def __init__(self, task):
self.repeats = task.get_custom_field('repeats')
self.data_files = task.get_custom_field('data_files')
if self.data_files is None:
self.data_files = []
self.raw_mode_args = task.get_custom_field('raw_mode_args')
super(TaskPlugin, self).__init__(task)
self.copasi_model = RWCopasiModel(
os.path.join(self.task.directory, self.task.original_model))
def __init__(self, task):
self.repeats = task.get_custom_field('repeats')
self.data_files = task.get_custom_field('data_files')
self.raw_mode_args = task.get_custom_field('raw_mode_args')
super(TaskPlugin, self).__init__(task)
self.copasi_model = RWCopasiModel(os.path.join(self.task.directory, self.task.original_model))
class TaskPlugin(BaseTask):
subtasks = 3
def __init__(self, task):
self.repeats = task.get_custom_field('repeats')
self.data_files = task.get_custom_field('data_files')
if self.data_files is None:
self.data_files = []
self.raw_mode_args = task.get_custom_field('raw_mode_args')
super(TaskPlugin, self).__init__(task)
self.copasi_model = RWCopasiModel(os.path.join(self.task.directory, self.task.original_model))
def validate(self):
#TODO:Abstract this to a new COPASI class in this plugin package
return self.copasi_model.is_valid('RW')
def initialize_subtasks(self):
#Create new subtask objects, and save them
#The main module
self.create_new_subtask('main')
#And a subtask to process any results
self.create_new_subtask('process', local=True)
self.task.result_view = False
self.task.result_download = False
self.task.save()
def prepare_subtask(self, index):
"""Prepare the indexed subtask"""
if index == 1:
return self.process_main_subtask()
elif index == 2:
return self.process_results_subtask()
else:
raise Exception('No subtasks remaining')
def process_main_subtask(self):
subtask = self.get_subtask(1)
#If no load balancing step required:
model_files, output_files = self.copasi_model.prepare_rw_jobs(self.repeats)
self.task.set_custom_field('output_files', output_files)
model_count = len(model_files)
self.task.set_custom_field('model_count', model_count)
self.task.save()
condor_pool = self.task.condor_pool
condor_job_file = self.copasi_model.prepare_rw_condor_job(condor_pool.pool_type, condor_pool.address, len(model_files), self.raw_mode_args, self.data_files, output_files, rank='0')
log.debug('Prepared copasi files %s'%model_files)
log.debug('Prepared condor job %s' %condor_job_file)
subtask.spec_file = condor_job_file
subtask.status = 'ready'
subtask.set_custom_field('job_output', '') # Job output is potentially >1 file. Currently can't check for this, so leave blank
subtask.save()
return subtask
def process_results_subtask(self):
subtask=self.get_subtask(2)
assert isinstance(subtask, Subtask)
subtask.start_time = now()
#Go through and collate the results
#This is reasonably computationally simple, so we run locally
directory = self.task.directory
output_files = self.task.get_custom_field('output_files')
model_count = self.task.get_custom_field('model_count')
collated_output_files = []
#Collate the output files back into their original name
for output_filename in output_files:
try:
output_file = open(os.path.join(directory, output_filename), 'w')
for partial_output in ['%d_%s' % (i, output_filename) for i in range(model_count)]:
partial_output_file = open(os.path.join(directory, partial_output), 'r')
for line in partial_output_file:
output_file.write(line)
partial_output_file.close()
output_file.close()
collated_output_files.append(output_filename)
except Exception, e:
raise e
pass
self.task.set_custom_field('collated_output_files', collated_output_files)
if len(collated_output_files) > 0:
self.task.result_view=True
self.task.save()
subtask.status = 'finished'
subtask.finish_time = now()
subtask.set_run_time(time_delta=subtask.finish_time-subtask.start_time)
subtask.save()
return subtask
class TaskPlugin(BaseTask):
subtasks = 3
def __init__(self, task):
self.repeats = task.get_custom_field('repeats')
self.data_files = task.get_custom_field('data_files')
