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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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@squirrelo
squirrelo committed Mar 18, 2015
commit 4a1e37c4a2831ee69e8ae8b444711865fe5bc69d
15 changes: 0 additions & 15 deletions qiita_db/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1144,21 +1144,6 @@ def study(self):
"processed_data_id=%s".format(self._study_processed_table),
[self._id])[0]

@property
def samples(self):
"""Returns samples available in this processed data

Returns
-------
generator of str
Sample_ids available according to the prep template
"""
# Get the samples available for the prep template
pid = PreprocessedData(self.preprocessed_data).prep_template
conn_handler = SQLConnectionHandler()
sql = "SELECT sample_id FROM qiita.prep_{0}".format(pid)
return (x[0] for x in conn_handler.execute_fetchall(sql))

def data_type(self, ret_id=False):
"""Returns the data_type or data_type_id

Expand Down
4 changes: 3 additions & 1 deletion qiita_pet/handlers/analysis_handlers.py
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Expand Up @@ -31,7 +31,8 @@
check_access_to_analysis_result,
get_table_cols,
filepath_ids_to_rel_paths)
from qiita_ware.search import search, count_metadata
from qiita_db.search import QiitaStudySearch
from qiita_ware.search import count_metadata
from qiita_db.exceptions import (
QiitaDBIncompatibleDatatypeError, QiitaDBUnknownIDError)

Expand Down Expand Up @@ -140,6 +141,7 @@ def post(self):

# run through action requested
if action == "search":
search = QiitaStudySearch()
query = str(self.get_argument("query"))
try:
results, meta_headers = search(query, user)
Expand Down
9 changes: 0 additions & 9 deletions qiita_ware/search.py
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Expand Up @@ -2,8 +2,6 @@

from future.utils import viewvalues

from qiita_db.search import QiitaStudySearch


def count_metadata(results, meta_cols):
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this is not counting anything, so the name and the description are misleading. Can you change the name to something like collapse_search_results or something similar? Also I'm unsure if this function should be exposed to qiita_pet or should be private and be included in the search function below, which will make it useful.

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It is counting the number of occurrences of each metadata value for each metadata column. It's there specifically for qiita_pet.

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Oh, sorry, I got confused with the code.

"""Counts the metadata found in a search, and returns these counts
Expand Down Expand Up @@ -50,10 +48,3 @@ def double_comprehension(results):
studycount[study_id][cat] = Counter(meta_vals[pos + 1])

return fullcount, studycount


def search(searchstr, user, study=None):
""" Passthrough for qiita_db search object. See object for documentation
"""
search = QiitaStudySearch()
return search(searchstr, user, study)