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rm artifacts from parameters listing #2374

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Merged
merged 2 commits into from
Oct 24, 2017
Merged

rm artifacts from parameters listing #2374

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7df64f3
rm artifacts from parameters listing
antgonza Oct 24, 2017
18bd7b6
fix flake8
antgonza Oct 24, 2017
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2 changes: 1 addition & 1 deletion qiita_db/test/test_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -931,7 +931,7 @@ def test_get_artifacts_information(self):
'data_type': '18S', 'prep_samples': 27,
'parameters': {
'reference': 1, 'similarity': 0.97, 'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000, 'input_data': 2, 'threads': 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,
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24 changes: 19 additions & 5 deletions qiita_db/util.py
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Expand Up @@ -1513,8 +1513,14 @@ def get_artifacts_information(artifact_ids, only_biom=True):
"""

sql_params = """SELECT default_parameter_set_id, command_id,
parameter_set_name, parameter_set AS param_set
FROM qiita.default_parameter_set"""
parameter_set_name, parameter_set AS param_set,
array_agg(parameter_name)
FROM qiita.default_parameter_set
LEFT JOIN qiita.command_parameter
USING (command_id)
WHERE parameter_type = 'artifact'
GROUP BY default_parameter_set_id, command_id,
parameter_set_name"""

sql_ts = """SELECT DISTINCT target_subfragment FROM qiita.prep_%s"""

Expand All @@ -1526,8 +1532,9 @@ def get_artifacts_information(artifact_ids, only_biom=True):
# to have a huge growth in the near future
qdb.sql_connection.TRN.add(sql_params)
params = defaultdict(list)
for _, cid, n, p in qdb.sql_connection.TRN.execute_fetchindex():
params[cid].append((n, list(p.iteritems())))
for row in qdb.sql_connection.TRN.execute_fetchindex():
_, cid, n, param, aparam = row
params[cid].append((n, list(param.iteritems()), aparam))

# now let's get the actual artifacts
ts = {}
Expand All @@ -1549,14 +1556,21 @@ def get_artifacts_information(artifact_ids, only_biom=True):
# the name of the parameter set
pparams = sorted(
[(pn, len([vv for vv in v if vv in pparams]))
for pn, v in params[pcid]], key=lambda x: x[1])[-1]
for pn, v, a in params[pcid]], key=lambda x: x[1])[-1]
pparams = 'N/A' if pparams[1] == 0 else pparams[0]
else:
pparams = 'N/A'
# - [0] due to the array_agg
aparams = aparams[0]
if aparams is None:
aparams = {}
else:
# we are gonna remove any artifacts from the parameters
# [0] cause there is only one element and [2] cause
# there is where the artifact types are stored
to_ignore = params[cid][0][2]
for ti in to_ignore:
del aparams[ti]
# - ignoring empty filepaths
if filepaths == [None]:
filepaths = []
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4 changes: 2 additions & 2 deletions qiita_pet/handlers/api_proxy/tests/test_artifact.py
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Expand Up @@ -230,7 +230,7 @@ def test_artifact_get_info(self):
'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, 'input_data': 2, 'threads': 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'],
Expand All @@ -240,7 +240,7 @@ def test_artifact_get_info(self):
'timestamp': '2012-10-02 17:30:00', 'prep_samples': 27,
'parameters': {
'reference': 1, 'similarity': 0.97, 'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000, 'input_data': 2, 'threads': 1,
'sortmerna_max_pos': 10000, 'threads': 1,
'sortmerna_coverage': 0.97}, 'name': 'BIOM'},
{'files': [], 'target_subfragment': ['V4'], 'algorithm': '',
'artifact_id': 7, 'data_type': '16S',
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2 changes: 1 addition & 1 deletion qiita_pet/handlers/study_handlers/tests/test_artifact.py
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Expand Up @@ -170,7 +170,7 @@ def test_get(self):
'algorithm': 'Pick closed-reference OTUs, QIIMEv1.9.1 | Defaults',
'parameters': {
'reference': 2, 'similarity': 0.97, 'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000, 'input_data': 2, 'threads': 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',
Expand Down