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2021-07-23Fix issue caught in `nearest` while testing `slink`Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * While running tests for slink, to try and understand what it is doing in order to write the appropriate tests for it, an issue arose that pointed a blindspot in the former understanding of now `nearest` should work. This commit fixes the issue found in both the expected data, and the code.
2021-07-23New function (`slink`): return [] on exceptionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add minimum code to pass new test * tests/unit/computations/test_slink.py: new test Add test to ensure that the new `slink` function return an empty list in case and exception is raised. Add the new `slink` function with minimum amount of code needed to pass the test.
2021-07-23Add dummy module documentationMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add initial dummy module documentation in form of a python docstring Update the names of what would be private methods/function to start with a double-underscore (__) so that they do not show up in the default python documentation.
2021-07-23Add docstring for `nearest' functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: add documentation for the `nearest` function in the `gn3.computations.slink` module in the form of a (hopefully correct) python docstring.
2021-07-22Get shortest distance from two lists/tuples of member coordinatesMuriithi Frederick Muriuki
* gn3/computations/slink.py: add code to ensure new test passes * tests/unit/computations/test_slink.py: new test This one is a little weird: from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L57-L63 It gets rid of the last coordinates in both the lists of the member coordinates, and uses the remaining coordinates to find the shortest members. For example, given the following member coordinates: - i=[0,1,2] and j=[5,7,9], it uses [0,1] and [5,7] - i=[3,6,1] and j=[7,13], it uses [3,6] and [7] to find the shortest distances. I (fredmanglis) am not sure why it does it this way, since I'd have expected it to use all the coordinates, however, since at this time we need to retain bug-compatibility with the older code, I have done it as it is done in the old code. I also add a statement to raise an exception in the case where i and j are not lists of integers, or integers
2021-07-22Extract common `is_list_or_tuple' functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Extract the common function `is_list_or_tuple' making it accessible to later parts of the code.
2021-07-22Test for shortest distance between members in a list and coordinateMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: add code to pass new test * tests/unit/computations/test_slink.py: new test Given a list of members in a group, and a coordinate for a member in the same group, find the distance of the closest member from the given coordinate in the group.
2021-07-22Merge branch 'main' of github.com:genenetwork/genenetwork3Muriithi Frederick Muriuki
2021-07-22Check that given list and both coordinates, we get shortest distanceMuriithi Frederick Muriuki
* gn3/computations/slink.py: Add code to compute the distance given the coordinate of both members on the parent list/tuple * tests/unit/computations/test_slink.py: * Change the name of the tests to more closely correspond to the business requirement the test is checking for * Update the comments to indicate some more things that might need to be done in the future
2021-07-22Check that all distances are positive or zeroMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that all distances between the 'somethings' are all either zero or positive. * tests/unit/computations/test_slink.py: * Remove data with all distances positive or zero, since it would fail the test * Change the expected message to more closely correspond to the business logic
2021-07-22Check that distance from A to B is same as from B to AMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that the distance from child A to B is the same as distance from child B to A. If not, throw an exception. * tests/unit/computations/test_slink.py: * Change the name of the test to more closely correspond to the business logic being tested. * Update the data in a separate test such that it does not error out due to failing to fulfill the expectations of separate requirement. - pass tests - Rename test - Fix errors: distances same both directions
2021-07-22Move sql updates into dirPjotr Prins
2021-07-22Check that child distance from itself is zeroMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Check that a child's distance from itself is zero. If not, throw an exception. The children lists are a list of distances of "something" from other "somethings". There is still some need to establish what those "somethings" are, so that the test names can reflect the ideas that are actually being tested for. * tests/unit/computations/test_slink.py: Change the name of the test so that it more closely corresponds to the business logic it is actually testing, and not the mechanics of testing the idea.
2021-07-22Check the child lengths are same as length of parentMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Check that the child lists/tuples are the same length as the parent list/tuple. If any of the children is not the same length as the parent, throw and exception.
2021-07-22Add docstringMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add docstring to the function, useful for generating automated developer documentation. We also surround the guard functions with some notification comments, to mark possible future places where change might be done.
2021-07-22Check that list and its direct children are not emptyMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add code to pass the test that the list/tuple passed to `nearest' and its direct children lists/tuples are not empty.
2021-07-22Implement check for lists or tuplesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Implement the code to pass the check that a list of lists is passed to the `nearest' function.
