| Age | Commit message (Expand) | Author |
|---|
| 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 | 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 |
| 2022-03-22 | 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 |
| 2022-03-18 | 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 |
| 2022-03-17 | 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 | 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 |
| 2022-03-14 | 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 |
| 2022-03-14 | Warn when someone uploads a csv file that has columns not in the db...* wqflask/wqflask/metadata_edits.py: Import "extract_invalid_csv_headers"
and "get_allowable_sampledata_headers".
(display_phenotype_metadata): Pass the allowable headers to the
template.
(update_phenotype): If a user uploads data with a column header that's
not in the db, don't upload the file, and send a warning message.
* wqflask/wqflask/templates/edit_phenotype.html: List the allowable
headers in the template.
| BonfaceKilz |
| 2022-03-14 | Remove button for "Edit Privileges"...This is a WIP.
| BonfaceKilz |
| 2022-03-14 | Reword link text for downloading csv sample data | BonfaceKilz |
| 2022-03-12 | Use "database_connection" within a context-manager...Using "database_connection" within a context-manager makes sure that
the SQL connection that is created is closed.
* wqflask/wqflask/metadata_edits.py (display_probeset_metadata):
Connect to the db within a context-manager.
(update_phenotype): Ditto.
(update_probeset): Ditto.
(approve_data): Ditto.
| BonfaceKilz |
| 2022-03-12 | Remove unused imports | BonfaceKilz |
| 2022-03-12 | Close a connection after it's use...* wqflask/wqflask/metadata_edits.py (approve_data): Explicitly close a
connection after it is used.
| BonfaceKilz |
| 2022-03-12 | Use updated `update_sample_data` from gn3 | BonfaceKilz |
