| Age | Commit message (Expand) | Author |
|---|
| 2022-10-28 | Add search....* gn3/api/search.py: New file.
* gn3/app.py: Register the search blueprint.
| 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 |
| 2022-10-25 | Reshape column major genotype database storage correctly....* gn3/genodb.py (matrix): Reshape column major genotype database storage as
ncols x nrows instead of as nrows x ncols.
| Arun Isaac |
| 2022-10-22 | fix issue;parsing sample data (#102) | Alexander Kabui |
| 2022-10-18 | Add xapian indexing script....* scripts/index-genenetwork: New file.
* setup.py (install_requires): Add click, pymonad and xapian-bindings.
(scripts): Add scripts/index-genenetwork.
| Arun Isaac |
| 2022-10-18 | Support server side SQL query retrieval....* gn3/monads.py: Import SSDictCursor from MySQLdb.cursors.
(query_sql): Add server_side argument.
| 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 |
| 2022-10-18 | Add monadic utilities....* gn3/monads.py: New file.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Munyoki Kilyungi |
| 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...* 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.
| Frederick Muriuki Muriithi |
| 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...Use the built-in csv module for file output in order to avoid subtle errors in
the formats.
| Frederick Muriuki Muriithi |
| 2022-09-06 | Update link to continuous deployment....* README.md: Update link to continuous deployment.
| Arun Isaac |
| 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()...* 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.
| Munyoki Kilyungi |
| 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 |
| 2022-08-12 | Add mandatory/expected fields to parsed data. | Frederick Muriuki Muriithi |
| 2022-08-10 | Fix returned value for 'parse_correlation_output'...* Always return dict
* Fix internal '__parse_line__' to always have a valid return
| Frederick Muriuki Muriithi |
| 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...* remove extra iteration that is unnecessary
* remove unnecessary variables
| Frederick Muriuki Muriithi |
| 2022-07-29 | New script to run sample correlations...* 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
| Frederick Muriuki Muriithi |
| 2022-07-29 | Fix failing tests...* 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
| Frederick Muriuki Muriithi |
| 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...* To help speed up the processing of the correlations, convert the
`compute_all_sample_correlation` function to use the multiprocessing module.
| Frederick Muriuki Muriithi |
| 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 |
| 2022-07-22 | delete dead_code;rename variables | Alexander_Kabui |
