Age | Commit message (Expand) | Author |
2023-07-19 | Make repository a guix channel....* .guix-channel: New file.
* guix.scm: Move to ...
* .guix/genenetwork3-package.scm: ... here. Convert into a module with public
package variables.
| Arun Isaac |
2023-07-19 | Extract code dealing with ProbeSets to their own module. | Frederick Muriuki Muriithi |
2023-07-19 | Extract reusable code to separate module...Extract the reusable function into a separate `query_tools` module for use in
other modules.
| Frederick Muriuki Muriithi |
2023-07-18 | Bug: Change from `_id` to `id_` to avoid downstream breakage....The downstream code expects `id_` not `_id`.
| Frederick Muriuki Muriithi |
2023-07-18 | Fix wrong import, and typing issues. | Frederick Muriuki Muriithi |
2023-07-18 | Fetch a single publication by `PublicationId` | Frederick Muriuki Muriithi |
2023-07-18 | Fetch metadata for a single phenotype. | Frederick Muriuki Muriithi |
2023-07-18 | Fetch single phenotype trait by `dataset_id` and `trait_name`. | Frederick Muriuki Muriithi |
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 |
2023-07-17 | Fix dict key name...Remove extra colon (:) at the end of the name that was leading to the number
of cases not being presented as expected.
| Frederick Muriuki Muriithi |
2023-07-12 | Bug: Set the `data_exists` variable within the context manager...The `cursor.fetchone()` call that was used as the condition to the `if` was
called outside of the context manager, and therefore would always give a
non-truthy value at best and an inconsistent result at worst.
This commit gets the value before the context manager has exited and stores it
for later use.
| 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 |
2023-07-12 | Move documentation comment to beginning of function | Frederick Muriuki Muriithi |
2023-07-11 | Revert "Skip tests broken by Python-3.10 temporarily"...This reverts commit f52247c15f3694f3dd5fd0fd79c3e15376137e07.
| Frederick Muriuki Muriithi |
2023-07-11 | Trigger CI | Munyoki Kilyungi |
2023-07-06 | Provide the client_id as part of the post request. | Frederick Muriuki Muriithi |
2023-07-05 | Skip tests broken by Python-3.10 temporarily...Skip the tests that have been broken by the migrations to Python-3.10
temporarily, until we can fix them.
| Frederick Muriuki Muriithi |
2023-07-05 | Update test: create throw-away variable...* Commit `b529c700` changes the return value to a tuple of values rather than
a single string value. Handle that in the test.
| Frederick Muriuki Muriithi |
2023-07-04 | Fix minor UI bug | Frederick Muriuki Muriithi |
2023-07-03 | Spruce up UI...Make UI somewhat consistent with the GN2 UI.
| Frederick Muriuki Muriithi |
2023-07-03 | Enable deletion of OAuth2 clients. | Frederick Muriuki Muriithi |
2023-06-30 | Edit some of the details of OAuth2 clients | Frederick Muriuki Muriithi |
2023-06-30 | List all OAuth2 clients. | Frederick Muriuki Muriithi |
2023-06-23 | Fetch all collections, rename variables...Fetch from `__REDIS_COLLECTION_KEY__` not `"collections"` to ensure all
collections are retrieved correctly.
Rename from `__*_DOC__` to `__REDIS_*_KEY__` to more clearly express what the
variables are about.
| Frederick Muriuki Muriithi |
2023-06-20 | Fix conflicts | zsloan |
2023-06-20 | Bug: Don't overwrite/delete old collections | Frederick Muriuki Muriithi |
2023-06-15 | Fetch genotypes from virtuoso...* gn3/api/metadata.py: Import get_genotype_metadata.
(genotype): New end-point.
* gn3/db/rdf.py (get_phenotype_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-13 | Namespace session variable...Extract the functions acting on the session into a separate module and
namespace the session variable to prevent conflicts.
| Frederick Muriuki Muriithi |
2023-06-12 | Delete unused import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-12 | Fetch phenotypes from virtuoso...* gn3/api/metadata.py: Import get_phenotype_metadata.
(phenotype): New end-point.
* gn3/db/rdf.py (get_phenotype_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-12 | Correct publication function docstring...* gn3/api/metadata.py (publication): Update docstring.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-12 | Delete unused get_trait_metadata function...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-08 | Fix bugs with accessing/creating collections | zsloan |
2023-06-08 | bug: Function expects pathlib.Path not str | Frederick Muriuki Muriithi |
2023-06-07 | auth: Remove "migrate-data" scope....Scope is superceded by CLI utility script.
| Frederick Muriuki Muriithi |
2023-06-07 | auth: Remove obsoleted scope | Frederick Muriuki Muriithi |
2023-06-07 | Add publication end-point...* gn3/api/metadata.py: Import get_publication_metadata
(publication): New endpoint.
* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-07 | Nest duplicate entries into a list from a sparql result...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-07 | Remove trait_metadata endpoint...* gn3/api/metadata.py: Remove get_trait_metadata import.
(trait_metadata): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-06 | Pass geoSeries as a URL...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-06 | Rename gn:geoPlatform -> gn:geoPlatformUrl...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-06 | Match how dataset metadata is fetched with GN1...* gn3/db/rdf.py (sparql_query): Parse CONSTRUCTS and SELECTS
differently.
(strip_url): Rename to ...
(get_url_local_name): ... this.
(get_dataset_metadata): Fetch extra fields in RDF.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-06 | Replace taxon prefix with ncbiTaxon which references NCBI...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-06 | Rename dataset_metadata -> dataset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-05 | Logging: Don't allow getting user info to stop application starting...In certain scenarios (probably due to host contamination) the effective UID of
the running application is not the expected "genenetwork" user, rather, it is
a user on the host system, which leads to the error:
KeyError: 'getpwuid(): uid not found: 1000'
This commit prevents the application from failing in such a case, but still
logs out such weirdness.
| Frederick Muriuki Muriithi |
2023-06-05 | Logging: Get user information. | Frederick Muriuki Muriithi |
2023-06-05 | Logging: Get guix profile information if present....Useful for debugging issues within the guix containers.
| Frederick Muriuki Muriithi |
2023-06-05 | Logging: Get info about python...This information is useful to assist with debugging issues within the guix
containers.
| Frederick Muriuki Muriithi |
2023-06-05 | Handle unhandled SQLite3 errors. | Frederick Muriuki Muriithi |
2023-06-02 | Replace SELECT with CONSTRUCT when fetching a dataset's metadata...* gn3/db/rdf.py: Importh pymonad.Nothing.
(get_dataset_metadata): Replace SELECT with CONSTRUCT.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |