Age | Commit message (Expand) | Author |
2023-06-22 | Update calls to `database_connection` function...Pass in the database URI at call time.
| Frederick Muriuki Muriithi |
2023-05-31 | Compute dataset type from name. | Frederick Muriuki Muriithi |
2023-05-19 | auth: Use auth privileges to control UI display...Use the privileges from the authorisation endpoint to control which
elements of the UI are displayed to the user.
* wqflask/base/trait.py: Remove unused import
* wqflask/wqflask/show_trait/show_trait.py: Unhook from GN-PROXY
* wqflask/wqflask/templates/show_trait.html: Display or hide UI
elements depending on the privileges the user has.
* wqflask/wqflask/templates/show_trait_details.html: Display or hide
UI elements depending on the privileges the user has.
* wqflask/wqflask/views.py: Pass privileges, user, and resource
details on to the UI template to be used for controlling UI element
display.
| Frederick Muriuki Muriithi |
2023-03-17 | Fix correlation bug caused by a NULL UPDATE_TIME in the DB | zsloan |
2023-02-17 | Use abbreviation as symbol for phenotypes in collection page | zsloan |
2023-02-17 | Default trait abbreviation to N/A and only set to pre/post_publication_abbrev... | zsloan |
2023-02-14 | Fix collection page error when ProbeSet/Publish traits don't have a mean | zsloan |
2023-01-12 | Add BXD-NIA-AD to list of BXD_GROUP_EXCEPTIONS (so the correct options show u... | zsloan |
2022-12-01 | Fix Exception that's raised when query_sql returns None...* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor.
(DataSet.get_accession_id): Handle a case where query_sql returns a
None value.
| Munyoki Kilyungi |
2022-11-30 | Remove check for shortnames/fullnames in probeset metadata query...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.
| Munyoki Kilyungi |
2022-11-10 | Use the Maybe Monad when fetching the accession_id of a dataset...* 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.
| Munyoki Kilyungi |
2022-11-08 | Remove string check for 'None' in HTML template...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'`.
| Munyoki Kilyungi |
2022-11-02 | Update Phenogen URL to rn7 | zsloan |
2022-10-28 | Refactor: Pass user id to `check_resource_availability`...* Pass the user_id for the current user to the
`check_resource_availability` function as an argument, rather than
using the global `g.user_session.user_id` value.
| Frederick Muriuki Muriithi |
2022-10-27 | init fix for querying for datasets | Alexander_Kabui |
2022-10-20 | Cleanup: Remove unused code...* Commit 49580eb9cd47bb2ce15fd44be11bb9580d85efef removed the use of
the gn-proxy, but left some code that was used expressly for use
with the gn-proxy. This commit removes that code.
| Frederick Muriuki Muriithi |
2022-10-18 | Change logic in retrieve_trait_info to account for situations where a marker ... | zsloan |
2022-10-17 | Fix bug when initializing Temp DatasetGroups | zsloan |
2022-10-14 | Add BXD_GROUP_EXCEPTIONS to webqtlConfig.py instead of having the groups hard......I'm not sure why this logic exists, so it might be removed entirely later. I'm asking Rob
| zsloan |
2022-10-12 | Use SQL to fetch trait metadata instead of gn-proxy, since it's dramatically ... | zsloan |
2022-10-12 | Include chr/mb values in jsonable trait | zsloan |
2022-10-04 | Add more information to exception to help in debugging | Frederick Muriuki Muriithi |
2022-09-26 | Remove unused database_connection import from species.py | zsloan |
2022-09-25 | Fix issue where the display name was used in the hmac for phenotype traits | zsloan |
2022-09-22 | Provide database cursor as argument for TheSpecies and Chromosomes...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.
| Frederick Muriuki Muriithi |
2022-09-21 | Added Markers/HumanMarkers import to datasetgroup.py and removed it from...__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
| zsloan |
2022-09-21 | Refactor: pass redis and db connections as argument...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.
| Frederick Muriuki Muriithi |
2022-09-20 | Remove global `Dataset_Getter` variable...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.
| Frederick Muriuki Muriithi |
2022-09-20 | Revert "Use member variable `self.conn` to avoid test failure"...This reverts commit 4fafdfd8487ddf61105b2a5ca92534c8014c1db4.
