| Age | Commit message (Expand) | Author |
|---|
| 2022-04-07 | Run python-black on file...* wqflask/wqflask/metadata_edits.py: Run "black -l 79
wqflask/wqflask/metadata_edits.py"
| BonfaceKilz |
| 2022-04-07 | Create a new page to display case-attributes and their descriptions...* wqflask/wqflask/metadata_edits.py: Import
"gn3.db.sample_data.get_case_attributes".
(show_case_attribute_columns): New function/ end-point to show
case-attributes.
* wqflask/tests/integration/wqflask/test_metadata_edits.py: New
integration tests for the above.
* wqflask/tests/integration/wqflask/__init__.py: New file.
* wqflask/wqflask/templates/case_attributes.html: New template file to
display the above.
| BonfaceKilz |
| 2022-04-06 | Changed some styling for the edit_phenotype template | zsloan |
| 2022-04-05 | Fix combined searches involving aliases...The logic for building the SQL query wasn't working correctly when
aliases were involved. The query also checks for a gene symbol's aliases
in the DB, but this wasn't properly handling the AND/OR logic, leading
to no results being shown when doing a "Get Combined" search involving a
gene symbol.
This also removed some unused code related to aliases.
| zsloan |
| 2022-04-04 | Return None in load_json_from_redis when the item doesn't exist...For some reason that isn't clear to me yet, a logged-in user session ID
was set even when a user wasn't logged in, causing the user session code
to attempt to fetch user information for a non-existent user ID
| zsloan |
| 2022-04-04 | Change UserSession to properly remove user session ID when not logged in...It's not entirely clear to me exactly why the previous logic wasn't
working correctly, but this change (that removes the user cookie when
there's no user_session after the request and returns None if there
aren't any user_details) appears to fix the issue.
The main confusing part is why the user_cookie still exists even when
not logged in
| zsloan |
| 2022-04-01 | Fix the way database_connection was being called in 2 places in...metadata_edits.py
For some reason there were two places where it wasn't being called as a
function. Fixing this appears to have fixed the error
| zsloan |
| 2022-03-31 | Add another check for >1 markers on a chromosome for interval mapping...There were two places this needed to be checked and I previously missed
this one
| zsloan |
| 2022-03-31 | Replace 'User Account Settings' with user's e-mail and add user_email...property to user_session
Also changed the order of the dropdowns to have Sign Out after the user
drop-down, to more closely match NCBI's style
| zsloan |
| 2022-03-31 | Fix the way database_connector is called...The function returns a call to mdb.connect, which only returns the
connection object. It was throwing an error due to trying to unpack
multiple items.
One thing I noticed while looking at this is that we should probably
decide on a single way to create these connections. In some other files,
we instead use database_connection from wqflask.database (instead of the
gn3 database_connector from gn3.db_utils)
| zsloan |
| 2022-03-30 | Merge pull request #690 from Alexanderlacuna/chore/ctl-wgcna-enhancements...Chore/ctl wgcna enhancements | Alexander Kabui |
| 2022-03-30 | Remove double-encoding to json...Passing the data into `requests.post` as a `json=...` argument will
automatically encode the data to JSON and set up the correct
Content-Type header.
The call `json.dumps(post_data)` was pre-encoding the data to a JSON
string, that was the re-encoded to JSON yet again, which is not what
we want. This commit fixes that.X
| Frederick Muriuki Muriithi |
| 2022-03-25 | Fix Spearman Rank correlation appearing as 'r' instead of 'rho' | zsloan |
| 2022-03-25 | Fix issues that prevented genotype traits from being added to collections...Some of this was caused by heatmaps supporting code; that code should probably pass the traits differently than the way it does in the "trait_info_str" function
| zsloan |
| 2022-03-24 | Merge pull request #691 from zsloan/bug/fix_qtlreaper_snp_order...Bug/fix qtlreaper snp order | zsloan |
| 2022-03-24 | Check if there's only one coordinate for interval mapping...This is meant to deal with edge cases where there's only a single coordinate for a chromosome when doing interval mapping (which causes an error, since interval mapping requires that markers be linked within each chromosome)
| zsloan |
| 2022-03-24 | Fix qtlreaper results sorting to deal with M as chromosome (should be at the ......Not sure how best to do this; I just had the sort algorithm change "M" to "z" (which will always be sorted last, behind X and Y)
| zsloan |
| 2022-03-24 | code refactoring | Alexander Kabui |
| 2022-03-24 | display parametric values used | Alexander Kabui |
| 2022-03-24 | rename template to gn3_wgcna_results | Alexander Kabui |
| 2022-03-22 | Merge pull request #608 from zsloan/feature/add_rqtl_pairscan...Feature/add rqtl pairscan | zsloan |
| 2022-03-22 | Fix logic for setting interval parameter...The parameter should never be interval if pair_scan is being run; not checking for this causes the --interval tag to pointlessly be included when running pair-scan, which also interferes with caching
| zsloan |
| 2022-03-22 | Fix way pair_scan is checked...Previously it would always register as True, due to being in the start_vars
| zsloan |
| 2022-03-22 | Set pair_scan to false when using regular R/qtl mapping | zsloan |
| 2022-03-22 | Change d3panels CSS/JS to min files | zsloan |
| 2022-03-22 | Merge remote-tracking branch 'origin/testing' into feature/add_rqtl_pairscan | zsloan |
| 2022-03-21 | Fix command in documentation...Add missing argument to the command in the documentation
| Frederick Muriuki Muriithi |
| 2022-03-18 | README: Update CI badge subdomain....The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org.
