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2021-12-13Return the primary and control traits in addition to results...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * In addition to the partial correlation results, this commit enables the return of the chosen primary trait and the selected control traits. This data is required for presentation on the results page. Frederick Muriuki Muriithi
2021-12-13Run partial correlations against chosen database...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Run the partial correlations against the database that the user selects, and not the one from which the primary trait is. This was a bug in the code. Frederick Muriuki Muriithi
2021-12-13Fix errors with query...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Use the correct format string paradigm: put f before opening quote. * Provide missing space just before 'FROM' clause Frederick Muriuki Muriithi
2021-12-10Remove pull request template....People are not using the pull request template properly. Often, the fields remain unfilled, and the placeholders are not deleted. This is cognitively taxing for reviewers. Also, most of our changes are better described in the commit log than in the pull request description. And, our reviews are quite cursory and don't need a detailed pull request description for the reviewer to act on. * .github/PULL_REQUEST_TEMPLATE.md: Delete file. Arun Isaac
2021-12-10Fix parameters...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Provide parameters as a dict of items (which works for MySQL), rather than as keywork arguments (as works in PostgreSQL). Frederick Muriuki Muriithi
2021-12-10format normalize function doc stringAlexander Kabui
2021-12-10minor pr fixesAlexander Kabui
2021-12-10rename variablesAlexander Kabui
2021-12-10try and catch for non matching sample keysAlexander Kabui
2021-12-10update function docs for normalizing strain valuesAlexander Kabui
2021-12-10refactor sample r unittestsAlexander Kabui
2021-12-10refactor unittest for normalizing sample valuesAlexander Kabui
2021-12-10fix bug:unpacking error when generator returns empty listAlexander Kabui
2021-12-09README: Link CI badge to CI status page....* README.md: Link CI badge to CI status page. Arun Isaac
2021-12-09README: Add CI badge....* README.md: Add CI badge. Arun Isaac
2021-12-09guix.scm: Inherit from (gn packages genenetwork)....We base this off the genenetwork3 package defined in (gn packages genenetwork). That way, we don't have to duplicate the package definition in multiple places. * guix.scm (genenetwork3): Inherit from genenetwork3 package definition in (gn packages genenetwork). Arun Isaac
2021-12-09Prevent error on no result. Fix indexing...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * If the dataset name is not found, don't cause an exception, instead, return the provided search name. * Use the correct inner object Frederick Muriuki Muriithi
2021-12-09Provide clearer error message...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * To help with debugging error conditions, provide the original name to help with figuring out why the error was raised Frederick Muriuki Muriithi
2021-12-08Provide group from primary trait...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * From the collections page, the group is not present, so this commit retrieves the group value from the primary trait. Frederick Muriuki Muriithi
2021-12-06Merge branch 'main' of github.com:genenetwork/genenetwork3Frederick Muriuki Muriithi
2021-12-06Merge branch 'partial-correlations'Frederick Muriuki Muriithi
2021-12-02Add a Guix operating-system configuration....* guix-system.scm: New file. Arun Isaac
2021-12-02Implement dataset metadata API endpoint....* guix.scm: Import (gnu packages rdf). (genenetwork3)[propagated-inputs]: Add python-sparqlwrapper. * gn3/settings.py (SPARQL_ENDPOINT): New variable. * gn3/api/general.py: Import datasets from gn3.db. (dataset_metadata): New API endpoint. * gn3/db/datasets.py: Import re, Template from string, Dict and Optional from typing, JSON and SPARQLWrapper from SPARQLWrapper, SPARQL_ENDPOINT from gn3.settings. (sparql_query, dataset_metadata): New functions. Arun Isaac
2021-11-29Merge branch 'main' into partial-correlationsMuriithi Frederick Muriuki
2021-11-29Update test for data changes...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-29Fix linting errors...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-29Provide entry-point function for the partial correlations...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Provide the entry-point function to the partial correlation feature. This is the function that ochestrates the fetching of the data, and processing it for output by the API endpoint (to be implemented). Frederick Muriuki Muriithi
2021-11-29Fix bugs in data...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Process the db_name and db_type values. * Return data correctly Frederick Muriuki Muriithi
2021-11-29Update return type...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Return the complete filename when found, or the boolean value False, when it is not found. Frederick Muriuki Muriithi
2021-11-29Return only values...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Return the values from the database, not the tuples. Frederick Muriuki Muriithi
2021-11-29Update typing notations on functions...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-29Fix query parametrisation...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Pass parameters to the query the way the MySQL driver expects. Frederick Muriuki Muriithi
2021-11-29Retrieve the species name given the group...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Migrate the `web.webqtl.dbFunction.webqtlDatabaseFunction.retrieveSpecies` in GeneNetwork1 to `gn3.db.species.species_name` in GeneNetwork3 to enable the retrieval of the species name, given the group name (formerly RISet). Frederick Muriuki Muriithi
2021-11-29db: traits: Support additions and deletions from csv fileBonfaceKilz
2021-11-29Add SQL statement to update json_diffBonfaceKilz
2021-11-29db: traits: Remove trailing ".0" in int valuesBonfaceKilz
2021-11-29db: traits: Remove "\n\n" when generating csv file...In excel, "\n\n" is replaced with ",,,," during upload. BonfaceKilz
2021-11-25db: traits: Support additions and deletions from csv fileBonfaceKilz
2021-11-24Add SQL statement to update json_diffBonfaceKilz
2021-11-24db: traits: Remove trailing ".0" in int valuesBonfaceKilz
2021-11-23db: traits: Remove "\n\n" when generating csv file...In excel, "\n\n" is replaced with ",,,," during upload. BonfaceKilz
2021-11-23Fix a myriad of linting errors...* Fix linting errors like: - Unused variables - Undeclared variable errors (mostly caused by typos, and wrong names) - Missing documentation strings for functions etc. Frederick Muriuki Muriithi
2021-11-23Migrate `getPartialCorrelationsNormal`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Migrate the `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsNormal` function in GN1. * Remove function obsoleted by newer implementation of the code Frederick Muriuki Muriithi
2021-11-23Update documentation for functions...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Document functions for posterity. Frederick Muriuki Muriithi
2021-11-22Add test to query builders...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add some tests for the query builders to ensure that the queries are built up correctly. Frederick Muriuki Muriithi
2021-11-22Migrate `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Migrate the `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function from GN1 to GN3. Frederick Muriuki Muriithi
2021-11-22Make the DB connection argument the first...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * To make the code more composable down the line, make the database connection argument the first argument for functions that access the database, since they will always require the connection. Frederick Muriuki Muriithi
2021-11-20Merge pull request #56 from genenetwork/partial-correlations...Partial correlationsMuriithi Frederick Muriuki
2021-11-19Replace guix environment with guix shell....* README.md, guix.scm: Replace guix environment with guix shell. Arun Isaac
2021-11-19Do not recommend GUIX_PACKAGE_PATH....* guix.scm: Do not recommend GUIX_PACKAGE_PATH. Arun Isaac
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