| Age | Commit message (Expand) | Author |
|---|
| 2023-09-05 | Remove un-necessary string concatenation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Replace "escape_string" with safe-query parameters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-17 | Fix tests to work with changes | zsloan |
| 2023-08-04 | Remove unused import | Frederick Muriuki Muriithi |
| 2023-08-04 | Remove tests for deleted function. | Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `insert` function...Remove the object-relation-mapping dependent `insert` function to prevent it
being used in the code down the line.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `fetchall` and `fetchone` functions...Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone`
so as to prevent theirs use in the code moving forward.
| Frederick Muriuki Muriithi |
| 2023-07-19 | Extract code dealing with ProbeSets to their own module. | Frederick Muriuki Muriithi |
| 2023-07-11 | Revert "Skip tests broken by Python-3.10 temporarily"...This reverts commit f52247c15f3694f3dd5fd0fd79c3e15376137e07.
| Frederick Muriuki Muriithi |
| 2023-07-05 | Skip tests broken by Python-3.10 temporarily...Skip the tests that have been broken by the migrations to Python-3.10
temporarily, until we can fix them.
| Frederick Muriuki Muriithi |
| 2023-03-20 | Fix get_all_species test | zsloan |
| 2022-05-27 | Move sql for CRUD operations on case-attrs from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Move sql for modifying case-attributes from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Return all the results from CaseAttributes column as is...* gn3/db/sample_data.py: Remove "collections" import. Add "Optional" import.
(get_case_attributes): Return the results of "fetchall" from the case
attributes.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Update failing
test.
| BonfaceKilz |
| 2022-05-26 | Add Endpoint to get menu items for use in UI | Frederick Muriuki Muriithi |
| 2022-04-12 | Test that a carriage return is removed when generating csv...* tests/unit/db/test_sample_data.py: import "get_trait_csv_sample_data".
(test_get_trait_csv_sample_data): New test function.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (delete_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_delete_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (insert_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_insert_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during updates...* gn3/db/sample_data.py: Import "parse_csv_column".
(update_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Add method for fetching the case_attributes...* gn3/db/sample_data.py (get_case_attributes): New function.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for
the above.
| BonfaceKilz |
| 2022-04-01 | Run python-black in file...* gn3/csvcmp.py: Run "black -l 79 ..."
* tests/unit/db/test_sample_data.py: Ditto.
* tests/unit/test_csvcmp.py: Ditto.
| BonfaceKilz |
| 2022-03-12 | Fix pylint errors in unit_tests | BonfaceKilz |
| 2022-03-12 | Append the strain name when extracting "actions"...* gn3/db/sample_data.py (__extract_actions): During updates, make sure that
the strain name is part of the returned string when extracting "actions".
* tests/unit/db/test_sample_data.py: Add test cases for the above.
| BonfaceKilz |
| 2022-03-12 | Apply auto-pep8 to sample_data.py and it's test file | BonfaceKilz |
| 2022-03-12 | Update how data is updated by re-using existing functions...* gn3/db/sample_data.py (get_sample_data_ids): Re-use "delete_sample_data" and
"insert_sample_data" when updating data; and also add logic for updating
modified data.
* tests/unit/db/test_sample_data.py: Add tests for the above.
| BonfaceKilz |
| 2022-03-12 | Create action dict that's created when updating data...* gn3/db/sample_data.py (__extract_actions): An update on a vector of data can
contain: inserts, deletes and updates. This functions extracts these actions
during an update.
* tests/unit/db/test_sample_data.py (test_extract_actions): Add test-case for
the above.
| BonfaceKilz |
| 2022-03-12 | Add test cases for inserting and deleting data...* tests/unit/db/test_sample_data.py (test_insert_sample_data): Test inserting
data.
(test_delete_sample_data): Test deleting data.
| BonfaceKilz |
| 2022-03-12 | Remove test cases related to sample data...Most of this functions were moved to their own module.
| BonfaceKilz |
| 2022-03-12 | Append case attributes to csv data if they exist | BonfaceKilz |
| 2022-02-21 | Fix minor issues introduced while fixing linting errors | Frederick Muriuki Muriithi |
| 2022-02-21 | Fix a myriad of linter issues...* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
| Frederick Muriuki Muriithi |
| 2022-02-21 | Add test to ensure samples are read correctly from .geno files...* tests/unit/db/test_genotypes2.py: New file
| Frederick Muriuki Muriithi |
| 2022-02-18 | Remove erroneous test based on wrong assumptions...Related to commit 75dcfe295af57b16428c586cc11dbaa827a5feba
This commit removes the related test that was checking for the wrong thing.
| Frederick Muriuki Muriithi |
| 2022-02-17 | Use pytest's "mark" feature to categorise tests...Use pytest's `mark` feature to explicitly categorise the tests and run them
per category
| Frederick Muriuki Muriithi |
| 2022-02-09 | Remove obsolete `PublishFreeze` table | Frederick Muriuki Muriithi |
| 2022-01-05 | test_traits.py: Update failing test | BonfaceKilz |
| 2021-12-14 | Provide expected values to use for tests | Frederick Muriuki Muriithi |
| 2021-11-23 | Fix a myriad of linting errors...* Fix linting errors like:
- Unused variables
- Undeclared variable errors (mostly caused by typos, and wrong names)
- Missing documentation strings for functions
etc.
| Frederick Muriuki Muriithi |
| 2021-11-22 | Add test to query builders...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add some tests for the query builders to ensure that the queries are built
up correctly.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Disable pylint issue...* Disable minor pylint issue.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `riset` to `group`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update terminology to use the appropriate domain terminology according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
| Frederick Muriuki Muriithi |
| 2021-09-23 | Refactor: Move common sample data to separate file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Move common sample test data into a separate file where it can be imported
from, to prevent pylint error R0801 which proved tricky to silence in any
other way.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix more pylint errors | Frederick Muriuki Muriithi |
| 2021-09-15 | Add missing sample file for tests...* tests/unit/db/data/genotypes/genotype_sample1.geno: new file
Add a missing sample data file needed for unit tests.
| Frederick Muriuki Muriithi |
| 2021-09-01 | Fix linting and typing issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Muriithi Frederick Muriuki |
| 2021-09-01 | Built top-level genotype file parsing function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype files
* tests/unit/db/test_genotypes.py: test parsing is correct
Add the overall genotype files parsing function and tests to check that the
parsing works as expected.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse data lines into markers...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse data lines in file to genetic markers.
* tests/unit/db/test_genotypes.py: test that parsing works.
Add some tests to check that the parsing of the markers works as expected,
and add the code to actually parse the markers.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse the genotype file's data header...* gn3/db/genotypes.py: parse data header
* tests/unit/db/test_genotypes.py: check that header's parse works correctly.
Add tests to check that the parser works as expected. Add code to implement
the parsing and pass the tests.
| Muriithi Frederick Muriuki |
