| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-12-21 | Make homology track display directional arrows based on query strand | zsloan | |
| 2022-12-21 | Fix homology source file path | zsloan | |
| Fix syntax error in multiline if statement | |||
| 2022-12-21 | Replace a couple other instances of hg38 with query | zsloan | |
| 2022-12-21 | Substitute mm10/hg38 with ref/source in display_mapping_results.py | zsloan | |
| 2022-12-21 | Change homology logic to include lines that start/end outside of the | zsloan | |
| given mb range This is to avoid a situation where a user zooms in and a bar should encompass the whole area but isn't displayed (because its start/end don't both fall within the given Mb range) This commit also renames mm10/hg38 to ref/query to be more generic | |||
| 2022-12-21 | Replace hard-coded homology source file | zsloan | |
| Remove limitation on when to show homology track | |||
| 2022-12-21 | Add code drawing homology band in mapping figure | zsloan | |
| 2022-12-21 | Add showHomology parameter to mapping endpoint | zsloan | |
| 2022-12-21 | Add code loading contents of homology file for given mb range | zsloan | |
| Currently this hard-codes the source file. Not sure how we want to store this data yet so just using a CSV file for now. | |||
| 2022-12-21 | Add homology band option to run_mapping.py | zsloan | |
| 2022-12-21 | Add homology band options to mapping template | zsloan | |
| 2022-12-15 | Add BXD-NIA-AD to list of BXD-equivalent groups in display_mapping_results.py | zsloan | |
| 2022-12-15 | Fix bug where changing a resource owner throws an error due to users without ↵ | zsloan | |
| email_addresses (can happen for orcid/github users currently) | |||
| 2022-12-15 | Change if blocks in template to allow changing owner when an owner isn't ↵ | zsloan | |
| currently set | |||
| 2022-12-14 | Add description to REST API /traits output for phenotypes | zsloan | |
| 2022-12-13 | Change default text_dir to TEXTDIR, since that points to the GN1 ↵ | zsloan | |
| ProbeSet_DataMatrix files | |||
| 2022-12-13 | add check for file in web/ProbeSetFreeze_DataMatrix folder (#758) | Alexander Kabui | |
| 2022-12-12 | Change logic in compute_correlation_rust so that it doesn't re-run the top ↵ | zsloan | |
| 500 correlations for sample correlations of non-probeset traits (which it was previously doing and caused many wrong results | |||
| 2022-12-06 | Use a dataset's name to fetch it's metadata | Munyoki Kilyungi | |
| * wqflask/wqflask/views.py (show_trait_page): Use a dataset's name - from the query parameters - to fetch metadata. | |||
| 2022-12-05 | Put metadata fetching for show_trait_page in try/except to get it working again | zsloan | |
| 2022-12-05 | scripts: add GN2 results parsing to parser script | Frederick Muriuki Muriithi | |
| * wqflask/scripts/parse_corr_gn1_results_to_csv.py: Rename script * wqflask/scripts/parse_corr_html_results_to_csv.py: * Use argparse to parse CLI arguments * Add parsing for GN2 results | |||
| 2022-12-03 | jobs: Add debug UI | Frederick Muriuki Muriithi | |
| * wqflask/scripts/run_external.py: Save the actual return code * wqflask/wqflask/__init__.py: Use new jobs blueprint * wqflask/wqflask/api/jobs.py: Add new jobs debug route * wqflask/wqflask/templates/jobs/debug.html: new template for when job is found * wqflask/wqflask/templates/jobs/no-such-job.html: new template for when the job is not found | |||
| 2022-12-02 | correlations: display "--" whenever "lit_corr" is None | Frederick Muriuki Muriithi | |
| * wqflask/wqflask/correlation/show_corr_results.py: Check for `None` and display "--" in its place. | |||
| 2022-12-02 | correlations: Fix description | Frederick Muriuki Muriithi | |
| * wqflask/wqflask/correlation/rust_correlation.py: Add `Probe_Target_Description` to the description field for "ProbeSet" traits. | |||
| 2022-12-02 | correlations: Format `sample_r` value correctly. | Frederick Muriuki Muriithi | |
| * wqflask/wqflask/correlation/show_corr_results.py: Use scientific notation with 2 decimal places | |||
| 2022-12-02 | correlation: Remove unused argument | Frederick Muriuki Muriithi | |
| * wqflask/wqflask/correlation/rust_correlation.py: The `get_sample_corr_data` function no longer has the `all_samples` parameter, thus passing the argument leads to a failure. This commit removes the argument from the call. | |||
