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2021-10-26Merge pull request #46 from genenetwork/partial-correlationsBonfaceKilz
Partial correlations
2021-10-25Start implementation of `fetch_tissue_correlations` and dependenciesFrederick Muriuki Muriithi
* 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.
2021-10-25Implement `partition_all` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/data_helpers.py: new function (partition_all) * tests/unit/test_data_helpers.py: tests for function `gn3.data_helpers.partition_all` As part of migrating some functions that access the database, this commit extracts generic processes that can be accomplished on data, and implements the `partition_all` function, that is equivalent to Clojure's `partition-all` function.
2021-10-25Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-10-25mypy:Incompatible types in assignment fixAlexander Kabui
2021-10-25mypy fix for none stdoutAlexander Kabui
2021-10-25pylint and pep8 formattingAlexander Kabui
2021-10-25fix unittestsAlexander Kabui
2021-10-25minor fixes for sript enable annotationsAlexander Kabui
2021-10-25add flask-socketio input to gn3Alexander Kabui
2021-10-25minor modification for emitting data:add namespacesAlexander Kabui
2021-10-25pep8 formatting,pylint fixesAlexander Kabui
2021-10-25add socket obj and emit processAlexander Kabui
2021-10-25fix issues serializing byte stringAlexander Kabui
2021-10-25script modification : add debug statementsAlexander Kabui
2021-10-25rename key to image_dataAlexander Kabui
2021-10-25add function to process imagesAlexander Kabui
2021-10-25add function to capture output in real timeAlexander Kabui
2021-10-25Implement `fetch_literature_correlations` and depedenciesFrederick Muriuki Muriithi
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.
2021-10-25Implement `get_filename` for correlationsFrederick Muriuki Muriithi
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
2021-10-21Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-10-21Implement `translate_to_mouse_gene_id` 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.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.
2021-10-21Implement `find_identical_traits` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement function `find_identical_traits` * tests/unit/test_partial_correlations.py: implement tests for function `find_identical_traits` Migrate `web.webqtl.correlation.correlationFunction.findIdenticalTraits` function in GN1 to here, adding in tests to ensure the migration works in a bug-compatible version with the original.
2021-10-21Document tests betterFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Document the issues better to help with understanding what each test checks for.
2021-10-19Implement remaining `fix_samples` functionalityFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement `fix_samples` function * tests/unit/test_partial_correlations.py: implement tests for `fix_samples` function Implement the remaining partial migration for the `web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
2021-10-19Implement `dictify_by_samples`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement `dictify_by_samples` function * tests/unit/test_partial_correlations.py: implement tests for `dictify_by_samples` function Implement the `dictify_by_samples` function as a partial migration of the `web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
2021-10-19Disable pylint issueFrederick Muriuki Muriithi
* Disable minor pylint issue.
2021-10-19Implement `control_samples` function as is in GN1Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement `control_samples` function * tests/unit/test_partial_correlations.py: add tests for `control_samples` function Implement the function `control_samples` and make it mostly bug-compatible with the `web/webqtl/correlation/correlationFunction.controlStrain` function in GN1. This implementation in GN3 does not do any calls to the database. It will rely on other functions to provide the data from the database to it.
2021-10-19Move `export_informative` function to `gn3.db.traits` moduleFrederick Muriuki Muriithi
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.
2021-10-19Move 'export_trait_data' to 'gn3.db.traits' moduleFrederick Muriuki Muriithi
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.
2021-10-19Migrate `export_informative` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement a mostly, bug-compatible `export_informative` function as part of migrating the partial correlations feature over to GN3 from GN1 * tests/unit/test_partial_correlations.py: Implement tests to ensure the code work in a similar manner as that one in GN1.
2021-10-19Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-10-19Implement remaining `fix_samples` functionalityFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement `fix_samples` function * tests/unit/test_partial_correlations.py: implement tests for `fix_samples` function Implement the remaining partial migration for the `web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
2021-10-19Fix some linting issuesFrederick Muriuki Muriithi
2021-10-19Allow CORS_ORIGINS to be configurable via the environmentFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * gn3/app.py: setup CORS after all the configuration sources are loaded. * gn3/settings.py: Parse CORS_ORIGINS from the environment variables. Enable the CORS_ORIGINS configuration to be set in the environment variables to give the application some flexibility when launching.
2021-10-19Enable vertical and horizontal heatmapsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Update the request endpoint, so that it produces a vertical or horizontal heatmap depending on the user's request.
2021-10-19Enable vertical orientation of heatmapsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Update the code to enable the generation of the heatmap in both the horizontal and vertical orientations.
2021-10-19Swap axis labelsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Switch the axis labels to make them less confusing for the user.
2021-10-19Add typing. Simplify arguments.Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Add type-hints to the functions * Merge the axis data and labels to simpler dict arguments to reduce number of parameters to the function.
2021-10-19Remove file I/O statementsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Remove file I/O from the function. If file I/O is needed, it will be provided outside of this function.
2021-10-19Implement `dictify_by_samples`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement `dictify_by_samples` function * tests/unit/test_partial_correlations.py: implement tests for `dictify_by_samples` function Implement the `dictify_by_samples` function as a partial migration of the `web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
2021-10-18Disable pylint issueFrederick Muriuki Muriithi
* Disable minor pylint issue.
2021-10-18Implement `control_samples` function as is in GN1Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement `control_samples` function * tests/unit/test_partial_correlations.py: add tests for `control_samples` function Implement the function `control_samples` and make it mostly bug-compatible with the `web/webqtl/correlation/correlationFunction.controlStrain` function in GN1. This implementation in GN3 does not do any calls to the database. It will rely on other functions to provide the data from the database to it.
2021-10-18Move `export_informative` function to `gn3.db.traits` moduleFrederick Muriuki Muriithi
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.
2021-10-18Move 'export_trait_data' to 'gn3.db.traits' moduleFrederick Muriuki Muriithi
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.
2021-10-18Migrate `export_informative` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement a mostly, bug-compatible `export_informative` function as part of migrating the partial correlations feature over to GN3 from GN1 * tests/unit/test_partial_correlations.py: Implement tests to ensure the code work in a similar manner as that one in GN1.
2021-10-14Fixed when model is set to account for situations with no covariateszsloan
2021-10-14Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.Rzsloan
2021-10-12Merge pull request #40 from zsloan/bug/fix_rqtl_covariateszsloan
Bug/fix rqtl covariates
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
bug/fix_rqtl_covariates
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