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path: root/gn3/db/species.py
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2023-09-05Replace "escape_string" with safe-query parameters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-03-17Change get_all_species query to order by Familyzsloan
2021-11-29Fix query parametrisation...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Pass parameters to the query the way the MySQL driver expects. Frederick Muriuki Muriithi
2021-11-29Retrieve the species name given the group...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Migrate the `web.webqtl.dbFunction.webqtlDatabaseFunction.retrieveSpecies` in GeneNetwork1 to `gn3.db.species.species_name` in GeneNetwork3 to enable the retrieval of the species name, given the group name (formerly RISet). Frederick Muriuki Muriithi
2021-11-04Add missing comma...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-04Remove if clauses: replace with dict...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Remove the if clauses to simplify the code flow: use a dictionary of queries and select the appropriate query from the dictionary instead. Frederick Muriuki Muriithi
2021-10-21Implement `translate_to_mouse_gene_id` function...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Migrate the `web.webqtl.correlation/CorrelationPage.translateToMouseGeneID` function in GN1 to GN3. This is a function that retrieves data from the database, and therefore uses a system outside of our code, therefore, the function does not have a corresponding unit test. This kind of function will probably need to be tested at the integration or system tests level, where we test that our code interacts correcly with any and all external systems that it should. Frederick Muriuki Muriithi
2021-05-10db: species: Add method for fetching all speciesBonfaceKilz
2021-05-08db: species: Fetch chromosomes using a group or species name...* gn3/db/species.py (get_chromosome): New function. BonfaceKilz