diff options
Diffstat (limited to 'gn_auth/auth')
| -rw-r--r-- | gn_auth/auth/authorisation/resources/__init__.py | 2 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/data.py | 29 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/genotype_resource.py | 70 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/models.py | 238 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/mrna_resource.py | 67 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/phenotype_resource.py | 69 |
6 files changed, 274 insertions, 201 deletions
diff --git a/gn_auth/auth/authorisation/resources/__init__.py b/gn_auth/auth/authorisation/resources/__init__.py index 869ab60..8037ca9 100644 --- a/gn_auth/auth/authorisation/resources/__init__.py +++ b/gn_auth/auth/authorisation/resources/__init__.py @@ -1,2 +1,2 @@ """Initialise the `gn3.auth.authorisation.resources` package.""" -from .models import Resource, ResourceCategory +from .base import Resource, ResourceCategory diff --git a/gn_auth/auth/authorisation/resources/data.py b/gn_auth/auth/authorisation/resources/data.py new file mode 100644 index 0000000..8f5e625 --- /dev/null +++ b/gn_auth/auth/authorisation/resources/data.py @@ -0,0 +1,29 @@ +""" +Utilities for handling data on resources. + +These are mostly meant for internal use. +""" +from uuid import UUID +from typing import Sequence +from functools import reduce + +import sqlite3 + +from .base import Resource + +def __attach_data__( + data_rows: Sequence[sqlite3.Row], + resources: Sequence[Resource]) -> Sequence[Resource]: + def __organise__(acc, row): + resource_id = UUID(row["resource_id"]) + return { + **acc, + resource_id: acc.get(resource_id, tuple()) + (dict(row),) + } + organised: dict[UUID, tuple[dict, ...]] = reduce(__organise__, data_rows, {}) + return tuple( + Resource( + resource.group, resource.resource_id, resource.resource_name, + resource.resource_category, resource.public, + organised.get(resource.resource_id, tuple())) + for resource in resources) diff --git a/gn_auth/auth/authorisation/resources/genotype_resource.py b/gn_auth/auth/authorisation/resources/genotype_resource.py new file mode 100644 index 0000000..03e2e68 --- /dev/null +++ b/gn_auth/auth/authorisation/resources/genotype_resource.py @@ -0,0 +1,70 @@ +"""Genotype data resources functions and utilities.""" +import uuid +from typing import Optional, Sequence + +import sqlite3 + +import gn_auth.auth.db.sqlite3 as db + +from .base import Resource +from .data import __attach_data__ + + +def resource_data( + cursor: db.DbCursor, + resource_id: uuid.UUID, + offset: int = 0, + limit: Optional[int] = None) -> Sequence[sqlite3.Row]: + """Fetch data linked to a Genotype resource""" + cursor.execute( + (("SELECT * FROM genotype_resources AS gr " + "INNER JOIN linked_genotype_data AS lgd " + "ON gr.data_link_id=lgd.data_link_id " + "WHERE gr.resource_id=?") + ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")), + (str(resource_id),)) + return cursor.fetchall() + +def link_data_to_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.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), + "data_link_id": str(data_link_id) + } + cursor.execute( + "INSERT INTO genotype_resources VALUES" + "(:group_id, :resource_id, :data_link_id)", + params) + return params + +def unlink_data_from_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.UUID) -> dict: + """Unlink data from Genotype resources""" + with db.cursor(conn) as cursor: + cursor.execute("DELETE FROM genotype_resources " + "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, + "data_link_id": data_link_id + } + +def attach_resources_data( + cursor, resources: Sequence[Resource]) -> Sequence[Resource]: + """Attach linked data to Genotype resources""" + placeholders = ", ".join(["?"] * len(resources)) + cursor.execute( + "SELECT * FROM genotype_resources AS gr " + "INNER JOIN linked_genotype_data AS lgd " + "ON gr.data_link_id=lgd.data_link_id " + f"WHERE gr.resource_id IN ({placeholders})", + tuple(str(resource.resource_id) for resource in resources)) + return __attach_data__(cursor.fetchall(), resources) diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py index 5718753..b5a6cd5 100644 --- a/gn_auth/auth/authorisation/resources/models.py +++ b/gn_auth/auth/authorisation/resources/models.py @@ -1,6 +1,5 @@ """Handle the management of resources.""" import json -import sqlite3 from uuid import UUID, uuid4 from functools import reduce, partial from typing import Dict, Sequence, Optional @@ -17,17 +16,34 @@ from ..errors import NotFoundError, AuthorisationError from ..groups.models import ( Group, GroupRole, user_group, group_by_id, is_group_leader) +from .checks import authorised_for +from .base import Resource, ResourceCategory +from .mrna_resource import ( + resource_data as mrna_resource_data, + attach_resources_data as mrna_attach_resources_data, + link_data_to_resource as mrna_link_data_to_resource, + unlink_data_from_resource as mrna_unlink_data_from_resource) +from .genotype_resource import ( + resource_data as genotype_resource_data, + attach_resources_data as genotype_attach_resources_data, + link_data_to_resource as genotype_link_data_to_resource, + unlink_data_from_resource as genotype_unlink_data_from_resource) +from .phenotype_resource import ( + resource_data as phenotype_resource_data, + attach_resources_data as phenotype_attach_resources_data, + link_data_to_resource as phenotype_link_data_to_resource, + unlink_data_from_resource as phenotype_unlink_data_from_resource) + class MissingGroupError(AuthorisationError): """Raised for any resource operation without a group.""" - -def __assign_resource_owner_role__(cursor, resource, user): +def __assign_resource_owner_role__(cursor, resource, user, group): """Assign `user` the 'Resource Owner' role for `resource`.""" cursor.execute( "SELECT gr.* FROM group_roles AS gr INNER JOIN roles AS r " "ON gr.role_id=r.role_id WHERE r.role_name='resource-owner' " "AND gr.group_id=?", - (str(resource.group.group_id),)) + (str(group.group_id),)) role = cursor.fetchone() if not role: cursor.execute("SELECT * FROM roles WHERE role_name='resource-owner'") @@ -36,7 +52,7 @@ def __assign_resource_owner_role__(cursor, resource, user): "INSERT INTO group_roles VALUES " "(:group_role_id, :group_id, :role_id)", {"group_role_id": str(uuid4()), - "group_id": str(resource.group.group_id), + "group_id": str(group.group_id), "role_id": role["role_id"]}) cursor.execute( @@ -44,7 +60,7 @@ def __assign_resource_owner_role__(cursor, resource, user): "VALUES (" ":group_id, :user_id, :role_id, :resource_id" ")", - {"group_id": str(resource.group.group_id), + {"group_id": str(resource.group_id), "user_id": str(user.user_id), "role_id": role["role_id"], "resource_id": str(resource.resource_id)}) @@ -63,15 +79,17 @@ def create_resource( if not group: raise MissingGroupError( "User with no group cannot create a resource.") - resource = Resource( - group, uuid4(), resource_name, resource_category, public) + resource = Resource(uuid4(), resource_name, resource_category, public) cursor.execute( - "INSERT INTO resources VALUES (?, ?, ?, ?, ?)", - (str(resource.group.group_id), str(resource.resource_id), + "INSERT INTO resources VALUES (?, ?, ?, ?)", + (str(resource.resource_id), resource_name, str(resource.resource_category.resource_category_id), 1 if resource.public else 0)) - __assign_resource_owner_role__(cursor, resource, user) + cursor.execute("INSERT INTO resource_ownership (group_id, resource_id) " + "VALUES (?, ?)", + (str(group.group_id), str(resource.resource_id))) + __assign_resource_owner_role__(cursor, resource, user, group) return