def process_request( request, header_text, button_text, callback, format_callback=None,
mode = 'mlgt', form_modifier = None, stdout=False, stderr=False ):
global task_ids
# check whether request have taskid as GET parameter
taskid = request.GET.get('taskid', None)
if taskid:
if taskid not in task_ids:
return error_page(request, 'task with ID %s is not registered in the system!')
(procid, login, title, current_route_path, format_callback, path_qs) = task_ids[taskid]
procunit = getproc(procid)
if procunit.status in ['D', 'U']:
result = procunit.result
if not result and procunit.exc:
raise procunit.exc
if format_callback:
output = format_callback(result, request)
html = output['html']
jscode = output['jscode']
refs = format_refs(output.get('refs', ''))
else:
html = result['html']
jscode = result['jscode']
refs = format_refs(result.get('refs', ''))
# dummy
sample_html, sample_code = result['sample_filtering']
marker_html, marker_code = result['marker_filtering']
return render_to_response("genaf:templates/tools/report.mako",
{ 'header_text': result['title'],
'sample_report': sample_html,
'marker_report': marker_html,
'html': html if html is not None else '',
'code': sample_code + marker_code + jscode if jscode is not None else '',
'path_qs': path_qs,
'refs': refs,
}, request = request )
clearproc(procid)
del task_ids[taskid]
else:
seconds = 5
ns = procunit.ns
return render_to_response('genaf:templates/tools/progress.mako',
{ 'msg': ns.cerr,
'title': title,
'taskid': taskid,
'seconds': seconds,
}, request = request )
# prepare form and/or process form
if not request.GET.get('_method', None) in ['_exec', '_yamlexec']:
queryform, javacode = create_form( request, mode )
if form_modifier:
queryform, javacode = form_modifier(queryform, javacode)
return render_to_response('genaf:templates/tools/index.mako',
{ 'header_text': header_text,
'queryform': queryform,
'code': javacode,
'yamlform': yaml_query_form(request),
}, request = request)
# process request
if request.GET.get('_method', None) == '_exec':
params = load_params(form2dict( request ))
elif request.GET.get('_method', None) == '_yamlexec':
params = load_yaml( request.params.get('yamlquery') )
if not asbool(request.registry.settings['genaf.concurrent.analysis']):
# set this to false for debugging in non-concurrent mode
result = mp_run_callback(request.registry.settings,
callback, params, request.user, mode)
if format_callback:
output = format_callback(result, request)
html = output['html']
jscode = output['jscode']
refs = format_refs(output.get('refs', ''))
else:
html = result['html']
jscode = result['jscode']
refs = format_refs(result.get('refs', ''))
# dummy
sample_html, sample_code = result['sample_filtering']
marker_html, marker_code = result['marker_filtering']
return render_to_response("genaf:templates/tools/report.mako",
{ 'header_text': result['title'],
'sample_report': sample_html,
'marker_report': marker_html,
'html': html if html is not None else '',
'code': sample_code + marker_code + jscode if jscode is not None else '',
'path_qs': request.path_qs,
'refs': refs,
}, request = request )
# this is code for concurrent mode
with glock:
procid, msg = subproc( request.user.login, None,
mp_run_callback, request.registry.settings, callback, params,
request.user, mode )
task_ids[procid] = ( procid, request.user.login, header_text,
request.current_route_path(), format_callback, request.path_qs )
return HTTPFound(location = request.current_route_path(_query = { 'taskid': procid }))
raise NotImplementedError()
## method stops here
q = Query( params, get_dbhandler() )
# callback needs to return (header_text, html, jscode) tuple
response = callback(q, request)
if type(response) != tuple:
return response
(header_text, html, code) = response
sample_html, sample_code = format_sample_summary( q.get_sample_summary(mode) )
marker_html, marker_code = format_marker_summary( q )
return render_to_response("genaf:templates/tools/report.mako",
{ 'header_text': header_text,
'sample_report': sample_html,
'marker_report': marker_html,
'html': html if html is not None else '',
'code': sample_code + marker_code + code if code is not None else '',
}, request = request )
def process(request):
batch_id = request.matchdict.get('id')
if batch_id in local_procs:
(procid, login, batch_code) = local_procs[batch_id]
if login != request.user.login:
seconds = 0
msg = div()[ p('Another task started by %s is currently running batch: %s' %
( login, batch_code ))
]
else:
procunit = getproc(procid)
if procunit.status in ['D', 'U']:
seconds = 0
if procunit.exc:
msg = div()[
p('Assay processing failed. Please see the following error:'),
p( procunit.exc ),
]
else:
result = procunit.result
msg = div()[ p('Assay processing finished.'),
p('Statistics: %s' % str(result[0]) ),
p()[ a(href=request.route_url('genaf.famgr-view',id=batch_id))[
span(class_='btn btn-success')[ 'Continue' ]
]
]
]
if result[1]:
msg.add( div()[ p( *result[1] ) ] )
del local_procs[batch_id]
else:
seconds = 10
msg = div()[ p('Output: %s' % procunit.ns.cout), p('Processing...') ]
else:
batch = get_dbhandler().get_batch_by_id(batch_id)
batch_code = batch.code
# check authorization
if not request.user.in_group( batch.group ):
error_page('You are not authorized to view this batch!')
if False:
# set the above to True for single-process debugging purpose
process_assays(batch_id, request.user.login, None)
with glock:
procid, msg = subproc( request.user.login, None,
mp_process_assays, request.registry.settings,
batch_id, request.user.login, request.user.id )
local_procs[batch_id] = (procid, request.user.login, batch_code)
msg = div()[ p('Starting assay processing task') ]
seconds = 10
return render_to_response('genaf:templates/famgr/process.mako',
{ 'msg': msg,
'batch_code': batch_code,
'seconds': seconds,
}, request = request )
