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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.
2022-11-11Parse metadata.about_data_processing correctlyMunyoki Kilyungi
2022-11-10Fix typo in probeset editing formMunyoki Kilyungi
2022-11-10Display a dataset's metadata in the "Trait Data and Analysis" pageMunyoki Kilyungi
* wqflask/wqflask/static/new/css/show_trait.css: Show a pointer when a user hovers over summary data. Add extra styling for the metadata table. * wqflask/wqflask/templates/search_result_page.html: Replace dataset.accession_id with metadata.accession_id. * wqflask/wqflask/templates/show_metadata_details.html: New template. file that displays a dataset's metadata in tabular form. * wqflask/wqflask/templates/show_trait.html: Sub-template 'show_metadata_details' conditionally. * wqflask/wqflask/views.py (show_trait_page): Explicitly pass metadata as a dictionary to the template.
2022-11-10Convert monadic_dict to normal dictionariesMunyoki Kilyungi
* wqflask/wqflask/correlation/show_corr_results.py (set_template_vars): Convert monadict_dict to a normal dictionary. (correlation_json_for_table): Ditto.
2022-11-10Rename dataset.as_dict to dataset.as_monadic_dictMunyoki Kilyungi
* wqflask/base/data_set/dataset.py (DataSet.as_dict): Rename this to ... (as_monadic_dict): ... this. * wqflask/wqflask/correlation/show_corr_results.py (set_template_vars): Rename as_dict to as_monadic_dict. (correlation_json_for_table): Ditto.
2022-11-10Use the Maybe Monad when fetching the accession_id of a datasetMunyoki Kilyungi
* wqflask/base/data_set/dataset.py: Import itertools, DictCursor, MonadicDict, Maybe, Nothing and query_sql. (DataSet.__init__): Initialize accession_id to Nothing. (DataSet.as_dict): Rename this to ... (Dataset.as_monadic_dict): ... this which returns a monadic dictionary. (DataSet.get_accession_id): Query for the accession_id and return it as a maybe monad.
2022-11-09delete unecessary codeAlexanderKabui
2022-11-09add filter checkersAlexanderKabui
2022-11-09refactor:apply use filtersAlexanderKabui
2022-11-09init code refactoringAlexanderKabui
2022-11-08Remove string check for 'None' in HTML templateMunyoki Kilyungi
In Jinja, you can use dot notation to check for values. If a value does not exist, you get None by default. * wqflask/base/data_set/dataset.py (Dataset.get_accession_id): Remove returning a string version of None. * wqflask/wqflask/templates/correlation_page.html: Delete `!= 'None'`.
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