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path: root/tests/unit/db/test_traits.py
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2021-10-19Disable pylint issue...* Disable minor pylint issue. Frederick Muriuki Muriithi
2021-10-19Move `export_informative` function to `gn3.db.traits` module...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/traits.py: Move `export_informative` function here * gn3/partial_correlations.py: Remove `export_informative` function * tests/unit/db/test_traits.py: Move `export_informative` function tests here * tests/unit/test_partial_correlations.py: Remove `export_informative` function tests The `export_informative` function relates more to the traits than to the partial correlations, and could find use in more than just the partial correlations stuff. This commit moves the function to the more traits-specific `gn3.db.traits` module. Frederick Muriuki Muriithi
2021-10-19Move 'export_trait_data' to 'gn3.db.traits' module...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/traits.py: Move function `export_trait_data` here * gn3/heatmaps.py: Remove function `export_trait_data` * tests/unit/db/test_traits.py: Move function `export_trait_data` tests here * tests/unit/test_heatmaps.py: Remove function `export_trait_data` here Function `export_trait_data` more closely corresponds to the traits and is used in more than just the `gn3.heatmaps` module. This commit moves the relevant code over to the `gn3.db.traits` module and also moves the tests to the corresponding tests modules. Frederick Muriuki Muriithi
2021-09-23Refactor: Move common sample data to separate file...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move common sample test data into a separate file where it can be imported from, to prevent pylint error R0801 which proved tricky to silence in any other way. Frederick Muriuki Muriithi
2021-09-22Fix more pylint errorsFrederick Muriuki Muriithi
2021-08-09Set up the trait dataset type correctly...* gn3/db/traits.py: setup `trait_dataset_type` * tests/unit/db/test_traits.py: fix tests The type ('Temp', 'Geno', 'Publish', and 'ProbeSet') relate to a trait's dataset, and not the trait itself. This commit updates the code to take this into consideration. The dataset type is also set up from a trait's full name, therefore this commit removes the `trait_type` argument from the `retrieve_trait_info` function. Muriithi Frederick Muriuki
2021-08-09Fix linting errors...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add module, class and function docstrings * Deactivate some irrelevant pylint errors * Fix indentations and line-lengths Muriithi Frederick Muriuki
2021-08-08Update tests...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. Muriithi Frederick Muriuki
2021-08-05Reorganise the database code...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 Muriithi Frederick Muriuki
2021-08-05Build up trait_name items from full name...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. Muriithi Frederick Muriuki
2021-08-04Fix issues caught by pylint...* 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 Muriithi Frederick Muriuki
2021-08-04Retrieve the RISet and RISet ID values...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. Muriithi Frederick Muriuki
2021-08-04Add tests for post-processing functions...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 Muriithi Frederick Muriuki
2021-08-04Update tests...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. Muriithi Frederick Muriuki
2021-07-30Remove extra space...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. Muriithi Frederick Muriuki
2021-07-30Return dict from query functions...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. Muriithi Frederick Muriuki
2021-07-29Merge branch 'main' into Feature/Update-db-from-csv-dataBonfaceKilz
2021-07-29Add method for updating values from a sample dataset...* gn3/db/traits.py (update_sample_data): New function. * tests/unit/db/test_traits.py: New test cases for ^^. BonfaceKilz
2021-07-29Retrieve trait information...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. Muriithi Frederick Muriuki
2021-07-29Make name retrieval more general...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. Muriithi Frederick Muriuki
2021-07-29Retrieve 'ProbeSet' trait name...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. Muriithi Frederick Muriuki