def get(self, request, tool_id):
"""
Get development scripts and files for tool
"""
jms = JobManager(user=request.user)
dir_listing = jms.GetToolFiles(tool_id)
return Response(dir_listing, status=200)
def get(self, request):
"""
Get queues
"""
jms = JobManager(user=request.user)
queues = jms.GetQueues()
return Response(json.dumps(queues, default=lambda o: o.__dict__))
def get(self, request):
"""
Get administrators
"""
jms = JobManager(user=request.user)
admins = jms.GetAdministrators()
return Response(json.dumps(admins, default=lambda o: o.__dict__))
def post(self, request, tool_id, file_name):
"""
Create a new file
"""
jms = JobManager(user=request.user)
jms.CreateToolFile(tool_id, file_name)
return Response(status=200)
def post(self, request, tool_id):
"""
Upload files for tool
"""
jms = JobManager(user=request.user)
dir_listing = jms.UploadToolFiles(tool_id, request.FILES)
return Response(dir_listing, status=200)
def delete(self, request, parameter_id):
"""
Delete parameter
"""
jms = JobManager(user=request.user)
jms.DeleteParameter(parameter_id)
return Response(status=200)
def delete(self, request, tool_id, user_name):
"""
Unshare a tool with a user
"""
jms = JobManager(user=request.user)
jms.UnshareTool(tool_id, user_name)
return Response()
def get(self, request):
"""
Get server settings
"""
jms = JobManager(user=request.user)
settings = jms.GetSettings()
return Response(json.dumps(settings, default=lambda o: o.__dict__, sort_keys=True))
def delete(self, request, category_id):
"""
Update tool category
"""
jms = JobManager(user=request.user)
jms.DeleteCategory(category_id)
return Response(status=200)
def delete(self, request, tool_id):
"""
Delete a tool
"""
jms = JobManager(user=request.user)
jms.DeleteTool(tool_id)
return Response(status=200)
def get(self, request):
"""
Get queue and node usage statistics for all nodes in the cluster
"""
jms = JobManager(user=request.user)
dashboard = jms.GetDashboard()
return Response(json.dumps(dashboard, default=lambda o: o.__dict__, sort_keys=True))
def get(self, request, job_id):
"""
Get the status ID of the job
"""
jms = JobManager(user=request.user)
stage = jms.GetJob(job_id).JobStages.all()[0]
return Response(stage.Status.StatusID)
def delete(self, request, cluster_id):
"""
Stop job
"""
jms = JobManager(user=request.user)
jms.StopClusterJob(cluster_id)
return Response()
def get(self, request, tool_id, file_name):
"""
Get file content
"""
jms = JobManager(user=request.user)
content = jms.ReadToolFile(tool_id, file_name)
return Response(content, status=200)
def delete(self, request, tool_id, file_name):
"""
Delete a file
"""
jms = JobManager(user=request.user)
jms.DeleteToolFile(tool_id, file_name)
return Response(status=200)
def delete(self, request, job_id):
"""
Delete job
"""
jms = JobManager(user=request.user)
job = jms.DeleteJob(job_id)
return Response()
def delete(self, request, workflow_id, user_name):
"""
Unshare a workflow with a user
"""
jms = JobManager(user=request.user)
jms.UnshareWorkflow(workflow_id, user_name)
return Response()
def delete(self, request, stage_id):
"""
Delete stage
"""
jms = JobManager(user=request.user)
stage = jms.DeleteStage(stage_id)
return Response()
def delete(self, request, workflow_id):
"""
Delete a workflow
"""
jms = JobManager(user=request.user)
jms.DeleteWorkflow(workflow_id)
return Response(status=200)
def delete(self, request, dependency_id):
"""
Delete stage dependency
"""
jms = JobManager(user=request.user)
stages = jms.DeleteStageDependency(dependency_id)
serializer = StageLevelSerializer(stages, many=True)
return Response(serializer.data)
def get(self, request, workflow_id, version_num):
"""
Get workflow stages
"""
jms = JobManager(user=request.user)
stages = jms.GetStages(workflow_id, version_num)
serializer = StageLevelSerializer(stages, many=True)
return Response(serializer.data)
def get(self, request, stage_id):
"""
Get stage details
"""
