| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | 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 | |
| 2022-10-12 | Include chr/mb values in jsonable trait | zsloan | |
| 2022-10-12 | Commit missing html page. | Frederick Muriuki Muriithi | |
| 2022-10-11 | Only compute Lit/Tissue corr when main trait's dataset is of type ProbeSet | zsloan | |
| 2022-10-11 | Fix block_by_index ID referenced in show_trait.js | zsloan | |
| 2022-10-11 | Change Interval Analyst table to use new GeneList table | zsloan | |
| 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. | |||
| 2022-10-11 | Remove logging from validation.js | zsloan | |
| 2022-10-10 | Replace GeneList table name with new table | zsloan | |
| 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) | |||
| 2022-10-08 | Added Shelby to credits | Pjotr Prins | |
| 2022-10-08 | Update link to public datasets | Pjotr Prins | |
| 2022-10-06 | DEBUG: More info | Frederick Muriuki Muriithi | |
| 2022-10-06 | DEBUG: More debug of CI/CD. | Frederick Muriuki Muriithi | |
| 2022-10-06 | DEBUG: Collect more info to debug CI/CD | Frederick Muriuki Muriithi | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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