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2021-08-08Update testsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix tests to take current changes into consideration.
2021-08-08Only load extra data if the traits have basic infoMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Only load the extra trait data if the basic trait information is found.
2021-08-08Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_decompose_db_retrieval
2021-08-07Add gunicorn support for productionPjotr Prins
2021-08-07Update info on running guix containerPjotr Prins
2021-08-05db: traits: Return unique values when fetching sample dataBonfaceKilz
2021-08-05Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_decompose_db_retrieval
2021-08-05Reorganise the database codeMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Reorganise the code to separate the datasets from the traits, and to more closely conform to the same flow as that in GN1
2021-08-05Build up trait_name items from full nameMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The full name of the traits from search contains multiple parts to it, and as such, we use it to retrieve the appropriate data and set it up in the final trait_info dictionary that is produced.
2021-08-04Fix issues caught by pylintMuriithi Frederick Muriuki
* gn3/computations/slink.py: remove unused imports * gn3/db/traits.py: remove unnecessary `else` clauses * tests/unit/db/test_traits.py: add docstrings for functions
2021-08-04Retrieve the RISet and RISet ID valuesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Retrieve the RISet and RISet ID values from the database.
2021-08-04Add tests for post-processing functionsMuriithi Frederick Muriuki
Issues: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add missing tests for some post-processing functions
2021-08-04sql: Add documentation extracted from within the database.Arun Isaac
It turns out there is documentation of the database within the database itself. I have dumped that it into an org file. * sql/schema-from-in-db-documentation.org: New file.
2021-08-04Update testsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the tests to deal with changes in the code.
2021-08-04Avoid string interpolation: use prepared statementMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Following Arun's comment at https://github.com/genenetwork/genenetwork3/pull/31#issuecomment-890915813 this commit eliminates string interpolation, and adds a map of tables for the various types of traits dataset names
2021-08-04Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_decompose_db_retrieval
2021-08-03guix.scm: Add csvdiff as a propagated inputBonfaceKilz
2021-08-02sql: Document the table Strain.Arun Isaac
* sql/schema.org (Strain): New section.
2021-07-31sql: Add schema description.Arun Isaac
* sql/schema.org: New file.
2021-07-30Rework db functions to enable postprocessingMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Rework the database functions to return a dict of key-value pairs, which eases the postprocessing of the trait information. The postprocessing is mainly to try an maintain data compatibility with the code that is at the following locations: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py This was mainly a proof-of-concept, and the functions do not have testing added for them: there is therefore need to add testing for the new functions, and probably even rework them if they are found to be complicated.
2021-07-30Remove extra spaceMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Remove extra space that was causing test to fail.
2021-07-30Add module for common utilitiesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/function_helpers.py: new file Provides a new module to hold common programming utilities that are generic enough that they will find use across the entire application. The first utility function provided in this commit is the `compose` function, whose purpose, as indicated by its name, is to take a number of functions and compose them into a single function, which when called, will return the same result that would have been got had the user called the functions in a chain from right to left.
2021-07-30Return dict from query functionsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: return dicts rather than tuples/list * tests/unit/db/test_traits.py: Update tests Return dicts with the key-value pairs set up so as to ease with the data manipulation down the pipeline. This is also useful to help with the retrieval of all other extra information that was left out in the first iteration. This commit also updates the tests by ensuring they expect dicts rather than tuples.
2021-07-30Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_decompose_db_retrieval Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi Fix merge conflicts in: * gn3/db/traits.py * tests/unit/db/test_traits.py
2021-07-29Merge pull request #30 from genenetwork/Feature/Update-db-from-csv-dataBonfaceKilz
Feature/update db from csv data
2021-07-29Merge branch 'main' into Feature/Update-db-from-csv-dataBonfaceKilz
2021-07-29Delete "update_raw" and it's test-casesBonfaceKilz
2021-07-29Add method for updating values from a sample datasetBonfaceKilz
* gn3/db/traits.py (update_sample_data): New function. * tests/unit/db/test_traits.py: New test cases for ^^.
2021-07-29Add partial type annotations for slink moduleMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add some type annotations for the `nearest` function. * Leave some comments regarding the issues experienced when trying to add some typing annotations to the function to help with future endeavours of the same.
