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2023-02-14Fix collection page error when ProbeSet/Publish traits don't have a meanzsloan
2023-01-12Add BXD-NIA-AD to list of BXD_GROUP_EXCEPTIONS (so the correct options show ↵zsloan
up in correlation drop-down)
2022-12-01Fix Exception that's raised when query_sql returns NoneMunyoki Kilyungi
* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor. (DataSet.get_accession_id): Handle a case where query_sql returns a None value.
2022-11-30Remove check for shortnames/fullnames in probeset metadata queryMunyoki Kilyungi
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.
2022-11-10Use the Maybe Monad when fetching the accession_id of a datasetMunyoki Kilyungi
* 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.
2022-11-08Remove string check for 'None' in HTML templateMunyoki Kilyungi
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'`.
2022-11-02Update Phenogen URL to rn7zsloan
2022-10-28Refactor: Pass user id to `check_resource_availability`Frederick Muriuki Muriithi
* 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.
2022-10-27init fix for querying for datasetsAlexander_Kabui
2022-10-20Cleanup: Remove unused codeFrederick Muriuki Muriithi
* 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.
2022-10-18Change logic in retrieve_trait_info to account for situations where a marker ↵zsloan
doesn't have a position in the DB
2022-10-17Fix bug when initializing Temp DatasetGroupszsloan
2022-10-14Add BXD_GROUP_EXCEPTIONS to webqtlConfig.py instead of having the groups ↵zsloan
hardcoded into show_trait.build_correlation_tools (+ add BXD-Heart-Metals to that list) I'm not sure why this logic exists, so it might be removed entirely later. I'm asking Rob
2022-10-12Use SQL to fetch trait metadata instead of gn-proxy, since it's dramatically ↵zsloan
faster
2022-10-12Include chr/mb values in jsonable traitzsloan
2022-10-04Add more information to exception to help in debuggingFrederick Muriuki Muriithi
2022-09-26Remove unused database_connection import from species.pyzsloan
2022-09-25Fix issue where the display name was used in the hmac for phenotype traitszsloan
2022-09-22Provide database cursor as argument for TheSpecies and ChromosomesFrederick Muriuki Muriithi
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.
2022-09-21Added Markers/HumanMarkers import to datasetgroup.py and removed it fromzsloan
__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
2022-09-21Refactor: pass redis and db connections as argumentFrederick Muriuki Muriithi
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.
2022-09-20Remove global `Dataset_Getter` variableFrederick Muriuki Muriithi
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.
2022-09-20Revert "Use member variable `self.conn` to avoid test failure"Frederick Muriuki Muriithi
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.
2022-09-20Use member variable `self.conn` to avoid test failureFrederick Muriuki Muriithi
Use the `self.conn` variable to prevent test from failing.
2022-09-20Decompose file into separate modulesrefactor-data_set_py-20220920Frederick Muriuki Muriithi
To ease future refactors on the code, decompose the file into a module with multiple modules that can be refactored semi-independently.
2022-09-12Fix query: Add comma to separate columns.Frederick Muriuki Muriithi
2022-09-12Fix query: remove wrongly-placed commaFrederick Muriuki Muriithi
2022-09-12Check db resultset before indexing into itFrederick Muriuki Muriithi
The assumption that the resultset will never be empty was leading to a lot of errors.
2022-09-09Fix bug in retrieve_other_nameszsloan
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)
2022-09-09tissue:fetch for query formattingAlexander_Kabui
2022-09-09Retain only a single import of the same moduleFrederick Muriuki Muriithi
2022-09-09Merge pull request #732 from BonfaceKilz/bug/fix-broken-correlationsMuriithi Frederick Muriuki
Bug/fix broken correlations
2022-09-09Fetch sample values correctlyMunyoki Kilyungi
* wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data): Fix indentation.
2022-09-09Add missing importMunyoki Kilyungi
* wqflask/base/trait.py: Import utility.hmac
2022-09-09Import missing module.Frederick Muriuki Muriithi
2022-09-09Filter out Samples without valuesFrederick Muriuki Muriithi
2022-09-09Use `database_connection()`Frederick Muriuki Muriithi
Call the `database_connection()` function to get a connection to the database.
2022-09-09Replace `g.db.execute` with `cursor.execute`Frederick Muriuki Muriithi
2022-09-08Simplify how chromosomes are fetchedMunyoki Kilyungi
* 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.
2022-09-08Remove redundant cursor.fetchone()Munyoki Kilyungi
* wqflask/base/data_set.py (DataSet.retrieve_other_names): Call cursor.fetchone() only once.
2022-09-08Use "%s" in sql queryMunyoki Kilyungi
* 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.
2022-09-08Inject database connection to mrna_assay_tissue_data classMunyoki Kilyungi
* 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.
2022-09-08Fix sql queriesMunyoki Kilyungi
"%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.
2022-09-08Add missing "," in cursor.execute()Munyoki Kilyungi
* wqflask/base/data_set.py (DatasetGroup.get_mapping_methods): Fix failing query by adding a missing ",".
2022-09-08Remove intermediate variables that are only used onceMunyoki Kilyungi
* 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.
2022-09-08Delete dead importsMunyoki Kilyungi
* 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.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* 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.
2022-09-08Delete logger importMunyoki Kilyungi
* wqflask/base/trait.py: Remove utility.logger
2022-09-08Replace assertion with Value Error for non-existent datasetMunyoki Kilyungi
* wqflask/base/trait.py (retrieve_trait_info): Wrap error message in ValueError.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* 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.
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