def add(self, input_name, input_value):
if self.input_name_prefix is not None:
if input_name.startswith(self.input_name_prefix):
input_name = input_name[len(self.input_name_prefix):]
else: # Skip inputs that don't start with prefix
return
if ':' in input_name:
input_class = input_name[input_name.find(':') + 1:]
input_name = input_name[:input_name.find(':')]
else:
input_class = None
if self.input_spec is not None:
if input_name not in self.input_spec:
raise Exception('Input field called ' + input_name + ' was not found in the input spec')
input_class = self.input_spec[input_name]['class']
if input_class is None:
done = False
try:
# Resolve "job-xxxx:output-name" syntax into a canonical job ref
job_id, field = split_unescaped(':', input_value)
if is_job_id(job_id) or is_localjob_id(job_id):
input_value = {"job": job_id, "field": field}
done = True
except:
pass
if not done:
try:
parsed_input_value = json.loads(input_value, object_pairs_hook=collections.OrderedDict)
if type(parsed_input_value) in (collections.OrderedDict, list, int, long, float):
input_value = parsed_input_value
else:
raise Exception()
except:
# Not recognized JSON (list or dict), so resolve it as a name
try:
project, folderpath, entity_result = resolve_existing_path(input_value,
expected='entity')
except:
# If not possible, then leave it as a string
project, folderpath, entity_result = None, None, None
if entity_result is not None:
if is_hashid(input_value):
input_value = {'$dnanexus_link': entity_result['id']}
else:
input_value = {"$dnanexus_link": {"project": entity_result['describe']['project'],
"id": entity_result['id']}}
self.inputs[input_name].append(input_value)
else:
# Input class is known. Respect the "array" class.
input_value = parse_input_or_jbor(input_class, input_value)
if input_class.startswith('array:'):
self.inputs[input_name].append(input_value)
else:
self.inputs[input_name] = input_value
def parse_obj(string, klass):
if string == '':
raise ValueError('Error: Nonempty string cannot be resolved')
project, path, entity_result = resolve_existing_path(string)
if entity_result is None:
raise TypeError('Could not resolve \"' + string + '\" to a name or ID')
if not entity_result['describe']['class'] == klass:
raise TypeError('Error: The given object is of class ' + entity_result['describe']['class'] + ' but an object of class ' + klass + ' was expected.')
if is_hashid(string):
return {'$dnanexus_link': entity_result['id']}
else:
return {'$dnanexus_link': {"project": entity_result['describe']['project'],
"id": entity_result['id']}}
def parse_obj(string, klass):
if string == '':
raise ValueError('Error: Nonempty string cannot be resolved')
project, path, entity_result = resolve_existing_path(string)
if entity_result is None:
raise TypeError('Could not resolve \"' + string + '\" to a name or ID')
if not entity_result['describe']['class'] == klass:
raise TypeError('Error: The given object is of class ' +
entity_result['describe']['class'] +
' but an object of class ' + klass + ' was expected.')
if is_hashid(string):
return {'$dnanexus_link': entity_result['id']}
else:
return {
'$dnanexus_link': {
"project": entity_result['describe']['project'],
"id": entity_result['id']
}
}
def add(self, input_name, input_value):
if self.input_name_prefix is not None:
if input_name.startswith(self.input_name_prefix):
input_name = input_name[len(self.input_name_prefix):]
else: # Skip inputs that don't start with prefix
return
if ':' in input_name:
input_class = input_name[input_name.find(':') + 1:]
input_name = input_name[:input_name.find(':')]
else:
input_class = None
if self.input_spec is not None:
if input_name not in self.input_spec and self._desc.get(
'class') != 'workflow':
raise Exception('Input field called ' + input_name +
' was not found in the input spec')
elif input_name in self.input_spec:
input_class = self.input_spec[input_name]['class']
if input_class is None:
done = False
try:
# Resolve "job-xxxx:output-name" syntax into a canonical job ref
job_id, field = split_unescaped(':', input_value)
if is_job_id(job_id) or is_localjob_id(job_id):
input_value = {"job": job_id, "field": field}
done = True
except:
pass
if not done:
try:
parsed_input_value = json.loads(
input_value, object_pairs_hook=collections.OrderedDict)
if type(parsed_input_value) in (collections.OrderedDict,
list, int, long, float):
input_value = parsed_input_value
else:
raise Exception()
except:
# Not recognized JSON (list or dict), so resolve it as a name
try:
project, folderpath, entity_result = resolve_existing_path(
input_value, expected='entity')
except:
# If not possible, then leave it as a string
project, folderpath, entity_result = None, None, None
if entity_result is not None:
if is_hashid(input_value):
input_value = {
'$dnanexus_link': entity_result['id']
}
else:
input_value = {
"$dnanexus_link": {
"project":
entity_result['describe']['project'],
"id": entity_result['id']
}
}
if isinstance(self.inputs[input_name], list) and \
not isinstance(self.inputs[input_name], basestring):
self.inputs[input_name].append(input_value)
else:
self.inputs[input_name] = input_value
else:
# Input class is known. Respect the "array" class.
input_value = parse_input_or_jbor(input_class, input_value)
if input_class.startswith('array:'):
self.inputs[input_name].append(input_value)
else:
self.inputs[input_name] = input_value
