def __init__(self,
executable=None,
input_name_prefix=None,
input_spec=None):
self.executable = executable
self._desc = {} if self.executable is None else executable.describe()
self.input_spec = collections.OrderedDict(
) if 'inputSpec' in self._desc or input_spec else None
self.required_inputs, self.optional_inputs, self.array_inputs = [], [], set(
)
self.input_name_prefix = input_name_prefix
if input_spec is None:
input_spec = self._desc.get('inputSpec', [])
for spec_atom in input_spec:
if spec_atom['class'].startswith('array:'):
self.array_inputs.add(spec_atom['name'])
self.input_spec[spec_atom['name']] = spec_atom
if "default" in spec_atom or spec_atom.get("optional") == True:
self.optional_inputs.append(spec_atom['name'])
else:
self.required_inputs.append(spec_atom['name'])
self.inputs = OrderedDefaultdict(list)
def __init__(self, executable=None, input_name_prefix=None):
self.executable = executable
self._desc = {} if self.executable is None else executable.describe()
self.input_spec = collections.OrderedDict() if 'inputSpec' in self._desc else None
self.required_inputs, self.optional_inputs, self.array_inputs = [], [], set()
self.input_name_prefix = input_name_prefix
for spec_atom in self._desc.get('inputSpec', []):
if spec_atom['class'].startswith('array:'):
self.array_inputs.add(spec_atom['name'])
self.input_spec[spec_atom['name']] = spec_atom
if "default" in spec_atom or spec_atom.get("optional") == True:
self.optional_inputs.append(spec_atom['name'])
else:
self.required_inputs.append(spec_atom['name'])
self.inputs = OrderedDefaultdict(list)
class ExecutableInputs(object):
def __init__(self, executable=None, input_name_prefix=None):
self.executable = executable
self._desc = {} if self.executable is None else executable.describe()
self.input_spec = collections.OrderedDict() if 'inputSpec' in self._desc else None
self.required_inputs, self.optional_inputs, self.array_inputs = [], [], set()
self.input_name_prefix = input_name_prefix
for spec_atom in self._desc.get('inputSpec', []):
if spec_atom['class'].startswith('array:'):
self.array_inputs.add(spec_atom['name'])
self.input_spec[spec_atom['name']] = spec_atom
if "default" in spec_atom or spec_atom.get("optional") == True:
self.optional_inputs.append(spec_atom['name'])
else:
self.required_inputs.append(spec_atom['name'])
self.inputs = OrderedDefaultdict(list)
def update(self, new_inputs, strip_prefix=True):
if strip_prefix and self.input_name_prefix is not None:
for i in new_inputs:
if i.startswith(self.input_name_prefix):
self.inputs[i[len(self.input_name_prefix):]] = new_inputs[i]
else:
self.inputs.update(new_inputs)
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):
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 init_completer(self):
try:
import readline
import rlcompleter
readline.parse_and_bind("tab: complete")
readline.set_completer_delims("")
readline.write_history_file(os.path.expanduser('~/.dnanexus_config/.dx_history'))
readline.clear_history()
readline.set_completer()
except:
pass
def uninit_completer(self):
try:
readline.set_completer()
readline.clear_history()
except:
pass
def prompt_for_missing(self):
# No-op if there is no input spec
if self.input_spec is None:
return
# If running from the command-line (not in the shell), bring up the tab-completer
self.init_completer()
# Select input interactively
no_prior_inputs = True if len(self.inputs) == 0 else False
for i in self.required_inputs:
if i not in self.inputs:
if len(self.inputs) == 0:
print 'Entering interactive mode for input selection.'