if self.data_files is None:
self.data_files = []
self.raw_mode_args = task.get_custom_field('raw_mode_args')
super(TaskPlugin, self).__init__(task)
self.copasi_model = RWCopasiModel(
os.path.join(self.task.directory, self.task.original_model))
def validate(self):
#TODO:Abstract this to a new COPASI class in this plugin package
return self.copasi_model.is_valid('RW')
def initialize_subtasks(self):
#Create new subtask objects, and save them
#The main module
self.create_new_subtask('main')
#And a subtask to process any results
self.create_new_subtask('process', local=True)
self.task.result_view = False
self.task.result_download = False
self.task.save()
def prepare_subtask(self, index):
"""Prepare the indexed subtask"""
if index == 1:
return self.process_main_subtask()
elif index == 2:
return self.process_results_subtask()
else:
raise Exception('No subtasks remaining')
def process_main_subtask(self):
subtask = self.get_subtask(1)
#If no load balancing step required:
model_files, output_files = self.copasi_model.prepare_rw_jobs(
self.repeats)
self.task.set_custom_field('output_files', output_files)
model_count = len(model_files)
self.task.set_custom_field('model_count', model_count)
self.task.save()
condor_pool = self.task.condor_pool
condor_job_file = self.copasi_model.prepare_rw_condor_job(
condor_pool.pool_type,
condor_pool.address,
len(model_files),
self.raw_mode_args,
self.data_files,
output_files,
rank='0')
log.debug('Prepared copasi files %s' % model_files)
log.debug('Prepared condor job %s' % condor_job_file)
subtask.spec_file = condor_job_file
subtask.status = 'ready'
subtask.set_custom_field(
'job_output', ''
) # Job output is potentially >1 file. Currently can't check for this, so leave blank
subtask.save()
return subtask
def process_results_subtask(self):
subtask = self.get_subtask(2)
assert isinstance(subtask, Subtask)
subtask.start_time = now()
#Go through and collate the results
#This is reasonably computationally simple, so we run locally
directory = self.task.directory
output_files = self.task.get_custom_field('output_files')
model_count = self.task.get_custom_field('model_count')
collated_output_files = []
#Collate the output files back into their original name
for output_filename in output_files:
try:
output_file = open(os.path.join(directory, output_filename),
'w')
for partial_output in [
'%d_%s' % (i, output_filename)
for i in range(model_count)
]:
partial_output_file = open(
os.path.join(directory, partial_output), 'r')
for line in partial_output_file:
output_file.write(line)
partial_output_file.close()
output_file.close()
collated_output_files.append(output_filename)
except Exception as e:
raise e
pass
self.task.set_custom_field('collated_output_files',
collated_output_files)
if len(collated_output_files) > 0:
self.task.result_view = True
self.task.save()
subtask.status = 'finished'
subtask.finish_time = now()
subtask.set_run_time(time_delta=subtask.finish_time -
subtask.start_time)
subtask.save()
return subtask
#===========================================================================
# Results download code. No results view page for this task
#===========================================================================
def get_results_view_template_name(self, request):
"""Return a string with the HTML code to be used in the task results view page
"""
#Get the name of the page we're displaying. If not specified, assume main
page_name = request.GET.get('name', 'main')
if page_name == 'main':
return self.get_template_name('results_view')
def get_results_view_data(self, request):
#Get the name of the page we're displaying. If not specified, assume main
page_name = request.GET.get('name', 'main')
if page_name == 'main':
collated_output_files = self.task.get_custom_field(
'collated_output_files')
output = {'output_files': collated_output_files}
return output
def get_results_download_data(self, request):
filename = request.GET.get('name')
if not filename in self.task.get_custom_field('collated_output_files'):
