| Age | Commit message (Expand) | Author |
|---|
| 2022-11-02 | Update Phenogen URL to rn7 | zsloan |
| 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...collection page
I think the Monad stuff Bonface/Arun are doing might address situations
like this better.
| zsloan |
| 2022-10-28 | Add `sample_data` argument to function call.run-corrs-in-external-process | Frederick Muriuki Muriithi |
| 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 |
