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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'`.
2022-11-08Remove unused importsMunyoki Kilyungi
* wqflask/wqflask/correlation/show_corr_results.py: Delete os, Path, TMPDIR, fetch_all_cached_metadata and cache_new_traits_metadata. * wqflask/wqflask/db_info.py: Remove http.client.
2022-11-08Use DictCursor to fetch results into a dictionaryMunyoki Kilyungi
* wqflask/wqflask/db_info.py: Import DictCursor. (InfoPage.get_info): Add aliases in SQL that will be used as keys later by DictCursor.. (process_query_results): Delete it.
2022-11-08De-duplicate fetching results after a queryMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): run cursor.fetchone() only once.
2022-11-08Delete unused JavaScript filesMunyoki Kilyungi
* wqflask/wqflask/static/new/javascript/dataset_select_menu.js: Delete. * wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js: Ditto.
2022-11-07Change sample correlations to use full samplelist, including f1s/parentszsloan
2022-11-07include f1 parents for correlationAlexanderKabui
2022-11-02Update Phenogen URL to rn7zsloan
2022-11-02Enable Verify button for Genotype traitszsloan
2022-10-31Fix error when there's no human data in GeneListzsloan
2022-10-31Only show Tissue in trait page for ProbeSet traitszsloan
2022-10-31Add md5 js file (needed for adding to collections)zsloan
2022-10-31Update Rat links to rn7zsloan
2022-10-30Address situations where Additive Effect is an empty string for viewzsloan
collection page I think the Monad stuff Bonface/Arun are doing might address situations like this better.
2022-10-28Add `sample_data` argument to function call.run-corrs-in-external-processFrederick Muriuki Muriithi
2022-10-28Fix importsFrederick Muriuki Muriithi
* Fix imports I broke when rebasing.
2022-10-28Refactor: run correlation computation externallyFrederick Muriuki Muriithi
* wqflask/scripts/corr_compute.py: move correlation computation to external script. * wqflask/wqflask/templates/loading_corrs.html: Provide UI to display while computation is still not complete. * wqflask/wqflask/views.py: Dispatch correlation computation to external script and display appropriate UI for each valid state of the computation.
2022-10-28Settings: Add the `REDIS_URL` setting.Frederick Muriuki Muriithi
2022-10-28Declutter stdoutFrederick Muriuki Muriithi
* wqflask/utility/tools.py: Output extraneous messages to stderr rather than stdout to avoid cluttering the output.
2022-10-28Refactor: Pass user id to `check_resource_availability`Frederick Muriuki Muriithi
* Pass the user_id for the current user to the `check_resource_availability` function as an argument, rather than using the global `g.user_session.user_id` value.
2022-10-28Add external process managerFrederick Muriuki Muriithi
* wqflask/jobs/__init__.py: New jobs module * wqflask/jobs/jobs.py: New jobs module * wqflask/scripts/run_external.py: new external process manager.
2022-10-28Query genenetwork3 API for search.Arun Isaac
genenetwork2 should be a thin wrapper web UI around the genenetwork3 API. Hence, this move. * etc/default_settings.py (XAPIAN_DB_PATH): Delete variable. * wqflask/wqflask/database.py: Remove xapian import. (xapian_database, xapian_writable_database): Delete functions. * wqflask/wqflask/gsearch.py: Do not import json, xapian, Nothing from pymonad.maybe, base, utility.authentication_tools and wqflask.database. Import MonadicDict from gn3.monads instead of utility.monads and GN3_LOCAL_URL from utility.tools. (GSearch.__init__): Query genenetwork3 search API instead of directly reading a Xapian index.
2022-10-28Remove xapian indexing script.Arun Isaac
The xapian indexing script has been moved to genenetwork3. All further development will happen there. * wqflask/scripts/index.py: Delete file.
2022-10-27init fix for querying for datasetsAlexander_Kabui
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