raise Exception('Output file not recognized')
request.session['errors'] = [
('Cannot Return Output',
'There was an internal error processing the results file')
]
return HttpResponseRedirect(
reverse_lazy('task_details', kwargs={'task_id': self.task.id}))
full_filename = os.path.join(self.task.directory, filename)
if not os.path.isfile(full_filename):
request.session['errors'] = [
('Cannot Return Output',
'There was an internal error processing the results file')
]
return HttpResponseRedirect(
reverse_lazy('task_details', kwargs={'task_id': self.task.id}))
result_file = open(full_filename, 'r')
response = HttpResponse(result_file, content_type='text/plain')
response['Content-Disposition'] = 'attachment; filename=%s' % (
filename.replace(' ', '_'))
response['Content-Length'] = os.path.getsize(full_filename)
return response
class TaskPlugin(BaseTask):
subtasks = 3
def __init__(self, task):
self.repeats = task.get_custom_field('repeats')
self.data_files = task.get_custom_field('data_files')
if self.data_files is None:
self.data_files = []
self.raw_mode_args = task.get_custom_field('raw_mode_args')
super(TaskPlugin, self).__init__(task)
self.copasi_model = RWCopasiModel(
os.path.join(self.task.directory, self.task.original_model))
def validate(self):
#TODO:Abstract this to a new COPASI class in this plugin package
return self.copasi_model.is_valid('RW')
def initialize_subtasks(self):
#Create new subtask objects, and save them
#The main module
self.create_new_subtask('main')
#And a subtask to process any results
self.create_new_subtask('process', local=True)
self.task.result_view = False
self.task.result_download = False
self.task.save()
def prepare_subtask(self, index):
"""Prepare the indexed subtask"""
if index == 1:
return self.process_main_subtask()
elif index == 2:
return self.process_results_subtask()
else:
raise Exception('No subtasks remaining')
def process_main_subtask(self):
subtask = self.get_subtask(1)
#If no load balancing step required:
model_files, output_files = self.copasi_model.prepare_rw_jobs(
self.repeats)
self.task.set_custom_field('output_files', output_files)
model_count = len(model_files)
self.task.set_custom_field('model_count', model_count)
self.task.save()
condor_pool = self.task.condor_pool
condor_job_file = self.copasi_model.prepare_rw_condor_job(
condor_pool.pool_type,
condor_pool.address,
len(model_files),
self.raw_mode_args,
self.data_files,
output_files,
rank='0')
log.debug('Prepared copasi files %s' % model_files)
log.debug('Prepared condor job %s' % condor_job_file)
subtask.spec_file = condor_job_file
subtask.status = 'ready'
subtask.set_custom_field(
'job_output', ''
) # Job output is potentially >1 file. Currently can't check for this, so leave blank
subtask.save()
return subtask
def process_results_subtask(self):
subtask = self.get_subtask(2)
assert isinstance(subtask, Subtask)
subtask.start_time = now()
#Go through and collate the results
#This is reasonably computationally simple, so we run locally
directory = self.task.directory
output_files = self.task.get_custom_field('output_files')
model_count = self.task.get_custom_field('model_count')
collated_output_files = []
#Collate the output files back into their original name
for output_filename in output_files:
try:
output_file = open(os.path.join(directory, output_filename),
'w')
for partial_output in [
'%d_%s' % (i, output_filename)
for i in range(model_count)
]:
partial_output_file = open(
os.path.join(directory, partial_output), 'r')
for line in partial_output_file:
output_file.write(line)
partial_output_file.close()
output_file.close()
collated_output_files.append(output_filename)
except Exception, e:
raise e
pass
self.task.set_custom_field('collated_output_files',
collated_output_files)
if len(collated_output_files) > 0:
self.task.result_view = True
self.task.save()
subtask.status = 'finished'
subtask.finish_time = now()
subtask.set_run_time(time_delta=subtask.finish_time -
subtask.start_time)
subtask.save()
return subtask
