def get_compile_msgs (request):
log = request.REQUEST ['log']
logger.debug ("getting compilation messages: log=%s", log)
process_username = ViewUtil.get_os_username ()
text = GraysonUtil.readFileAsString (log)
text = unicode (text.replace ('\n', '<br/>')) if text else 'An unknown error occurred compiling the model.'
return ViewUtil.get_text_response (text)
def get_flow_status (request):
path = os.path.join (settings.GRAYSONWEB_WORKFLOW_ROOT,
request.REQUEST ['path'])
output = []
executor = Executor ({ 'flowPath' : path })
pegasus = os.environ ['PEGASUS_HOME']
executor.execute (command = "%s/bin/pegasus-status -l ${flowPath}" % pegasus,
pipe = True,
processor = lambda n : output.append (n))
return ViewUtil.get_text_response (''.join (output))
def get_flow_file (request):
username = ''
if 'addUser' in request.REQUEST:
user = ViewUtil.get_user (request)
username = user.username
path = os.path.join (settings.GRAYSONWEB_WORKFLOW_ROOT, username, request.REQUEST ['path'])
text = GraysonUtil.readFileAsString (path) if os.path.exists (path) else ''
print ("path: %s", path)
return ViewUtil.get_text_response (text)
def runs (request):
flow = request.REQUEST ['flow']
response = ViewUtil.get_text_response ('fail')
if flow:
flows = get_flows (request)
for f in flows:
logger.error ('argh %s', f)
print 'argh %s' % f
name = f ['flow']
if flow == name:
context = {
'flow' : f
}
response = ViewUtil.get_response (get_template_name ('runs.html'), request, context)
break
return response
def get_job_output (request):
user = ViewUtil.get_user (request)
workdir = request.REQUEST ['workdir']
workflow_id = request.REQUEST ['workflowid']
job_id = request.REQUEST ['jobid']
run_id = request.REQUEST ['runid']
if not run_id:
run_id = ""
if not workflow_id:
workflow_id = ""
logger.debug ("getting job output: workdir=%s, workflowid: %s, runid: %s, jobid: %s", workdir, workflow_id, run_id, job_id)
process_username = ViewUtil.get_os_username ()
workdirPath = GraysonUtil.form_workdir_path (workdir, process_username, workflow_id, run_id)
workdirPath = ViewUtil.form_workflow_path (user, workdirPath)
logger.debug ("workdirPath: %s", workdirPath)
text = ""
if job_id.startswith ('/'):
job_id = job_id [1:]
concrete = os.path.join (workdirPath, job_id)
logger.debug ('concrete: --- %s', concrete)
if os.path.exists (concrete):
logger.debug ("concrete --- : %s", concrete)
text = GraysonUtil.readFile (concrete)
else:
logger.debug ("regex: --- : %s", concrete)
workflow = GridWorkflow (workdirPath)
outputs = workflow.getOutputFiles (subworkflows = [ workdirPath ], item = job_id)
jobOutput = None
if outputs and len (outputs) > 0:
jobOutput = outputs [0]
logger.debug ("got job output: %s \n for job_id: %s", jobOutput, job_id)
if jobOutput:
text = GraysonUtil.readFileAsString (jobOutput)
return ViewUtil.get_text_response (text)
def getfile (request):
# TODO: construct path dynamically and selectively for security purposes.
return ViewUtil.get_text_response (GraysonUtil.readFile (request.REQUEST ['file']))