While using `self.conn.cursor()` works in the tests, it will not work
in the application since the point of initialisation could be very
different from the point where the 'property' is called.
| Frederick Muriuki Muriithi |
2022-09-20 | Use member variable `self.conn` to avoid test failure...Use the `self.conn` variable to prevent test from failing.
| Frederick Muriuki Muriithi |
2022-09-20 | Decompose file into separate modules...To ease future refactors on the code, decompose the file into a module
with multiple modules that can be refactored semi-independently.
refactor-data_set_py-20220920 | Frederick Muriuki Muriithi |
2022-09-12 | Fix query: Add comma to separate columns. | Frederick Muriuki Muriithi |
2022-09-12 | Fix query: remove wrongly-placed comma | Frederick Muriuki Muriithi |
2022-09-12 | Check db resultset before indexing into it...The assumption that the resultset will never be empty was leading to a
lot of errors.
| Frederick Muriuki Muriithi |
2022-09-09 | Fix bug in retrieve_other_names...After a recent change, it always tries to unpack 6 values from the
query, but it should only be unpacking 4 values if not type ProbeSet (so
it was throwing an error for anything not ProbeSet)
| zsloan |
2022-09-09 | tissue:fetch for query formatting | Alexander_Kabui |
2022-09-09 | Retain only a single import of the same module | Frederick Muriuki Muriithi |
2022-09-09 | Merge pull request #732 from BonfaceKilz/bug/fix-broken-correlations...Bug/fix broken correlations | Muriithi Frederick Muriuki |
2022-09-09 | Fetch sample values correctly...* wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data):
Fix indentation.
| Munyoki Kilyungi |
2022-09-09 | Add missing import...* wqflask/base/trait.py: Import utility.hmac
| Munyoki Kilyungi |
2022-09-09 | Import missing module. | Frederick Muriuki Muriithi |
2022-09-09 | Filter out Samples without values | Frederick Muriuki Muriithi |
2022-09-09 | Use `database_connection()`...Call the `database_connection()` function to get a connection to the
database.
| Frederick Muriuki Muriithi |
2022-09-09 | Replace `g.db.execute` with `cursor.execute` | Frederick Muriuki Muriithi |
2022-09-08 | Simplify how chromosomes are fetched...* wqflask/base/species.py: Import "Any" and "Union".
(TheSpecies): Add type hints. Get rid of redundant "if ... else"
statement.
(IndChromosome.mb_length): Add type hints.
(Chromosomes): Inject conn and add type hints.
| Munyoki Kilyungi |
2022-09-08 | Remove redundant cursor.fetchone()...* wqflask/base/data_set.py (DataSet.retrieve_other_names): Call
cursor.fetchone() only once.
| Munyoki Kilyungi |
2022-09-08 | Use "%s" in sql query...* wqflask/base/mrna_assay_tissue_data.py: Delete db_tools.
(MrnaAssayTissueData.get_symbol_values_pairs): Re-format query.
* wqflask/tests/unit/base/test_mrna_assay_tissue_data.py:
(test_get_trait_symbol_and_tissue_values): Add test for above.
| Munyoki Kilyungi |
2022-09-08 | Inject database connection to mrna_assay_tissue_data class...* wqflask/base/mrna_assay_tissue_data.py: Imports: Delete
database_connection, escape, and database_connector.
(MrnaAssayTissueData): Inject conn. Re-format queries. Rework 'if
... else' logic. Re-work how results are assigned to
'self.data[symbol]' - remove dot-notation.
(MrnaAssayTissueData.get_symbol_values_pairs): Move box-comments to
doc-string. Rework how results are assigned to 'symbol_values_dict' -
remove dot-notation.
* wqflask/tests/unit/base/test_mrna_assay_tissue_data.py
(test_mrna_assay_tissue_data_initialisation): New test.
* wqflask/wqflask/correlation/correlation_functions.py: Import
database_connection.
(get_trait_symbol_and_tissue_values): Inject conn object.
| Munyoki Kilyungi |
2022-09-08 | Fix sql queries..."%s" should only be used outside table names and column names
otherwise a string literal will be inserted thereby leading to errors
in the sql statements.
* wqflask/base/data_set.py (geno_mrna_confidentiality): Use f-strings
for table/columns/clause.
* wqflask/base/trait.py (retrieve_trait_info): Ditto.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto.
* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Ditto.
* wqflask/wqflask/snp_browser/snp_browser.py
(SnpBrowser.get_browser_results): Ditto.
| Munyoki Kilyungi |
2022-09-08 | Add missing "," in cursor.execute()...* wqflask/base/data_set.py (DatasetGroup.get_mapping_methods): Fix
failing query by adding a missing ",".
| Munyoki Kilyungi |