resource @@ -201,50 +219,6 @@ def attach_resource_data(cursor: db.DbCursor, resource: Resource) -> Resource: resource.group, resource.resource_id, resource.resource_name, resource.resource_category, resource.public, data_rows) -def mrna_resource_data(cursor: db.DbCursor, - resource_id: UUID, - offset: int = 0, - limit: Optional[int] = None) -> Sequence[sqlite3.Row]: - """Fetch data linked to a mRNA resource""" - cursor.execute( - (("SELECT * FROM mrna_resources AS mr " - "INNER JOIN linked_mrna_data AS lmr " - "ON mr.data_link_id=lmr.data_link_id " - "WHERE mr.resource_id=?") + ( - f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")), - (str(resource_id),)) - return cursor.fetchall() - -def genotype_resource_data( - cursor: db.DbCursor, - resource_id: UUID, - offset: int = 0, - limit: Optional[int] = None) -> Sequence[sqlite3.Row]: - """Fetch data linked to a Genotype resource""" - cursor.execute( - (("SELECT * FROM genotype_resources AS gr " - "INNER JOIN linked_genotype_data AS lgd " - "ON gr.data_link_id=lgd.data_link_id " - "WHERE gr.resource_id=?") + ( - f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")), - (str(resource_id),)) - return cursor.fetchall() - -def phenotype_resource_data( - cursor: db.DbCursor, - resource_id: UUID, - offset: int = 0, - limit: Optional[int] = None) -> Sequence[sqlite3.Row]: - """Fetch data linked to a Phenotype resource""" - cursor.execute( - ("SELECT * FROM phenotype_resources AS pr " - "INNER JOIN linked_phenotype_data AS lpd " - "ON pr.data_link_id=lpd.data_link_id " - "WHERE pr.resource_id=?") + ( - f" LIMIT {limit} OFFSET {offset}" if bool(limit) else ""), - (str(resource_id),)) - return cursor.fetchall() - def resource_by_id( conn: db.DbConnection, user: User, resource_id: UUID) -> Resource: """Retrieve a resource by its ID.""" @@ -268,51 +242,6 @@ 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, 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), - "data_link_id": str(data_link_id) - } - cursor.execute( - "INSERT INTO mrna_resources VALUES" - "(:group_id, :resource_id, :data_link_id)", - params) - return params - -def __link_geno_data_to_resource__( - 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), - "data_link_id": str(data_link_id) - } - cursor.execute( - "INSERT INTO genotype_resources VALUES" - "(:group_id, :resource_id, :data_link_id)", - params) - return params - -def __link_pheno_data_to_resource__( - 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), - "data_link_id": str(data_link_id) - } - cursor.execute( - "INSERT INTO phenotype_resources VALUES" - "(: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, data_link_id: UUID) -> dict: @@ -327,50 +256,11 @@ def link_data_to_resource( resource = with_db_connection(partial( resource_by_id, user=user, resource_id=resource_id)) return { - "mrna": __link_mrna_data_to_resource__, - "genotype": __link_geno_data_to_resource__, - "phenotype": __link_pheno_data_to_resource__, + "mrna": mrna_link_data_to_resource, + "genotype": genotype_link_data_to_resource, + "phenotype": phenotype_link_data_to_resource, }[dataset_type.lower()](conn, resource, data_link_id) -def __unlink_mrna_data_to_resource__( - 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 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, - "data_link_id": data_link_id - } - -def __unlink_geno_data_to_resource__( - 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 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, - "data_link_id": data_link_id - } - -def __unlink_pheno_data_to_resource__( - 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 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, - "data_link_id": str(data_link_id) - } - def unlink_data_from_resource( conn: db.DbConnection, user: User, resource_id: UUID, data_link_id: UUID): """Unlink data from resource.""" @@ -385,9 +275,9 @@ def unlink_data_from_resource( resource_by_id, user=user, resource_id=resource_id)) dataset_type = resource.resource_category.resource_category_key return { - "mrna": __unlink_mrna_data_to_resource__, - "genotype": __unlink_geno_data_to_resource__, - "phenotype": __unlink_pheno_data_to_resource__, + "mrna": mrna_unlink_data_from_resource, + "genotype": genotype_unlink_data_from_resource, + "phenotype": phenotype_unlink_data_from_resource, }[dataset_type.lower()](conn, resource, data_link_id) def organise_resources_by_category(resources: Sequence[Resource]) -> dict[ @@ -401,66 +291,14 @@ def organise_resources_by_category(resources: Sequence[Resource]) -> dict[ } return reduce(__organise__, resources, {}) -def __attach_data__( - data_rows: Sequence[sqlite3.Row], - resources: Sequence[Resource]) -> Sequence[Resource]: - def __organise__(acc, row): - resource_id = UUID(row["resource_id"]) - return { - **acc, - resource_id: acc.get(resource_id, tuple()) + (dict(row),) - } - organised: dict[UUID, tuple[dict, ...]] = reduce(__organise__, data_rows, {}) - return tuple( - Resource( - resource.group, resource.resource_id, resource.resource_name, - resource.resource_category, resource.public, - organised.get(resource.resource_id, tuple())) - for resource in resources) - -def attach_mrna_resources_data( - cursor, resources: Sequence[Resource]) -> Sequence[Resource]: - """Attach linked data to mRNA Assay resources""" - placeholders = ", ".join(["?"] * len(resources)) - cursor.execute( - "SELECT * FROM mrna_resources AS mr INNER JOIN linked_mrna_data AS lmd" - " ON mr.data_link_id=lmd.data_link_id " - f"WHERE mr.resource_id IN ({placeholders})", - tuple(str(resource.resource_id) for resource in resources)) - return __attach_data__(cursor.fetchall(), resources) - -def attach_genotype_resources_data( - cursor, resources: Sequence[Resource]) -> Sequence[Resource]: - """Attach linked data to Genotype resources""" - placeholders = ", ".join(["?"] * len(resources)) - cursor.execute( - "SELECT * FROM genotype_resources AS gr " - "INNER JOIN linked_genotype_data AS lgd " - "ON gr.data_link_id=lgd.data_link_id " - f"WHERE gr.resource_id IN ({placeholders})", - tuple(str(resource.resource_id) for resource in resources)) - return __attach_data__(cursor.fetchall(), resources) - -def attach_phenotype_resources_data( - cursor, resources: Sequence[Resource]) -> Sequence[Resource]: - """Attach linked data to Phenotype resources""" - placeholders = ", ".join(["?"] * len(resources)) - cursor.execute( - "SELECT * FROM phenotype_resources AS pr " - "INNER JOIN linked_phenotype_data AS lpd " - "ON pr.data_link_id=lpd.data_link_id " - f"WHERE pr.resource_id IN ({placeholders})", - tuple(str(resource.resource_id) for resource in resources)) - return __attach_data__(cursor.fetchall(), resources) - def attach_resources_data( conn: db.DbConnection, resources: Sequence[Resource]) -> Sequence[ Resource]: """Attach linked data for each resource in `resources`""" resource_data_function = { - "mrna": attach_mrna_resources_data, - "genotype": attach_genotype_resources_data, - "phenotype": attach_phenotype_resources_data + "mrna": mrna_attach_resources_data, + "genotype": genotype_attach_resources_data, + "phenotype": phenotype_attach_resources_data } organised = organise_resources_by_category(resources) with db.cursor(conn) as cursor: diff --git a/gn_auth/auth/authorisation/resources/mrna_resource.py b/gn_auth/auth/authorisation/resources/mrna_resource.py new file mode 100644 index 0000000..77295f3 --- /dev/null +++ b/gn_auth/auth/authorisation/resources/mrna_resource.py @@ -0,0 +1,67 @@ +"""mRNA data resources functions and utilities""" +import uuid +from typing import Optional, Sequence + +import sqlite3 + +import gn_auth.auth.db.sqlite3 as db + +from .base import Resource +from .data import __attach_data__ + +def resource_data(cursor: db.DbCursor, + resource_id: uuid.UUID, + offset: int = 0, + limit: Optional[int] = None) -> Sequence[sqlite3.Row]: + """Fetch data linked to a mRNA resource""" + cursor.execute( + (("SELECT * FROM mrna_resources AS mr " + "INNER JOIN linked_mrna_data AS lmr " + "ON mr.data_link_id=lmr.data_link_id " + "WHERE mr.resource_id=?") + ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")), + (str(resource_id),)) + return cursor.fetchall() + +def link_data_to_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.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), + "data_link_id": str(data_link_id) + } + cursor.execute( + "INSERT INTO mrna_resources VALUES" + "(:group_id, :resource_id, :data_link_id)", + params) + return params + +def unlink_data_from_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.UUID) -> dict: + """Unlink data from mRNA Assay resources""" + with db.cursor(conn) as cursor: + cursor.execute("DELETE FROM mrna_resources " + "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, + "data_link_id": data_link_id + } + +def attach_resources_data( + cursor, resources: Sequence[Resource]) -> Sequence[Resource]: + """Attach linked data to mRNA Assay resources""" + placeholders = ", ".join(["?"] * len(resources)) + cursor.execute( + "SELECT * FROM mrna_resources AS mr INNER JOIN linked_mrna_data AS lmd" + " ON mr.data_link_id=lmd.data_link_id " + f"WHERE mr.resource_id IN ({placeholders})", + tuple(str(resource.resource_id) for resource in resources)) + return __attach_data__(cursor.fetchall(), resources) diff --git a/gn_auth/auth/authorisation/resources/phenotype_resource.py b/gn_auth/auth/authorisation/resources/phenotype_resource.py new file mode 100644 index 0000000..cf33579 --- /dev/null +++ b/gn_auth/auth/authorisation/resources/phenotype_resource.py @@ -0,0 +1,69 @@ +"""Phenotype data resources functions and utilities.""" +import uuid +from typing import Optional, Sequence + +import sqlite3 + +import gn_auth.auth.db.sqlite3 as db + +from .base import Resource +from .data import __attach_data__ + +def resource_data( + cursor: db.DbCursor, + resource_id: uuid.UUID, + offset: int = 0, + limit: Optional[int] = None) -> Sequence[sqlite3.Row]: + """Fetch data linked to a Phenotype resource""" + cursor.execute( + ("SELECT * FROM phenotype_resources AS pr " + "INNER JOIN linked_phenotype_data AS lpd " + "ON pr.data_link_id=lpd.data_link_id " + "WHERE pr.resource_id=?") + ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else ""), + (str(resource_id),)) + return cursor.fetchall() + +def link_data_to_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.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), + "data_link_id": str(data_link_id) + } + cursor.execute( + "INSERT INTO phenotype_resources VALUES" + "(:group_id, :resource_id, :data_link_id)", + params) + return params + +def unlink_data_from_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.UUID) -> dict: + """Unlink data from Phenotype resources""" + with db.cursor(conn) as cursor: + cursor.execute("DELETE FROM phenotype_resources " + "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, + "data_link_id": str(data_link_id) + } + +def attach_resources_data( + cursor, resources: Sequence[Resource]) -> Sequence[Resource]: + """Attach linked data to Phenotype resources""" + placeholders = ", ".join(["?"] * len(resources)) + cursor.execute( + "SELECT * FROM phenotype_resources AS pr " + "INNER JOIN linked_phenotype_data AS lpd " + "ON pr.data_link_id=lpd.data_link_id " + f"WHERE pr.resource_id IN ({placeholders})", + tuple(str(resource.resource_id) for resource in resources)) + return __attach_data__(cursor.fetchall(), resources) |