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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
2021-11-19Remove gemma specific instructions from guix.scm....* guix.scm: Remove gemma specific instructions. Arun Isaac
2021-11-19Sort inputs in package definition....* guix.scm (genenetwork3)[propagated-inputs]: Sort. Arun Isaac
2021-11-19Remove duplicated python-plotly dependency....* guix.scm (genenetwork3)[propagated-inputs]: Remove python-plotly. Arun Isaac
2021-11-19Avoid rounding: compare floats approximately...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. Frederick Muriuki Muriithi
2021-11-19Replace use of assert_allclose. Disable linter error...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. Frederick Muriuki Muriithi
2021-11-19Use latest version of Pengouin...Notes: https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918 * Pingouin 0.3.12 is buggy, as noted in the comment noted above. One of the bugs is that the Spearman correlations might give the wrong results under some circumstances. This commit removes the pinned version so that the system gets the latest version for testing. Frederick Muriuki Muriithi
2021-11-18Fix some linting errors...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 Frederick Muriuki Muriithi
2021-11-18Replace code migrated from R with pingouin functions...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. Frederick Muriuki Muriithi
2021-11-16Remove sqlalchemy....* gn3/settings.py (SQLALCHEMY_TRACK_MODIFICATIONS): Delete variable. * guix.scm (genenetwork3)[propagated-inputs]: Remove python-sqlalchemy-stubs. * setup.py: Remove sqlalchemy-stubs from install_requires. Arun Isaac
2021-11-15Fix bugs in recursive partial correlations...* 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. Frederick Muriuki Muriithi
2021-11-15Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre...Frederick Muriuki Muriithi
2021-11-15Fix the columns in built data frame...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. Frederick Muriuki Muriithi
2021-11-13Do not shadow global symbol uuid....* gn3/authentication.py (get_groups_by_user_uid): Rename local symbol uuid to group_uuid. (get_user_info_by_key): Rename local symbol uuid to user_uuid. Arun Isaac
2021-11-13Reformat condition on a single line....* gn3/authentication.py (get_user_info_by_key): Reformat so that condition is on a single line. Arun Isaac
2021-11-13Do not use dangerous default argument []....Default arguments get evaluated only once when the function is defined, and are then shared across all instances of the function. If the argument is then mutated, this can cause hard to find bugs. See https://docs.python.org/3/tutorial/controlflow.html#default-argument-values * gn3/authentication.py (create_group): Do not use [] as the default argument. Arun Isaac
2021-11-12Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre...Frederick Muriuki Muriithi
2021-11-12Pass in parser function for flexibility...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. Frederick Muriuki Muriithi
2021-11-11Remove redundant check on the Pearson correlation coefficient....The Pearson correlation coefficient always has a value between -1 and 1. So, this check is redundant. * gn3/heatmaps.py (cluster_traits.__compute_corr): Remove redundant check on the Pearson correlation coefficient. Arun Isaac
2021-11-11Reimplement correlations2.compute_correlation using pearsonr....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. Arun Isaac
2021-11-11Reimplement __items_with_values using list comprehension....* gn3/computations/correlations2.py: Remove import of reduce from functools. (__items_with_values): Reimplement using list comprehension. Arun Isaac
2021-11-11Compare floats approximately....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. Arun Isaac
2021-11-11pep8 formatting;update unittestsAlexander Kabui
2021-11-11pylint fixes and pep8 formattingAlexander Kabui
2021-11-11fix target and base sample data orderAlexander Kabui
2021-11-11fix:spawned processes memory issuesAlexander Kabui
2021-11-11replace list with generatorsAlexander Kabui
2021-11-11Disuse absolute paths to guix....It is safe to assume that the user has correctly set up guix in their PATH. * README.md: Disuse absolute paths to guix in command invocations. Arun Isaac
2021-11-11Disuse GUIX_PACKAGE_PATH....guix-bioinformatics is a Guix channel that is set up by `guix pull'. There is no need to specify it explicitly using GUIX_PACKAGE_PATH. * README.md: Do not explicitly set GUIX_PACKAGE_PATH for any command. Arun Isaac
2021-11-11Update PULL_REQUEST_TEMPLATE.md.Arun Isaac
2021-11-10Remove repeated input python-flask-cors....* guix.scm (genenetwork3)[propagated-inputs]: Remove python-flask-cors. Arun Isaac
2021-11-10Indent guix.scm use-modules better....* guix.scm: Indent use-modules better, the more conventional way. Arun Isaac