| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-07-26 | db: traits: Remove unused functions | BonfaceKilz | |
| 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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