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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
2021-12-09Prevent 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
2021-12-06Merge branch 'main' of github.com:genenetwork/genenetwork3Frederick Muriuki Muriithi
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
2021-11-29Fix 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
2021-11-29db: 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
2021-11-24db: 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
2021-11-23Update 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
2021-11-04Add some condition checking functions...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add the `check_for_literature_info` and `check_symbol_for_tissue_correlation` functions to check for the presence of specific data. Frederick Muriuki Muriithi
2021-11-04Fix linting and typing errors...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-04Rework sorting: remove `compare_tissue_correlation_absolute_values`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/correlations.py: Remove the `compare_tissue_correlation_absolute_values` function which is no longer needed. Frederick Muriuki Muriithi
2021-11-04Complete `build_temporary_tissue_correlations_table`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: Remove comments after updating usage of the function at call point * gn3/db/correlations.py: Complete the implementation of the `build_temporary_tissue_correlations_table` function Frederick Muriuki Muriithi
2021-11-04Move `correlations_of_all_tissue_traits`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: new function (`correlations_of_all_tissue_traits`). * gn3/db/correlations.py: delete function (`correlations_of_all_tissue_traits`). Move the function to `gn3.computations.partial_correlations` module and comment out the db-access code. Rework it to receive, as arguments, the data it previously fetched from the database, and add comments on future rework to get the function working again. Frederick Muriuki Muriithi
2021-11-04Add missing comma...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-04Move the function to computations module...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The function `batch_computed_tissue_correlation` is a pure computations function with no expressions accessing the database, as far as I can tell, therefore, this commit moves the function over to the gn3.computations.partial_correlations module that holds the pure computation functions. Frederick Muriuki Muriithi
2021-11-04Remove if clauses: replace with dict...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Remove the if clauses to simplify the code flow: use a dictionary of queries and select the appropriate query from the dictionary instead. Frederick Muriuki Muriithi
2021-11-04Stub out `batch_computed_tissue_correlation` function...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Stub out `batch_computed_tissue_correlation` function to be used in implementing the function down the line. Frederick Muriuki Muriithi
2021-11-04Complete `correlations_of_all_tissue_traits`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Complete the implementation of the `correlations_of_all_tissue_traits` function by providing a call to a non-implemented function. Frederick Muriuki Muriithi
2021-11-04Implement `fetch_gene_symbol_tissue_value_dict_for_trait`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Implement `fetch_gene_symbol_tissue_value_dict_for_trait` function which is a migration of the `web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDictForTrait` function in GeneNetwork1. Frederick Muriuki Muriithi
2021-10-25Start implementation of `fetch_tissue_correlations` and dependencies...* compare_tissue_correlation_absolute_values: New function. Complete. Used for sorting of tissue correlation values * fetch_symbol_value_pair_dict: New function. Complete. Maps gene symbols to tissue expression data * fetch_gene_symbol_tissue_value_dict: New function. Complete. Wrapper for `gn3.db.correlations.fetch_symbol_value_pair_dict` function * fetch_tissue_probeset_xref_info: New function. Complete. Retrieves the Probeset XRef information for tissues from the database. * correlations_of_all_tissue_traits: Stub. Dependencies not completed yet. * build_temporary_tissue_correlations_table: Stub. Dependencies not completed yet. * fetch_tissue_correlations: New function. Incomplete. This function calls (a) stub(s) function(s) which is/are under development still. Frederick Muriuki Muriithi
2021-10-25Implement `fetch_literature_correlations` and depedencies...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Migrate: * `web.webqtl.correlation.CorrelationPage.getTempLiteratureTable` * `web.webqtl.correlation.CorrelationPage.fetchLitCorrelations` from GeneNetwork1. The first function creates and populates a temporary table with the literature correlations data. The second function uses the data in the newly created temporary table to link the trait with the correlation value. Frederick Muriuki Muriithi
2021-10-25Implement `get_filename` for correlations...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Implement `get_filename` for the correlations, to be used to determine whether to do fast or normal correlations. This is a migration of the `web.webqtl.correlation.CorrelationPage.getFileName` function in GN1 Frederick Muriuki Muriithi
2021-10-21Implement `translate_to_mouse_gene_id` 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.translateToMouseGeneID` function in GN1 to GN3. This is a function that retrieves data from the database, and therefore uses a system outside of our code, therefore, the function does not have a corresponding unit test. This kind of function will probably need to be tested at the integration or system tests level, where we test that our code interacts correcly with any and all external systems that it should. Frederick Muriuki Muriithi
2021-10-18Move `export_informative` function to `gn3.db.traits` module...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/traits.py: Move `export_informative` function here * gn3/partial_correlations.py: Remove `export_informative` function * tests/unit/db/test_traits.py: Move `export_informative` function tests here * tests/unit/test_partial_correlations.py: Remove `export_informative` function tests The `export_informative` function relates more to the traits than to the partial correlations, and could find use in more than just the partial correlations stuff. This commit moves the function to the more traits-specific `gn3.db.traits` module. Frederick Muriuki Muriithi
2021-10-18Move 'export_trait_data' to 'gn3.db.traits' module...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/traits.py: Move function `export_trait_data` here * gn3/heatmaps.py: Remove function `export_trait_data` * tests/unit/db/test_traits.py: Move function `export_trait_data` tests here * tests/unit/test_heatmaps.py: Remove function `export_trait_data` here Function `export_trait_data` more closely corresponds to the traits and is used in more than just the `gn3.heatmaps` module. This commit moves the relevant code over to the `gn3.db.traits` module and also moves the tests to the corresponding tests modules. Frederick Muriuki Muriithi
2021-09-27Update terminology: `riset` to `group`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update terminology to use the appropriate domain terminology according to Zachary's direction at https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744 Frederick Muriuki Muriithi
2021-09-27Update terminology: `strain` to `sample`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the terminology used: use `sample` in place of `strain` according to Zachary's direction at https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306 Frederick Muriuki Muriithi
2021-09-22Fix more pylint errorsFrederick Muriuki Muriithi
2021-09-22Fix typing issues...* Ignore some errors * Update typing definitions for some portions of code * Add missing imports Frederick Muriuki Muriithi
2021-09-22Fix pylint errors...* Add missing function and module docstrings * Remove unused imports * Fix import order * Rework some code sections to fix issues * Disable some pylint errors. Frederick Muriuki Muriithi
2021-09-17Fix a number of linting issues...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi Frederick Muriuki Muriithi
2021-09-01Fix linting and typing issues...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi Muriithi Frederick Muriuki
2021-09-01Built top-level genotype file parsing function...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/genotypes.py: parse genotype files * tests/unit/db/test_genotypes.py: test parsing is correct Add the overall genotype files parsing function and tests to check that the parsing works as expected. Muriithi Frederick Muriuki