Omics - re-do frontend, added to environment, clean-up code, naming c…

…onventions, json prettify

backend/dataall/modules/omics/api/mutations.py

@@ -30,5 +30,3 @@
 #     ],
 #     resolver=delete_omics_run,
 # )
-
-

backend/dataall/modules/omics/api/queries.py

@@ -12,7 +12,7 @@
 
 getOmicsWorkflow = gql.QueryField(
     name="getOmicsWorkflow",
-    args=[gql.Argument(name="workflowId", type=gql.NonNullableType(gql.String))],
+    args=[gql.Argument(name="workflowUri", type=gql.NonNullableType(gql.String))],
     type=gql.Ref("OmicsWorkflow"),
     resolver=get_omics_workflow,
 )

backend/dataall/modules/omics/api/resolvers.py

@@ -1,12 +1,13 @@
 import logging
 from dataall.base.api.context import Context
-from dataall.core.stacks.api import stack_helper
 from dataall.base.db import exceptions
 from dataall.modules.omics.services.omics_service import OmicsService
+from dataall.modules.omics.services.omics_enums import OmicsWorkflowType
 from dataall.modules.omics.db.models import OmicsRun, OmicsWorkflow
 
 log = logging.getLogger(__name__)
 
+
 class RequestValidator:
     """Aggregates all validation logic for operating with omics"""
     @staticmethod
@@ -30,6 +31,7 @@ def _required(data: dict, name: str):
         if not data.get(name):
             raise exceptions.RequiredParameter(name)
 
+
 def create_omics_run(context: Context, source, input=None):
     RequestValidator.validate_creation_request(input)
     # request = OmicsRunCreationRequest.from_dict(input)
@@ -52,13 +54,10 @@ def list_omics_workflows(context: Context, source, filter: dict = None):
     return OmicsService.list_omics_workflows(filter)
 
 
-def get_omics_workflow(context: Context, source, workflowId: str = None):
-    RequestValidator.required_uri(workflowId)
-    return OmicsService.get_omics_workflow(workflowId)
+def get_omics_workflow(context: Context, source, workflowUri: str = None):
+    RequestValidator.required_uri(workflowUri)
+    return OmicsService.get_omics_workflow(workflowUri)
 
-def run_omics_workflow(context: Context, source, workflowId: str = None, workflowType: str = 'READY2RUN', roleArn: str = None, parameters: str = None):
-    RequestValidator.required_uri(workflowId)
-    return OmicsService.run_omics_workflow(workflowId,workflowType,roleArn,parameters)
 
 def delete_omics_run(context: Context, source, runUri: str = None, deleteFromAWS: bool = None):
     RequestValidator.required_uri(runUri)
@@ -67,11 +66,10 @@ def delete_omics_run(context: Context, source, runUri: str = None, deleteFromAWS
         delete_from_aws=deleteFromAWS
     )
 
+
 def resolve_omics_workflow(context, source: OmicsRun, **kwargs):
-    return OmicsService.get_omics_workflow(source.workflowId)
+    return OmicsService.get_omics_workflow(source.workflowUri)
 
 
 def resolve_omics_run_details(context, source: OmicsRun, **kwargs):
     return OmicsService.get_omics_run_from_aws(source.runUri)
-
-

backend/dataall/modules/omics/api/types.py

@@ -6,13 +6,14 @@
 OmicsWorkflow = gql.ObjectType(
     name="OmicsWorkflow",
     fields=[
-        gql.Field(name="arn", type=gql.String),
+        gql.Field(name="workflowUri", type=gql.String),
         gql.Field(name="id", type=gql.String),
+        gql.Field(name="arn", type=gql.String),
         gql.Field(name="name", type=gql.String),
-        gql.Field(name="status", type=gql.String),
+        gql.Field(name="label", type=gql.String),
         gql.Field(name="type", type=gql.String),
         gql.Field(name="description", type=gql.String),
-        gql.Field(name="parameterTemplate", type=gql.String), # from the omics client
+        gql.Field(name="parameterTemplate", type=gql.String),
         gql.Field(name="environmentUri", type=gql.String),
     ],
 )
@@ -29,21 +30,13 @@
     ],
 )
 
-# TODO: not used at the moment
-# OmicsRunStatus = gql.ObjectType(
-#     name="OmicsRunStatus",
-#     fields=[
-#         gql.Field(name="arn", type=gql.String),
-#         gql.Field(name="id", type=gql.String),
-#         gql.Field(name="status", type=gql.String),
-#         gql.Field(name="runId", type=gql.String),
-#         gql.Field(name="roleArn", type=gql.String),
-#         gql.Field(name="statusMessage", type=gql.String),
-#         gql.Field(name="creationTime", type=gql.String),
-#         gql.Field(name="startTime", type=gql.String),
-#         gql.Field(name="stopTime", type=gql.String),
-#     ],
-# )
+OmicsRunStatus = gql.ObjectType(
+    name="OmicsRunStatus",
+    fields=[
+        gql.Field(name="status", type=gql.String),
+        gql.Field(name="statusMessage", type=gql.String)
+    ],
+)
 
