diff options
Diffstat (limited to 'gn3/auth/authorisation/resources/models.py')
| -rw-r--r-- | gn3/auth/authorisation/resources/models.py | 53 |
1 files changed, 25 insertions, 28 deletions
diff --git a/gn3/auth/authorisation/resources/models.py b/gn3/auth/authorisation/resources/models.py index 2e2ff53..bc88691 100644 --- a/gn3/auth/authorisation/resources/models.py +++ b/gn3/auth/authorisation/resources/models.py @@ -269,56 +269,53 @@ def resource_by_id( raise NotFoundError(f"Could not find a resource with id '{resource_id}'") def __link_mrna_data_to_resource__( - conn: db.DbConnection, resource: Resource, dataset_id: str) -> dict: + conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict: """Link mRNA Assay data with a resource.""" with db.cursor(conn) as cursor: params = { "group_id": str(resource.group.group_id), "resource_id": str(resource.resource_id), - "dataset_type": "mRNA", - "dataset_id": dataset_id + "data_link_id": str(data_link_id) } cursor.execute( "INSERT INTO mrna_resources VALUES" - "(:group_id, :resource_id, :dataset_type, :dataset_id)", + "(:group_id, :resource_id, :data_link_id)", params) return params def __link_geno_data_to_resource__( - conn: db.DbConnection, resource: Resource, dataset_id: str) -> dict: + conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict: """Link Genotype data with a resource.""" with db.cursor(conn) as cursor: params = { "group_id": str(resource.group.group_id), "resource_id": str(resource.resource_id), - "dataset_type": "Genotype", - "trait_id": dataset_id + "data_link_id": str(data_link_id) } cursor.execute( "INSERT INTO genotype_resources VALUES" - "(:group_id, :resource_id, :dataset_type, :trait_id)", + "(:group_id, :resource_id, :data_link_id)", params) return params def __link_pheno_data_to_resource__( - conn: db.DbConnection, resource: Resource, dataset_id: str) -> dict: + conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict: """Link Phenotype data with a resource.""" with db.cursor(conn) as cursor: params = { "group_id": str(resource.group.group_id), "resource_id": str(resource.resource_id), - "dataset_type": "Phenotype", - "trait_id": dataset_id + "data_link_id": str(data_link_id) } cursor.execute( "INSERT INTO phenotype_resources VALUES" - "(:group_id, :resource_id, :dataset_type, :trait_id)", + "(:group_id, :resource_id, :data_link_id)", params) return params def link_data_to_resource( conn: db.DbConnection, user: User, resource_id: UUID, dataset_type: str, - dataset_id: str): + data_link_id: UUID) -> dict: """Link data to resource.""" if not authorised_for( conn, user, ("group:resource:edit-resource",), @@ -333,49 +330,49 @@ def link_data_to_resource( "mrna": __link_mrna_data_to_resource__, "genotype": __link_geno_data_to_resource__, "phenotype": __link_pheno_data_to_resource__, - }[dataset_type.lower()](conn, resource, dataset_id) + }[dataset_type.lower()](conn, resource, data_link_id) def __unlink_mrna_data_to_resource__( - conn: db.DbConnection, resource: Resource, dataset_id: str) -> dict: + conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict: """Unlink data from mRNA Assay resources""" with db.cursor(conn) as cursor: cursor.execute("DELETE FROM mrna_resources " - "WHERE resource_id=? AND dataset_id=?", - (str(resource.resource_id), dataset_id)) + "WHERE resource_id=? AND data_link_id=?", + (str(resource.resource_id), str(data_link_id))) return { "resource_id": str(resource.resource_id), "dataset_type": resource.resource_category.resource_category_key, - "dataset_id": dataset_id + "data_link_id": data_link_id } def __unlink_geno_data_to_resource__( - conn: db.DbConnection, resource: Resource, trait_id: str) -> dict: + conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict: """Unlink data from Genotype resources""" with db.cursor(conn) as cursor: cursor.execute("DELETE FROM genotype_resources " - "WHERE resource_id=? AND trait_id=?", - (str(resource.resource_id), trait_id)) + "WHERE resource_id=? AND data_link_id=?", + (str(resource.resource_id), str(data_link_id))) return { "resource_id": str(resource.resource_id), "dataset_type": resource.resource_category.resource_category_key, - "dataset_id": trait_id + "data_link_id": data_link_id } def __unlink_pheno_data_to_resource__( - conn: db.DbConnection, resource: Resource, trait_id: str) -> dict: + conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict: """Unlink data from Phenotype resources""" with db.cursor(conn) as cursor: cursor.execute("DELETE FROM phenotype_resources " - "WHERE resource_id=? AND trait_id=?", - (str(resource.resource_id), trait_id)) + "WHERE resource_id=? AND data_link_id=?", + (str(resource.resource_id), str(data_link_id))) return { "resource_id": str(resource.resource_id), "dataset_type": resource.resource_category.resource_category_key, - "dataset_id": trait_id + "data_link_id": str(data_link_id) } def unlink_data_from_resource( - conn: db.DbConnection, user: User, resource_id: UUID, dataset_id: str): + conn: db.DbConnection, user: User, resource_id: UUID, data_link_id: UUID): """Unlink data from resource.""" if not authorised_for( conn, user, ("group:resource:edit-resource",), @@ -391,7 +388,7 @@ def unlink_data_from_resource( "mrna": __unlink_mrna_data_to_resource__, "genotype": __unlink_geno_data_to_resource__, "phenotype": __unlink_pheno_data_to_resource__, - }[dataset_type.lower()](conn, resource, dataset_id) + }[dataset_type.lower()](conn, resource, data_link_id) def organise_resources_by_category(resources: Sequence[Resource]) -> dict[ ResourceCategory, tuple[Resource]]: |