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2022-03-08Fix tests, and issues caught by testsFrederick Muriuki Muriithi
Fix some issues caught by tests due to changes introducing the hand-off of the partial correlations computations to an external process Fix some issues due to the changes that introduce context managers for database connections Update some tests to take the above two changes into consideration
2022-02-24gn3: Explicitly specify UTF-8 to be the file encoding.Arun Isaac
When the encoding is not specified explicitly, the system default encoding is used. This is not recommended. * gn3/computations/ctl.py (call_ctl_script), gn3/computations/gemma.py (generate_pheno_txt_file), gn3/computations/parsers.py (parse_genofile), gn3/computations/partial_correlations.py (partial_correlations_fast), gn3/computations/rqtl.py (process_rqtl_output, process_perm_output), gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script), gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file encoding. * tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file), tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test for call to open with encoding='utf-8' argument.
2022-02-21Fix minor issues introduced while fixing linting errorsFrederick Muriuki Muriithi
2022-02-21Fix a myriad of linter issuesFrederick Muriuki Muriithi
* Use `with` in place of plain `open` * Use f-strings in place of `str.format()` * Remove string interpolation from queries - provide data as query parameters * other minor fixes
2022-02-21Add test to ensure samples are read correctly from .geno filesFrederick Muriuki Muriithi
* tests/unit/db/test_genotypes2.py: New file
2022-02-21Test partial corrs API with mix of existing and non-existing control traitsFrederick Muriuki Muriithi
Test that the partial correlations endpoint handles a mix of existing and non-existing control traits gracefully and issues a warning to the user. Summary of changes: * gn3/computations/partial_correlations.py: Issue a warning for all non-existing control traits * gn3/db/partial_correlations.py: update queries - use `INNER JOIN` for tables instead of comma-separated list of tables * tests/integration/conftest.py: Add `db_conn` fixture to provide a database connection to the tests. This will probably be changed in the future to connect to a temporary database for tests. * tests/integration/test_partial_correlations.py: Add test to check for correct behaviour with a mix of existing and non-existing control traits
2022-02-19Test partial corrs endpoint with non-existing control traitsFrederick Muriuki Muriithi
Test that if the endpoint is queried and not a single one of the control traits exists in the database, then the endpoint will respond with a 404 (not-found) status code. Summary of changes: * gn3/computations/partial_correlations.py: Check whether any control trait is found. If none is found, return "not-found" message. * gn3/db/partial_correlations.py: Fix bug in Geno query. * tests/integration/test_partial_correlations.py: Add test for non-existing control traits. Rename function to make it clearer what it is testing for. Remove obsoleted comments.
2022-02-18Remove erroneous test based on wrong assumptionsFrederick Muriuki Muriithi
Related to commit 75dcfe295af57b16428c586cc11dbaa827a5feba This commit removes the related test that was checking for the wrong thing.
2022-02-18Test partial correlations endpoint with non-existent primary traitsFrederick Muriuki Muriithi
Test that the partial correlations endpoint responds with an appropriate "not-found" message and the corresponding 404 status code in the case where a request is made and the primary trait requested for does not exist in the database. Summary of the changes in each file: * gn3/api/correlation.py: generalise the building of the response * gn3/computations/partial_correlations.py: return with a "not-found" if the primary trait does not exist in the database * gn3/db/partial_correlations.py: Fix a number of bugs that led to exceptions in the case that the primary trait did not exist * pytest.ini: register a `slow` pytest marker * tests/integration/test_partial_correlations.py: Add a new test to check for an appropriate 404 response in case of a primary trait that does not exist in the database.
2022-02-17Test partial correlations endpoint with missing data in POST requestFrederick Muriuki Muriithi
Add a test for the partial correlations endpoint, with: - no data in the request - missing items in the data Fix the bugs caught by the test
2022-02-17Create client fixture for integration testsFrederick Muriuki Muriithi
Create a client fixture to help with the integration tests
2022-02-17Use pytest's "mark" feature to categorise testsFrederick Muriuki Muriithi
Use pytest's `mark` feature to explicitly categorise the tests and run them per category
2022-02-17Add property tests for `dictify_by_samples`Frederick Muriuki Muriithi
Add property tests using pytest and hypothesis to test that the expected properties hold for the `gn3.computations.partial_correlations.dictify_by_samples` function.
2022-02-09Remove obsolete `PublishFreeze` tableFrederick Muriuki Muriithi
2022-01-05test_traits.py: Update failing testBonfaceKilz
2021-12-14linting: Fix obvious linting issuesFrederick Muriuki Muriithi
2021-12-14Provide expected values to use for testsFrederick Muriuki Muriithi
2021-12-10refactor sample r unittestsAlexander Kabui
2021-12-10refactor unittest for normalizing sample valuesAlexander Kabui
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
2021-11-23Fix 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.
2021-11-22Add 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.
2021-11-19Avoid rounding: compare floats approximatelyFrederick Muriuki Muriithi
Notes: https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918 * As mentioned in the notes, rather than rounding to an arbitrary number of decimal places, it is a much better practice to use approximate comparisons of floats for the tests.
2021-11-19Replace use of assert_allclose. Disable linter errorFrederick Muriuki Muriithi
Notes: https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918 * From the notes above, the assert_allclose is a better function for figuring out what failed, unlike the allclose that simply just returns a True/False value. This commit restores the use of the assert_allclose function, and then disables the linter error due to the fact that there is no use of the `self` keyword.
2021-11-18Fix some linting errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Fix some obvious linting errors and remove obsolete code
2021-11-18Replace code migrated from R with pingouin functionsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace the code that was in the process of being migrated from R in GeneNetwork1 with calls to pingouin functions that achieve the same thing. Since the functions in this case are computing correlations and partial correlations, rather than having home-rolled functions to do that, this commit makes use of the tried and tested pingouin functions. This avoids complicating our code with edge-case checks, and leverages the performance optimisations done in pingouin.
2021-11-15Fix bugs in recursive partial correlationsFrederick Muriuki Muriithi
* gn3/computations/partial_correlations.py: Remove rounding. Fix computation of remaining covariates * tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt: reduce the number of covariates to between one (1) and three (3) * tests/unit/computations/test_partial_correlations.py: fix some minor bugs It turns out that the computation complexity increases exponentially, with the number of covariates. Therefore, to get a somewhat sensible test time, while retaining a large-ish number of tests, this commit reduces the number of covariates to between 1 and 3.
2021-11-15Fix the columns in built data frameFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * When the z value is a Sequence of sequences of values, each of the internal sequences should form a column of its own, and not a row, as it was originally set up to do.
2021-11-12Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-11-12Pass in parser function for flexibilityFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * To improve the usefulness of already existing code, provide the parser function as an argument to the `parse_input_line` function. This was found to be useful when writing code to compare the `pcor.test` function in GN1 and the `pingouin.partial_corr` function. The format of the data generated when getting results for the `pcor.test` function shared a lot with that of the `pcor.rec` function, but it was different in a few, places, and the differences were non-trivial, needing different parsing processes. In such a case, it was found necessary to just pass in the function to do the actual parsing, rather than create code with the same form as the existing one, save for the function being called.
2021-11-11Reimplement correlations2.compute_correlation using pearsonr.Arun Isaac
correlations2.compute_correlation computes the Pearson correlation coefficient. Outsource this computation to scipy.stats.pearsonr. When the inputs are constant, the Pearson correlation coefficient does not exist and is represented by NaN. Update the tests to reflect this. * gn3/computations/correlations2.py: Remove import of sqrt from math. (compute_correlation): Reimplement using scipy.stats.pearsonr. * tests/unit/computations/test_correlation.py: Import math. (TestCorrelation.test_compute_correlation): When inputs are constant, set expected correlation coefficient to NaN.
2021-11-11Compare floats approximately.Arun Isaac
Floating point numbers should only be compared approximately. Different implementations of functions might produce slightly different results. * tests/unit/computations/test_correlation.py: Import assert_almost_equal from numpy.testing. (TestCorrelation.test_compute_correlation): Compare floats using assert_almost_equal instead of assertEqual. * tests/unit/test_heatmaps.py: Import assert_allclose from numpy.testing. (TestHeatmap.test_cluster_traits): Use assert_allclose instead of assertEqual.
