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Merged
merged 49 commits into from
Mar 27, 2015
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be2186b
Modifying the database
josenavas Mar 2, 2015
5188ef0
Modifying populate_test_db.sql to support the new db schema
josenavas Mar 2, 2015
905b14b
Fixing column naming
josenavas Mar 3, 2015
93a8760
Fixing study object
josenavas Mar 3, 2015
6c3d5a0
Fixing the ProcessedData object
josenavas Mar 3, 2015
60e5276
Fixing the tests for base.py
josenavas Mar 3, 2015
2d7fff4
Fixing more tests
josenavas Mar 3, 2015
5db7e9e
Fixing all qiita_db tests
josenavas Mar 3, 2015
90da22c
All tests passing again
josenavas Mar 3, 2015
2db9c91
Solving merge conflicts
josenavas Mar 4, 2015
5e7d687
Moving status changer buttons from the study to the processed data
josenavas Mar 6, 2015
09c7586
Easy status on processed data
josenavas Mar 6, 2015
688c250
Adding status to preprocessed data
josenavas Mar 6, 2015
d9c73ca
Easy status on preprocessed data
josenavas Mar 6, 2015
ef7b3ec
Adding status to prep template
josenavas Mar 7, 2015
ba42a92
Easy status on prep template
josenavas Mar 10, 2015
b13055a
Adding status to raw data
josenavas Mar 10, 2015
f32d47b
Easy status on raw data
josenavas Mar 10, 2015
fe9c860
Merge branch 'master' of github.com:qiime/QiiTa into issue-855
josenavas Mar 10, 2015
a9085dd
Fixing test failure
josenavas Mar 10, 2015
f851b8d
Expose only public *data through public study access
josenavas Mar 11, 2015
b849eaf
solving merge conflicts
josenavas Mar 11, 2015
b93d037
Adding get_by_status and get_by_status_group_by_study funcs to proces…
josenavas Mar 17, 2015
591e004
Change the awaiting approval list to retrieve the information by proc…
josenavas Mar 17, 2015
2382017
BUG: the admin user now have access to all data again...
josenavas Mar 17, 2015
fdac7da
Fixing merge conflicts
josenavas Mar 17, 2015
4da919c
Fixing merge conflicts
josenavas Mar 18, 2015
b8b205f
Fixing merge conflicts
josenavas Mar 19, 2015
51696a8
Changing meta_util to reflect status change
josenavas Mar 19, 2015
2c70328
Removing commented code
josenavas Mar 19, 2015
9a5d14f
Update dbschema and html to reflect the current database layout
josenavas Mar 19, 2015
0924257
Fixing bug
josenavas Mar 19, 2015
5de46d2
Pep 8 ...
josenavas Mar 19, 2015
ee95fe4
Fixing commands.sh
josenavas Mar 19, 2015
736ad4e
Fixing commands.sh
josenavas Mar 20, 2015
32a6984
Flake 8 again...
josenavas Mar 20, 2015
bb0cb32
Addressing @squirrelo's comments
josenavas Mar 20, 2015
78b8aea
Merge branch 'master' of github.com:qiime/QiiTa into issue-855
josenavas Mar 23, 2015
d17f9a1
ON to USING
josenavas Mar 25, 2015
8281e3c
Extracting status inference code to its own function to avoid code du…
josenavas Mar 25, 2015
57df5c7
Modify status functions to use the util infer status
josenavas Mar 25, 2015
bb1dd25
Adding test for non-status value
josenavas Mar 25, 2015
f9a9e10
Addressing remaining comments
josenavas Mar 25, 2015
84a9ed4
Addressing @ElDeveloper's comments
josenavas Mar 26, 2015
67d8fb2
Addressing @antgonza's comments
josenavas Mar 26, 2015
a09f97f
Increasing timeout
josenavas Mar 26, 2015
68bc8ae
Checking another version of tornado
josenavas Mar 26, 2015
46b84ef
Trying with docker containers
josenavas Mar 26, 2015
3bca14e
Changing back the tornado version
josenavas Mar 26, 2015
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Addressing @squirrelo's comments
  • Loading branch information
josenavas committed Mar 20, 2015
commit bb0cb324edd5a95866f7b9d75e01917f12c529c9
6 changes: 3 additions & 3 deletions qiita_db/data.py
Original file line number Diff line number Diff line change
Expand Up @@ -642,7 +642,7 @@ def status(self, study):
"""
if self._id not in study.raw_data():
raise QiitaDBStatusError(
"The study %s do not have access to the raw data %s"
"The study %s does not have access to the raw data %s"
% (study.id, self.id))

conn_handler = SQLConnectionHandler()
Expand Down Expand Up @@ -1176,7 +1176,7 @@ def get_by_status_grouped_by_study(cls, status):
JOIN qiita.study_processed_data spd
ON spd.processed_data_id=pd.processed_data_id
WHERE pds.processed_data_status = %s
GROUP BY study_id;"""
GROUP BY spd.study_id;"""
return dict(conn_handler.execute_fetchall(sql, (status,)))

@classmethod
Expand Down Expand Up @@ -1336,7 +1336,7 @@ def processed_date(self):
@property
def status(self):
conn_handler = SQLConnectionHandler()
sql = """SELECT processed_data_status
sql = """SELECT pds.processed_data_status
FROM qiita.processed_data_status pds
JOIN qiita.processed_data pd
ON pd.processed_data_status_id=pds.processed_data_status_id
Expand Down
2 changes: 1 addition & 1 deletion qiita_db/support_files/patches/18.sql
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
-- March 18, 2015
-- Add column to analysis table to mark shopping cart
ALTER TABLE qiita.analysis ADD dflt bool NOT NULL DEFAULT false;
ALTER TABLE qiita.analysis ADD dflt bool NOT NULL DEFAULT false;
4 changes: 2 additions & 2 deletions qiita_pet/handlers/study_handlers/description_handlers.py
Original file line number Diff line number Diff line change
Expand Up @@ -107,8 +107,8 @@ def _get_study_and_check_access(self, study_id):
else:
check_access(user, study, raise_error=True)

full_access = (study.id in user.user_studies | user.shared_studies or
user.level == 'admin')
full_access = (user.level == 'admin' or
study.id in user.user_studies | user.shared_studies)

return study, user, full_access

Expand Down