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2022-10-20Clean Up: Remove unused functionFrederick Muriuki Muriithi
* The function `generate_corr_json` was not used anywhere in the code.
2022-10-19Remove `/test_corr_compute' endpointFrederick Muriuki Muriithi
* Remove the `/test_corr_compute` endpoint that has been superceded by the `/corr_compute` endpoint.
2022-10-18Change qtlreaper default settings to 1000 permutations and 0 bootstrapszsloan
2022-10-18Convert LRS to LOD/-logP for global search resultszsloan
2022-10-18Change logic in retrieve_trait_info to account for situations where a marker ↵zsloan
doesn't have a position in the DB
2022-10-18Change bnw link to https, which seems to fix itzsloan
2022-10-18In collection table, show the trait name in the Symbol column if there's no ↵zsloan
symbol, and show location or name in the Description column if there's no description
2022-10-18Sanitise generated filenamesFrederick Muriuki Muriithi
* wqflask/wqflask/correlation/pre_computes.py: Sanitise the generated filenames to get rid of characters that have special meanings in a file path, and other characters that are just a nuisance.
2022-10-17Fix correlation filter logiczsloan
2022-10-17Fix bug when initializing Temp DatasetGroupszsloan
2022-10-14Add BXD_GROUP_EXCEPTIONS to webqtlConfig.py instead of having the groups ↵zsloan
hardcoded into show_trait.build_correlation_tools (+ add BXD-Heart-Metals to that list) I'm not sure why this logic exists, so it might be removed entirely later. I'm asking Rob
2022-10-14Add redis_conn as argument to get_samplelist callszsloan
2022-10-14Declare search prefixes as boolean.Arun Isaac
Boolean search prefixes are used to filter the result set whereas non-boolean search prefixes merely contribute to the relevance score of the document. * wqflask/wqflask/gsearch.py (GSearch.__init__): Declare all search prefixes except description as boolean.
2022-10-14Update mock: Return correct test data.Frederick Muriuki Muriithi
2022-10-14Use f-strings to do string interpolationFrederick Muriuki Muriithi
2022-10-14Set up year of publication correctly.Frederick Muriuki Muriithi
2022-10-13Set scrollX to 100% in DataTables default settingszsloan
This should fix the issue where horizontal scrolling ruins the header/row alignment
2022-10-12Use SQL to fetch trait metadata instead of gn-proxy, since it's dramatically ↵zsloan
faster
2022-10-12Add filtering logic for correlation resultszsloan
2022-10-12Include chr/mb in trait metadatazsloan
2022-10-12Account for empty strings in get_string functionzsloan
2022-10-12Remove Test Correlation button and Biweight Midcorrelation optionzsloan
2022-10-12Include chr/mb values in jsonable traitzsloan
2022-10-12Commit missing html page.Frederick Muriuki Muriithi
2022-10-11Only compute Lit/Tissue corr when main trait's dataset is of type ProbeSetzsloan
2022-10-11Fix block_by_index ID referenced in show_trait.jszsloan
2022-10-11Change Interval Analyst table to use new GeneList tablezsloan
The query changes in GeneUtil.pyi (to insert column names using string formatting) are definitely some sort of SQL injection issue, but I'm not sure how else to do it Also, the table name will be changed later, once the new table has been tested for a while.
2022-10-11Remove logging from validation.jszsloan
2022-10-10Replace GeneList table name with new tablezsloan
Once this is confirmed to be working as expected, it will be changed back to GeneList (and the old table's name will be changed)
2022-10-08Added Shelby to creditsPjotr Prins
2022-10-08Update link to public datasetsPjotr Prins
2022-10-06DEBUG: More infoFrederick Muriuki Muriithi
2022-10-06DEBUG: More debug of CI/CD.Frederick Muriuki Muriithi
2022-10-06DEBUG: Collect more info to debug CI/CDFrederick Muriuki Muriithi
2022-10-06Check for incompatible datasets for various correlation types.Frederick Muriuki Muriithi
2022-10-05fix bug use target dataset for top n correlationAlexander_Kabui
2022-10-05remove data preprocessing for top n samplesAlexander_Kabui
2022-10-05Handle correlation errorFrederick Muriuki Muriithi
* Handle the correlation error such that it gives the user a better message for the cause of the error, instead of displaying the exception.
2022-10-05Bug: Check for compatible datasets for a correlation typeFrederick Muriuki Muriithi
2022-10-05bug: Use target dataset when computing tissue correlationsFrederick Muriuki Muriithi
2022-10-04Fix bug where dataset_name was being passed into get_samplelist query ↵zsloan
instead of group_id
2022-10-04Pass redis_conn to get_samplelistzsloan
2022-10-04Initialize result_list for /traits endpoint JSON outputzsloan
2022-10-04Remove unnecessary variableFrederick Muriuki Muriithi
Just assign the value of the function call directly to the dictionary key rather than using an intermediate variable.
2022-10-04Add more information to exception to help in debuggingFrederick Muriuki Muriithi
2022-10-03Bug: Don't process data for output earlyFrederick Muriuki Muriithi
* The ",".join(...) call was processing the data for output to file, way too early, which would lead to errors down the line, very far removed from the actual cause of the error.
2022-09-30Reformat statementFrederick Muriuki Muriithi
2022-09-30Remove unused table and simplify queryFrederick Muriuki Muriithi
2022-09-30Raise hard-limit on search results to 10k.Arun Isaac
* wqflask/wqflask/gsearch.py (MAX_SEARCH_RESULTS): Set to 10k.
2022-09-30Disregard permissions when displaying search results.Arun Isaac
* wqflask/wqflask/gsearch.py: Do not import types. (is_permitted_for_listing): Delete function. (GSearch.__init__): Do not call is_permitted_for_listing.
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