2021-07-29Add type annotations to the functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add some type annotations to the functions to reduce the chances of bugs creeping into the code.
2021-07-29Retrieve trait informationMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: add functions to retrieve traits information * tests/unit/db/test_traits.py: add tests for new function Add functions to retrieve traits information as is done in genenetwork1 https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456 At this point, the data retrieval functions are probably incomplete, as there is more of the `retrieveInfo` function in GN1 that has not been considered as of this commit.
2021-07-29Make name retrieval more generalMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: make function more general * tests/unit/db/test_traits.py: parametrize the tests Make the name retrieval more general for the different types of traits by changing the column specification and table as appropriate.
2021-07-29Retrieve 'ProbeSet' trait nameMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: new function (retrieve_probeset_trait_name) * tests/unit/db/test_traits.py: test(s) for new function Add a function to retrieve the name of a 'ProbeSet' trait in a manner similar to genenetwork1's retrieval of the same, as implemented here https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154 Unlike in genenetwork1, we do not mutate an object, instead, we return the values as retrieved from the database, and the caller will deal with the returned values as appropriate.
2021-07-29Add partial type annotations for slink moduleMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add some type annotations for the `nearest` function. * Leave some comments regarding the issues experienced when trying to add some typing annotations to the function to help with future endeavours of the same.
2021-07-29Add type annotations to the functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add some type annotations to the functions to reduce the chances of bugs creeping into the code.
2021-07-29db: traits: Remove publishdata columnBonfaceKilz
2021-07-28Retrieve trait informationMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: add functions to retrieve traits information * tests/unit/db/test_traits.py: add tests for new function Add functions to retrieve traits information as is done in genenetwork1 https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456 At this point, the data retrieval functions are probably incomplete, as there is more of the `retrieveInfo` function in GN1 that has not been considered as of this commit.
2021-07-28Make name retrieval more generalMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: make function more general * tests/unit/db/test_traits.py: parametrize the tests Make the name retrieval more general for the different types of traits by changing the column specification and table as appropriate.
2021-07-28Retrieve 'ProbeSet' trait nameMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: new function (retrieve_probeset_trait_name) * tests/unit/db/test_traits.py: test(s) for new function Add a function to retrieve the name of a 'ProbeSet' trait in a manner similar to genenetwork1's retrieval of the same, as implemented here https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154 Unlike in genenetwork1, we do not mutate an object, instead, we return the values as retrieved from the database, and the caller will deal with the returned values as appropriate.
2021-07-26tests: test_db: Add test case for "update_raw"BonfaceKilz
2021-07-26gn3: db: Create a raw update queryBonfaceKilz
* gn3/db/__init__.py (update_raw): New function.
2021-07-26db: traits: Fetch sample_data from a trait in csv formBonfaceKilz
2021-07-26Merge branch 'main' of github.com:genenetwork/genenetwork3Muriithi Frederick Muriuki
2021-07-26Fix issues caught by pylintMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix a myriad of issues caught by pylint to ensure the code passes all tests.
2021-07-26db: traits: Remove unused functionsBonfaceKilz
2021-07-26Check if corr_coefficient is NaN, since apparently it's stored as NaN ↵zsloan
instead of None when it can't be calculcated (which was messing up sorting); it may also be okay to remove the None check, but leaving it for now (#28)
2021-07-23sql: metadata_audit: Make char-set encoding explicit(utf8mb4)BonfaceKilz
See: https://www.eversql.com/mysql-utf8-vs-utf8mb4-whats-the-difference-between-utf8-and-utf8mb4/
2021-07-23Add data examples for `slink`. Implement function.Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Copy the function, mostly verbatim from genenetwork1. See: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L107-L138 * tests/unit/computations/test_slink.py: Add a test with some example data to test that the implementation gives the same results as that in genenetwork1
2021-07-23Add more test dataMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
2021-07-23Iterate through all valid pairsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Fix the iteration construct. Given two lists of member coordinates, such as [0, 1] and [3, 5], the initial code would iterate over the pairs [0, 3] and [1, 5]. This commit fixes the iteration constructs such that the new code iterates over the pairs [0, 3], [0, 5], [1, 3] and [1, 5].
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