diff options
Diffstat (limited to 'gn_auth/auth/authorisation/resources/mrna_resource.py')
-rw-r--r-- | gn_auth/auth/authorisation/resources/mrna_resource.py | 67 |
1 files changed, 67 insertions, 0 deletions
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) |