| 2022-12-01 | Return Chr and Mb separately for phenotype /traits API request | zsloan | |
| 2022-12-01 | Fix Exception that's raised when query_sql returns None | Munyoki Kilyungi | |
| * wqflask/base/data_set/dataset.py: Delete itertools, DictCursor. (DataSet.get_accession_id): Handle a case where query_sql returns a None value. | |||
| 2022-12-01 | Reproduce ValueError when query_sql returns None | Munyoki Kilyungi | |
| * wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId): New test cases. | |||
| 2022-12-01 | Delete complicated unmaintainable test-cases marked for skipping | Munyoki Kilyungi | |
| * wqflask/tests/unit/base/test_data_set.py (TestDataSetTypes) [test_set_dataset_key_mrna, test_set_dataset_key_pheno, test_set_dataset_geno]: Delete. | |||
| 2022-12-01 | Change API Phenotype query to get other fields, including Locus position | zsloan | |
| 2022-12-01 | Variety of changes to basic stats figures | zsloan | |
| - Left-aligned bar-chart title - Changed y-axis label for Violin Plot to 'Density' - Always display modebar options - Increase font size for y axis label for Violin Plot | |||
| 2022-12-01 | Prevent error when user account doesn't have an email address (which is ↵ | zsloan | |
| currently the case if you use Github or ORCID to log-in) | |||
| 2022-12-01 | Fix group-management URL | zsloan | |
| 2022-12-01 | Remove min-width for trait page main div | zsloan | |
| 2022-12-01 | Increase width of email/password inputs on login page + change some text | zsloan | |
| 2022-12-01 | Add line-break below probability plot | zsloan | |
| 2022-11-30 | Remove box plot (violin plot is enough) | zsloan | |
| 2022-11-30 | Remove check for shortnames/fullnames in probeset metadata query | Munyoki Kilyungi | |
| Some rows in InfoFiles have NULL values thereby causing an exception to be raised. All InfoFiles.DB_Name are unique. * wqflask/base/data_set/dataset.py (DataSet.get_accession_id): Remove shortname/fullname check in query. | |||
| 2022-11-29 | remove unnecessary function argument (#754) | Alexander Kabui | |
| 2022-11-29 | mechanical-rob: Activate correctness checks | Frederick Muriuki Muriithi | |
| * test/requests/test-website.py: allow the correlation correctness tests to run on CI. | |||
| 2022-11-28 | Fix bugs in show_corr_results.py | zsloan | |
| 2022-11-28 | Convert trait name to str, since phenotype trait names being numerical was ↵ | zsloan | |
| causing them to not work as dict keys | |||
| 2022-11-28 | this commit remove the stage for parsing rows to remove nan values | AlexanderKabui | |
| * this stage is already handled by the rust code hence doing positional comparison lead to different results than expected | |||
| 2022-11-28 | Fix bug where single chromosome mapping view wouldn't work for the X chromosome | zsloan | |
| 2022-11-28 | Fetch the accession_id from the dataset object | Munyoki Kilyungi | |
| * wqflask/wqflask/templates/search_result_page.html: Replace metadata.accession_id with dataset.accession_id. * wqflask/wqflask/templates/show_trait.html: Ditto. | |||
| 2022-11-28 | mechanical-rob: Add more tests for correctness | Frederick Muriuki Muriithi | |
| 2022-11-28 | mechanical-rob: First test for correlations correctness | Frederick Muriuki Muriithi | |
| * test/requests/correlation_tests.py: Add proof-of-concept code to run the checks for correctness. * test/requests/test-website.py: Add a way to manually run the tests from the CLI | |||
| 2022-11-25 | mechanical-rob: Parser for GN1 results and some sample results | Frederick Muriuki Muriithi | |
| * test/requests/correlation_results_text_files/*results.csv: csv files with sample results from GN1 for the trait `1435464_at` in dataset `HC_M2_0606_P`. * wqflask/scripts/parse_corr_gn1_results_to_csv.py: parser for results from GN1 when saved to a html file. | |||
| 2022-11-23 | Make some changes to prevent show_corr_results.py bugs (details below) | zsloan | |
| At one point the MonadicDict of the dataset ob was being passed to create_trait, which does not work. I changed it back to passing the object Another place calls "as_dict" on the dataset ob, which doesn't work; I had to call as_monadic_dict().data for that Some traits are also None for some reason, which caused an error in the filter. For now I just used an if/else, but someone can deal with this differently later | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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