def submit(self, allow_invalid=False):
self.db_desc = Descriptor()
self.db_desc.is_public = self.is_public
self.db_desc.user_id = self.user
file = create_temporary_file(self.container.get_data())
if (isinstance(self.container, DescriptorDataCandidateURLContainer)):
self.db_desc.data_url = self.container.get_url()
self.db_desc.automatic_updating = self.automatic_updating
else:
self.db_desc.data_url = ""
filename = uuid.uuid4().hex
self.db_desc.data_file.save(filename,
ContentFile(self.container.get_data()))
self.db_desc.md5 = calculate_MD5(self.container.get_data())
if (self.carmin_platform):
self.db_desc.carmin_platform = self.carmin_platform
# Validation
try:
bosh.validate(file.name)
self.validated = True
except Exception as exc:
self.validated = False
file.close()
if (not allow_invalid):
# An invalid descriptor is allowed on submission only if the 'allow_invalid' argument is set
return False
# Add error message to desc
self.db_desc.execution_status = EXECUTION_STATUS_ERROR
self.db_desc.error_message = str(exc).replace('\n', '<br>')
self.db_desc.last_updated = datetime.date.today()
self.db_desc.save()
return True
self.db_desc.execution_status = EXECUTION_STATUS_UNCHECKED
desc_JSON = json.loads(file.read())
self.db_desc.tool_name = desc_JSON["name"]
self.db_desc.version = desc_JSON["tool-version"]
self.db_desc.last_updated = datetime.date.today()
self.db_desc.save()
# Generate all the test profiles.
desc_entry = DescriptorEntry(self.db_desc)
desc_entry.generate_tests()
return True
def _get_valid_descriptor_count(self, raw_descriptors):
count = 0
for raw_descriptor in raw_descriptors:
descriptor_file = create_temporary_file(raw_descriptor)
try:
bosh.validate(descriptor_file.name)
count += 1
descriptor_file.close()
except:
descriptor_file.close()
return count
def function(descriptor):
'''
Returns a function to invoke bosh.execute on a descriptor.
args:
descriptor: Zenodo id, file name, or JSON string representing a
descriptor.
name: name of the function to create. Defaults to the tool name in the
descriptor.
'''
validate(descriptor)
descriptor_json = loadJson(descriptor)
def f(*args, **kwargs):
# Set default mode to 'launch'
if len(args) > 0:
mode = args[0]
else:
mode = 'launch'
if mode not in ['launch', 'simulate']:
mode = 'launch'
else:
args = args[1:]
# Call bosh execute
if mode == 'launch':
return execute(mode, descriptor, json.dumps(kwargs), *args)
if len(kwargs) > 0:
return execute(mode, descriptor, '-i', json.dumps(kwargs), *args)
return execute(mode, descriptor, *args)
f.__name__ = str(descriptor_json['name'])
# Documentation
doc = []
doc.append(r'''Runs {0} through its Boutiques interface.
*args:
- mode: 'launch' or 'simulate'. Defaults to 'launch'.
- other arguments: will be passed to bosh execute. Examples: '-s',
'-x'. See help(bosh.execute) for a complete list.
*kwargs:
{1} arguments as defined in the Boutiques descriptor, referenced
from input ids. Example: {2}='some_value'. See complete
list in descriptor help below.
'''.format(f.__name__, f.__name__, descriptor_json['inputs'][0]['id']))
doc.append(pprint(descriptor))
f.__doc__ = ''.join(doc)
return f
def validate(self):
# This is here in case we have a URL container
if (self.container.is_medium_erroneous()):
self.validated = False
self.message = self.container.get_error()
return False
else:
desc_content = self.container.get_data()
# Call bosh validate on the data
file = create_temporary_file(desc_content)
#backedup = sys.tracebacklimit
#sys.tracebacklimit = None
try:
bosh.validate(file.name)
self.validated = True
except Exception as exc:
self.validated = False
error = str(exc).replace('\n', '<br>')
#sys.tracebacklimit = backedup
if (self.validated == True):
desc = json.loads(file.read())
if (desc.get("tests") == None):
n_tests = 0
else:
n_tests = len(desc["tests"])
self.message = "Associated descriptor is valid.<br><b>" + str(
n_tests) + "</b> tests found defined inside descriptor."
else:
self.message = "<b> Validation failure.<br>Boutiques returned the following error(s):</b><br>" + error
file.close()
return self.validated
def test_demo_descriptor_valid(self):
self.assertFalse(boutiques.validate(self.get_json_descriptor(),"-b"))
def test_pythoninterface_validate(self):
fil = op.join(op.split(bfile)[0], 'schema/examples/good.json')
self.assertIsNone(boutiques.validate(fil))