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-rw-r--r--gn3/auth/authorisation/resources/data.py96
-rw-r--r--gn3/auth/authorisation/resources/views.py34
-rw-r--r--gn3/db_utils.py2
3 files changed, 119 insertions, 13 deletions
diff --git a/gn3/auth/authorisation/resources/data.py b/gn3/auth/authorisation/resources/data.py
index 7598f34..93b8e1d 100644
--- a/gn3/auth/authorisation/resources/data.py
+++ b/gn3/auth/authorisation/resources/data.py
@@ -5,7 +5,9 @@ from MySQLdb.cursors import DictCursor
from gn3 import db_utils as gn3db
from gn3.auth import db as authdb
-from gn3.auth.authorisation.errors import InvalidData
+from gn3.auth.authorisation.groups import Group
+from gn3.auth.authorisation.checks import authorised_p
+from gn3.auth.authorisation.errors import InvalidData, NotFoundError
def __fetch_grouped_data__(
conn: authdb.DbConnection, dataset_type: str) -> Sequence[dict[str, Any]]:
@@ -31,7 +33,7 @@ def __fetch_ungrouped_mrna_data__(
params = tuple(item["dataset_or_trait_id"] for item in grouped_data)
query = f"{query} LIMIT 100 OFFSET %s"
- with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg]
+ with conn.cursor(DictCursor) as cursor:
cursor.execute(query, (params + (offset,)))
return tuple(dict(row) for row in cursor.fetchall())
@@ -49,7 +51,7 @@ def __fetch_ungrouped_geno_data__(
params = tuple(item["dataset_or_trait_id"] for item in grouped_data)
query = f"{query} LIMIT 100 OFFSET %s"
- with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg]
+ with conn.cursor(DictCursor) as cursor:
cursor.execute(query, (params + (offset,)))
return tuple(dict(row) for row in cursor.fetchall())
@@ -67,7 +69,7 @@ def __fetch_ungrouped_pheno_data__(
params = tuple(item["dataset_or_trait_id"] for item in grouped_data)
query = f"{query} LIMIT 100 OFFSET %s"
- with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg]
+ with conn.cursor(DictCursor) as cursor:
cursor.execute(query, (params + (offset,)))
return tuple(dict(row) for row in cursor.fetchall())
@@ -82,6 +84,11 @@ def __fetch_ungrouped_data__(
}
return fetch_fns[dataset_type](conn, ungrouped)
+@authorised_p(("system:data:link-to-group",),
+ error_description=(
+ "You do not have sufficient privileges to link data to (a) "
+ "group(s)."),
+ oauth2_scope="profile group resource")
def retrieve_ungrouped_data(
authconn: authdb.DbConnection,
gn3conn: gn3db.Connection,
@@ -92,5 +99,84 @@ def retrieve_ungrouped_data(
"Requested dataset type is invalid. Expected one of "
"'mrna', 'genotype' or 'phenotype'.")
grouped_data = __fetch_grouped_data__(authconn, dataset_type)
- print(f"GROUPED DATA: {grouped_data}")
return __fetch_ungrouped_data__(gn3conn, dataset_type, grouped_data)
+
+def __fetch_mrna_data_by_id__(conn: gn3db.Connection, dataset_id: str) -> dict:
+ """Fetch mRNA Assay data by ID."""
+ with conn.cursor(DictCursor) as cursor:
+ cursor.execute(
+ "SELECT psf.Id, psf.Name, psf.FullName, "
+ "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf "
+ "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName "
+ "WHERE psf.Id=%s",
+ (dataset_id,))
+ res = cursor.fetchone()
+ if res:
+ return dict(res)
+ raise NotFoundError("Could not find mRNA Assay data with the given ID.")
+
+def __fetch_geno_data_by_id__(conn: gn3db.Connection, dataset_id: str) -> dict:
+ """Fetch genotype data by ID."""
+ with conn.cursor(DictCursor) as cursor:
+ cursor.execute(
+ "SELECT gf.Id, gf.Name, gf.FullName, "
+ "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf "
+ "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName "
+ "WHERE gf.Id=%s",
+ (dataset_id,))
+ res = cursor.fetchone()
+ if res:
+ return dict(res)
+ raise NotFoundError("Could not find Genotype data with the given ID.")
+
+def __fetch_pheno_data_by_id__(conn: gn3db.Connection, dataset_id: str) -> dict:
+ """Fetch phenotype data by ID."""
+ with conn.cursor(DictCursor) as cursor:
+ cursor.execute(
+ "SELECT pf.Id, pf.Name, pf.FullName, "
+ "ifiles.GN_AccesionId AS accession_id FROM PublishFreeze AS pf "
+ "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName "
+ "WHERE pf.Id=%s",
+ (dataset_id,))
+ res = cursor.fetchone()
+ if res:
+ return dict(res)
+ raise NotFoundError(
+ "Could not find Phenotype/Publish data with the given ID.")
