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Start improving search #988

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8c37d53
break up search object and move stats to qiita_ware
squirrelo Mar 16, 2015
d1390c5
update sql connection handler
squirrelo Mar 16, 2015
ff58d42
add helper utilities
squirrelo Mar 16, 2015
0c2d23a
revert change to sqlconnectionhandler
squirrelo Mar 16, 2015
8ab20c7
add samples property to ProcessedData object
squirrelo Mar 16, 2015
929d27b
flake8
squirrelo Mar 16, 2015
de8a466
revamp search object to use giant join table
squirrelo Mar 17, 2015
ff6731d
search prep templates and data_types
squirrelo Mar 17, 2015
ae6dd10
bit of rearrangement
squirrelo Mar 17, 2015
586a18e
refine search more
squirrelo Mar 18, 2015
0de4037
update search for changes
squirrelo Mar 18, 2015
056d4d0
update qiita_ware search to reflect changes
squirrelo Mar 18, 2015
56f8175
merge upstream/master
squirrelo Mar 18, 2015
3d29605
remove unused imports
squirrelo Mar 18, 2015
58cabfa
update search help page
squirrelo Mar 18, 2015
4a1e37c
address comments
squirrelo Mar 18, 2015
112f73e
add disallowed column checks for sample and prep templates
squirrelo Mar 18, 2015
db3d334
add data patch to remove offending cols
squirrelo Mar 18, 2015
f8d3fce
rename instead of drop
squirrelo Mar 18, 2015
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bit of rearrangement
  • Loading branch information
@squirrelo
squirrelo committed Mar 17, 2015
commit ae6dd10b5b22539636895d0296a361b3054fe0e2
18 changes: 7 additions & 11 deletions qiita_db/search.py
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Original file line number Diff line number Diff line change
Expand Up @@ -203,15 +203,10 @@ def __call__(self, searchstr, user, study=None):
raise ParseException('Can not search over string and '
'integer/float for same field!')

dyn_headers = meta_headers - self.req_samp_cols - self.study_cols - \
self.prep_info_cols

# remove metadata headers that come from non-dynamic tables
# get the list of dynamic table columns for sample + prep templates
conn_handler = SQLConnectionHandler()
sql = """SELECT DISTINCT column_name FROM qiita.study_sample_columns"""
sample_headers = meta_headers.intersection(
c[0] for c in conn_handler.execute_fetchall(sql))
dyn_headers = meta_headers - self.req_samp_cols - self.study_cols - \
self.prep_info_cols

if study:
sql = ["%d" % study.id]
Expand All @@ -227,8 +222,10 @@ def __call__(self, searchstr, user, study=None):
if user.level == 'user':
# trim to accessable studies
sql.append("SELECT study_id FROM qiita.study_users WHERE "
"email = '{0}' UNION SELECT study_id FROM qiita.study WHERE email = '{0}' OR"
" study_status_id = {1}".format(user.id, convert_to_id('public', 'study_status')))
"email = '{0}' UNION SELECT study_id "
"FROM qiita.study WHERE email = '{0}' OR"
" study_status_id = {1}".format(
user.id, convert_to_id('public', 'study_status')))
if sql:
st_sql = " WHERE srd.study_id in (%s)" % ' INTERSECT '.join(sql)
else:
Expand All @@ -238,8 +235,8 @@ def __call__(self, searchstr, user, study=None):
"ORDER BY srd.study_id) FROM qiita.study_raw_data srd "
"JOIN qiita.prep_template pt USING (raw_data_id)%s "
"GROUP BY study_id" % st_sql)
conn_handler = SQLConnectionHandler()
studies = conn_handler.execute_fetchall(sql)
print studies

if not studies:
# No studies found, so no need to continue
Expand Down Expand Up @@ -273,7 +270,6 @@ def __call__(self, searchstr, user, study=None):

conn_handler.add_to_queue('search', ' '.join(sql).format(
','.join(header_info)))
print 'search', ' '.join(sql).format(','.join(header_info))
results = self._process_to_dict(conn_handler.execute_queue('search'),
len(header_info))
return results, meta_headers
Expand Down