 
 OmicsRun = gql.ObjectType(
@@ -54,17 +47,15 @@
         gql.Field("organizationUri", type=gql.String),
         gql.Field("name", type=gql.String),
         gql.Field("label", type=gql.String),
-        gql.Field("description", type=gql.String),
-        gql.Field("tags", type=gql.ArrayType(gql.String)),
         gql.Field("created", type=gql.String),
         gql.Field("updated", type=gql.String),
         gql.Field("owner", type=gql.String),
         gql.Field("AwsAccountId", type=gql.String),
         gql.Field("region", type=gql.String),
-        gql.Field("workflowId", type=gql.String),
+        gql.Field("workflowUri", type=gql.String),
         gql.Field("SamlAdminGroupName", type=gql.String),
         gql.Field("parameterTemplate", type=gql.String),
-        gql.Field("outputUri", type=gql.String),
+        gql.Field("outputDatasetUri", type=gql.String),
         gql.Field(
             name='environment',
             type=gql.Ref('Environment'),
@@ -100,5 +91,3 @@
         gql.Field(name="nodes", type=gql.ArrayType(OmicsRun)),
     ],
 )
-
-

backend/dataall/modules/omics/aws/omics_client.py

@@ -21,64 +21,63 @@ class OmicsClient:
     def client(awsAccountId: str, region: str):
         session = SessionHelper.remote_session(awsAccountId)
         return session.client('omics', region_name=region)
-        
+
     @staticmethod
-    def get_omics_workflow(id: str, session):
-        workflow = OmicsRepository(session).get_workflow(id=id)
+    def get_omics_workflow(workflowUri: str, session):
+        workflow = OmicsRepository(session).get_workflow(workflowUri=workflowUri)
         environment = EnvironmentRepository.get_environment_by_uri(session=session, uri=workflow.environmentUri)
         client = OmicsClient.client(awsAccountId=environment.AwsAccountId, region=environment.region)
         try:
             response = client.get_workflow(
-                id=id,
+                id=workflow.id,
                 type='READY2RUN'
             )
             return response
         except ClientError as e:
             logger.error(
                 f'Could not retrieve Ready2Run Omics Workflows status due to: {e} '
             )
-            return 'ERROR LISTING WORKFLOWS'
+            raise e
 
     @staticmethod
     def get_omics_run(session, runUri: str):
         omics_db = OmicsRepository(session)
         omics_run = omics_db.get_omics_run(runUri=runUri)
-        workflow = omics_db.get_workflow(id=omics_run.workflowId)
+        workflow = omics_db.get_workflow(workflowUri=omics_run.workflowUri)
         environment = EnvironmentRepository.get_environment_by_uri(session=session, uri=workflow.environmentUri)
         client = OmicsClient.client(awsAccountId=environment.AwsAccountId, region=environment.region)
         try:
-            response = client.get_run(id=omics_run.runUri
-            )
+            response = client.get_run(id=omics_run.runUri)
+            # TODO: remove prints
             print(response)
             return response
         except ClientError as e:
             logger.error(
                 f'Could not retrieve workflow run status due to: {e} '
             )
-            return 'ERROR GETTING WORKFLOW RUN'    
-
+            return 'ERROR GETTING WORKFLOW RUN'
 
     @staticmethod
     def run_omics_workflow(omics_run: OmicsRun, session):
         group = EnvironmentService.get_environment_group(session, omics_run.SamlAdminGroupName, omics_run.environmentUri)
+        workflow = OmicsRepository(session=session).get_workflow(workflowUri=omics_run.workflowUri)
         client = OmicsClient.client(awsAccountId=omics_run.AwsAccountId, region=omics_run.region)
         try:
             response = client.start_run(
-                workflowId=omics_run.workflowId,
-                workflowType='READY2RUN',
+                workflowId=workflow.id,
+                workflowType=workflow.type,
                 roleArn=group.environmentIAMRoleArn,
                 parameters=json.loads(omics_run.parameterTemplate),
                 outputUri=omics_run.outputUri
             )
             return response
         except ClientError as e:
+            # TODO: Check if we need to raise an error!
             logger.error(
                 f'Could not retrieve workflow run status due to: {e} '
             )
-            return 'ERROR RUNNING OMICS WORKFLOW'           
-
+            return 'ERROR RUNNING OMICS WORKFLOW'
 
-
     @staticmethod
     def list_workflows(awsAccountId, region, type) -> list:
         try:

backend/dataall/modules/omics/cdk/omics_policy.py

@@ -1,6 +1,6 @@
 from aws_cdk import aws_iam as iam
 
-from dataall.core.environment.cdk.env_role_core_policies.service_policy import ServicePolicy 
+from dataall.core.environment.cdk.env_role_core_policies.service_policy import ServicePolicy
 from dataall.modules.omics.services.omics_permissions import CREATE_OMICS_RUN
 
