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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.
2021-11-23Fix 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.
2021-11-19Sort inputs in package definition.Arun Isaac
* guix.scm (genenetwork3)[propagated-inputs]: Sort.
2021-11-19Remove duplicated python-plotly dependency.Arun Isaac
* guix.scm (genenetwork3)[propagated-inputs]: Remove python-plotly.
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.
2021-11-19Use latest version of PengouinFrederick Muriuki Muriithi
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.
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.
2021-11-16Remove sqlalchemy.Arun Isaac
* 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.
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.
2021-11-15Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
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.
2021-11-13Do not shadow global symbol uuid.Arun Isaac
* 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.
2021-11-13Reformat condition on a single line.Arun Isaac
* gn3/authentication.py (get_user_info_by_key): Reformat so that condition is on a single line.
2021-11-13Do not use dangerous default argument [].Arun Isaac
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.
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.
2021-11-11Remove redundant check on the Pearson correlation coefficient.Arun Isaac
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.
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.
2021-11-11Reimplement __items_with_values using list comprehension.Arun Isaac
* gn3/computations/correlations2.py: Remove import of reduce from functools. (__items_with_values): Reimplement using list comprehension.
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
2021-11-11pylint 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.Arun Isaac
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.
2021-11-11Disuse GUIX_PACKAGE_PATH.Arun Isaac
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.
2021-11-11Update PULL_REQUEST_TEMPLATE.md.Arun Isaac
2021-11-10Remove repeated input python-flask-cors.Arun Isaac
* guix.scm (genenetwork3)[propagated-inputs]: Remove python-flask-cors.
2021-11-10Indent guix.scm use-modules better.Arun Isaac
* guix.scm: Indent use-modules better, the more conventional way.
2021-11-10Set version to 0.1.0.Arun Isaac
Semantic versioning begins at 0.1.0, not 0.0.1. * guix.scm: Set genenetwork package version to 0.1.0.
2021-11-10Name source checkout in the store.Arun Isaac
* guix.scm: Name source checkout in the store to "genenetwork3-checkout".
2021-11-10Use git-predicate in guix.scm.Arun Isaac
* guix.scm: Do not import (srfi srfi-1), (srfi srfi-26), (ice-9 match), (ice-9 popen) and (ice-9 rdelim). Use git-predicate instead of git-file?. (git-file?): Delete function.
2021-11-09Add functions for updating groupsBonfaceKilz
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