact_processing_id': 3,
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'artifact_processing_name': 'Pick closed-reference OTUs',
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'artifact_processing_arguments': {'input_data': '2',
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'reference': '1',
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'sortmerna_e_value': '1',
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'sortmerna_max_pos': '10000',
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'similarity': '0.97',
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'sortmerna_coverage': '0.97',
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'threads': '1'},
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'artifact_filepaths': [{'artifact_filepath_id': 9,
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'artifact_filepath': IGNORE,
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'artifact_filepath_type': 'biom'}]},
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{'artifact_id': 6,
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'artifact_parent_ids': [2],
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'artifact_basal_id': 1,
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'artifact_processing_id': 3,
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'artifact_processing_name': 'Pick closed-reference OTUs',
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'artifact_processing_arguments': {'input_data': '2',
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'reference': '2',
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'sortmerna_e_value': '1',
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'sortmerna_max_pos': '10000',
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'similarity': '0.97',
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'sortmerna_coverage': '0.97',
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'threads': '1'},
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'artifact_filepaths': [{'artifact_filepath_id': 12,
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'artifact_filepath': IGNORE,
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'artifact_filepath_type': 'biom'}]}]},
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{'prep_id': 2,
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'prep_filepath': IGNORE,
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'prep_datatype': '18S',
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'prep_human_filtering': None,
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'prep_artifacts': [{'artifact_id': 7,
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'artifact_parent_ids': [],
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'artifact_basal_id': 7,
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'artifact_processing_id': None,
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'artifact_processing_name': None,
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'artifact_processing_arguments': None,
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'artifact_filepaths': [{'artifact_filepath_id': 22,
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'artifact_filepath': IGNORE,
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'artifact_filepath_type': 'biom'}]}]}]}
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response = self.get('/api/v1/study-association/1', headers=self.headers)
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self.assertEqual(response.code, 200)
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obs = json_decode(response.body)
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self.assertEqual(obs, exp)
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def test_get_invalid(self):
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response = self.get('/api/v1/study-association/0', headers=self.headers)
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self.assertEqual(response.code, 404)
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self.assertEqual(json_decode(response.body),
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{'message': 'Study not found'})
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if __name__ == '__main__':
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main()

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