| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-08-31 | Add qnorm option to mapping api | zsloan | |
| 2022-08-31 | Move normf function out of quantile_normalize_vals so it can be imported by ↵ | zsloan | |
| mapping api | |||
| 2022-08-31 | Fix failing api/test_mapping.py test | zsloan | |
| 2022-08-31 | Re-add read_from_pyfile | Munyoki Kilyungi | |
| * wqflask/wqflask/database.py (read_from_pyfile): Re-add it. This is used in the sql_uri() function. | |||
| 2022-08-30 | Remove logging and unused imports from api/mapping.py | zsloan | |
| 2022-08-30 | Add genofile parameter to mapping API endpoint | zsloan | |
| 2022-08-30 | Close a database connection only once | Munyoki Kilyungi | |
| * wqflask/wqflask/database.py (database_connection): Close connection only once; otherwise an error is raised. | |||
| 2022-08-25 | Merge branch 'chores/gn2-queries-optimization' of ↵ | Frederick Muriuki Muriithi | |
| github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/gn2-queries-optimization | |||
| 2022-08-24 | Fix issue where literature correlations were always run against their own ↵ | zsloan | |
| dataset, instead of the target dataset | |||
| 2022-08-24 | Limit literature correlation results to top N as specified in the form | zsloan | |
| 2022-08-23 | Add support for database rollbacks if the db engine supports it. | Munyoki Kilyungi | |
| * wqflask/wqflask/database.py: Import contextlib. (database_connection): Refactor to support roll-backs. | |||
| 2022-08-23 | Delete unused function and imports. | Munyoki Kilyungi | |
| * wqflask/wqflask/database.py: Remove unused sqlalchemy imports. (read_from_pyfile): Delete it. | |||
| 2022-08-23 | integrate code for fetching traits metadata | Alexander_Kabui | |
| 2022-08-23 | function to fetch metadata | Alexander_Kabui | |
| 2022-08-20 | Divide GEMMA additive effect by 2 | zsloan | |
| 2022-08-20 | Fix JS for opening new tabs (or not) for collection page tools/options | zsloan | |
| 2022-08-18 | bulk fetch n number of traits type probeset | Alexander_Kabui | |
| 2022-08-17 | Use context managers for database cursors | Frederick Muriuki Muriithi | |
| 2022-08-17 | Merge branch 'chores/rust-enhancements' of ↵ | Frederick Muriuki Muriithi | |
| github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/rust-enhancements | |||
| 2022-08-16 | Merge dicts into single result | Frederick Muriuki Muriithi | |
| 2022-08-16 | Convert list items to single dict | Frederick Muriuki Muriithi | |
| 2022-08-16 | rename boolean variables | Alexander_Kabui | |
| 2022-08-16 | linter fixes | Alexander_Kabui | |
| 2022-08-16 | enable compute all for test | Alexander_Kabui | |
| 2022-08-16 | index error fix | Alexander_Kabui | |
| 2022-08-16 | remove flask g object | Alexander_Kabui | |
| 2022-08-16 | minor fixes for computing all correlations | Alexander_Kabui | |
| 2022-08-15 | add default values for num overlap,corr_coeff | Alexander_Kabui | |
| 2022-08-14 | init:perform top n sample for probes | Alexander_Kabui | |
| 2022-08-12 | Revert "Check for keys before using them." | Frederick Muriuki Muriithi | |
| This reverts commit a1cbc12f843bbdc1759d5acac5ae3630fb5d4b81. | |||
| 2022-08-12 | Add a profiling script | Frederick Muriuki Muriithi | |
| Add a script to enable profiling the code. | |||
| 2022-08-12 | Fix some issues with the tests. Add notes in code for improvements. | Frederick Muriuki Muriithi | |
| 2022-08-12 | Refactor: separate the three correlation types | Frederick Muriuki Muriithi | |
| Refactor the code such that each correlation type (sample, tissue, literature) is computed in its own function. This makes the code clearer, and helps reduce repetition. | |||
| 2022-08-12 | Check for keys before using them. | Frederick Muriuki Muriithi | |
| 2022-08-12 | Update format to prevent tissue correlation from failing | Frederick Muriuki Muriithi | |
| Update the data format of returned values so that it conforms with expectatitions. | |||
| 2022-08-12 | Fix formatting for legibility | Frederick Muriuki Muriithi | |
| 2022-08-12 | code to merge results;minor fixes | Alexander_Kabui | |
| 2022-08-12 | compute top n tissue results | Alexander_Kabui | |
| 2022-08-12 | add code to compute top n tissue results | Alexander_Kabui | |
| 2022-08-12 | Fix minor bug. | Frederick Muriuki Muriithi | |
| 2022-08-12 | Integrate rust correlations. Deduplicate similar code. | Frederick Muriuki Muriithi | |
| - Use rust correlations rather than the slower python one - Remove code duplicated in the `wqflask/wqflask/correlation/rust_correlation.py` module within the `compute_correlation_rust` function. | |||
| 2022-08-11 | Add data-trait-info attribute to checkboxes on search results page | zsloan | |
| Currently there's a separate trait_info_str function in search_results.py, because search_results.py doesn't build the trait objects (so it can't use the one in collect.py unless I change that to accept traits as either a GeneralTrait class or dict - which might be better, I'm not sure) | |||
| 2022-08-09 | Display the probeset name in the editing form | Munyoki Kilyungi | |
| * wqflask/wqflask/templates/edit_probeset.html: Add probeset.name to the h1 tag. | |||
| 2022-08-09 | Make edit_probeset.html similar to corresponding phenotype page | Munyoki Kilyungi | |
| * wqflask/wqflask/templates/edit_probeset.html: Remove "reset" button. Make button green. Move form element into the "container" div. Add "container" class to form. Left justify labels, and the button. Remove ":" from labels. | |||
| 2022-08-09 | Delete "diff" section | Munyoki Kilyungi | |
| For both the edit phenotype and probeset pages, the diffs can be viewed from history.html. * wqflask/wqflask/templates/edit_phenotype.html: Delete "diffs" section. * wqflask/wqflask/templates/edit_probeset.html: Ditto. | |||
| 2022-08-09 | Remove "diff" logic from edit_probeset | Munyoki Kilyungi | |
| * wqflask/wqflask/metadata_edits.py (edit_probeset): Delete logic for fetching diff. Move that... (show_history): ... here * wqflask/wqflask/templates/edit_probeset.html: Update template to show diffs in a history.html. Reposition and rename the h1 tag of this page. | |||
| 2022-08-09 | Update h1 title of history page | Munyoki Kilyungi | |
| ATM, we don't show the name of the phenotype whose history we are changing. That may be updated in a future commit. * wqflask/wqflask/templates/edit_history.html: Reword h1 and remove "{{}}" which results in a jinja error. | |||
| 2022-08-09 | Fix circular import issue | Frederick Muriuki Muriithi | |
| 2022-08-09 | Integrate rust correlation for "sample" correlation selection | Frederick Muriuki Muriithi | |
| Integrate the use of the rust code to compute the correlations for the "sample" correlation selection. | |||
| 2022-08-09 | Pass trait values (X) as list not string | Frederick Muriuki Muriithi | |
| The trait values (X values) are converted to JSON within the `run_correlation` call. Since JSON has the ability to represent lists of objects, there is no point for the added conversion to and from strings. | |||
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