genenetwork2/wqflask/base/data_set, branch lmdb-code/refactoringGeneNetwork (2nd generation)
http://git.genenetwork.org/genenetwork2/atom?h=lmdb-code%2Frefactoring2023-03-17T16:25:51+00:00Fix correlation bug caused by a NULL UPDATE_TIME in the DB2023-03-17T16:25:51+00:00zsloan2023-03-17T16:25:51+00:00urn:sha1:b414da7ff3c84564931388e81c729f0dfd06d0c3Fix Exception that's raised when query_sql returns None2022-12-01T21:11:13+00:00Munyoki Kilyungi2022-12-01T16:34:33+00:00urn:sha1:fb0fffb7a3470c648cef8effeb1792e6ac3c7504
* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor.
(DataSet.get_accession_id): Handle a case where query_sql returns a
None value.
Remove check for shortnames/fullnames in probeset metadata query2022-11-30T13:45:25+00:00Munyoki Kilyungi2022-11-30T13:34:58+00:00urn:sha1:9c5b1f48914da17c08fc95da858e3d06e41721bb
Some rows in InfoFiles have NULL values thereby causing an exception
to be raised. All InfoFiles.DB_Name are unique.
* wqflask/base/data_set/dataset.py (DataSet.get_accession_id): Remove
shortname/fullname check in query.
Use the Maybe Monad when fetching the accession_id of a dataset2022-11-10T06:00:04+00:00Munyoki Kilyungi2022-10-09T11:04:29+00:00urn:sha1:30c31955df6a9d20c28e0dcd9f99f06cbfd51a77
* wqflask/base/data_set/dataset.py: Import itertools, DictCursor, MonadicDict,
Maybe, Nothing and query_sql.
(DataSet.__init__): Initialize accession_id to Nothing.
(DataSet.as_dict): Rename this to ...
(Dataset.as_monadic_dict): ... this which returns a monadic
dictionary.
(DataSet.get_accession_id): Query for the accession_id and return it
as a maybe monad.
Remove string check for 'None' in HTML template2022-11-08T08:22:05+00:00Munyoki Kilyungi2022-10-09T16:38:13+00:00urn:sha1:d09a9485aebe0fa40c9fed2064a975a7cdd06e87
In Jinja, you can use dot notation to check for values. If a value
does not exist, you get None by default.
* wqflask/base/data_set/dataset.py (Dataset.get_accession_id): Remove
returning a string version of None.
* wqflask/wqflask/templates/correlation_page.html: Delete `!= 'None'`.
Fix bug when initializing Temp DatasetGroups2022-10-17T18:35:50+00:00zsloan2022-10-17T18:35:50+00:00urn:sha1:619548466f49c985ad77183e3722a3c47ab85425Provide database cursor as argument for TheSpecies and Chromosomes2022-09-22T03:33:47+00:00Frederick Muriuki Muriithi2022-09-22T03:33:47+00:00urn:sha1:30f305c1b87b4b6c4f308b15d5ae9248dc367e14
Provide the database cursor as an argument to the methods of the two
classes:
* wqflask.base.species.TheSpecies
* wqflask.base.species.Chromosomes
Also update dependent code to initialise and pass the cursor where
these classes are used.
Added Markers/HumanMarkers import to datasetgroup.py and removed it from2022-09-21T18:43:33+00:00zsloan2022-09-21T18:42:13+00:00urn:sha1:1292d94abbf2e10698344dd98b7d887ea6bc5221
__init__.py
Previously it threw an error when it tried to use Markers/HumanMarkers
in datasetgroup.py; since Markers/HumanMarkers doesn't seem to be used
anywhere else, I think it's okay for the import to only be in
datasetgroup.py
Refactor: pass redis and db connections as argument2022-09-21T09:37:36+00:00Frederick Muriuki Muriithi2022-09-21T09:33:20+00:00urn:sha1:8a51d58ed66593a420740b347ef841454e254237
Pass the redis and database connection/cursors as arguments to the
class methods, and do not retain a copy of the connections/cursors.
This allows us to do the connection management in the context
managers elsewhere - ideally, at the top-level. For now the context
manager is within the `create_dataset` function, but this should be
moved out to a higher level once the lower levels are verified to be
working as expected.
Remove global `Dataset_Getter` variable2022-09-20T19:56:55+00:00Frederick Muriuki Muriithi2022-09-20T19:56:55+00:00urn:sha1:d0b01d0be72ff541e72373cd085a58c3af2b4fed
Since the `__post_init__` method in the 'DatasetType' class checks
whether data is in redis before hitting the database, it does not
matter whether there is a global object of the type, as long as we
make sure to call the object correctly.
This commit makes that happen.