| Age | Commit message (Expand) | Author |
|---|
| 2023-08-17 | Fix queries for fetching group names | zsloan |
| 2023-08-17 | Fix query for retrieving mrna dataset group name | zsloan |
| 2023-08-17 | Fix mrna group name query | zsloan |
| 2023-08-17 | Add function for retrieving mRNA Assay group name | zsloan |
| 2023-07-18 | Bug: Fetch group name by dataset_id...Change the code to fetch the group name by the dataset ID, since according to
usage[1] of the `retrieve_group_name` function, the value passed in is the
`dataset_id` and not the `group_id`.
Change the name from `retrieve_group_name` to `retrieve_phenotype_group_name`
to more clearly indicate that this function concerns itself with the groups
that relate to phenotypes.
[1](https://github.com/genenetwork/genenetwork2/blob/1bbb0430732b7fa5102d7dcbda80ebda252f5424/wqflask/wqflask/metadata_edits.py)
| Frederick Muriuki Muriithi |
| 2023-07-12 | Bug: Retrieve configs from app, not environment...Retrieve the configuration values from the application object, not from the
environment. We are assured of having the configuration values set in the
application - we do not have that assurance for the environment.
| Frederick Muriuki Muriithi |
| 2023-05-22 | Use string literal concatenation to make genofile_path line shorter | zsloan |
| 2023-05-22 | Fix quotes when setting genofile_path | zsloan |
| 2023-05-22 | Change type from 'any' to 'Any' | zsloan |
| 2023-05-22 | Use f-string for setting genofile_path...Also set default value for os.environ.get("GENENETWORK_FILES")
| zsloan |
| 2023-05-22 | Include encoding in open statement to address pylint W1514 | zsloan |
| 2023-05-22 | Initialize 'line'; previous pylint complained because line might not be initi... | zsloan |
| 2023-05-22 | Use 'with open()' syntax...Initialize samplelist variable
| zsloan |
| 2023-05-22 | Fix retrieve_sample_list function to correctly get genofile_path | zsloan |
| 2023-05-22 | Add function for retrieving group name (given group ID) | zsloan |
| 2023-05-22 | Add function for retrieving samplelist from .geno file | zsloan |
| 2022-11-02 | Re-implement RDF related code to use monads in its own module...* gn3/api/general.py: Replace gn3.db.datasets import with gn3.db.rdf.
(dataset_metadata) <jsonify>: Replace datasets.dataset_metadata with
rdf.get_dataset_metadata.
* gn3/db/datasets.py: Remove unused imports.
(sparql_query, dataset_metadata): Delete.
* gn3/db/rdf.py: (sparql_query, get_dataset_metadata): New functions.
| Munyoki Kilyungi |
| 2022-06-21 | db: datasets.py: Ignore results from sparql.queryAndConvert...ATM, it's very difficult to work the correct type that is returned. Ignore
this for now and fix this later.
| BonfaceKilz |
| 2022-02-21 | Fix a myriad of linter issues...* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
| Frederick Muriuki Muriithi |
| 2022-02-18 | Remove code trying to query non-existent `TempFreeze` table...The code was migrated from GN1 with a faulty assumption that all trait types
have a corresponding `*Freeze` table in the database. This assumption is not
true for the `Temp` traits.
This commit removes the buggy code.
| Frederick Muriuki Muriithi |
| 2021-12-23 | db: Assist mypy with explicit type declaration....* gn3/db/datasets.py (dataset_metadata): Assist mypy by explicitly declaring
type of return dictionary.
| Arun Isaac |
| 2021-12-23 | db: Fix sparql_query return type....* gn3/db/datasets.py: Import List from typing.
(sparql_query): Set return type to List[Dict[str, Any]].
| Arun Isaac |
| 2021-12-23 | db: Fix wrong continued indentation....* gn3/db/datasets.py (dataset_metadata): Fix wrong continued indentation.
| Arun Isaac |
| 2021-12-09 | Prevent error on no result. Fix indexing...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* If the dataset name is not found, don't cause an exception, instead, return
the provided search name.
* Use the correct inner object
| Frederick Muriuki Muriithi |
| 2021-12-02 | Implement dataset metadata API endpoint....* guix.scm: Import (gnu packages rdf).
(genenetwork3)[propagated-inputs]: Add python-sparqlwrapper.
* gn3/settings.py (SPARQL_ENDPOINT): New variable.
* gn3/api/general.py: Import datasets from gn3.db.
(dataset_metadata): New API endpoint.
* gn3/db/datasets.py: Import re, Template from string, Dict and Optional from
typing, JSON and SPARQLWrapper from SPARQLWrapper, SPARQL_ENDPOINT from
gn3.settings.
(sparql_query, dataset_metadata): New functions.
| Arun Isaac |
| 2021-09-27 | Update terminology: `riset` to `group`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update terminology to use the appropriate domain terminology according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
| Frederick Muriuki Muriithi |
| 2021-08-17 | Fix 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 |
| 2021-08-09 | Fix 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 |
| 2021-08-05 | Reorganise 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 |
