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fix generate_biom_and_metadata_release #2072

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Merged
merged 2 commits into from
Feb 7, 2017
Merged

fix generate_biom_and_metadata_release #2072

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4a8304d
fix generate_biom_and_metadata_release
antgonza Feb 6, 2017
13c4b2b
addressing @ElDeveloper comment
antgonza Feb 6, 2017
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11 changes: 3 additions & 8 deletions qiita_db/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1574,14 +1574,11 @@ def generate_biom_and_metadata_release(study_status='public'):
working_dir = qiita_config.working_dir
portal = qiita_config.portal
bdir = qdb.util.get_db_files_base_dir()
bdir_len = len(bdir) + 1

data = []
for s in studies:
# [0] latest is first, [1] only getting the filepath
sample_fp = s.sample_template.get_filepaths()[0][1]
if sample_fp.startswith(bdir):
sample_fp = sample_fp[bdir_len:]
sample_fp = relpath(s.sample_template.get_filepaths()[0][1], bdir)

for a in s.artifacts(artifact_type='BIOM'):
if a.processing_parameters is None:
Expand All @@ -1605,16 +1602,14 @@ def generate_biom_and_metadata_release(study_status='public'):
for _, fp, fp_type in a.filepaths:
if fp_type != 'biom' or 'only-16s' in fp:
continue
if fp.startswith(bdir):
fp = fp[bdir_len:]
fp = relpath(fp, bdir)
# format: (biom_fp, sample_fp, prep_fp, qiita_artifact_id,
# human readable name)
for pt in a.prep_templates:
for _, prep_fp in pt.get_filepaths():
if 'qiime' not in prep_fp:
break
if prep_fp.startswith(bdir):
prep_fp = prep_fp[bdir_len:]
prep_fp = relpath(prep_fp, bdir)
data.append((fp, sample_fp, prep_fp, a.id, human_cmd))

# writing text and tgz file
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