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2023-07-08guile server: adding docstringsPjotr Prins
2023-07-08guile server: more meta infoPjotr Prins
2023-07-08guile server: updated README to run interactive development with emacs-geiserPjotr Prins
2023-07-08guile server: try meta examplePjotr Prins
2023-07-08guile server: indentPjotr Prins
2023-07-06guile server: switching to fiber webPjotr Prins
2023-07-06guile server: switching to fiber webPjotr Prins
2023-07-06guile: propose adding end points to outputPjotr Prins
2023-07-05Kicked of guile REST APIPjotr Prins
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
2023-05-31scripts: Introduce SQLTableClause....* scripts/index-genenetwork (SQLTableClause): New variable. (genes_query, phenotypes_query): Express tables using SQLTableClause. (serialize_sql): Serialize SQLTableClause. Arun Isaac
2023-05-31scripts: Fold long lines....* scripts/index-genenetwork (write_document, index_query): Fold long lines. Arun Isaac
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