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2023-07-18Fetch a single publication by `PublicationId`Frederick Muriuki Muriithi
2023-07-18Fetch metadata for a single phenotype.Frederick Muriuki Muriithi
2023-07-18Fetch single phenotype trait by `dataset_id` and `trait_name`.Frederick Muriuki Muriithi
2023-07-18Bug: 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
2023-07-17Fix 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
2023-07-12Bug: 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
2023-07-12Bug: 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
2023-07-12Move documentation comment to beginning of functionFrederick Muriuki Muriithi
2023-07-11Revert "Skip tests broken by Python-3.10 temporarily"...This reverts commit f52247c15f3694f3dd5fd0fd79c3e15376137e07. Frederick Muriuki Muriithi
2023-07-11Trigger CIMunyoki Kilyungi
2023-07-06Provide the client_id as part of the post request.Frederick Muriuki Muriithi
2023-07-05Skip 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
2023-07-05Update 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
2023-07-04Fix minor UI bugFrederick Muriuki Muriithi
2023-07-03Spruce up UI...Make UI somewhat consistent with the GN2 UI. Frederick Muriuki Muriithi
2023-07-03Enable deletion of OAuth2 clients.Frederick Muriuki Muriithi
2023-06-30Edit some of the details of OAuth2 clientsFrederick Muriuki Muriithi
2023-06-30List all OAuth2 clients.Frederick Muriuki Muriithi
2023-06-23Fetch 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
2023-06-20Fix conflictszsloan
2023-06-20Bug: Don't overwrite/delete old collectionsFrederick Muriuki Muriithi
2023-06-15Fetch 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
2023-06-13Namespace session variable...Extract the functions acting on the session into a separate module and namespace the session variable to prevent conflicts. Frederick Muriuki Muriithi
2023-06-12Delete unused import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Fetch 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
2023-06-12Correct publication function docstring...* gn3/api/metadata.py (publication): Update docstring. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Delete unused get_trait_metadata function...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-08Fix bugs with accessing/creating collectionszsloan
2023-06-08bug: Function expects pathlib.Path not strFrederick Muriuki Muriithi
2023-06-07auth: Remove "migrate-data" scope....Scope is superceded by CLI utility script. Frederick Muriuki Muriithi
2023-06-07auth: Remove obsoleted scopeFrederick Muriuki Muriithi
2023-06-07Add 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
2023-06-07Nest duplicate entries into a list from a sparql result...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-07Remove 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
2023-06-06Pass geoSeries as a URL...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-06Rename gn:geoPlatform -> gn:geoPlatformUrl...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-06Match 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
2023-06-06Replace taxon prefix with ncbiTaxon which references NCBI...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-06Rename dataset_metadata -> dataset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-05Logging: 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
2023-06-05Logging: Get user information.Frederick Muriuki Muriithi
2023-06-05Logging: Get guix profile information if present....Useful for debugging issues within the guix containers. Frederick Muriuki Muriithi
2023-06-05Logging: Get info about python...This information is useful to assist with debugging issues within the guix containers. Frederick Muriuki Muriithi
2023-06-05Handle unhandled SQLite3 errors.Frederick Muriuki Muriithi
2023-06-02Replace 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
2023-06-02Create a function for stripping the last bit from a URL...* gn3/db/rdf.py: Import unquote and urlparse. (strip_url): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-02auth: Increase limit to 100K recordsFrederick Muriuki Muriithi
2023-06-02auth: Add delay between DB inserts...Add delays to avoid overwhelming the DB server. Frederick Muriuki Muriithi
2023-06-02Auth: Bug: Display all admins before taking choiceFrederick Muriuki Muriithi
2023-05-31scripts: Write table checksums into index....* scripts/index-genenetwork (main): Write table checksums into index. Arun Isaac
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