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authorFrederick Muriuki Muriithi2023-09-13 08:04:55 +0300
committerFrederick Muriuki Muriithi2023-09-26 03:44:29 +0300
commit4b36031859d1f2e0d4a255741b543afecfe3cecd (patch)
treefbe29b6dfd2bdf63f0dc6bac9542ca630b4c7312 /gn_auth/auth/authorisation
parent9a3b628e2744b658ade8902c1cd33deccbd48b63 (diff)
downloadgn-auth-4b36031859d1f2e0d4a255741b543afecfe3cecd.tar.gz
Extract resource-type-specific code into separate modules
For easier maintenance, extract the code that relates to specific resource types/categories into separate modules, each dealing with a single resource type/category.
Diffstat (limited to 'gn_auth/auth/authorisation')
-rw-r--r--gn_auth/auth/authorisation/resources/__init__.py2
-rw-r--r--gn_auth/auth/authorisation/resources/data.py29
-rw-r--r--gn_auth/auth/authorisation/resources/genotype_resource.py70
-rw-r--r--gn_auth/auth/authorisation/resources/models.py238
-rw-r--r--gn_auth/auth/authorisation/resources/mrna_resource.py67
-rw-r--r--gn_auth/auth/authorisation/resources/phenotype_resource.py69
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)