def add_job(self, job_dict):
assert (job_dict)
assert (job_dict["toolName"])
logger.debug(job_dict["toolName"])
template = CommandTemplate()
template.setup(self, job_dict)
template.parse_parameter_description()
self.job_dict = job_dict
if "toolId" not in job_dict:
raise InvalidRequestError("Submitted job %s lacks toolId" %
job_dict["toolName"])
self.tool = Tool.objects.get(id=job_dict["toolId"])
if not self.tool.enabled:
raise InvalidRequestError(
"Can't process workflow with disabled tool '%s'" %
self.tool.name)
if not self.tool.does_user_have_access_to(self.user):
raise InvalidRequestError(
"Can't process workflow with inaccessible tool '%s'" %
self.tool.name)
# lets work out the highest copy level supported by this tool and store it in job. This makes no account for the backends capabilities.
# that will be resolved later when the stagein is created during the walk
self.preferred_stagein_method = 'link' if self.tool.link_supported else 'lcopy' if self.tool.lcopy_supported else 'copy'
self.preferred_stageout_method = 'lcopy' if self.tool.lcopy_supported else 'copy' # stageouts should never be linked. Only local copy or remote copy
# cache job for later reference
self.command_template = template.serialise()
self.command = str(template) # text description of command
self.status = const.STATUS_PENDING
self.stageout = "%s%s/" % (
self.workflow.stageout, "%d - %s" %
(self.order + 1, self.tool.get_display_name()))
self.exec_backend = self.get_backend_uri(self.exec_credential)
self.fs_backend = self.get_backend_uri(self.fs_credential)
self.cpus = self.tool.cpus
self.walltime = self.tool.walltime
self.module = self.tool.module
self.queue = self.tool.queue
self.max_memory = self.tool.max_memory
self.job_type = self.tool.job_type
self.save()
def add_job(self, job_dict):
assert(job_dict)
assert(job_dict["toolName"])
logger.debug(job_dict["toolName"])
template = CommandTemplate()
template.setup(self, job_dict)
template.parse_parameter_description()
self.job_dict = job_dict
if "toolId" not in job_dict:
raise InvalidRequestError("Submitted job %s lacks toolId" % job_dict["toolName"])
self.tool = Tool.objects.get(id=job_dict["toolId"])
if not self.tool.enabled:
raise InvalidRequestError("Can't process workflow with disabled tool '%s'" % self.tool.name)
if not self.tool.does_user_have_access_to(self.user):
raise InvalidRequestError("Can't process workflow with inaccessible tool '%s'" % self.tool.name)
# lets work out the highest copy level supported by this tool and store it in job. This makes no account for the backends capabilities.
# that will be resolved later when the stagein is created during the walk
self.preferred_stagein_method = 'link' if self.tool.link_supported else 'lcopy' if self.tool.lcopy_supported else 'copy'
self.preferred_stageout_method = 'lcopy' if self.tool.lcopy_supported else 'copy' # stageouts should never be linked. Only local copy or remote copy
# cache job for later reference
self.command_template = template.serialise()
self.command = str(template) # text description of command
self.status = const.STATUS_PENDING
self.stageout = "%s%s/" % (self.workflow.stageout, "%d - %s" % (self.order + 1, self.tool.get_display_name()))
self.exec_backend = self.get_backend_uri(self.exec_credential)
self.fs_backend = self.get_backend_uri(self.fs_credential)
self.cpus = self.tool.cpus
self.walltime = self.tool.walltime
self.module = self.tool.module
self.queue = self.tool.queue
self.max_memory = self.tool.max_memory
self.job_type = self.tool.job_type
self.save()
class CommandLineTemplateTest(unittest.TestCase):
def setUp(self):
demo_user = m.User.objects.get(name='demo')
workflow = mommy.make('Workflow', user=demo_user)
self.job = mommy.make('Job', workflow=workflow, order=0)
self.td = mommy.make('ToolDesc', name='my-tool')
self.tool = mommy.make('Tool', desc=self.td, path='tool.sh')
combined_with_equals = ParameterSwitchUse.objects.get(
display_text='combined with equals')
value_only = ParameterSwitchUse.objects.get(display_text='valueOnly')
mommy.make('ToolParameter',
tool=self.td,
switch="-arg1",
switch_use=combined_with_equals,
rank=2)
mommy.make('ToolParameter',
tool=self.td,
switch="-arg2",
switch_use=value_only,
rank=1)
mommy.make('ToolParameter',
tool=self.td,
switch="-arg3",
switch_use=value_only,
file_assignment='batch')
self.template = CommandTemplate()
self.job_1_dict = {
"jobId": 1,
"toolName": "my-tool",
"toolId": self.tool.id,
"parameterList": {
"parameter": []
}
}
def tearDown(self):
self.job.workflow.delete()
self.td.delete()
def job_dict_with_params(self, *params):
import copy
d = copy.copy(self.job_1_dict)
if params:
d['parameterList']['parameter'] = params
return d
def render_command(self, job, job_dict, uri_conversion=None):
self.template.setup(job, job_dict)
self.template.parse_parameter_description()
if uri_conversion is not None:
self.template.set_uri_conversion(uri_conversion)
return self.template.render()
def test_no_params(self):
job_dict = self.job_1_dict
command = self.render_command(self.job, job_dict)
self.assertEquals("tool.sh", command)
def test_param_combined_with_equals(self):
job_dict = self.job_dict_with_params({
'switchName': '-arg1',
'valid': True,
'value': ['value']
})
command = self.render_command(self.job, job_dict)
self.assertEquals('tool.sh -arg1=value', command)
def test_param_value_only(self):
job_dict = self.job_dict_with_params({
'switchName': '-arg2',
'valid': True,
'value': ['a value']
})
command = self.render_command(self.job, job_dict)
self.assertEquals("tool.sh 'a value'", command)
def test_rank_respected(self):
job_dict = self.job_dict_with_params(
{
'switchName': '-arg1',
'valid': True,
'value': ['value']
}, {
'switchName': '-arg2',
'valid': True,
'value': ['other value']
})
command = self.render_command(self.job, job_dict)
self.assertEquals("tool.sh 'other value' -arg1=value", command)
def test_direct_file_reference(self):
job_dict = self.job_dict_with_params({
'switchName':
'-arg3',
'valid':
True,
'value': [{
'path': ['some', 'path'],
'root': 'sftp://demo@localhost:22/',
'type': 'file',
'filename': 'a file.txt'
}]
})
command = self.render_command(
self.job,
job_dict,
uri_conversion='/tools/workdir/input/%(filename)s')
self.assertEquals("tool.sh '/tools/workdir/input/a file.txt'", command)
