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Added permissions to Omics
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@dlpzx
dlpzx committed Jan 25, 2024
1 parent 1d8c672 commit 6149e35
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Showing 2 changed files with 29 additions and 36 deletions.
4 changes: 1 addition & 3 deletions backend/dataall/modules/omics/services/omics_permissions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@
Contains permissions for Omics RUNs
"""

# TODO: THIS HAS NOT BEEN IMPLEMENTED AT ALL AND NEEDS TO BE IMPLEMENTED
from dataall.core.permissions.permissions import (
ENVIRONMENT_ALL,
ENVIRONMENT_INVITED,
Expand Down Expand Up @@ -44,7 +43,6 @@
RESOURCES_ALL.append(LIST_ENVIRONMENT_OMICS_RUNS)

RESOURCES_ALL_WITH_DESC[CREATE_OMICS_RUN] = "Create Omics workflow runs on this environment"
RESOURCES_ALL_WITH_DESC[LIST_ENVIRONMENT_OMICS_RUNS] = "List Omics workflow runs on this environment"
RESOURCES_ALL_WITH_DESC[GET_OMICS_RUN] = "General permission to list Omics workflow runs"
RESOURCES_ALL_WITH_DESC[GET_OMICS_RUN] = "Permission to get Omics workflow runs"
RESOURCES_ALL_WITH_DESC[DELETE_OMICS_RUN] = "Permission to delete Omics workflow runs"
RESOURCES_ALL_WITH_DESC[UPDATE_OMICS_RUN] = "Permission to edit Omics workflow runs"
61 changes: 28 additions & 33 deletions backend/dataall/modules/omics/services/omics_service.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,9 +61,9 @@ class OmicsService:
"""

@staticmethod
# @has_tenant_permission(MANAGE_OMICS_RUNS)
# @has_resource_permission(CREATE_OMICS_RUN)
# @has_group_permission(CREATE_OMICS_RUN)
@has_tenant_permission(MANAGE_OMICS_RUNS)
@has_resource_permission(CREATE_OMICS_RUN)
@has_group_permission(CREATE_OMICS_RUN)
def create_omics_run(*, uri: str, admin_group: str, data: dict) -> OmicsRun:
"""
Creates an omics_run and attach policies to it
Expand All @@ -73,13 +73,13 @@ def create_omics_run(*, uri: str, admin_group: str, data: dict) -> OmicsRun:
with _session() as session:
environment = EnvironmentService.get_environment_by_uri(session, uri)
dataset = DatasetRepository.get_dataset_by_uri(session, data['destination'])
# enabled = EnvironmentService.get_boolean_env_param(session, environment, "omicsEnabled")
enabled = EnvironmentService.get_boolean_env_param(session, environment, "omicsEnabled")

# if not enabled and enabled.lower() != "true":
# raise exceptions.UnauthorizedOperation(
# action=CREATE_OMICS_RUN,
# message=f'OMICS_RUN feature is disabled for the environment {environment.label}',
# )
if not enabled and enabled.lower() != "true":
raise exceptions.UnauthorizedOperation(
action=CREATE_OMICS_RUN,
message=f'OMICS_RUN feature is disabled for the environment {environment.label}',
)

omics_run = OmicsRun(
owner=get_context().username,
Expand All @@ -95,44 +95,39 @@ def create_omics_run(*, uri: str, admin_group: str, data: dict) -> OmicsRun:
)

OmicsRepository(session).save_omics_run(omics_run)
ResourcePolicy.attach_resource_policy(
session=session,
group=omics_run.SamlAdminGroupName,
permissions=OMICS_RUN_ALL,
resource_uri=omics_run.runUri,
resource_type=OmicsRun.__name__,
)

response = OmicsClient.run_omics_workflow(omics_run, session)
print(response)

if response:
omics_run.runUri = response['id']
OmicsRepository(session).save_omics_run(omics_run)
# ResourcePolicy.attach_resource_policy(
# session=session,
# group=request.SamlAdminGroupName,
# permissions=OMICS_RUN_ALL,
# resource_uri=omics_run.runUri,
# resource_type=OmicsRun.__name__,
# )

# if environment.SamlGroupName != admin_group:
# ResourcePolicy.attach_resource_policy(
# session=session,
# group=environment.SamlGroupName,
# permissions=OMICS_RUN_ALL,
# resource_uri=omics_run.runUri,
# resource_type=OmicsRun.__name__,
# )

return True
# TODO: in case of failure do we want to delete the object or do we want to show it in UI?
OmicsRepository(session).delete_omics_run(omics_run)
return False

@staticmethod
#@has_resource_permission(GET_OMICS_RUN)
@has_resource_permission(GET_OMICS_RUN)
def get_omics_run(*, uri: str):
with _session() as session:
return OmicsRepository.get_omics_run(session, uri)

@staticmethod
@has_resource_permission(GET_OMICS_RUN)
def get_omics_run_from_aws(uri: str):
with _session() as session:
return OmicsClient.get_omics_run(session, uri)

@staticmethod
@has_tenant_permission(MANAGE_OMICS_RUNS)
def get_omics_workflow(workflowId: str) -> dict:
"""List Omics workflows."""
with _session() as session:
Expand All @@ -142,13 +137,15 @@ def get_omics_workflow(workflowId: str) -> dict:
return response

@staticmethod
@has_tenant_permission(MANAGE_OMICS_RUNS)
def run_omics_workflow(workflowId: str, workflowType: str, roleArn: str, parameters: str) -> dict:
"""List Omics workflows."""
with _session() as session:
response = OmicsClient.run_omics_workflow(workflowId,workflowType, roleArn, parameters, session)
return response

@staticmethod
@has_tenant_permission(MANAGE_OMICS_RUNS)
def list_user_omics_runs(filter: dict) -> dict:
"""List existed user Omics pipelines. Filters only required omics_runs by the filter param"""
with _session() as session:
Expand All @@ -159,6 +156,7 @@ def list_user_omics_runs(filter: dict) -> dict:
)

@staticmethod
@has_tenant_permission(MANAGE_OMICS_RUNS)
def list_omics_workflows(filter: dict) -> dict:
"""List Omics workflows."""
with _session() as session:
Expand All @@ -167,9 +165,9 @@ def list_omics_workflows(filter: dict) -> dict:
)

@staticmethod
#@has_resource_permission(DELETE_OMICS_RUN)
def delete_omics_run(*, uri: str):
##T TODO: IMPLEMENT IN omics_repository
@has_resource_permission(DELETE_OMICS_RUN)
def delete_omics_run(uri: str):
## TODO: IMPLEMENT IN omics_repository
"""Deletes Omics project from the database and if delete_from_aws is True from AWS as well"""
with _session() as session:
omics_run = OmicsService._get_omics_run(session, uri)
Expand All @@ -183,8 +181,5 @@ def delete_omics_run(*, uri: str):
group=omics_run.SamlAdminGroupName,
)




def _session():
return get_context().db_engine.scoped_session()

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