| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-11-02 | Enable Verify button for Genotype traits | zsloan | |
| 2022-10-31 | Fix error when there's no human data in GeneList | zsloan | |
| 2022-10-31 | Only show Tissue in trait page for ProbeSet traits | zsloan | |
| 2022-10-31 | Add md5 js file (needed for adding to collections) | zsloan | |
| 2022-10-31 | Update Rat links to rn7 | zsloan | |
| 2022-10-30 | Address situations where Additive Effect is an empty string for view | zsloan | |
| collection page I think the Monad stuff Bonface/Arun are doing might address situations like this better. | |||
| 2022-10-28 | Increase back-off time before mechanical-rob tests run | Frederick Muriuki Muriithi | |
| 2022-10-28 | Fix typo | Frederick Muriuki Muriithi | |
| 2022-10-28 | Add `sample_data` argument to function call.run-corrs-in-external-process | Frederick Muriuki Muriithi | |
| 2022-10-28 | Fix imports | Frederick Muriuki Muriithi | |
| * Fix imports I broke when rebasing. | |||
| 2022-10-28 | Wait until results page is loaded before returning the results | Frederick Muriuki Muriithi | |
| 2022-10-28 | Refactor: run correlation computation externally | Frederick Muriuki Muriithi | |
| * 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. | |||
| 2022-10-28 | Settings: Add the `REDIS_URL` setting. | Frederick Muriuki Muriithi | |
| 2022-10-28 | Declutter stdout | Frederick Muriuki Muriithi | |
| * wqflask/utility/tools.py: Output extraneous messages to stderr rather than stdout to avoid cluttering the output. | |||
| 2022-10-28 | Refactor: Pass user id to `check_resource_availability` | Frederick Muriuki Muriithi | |
| * 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. | |||
| 2022-10-28 | Add external process manager | Frederick Muriuki Muriithi | |
| * wqflask/jobs/__init__.py: New jobs module * wqflask/jobs/jobs.py: New jobs module * wqflask/scripts/run_external.py: new external process manager. | |||
| 2022-10-28 | Query genenetwork3 API for search. | Arun Isaac | |
| 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. | |||
| 2022-10-28 | Remove xapian indexing script. | Arun Isaac | |
| The xapian indexing script has been moved to genenetwork3. All further development will happen there. * wqflask/scripts/index.py: Delete file. | |||
| 2022-10-27 | init fix for querying for datasets | Alexander_Kabui | |
| 2022-10-26 | Remove Owner from phenotype editing, since it only applies to the GN1 Owner ↵ | zsloan | |
| field and is misleading in GN2 | |||
| 2022-10-26 | Add Edit Privileges button to trait page | zsloan | |
| 2022-10-26 | Fix group manager link | zsloan | |
| 2022-10-23 | Inlcude redis_conn in MockGroup for get_samplelist | zsloan | |
| 2022-10-23 | Fix Variant Browser's db_cursor issues | zsloan | |
| 2022-10-22 | Merge pull request #739 from Alexanderlacuna/fix/samplelist-parsing | Alexander Kabui | |
| fix issue;parsing sample data | |||
| 2022-10-22 | fix issue;parsing sample data | Alexander_Kabui | |
| 2022-10-21 | Fix logic for determining samplelist in correlations | zsloan | |
| 2022-10-20 | Cleanup: Remove unused code | Frederick Muriuki Muriithi | |
| * 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. | |||
| 2022-10-20 | Clean Up: Remove unused function | Frederick Muriuki Muriithi | |
| * The function `generate_corr_json` was not used anywhere in the code. | |||
| 2022-10-19 | Remove `/test_corr_compute' endpoint | Frederick Muriuki Muriithi | |
| * Remove the `/test_corr_compute` endpoint that has been superceded by the `/corr_compute` endpoint. | |||
| 2022-10-18 | Change qtlreaper default settings to 1000 permutations and 0 bootstraps | zsloan | |
| 2022-10-18 | Convert LRS to LOD/-logP for global search results | zsloan | |
| 2022-10-18 | Change logic in retrieve_trait_info to account for situations where a marker ↵ | zsloan | |
| doesn't have a position in the DB | |||
| 2022-10-18 | Change bnw link to https, which seems to fix it | zsloan | |
| 2022-10-18 | In 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 | |||
| 2022-10-18 | Sanitise generated filenames | Frederick 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. | |||
| 2022-10-17 | Fix correlation filter logic | zsloan | |
| 2022-10-17 | Fix bug when initializing Temp DatasetGroups | zsloan | |
| 2022-10-14 | Add 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 | |||
| 2022-10-14 | Add redis_conn as argument to get_samplelist calls | zsloan | |
| 2022-10-14 | Declare 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. | |||
| 2022-10-14 | Update mock: Return correct test data. | Frederick Muriuki Muriithi | |
| 2022-10-14 | Use f-strings to do string interpolation | Frederick Muriuki Muriithi | |
| 2022-10-14 | Set up year of publication correctly. | Frederick Muriuki Muriithi | |
| 2022-10-13 | Set scrollX to 100% in DataTables default settings | zsloan | |
| This should fix the issue where horizontal scrolling ruins the header/row alignment | |||
| 2022-10-12 | Use SQL to fetch trait metadata instead of gn-proxy, since it's dramatically ↵ | zsloan | |
| faster | |||
| 2022-10-12 | Add filtering logic for correlation results | zsloan | |
| 2022-10-12 | Include chr/mb in trait metadata | zsloan | |
| 2022-10-12 | Account for empty strings in get_string function | zsloan | |
| 2022-10-12 | Remove Test Correlation button and Biweight Midcorrelation option | zsloan | |
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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