| Age | Commit message (Expand) | Author |
|---|
| 2021-07-30 | Return dict from query functions•••Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: return dicts rather than tuples/list
* tests/unit/db/test_traits.py: Update tests
Return dicts with the key-value pairs set up so as to ease with the data
manipulation down the pipeline.
This is also useful to help with the retrieval of all other extra
information that was left out in the first iteration.
This commit also updates the tests by ensuring they expect dicts rather than
tuples.
| Muriithi Frederick Muriuki |
| 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•••* gn3/db/traits.py (update_sample_data): New function.
* tests/unit/db/test_traits.py: New test cases for ^^.
| BonfaceKilz |
| 2021-07-29 | Retrieve trait information•••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.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Make name retrieval more general•••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.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Retrieve 'ProbeSet' trait name•••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.
| Muriithi Frederick Muriuki |
| 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 |
