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authorFrederick Muriuki Muriithi2023-04-10 12:57:08 +0300
committerFrederick Muriuki Muriithi2023-04-10 12:57:08 +0300
commit54e8769a8cfbf12967c26598b97ce0e88d891e86 (patch)
tree85b16e816ebb15e06d44b6caf9750a8df4daa42b
parent6006526069803a8a906b4fd19f372ca721f7b29c (diff)
downloadgenenetwork3-54e8769a8cfbf12967c26598b97ce0e88d891e86.tar.gz
Add search and link for mRNA Assay datasets.
-rw-r--r--gn3/auth/authorisation/data/mrna.py100
-rw-r--r--gn3/auth/authorisation/data/views.py36
2 files changed, 135 insertions, 1 deletions
diff --git a/gn3/auth/authorisation/data/mrna.py b/gn3/auth/authorisation/data/mrna.py
new file mode 100644
index 0000000..bdfc5c1
--- /dev/null
+++ b/gn3/auth/authorisation/data/mrna.py
@@ -0,0 +1,100 @@
+"""Handle linking of mRNA Assay data to the Auth(entic|oris)ation system."""
+import uuid
+from typing import Iterable
+from MySQLdb.cursors import DictCursor
+
+import gn3.auth.db as authdb
+import gn3.db_utils as gn3db
+from gn3.auth.dictify import dictify
+from gn3.auth.authorisation.checks import authorised_p
+from gn3.auth.authorisation.groups.models import Group
+
+def linked_mrna_data(conn: authdb.DbConnection) -> Iterable[dict]:
+ """Retrieve mRNA Assay data that is linked to user groups."""
+ with authdb.cursor(conn) as cursor:
+ cursor.execute("SELECT * FROM linked_mrna_data")
+ return (dict(row) for row in cursor.fetchall())
+
+@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 ungrouped_mrna_data(# pylint: disable=[too-many-arguments]
+ authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
+ search_query: str, selected: tuple[dict, ...] = tuple(),
+ limit: int = 10000, offset: int = 0) -> tuple[
+ dict, ...]:
+ """Retrieve mrna data that is not linked to any user group."""
+ params = tuple(
+ (row["SpeciesId"], row["InbredSetId"], row["ProbeFreezeId"],
+ row["ProbeSetFreezeId"])
+ for row in linked_mrna_data(authconn)) + tuple(
+ (row["SpeciesId"], row["InbredSetId"], row["ProbeFreezeId"],
+ row["ProbeSetFreezeId"])
+ for row in selected)
+ query = (
+ "SELECT s.SpeciesId, iset.InbredSetId, iset.InbredSetName, "
+ "pf.ProbeFreezeId, pf.Name AS StudyName, psf.Id AS ProbeSetFreezeId, "
+ "psf.Name AS dataset_name, psf.FullName AS dataset_fullname, "
+ "psf.ShortName AS dataset_shortname "
+ "FROM Species AS s INNER JOIN InbredSet AS iset "
+ "ON s.SpeciesId=iset.SpeciesId INNER JOIN ProbeFreeze AS pf "
+ "ON iset.InbredSetId=pf.InbredSetId INNER JOIN ProbeSetFreeze AS psf "
+ "ON pf.ProbeFreezeId=psf.ProbeFreezeId ") + (
+ "WHERE " if (len(params) > 0 or bool(search_query)) else "")
+
+ if len(params) > 0:
+ paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(params))
+ query = query + (
+ "(s.SpeciesId, iset.InbredSetId, pf.ProbeFreezeId, psf.Id) "
+ f"NOT IN ({paramstr}) "
+ ) + ("AND " if bool(search_query) else "")
+
+ if bool(search_query):
+ query = query + (
+ "CONCAT(pf.Name, psf.Name, ' ', psf.FullName, ' ', psf.ShortName) "
+ "LIKE %s ")
+ params = params + ((f"%{search_query}%",),)# type: ignore[operator]
+
+ query = query + f"LIMIT {int(limit)} OFFSET {int(offset)}"
+ with gn3conn.cursor(DictCursor) as cursor:
+ cursor.execute(
+ query, tuple(item for sublist in params for item in sublist))
+ return tuple(row for row in cursor.fetchall())
+
+@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_mrna_data(
+ conn: authdb.DbConnection, group: Group, datasets: dict) -> dict:
+ """Link genotye `datasets` to `group`."""
