| Age | Commit message (Expand) | Author |
|---|
| 2022-11-02 | Fix pylint and mypy errors...* gn3/db/sample_data.py (get_trait_csv_sample_data): Pass __query
directly to cursor.execute. Rename value to _value in for loop to
make mypy pass.
* gn3/db_utils.py (Connection): Add class docstring.
(Connection.cursor): Add docstring.
* mypy.ini: Add an entry for xapian.
| Munyoki Kilyungi |
| 2022-10-28 | Use Xapian index path from app settings....App settings should be accessed from current_app. It should not be hard-coded
to a variable in a module.
* gn3/db_utils.py: Do not import XAPIAN_DB_PATH from gn3.settings.
(xapian_database): Accept path argument.
* gn3/api/search.py: Import current_app from flask.
(search_results): Pass Xapian index path to xapian_database.
| Arun Isaac |
| 2022-10-28 | Disable various pylint checks on Connection class....* gn3/db_utils.py (Connection): Disable missing-class-docstring,
missing-function-docstring and too-few-public-methods pylint checks.
| Arun Isaac |
| 2022-10-26 | Add xapian database connection context manager....* gn3/settings.py (XAPIAN_DB_PATH): New variable.
* gn3/db_utils.py: Import xapian and XAPIAN_DB_PATH from gn3.settings.
(xapian_database): New function.
| Arun Isaac |
| 2022-10-18 | Add database connection context manager....* gn3/db_utils.py: Import contextlib. Import Any, Iterator, Protocol and Tuple
from typing.
(database_connector): Deprecate function.
(Connection): New class.
(database_connection): New function.
| Arun Isaac |
| 2022-08-22 | Use non-default MySQL port if present...By default, MySQL/Mariadb connects at port 3306, however, the configuration
variable `SQL_URI` could contain a different port. In that case, this commit
allows the system to connect to the non-default port.
| Frederick Muriuki Muriithi |
| 2022-03-11 | Fix some linting issues | Frederick Muriuki Muriithi |
| 2022-03-08 | Create database connections within context managers...Use the `with` context manager to open database connections, so as to ensure
that those connections are closed once the call is completed. This hopefully
avoids the 'too many connections' error
| Frederick Muriuki Muriithi |
| 2021-05-08 | gn3: db_utils: Remove mypy ignore stub...MySQLdb is already ignored in ".mypy.ini", added in 88c33df.
| BonfaceKilz |
| 2021-05-08 | Fix pep-8 errors | BonfaceKilz |
| 2021-04-12 | Integrate correlation API...- add new api for gn2-gn3 sample r integration
- delete map for sample list to values
- add db util file
- add python msql-client dependency
- add db for fetching lit correlation results
- add unittests for db utils
- add tests for db_utils
- modify api for fetching lit correlation results
- refactor Mock Database Connector and unittests
- add sql url parser
- add SQL URI env variable
- refactor code for db utils
- modify return data for lit correlation
- refactor tissue correlation endpoint
- replace db_instance with conn | Alexander Kabui |