2021-11-11pep8 formatting;update unittestsAlexander Kabui
2021-11-09Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-11-09Implement remaining part of `partial_correlation_recursive` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: implement remaining portion of `partial_correlation_recursive` function. * tests/unit/computations/test_partial_correlations.py: add parsing for new data format and update tests
2021-11-09Update test data: have both vectors and matricesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Delete the older test data that was only testing with `z` being a vector and replace it with data that has `z` being a vector or matrix from data item to data item.
2021-11-09Add new data processing utilityFrederick 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_by`) * tests/unit/test_data_helpers.py: Tests for new function Add a function that approximates Clojure's `partition-by` function, to help with processing the data in a more functional way.
2021-11-04test_partial_correlations: skip failing testsBonfaceKilz
Fix these later. I need a passing test suite so as to update the gn2 docker image.
2021-11-04Create blackbox tests for some functions migrated from RFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: new stub functions (partial_correlation_matrix, partial_correlation_recursive) * tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv: blackbox sample data and results for variance-covariance matrix method * tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv: blackbox sample data and results for recursive method * tests/unit/computations/test_partial_correlations.py: Tests for new function Provide some blackbox testing sample data for checking the operation of the functions migrated from R.
2021-11-04Retrieve indices of the selected samplesFrederick Muriuki Muriithi
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 (good_dataset_samples_indexes). * tests/unit/computations/test_partial_correlations.py: Tests for new function (good_dataset_samples_indexes) Get the indices of the selected samples. This is a partial migration of the `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` function in GN1.
2021-11-04Parse single line from CSV fileFrederick 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 (parse_csv_line) * tests/unit/test_data_helpers.py: Add tests for new function (parse_csv_line) Add a function to parse a single line from a CSV file.
2021-11-04Specify ten (10) decimal placesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: specify 10 decimal places * tests/unit/computations/test_partial_correlations.py: update examples Slight differences in python implementations, possibly hardware and operating systems could cause the value of float (double) values to be different in the less significant parts of the decimal places. This commit limits the usable part of the decimals to the first 10 decimal places for now.
2021-11-04Fix some linting errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-04Implement `tissue_correlation` functionFrederick Muriuki Muriithi
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 (tissue_correlation) * tests/unit/test_partial_correlations.py -> tests/unit/computations/test_partial_correlations.py: Move module. Implement tests for new function Migrate the `cal_tissue_corr` function embedded in the `web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in GN1 and implement tests to ensure it works correctly.
2021-11-04Partially implement `partial_correlation_recursive`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: Implement one path for the `gn3.computations.partial_correlations.partial_correlation_recursive` function. * gn3/settings.py: Add a setting for how many decimal places to round to * tests/unit/computations/test_partial_correlations.py: Update test to take the number of decimal places into consideration Implement a single path (where the z value is a vector and not a matrix) for the `partial_correlation_recursive` function.
2021-11-04Implement `build_data_frame`Frederick Muriuki Muriithi
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 (`build_data_frame`) * tests/unit/computations/test_partial_correlations.py: Add tests for new function Add a new function to build a pandas DataFrame object from the provided values: - x: a vector of floats (represented with a tuple of floats) - y: a vector of floats (represented with a tuple of floats) - z: a vector OR matrix of floats (represented with a tuple of floats or a tuple of tuples of floats)
2021-11-04Create blackbox tests for some functions migrated from RFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: new stub functions (partial_correlation_matrix, partial_correlation_recursive) * tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv: blackbox sample data and results for variance-covariance matrix method * tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv: blackbox sample data and results for recursive method * tests/unit/computations/test_partial_correlations.py: Tests for new function Provide some blackbox testing sample data for checking the operation of the functions migrated from R.
2021-11-01Add test cases for gn3.authenticationBonfaceKilz
2021-11-01Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-11-01Retrieve indices of the selected samplesFrederick Muriuki Muriithi
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 (good_dataset_samples_indexes). * tests/unit/computations/test_partial_correlations.py: Tests for new function (good_dataset_samples_indexes) Get the indices of the selected samples. This is a partial migration of the `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` function in GN1.
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