+ with authdb.cursor(conn) as cursor:
+ cursor.executemany(
+ "INSERT INTO linked_mrna_data VALUES "
+ "(:data_link_id, :group_id, :SpeciesId, :InbredSetId, "
+ ":ProbeFreezeId, :ProbeSetFreezeId, :dataset_name, "
+ ":dataset_fullname, :dataset_shortname) "
+ "ON CONFLICT "
+ "(SpeciesId, InbredSetId, ProbeFreezeId, ProbeSetFreezeId) "
+ "DO NOTHING",
+ tuple({
+ "data_link_id": str(uuid.uuid4()),
+ "group_id": str(group.group_id),
+ **{
+ key: value for key,value in dataset.items() if key in (
+ "SpeciesId", "InbredSetId", "ProbeFreezeId",
+ "ProbeSetFreezeId", "dataset_fullname", "dataset_name",
+ "dataset_shortname")
+ }
+ } for dataset in datasets))
+ return {
+ "description": (
+ f"Successfully linked {len(datasets)} to group "
+ f"'{group.group_name}'."),
+ "group": dictify(group),
+ "datasets": datasets
+ }
diff --git a/gn3/auth/authorisation/data/views.py b/gn3/auth/authorisation/data/views.py
index a30096d..1a4c031 100644
--- a/gn3/auth/authorisation/data/views.py
+++ b/gn3/auth/authorisation/data/views.py
@@ -40,6 +40,7 @@ from gn3.auth.authorisation.errors import ForbiddenAccess
from gn3.auth.authentication.oauth2.resource_server import require_oauth
from gn3.auth.authentication.users import User, user_by_email, set_user_password
+from gn3.auth.authorisation.data.mrna import link_mrna_data, ungrouped_mrna_data
from gn3.auth.authorisation.data.genotypes import (
link_genotype_data, ungrouped_genotype_data)
@@ -311,7 +312,15 @@ def migrate_users_data() -> Response:
status=500, mimetype="application/json")
def __search_mrna__():
- pass
+ query = __request_key__("query", "")
+ limit = int(__request_key__("limit", 10000))
+ offset = int(__request_key__("offset", 0))
+ with gn3db.database_connection() as gn3conn:
+ __ungrouped__ = partial(
+ ungrouped_mrna_data, gn3conn=gn3conn, search_query=query,
+ selected=__request_key_list__("selected"),
+ limit=limit, offset=offset)
+ return jsonify(with_db_connection(__ungrouped__))
def __request_key__(key: str, default: Any = ""):
if bool(request.json):
@@ -377,3 +386,28 @@ def link_genotypes() -> Response:
return jsonify(with_db_connection(
partial(__link__, **__values__(request.json))))
+
+@data.route("/link/mrna", methods=["POST"])
+def link_mrna() -> Response:
+ """Link mrna data to group."""
+ def __values__(form) -> dict[str, Any]:
+ if not bool(form.get("species_name", "").strip()):
+ raise InvalidData("Expected 'species_name' not provided.")
+ if not bool(form.get("group_id")):
+ raise InvalidData("Expected 'group_id' not provided.",)
+ try:
+ _group_id = uuid.UUID(form.get("group_id"))
+ except TypeError as terr:
+ raise InvalidData("Expected a UUID for 'group_id' value.") from terr
+ if not bool(form.get("selected")):
+ raise InvalidData("Expected at least one dataset to be provided.")
+ return {
+ "group_id": uuid.UUID(form.get("group_id")),
+ "datasets": form.get("selected")
+ }
+
+ def __link__(conn: db.DbConnection, group_id: uuid.UUID, datasets: dict):
+ return link_mrna_data(conn, group_by_id(conn, group_id), datasets)
+
+ return jsonify(with_db_connection(
+ partial(__link__, **__values__(request.json))))