 
@@ -15,10 +15,10 @@ def get_statements(self, group_permissions, **kwargs):
             return []
 
         return [
-                iam.PolicyStatement(
-                    actions=[
+            iam.PolicyStatement(
+                actions=[
                     "omics:*"
-                    ],
-                    resources=['*'],
-                ),
+                ],
+                resources=['*'],
+            ),
         ]

backend/dataall/modules/omics/db/models.py

@@ -1,37 +1,27 @@
 import enum
 
 from sqlalchemy import Column, String, ForeignKey
-from sqlalchemy.dialects.postgresql import JSON
-from sqlalchemy.orm import query_expression, relationship
 
 from dataall.base.db import Base
 from dataall.base.db import Resource, utils
 
 
-class OmicsWorkflowType(enum.Enum):
-    PRIVATE = "PRIVATE"
-    READY2RUN = "READY2RUN"
-
 class OmicsWorkflow(Resource, Base):
     __tablename__ = "omics_workflow"
+    workflowUri = Column(String, primary_key=True, default=utils.uuid("omicsWorkflowUri"))
     arn = Column(String, nullable=False)
-    id = Column(String, nullable=False, primary_key=True, default=utils.uuid("omicsWorkflowUri"))
-    label = Column(String, nullable=False, default=utils.uuid("omicsWorkflowUri"))
-    owner = Column(String, nullable=False, default=utils.uuid("omicsWorkflowUri"))
-    name = Column(String, nullable=False)
-    status = Column(String, nullable=False)
+    id = Column(String, nullable=False)
     type = Column(String, nullable=False)
-    description = Column(String, nullable=True)
-    environmentUri = Column(String, nullable=False)
+    environmentUri = Column(String, nullable=True)
+
 
 class OmicsRun(Resource, Base):
     __tablename__ = "omics_run"
     runUri = Column(String, nullable=False, primary_key=True, default=utils.uuid("runUri"))
     organizationUri = Column(String, nullable=False)
     environmentUri = Column(String, ForeignKey("environment.environmentUri", ondelete="cascade"), nullable=False)
-    region = Column(String, default="eu-west-1")
-    AwsAccountId = Column(String, nullable=False)
+    workflowUri = Column(String, ForeignKey("omics_workflow.workflowUri", ondelete="cascade"), nullable=False)
     SamlAdminGroupName = Column(String, nullable=False)
-    workflowId = Column(String, nullable=False)
     parameterTemplate = Column(String, nullable=False)
     outputUri = Column(String, nullable=True)
+    outputDatasetUri = Column(String, nullable=True)

backend/dataall/modules/omics/db/omics_repository.py

@@ -39,18 +39,15 @@ def delete_omics_workflow(self, omics_workflow):
         self._session.delete(omics_workflow)
         self._session.commit()
 
-
-    def get_workflow(self, id: str):
-        return self._session.query(OmicsWorkflow).get(id)
-
+    def get_workflow(self, workflowUri: str):
+        return self._session.query(OmicsWorkflow).get(workflowUri)
 
     def get_omics_run(self, runUri: str):
         omics_run = self._session.query(OmicsRun).get(runUri)
         if not omics_run:
             raise exceptions.ObjectNotFound("OmicsRun", runUri)
         return omics_run
 
-
     def _query_workflows(self, filter) -> Query:
         query = self._session.query(OmicsWorkflow)
         if filter and filter.get("term"):
@@ -60,17 +57,15 @@ def _query_workflows(self, filter) -> Query:
                     OmicsWorkflow.name.ilike(filter.get("term") + "%%"),
                 )
             )
-        print(query)    
         return query
-    
-    def paginated_omics_workflows(self,filter=None) -> dict:
+
+    def paginated_omics_workflows(self, filter=None) -> dict:
         return paginate(
             query=self._query_workflows(filter),
             page=filter.get('page', OmicsRepository._DEFAULT_PAGE),
             page_size=filter.get('pageSize', OmicsRepository._DEFAULT_PAGE_SIZE),
         ).to_dict()
 
-
     def _query_user_runs(self, username, groups, filter) -> Query:
         query = self._session.query(OmicsRun).filter(
             or_(
@@ -87,7 +82,6 @@ def _query_user_runs(self, username, groups, filter) -> Query:
             )
         return query
 
-
     def paginated_user_runs(self, username, groups, filter=None) -> dict:
         return paginate(
             query=self._query_user_runs(username, groups, filter),
@@ -97,7 +91,6 @@ def paginated_user_runs(self, username, groups, filter=None) -> dict:
 
     # TODO: IMPLEMENT COUNT_RESOUCES
 
-
     # def count_resources(self, environment, group_uri):
     #     return (
     #         self._session.query(OmicsRun)
@@ -108,4 +101,4 @@ def paginated_user_runs(self, username, groups, filter=None) -> dict:
     #             )
     #         )
     #         .count()
-    #     )
+    #     )

backend/dataall/modules/omics/services/omics_enums.py

@@ -0,0 +1,6 @@
+import enum
+
+
+class OmicsWorkflowType(enum.Enum):
+    PRIVATE = "PRIVATE"
+    READY2RUN = "READY2RUN"