aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--gn3/auth/authorisation/resources/models.py62
-rw-r--r--gn3/auth/authorisation/resources/views.py35
2 files changed, 80 insertions, 17 deletions
diff --git a/gn3/auth/authorisation/resources/models.py b/gn3/auth/authorisation/resources/models.py
index 5ff5983..b634a35 100644
--- a/gn3/auth/authorisation/resources/models.py
+++ b/gn3/auth/authorisation/resources/models.py
@@ -3,7 +3,7 @@ import json
import sqlite3
from uuid import UUID, uuid4
from functools import reduce, partial
-from typing import Any, Dict, Sequence, NamedTuple
+from typing import Any, Dict, Sequence, Optional, NamedTuple
from gn3.auth import db
from gn3.auth.dictify import dictify
@@ -201,6 +201,22 @@ def user_resources(conn: db.DbConnection, user: User) -> Sequence[Resource]:
return user_group(conn, user).map(__all_resources__).maybe(# type: ignore[arg-type,misc]
public_resources(conn), lambda res: res)# type: ignore[arg-type,return-value]
+def resource_data(conn, resource, offset: int = 0, limit: Optional[int] = None) -> tuple[dict, ...]:
+ """
+ Retrieve the data for `resource`, optionally limiting the number of items.
+ """
+ resource_data_function = {
+ "mrna": mrna_resource_data,
+ "genotype": genotype_resource_data,
+ "phenotype": phenotype_resource_data
+ }
+ with db.cursor(conn) as cursor:
+ return tuple(
+ dict(data_row) for data_row in
+ resource_data_function[
+ resource.resource_category.resource_category_key](
+ cursor, resource.resource_id, offset, limit))
+
def attach_resource_data(cursor: db.DbCursor, resource: Resource) -> Resource:
"""Attach the linked data to the resource"""
resource_data_function = {
@@ -217,35 +233,49 @@ 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) -> Sequence[sqlite3.Row]:
+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=?",
+ (("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}" if bool(limit) else "") (
+ 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) -> Sequence[sqlite3.Row]:
+ 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=?",
+ (("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) -> Sequence[sqlite3.Row]:
+ cursor: db.DbCursor,
+ resource_id: UUID,
+ offset: int = 0,
+ limit: Optional[int] = None) -> Sequence[sqlite3.Row]:
"""Fetch data linked to a Phenotype resource"""
+ from gn3.debug import __pk__
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=?",
+ ("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()
diff --git a/gn3/auth/authorisation/resources/views.py b/gn3/auth/authorisation/resources/views.py
index 396a57e..2e6c244 100644
--- a/gn3/auth/authorisation/resources/views.py
+++ b/gn3/auth/authorisation/resources/views.py
@@ -10,7 +10,7 @@ from gn3.auth.db_utils import with_db_connection
from .checks import authorised_for
from .models import (
- Resource, save_resource, resource_by_id, resource_categories,
+ Resource, save_resource, resource_data, resource_by_id, resource_categories,
assign_resource_user, link_data_to_resource, unassign_resource_user,
resource_category_by_id, unlink_data_from_resource,
create_resource as _create_resource)
@@ -72,6 +72,39 @@ def view_resource(resource_id: uuid.UUID) -> Response:
return jsonify(dictify(resource_by_id(
conn, the_token.user, resource_id)))
+def __safe_get_requests_page__(key: str = "page") -> int:
+ """Get the results page if it exists or default to the first page."""
+ try:
+ return abs(int(request.args.get(key, "1"), base=10))
+ except ValueError as _valerr:
+ return 1
+
+def __safe_get_requests_count__(key: str = "count_per_page") -> int:
+ """Get the results page if it exists or default to the first page."""
+ try:
+ count = request.args.get(key)
+ if count is None:
+ return None
+ return abs(int(count, base=10))
+ except ValueError as _valerr:
+ return None
+
+@resources.route("/view/<uuid:resource_id>/data")
+@require_oauth("profile group resource")
+def view_resource_data(resource_id: uuid.UUID) -> Response:
+ """Retrieve a particular resource's data."""
+ with require_oauth.acquire("profile group resource") as the_token:
+ db_uri = app.config["AUTH_DB"]
+ count_per_page = __safe_get_requests_count__("count_per_page")
+ page = (__safe_get_requests_page__("page") - 1)
+ with db.connection(db_uri) as conn:
+ resource = resource_by_id(conn, the_token.user, resource_id)
+ return jsonify(resource_data(
+ conn,
+ resource,
+ ((page * count_per_page) if bool(count_per_page) else page),
+ count_per_page))
+
@resources.route("/data/link", methods=["POST"])
@require_oauth("profile group resource")
def link_data():