| Age | Commit message (Expand) | Author |
|---|
| 2022-04-19 | Add scatterplot link for additive effect in mapping results | zsloan |
| 2022-04-18 | Add BXD-Micturition to BXD-equivalent groups...This is necessary for the coloring of the gene band rectangles to work
correctly (because a query it runs needs the BXD strain ID)
| zsloan |
| 2022-04-14 | Adjust mapping results page to prevent the mapping options at the top of...the page from being too far to the right
| zsloan |
| 2022-04-14 | Add group code to loading pages when applicable...This adds the group code to phenotype traits on loading pages, and also
sets the group code as an attribute of the dataset.group class.
| zsloan |
| 2022-04-14 | Increase tool-button-container min-width...This increases the min-width for the search/collection page tool button
container, since previously the Partial Correlation button would get
shoved below when the window was too narrow. It needed to be increased
to account for that button.
| zsloan |
| 2022-04-14 | wqflask: Mock db connection when fetching case attributes...* wqflask/tests/integration/wqflask/test_metadata_edits.py
(test_show_case_attributes): Mock
"database_connection". Fixes this failing test:
<https://ci.genenetwork.org/jobs/genenetwork2/223>
| BonfaceKilz |
| 2022-04-14 | Register the port in the app configs | Frederick Muriuki Muriithi |
| 2022-04-14 | Provide db port when present...Sometimes the system uses a port to connect to the database, rather
than a socket, so if the port is present, provide it as part of the
connection arguments.
| Frederick Muriuki Muriithi |
| 2022-04-14 | Trigger the CI after mariadb restart | Frederick Muriuki Muriithi |
| 2022-04-14 | Use `MySQLdb.connect` rather than `MySQLdb.Connect` | Frederick Muriuki Muriithi |
| 2022-04-14 | Debug: Add logging to track db connection creation and stopping...As part of debugging the "Too many connections" error to the database,
this commit adds logging to track the creation of connections to the
database, and their eventual closing.
debug-too-many-connections-error | Frederick Muriuki Muriithi |
| 2022-04-12 | Replace get_allowable_sampledata_headers with get_case_attributes...* wqflask/wqflask/metadata_edits.py: Remove
"get_allowable_sampledata_headers" import.
(display_phenotype_metadata): Use
"get_case_attributes" to fetch all the allowable
case attributes.
| BonfaceKilz |
| 2022-04-12 | List out case-attrs from database; and add link to case-attr page | BonfaceKilz |
| 2022-04-12 | Don't create db engine for static files...There is no need to create a database engine for requests for static
files like CSS files and javascript files. This commit checks for and
skips the creation of the engine for such requests.
| Frederick Muriuki Muriithi |
| 2022-04-12 | Remove unused database code...Remove code for connecting to the database that is not actually used
in the application in any sensible form.
| Frederick Muriuki Muriithi |
| 2022-04-07 | Add submit buttons to the top of the edit page | BonfaceKilz |
| 2022-04-07 | Fix "Pubmed" spelling to "PubMed" | BonfaceKilz |
| 2022-04-07 | Add left space to content by making the "form" a container | BonfaceKilz |
| 2022-04-07 | Remove ":" after a header | BonfaceKilz |
| 2022-04-07 | Make case-attribute table a "data table" | BonfaceKilz |
| 2022-04-07 | Pass missing "conn" when getting case attributes...* wqflask/wqflask/metadata_edits.py (show_case_attribute_columns):
Create a connection and pass it to "get_case_attributes".
| BonfaceKilz |
| 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 |
