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2022-10-30Address situations where Additive Effect is an empty string for view...collection page I think the Monad stuff Bonface/Arun are doing might address situations like this better. zsloan
2022-10-28Increase back-off time before mechanical-rob tests runFrederick Muriuki Muriithi
2022-10-28Fix typoFrederick Muriuki Muriithi
2022-10-28Add `sample_data` argument to function call.run-corrs-in-external-processFrederick Muriuki Muriithi
2022-10-28Fix imports...* Fix imports I broke when rebasing. Frederick Muriuki Muriithi
2022-10-28Wait until results page is loaded before returning the resultsFrederick Muriuki Muriithi
2022-10-28Refactor: run correlation computation externally...* wqflask/scripts/corr_compute.py: move correlation computation to external script. * wqflask/wqflask/templates/loading_corrs.html: Provide UI to display while computation is still not complete. * wqflask/wqflask/views.py: Dispatch correlation computation to external script and display appropriate UI for each valid state of the computation. Frederick Muriuki Muriithi
2022-10-28Settings: Add the `REDIS_URL` setting.Frederick Muriuki Muriithi
2022-10-28Declutter stdout...* wqflask/utility/tools.py: Output extraneous messages to stderr rather than stdout to avoid cluttering the output. Frederick Muriuki Muriithi
2022-10-28Refactor: Pass user id to `check_resource_availability`...* Pass the user_id for the current user to the `check_resource_availability` function as an argument, rather than using the global `g.user_session.user_id` value. Frederick Muriuki Muriithi
2022-10-28Add external process manager...* wqflask/jobs/__init__.py: New jobs module * wqflask/jobs/jobs.py: New jobs module * wqflask/scripts/run_external.py: new external process manager. Frederick Muriuki Muriithi
2022-10-28Query genenetwork3 API for search....genenetwork2 should be a thin wrapper web UI around the genenetwork3 API. Hence, this move. * etc/default_settings.py (XAPIAN_DB_PATH): Delete variable. * wqflask/wqflask/database.py: Remove xapian import. (xapian_database, xapian_writable_database): Delete functions. * wqflask/wqflask/gsearch.py: Do not import json, xapian, Nothing from pymonad.maybe, base, utility.authentication_tools and wqflask.database. Import MonadicDict from gn3.monads instead of utility.monads and GN3_LOCAL_URL from utility.tools. (GSearch.__init__): Query genenetwork3 search API instead of directly reading a Xapian index. Arun Isaac
2022-10-28Remove xapian indexing script....The xapian indexing script has been moved to genenetwork3. All further development will happen there. * wqflask/scripts/index.py: Delete file. Arun Isaac
2022-10-27init fix for querying for datasetsAlexander_Kabui
2022-10-26Remove Owner from phenotype editing, since it only applies to the GN1 Owner f...zsloan
2022-10-26Add Edit Privileges button to trait pagezsloan
2022-10-26Fix group manager linkzsloan
2022-10-23Inlcude redis_conn in MockGroup for get_samplelistzsloan
2022-10-23Fix Variant Browser's db_cursor issueszsloan
2022-10-22Merge pull request #739 from Alexanderlacuna/fix/samplelist-parsing...fix issue;parsing sample dataAlexander Kabui
2022-10-22fix issue;parsing sample dataAlexander_Kabui
2022-10-21Fix logic for determining samplelist in correlationszsloan
2022-10-20Cleanup: Remove unused code...* Commit 49580eb9cd47bb2ce15fd44be11bb9580d85efef removed the use of the gn-proxy, but left some code that was used expressly for use with the gn-proxy. This commit removes that code. Frederick Muriuki Muriithi
2022-10-20Clean Up: Remove unused function...* The function `generate_corr_json` was not used anywhere in the code. Frederick Muriuki Muriithi
2022-10-19Remove `/test_corr_compute' endpoint...* Remove the `/test_corr_compute` endpoint that has been superceded by the `/corr_compute` endpoint. Frederick Muriuki Muriithi
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
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 s...zsloan
2022-10-18Sanitise generated filenames...* 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. Frederick Muriuki Muriithi
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 hard......I'm not sure why this logic exists, so it might be removed entirely later. I'm asking Rob zsloan
2022-10-14Add redis_conn as argument to get_samplelist callszsloan
2022-10-14Declare search prefixes as boolean....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. Arun Isaac
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 settings...This should fix the issue where horizontal scrolling ruins the header/row alignment zsloan
2022-10-12Use SQL to fetch trait metadata instead of gn-proxy, since it's dramatically ...zsloan
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 table...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. zsloan