| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-07-29 | Retrieve 'ProbeSet' trait name | Muriithi 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. | |||
| 2021-07-10 | gn3: db: Use correct type for columns arg in fetch functions | BonfaceKilz | |
| 2021-07-10 | Fix pylint issues | BonfaceKilz | |
| 2021-07-10 | gn3: db: Add extra argument to specify column in fetch statements | BonfaceKilz | |
| 2021-07-10 | db: phenotypes: Add Probeset data structures | BonfaceKilz | |
| * gn3/db/phenotypes.py (Probeset): New dataclass. (probeset_mapping): New dict. * gn3/db/__init__.py: Add probeset_mapping and Probeset. | |||
| 2021-06-07 | Rename json_data column to json_diff_data | BonfaceKilz | |
| 2021-06-07 | gn3: db: Fix how columns from tables is resolved | BonfaceKilz | |
| 2021-06-07 | gn3: db: Add "id_" property to metadata_audit class and mapping | BonfaceKilz | |
| 2021-06-07 | gn3: db: Add "fetchall" method. | BonfaceKilz | |
| 2021-06-07 | gn3: metadata_audit: Make props for MetadataAudit class optional | BonfaceKilz | |
| 2021-06-07 | gn3: db: Make "WHERE" clause optional | BonfaceKilz | |
| * gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg. | |||
| 2021-06-07 | gn3: db: Use correct DATACLASSMAP entry from metadata_audit | BonfaceKilz | |
| 2021-06-07 | gn3: db: sort imports | BonfaceKilz | |
| 2021-06-03 | gn3: db: Remove "escape_string" from imports | BonfaceKilz | |
| We use prepared statements, so no need to have this. | |||
| 2021-06-03 | Use prepared statements for FETCH sql function | BonfaceKilz | |
| 2021-06-03 | gn3: db: Replace items() with keys() | BonfaceKilz | |
| * gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict! | |||
| 2021-06-03 | Use prepared statements for UPDATE sql function | BonfaceKilz | |
| 2021-06-03 | gn3: db: Add new function for doing sql INSERT | BonfaceKilz | |
| 2021-06-03 | Add data structures for the table metadata_audit | BonfaceKilz | |
| 2021-06-03 | gn3: db: Add spacing before around "AND" in sql clause | BonfaceKilz | |
| 2021-06-03 | Get the diff between 2 dicts and return that as a dict | BonfaceKilz | |
| 2021-06-03 | gn3: db: Return None if data and where are empty | BonfaceKilz | |
| 2021-05-26 | Move the methods, "update" and "fetch", to gn3.db | BonfaceKilz | |
| 2021-05-26 | db: phenotypes: Fix publication_mapping | BonfaceKilz | |
| 2021-05-26 | db: phenotypes: Fix typo | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Add function for fetching a single result | BonfaceKilz | |
| * gn3/db/phenotypes.py (fetchone): New function. | |||
| 2021-05-20 | db: phenotypes: Add a dataclass map | BonfaceKilz | |
| Maps a string to it's dataclass. | |||
| 2021-05-20 | db: phenotypes: Add Publication table mapping | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Rename phenotype_column_mapping | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Add Publication dataclass and mapping | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Generalise the update function | BonfaceKilz | |
| * gn3/db/phenotypes.py (update_phenotype): Delete it. (update): New, more general function. | |||
| 2021-05-20 | db: phenotypes: Map a table to it's relevant dict mapping | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Add type for Dataclass | BonfaceKilz | |
| See: https://www.py4u.net/discuss/188952 | |||
| 2021-05-20 | db: phenotypes: Put mapping def after dataclass | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Add phenotype table mapping | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Add dataclass to represent PublishXRef | BonfaceKilz | |
| 2021-05-20 | db: phenotype: Make "pylint: disable=[R0902]" global for file | BonfaceKilz | |
| 2021-05-20 | db: phenotypes: Add a way of updating the Phenotype table | BonfaceKilz | |
| * gn3/db/phenotypes.py (Phenotype): New dataclass. (update_phenotype): New function. [phenotype_column_mapping]: New variable. | |||
| 2021-05-10 | db: species: Add method for fetching all species | BonfaceKilz | |
| 2021-05-08 | db: species: Fetch chromosomes using a group or species name | BonfaceKilz | |
| * gn3/db/species.py (get_chromosome): New function. | |||
| 2021-05-08 | Fix pep-8 errors | BonfaceKilz | |
| 2021-05-08 | db: traits: Add extra method for looking up webqtl datasets | BonfaceKilz | |
| 2021-05-08 | db: traits: Update method for inserting publication method | BonfaceKilz | |
| 2021-05-08 | Add method for inserting publication_data | BonfaceKilz | |
| 2021-05-08 | Add webqtlCaseData DS to keep track of case data in one trait | BonfaceKilz | |
| 2021-05-08 | Replace namedtuple with a dataclass | BonfaceKilz | |
| 2021-05-08 | Add method for inserting phenotypes | BonfaceKilz | |
| 2021-05-08 | Add method for inserting publications | BonfaceKilz | |
| 2021-05-08 | Add method to fetch riset name and id | BonfaceKilz | |
| 2021-03-16 | delete unwanted correlation stuff (#5) | Alexander Kabui | |
| * delete unwanted correlation stuff * Refactor/clean up correlations (#4) * initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com> * update guix scm file * fix pylint error for correlations api Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com> | |||
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