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2022-12-21Add code loading contents of homology file for given mb rangezsloan
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.
2022-12-21Add homology band option to run_mapping.pyzsloan
2022-12-21Add homology band options to mapping templatezsloan
2022-12-15Add BXD-NIA-AD to list of BXD-equivalent groups in display_mapping_results.pyzsloan
2022-12-15Fix bug where changing a resource owner throws an error due to users without ↵zsloan
email_addresses (can happen for orcid/github users currently)
2022-12-15Change if blocks in template to allow changing owner when an owner isn't ↵zsloan
currently set
2022-12-14Add description to REST API /traits output for phenotypeszsloan
2022-12-13Change default text_dir to TEXTDIR, since that points to the GN1 ↵zsloan
ProbeSet_DataMatrix files
2022-12-13add check for file in web/ProbeSetFreeze_DataMatrix folder (#758)Alexander Kabui
2022-12-12Change 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
2022-12-06Use a dataset's name to fetch it's metadataMunyoki Kilyungi
* wqflask/wqflask/views.py (show_trait_page): Use a dataset's name - from the query parameters - to fetch metadata.
2022-12-05Put metadata fetching for show_trait_page in try/except to get it working againzsloan
2022-12-05scripts: add GN2 results parsing to parser scriptFrederick 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
2022-12-03jobs: Add debug UIFrederick 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
2022-12-02correlations: display "--" whenever "lit_corr" is NoneFrederick Muriuki Muriithi
* wqflask/wqflask/correlation/show_corr_results.py: Check for `None` and display "--" in its place.
2022-12-02correlations: Fix descriptionFrederick Muriuki Muriithi
* wqflask/wqflask/correlation/rust_correlation.py: Add `Probe_Target_Description` to the description field for "ProbeSet" traits.
2022-12-02correlations: Format `sample_r` value correctly.Frederick Muriuki Muriithi
* wqflask/wqflask/correlation/show_corr_results.py: Use scientific notation with 2 decimal places
2022-12-02correlation: Remove unused argumentFrederick 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.
2022-12-01Return Chr and Mb separately for phenotype /traits API requestzsloan
2022-12-01Fix Exception that's raised when query_sql returns NoneMunyoki Kilyungi
* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor. (DataSet.get_accession_id): Handle a case where query_sql returns a None value.
2022-12-01Reproduce ValueError when query_sql returns NoneMunyoki Kilyungi
* wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId): New test cases.
2022-12-01Delete complicated unmaintainable test-cases marked for skippingMunyoki 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.
2022-12-01Change API Phenotype query to get other fields, including Locus positionzsloan
2022-12-01Variety of changes to basic stats figureszsloan
- 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
2022-12-01Prevent 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)
2022-12-01Fix group-management URLzsloan
2022-12-01Remove min-width for trait page main divzsloan
2022-12-01Increase width of email/password inputs on login page + change some textzsloan
2022-12-01Add line-break below probability plotzsloan
2022-11-30Remove box plot (violin plot is enough)zsloan
2022-11-30Remove check for shortnames/fullnames in probeset metadata queryMunyoki 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.
2022-11-29remove unnecessary function argument (#754)Alexander Kabui
2022-11-28Fix bugs in show_corr_results.pyzsloan
2022-11-28Convert trait name to str, since phenotype trait names being numerical was ↵zsloan
causing them to not work as dict keys
2022-11-28this commit remove the stage for parsing rows to remove nan valuesAlexanderKabui
* this stage is already handled by the rust code hence doing positional comparison lead to different results than expected
2022-11-28Fix bug where single chromosome mapping view wouldn't work for the X chromosomezsloan
2022-11-28Fetch the accession_id from the dataset objectMunyoki Kilyungi
* wqflask/wqflask/templates/search_result_page.html: Replace metadata.accession_id with dataset.accession_id. * wqflask/wqflask/templates/show_trait.html: Ditto.
2022-11-25mechanical-rob: Parser for GN1 results and some sample resultsFrederick 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.
2022-11-23Make 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
2022-11-23Replace GN3 library rdf queries with a call to a gn3 endpointMunyoki Kilyungi
* wqflask/wqflask/database.py: Delete SPARQLWrapper, JSON imports (sparql_connection): Delete. * wqflask/wqflask/views.py: Import requests and urljoin. Delete get_dataset_metadata and sparql_connection import. (show_trait_page): Fetch metadata by calling a GN enpoint.
2022-11-23bug: Fix syntax error: missing commaFrederick Muriuki Muriithi
2022-11-22Merge branch 'bugfix/metadata-fetching' of ↵Frederick Muriuki Muriithi
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-bugfix/metadata-fetching
2022-11-22Merge branch 'chores/code-refactoring' of ↵Frederick Muriuki Muriithi
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/code-refactoring
2022-11-22Merge branch 'bugfix/use-f1-parents' of ↵Frederick Muriuki Muriithi
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-bugfix/use-f1-parents
2022-11-21fix merge conflictsAlexanderKabui
2022-11-21minor refactoringAlexanderKabui
2022-11-16Pass a sparql connection object to get_dataset_metadataMunyoki Kilyungi
* wqflask/wqflask/database.py (database_connection): New function. * wqflask/wqflask/views.py: Import sparql_connection (show_trait_page): Pass sparql_connection object to get_dataset_metadata.
2022-11-13add check when parsing floatsAlexanderKabui
2022-11-13add check for dataset typeAlexanderKabui
2022-11-11Notify user when they modify probeset dataMunyoki Kilyungi
* wqflask/wqflask/metadata_edits.py (update_probeset): Flash a success messages when user updates something. Otherwise flash a warning message * wqflask/wqflask/templates/edit_probeset.html: Display flash messages.
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