From 98147eb8c6488bac6e4e8adafa3aca2c0585f3bc Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Fri, 24 Sep 2021 18:17:12 +0200
Subject: [PATCH] Create an url to list cc-qtl workflow
---
server/api/views.py | 50 ++++++++++++++++++++++++++++++++++-----------
1 file changed, 38 insertions(+), 12 deletions(-)
diff --git a/server/api/views.py b/server/api/views.py
index 1c9398d6..90f5fd6d 100644
--- a/server/api/views.py
+++ b/server/api/views.py
@@ -17,7 +17,7 @@ from guardian.shortcuts import assign_perm, get_perms
import pandas as pd
# DRF
-from rest_framework import viewsets, status, serializers, mixins
+from rest_framework import views, viewsets, status, serializers, mixins, authentication
from rest_framework.permissions import IsAuthenticated
@@ -25,11 +25,16 @@ from rest_framework.permissions import IsAuthenticated
from rest_framework.response import Response
from rest_framework.decorators import action
+
+from rest_framework_simplejwt.authentication import JWTAuthentication
+
# DRF guardian
from rest_framework_guardian import filters
from .exceptions import RessourceAlreadyExists
+from bioblend import ConnectionError
+
# Serializers
from .serializers import (
FounderSerializer,
@@ -812,19 +817,29 @@ def tools_parameters(request):
return JsonResponse(job, safe=False)
-def workflow_tools(request):
- runner = GalaxyRunner()
- gi = runner.galaxy_instance
+class WorkflowTools(views.APIView):
+ authentication_classes = [JWTAuthentication, authentication.SessionAuthentication]
+ permission_classes = [IsAuthenticated]
- # TODO worflow_id should be a parameter
+ def get(self, request, *args, **kwargs):
+ wf_id = kwargs["wf_id"]
+ runner = GalaxyRunner()
+ gi = runner.galaxy_instance
- # workflow_id = request["workflow_id"]
- wf = gi.workflows.get_workflows(name="cc-qtl-wf")[0]
- wf_with_details = gi.workflows.show_workflow(wf["id"])
- wf_step_tool_ids = [
- (step_id, step["tool_id"]) for step_id, step in wf_with_details["steps"].items()
- ]
- return JsonResponse(dict(get_job_params(wf_step_tool_ids, gi)))
+ # TODO worflow_id should be a parameter
+
+ # workflow_id = request["workflow_id"]
+ try:
+ wf_with_details = gi.workflows.show_workflow(wf_id)
+ wf_step_tool_ids = [
+ (step_id, step["tool_id"])
+ for step_id, step in wf_with_details["steps"].items()
+ ]
+ return Response(dict(get_job_params(wf_step_tool_ids, gi)))
+ except ConnectionError as e:
+ return Response(
+ status=status.HTTP_400_BAD_REQUEST, data=json.loads(e.body)["err_msg"]
+ )
def workflow_default_parameters(request):
@@ -862,3 +877,14 @@ def get_job_params(job_ids, gi):
gi.tools.show_tool(job_id, io_details=True),
)
+
+class CcQtlWorkflows(views.APIView):
+
+ authentication_classes = [JWTAuthentication, authentication.SessionAuthentication]
+ permission_classes = [IsAuthenticated]
+
+ def get(self, request, *args, **kwargs):
+ runner = GalaxyRunner()
+ gi = runner.galaxy_instance
+ wf = gi.workflows.get_workflows()
+ return Response(wf)
--
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