2021-07-22sql: Add schema and schema map.Arun Isaac
* sql/map-database.sh, sql/schema-original.sql, sql/schema.png, sql/schema.sql, sql/schema.svg: New files.
2021-07-21Extract tests from code in GN1Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add dummy `nearest' function * tests/unit/computations/test_slink.py: Add some tests This commit adds tests to try and reproduce the working of the `nearest' function in: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py This commit might not yet have extracted all the expected behaviour of the `nearest' function, and therefore, there is a possibility of a later commit augmenting the work in this commit.
2021-07-20Implement the correlation functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Implement the correlation computation function, such that it passes the tests created previously.
2021-07-20Add test for code to move over from GN1Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * .gitignore: ignore emacs temporary files * gn3/computations/correlations2.py: add a dummy function * tests/unit/computations/test_correlation.py: add unit tests for the function As part of the move of the clustering and heatmap code over from GN1 to GN3, this commit begins by providing some unit tests for the correlation function used to ensure that the implementation that is built up here corresponds, and produces the same results as the original. This tests and the function might change in the new system, but for now, we try and maintain bug-to-bug compatibility.
2021-07-10gn3: db: Use correct type for columns arg in fetch functionsBonfaceKilz
2021-07-10Fix pylint issuesBonfaceKilz
2021-07-10db: test_db: Test that a fetch is correct when columns are specifiedBonfaceKilz
2021-07-10gn3: db: Add extra argument to specify column in fetch statementsBonfaceKilz
2021-07-10db: phenotypes: Add Probeset data structuresBonfaceKilz
* gn3/db/phenotypes.py (Probeset): New dataclass. (probeset_mapping): New dict. * gn3/db/__init__.py: Add probeset_mapping and Probeset.
2021-06-29Replace list with a tuple as an argument when setting success_codesBonfaceKilz
* gn3/commands.py (run_cmd): Replace type of success_codes from List to Tuple * gn3/computations/diff.py (generate_diff): Pass success_codes as a Tuple when calling "run_cmd".
2021-06-29guix: Add diffutils as a propagated inputBonfaceKilz
2021-06-29guix: Remove commented out hunkBonfaceKilz
2021-06-29gn3: diff: Set success_codes when running the diff toolBonfaceKilz
2021-06-29gn3: commands: Add extra arg that sets the success codes to checkBonfaceKilz
* gn3/commands.py (run_cmd): Some commands like "diff" return non-standard error codes. To make this fn more robust, add an extra optional argument that sets what successful codes to check.
2021-06-29tests: test_commands: Add extra check for when an error occursBonfaceKilz
2021-06-29Add a diffing functionBonfaceKilz
For now the diff function uses the Linux tool "diff" to generate the diff since it is efficient and straightforward. * gn3/computations/diff.py (generate_diff): New function. * tests/unit/computations/test_diff.py: Test cases for ☝🏾.
2021-06-29tests: test_data: Add test data that contains trait data for 10007BonfaceKilz
2021-06-25Check for the correct result codeBonfaceKilz
When programs terminate with an error, they usually return a -1!
2021-06-23Merge pull request #21 from genenetwork/fix/biweight-errorsBonfaceKilz
Fix/biweight errors
2021-06-23fix pylint issuesAlexander Kabui
2021-06-23minor fixes for biweight scriptAlexander Kabui
2021-06-22scripts: laminar: Add json with hooks for running a linterBonfaceKilz
2021-06-22scripts: laminar: Add sh scripts for CIBonfaceKilz
2021-06-21Merge pull request #20 from genenetwork/feature/biweight-correlationBonfaceKilz
add biweight r script and tests
2021-06-20minor fix docstringAlexander Kabui
2021-06-20merge mainAlexander Kabui
2021-06-20fix conflictAlexander Kabui
2021-06-20make requested changes to biweightAlexander Kabui
2021-06-18Merge pull request #13 from zsloan/feature/add_rqtl_endpointszsloan
Feature/add rqtl endpoints
2021-06-18Fixed another error where test_generate_rqtl_command didn't include the ↵zsloan
filename argument (not sure why running unit tests locally doesn't detect this)
2021-06-18Fixed file type from json to csv for test_generate_rqtl_commandzsloan
2021-06-18Fixed test_rqtl.py to include Rscript in the commandzsloan
2021-06-18Fixed test_compose_rqtl_command test; forgot to include Rscript in the commandzsloan
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