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Patch 61 - transfer all parameters to str #2379

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merged 2 commits into from
Oct 30, 2017
Merged

Patch 61 - transfer all parameters to str #2379

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61f620a
Patch 61 - transfer all parameters to str
josenavas Oct 30, 2017
4273533
Fixing errors
josenavas Oct 30, 2017
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4 changes: 2 additions & 2 deletions qiita_db/handlers/tests/test_artifact.py
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Expand Up @@ -103,8 +103,8 @@ def test_get_artifact(self):
'prep_information': [],
'study': None,
'analysis': 1,
'processing_parameters': {'biom_table': 8, 'depth': 9000,
'subsample_multinomial': False},
'processing_parameters': {'biom_table': '8', 'depth': '9000',
'subsample_multinomial': 'False'},
'files': exp_fps}
obs = loads(obs.body)
# The timestamp is genreated at patch time, so we can't check for it
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2 changes: 2 additions & 0 deletions qiita_db/support_files/patches/61.sql
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@@ -0,0 +1,2 @@
-- October 30th, 2017
SELECT 42;
28 changes: 28 additions & 0 deletions qiita_db/support_files/patches/python_patches/61.py
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@@ -0,0 +1,28 @@
# October 30th, 2017
# A change introduced in July made all the parameters to be stored as strings
# The DB needs to be patched so all the artifacts follow this structure

from json import dumps

from qiita_db.sql_connection import TRN

with TRN:
sql = """SELECT *
FROM qiita.artifact
JOIN qiita.artifact_output_processing_job
USING (artifact_id)
WHERE command_id IS NOT NULL"""
TRN.add(sql)