jms = JobManager(user=request.user)
stage = jms.GetStage(stage_id)
serializer = StageListSerializer(stage)
return Response(serializer.data)
def delete(self, request, workflow_id):
"""
Make workflow private
"""
jms = JobManager(user=request.user)
workflow = jms.UpdateWorkflowAvailability(workflow_id, False)
serializer = WorkflowPermissionSerializer(workflow)
return Response(serializer.data)
def put(self, request, workflow_id):
"""
Make workflow publically available
"""
jms = JobManager(user=request.user)
workflow = jms.UpdateWorkflowAvailability(workflow_id, True)
serializer = WorkflowPermissionSerializer(workflow)
return Response(serializer.data)
def get(self, request, workflow_id):
"""
Get the access permissions for a workflow
"""
jms = JobManager(user=request.user)
workflow = jms.GetWorkflow(workflow_id)
serializer = WorkflowPermissionSerializer(workflow)
return Response(serializer.data)
def get(self, request, workflow_id, version_num):
"""
Get a workflow version based on the WorkflowID and WorkflowVersionNum fields
"""
jms = JobManager(user=request.user)
version = jms.GetWorkflowVersion(jms.GetWorkflow(workflow_id), version_num)
serializer = WorkflowVersionDetailSerializer(version)
return Response(serializer.data)
def get(self, request, workflow_id):
"""
Get all versions of a workflow
"""
jms = JobManager(user=request.user)
versions = jms.GetWorkflowVersions(workflow_id)
serializer = WorkflowVersionListSerializer(versions, many=True)
return Response(serializer.data)
def get(self, request, workflow_id):
"""
Fetch workflow
"""
jms = JobManager(user=request.user)
workflow = jms.GetWorkflow(tool_id)
serializer = WorkflowListSerializer(workflow)
return Response(serializer.data)
def delete(self, request, node_name):
"""
Delete node
"""
jms = JobManager(user=request.user)
jms.DeleteNode(node_name)
nodes = jms.GetNodes()
return Response(json.dumps(nodes, default=lambda o: o.__dict__))
def get(self, request, job_stage_id):
"""
List job directory contents
"""
path = request.GET.get("path", "/")
jms = JobManager(user=request.user)
data = jms.get_job_directory_listing(job_stage_id, path)
return Response(data)
def get(self, request):
"""
Get all workflows accessible to user
"""
jms = JobManager(user=request.user)
workflows = jms.GetWorkflows()
serializer = WorkflowListSerializer(workflows, many=True)
return Response(serializer.data)
def get(self, request, job_stage_id):
"""
Get job file contents
"""
log = request.GET.get("log", None)
if not log:
#We are fetching a job file
try:
jms = JobManager(user=request.user)
#create a temp copy
filepath = request.GET.get("path", '')
tmp_path = jms.get_tmp_job_file(job_stage_id, filepath)
#Get file type
mimetypes.init()
name, file_ext = os.path.splitext(os.path.basename(filepath))
type = mimetypes.types_map.get(file_ext.lower(), "text/plain")
if type == "application/javascript":
type = "text/plain"
if request.method == "HEAD":
response = HttpResponse("", content_type=type)
return response
else:
wrapper = FileWrapper(open(tmp_path, "rb"))
response = HttpResponse(wrapper, content_type=type)
response['Content-Length'] = os.path.getsize(tmp_path)
return response
except Exception, err:
f = open("/tmp/file.txt", "w")
f.write(str(err))
f.close()
return Response(str(err), status=400)
return response
else:
wrapper = FileWrapper(open(tmp_path, "rb"))
response = HttpResponse(wrapper, content_type=type)
response['Content-Length'] = os.path.getsize(tmp_path)
return response
except Exception, err:
f = open("/tmp/file.txt", "w")
f.write(str(err))
f.close()
return Response(str(err), status=400)
else:
#We are fetching a log file
jms = JobManager(user=request.user)
if log.lower() == "error":
data = jms.get_job_error(job_stage_id)
elif log.lower() == "output":
data = jms.get_job_output(job_stage_id)
return Response(data)
class DirectoryDetail(APIView):
permission_classes = (IsAuthenticated,)
def get(self, request, job_stage_id):
"""
