def RunWorkflowJob(self, job, stages, files):
stage_levels = {}
executed_stages = {}
#create job stages
for i, s in enumerate(stages):
stage = Stages.GetStage(self.user, s["StageID"])
if not stage_levels.get(stage.StageLevel):
stage_levels[stage.StageLevel] = []
stage_obj = { "stage": stage, "parameters": s["Parameters"] }
stage_levels[stage.StageLevel].append(stage_obj)
for stages in sorted(stage_levels):
for s in stage_levels[stages]:
stage = s["stage"]
parameters = s["parameters"]
jobstage = self.RunToolJob(job, parameters, files.get("stage_%d" % stage.StageID, []), stage, i)
executed_stages[stage.StageID] = jobstage.JobStageID
for dep in jobstage.Stage.StageDependencies.all():
JobStageDependency.objects.create(
JobStageOI=jobstage,
DependantOn_id=executed_stages[dep.DependantOn.StageID],
Condition_id=dep.Condition.ConditionID,
ExitCodeValue=dep.ExitCodeValue
)
def DeleteStageDependency(self, dependency_id):
with transaction.atomic():
dep = StageDependencies.GetStageDependency(self.user, dependency_id)
StageDependencies.DeleteStageDependency(self.user, dep)
Stages.UpdateStageLevel(dep.StageOI)
return self.GetStages(dep.StageOI.WorkflowVersion.Workflow.WorkflowID,
"dev")
def AddStage(self, workflow_id, stage):
workflow = self.GetWorkflow(workflow_id)
version = self.GetWorkflowVersion(workflow, "dev")
tool = self.GetTool(stage["ID"])
tool_version = self.GetToolVersion(tool, stage["VersionNum"])
return Stages.AddStage(self.user, version, tool_version, None, False,
stage["Left"], stage["Top"])
def AddStageDependency(self, stage_id, dependency):
with transaction.atomic():
stage = self.GetStage(stage_id)
stage_dependency = StageDependencies.AddStageDependency(self.user,
stage, dependency['DependantOn'], dependency['Condition'],
dependency['ExitCodeValue'])
Stages.UpdateStageLevel(stage)
return stage_dependency
def UpdateStage(self, stage_id, stage_details):
with transaction.atomic():
stage = self.GetStage(stage_id)
tool = stage.ToolVersion.Tool
version = self.GetToolVersion(tool, stage_details["VersionNum"])
stage = Stages.UpdateStage(self.user, stage, version, None,
stage_details["Checkpoint"])
StageParameters.UpdateStageParameters(self.user, stage,
stage_details["StageParameters"])
return stage
def DeleteStage(self, stage_id):
stage = self.GetStage(stage_id)
Stages.DeleteStage(self.user, stage)
def MoveStage(self, stage_id, stage_pos):
stage = self.GetStage(stage_id)
return Stages.MoveStage(self.user, stage, stage_pos['Left'],
stage_pos['Top'])
def GetStage(self, stage_id):
return Stages.GetStage(self.user, stage_id)
def GetStages(self, workflow_id, version_num):
workflow = self.GetWorkflow(workflow_id)
version = self.GetWorkflowVersion(workflow, version_num)
return Stages.GetStages(version)