self.inputs[i] = self.prompt_for_input(i)
if no_prior_inputs and len(self.optional_inputs) > 0:
self.prompt_for_optional_inputs()
self.uninit_completer()
def prompt_for_input(self, input_name):
if input_name in self.array_inputs:
return get_input_array(self.input_spec[input_name])
else:
return get_input_single(self.input_spec[input_name])
def prompt_for_optional_inputs(self):
while True:
print '\n' + fill('Select an optional parameter to set by its # (^D or <ENTER> to finish):') + '\n'
for i in range(len(self.optional_inputs)):
opt_str = ' [' + str(i) + '] ' + \
get_optional_input_str(self.input_spec[self.optional_inputs[i]])
if self.optional_inputs[i] in self.inputs:
opt_str += ' [=' + GREEN()
opt_str += json.dumps(self.inputs[self.optional_inputs[i]])
opt_str += ENDC() + ']'
elif 'default' in self.input_spec[self.optional_inputs[i]]:
opt_str += ' [default=' + json.dumps(self.input_spec[self.optional_inputs[i]]['default']) + ']'
print opt_str
print ""
try:
while True:
selected = raw_input('Optional param #: ')
if selected == '':
return
try:
opt_num = int(selected)
if opt_num < 0 or opt_num >= len(self.optional_inputs):
raise ValueError('Error: Selection is out of range')
break
except ValueError as details:
print unicode(details)
continue
except EOFError:
return
try:
self.inputs[self.optional_inputs[opt_num]] = self.prompt_for_input(self.optional_inputs[opt_num])
except:
pass
def update_from_args(self, args):
if args.filename is not None:
try:
if args.filename == "-":
data = sys.stdin.read()
else:
with open(args.filename, 'r') as fd:
data = fd.read()
self.update(json.loads(data, object_pairs_hook=collections.OrderedDict))
except Exception as e:
raise Exception('Error while parsing input JSON file: %s' % unicode(e))
if args.input_json is not None:
try:
self.update(json.loads(args.input_json, object_pairs_hook=collections.OrderedDict))
except Exception as e:
raise Exception('Error while parsing input JSON: %s' % unicode(e))
if args.input is not None:
for keyeqval in args.input:
try:
first_eq_pos = get_first_pos_of_char('=', keyeqval)
if first_eq_pos == -1:
raise
name = split_unescaped('=', keyeqval)[0]
value = keyeqval[first_eq_pos + 1:]
except:
raise Exception('An input was found that did not conform to the syntax: -i<input name>=<input value>')
self.add(name, value)
if self.input_spec is None:
for i in self.inputs:
if type(self.inputs[i]) == list and len(self.inputs[i]) == 1:
self.inputs[i] = self.inputs[i][0]
if sys.stdout.isatty():
self.prompt_for_missing()
elif not all(i in self.inputs for i in self.required_inputs):
raise Exception('Some inputs are missing, and interactive mode is not available')
class ExecutableInputs(object):
def __init__(self,
executable=None,
input_name_prefix=None,
input_spec=None):
self.executable = executable
self._desc = {} if self.executable is None else executable.describe()
self.input_spec = collections.OrderedDict(
) if 'inputSpec' in self._desc or input_spec else None
self.required_inputs, self.optional_inputs, self.array_inputs = [], [], set(
)
self.input_name_prefix = input_name_prefix
if input_spec is None:
input_spec = self._desc.get('inputSpec', [])
for spec_atom in input_spec:
if spec_atom['class'].startswith('array:'):
self.array_inputs.add(spec_atom['name'])
self.input_spec[spec_atom['name']] = spec_atom
if "default" in spec_atom or spec_atom.get("optional") == True:
self.optional_inputs.append(spec_atom['name'])
else:
self.required_inputs.append(spec_atom['name'])
self.inputs = OrderedDefaultdict(list)
def update(self, new_inputs, strip_prefix=True):
if strip_prefix and self.input_name_prefix is not None:
for i in new_inputs:
if i.startswith(self.input_name_prefix):
self.inputs[
i[len(self.input_name_prefix):]] = new_inputs[i]
else:
self.inputs.update(new_inputs)
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
def init_completer(self):
try:
import readline
import rlcompleter
readline.parse_and_bind("tab: complete")
readline.set_completer_delims("")
readline.write_history_file(
os.path.expanduser('~/.dnanexus_config/.dx_history'))
readline.clear_history()
readline.set_completer()
except:
pass
def uninit_completer(self):
try:
readline.set_completer()
readline.clear_history()
except:
pass
def prompt_for_missing(self):
# No-op if there is no input spec
if self.input_spec is None:
return
# If running from the command-line (not in the shell), bring up the tab-completer
self.init_completer()
# Select input interactively
no_prior_inputs = True if len(self.inputs) == 0 else False
for i in self.required_inputs:
if i not in self.inputs:
if len(self.inputs) == 0:
print 'Entering interactive mode for input selection.'
