def test_addToCollection(self):
db.create_collection('test.collection')
data = {'_id': '1234567890', 'content': 'testcontent'}
db.add_oneDictIntoCollection(data, 'test.collection')
db.get_db().drop_collection('test.collection')
db.add_oneDictIntoCollection(data, 'test.collection')
def createObjectReferencesRecursive(self, data):
if isinstance(data, dict):
aDict = data
new_dict = {}
if "_id" in data: # data is a DB Object: Store as data only as DBRef
# check data for more potential db_refs and remove them before this data dict is stored.
for k, v in data.items():
new_dict[k] = self.createObjectReferencesRecursive(v)
assert new_dict['_id'] is not None, "if objects _id is set it is not allowed to be None"
ref = DBRef(str(new_dict['caemlType'][0]), new_dict['_id'])
res = dereference(ref) # is referenced object already in the db?
if res is None:
add_oneDictIntoCollection(new_dict, ref.collection)
else:
replace_oneDictInCollection(new_dict, ref.collection)
return ref
else: # check nested dicts items for potentials DBRefs
for k, v in data.items():
new_dict[k] = self.createObjectReferencesRecursive(v)
return new_dict
elif isinstance(data, list): # check nested list items for potentials DBRefs
new_list = [self.createObjectReferencesRecursive(l) for l in data]
return new_list
else: # data is not a dict
return data
def test_oneDictByIdWithUnKnownCollection(self):
data = {'_id': '1234567890', 'content': 'testcontent'}
db.add_oneDictIntoCollection(data, 'test.collection')
aDict = db.get_dictById('1234567890')
self.assertIsNotNone(aDict)
self.assertEqual(data['_id'], aDict['_id'])
self.assertIsNone(
db.get_dictById('no.tool.will.ever.have.an.id.like.this'))
def test_replace(self):
data = {'_id': '1234567890', 'content': 'testcontent'}
db.add_oneDictIntoCollection(data, 'test.collection')
first_load = db.get_dictById(data['_id'])
data = {'_id': '1234567890', 'content': 'newtestcontent'}
db.replace_oneDictInCollection(data, 'test.collection')
second_load = db.get_dictById(data['_id'])
self.assertEqual(second_load['_id'], first_load['_id'])
self.assertEqual(first_load['content'], 'testcontent')
self.assertEqual(second_load['content'], 'newtestcontent')
def initCmdTool(self, path: str):
create_collection('caeml.common.tools')
try:
with open(path, 'r') as f:
data = yaml.load(f)
if not 'dockerImageId' in data:
data['baseCommand'] = \
os.path.abspath(os.path.join(os.path.dirname(path), data['baseCommand'].format(path)))
elif 'scriptPath' in data:
data['scriptPath'] = os.path.abspath(os.path.join(os.path.dirname(path), data['scriptPath']))
for k, v in data['inputParameters'].items():
v['caemlType'] = 'caeml.common.process.Parameter'
if 'inputBinding' in v:
v['inputBinding']['caemlType'] = "caeml.common.process.InputBinding"
if '[]' == v['parameterType'] or isinstance(v['parameterType'],
list): # TODO: allow typed list (eg int[])
v['parameterType'] = 'list'
if 'file' == v['parameterType']:
v['parameterType'] = 'caeml.files.file.File'
for k, v in data['outputParameters'].items():
v['caemlType'] = "caeml.common.process.Parameter"
if 'outputBinding' in v:
v['outputBinding']['caemlType'] = "caeml.common.process.OutputBinding"
if '[]' == v['parameterType'] or isinstance(v['parameterType'], list):
v['parameterType'] = 'list'
if 'file' == v['parameterType']:
v['parameterType'] = 'caeml.files.file.File'
if not 'name' in data:
raise LookupError("YAML file needs to specify tool name for tool at path: {}".format(path))
except Exception as e:
raise Exception("Error from Tool: {}: {}".format(path, str(e)))
loaded_data = get_dictByQuery({"name": data['name']}, 'caeml.common.tools')
if loaded_data is None:
data['_id'] = str(uuid.uuid4())
add_oneDictIntoCollection(data, 'caeml.common.tools')
else:
data['_id'] = loaded_data['_id']
replace_oneDictInCollection(data, 'caeml.common.tools')
if data['name'] in self.inserted_names:
logging.getLogger('init').warning(
"Tool with name: {} already exists in database and has been overwritten".format(data['name']))
self.inserted_names.append(data['name'])
pass
def test_dereference(self):
data = {'_id': '1234567890', 'content': 'testcontent'}
ref = DBRef('test.collection', '1234567890')
db.add_oneDictIntoCollection(data, 'test.collection')
self.assertEqual(data, db.dereference(ref))