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fix get_studies #2052

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Merged
merged 2 commits into from
Jan 23, 2017
Merged

fix get_studies #2052

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d12ccfe
fix get_studies
antgonza Jan 20, 2017
b33983b
flake8
antgonza Jan 20, 2017
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23 changes: 9 additions & 14 deletions qiita_db/meta_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,6 @@
# -----------------------------------------------------------------------------
from __future__ import division

from itertools import chain

from qiita_core.qiita_settings import qiita_config
import qiita_db as qdb

Expand Down Expand Up @@ -136,6 +134,7 @@ def get_lat_longs():
s.id for s in qdb.portal.Portal(qiita_config.portal).get_studies()]

with qdb.sql_connection.TRN:
# getting all tables in the portal
sql = """SELECT DISTINCT table_name
FROM information_schema.columns
WHERE table_name SIMILAR TO 'sample_[0-9]+'
Expand All @@ -144,16 +143,12 @@ def get_lat_longs():
AND SPLIT_PART(table_name, '_', 2)::int IN %s;"""
qdb.sql_connection.TRN.add(sql, [tuple(portal_table_ids)])

sql = """SELECT CAST(latitude AS FLOAT), CAST(longitude AS FLOAT)
FROM qiita.{0}
WHERE isnumeric(latitude) AND isnumeric(latitude)"""
idx = qdb.sql_connection.TRN.index

portal_tables = qdb.sql_connection.TRN.execute_fetchflatten()

ebi_null = tuple(qdb.metadata_template.constants.EBI_NULL_VALUES)
for table in portal_tables:
qdb.sql_connection.TRN.add(sql.format(table), [ebi_null, ebi_null])
sql = [('SELECT CAST(latitude AS FLOAT), '
' CAST(longitude AS FLOAT) '
'FROM qiita.%s '
'WHERE isnumeric(latitude) AND isnumeric(latitude)' % s)
for s in qdb.sql_connection.TRN.execute_fetchflatten()]
sql = ' UNION '.join(sql)
qdb.sql_connection.TRN.add(sql)

return list(
chain.from_iterable(qdb.sql_connection.TRN.execute()[idx:]))
return qdb.sql_connection.TRN.execute_fetchindex()