Age | Commit message (Collapse) | Author | |
---|---|---|---|
2022-10-28 | Disable various pylint checks on Connection class. | Arun Isaac | |
* gn3/db_utils.py (Connection): Disable missing-class-docstring, missing-function-docstring and too-few-public-methods pylint checks. | |||
2022-10-28 | Add search. | Arun Isaac | |
* gn3/api/search.py: New file. * gn3/app.py: Register the search blueprint. | |||
2022-10-26 | Add xapian database connection context manager. | Arun Isaac | |
* 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. | |||
2022-10-25 | Reshape column major genotype database storage correctly. | Arun Isaac | |
* gn3/genodb.py (matrix): Reshape column major genotype database storage as ncols x nrows instead of as nrows x ncols. | |||
2022-10-22 | fix issue;parsing sample data (#102) | Alexander Kabui | |
2022-10-18 | Add xapian indexing script. | Arun Isaac | |
* scripts/index-genenetwork: New file. * setup.py (install_requires): Add click, pymonad and xapian-bindings. (scripts): Add scripts/index-genenetwork. | |||
2022-10-18 | Support server side SQL query retrieval. | Arun Isaac | |
* gn3/monads.py: Import SSDictCursor from MySQLdb.cursors. (query_sql): Add server_side argument. | |||
2022-10-18 | Add database connection context manager. | Arun Isaac | |
* 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. | |||
2022-10-18 | Add monadic utilities. | Munyoki Kilyungi | |
* gn3/monads.py: New file. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net> | |||
2022-10-08 | README: a note on design | Pjotr Prins | |
2022-10-06 | DEBUG: Collect more info for debugging | Frederick Muriuki Muriithi | |
2022-10-06 | DEBUG: Collect more information on possible failure. | Frederick Muriuki Muriithi | |
2022-10-03 | Bug: Do not process data for output too early | Frederick Muriuki Muriithi | |
* gn3/computations/rust_correlation.py: (parse_tissue_corr_data): The function was parsing data from a file, and then converting the parsed values into a comma-separated string for output, despite the fact that the data parsed is not output in this specific function. This is a really bad idea, and leads to errors showing up down the line, far removed from the cause. | |||
2022-09-30 | Add escape char to avoid error notice. | Frederick Muriuki Muriithi | |
2022-09-29 | Use the built-in csv module for file output | Frederick Muriuki Muriithi | |
Use the built-in csv module for file output in order to avoid subtle errors in the formats. | |||
2022-09-06 | Update link to continuous deployment. | Arun Isaac | |
* README.md: Update link to continuous deployment. | |||
2022-08-30 | Update test: include port in parsed data from mysql uri | Frederick Muriuki Muriithi | |
2022-08-25 | revert for commit 6db3b2af8fc09999996d3acc09890a06f179c669;Bug | Alexander_Kabui | |
2022-08-23 | Remove conn.commit() and conn.rollback() | Munyoki Kilyungi | |
* gn3/db/__init__.py (update): Delete conn.commit() and conn.rollback() (insert): Ditto. * gn3/db/case_attributes.py (insert_case_attribute_audit): Ditto. (reject_case_attribute): Ditto. (approve_case_attribute): Ditto. * gn3/db/sample_data.py (update_sample_data): Ditto. (delete_sample_data): Ditto. (insert_sample_data): Ditto. | |||
2022-08-22 | Use non-default MySQL port if present | Frederick Muriuki Muriithi | |
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. | |||
2022-08-12 | Add mandatory/expected fields to parsed data. | Frederick Muriuki Muriithi | |
2022-08-10 | Fix returned value for 'parse_correlation_output' | Frederick Muriuki Muriithi | |
* Always return dict * Fix internal '__parse_line__' to always have a valid return | |||
2022-08-10 | code refactoring | Frederick Muriuki Muriithi | |
2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui | |
2022-08-10 | code refactoring | Frederick Muriuki Muriithi | |
2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui | |
2022-08-10 | enhancements for rust tissue | Frederick Muriuki Muriithi | |
2022-08-10 | pylint fixes | Alexander_Kabui | |
2022-08-10 | update test;parse output | Alexander_Kabui | |
2022-08-10 | code refactoring | Alexander_Kabui | |
2022-08-10 | remove unnessary code | Alexander_Kabui | |
2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui | |
2022-08-10 | merge for results | Alexander_Kabui | |
2022-08-10 | enhancements for rust tissue | Alexander_Kabui | |
2022-08-03 | Refactor: Remove unnecessary whitespace and name | Frederick Muriuki Muriithi | |
2022-08-03 | Refactor: Remove unnecessary iterations and name | Frederick Muriuki Muriithi | |
* remove extra iteration that is unnecessary * remove unnecessary variables | |||
2022-07-29 | New script to run sample correlations | Frederick Muriuki Muriithi | |
* README.md: update mypy's invocation * scripts/argparse_actions.py: new file - implement custom FileCheck action for argparse * scripts/sample_correlations.py: new file - implement new script to run sample correlations in an external process | |||
2022-07-29 | Fix failing tests | Frederick Muriuki Muriithi | |
* gn3/computations/correlations.py: rename function * mypy.ini: deactivate mypy error about missing imports * tests/integration/test_correlation.py: mock correct function * tests/unit/computations/test_correlation.py: test correct function | |||
2022-07-28 | Add command to run the sample correlations in an external process | Frederick Muriuki Muriithi | |
2022-07-28 | Update sample correlations code to use multiprocessing | Frederick Muriuki Muriithi | |
* To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module. | |||
2022-07-22 | mypy fixes | Alexander_Kabui | |
2022-07-22 | pep8 fixes | Alexander_Kabui | |
2022-07-22 | linting and tests fixes | Alexander_Kabui | |
2022-07-22 | import rust_correlation when running gn3 as lib | Alexander_Kabui | |
2022-07-22 | compute num overlap | Alexander_Kabui | |
2022-07-22 | fix for bug splitting list data | Alexander_Kabui | |
2022-07-22 | minor fixes for parsing data | Alexander_Kabui | |
2022-07-22 | code to parse tissue correlation input | Alexander_Kabui | |
2022-07-22 | mypy pylint fixes | Alexander_Kabui | |
2022-07-22 | code to fetch correct sample corr data | Alexander_Kabui | |