| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-09-08 | Remove intermediate variables that are only used once...* wqflask/base/data_set.py (DatasetGroup.__init__): Remove "query"
variable.
(DataSet.chunk_dataset): Fix indentation.
* wqflask/wqflask/search_results.py (get_GO_symbols): Remove
"this_term" variable.
* wqflask/wqflask/views.py (search_page): Remove "the_search"
variable.
| Munyoki Kilyungi |
| 2022-09-08 | Delete dead imports...* wqflask/base/data_set.py: Remove un-used imports.
* wqflask/base/trait.py: Ditto.
wqflask/tests/wqflask/show_trait/test_show_trait.py: Ditto.
* wqflask/wqflask/show_trait/show_trait.py: Ditto.
* wqflask/wqflask/views: Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Replace g.db with database_connection() context manager...* wqflask/base/data_set.py (DatasetType.set_dataset_key): Replace g.db
with "database_connection()".
(DatasetGroup.get_mapping_methods): Ditto.
(DataSet.get_accession_id): Ditto.
(DataSet.retrieve_other_names): Rework "if ... else" logic to get rid
of "query" and "_vars" variables. Also, nest "try ... except" block
within "database_connection".
(DataSet.chunk_dataset): Replace g.db with "database_connection()".
(DataSet.get_probeset_data): Ditto.
(DataSet.get_trait_data): Ditto.
(PhenotypeDataSet.get_trait_info): Ditto.
(PhenotypeDataSet.retrieve_sample_data): Ditto.
(GenotypeDataSet.retrieve_sample_data): Ditto.
(MrnaAssayDataSet.get_trait_info): Ditto.
(MrnaAssayDataSet.retrieve_sample_data): Ditto.
(MrnaAssayDataSet.retrieve_genes): Ditto.
(TempDataSet): Ditto.
(geno_mrna_confidentiality): Ditto.
(query_table_timestamp): Ditto.
* wqflask/wqflask/api/router.py: Replace "flask.g" with
database_connection import.
(get_species_list): Replace g.db
with "database_connection()".
(get_species_info): Ditto.
(get_groups_list): Ditto.
(get_group_info): Ditto.
(get_datasets_for_group): Ditto.
(get_dataset_info): Ditto.
(fetch_traits): Ditto.
(all_sample_data): Ditto.
(trait_sample_data): Ditto.
(get_trait_info): Ditto.
(get_dataset_trait_ids): Ditto.
(get_samplelist): Ditto.
(get_group_id_from_dataset): Ditto.
(get_group_id): Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Delete logger import...* wqflask/base/trait.py: Remove utility.logger
| Munyoki Kilyungi |
| 2022-09-08 | Replace assertion with Value Error for non-existent dataset...* wqflask/base/trait.py (retrieve_trait_info): Wrap error message in
ValueError.
| Munyoki Kilyungi |
| 2022-09-08 | Replace g.db with database_connection() context manager...* wqflask/base/mrna_assay_tissue_data.py: Replace "flask.g" with database_connection.
(MrnaAssayTissueData.__init__): Use database_connection.
(MrnaAssayTissueData.get_symbol_values_pairs): Ditto.
* wqflask/base/species.py: Replace "Flask.g" imports with
"database_connection".
(Chromosomes.chromosomes): Use database_connection.
* wqflask/base/trait.py: Import database_connection.
(retrieve_trait_info): Use database_connection.
* wqflask/utility/authentication_tools.py: Replace "flask.g" with
database_connection.
(get_group_code): Use database_connection.
* wqflask/utility/helper_functions.py: Replace "flask.g" with
"database_connection".
(get_species_groups): Use database_connection.
* wqflask/wqflask/db_info.py: Replace "Flask" and "g" with
"database_connection".
(InfoPage.get_info): Use database_connection.
* wqflask/wqflask/do_search.py (DoSearch.execute): Use
database_connection().
* wqflask/wqflask/external_tools/send_to_geneweaver.py: Replace
"Flask" and "g" import with database_connection.
(test_chip): Use database_connection.
* wqflask/wqflask/external_tools/send_to_webgestalt.py: Replace
"Flask, g" imports with database_connection.
(test_chip): Use database_connection.
* wqflask/wqflask/gsearch.py: Replace "Flask" and "g" import with
database_connection.
(GSearch.__init__): Use database_connection.
* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes):
Use database_connection().
* wqflask/wqflask/show_trait/SampleList.py: Replace "flask.g import"
with database_connection.
(SampleList.get_attributes): Use database_connection.
(SampleList.get_extra_attribute_values): Ditto.
* wqflask/wqflask/show_trait/show_trait.py: Replace "Flask" and "g"
import with database_connection.
(ShowTrait.__init__): Use database_connection.
(ShowTrait.get_external_links): Ditto.
(get_nearest_marker): Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Merge pull request #727 from Alexanderlacuna/feature/use-textfiles...use text files for Probeset | Alexander Kabui |
