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2021-08-31Update `heatmap_data` function: remove extraneous data...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: update function * gn3/db/traits.py: new function Remove extraneous data and arguments from the function. - Load the genotype file - Generate traits file - Provide both raw traits data, and exported traits data in return Muriithi Frederick Muriuki
2021-08-31Provide utilities for genotype files...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/genotypes.py: New module * gn3/settings.py: Add new configuration variable * qtlfilesexport.py: Test out new code Add a module containing functions dealing with the genotype files. Add a configuration variable to point to the location of the genotype files. Muriithi Frederick Muriuki
2021-08-17Provide top-level `riset` key-value pair...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Provide the expected, top-level `riset` key-value pair and eliminate the redundant key-value pair. Muriithi Frederick Muriuki
2021-08-17Fix errors: add in missing parenthesis...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Call the `cursor.fetchone()` function to get results. Without the parenthesis, the code was trying to use the function itself as the results, which was a bug, and would lead to failure. Muriithi Frederick Muriuki
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
2021-08-09Retrieve the trait data...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add functions to retrieve the `value`, `variance`, and `ndata` values for any given trait. Muriithi Frederick Muriuki
2021-08-09Add missing arguments. Fix typo....Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix minor bugs in the code. 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
2021-08-08Only load extra data if the traits have basic info...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. Muriithi Frederick Muriuki
2021-08-08Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_decom...Muriithi Frederick Muriuki
2021-08-05db: traits: Return unique values when fetching sample dataBonfaceKilz
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
2021-08-04Avoid 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
2021-07-29Delete "update_raw" and it's test-casesBonfaceKilz
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
2021-07-26gn3: db: Create a raw update query...* gn3/db/__init__.py (update_raw): New function. BonfaceKilz
2021-07-26db: traits: Fetch sample_data from a trait in csv formBonfaceKilz
2021-07-26db: traits: Remove unused functionsBonfaceKilz
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 structures...* gn3/db/phenotypes.py (Probeset): New dataclass. (probeset_mapping): New dict. * gn3/db/__init__.py: Add probeset_mapping and Probeset. BonfaceKilz
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 optional...* gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg. BonfaceKilz
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 imports...We use prepared statements, so no need to have this. BonfaceKilz
2021-06-03Use prepared statements for FETCH sql functionBonfaceKilz
2021-06-03gn3: db: Replace items() with keys()...* gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict! BonfaceKilz
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