| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-07-29 | Merge branch 'main' into Feature/Update-db-from-csv-data | BonfaceKilz | |
| 2021-07-29 | Delete "update_raw" and it's test-cases | BonfaceKilz | |
| 2021-07-29 | Add method for updating values from a sample dataset | BonfaceKilz | |
| * gn3/db/traits.py (update_sample_data): New function. * tests/unit/db/test_traits.py: New test cases for ^^. | |||
| 2021-07-29 | Retrieve trait information | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: add functions to retrieve traits information * tests/unit/db/test_traits.py: add tests for new function Add functions to retrieve traits information as is done in genenetwork1 https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456 At this point, the data retrieval functions are probably incomplete, as there is more of the `retrieveInfo` function in GN1 that has not been considered as of this commit. | |||
| 2021-07-29 | Make name retrieval more general | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: make function more general * tests/unit/db/test_traits.py: parametrize the tests Make the name retrieval more general for the different types of traits by changing the column specification and table as appropriate. | |||
| 2021-07-29 | Retrieve 'ProbeSet' trait name | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: new function (retrieve_probeset_trait_name) * tests/unit/db/test_traits.py: test(s) for new function Add a function to retrieve the name of a 'ProbeSet' trait in a manner similar to genenetwork1's retrieval of the same, as implemented here https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154 Unlike in genenetwork1, we do not mutate an object, instead, we return the values as retrieved from the database, and the caller will deal with the returned values as appropriate. | |||
| 2021-07-26 | tests: test_db: Add test case for "update_raw" | BonfaceKilz | |
| 2021-07-10 | Fix pylint issues | BonfaceKilz | |
| 2021-07-10 | db: test_db: Test that a fetch is correct when columns are specified | BonfaceKilz | |
| 2021-06-07 | db: test_db: Add extra variable in test data for "id" | BonfaceKilz | |
| 2021-06-07 | Rename json_data column to json_diff_data | BonfaceKilz | |
| 2021-06-07 | tests: test_db: Add a test-case for fetchall | BonfaceKilz | |
| 2021-06-07 | tests: test_db: Rename TestPhenotype | BonfaceKilz | |
| 2021-06-07 | tests: test_phenotype: Rename to test_db | BonfaceKilz | |
| 2021-06-03 | Use prepared statements for FETCH sql function | BonfaceKilz | |
| 2021-06-03 | Use prepared statements for UPDATE sql function | BonfaceKilz | |
| 2021-06-03 | tests: test_audit: Update test case to check for prepared statements | BonfaceKilz | |
| 2021-06-03 | Add data structures for the table metadata_audit | BonfaceKilz | |
| 2021-06-03 | unit: test_phenotypes: Test for multiple "WHERE" clauses | BonfaceKilz | |
| 2021-06-03 | Get the diff between 2 dicts and return that as a dict | BonfaceKilz | |
| 2021-05-26 | Move the methods, "update" and "fetch", to gn3.db | BonfaceKilz | |
| 2021-05-20 | tests: test_phenotype: Add function that tests "fetchone" | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Update failing tests | BonfaceKilz | |
| 2021-05-20 | tests: test_phenotypes: New test cases for loading phenotypes | BonfaceKilz | |
| 2021-05-10 | tests: test_species: Add test for `get_all_species` | BonfaceKilz | |
| 2021-05-08 | tests: test_species: New tests | BonfaceKilz | |
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
| aboutsummaryrefslogtreecommitdiff |