self.inputs[i] = self.prompt_for_input(i)
if no_prior_inputs and len(self.optional_inputs) > 0:
self.prompt_for_optional_inputs()
self.uninit_completer()
def prompt_for_input(self, input_name):
if input_name in self.array_inputs:
return get_input_array(self.input_spec[input_name])
else:
return get_input_single(self.input_spec[input_name])
def prompt_for_optional_inputs(self):
while True:
print '\n' + fill(
'Select an optional parameter to set by its # (^D or <ENTER> to finish):'
) + '\n'
for i in range(len(self.optional_inputs)):
opt_str = ' [' + str(i) + '] ' + \
get_optional_input_str(self.input_spec[self.optional_inputs[i]])
if self.optional_inputs[i] in self.inputs:
opt_str += ' [=' + GREEN()
opt_str += json.dumps(self.inputs[self.optional_inputs[i]])
opt_str += ENDC() + ']'
elif 'default' in self.input_spec[self.optional_inputs[i]]:
opt_str += ' [default=' + json.dumps(self.input_spec[
self.optional_inputs[i]]['default']) + ']'
print opt_str
print ""
try:
while True:
selected = raw_input('Optional param #: ')
if selected == '':
return
try:
opt_num = int(selected)
if opt_num < 0 or opt_num >= len(self.optional_inputs):
raise ValueError(
'Error: Selection is out of range')
break
except ValueError as details:
print unicode(details)
continue
except EOFError:
return
try:
self.inputs[
self.optional_inputs[opt_num]] = self.prompt_for_input(
self.optional_inputs[opt_num])
except:
pass
def update_from_args(self, args):
if args.filename is not None:
try:
if args.filename == "-":
data = sys.stdin.read()
else:
with open(args.filename, 'r') as fd:
data = fd.read()
self.update(
json.loads(data,
object_pairs_hook=collections.OrderedDict))
except Exception as e:
raise Exception('Error while parsing input JSON file: %s' %
unicode(e))
if args.input_json is not None:
try:
self.update(
json.loads(args.input_json,
object_pairs_hook=collections.OrderedDict))
except Exception as e:
raise Exception('Error while parsing input JSON: %s' %
unicode(e))
if args.input is not None:
for keyeqval in args.input:
try:
first_eq_pos = get_first_pos_of_char('=', keyeqval)
if first_eq_pos == -1:
raise
name = split_unescaped('=', keyeqval)[0]
value = keyeqval[first_eq_pos + 1:]
except:
raise Exception(
'An input was found that did not conform to the syntax: -i<input name>=<input value>'
)
self.add(self.executable._get_input_name(name) if \
self._desc.get('class') == 'workflow' else name, value)
if self.input_spec is None:
for i in self.inputs:
if type(self.inputs[i]) == list and len(self.inputs[i]) == 1:
self.inputs[i] = self.inputs[i][0]
# For now, we do not handle prompting for workflow inputs nor
# recognizing when not all inputs haven't been bound
if sys.stdout.isatty() and self._desc.get('class') != 'workflow':
self.prompt_for_missing()
elif self._desc.get('class') != 'workflow':
missing_required_inputs = set(self.required_inputs) - set(
self.inputs.keys())
if missing_required_inputs:
raise Exception(
'Some inputs (%s) are missing, and interactive mode is not available'
% (', '.join(missing_required_inputs)))
