| Age | Commit message (Expand) | Author |
|---|
| 2022-10-28 | Fix imports...* Fix imports I broke when rebasing.
| Frederick Muriuki Muriithi |
| 2022-10-28 | Refactor: 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 |
| 2022-10-28 | Settings: Add the `REDIS_URL` setting. | Frederick Muriuki Muriithi |
| 2022-10-28 | Declutter stdout...* wqflask/utility/tools.py: Output extraneous messages to stderr
rather than stdout to avoid cluttering the output.
| Frederick Muriuki Muriithi |
| 2022-10-28 | Refactor: 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 |
| 2022-10-28 | Add 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 |
| 2022-10-28 | Query 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 |
| 2022-10-28 | Remove 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 |
| 2022-10-27 | init fix for querying for datasets | Alexander_Kabui |
| 2022-10-26 | Remove Owner from phenotype editing, since it only applies to the GN1 Owner f... | zsloan |
| 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...* 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 |
| 2022-10-20 | Clean Up: Remove unused function...* The function `generate_corr_json` was not used anywhere in the code.
| Frederick Muriuki Muriithi |
| 2022-10-19 | Remove `/test_corr_compute' endpoint...* Remove the `/test_corr_compute` endpoint that has been superceded by
the `/corr_compute` endpoint.
| Frederick Muriuki Muriithi |
| 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 |
| 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 s... | zsloan |
| 2022-10-18 | Sanitise 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 |
| 2022-10-17 | 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 hard......I'm not sure why this logic exists, so it might be removed entirely later. I'm asking Rob
| zsloan |
| 2022-10-14 | Add redis_conn as argument to get_samplelist calls | zsloan |
| 2022-10-14 | Declare 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 |
| 2022-10-14 | 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...This should fix the issue where horizontal scrolling ruins the header/row alignment
| zsloan |
| 2022-10-12 | Use SQL to fetch trait metadata instead of gn-proxy, since it's dramatically ... | zsloan |
| 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...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 |
| 2022-10-11 | Remove logging from validation.js | zsloan |
| 2022-10-10 | Replace GeneList table name with new table...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)
| zsloan |
| 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 |