* README.md: Update CI badge subdomain.
| Arun Isaac |
| 2022-03-18 | Merge pull request #689 from Alexanderlacuna/chore/gn2-enhancements...Chore/gn2 enhancements | Alexander Kabui |
| 2022-03-18 | add uniform font for title | Alexander Kabui |
| 2022-03-18 | remove correlation test button | Alexander Kabui |
| 2022-03-18 | fixes for ImageButtonOptions | Alexander Kabui |
| 2022-03-18 | code to fetch scree data from gn3 | Alexander Kabui |
| 2022-03-18 | integrate scree plot | Alexander Kabui |
| 2022-03-18 | Merge pull request #671 from Alexanderlacuna/feature/gn3-pca...Replace pca rpy2 code | Alexander Kabui |
| 2022-03-18 | Apply "python-black" on file...* test/requests/test-website.py: Run "black test/requests/test
test-website.py".
| BonfaceKilz |
| 2022-03-18 | Remove outdated integration tests on different login mechanisms...* test/requests/test-website.py: Delete parser option "-i" for running
integration tests.
(integration_tests): Delete it.
(integration_suite): Ditto.
(run_integration_tests): Ditto.
* test/requests/test_registration.py: Delete it.
| BonfaceKilz |
| 2022-03-18 | Delete deprecated modules...* test/requests/test-website: These imports were deleted in an earlier
PR here: <https://github.com/genenetwork/genenetwork2/pull/574>
| BonfaceKilz |
| 2022-03-18 | Delete "app" import in MR...* test/requests/test-website.py: Delete "from wqflask import
app". This has the undesired effect of starting an instance of
Genenetwork2.
| BonfaceKilz |
| 2022-03-18 | Document configurations...Document the configurations for the service, and how to use them when
invoking the service.
| Frederick Muriuki Muriithi |
| 2022-03-17 | Fix/change Authors column in phenotype search results...- Limit number of full names to 2 followed by "et al."
- Fix wrong logic that was using the full length of the authors string instead of the truncated length when determining the width of the column, resulting in it always being at least 500px wide
| zsloan |
| 2022-03-17 | Set min-width for table container, so the table never ends up so narrow it lo... | zsloan |
| 2022-03-17 | Fix authentication for phenotype search results...Previously authentication didn't work correctly if users had "edit" privileges, because the code specifically looked for just "view"; this changes it to check for either "view" or "edit"
| zsloan |
| 2022-03-17 | Lint some test files | BonfaceKilz |
| 2022-03-17 | Fix failing test | BonfaceKilz |
| 2022-03-17 | Create a db connection correctly...* wqflask/maintenance/quantile_normalize.py: Fix how the cursor is
created.
| BonfaceKilz |
| 2022-03-17 | Skip unittests...These tests touch on core data-structures in gn2; and there's a chance
that refactoring said data-structures may break many things.
| BonfaceKilz |
| 2022-03-17 | Replace "g.db" object with a proper database connection...* wqflask/tests/unit/wqflask/api/test_correlation.py: Use proper
database connection instead of the db connection attached at "g.db".
* wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py: Ditto.
* wqflask/wqflask/api/correlation.py: Ditto.
* wqflask/wqflask/snp_browser/snp_browser.py: Ditto.
| BonfaceKilz |
| 2022-03-17 | Delete dead code | BonfaceKilz |
| 2022-03-17 | Delete unused "logger" import...* wqflask/wqflask/snp_browser/snp_browser.py: Remove "getLogger".
| BonfaceKilz |
