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-rw-r--r--scripts/migrate_existing_data.py50
1 files changed, 24 insertions, 26 deletions
diff --git a/scripts/migrate_existing_data.py b/scripts/migrate_existing_data.py
index c9ac343..ab3e739 100644
--- a/scripts/migrate_existing_data.py
+++ b/scripts/migrate_existing_data.py
@@ -19,7 +19,8 @@ from gn_auth.auth.authentication.users import User
from gn_auth.auth.authorisation.roles.models import (
revoke_user_role_by_name, assign_user_role_by_name)
-from gn_auth.auth.authorisation.resources.groups.models import Group, save_group
+from gn_auth.auth.authorisation.resources.groups.models import (
+ Group, save_group, add_resources_to_group)
from gn_auth.auth.authorisation.resources.models import (
Resource, ResourceCategory, __assign_resource_owner_role__)
@@ -128,8 +129,7 @@ def __resource_category_by_key__(
row["resource_category_key"],
row["resource_category_description"])
-def __create_resources__(cursor: authdb.DbCursor, group: Group) -> tuple[
- Resource, ...]:
+def __create_resources__(cursor: authdb.DbCursor) -> tuple[Resource, ...]:
"""Create default resources."""
resources = tuple(Resource(
uuid4(), name, __resource_category_by_key__(cursor, catkey),
@@ -139,20 +139,13 @@ def __create_resources__(cursor: authdb.DbCursor, group: Group) -> tuple[
("pheno-xboecp", "phenotype"),
("geno-welphd", "genotype")))
cursor.executemany(
- "INSERT INTO resources VALUES (:gid, :rid, :rname, :rcid, :pub)",
+ "INSERT INTO resources VALUES (:rid, :rname, :rcid, :pub)",
tuple({
- "gid": str(group.group_id),
"rid": str(res.resource_id),
"rname": res.resource_name,
"rcid": str(res.resource_category.resource_category_id),
"pub": 1
} for res in resources))
- cursor.executemany("INSERT INTO resource_ownership(group_id, resource_id) "
- "VALUES (:group_id, :resource_id)",
- tuple({
- "group_id": str(group.group_id),
- "resource_id": str(resource.resource_id)
- } for resource in resources))
return resources
def default_resources(conn: authdb.DbConnection, group: Group) -> tuple[
@@ -161,14 +154,16 @@ def default_resources(conn: authdb.DbConnection, group: Group) -> tuple[
with authdb.cursor(conn) as cursor:
cursor.execute(
"SELECT r.resource_id, r.resource_name, r.public, rc.* "
- "FROM resources AS r INNER JOIN resource_categories AS rc "
+ "FROM resource_ownership AS ro INNER JOIN resources AS r "
+ "ON ro.resource_id=r.resource_id "
+ "INNER JOIN resource_categories AS rc "
"ON r.resource_category_id=rc.resource_category_id "
- "WHERE r.group_id=? AND r.resource_name IN "
+ "WHERE ro.group_id=? AND r.resource_name IN "
"('mRNA-euhrin', 'pheno-xboecp', 'geno-welphd')",
(str(group.group_id),))
rows = cursor.fetchall()
if len(rows) == 0:
- return __create_resources__(cursor, group)
+ return __create_resources__(cursor)
return tuple(Resource(
UUID(row["resource_id"]),
@@ -216,12 +211,12 @@ def __unassigned_mrna__(bioconn, assigned):
cursor.execute(query, tuple(item for row in assigned for item in row))
return (row for row in cursor.fetchall())
-def __assign_mrna__(authconn, bioconn, resource):
+def __assign_mrna__(authconn, bioconn, resource, group):
"Assign any unassigned mRNA data to resource."
while True:
unassigned = tuple({
"data_link_id": str(uuid4()),
- "group_id": str(resource.group.group_id),
+ "group_id": str(group.group_id),
"resource_id": str(resource.resource_id),
**row
} for row in __unassigned_mrna__(
@@ -239,7 +234,7 @@ def __assign_mrna__(authconn, bioconn, resource):
unassigned)
cursor.executemany(
"INSERT INTO mrna_resources VALUES "
- "(:group_id, :resource_id, :data_link_id)",
+ "(:resource_id, :data_link_id)",
unassigned)
print(f"-> mRNA: Linked {len(unassigned)}")
delay()
@@ -274,12 +269,12 @@ def __unassigned_geno__(bioconn, assigned):
cursor.execute(query, tuple(item for row in assigned for item in row))
return (row for row in cursor.fetchall())
-def __assign_geno__(authconn, bioconn, resource):
+def __assign_geno__(authconn, bioconn, resource, group):
"Assign any unassigned Genotype data to resource."
while True:
unassigned = tuple({
"data_link_id": str(uuid4()),
- "group_id": str(resource.group.group_id),
+ "group_id": str(group.group_id),
"resource_id": str(resource.resource_id),
**row
} for row in __unassigned_geno__(
@@ -297,7 +292,7 @@ def __assign_geno__(authconn, bioconn, resource):
unassigned)
cursor.executemany(
"INSERT INTO genotype_resources VALUES "
- "(:group_id, :resource_id, :data_link_id)",
+ "(:resource_id, :data_link_id)",
unassigned)
print(f"-> Genotype: Linked {len(unassigned)}")
delay()
@@ -338,12 +333,12 @@ def __unassigned_pheno__(bioconn, assigned):
cursor.execute(query, tuple(item for row in assigned for item in row))
return (row for row in cursor.fetchall())
-def __assign_pheno__(authconn, bioconn, resource):
+def __assign_pheno__(authconn, bioconn, resource, group):
"""Assign any unassigned Phenotype data to resource."""
while True:
unassigned = tuple({
"data_link_id": str(uuid4()),
- "group_id": str(resource.group.group_id),
+ "group_id": str(group.group_id),
"resource_id": str(resource.resource_id),
**row
} for row in __unassigned_pheno__(
@@ -361,12 +356,13 @@ def __assign_pheno__(authconn, bioconn, resource):
unassigned)
cursor.executemany(
"INSERT INTO phenotype_resources VALUES "
- "(:group_id, :resource_id, :data_link_id)",
+ "(:resource_id, :data_link_id)",
unassigned)
print(f"-> Phenotype: Linked {len(unassigned)}")
delay()
-def assign_data_to_resource(authconn, bioconn, resource: Resource):
+def assign_data_to_resource(
+ authconn, bioconn, resource: Resource, group: Group):
"""Assign existing data, not linked to any group to the resource."""
assigner_fns = {
"mrna": __assign_mrna__,
@@ -374,7 +370,7 @@ def assign_data_to_resource(authconn, bioconn, resource: Resource):
"phenotype": __assign_pheno__
}
return assigner_fns[resource.resource_category.resource_category_key](
- authconn, bioconn, resource)
+ authconn, bioconn, resource, group)
def entry(authdbpath, mysqldburi):
"""Entry-point for data migration."""
@@ -390,8 +386,10 @@ def entry(authdbpath, mysqldburi):
the_admin_group = admin_group(authconn, admin)
resources = default_resources(
authconn, the_admin_group)
+ add_resources_to_group(authconn, resources, the_admin_group)
for resource in resources:
- assign_data_to_resource(authconn, bioconn, resource)
+ assign_data_to_resource(
+ authconn, bioconn, resource, the_admin_group)
with authdb.cursor(authconn) as cursor:
__assign_resource_owner_role__(
cursor, resource, admin, the_admin_group)