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path: root/gn3/db/traits.py
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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
2021-08-04Avoid string interpolation: use prepared statement...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 Muriithi Frederick Muriuki
2021-07-30Rework db functions to enable postprocessing...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. 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
2021-07-29Add type annotations to the function...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. Muriithi Frederick Muriuki
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
2021-07-29db: traits: Remove publishdata columnBonfaceKilz
2021-07-26db: traits: Fetch sample_data from a trait in csv formBonfaceKilz
2021-07-26db: traits: Remove unused functionsBonfaceKilz
2021-05-08Fix pep-8 errorsBonfaceKilz
2021-05-08db: traits: Add extra method for looking up webqtl datasetsBonfaceKilz
2021-05-08db: traits: Update method for inserting publication methodBonfaceKilz
2021-05-08Add method for inserting publication_dataBonfaceKilz
2021-05-08Add webqtlCaseData DS to keep track of case data in one traitBonfaceKilz
2021-05-08Replace namedtuple with a dataclassBonfaceKilz
2021-05-08Add method for inserting phenotypesBonfaceKilz
2021-05-08Add method for inserting publicationsBonfaceKilz
2021-05-08Add method to fetch riset name and idBonfaceKilz