+
+def __fetch_data_by_id(
+ conn: gn3db.Connection, dataset_type: str, dataset_id: str) -> dict:
+ """Fetch data from MySQL by ID."""
+ fetch_fns = {
+ "mrna": __fetch_mrna_data_by_id__,
+ "genotype": __fetch_geno_data_by_id__,
+ "phenotype": __fetch_pheno_data_by_id__
+ }
+ return fetch_fns[dataset_type](conn, dataset_id)
+
+@authorised_p(("system:data:link-to-group",),
+ error_description=(
+ "You do not have sufficient privileges to link data to (a) "
+ "group(s)."),
+ oauth2_scope="profile group resource")
+def link_data_to_group(
+ authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
+ dataset_type: str, dataset_id: str, group: Group) -> dict:
+ """Link the given data to the specified group."""
+ the_data = __fetch_data_by_id(gn3conn, dataset_type, dataset_id)
+ with authdb.cursor(authconn) as cursor:
+ params = {
+ "group_id": str(group.group_id), "dataset_type": {
+ "mrna": "mRNA", "genotype": "Genotype",
+ "phenotype": "Phenotype"
+ }[dataset_type],
+ "dataset_or_trait_id": dataset_id, "dataset_name": the_data["Name"],
+ "dataset_fullname": the_data["FullName"],
+ "accession_id": the_data["accession_id"]
+ }
+ cursor.execute(
+ "INSERT INTO linked_group_data VALUES"
+ "(:group_id, :dataset_type, :dataset_or_trait_id, :dataset_name, "
+ ":dataset_fullname, :accession_id)",
+ params)
+ return params
diff --git a/gn3/auth/authorisation/resources/views.py b/gn3/auth/authorisation/resources/views.py
index 44e2c4e..e373182 100644
--- a/gn3/auth/authorisation/resources/views.py
+++ b/gn3/auth/authorisation/resources/views.py
@@ -7,13 +7,13 @@ from flask import request, jsonify, Response, Blueprint, current_app as app
from gn3 import db_utils as gn3dbutils
from gn3.auth.db_utils import with_db_connection
-from .data import retrieve_ungrouped_data
+from .data import link_data_to_group, retrieve_ungrouped_data
from .models import (
resource_by_id, resource_categories, resource_category_by_id,
create_resource as _create_resource)
-from ..errors import AuthorisationError
-from ..groups.models import user_group, DUMMY_GROUP
+from ..errors import InvalidData, AuthorisationError
+from ..groups.models import user_group, DUMMY_GROUP, group_by_id
from ... import db
from ...dictify import dictify
@@ -115,7 +115,27 @@ def ungrouped_data(dataset_type: str) -> Response:
if dataset_type not in ("all", "mrna", "genotype", "phenotype"):
raise AuthorisationError(f"Invalid dataset type {dataset_type}")
- with gn3dbutils.database_connection() as gn3conn:
- return jsonify(with_db_connection(partial(
- retrieve_ungrouped_data, gn3conn=gn3conn,
- dataset_type=dataset_type)))
+ with require_oauth.acquire("profile group resource") as _the_token:
+ with gn3dbutils.database_connection() as gn3conn:
+ return jsonify(with_db_connection(partial(
+ retrieve_ungrouped_data, gn3conn=gn3conn,
+ dataset_type=dataset_type)))
+
+@resources.route("/data/link", methods=["POST"])
+@require_oauth("profile group resource")
+def link_data() -> Response:
+ """Link selected data to specified group."""
+ with require_oauth.acquire("profile group resource") as _the_token:
+ form = request.form
+ group_id = uuid.UUID(form["group_id"])
+ dataset_id = form["dataset_id"]
+ dataset_type = form.get("dataset_type")
+ if dataset_type not in ("mrna", "genotype", "phenotype"):
+ raise InvalidData("Unexpected dataset type requested!")
+ def __link__(conn: db.DbConnection):
+ group = group_by_id(conn, group_id)
+ with gn3dbutils.database_connection() as gn3conn:
+ return link_data_to_group(
+ conn, gn3conn, dataset_type, dataset_id, group)
+
+ return jsonify(with_db_connection(__link__))
diff --git a/gn3/db_utils.py b/gn3/db_utils.py
index 23a570b..ad934d7 100644
--- a/gn3/db_utils.py
+++ b/gn3/db_utils.py
@@ -28,7 +28,7 @@ def database_connector() -> mdb.Connection:
# pylint: disable=missing-class-docstring, missing-function-docstring, too-few-public-methods
class Connection(Protocol):
"""Type Annotation for MySQLdb's connection object"""
- def cursor(self) -> Any:
+ def cursor(self, *args) -> Any:
"""A cursor in which queries may be performed"""
...
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 08:55:10 +0000