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2021-12-13Run partial correlations against chosen databaseFrederick Muriuki Muriithi
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.
2021-12-13Fix errors with queryFrederick Muriuki Muriithi
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
2021-12-10Remove pull request template.Arun Isaac
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.
2021-12-10Fix parametersFrederick Muriuki Muriithi
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).
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.Arun Isaac
* README.md: Link CI badge to CI status page.
2021-12-09README: Add CI badge.Arun Isaac
* README.md: Add CI badge.
2021-12-09guix.scm: Inherit from (gn packages genenetwork).Arun Isaac
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).
2021-12-09Prevent error on no result. Fix indexingFrederick Muriuki Muriithi
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
2021-12-09Provide clearer error messageFrederick Muriuki Muriithi
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
2021-12-08Provide group from primary traitFrederick Muriuki Muriithi
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.
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.Arun Isaac
* guix-system.scm: New file.
2021-12-02Implement dataset metadata API endpoint.Arun Isaac
* 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.
2021-11-29Merge branch 'main' into partial-correlationsMuriithi Frederick Muriuki
2021-11-29Update test for data changesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-29Fix linting errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-29Provide entry-point function for the partial correlationsFrederick Muriuki Muriithi
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).
2021-11-29Fix bugs in dataFrederick Muriuki Muriithi
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
2021-11-29Update return typeFrederick Muriuki Muriithi
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.
2021-11-29Return only valuesFrederick Muriuki Muriithi
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.
2021-11-29Update typing notations on functionsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-29Fix query parametrisationFrederick Muriuki Muriithi
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.
2021-11-29Retrieve the species name given the groupFrederick Muriuki Muriithi
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).
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 fileBonfaceKilz
In excel, "\n\n" is replaced with ",,,," during upload.
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 fileBonfaceKilz
In excel, "\n\n" is replaced with ",,,," during upload.
2021-11-23Fix a myriad of linting errorsFrederick Muriuki Muriithi
* Fix linting errors like: - Unused variables - Undeclared variable errors (mostly caused by typos, and wrong names) - Missing documentation strings for functions etc.
2021-11-23Migrate `getPartialCorrelationsNormal`Frederick Muriuki Muriithi
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
2021-11-23Update documentation for functionsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Document functions for posterity.
2021-11-22Add test to query buildersFrederick Muriuki Muriithi
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.
2021-11-22Migrate `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` functionFrederick Muriuki Muriithi
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.
2021-11-22Make the DB connection argument the firstFrederick Muriuki Muriithi
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.
2021-11-20Merge pull request #56 from genenetwork/partial-correlationsMuriithi Frederick Muriuki
Partial correlations
2021-11-19Replace guix environment with guix shell.Arun Isaac
* README.md, guix.scm: Replace guix environment with guix shell.
2021-11-19Do not recommend GUIX_PACKAGE_PATH.Arun Isaac
* guix.scm: Do not recommend GUIX_PACKAGE_PATH.
2021-11-19Remove gemma specific instructions from guix.scm.Arun Isaac
* guix.scm: Remove gemma specific instructions.
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