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Merged
merged 3 commits into from
Jul 10, 2017
Merged

WIP: using new info to merge bioms #2167

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daa45c8
using new info to merge bioms
antgonza Jul 10, 2017
127462e
fix errors
antgonza Jul 10, 2017
c9cf2e0
flake8
antgonza Jul 10, 2017
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62 changes: 35 additions & 27 deletions qiita_db/analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -771,6 +771,9 @@ def build_files(self, merge_duplicated_sample_ids):
# make testing much harder as we will need to have analyses at
# different stages and possible errors.
samples = self.samples
# gettin the info of all the artifacts to save SQL time
bioms_info = qdb.util.get_artifacts_bioms_information(
samples.keys())

# figuring out if we are going to have duplicated samples, again
# doing it here cause it's computational cheaper
Expand All @@ -780,20 +783,32 @@ def build_files(self, merge_duplicated_sample_ids):
# are going to create
rename_dup_samples = False
grouped_samples = {}
for k, v in viewitems(samples):
a = qdb.artifact.Artifact(k)
p = a.processing_parameters
if p is not None and p.command is not None:
ref = (str(p.values['reference'])
if 'reference' in p.values else 'na')
cid = str(p.command.id)
for aid, asamples in viewitems(samples):
# find the artifat info, [0] there should be only 1 info
ainfo = [bi for bi in bioms_info
if bi['artifact_id'] == aid][0]

data_type = ainfo['data_type']
algorithm = ainfo['algorithm']
target_subfragment = ainfo['target_subfragment']
parameters = ['%s: %s' % (k, v)
for k, v in viewitems(ainfo['parameters'])]
files = ainfo['files']

l = "%s || %s || %s || %s" % (
data_type, algorithm, ','.join(target_subfragment),
', '.join(parameters))
# deblur special case, we need to account for file name
if 'deblur-workflow' in algorithm:
# [0] there is always just one biom
l += " || %s" % [f for f in files
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In other formatting instances the list is joined (''.join(some_list)), any reason why you are not joining this list?

if f.endswith('.biom')][0]
else:
ref = 'na'
cid = 'na'
l = "%s.%s.%s" % (a.data_type, ref, cid)
l += " ||"

if l not in grouped_samples:
grouped_samples[l] = []
grouped_samples[l].append((k, v))
grouped_samples[l].append((aid, asamples))
# 2. if rename_dup_samples is still False, make sure that we don't
# need to rename samples by checking that there are not
# duplicated samples per group
Expand Down Expand Up @@ -826,7 +841,9 @@ def _build_biom_tables(self, grouped_samples, rename_dup_samples=False):

biom_files = []
for label, tables in viewitems(grouped_samples):
data_type, reference_id, command_id = label.split('.')
data_type, algorithm, target_subfragment, \
parameters, files = [l.strip() for l in label.split('||')]

new_table = None
artifact_ids = []
for aid, samples in tables:
Expand Down Expand Up @@ -873,25 +890,16 @@ def _build_biom_tables(self, grouped_samples, rename_dup_samples=False):
raise RuntimeError("All samples filtered out from "
"analysis due to rarefaction level")

# add the metadata column for study the samples come from,
# this is useful in case the user download the bioms
study_md = {'study': artifact.study.title,
'artifact_ids': ', '.join(artifact_ids),
'reference_id': reference_id,
'command_id': command_id}
samples_md = {sid: study_md for sid in new_table.ids()}
new_table.add_metadata(samples_md, axis='sample')

# write out the file
fn = "%d_analysis_dt-%s_r-%s_c-%s.biom" % (
self._id, data_type, reference_id, command_id)
info = "%s_%s_%s_%s_%s" % (
data_type, algorithm, target_subfragment, parameters,
files)
fn = "%d_analysis_%s.biom" % (self._id, info)
biom_fp = join(base_fp, fn)
with biom_open(biom_fp, 'w') as f:
new_table.to_hdf5(
f, "Generated by Qiita. Analysis %d Datatype %s "
"Reference %s Command %s" % (self._id, data_type,
reference_id, command_id))

f, "Generated by Qiita, analysis id: %d, info: %s" % (
self._id, label))
biom_files.append((data_type, biom_fp))
return biom_files

Expand Down
35 changes: 17 additions & 18 deletions qiita_db/test/test_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def setUp(self):
self.map_exp_fp = self.get_fp("1_analysis_mapping_exp.txt")

from glob import glob
conf_files = glob(join(qiita_config.plugin_dir, "*.conf"))
conf_files = glob(join(qiita_config.plugin_dir, "BIOM*.conf"))
for i, fp in enumerate(conf_files):
qdb.software.Software.from_file(fp, update=True)

Expand Down Expand Up @@ -413,10 +413,13 @@ def test_build_mapping_file_duplicated_samples_merge(self):

def test_build_biom_tables(self):
analysis = self._create_analyses_with_samples()
grouped_samples = {'18S.1.3': [(
4, ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'])]}
grouped_samples = {
'18S || algorithm || target_subfragment || parameters '
'|| files': [(4, ['1.SKB8.640193', '1.SKD8.640184',
'1.SKB7.640196'])]}
obs_bioms = analysis._build_biom_tables(grouped_samples)
biom_fp = self.get_fp("%s_analysis_dt-18S_r-1_c-3.biom" % analysis.id)
biom_fp = self.get_fp("%s_analysis_18S_algorithm_target_subfra"
"gment_parameters_files.biom" % analysis.id)
obs = [(a, basename(b)) for a, b in obs_bioms]
self.assertEqual(obs, [('18S', basename(biom_fp))])

Expand All @@ -425,22 +428,16 @@ def test_build_biom_tables(self):
exp = {'1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'}
self.assertEqual(obs, exp)

obs = table.metadata('1.SKB8.640193')
exp = {'study':
'Identification of the Microbiomes for Cannabis Soils',
'artifact_ids': '4',
'reference_id': '1',
'command_id': '3'}
self.assertEqual(obs, exp)

def test_build_biom_tables_duplicated_samples_not_merge(self):
analysis = self._create_analyses_with_samples()
grouped_samples = {'18S.1.3': [
(4, ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']),
(5, ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'])]}
grouped_samples = {
'18S || algorithm || target_subfragment || parameters || files': [
(4, ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']),
(5, ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'])]}
obs_bioms = analysis._build_biom_tables(grouped_samples, True)
obs = [(a, basename(b)) for a, b in obs_bioms]
biom_fp = "%s_analysis_dt-18S_r-1_c-3.biom" % analysis.id
biom_fp = ("%s_analysis_18S_algorithm_target_subfragment_"
"parameters_files.biom" % analysis.id)
self.assertEqual(obs, [('18S', biom_fp)])

table = load_table(obs_bioms[0][1])
Expand All @@ -450,8 +447,10 @@ def test_build_biom_tables_duplicated_samples_not_merge(self):
self.assertItemsEqual(obs, exp)

def test_build_biom_tables_raise_error_due_to_sample_selection(self):
grouped_samples = {'18S.1.3': [
(4, ['sample_name_1', 'sample_name_2', 'sample_name_3'])]}
grouped_samples = {
'18S || algorithm || target_subfragment || parameters '
'|| files': [(4, ['sample_name_1', 'sample_name_2',
'sample_name_3'])]}
with self.assertRaises(RuntimeError):
self.analysis._build_biom_tables(grouped_samples)

Expand Down