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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.
2021-07-10gn3: db: Use correct type for columns arg in fetch functionsBonfaceKilz
2021-07-10Fix pylint issuesBonfaceKilz
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.
2021-06-07Rename json_data column to json_diff_dataBonfaceKilz
2021-06-07gn3: db: Fix how columns from tables is resolvedBonfaceKilz
2021-06-07gn3: db: Add "id_" property to metadata_audit class and mappingBonfaceKilz
2021-06-07gn3: db: Add "fetchall" method.BonfaceKilz
2021-06-07gn3: metadata_audit: Make props for MetadataAudit class optionalBonfaceKilz
2021-06-07gn3: db: Make "WHERE" clause optionalBonfaceKilz
* gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg.
2021-06-07gn3: db: Use correct DATACLASSMAP entry from metadata_auditBonfaceKilz
2021-06-07gn3: db: sort importsBonfaceKilz
2021-06-03gn3: db: Remove "escape_string" from importsBonfaceKilz
We use prepared statements, so no need to have this.
2021-06-03Use prepared statements for FETCH sql functionBonfaceKilz
2021-06-03gn3: db: Replace items() with keys()BonfaceKilz
* gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict!
2021-06-03Use prepared statements for UPDATE sql functionBonfaceKilz
2021-06-03gn3: db: Add new function for doing sql INSERTBonfaceKilz
2021-06-03Add data structures for the table metadata_auditBonfaceKilz
2021-06-03gn3: db: Add spacing before around "AND" in sql clauseBonfaceKilz
2021-06-03Get the diff between 2 dicts and return that as a dictBonfaceKilz
2021-06-03gn3: db: Return None if data and where are emptyBonfaceKilz
2021-05-26Move the methods, "update" and "fetch", to gn3.dbBonfaceKilz
2021-05-26db: phenotypes: Fix publication_mappingBonfaceKilz
2021-05-26db: phenotypes: Fix typoBonfaceKilz
2021-05-20db: phenotypes: Add function for fetching a single resultBonfaceKilz
* gn3/db/phenotypes.py (fetchone): New function.
2021-05-20db: phenotypes: Add a dataclass mapBonfaceKilz
Maps a string to it's dataclass.
2021-05-20db: phenotypes: Add Publication table mappingBonfaceKilz
2021-05-20db: phenotypes: Rename phenotype_column_mappingBonfaceKilz
2021-05-20db: phenotypes: Add Publication dataclass and mappingBonfaceKilz
2021-05-20db: phenotypes: Generalise the update functionBonfaceKilz
* gn3/db/phenotypes.py (update_phenotype): Delete it. (update): New, more general function.
2021-05-20db: phenotypes: Map a table to it's relevant dict mappingBonfaceKilz
2021-05-20db: phenotypes: Add type for DataclassBonfaceKilz
See: https://www.py4u.net/discuss/188952
2021-05-20db: phenotypes: Put mapping def after dataclassBonfaceKilz
2021-05-20db: phenotypes: Add phenotype table mappingBonfaceKilz
2021-05-20db: phenotypes: Add dataclass to represent PublishXRefBonfaceKilz
2021-05-20db: phenotype: Make "pylint: disable=[R0902]" global for fileBonfaceKilz
2021-05-20db: phenotypes: Add a way of updating the Phenotype tableBonfaceKilz
* gn3/db/phenotypes.py (Phenotype): New dataclass. (update_phenotype): New function. [phenotype_column_mapping]: New variable.
2021-05-10db: species: Add method for fetching all speciesBonfaceKilz
2021-05-08db: species: Fetch chromosomes using a group or species nameBonfaceKilz
* gn3/db/species.py (get_chromosome): New function.
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
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