sql_update_artifact = """UPDATE qiita.artifact
SET command_parameters = %s
WHERE artifact_id = %s"""
sql_update_job = """UPDATE qiita.processing_job
SET command_parameters = %s
WHERE processing_job_id = %s"""
for ainfo in TRN.execute_fetchindex():
ainfo = dict(ainfo)
params = dumps(
{k: str(v) for k, v in ainfo['command_parameters'].items()})
TRN.add(sql_update_artifact, [params, ainfo['artifact_id']])
TRN.add(sql_update_job, [params, ainfo['processing_job_id']])
24 changes: 12 additions & 12 deletions qiita_db/test/test_artifact.py
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Expand Up @@ -96,24 +96,24 @@ def test_processing_parameters(self):
obs = qdb.artifact.Artifact(2).processing_parameters
exp = qdb.software.Parameters.load(
qdb.software.Command(1),
values_dict={'max_barcode_errors': 1.5, 'sequence_max_n': 0,
'max_bad_run_length': 3, 'rev_comp': False,
'phred_quality_threshold': 3, 'input_data': 1,
'rev_comp_barcode': False,
'rev_comp_mapping_barcodes': False,
'min_per_read_length_fraction': 0.75,
values_dict={'max_barcode_errors': '1.5', 'sequence_max_n': '0',
'max_bad_run_length': '3', 'rev_comp': 'False',
'phred_quality_threshold': '3', 'input_data': '1',
'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'False',
'min_per_read_length_fraction': '0.75',
'barcode_type': 'golay_12',
'phred_offset': 'auto'})
self.assertEqual(obs, exp)
obs = qdb.artifact.Artifact(3).processing_parameters
exp = qdb.software.Parameters.load(
qdb.software.Command(1),
values_dict={'max_barcode_errors': 1.5, 'sequence_max_n': 0,
'max_bad_run_length': 3, 'rev_comp': False,
'phred_quality_threshold': 3, 'input_data': 1,
'rev_comp_barcode': False,
'rev_comp_mapping_barcodes': True,
'min_per_read_length_fraction': 0.75,
values_dict={'max_barcode_errors': '1.5', 'sequence_max_n': '0',
'max_bad_run_length': '3', 'rev_comp': 'False',
'phred_quality_threshold': '3', 'input_data': '1',
'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'True',
'min_per_read_length_fraction': '0.75',
'barcode_type': 'golay_12',
'phred_offset': 'auto'})
self.assertEqual(obs, exp)
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6 changes: 3 additions & 3 deletions qiita_db/test/test_util.py
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Expand Up @@ -930,9 +930,9 @@ def test_get_artifacts_information(self):
'Pick closed-reference OTUs, QIIMEv1.9.1 | Defaults'),
'data_type': '18S', 'prep_samples': 27,
'parameters': {
'reference': 1, 'similarity': 0.97, 'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000, 'threads': 1,
'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
'reference': '1', 'similarity': '0.97',
'sortmerna_e_value': '1', 'sortmerna_max_pos': '10000',
'threads': '1', 'sortmerna_coverage': '0.97'}, 'name': 'BIOM'},
{'files': [], 'target_subfragment': ['V4'], 'algorithm': '',
'artifact_id': 7, 'data_type': '16S', 'prep_samples': 27,
'parameters': {}, 'name': 'BIOM'},
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12 changes: 6 additions & 6 deletions qiita_pet/handlers/api_proxy/tests/test_artifact.py
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Expand Up @@ -229,19 +229,19 @@ def test_artifact_get_info(self):
'artifact_id': 6, 'data_type': '16S',
'timestamp': '2012-10-02 17:30:00', 'prep_samples': 27,
'parameters': {
'reference': 2, 'similarity': 0.97, u'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000, 'threads': 1,
'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
'reference': '2', 'similarity': '0.97',
'sortmerna_e_value': '1', 'sortmerna_max_pos': '10000',
'threads': '1', 'sortmerna_coverage': '0.97'}, 'name': 'BIOM'},
{'files': ['1_study_1001_closed_reference_otu_table.biom'],
'target_subfragment': ['V4'],
'algorithm': (
'Pick closed-reference OTUs, QIIMEv1.9.1 | Defaults'),
'artifact_id': 5, 'data_type': '18S',
'timestamp': '2012-10-02 17:30:00', 'prep_samples': 27,
'parameters': {
'reference': 1, 'similarity': 0.97, 'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000, 'threads': 1,
'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
'reference': '1', 'similarity': '0.97',
'sortmerna_e_value': '1', 'sortmerna_max_pos': '10000',
'threads': '1', 'sortmerna_coverage': '0.97'}, 'name': 'BIOM'},
{'files': [], 'target_subfragment': ['V4'], 'algorithm': '',
'artifact_id': 7, 'data_type': '16S',
'timestamp': '2012-10-02 17:30:00', 'prep_samples': 27,
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12 changes: 6 additions & 6 deletions qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py
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Expand Up @@ -240,12 +240,12 @@ def test_artifact_summary_get_request(self):
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'processing_parameters': {
'max_barcode_errors': 1.5, 'sequence_max_n': 0,
'max_bad_run_length': 3, 'phred_offset': u'auto',
'rev_comp': False, 'phred_quality_threshold': 3,
'input_data': 1, 'rev_comp_barcode': False,
'rev_comp_mapping_barcodes': False,
'min_per_read_length_fraction': 0.75,
'max_barcode_errors': '1.5', 'sequence_max_n': '0',
'max_bad_run_length': '3', 'phred_offset': u'auto',
'rev_comp': 'False', 'phred_quality_threshold': '3',
'input_data': '1', 'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'False',
'min_per_read_length_fraction': '0.75',
'barcode_type': u'golay_12'},
'files': exp_files,
'is_from_analysis': False,
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6 changes: 3 additions & 3 deletions qiita_pet/handlers/study_handlers/tests/test_artifact.py
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Expand Up @@ -169,9 +169,9 @@ def test_get(self):
'prep_samples': 27,
'algorithm': 'Pick closed-reference OTUs, QIIMEv1.9.1 | Defaults',
'parameters': {
'reference': 2, 'similarity': 0.97, 'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000, 'threads': 1,
'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
'reference': '2', 'similarity': '0.97',
'sortmerna_e_value': '1', 'sortmerna_max_pos': '10000',
'threads': '1', 'sortmerna_coverage': '0.97'}, 'name': 'BIOM'},
{'files': [], 'target_subfragment': ['V4'], 'artifact_id': 7,
'data_type': '16S', 'timestamp': '2012-10-02 17:30:00',
'prep_samples': 27, 'algorithm': '', 'parameters': {},
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