| Age | Commit message (Expand) | Author |
|---|
| 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| 2022-03-18 | Remove outdated integration tests on different login mechanisms...* test/requests/test-website.py: Delete parser option "-i" for running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 |
| 2022-03-17 | Document how to run tests...Add documentation on how to run the tests - this was no clear from the
existing documentation up to this point.
| Frederick Muriuki Muriithi |
| 2022-03-17 | Provide path to default settings/configuration file as a fallback...If the GN2_SETTINGS environment variable, is for some reason, not set,
and the application actually ever tries to get a connection to the
database, then use the default settings/configuration file.
| Frederick Muriuki Muriithi |
| 2022-03-16 | Remove unnecessary print statement | zsloan |
| 2022-03-16 | Replace top comment with docstring | zsloan |
| 2022-03-16 | Add code generating the new genotype files...Also made a large number of other fixes that proved necessary during
testing
| zsloan |
| 2022-03-16 | Generate JSON file for target genotypes...Also store parents/type metadata from source genofiles
| zsloan |
| 2022-03-16 | Fix the way target/source genofiles were being processed + some other changes...- I was mixing up source/target genofiles previously; the JSON file is for the source genofiles
- references to the app context are removed in favor of just taking input as arguments or environment variables
- Updated example commands
| zsloan |
| 2022-03-16 | Add function for mapping strain to sample pos + begin creating generate_new_g... | zsloan |
| 2022-03-16 | Add function for getting strain name from sample name | zsloan |
| 2022-03-16 | Change EOL from CRLF to LF | zsloan |
| 2022-03-16 | Minor changes/bug fixes...- Removed some unused code
- Strip marker genotype to avoid newline character at end
- Convert zip to list for marker genotypes
- Add typing to group_samples
- Rename strain_genofile to source_genofile
| zsloan |
| 2022-03-16 | Add in-progress gen_ind_genofiles.py...gen_ind_genofiles.py is a command line script to generate genotype files for groups of
individuals/samples, taking a source .geno or .json file and a target 'dummy' .geno file as input
| zsloan |
| 2022-03-16 | Delete unused issue templates...* .github/ISSUE_TEMPLATE/: Delete this directory.
| BonfaceKilz |
| 2022-03-16 | Delete GitHub CI runner...We have moved to Laminar. See: <https://penguin2.genenetwork.org/>
* .github/workflows/main.yml: Delete it.
| BonfaceKilz |
| 2022-03-14 | instantiate plotly object | Alexander Kabui |
| 2022-03-14 | add custom configs for scree plot | Alexander Kabui |
| 2022-03-14 | add scree plot data | Alexander Kabui |
| 2022-03-14 | add scree plot layout | Alexander Kabui |
| 2022-03-14 | add plotly | Alexander Kabui |
| 2022-03-14 | init scree plot template | Alexander Kabui |
