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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 temporarilyFrederick Muriuki Muriithi
Skip the tests that have been broken by the migrations to Python-3.10 temporarily, until we can fix them.
2023-07-05Update test: create throw-away variableFrederick Muriuki Muriithi
* Commit `b529c700` changes the return value to a tuple of values rather than a single string value. Handle that in the test.
2023-07-04Fix minor UI bugFrederick Muriuki Muriithi
2023-07-03Spruce up UIFrederick Muriuki Muriithi
Make UI somewhat consistent with the GN2 UI.
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 variablesFrederick Muriuki Muriithi
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.
2023-06-20Fix conflictszsloan
2023-06-20Bug: Don't overwrite/delete old collectionsFrederick Muriuki Muriithi
2023-06-15Fetch genotypes from virtuosoMunyoki Kilyungi
* 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>
2023-06-13Namespace session variableFrederick Muriuki Muriithi
Extract the functions acting on the session into a separate module and namespace the session variable to prevent conflicts.
2023-06-12Delete unused importMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Fetch phenotypes from virtuosoMunyoki Kilyungi
* 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>
2023-06-12Correct publication function docstringMunyoki Kilyungi
* gn3/api/metadata.py (publication): Update docstring. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Delete unused get_trait_metadata functionMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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.Frederick Muriuki Muriithi
Scope is superceded by CLI utility script.
2023-06-07auth: Remove obsoleted scopeFrederick Muriuki Muriithi
2023-06-07Add publication end-pointMunyoki Kilyungi
* 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>
2023-06-07Nest duplicate entries into a list from a sparql resultMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-07Remove trait_metadata endpointMunyoki Kilyungi
* gn3/api/metadata.py: Remove get_trait_metadata import. (trait_metadata): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Pass geoSeries as a URLMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Rename gn:geoPlatform -> gn:geoPlatformUrlMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Match how dataset metadata is fetched with GN1Munyoki Kilyungi
* 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>
2023-06-06Replace taxon prefix with ncbiTaxon which references NCBIMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Rename dataset_metadata -> datasetMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-05Logging: Don't allow getting user info to stop application startingFrederick Muriuki Muriithi
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.
2023-06-05Logging: Get user information.Frederick Muriuki Muriithi
2023-06-05Logging: Get guix profile information if present.Frederick Muriuki Muriithi
Useful for debugging issues within the guix containers.
2023-06-05Logging: Get info about pythonFrederick Muriuki Muriithi
This information is useful to assist with debugging issues within the guix containers.
2023-06-05Handle unhandled SQLite3 errors.Frederick Muriuki Muriithi
2023-06-02Replace SELECT with CONSTRUCT when fetching a dataset's metadataMunyoki Kilyungi
* gn3/db/rdf.py: Importh pymonad.Nothing. (get_dataset_metadata): Replace SELECT with CONSTRUCT. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-02Create a function for stripping the last bit from a URLMunyoki Kilyungi
* gn3/db/rdf.py: Import unquote and urlparse. (strip_url): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-02auth: Increase limit to 100K recordsFrederick Muriuki Muriithi
2023-06-02auth: Add delay between DB insertsFrederick Muriuki Muriithi
Add delays to avoid overwhelming the DB server.
2023-06-02Auth: Bug: Display all admins before taking choiceFrederick Muriuki Muriithi
2023-05-31scripts: Write table checksums into index.Arun Isaac
* scripts/index-genenetwork (main): Write table checksums into index.
2023-05-31scripts: Introduce SQLTableClause.Arun Isaac
* scripts/index-genenetwork (SQLTableClause): New variable. (genes_query, phenotypes_query): Express tables using SQLTableClause. (serialize_sql): Serialize SQLTableClause.
2023-05-31scripts: Fold long lines.Arun Isaac
* scripts/index-genenetwork (write_document, index_query): Fold long lines.
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