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2022-08-30Close a database connection only onceMunyoki Kilyungi
* wqflask/wqflask/database.py (database_connection): Close connection only once; otherwise an error is raised.
2022-08-25Merge branch 'Alexanderlacuna-chores/gn2-queries-optimization' into testingFrederick Muriuki Muriithi
2022-08-25Merge branch 'chores/gn2-queries-optimization' of ↵Frederick Muriuki Muriithi
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/gn2-queries-optimization
2022-08-24Fix issue where literature correlations were always run against their own ↵zsloan
dataset, instead of the target dataset
2022-08-24Limit literature correlation results to top N as specified in the formzsloan
2022-08-23Add 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.
2022-08-23Delete unused function and imports.Munyoki Kilyungi
* wqflask/wqflask/database.py: Remove unused sqlalchemy imports. (read_from_pyfile): Delete it.
2022-08-23integrate code for fetching traits metadataAlexander_Kabui
2022-08-23function to fetch metadataAlexander_Kabui
2022-08-20Divide GEMMA additive effect by 2zsloan
2022-08-20Fix JS for opening new tabs (or not) for collection page tools/optionszsloan
2022-08-19Fix message and function keyFrederick Muriuki Muriithi
2022-08-18bulk fetch n number of traits type probesetAlexander_Kabui
2022-08-17Reduce incremental backoff timeFrederick Muriuki Muriithi
2022-08-17Do incremental backoff for mechanical rob testsFrederick Muriuki Muriithi
Sometimes the tests might be run before the service has began running. This commit delays the running of the tests for a while.
2022-08-17Merge branch 'Alexanderlacuna-chores/rust-enhancements' into testingFrederick Muriuki Muriithi
2022-08-17Use context managers for database cursorsFrederick Muriuki Muriithi
2022-08-17Merge branch 'chores/rust-enhancements' of ↵Frederick Muriuki Muriithi
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/rust-enhancements
2022-08-16Merge dicts into single resultFrederick Muriuki Muriithi
2022-08-16Convert list items to single dictFrederick Muriuki Muriithi
2022-08-16rename boolean variablesAlexander_Kabui
2022-08-16linter fixesAlexander_Kabui
2022-08-16enable compute all for testAlexander_Kabui
2022-08-16index error fixAlexander_Kabui
2022-08-16remove flask g objectAlexander_Kabui
2022-08-16minor fixes for computing all correlationsAlexander_Kabui
2022-08-16Setup default GN_PROXY settingFrederick Muriuki Muriithi
2022-08-15add default values for num overlap,corr_coeffAlexander_Kabui
2022-08-14init:perform top n sample for probesAlexander_Kabui
2022-08-12Update to newer lxml APIFrederick Muriuki Muriithi
2022-08-12Revert "Check for keys before using them."Frederick Muriuki Muriithi
This reverts commit a1cbc12f843bbdc1759d5acac5ae3630fb5d4b81.
2022-08-12Merge branch 'integrate-rust-correlations' of ↵Frederick Muriuki Muriithi
github.com:genenetwork/genenetwork2 into integrate-rust-correlations
2022-08-12Add a profiling scriptFrederick Muriuki Muriithi
Add a script to enable profiling the code.
2022-08-12Fix some issues with the tests. Add notes in code for improvements.Frederick Muriuki Muriithi
2022-08-12Refactor: separate the three correlation typesFrederick 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.
2022-08-12Fix correlation tests: Fix the test message.Frederick Muriuki Muriithi
2022-08-12Check for keys before using them.Frederick Muriuki Muriithi
2022-08-12Update format to prevent tissue correlation from failingFrederick Muriuki Muriithi
Update the data format of returned values so that it conforms with expectatitions.
2022-08-12Check that the correlations work as expected.Frederick Muriuki Muriithi
2022-08-12Fix formatting for legibilityFrederick Muriuki Muriithi
2022-08-12code to merge results;minor fixesAlexander_Kabui
2022-08-12compute top n tissue resultsAlexander_Kabui
2022-08-12add code to compute top n tissue resultsAlexander_Kabui
2022-08-12Fix minor bug.Frederick Muriuki Muriithi
2022-08-12Integrate 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.
2022-08-12Add a profiling scriptFrederick Muriuki Muriithi
Add a script to enable profiling the code.
2022-08-12Fix some issues with the tests. Add notes in code for improvements.Frederick Muriuki Muriithi
2022-08-11Add data-trait-info attribute to checkboxes on search results pagezsloan
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)
2022-08-11Refactor: separate the three correlation typesFrederick 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.
2022-08-11Fix correlation tests: Fix the test message.Frederick Muriuki Muriithi
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-19 14:35:54 +0000