| Age | Commit message (Expand) | Author |
|---|
| 2021-07-29 | Add 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 |
| 2021-07-29 | Retrieve 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 |
| 2021-07-29 | Make 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 |
| 2021-07-29 | Retrieve '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 |
| 2021-07-10 | 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...* gn3/db/phenotypes.py (Probeset): New dataclass.
(probeset_mapping): New dict.
* gn3/db/__init__.py: Add probeset_mapping and Probeset.
| BonfaceKilz |
| 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...* gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg.
| BonfaceKilz |
| 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...We use prepared statements, so no need to have this.
| BonfaceKilz |
| 2021-06-03 | Use prepared statements for FETCH sql function | BonfaceKilz |
| 2021-06-03 | gn3: db: Replace items() with keys()...* gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict!
| BonfaceKilz |
| 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...* gn3/db/phenotypes.py (fetchone): New function.
| BonfaceKilz |
| 2021-05-20 | db: phenotypes: Add a dataclass map...Maps a string to it's dataclass.
| BonfaceKilz |
| 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...* gn3/db/phenotypes.py (update_phenotype): Delete it.
(update): New, more general function.
| BonfaceKilz |
| 2021-05-20 | db: phenotypes: Map a table to it's relevant dict mapping | BonfaceKilz |
| 2021-05-20 | db: phenotypes: Add type for Dataclass...See: https://www.py4u.net/discuss/188952
| BonfaceKilz |
| 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...* gn3/db/phenotypes.py (Phenotype): New dataclass.
(update_phenotype): New function.
[phenotype_column_mapping]: New variable.
| BonfaceKilz |
| 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...* gn3/db/species.py (get_chromosome): New function.
| BonfaceKilz |
| 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 |
