From e19b01571ce61e01f482a1dadeeb2fd835fda939 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 14 Sep 2023 12:06:23 +0300
Subject: Move `groups` package under `resources` package

With user groups being resources that users can act on (with the
recent changes), this commit moves the `groups` module to under the
`resources` module.

It also renames the `*_resources.py` modules by dropping the
`_resources` part since the code is under the `resources` module
anyway.
---
 gn_auth/auth/authorisation/groups/data.py | 107 ------------------------------
 1 file changed, 107 deletions(-)
 delete mode 100644 gn_auth/auth/authorisation/groups/data.py

(limited to 'gn_auth/auth/authorisation/groups/data.py')

diff --git a/gn_auth/auth/authorisation/groups/data.py b/gn_auth/auth/authorisation/groups/data.py
deleted file mode 100644
index 1650405..0000000
--- a/gn_auth/auth/authorisation/groups/data.py
+++ /dev/null
@@ -1,107 +0,0 @@
-"""Handles the resource objects' data."""
-from MySQLdb.cursors import DictCursor
-
-from ..groups import Group
-from ..checks import authorised_p
-from ..errors import NotFoundError
-
-from ...db import mariadb as gn3db
-from ...db import sqlite3 as authdb
-
-def __fetch_mrna_data_by_ids__(
-        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
-            dict, ...]:
-    """Fetch mRNA Assay data by ID."""
-    with conn.cursor(DictCursor) as cursor:
-        paramstr = ", ".join(["%s"] * len(dataset_ids))
-        cursor.execute(
-            "SELECT psf.Id, psf.Name AS dataset_name, "
-            "psf.FullName AS dataset_fullname, "
-            "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf "
-            "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName "
-            f"WHERE psf.Id IN ({paramstr})",
-            dataset_ids)
-        res = cursor.fetchall()
-        if res:
-            return tuple(dict(row) for row in res)
-        raise NotFoundError("Could not find mRNA Assay data with the given ID.")
-
-def __fetch_geno_data_by_ids__(
-        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
-            dict, ...]:
-    """Fetch genotype data by ID."""
-    with conn.cursor(DictCursor) as cursor:
-        paramstr = ", ".join(["%s"] * len(dataset_ids))
-        cursor.execute(
-            "SELECT gf.Id, gf.Name AS dataset_name, "
-            "gf.FullName AS dataset_fullname, "
-            "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf "
-            "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName "
-            f"WHERE gf.Id IN ({paramstr})",
-            dataset_ids)
-        res = cursor.fetchall()
-        if res:
-            return tuple(dict(row) for row in res)
-        raise NotFoundError("Could not find Genotype data with the given ID.")
-
-def __fetch_pheno_data_by_ids__(
-        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
-            dict, ...]:
-    """Fetch phenotype data by ID."""
-    with conn.cursor(DictCursor) as cursor:
-        paramstr = ", ".join(["%s"] * len(dataset_ids))
-        cursor.execute(
-            "SELECT pxf.Id, iset.InbredSetName, pf.Id AS dataset_id, "
-            "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, "
-            "ifiles.GN_AccesionId AS accession_id "
-            "FROM PublishXRef AS pxf "
-            "INNER JOIN InbredSet AS iset ON pxf.InbredSetId=iset.InbredSetId "
-            "INNER JOIN PublishFreeze AS pf ON iset.InbredSetId=pf.InbredSetId "
-            "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName "
-            f"WHERE pxf.Id IN ({paramstr})",
-            dataset_ids)
-        res = cursor.fetchall()
-        if res:
-            return tuple(dict(row) for row in res)
-        raise NotFoundError(
-            "Could not find Phenotype/Publish data with the given IDs.")
-
-def __fetch_data_by_id(
-        conn: gn3db.DbConnection, dataset_type: str,
-        dataset_ids: tuple[str, ...]) -> tuple[dict, ...]:
-    """Fetch data from MySQL by IDs."""
-    fetch_fns = {
-        "mrna": __fetch_mrna_data_by_ids__,
-        "genotype": __fetch_geno_data_by_ids__,
-        "phenotype": __fetch_pheno_data_by_ids__
-    }
-    return fetch_fns[dataset_type](conn, dataset_ids)
-
-@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.DbConnection,
-        dataset_type: str, dataset_ids: tuple[str, ...], group: Group) -> tuple[
-            dict, ...]:
-    """Link the given data to the specified group."""
-    the_data = __fetch_data_by_id(gn3conn, dataset_type, dataset_ids)
-    with authdb.cursor(authconn) as cursor:
-        params = tuple({
-            "group_id": str(group.group_id), "dataset_type": {
-                "mrna": "mRNA", "genotype": "Genotype",
-                "phenotype": "Phenotype"
-            }[dataset_type],
-            "dataset_or_trait_id": item["Id"],
-            "dataset_name": item["dataset_name"],
-            "dataset_fullname": item["dataset_fullname"],
-            "accession_id": item["accession_id"]
-        } for item in the_data)
-        cursor.executemany(
-            "INSERT INTO linked_group_data VALUES"
-            "(:group_id, :dataset_type, :dataset_or_trait_id, :dataset_name, "
-            ":dataset_fullname, :accession_id)",
-            params)
-        return params
-- 
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