def export_to_gui(self, soma_workflow_dirpath, **Xy):
'''
Example
-------
see the directory of "examples/run_somaworkflow_gui.py" in epac
'''
try:
from soma.workflow.client import Job, Workflow
from soma.workflow.client import Helper, FileTransfer
except ImportError:
errmsg = "No soma-workflow is found. "\
"Please verify your soma-worklow"\
"on your computer (e.g. PYTHONPATH) \n"
sys.stderr.write(errmsg)
sys.stdout.write(errmsg)
raise NoSomaWFError
if not os.path.exists(soma_workflow_dirpath):
os.makedirs(soma_workflow_dirpath)
tmp_work_dir_path = soma_workflow_dirpath
cur_work_dir = os.getcwd()
os.chdir(tmp_work_dir_path)
ft_working_directory = FileTransfer(is_input=True,
client_path=tmp_work_dir_path,
name="working directory")
## Save the database and tree to working directory
## ===============================================
np.savez(os.path.join(tmp_work_dir_path,
SomaWorkflowEngine.dataset_relative_path), **Xy)
store = StoreFs(dirpath=os.path.join(
tmp_work_dir_path,
SomaWorkflowEngine.tree_root_relative_path))
self.tree_root.save_tree(store=store)
## Subtree job allocation on disk
## ==============================
node_input = NodesInput(self.tree_root.get_key())
split_node_input = SplitNodesInput(self.tree_root,
num_processes=self.num_processes)
nodesinput_list = split_node_input.split(node_input)
keysfile_list = self._save_job_list(tmp_work_dir_path,
nodesinput_list)
## Build soma-workflow
## ===================
jobs = [Job(command=[u"epac_mapper",
u'--datasets', '"%s"' %
(SomaWorkflowEngine.dataset_relative_path),
u'--keysfile', '"%s"' %
(nodesfile)],
referenced_input_files=[ft_working_directory],
referenced_output_files=[ft_working_directory],
name="epac_job_key=%s" % (nodesfile),
working_directory=ft_working_directory)
for nodesfile in keysfile_list]
soma_workflow = Workflow(jobs=jobs)
if soma_workflow_dirpath and soma_workflow_dirpath != "":
out_soma_workflow_file = os.path.join(soma_workflow_dirpath,
SomaWorkflowEngine.open_me_by_soma_workflow_gui)
Helper.serialize(out_soma_workflow_file, soma_workflow)
os.chdir(cur_work_dir)
def _submit_graph(self, pyfiles, dependencies, nodes):
jobs = []
soma_deps = []
for idx, fname in enumerate(pyfiles):
name = os.path.splitext(os.path.split(fname)[1])[0]
jobs.append(Job(command=[sys.executable, fname], name=name))
for key, values in list(dependencies.items()):
for val in values:
soma_deps.append((jobs[val], jobs[key]))
wf = Workflow(jobs, soma_deps)
logger.info('serializing workflow')
Helper.serialize('workflow', wf)
controller = WorkflowController()
logger.info('submitting workflow')
wf_id = controller.submit_workflow(wf)
Helper.wait_workflow(wf_id, controller)
def _submit_graph(self, pyfiles, dependencies, nodes):
jobs = []
soma_deps = []
for idx, fname in enumerate(pyfiles):
name = os.path.splitext(os.path.split(fname)[1])[0]
jobs.append(Job(command=[sys.executable, fname], name=name))
for key, values in list(dependencies.items()):
for val in values:
soma_deps.append((jobs[val], jobs[key]))
wf = Workflow(jobs, soma_deps)
logger.info('serializing workflow')
Helper.serialize('workflow', wf)
controller = WorkflowController()
logger.info('submitting workflow')
wf_id = controller.submit_workflow(wf)
Helper.wait_workflow(wf_id, controller)
def export_to_gui(self, soma_workflow_dirpath, **Xy):
'''
Example
-------
see the directory of "examples/run_somaworkflow_gui.py" in epac
'''
try:
from soma.workflow.client import Job, Workflow
from soma.workflow.client import Helper, FileTransfer
except ImportError:
errmsg = "No soma-workflow is found. "\
"Please verify your soma-worklow"\
"on your computer (e.g. PYTHONPATH) \n"
sys.stderr.write(errmsg)
sys.stdout.write(errmsg)
raise NoSomaWFError
if not os.path.exists(soma_workflow_dirpath):
os.makedirs(soma_workflow_dirpath)
tmp_work_dir_path = soma_workflow_dirpath
cur_work_dir = os.getcwd()
os.chdir(tmp_work_dir_path)
ft_working_directory = FileTransfer(is_input=True,
client_path=tmp_work_dir_path,
name="working directory")
## Save the database and tree to working directory
## ===============================================
np.savez(
os.path.join(tmp_work_dir_path,
SomaWorkflowEngine.dataset_relative_path), **Xy)
store = StoreFs(dirpath=os.path.join(
tmp_work_dir_path, SomaWorkflowEngine.tree_root_relative_path))
self.tree_root.save_tree(store=store)
## Subtree job allocation on disk
## ==============================
node_input = NodesInput(self.tree_root.get_key())
split_node_input = SplitNodesInput(self.tree_root,
num_processes=self.num_processes)
nodesinput_list = split_node_input.split(node_input)
keysfile_list = self._save_job_list(tmp_work_dir_path, nodesinput_list)
## Build soma-workflow
## ===================
jobs = [
Job(command=[
u"epac_mapper", u'--datasets',
'"%s"' % (SomaWorkflowEngine.dataset_relative_path),
u'--keysfile',
'"%s"' % (nodesfile)
],
referenced_input_files=[ft_working_directory],
referenced_output_files=[ft_working_directory],
name="epac_job_key=%s" % (nodesfile),
working_directory=ft_working_directory)
for nodesfile in keysfile_list
]
soma_workflow = Workflow(jobs=jobs)
if soma_workflow_dirpath and soma_workflow_dirpath != "":
out_soma_workflow_file = os.path.join(
soma_workflow_dirpath,
SomaWorkflowEngine.open_me_by_soma_workflow_gui)
Helper.serialize(out_soma_workflow_file, soma_workflow)
os.chdir(cur_work_dir)
workflows.append(("multiple", simple_wf_examples.multiple_simple_example()))
workflows.append(("special_command", simple_wf_examples.special_command()))
workflows.append(("mutiple_transfer", tr_wf_examples.multiple_simple_example()))
workflows.append(("special_command_transfer", tr_wf_examples.special_command()))
workflows.append(("special_transfer", tr_wf_examples.special_transfer()))
workflows.append(("mutiple_crp", srp_wf_examples.multiple_simple_example()))
workflows.append(("special_command_crp", srp_wf_examples.special_command()))
ret_value = 0
for workflow_name, workflow in workflows:
print "--------------------------------------------------------------"
print workflow_name
file_path = os.path.join(directory, "json_" + workflow_name + ".wf")
Helper.serialize(file_path, workflow)
new_workflow = Helper.unserialize(file_path)
if not new_workflow.attributs_equal(workflow):
print "FAILED !!"
ret_value = 1
else:
print "OK"
try:
os.remove(file_path)
except IOError:
pass
if ret_value == 0:
