#
# # did validate
# else:
# # inform the user of the success
# print('Validation of ' + object_id + ' succeeded.')
#
# # post the new object(s). SHOULD HANDLE ERRORS GRACEFULLY
# response = new_ENCODE(object_collection,new_object)
# if object is not found, verify and post it
if (old_object.get(u'title') == u'Not Found') | (old_object.get(u'title') == u'Home'):
# clean object of unpatchable or nonexistent properties. SHOULD INFORM USER OF ANYTHING THAT DOESN"T GET POSTED.
new_object = CleanJSON(new_object,object_schema,'POST')
new_object = FlatJSON(new_object,keys)
print(new_object)
# test the new object
if ValidJSON(object_type,object_id,new_object,keys):
# post the new object(s). SHOULD HANDLE ERRORS GRACEFULLY
new_object = CleanJSON(new_object,object_schema,'POST')
response = new_ENCODE(object_type,new_object,keys)
object_check = GetENCODE(str(response[u'@graph'][0][u'@id']),keys)
print(object_check[u'@id'], object_check[u'uuid'])
# if object is found, check for differences and patch it if needed/valid.
elif put_status:
# clean object of unpatchable or nonexistent properties. SHOULD INFORM USER OF ANYTHING THAT DOESN"T GET PUT.
new_object = CleanJSON(new_object,object_schema,'POST')
email = "*****@*****.**" # Stanford accounts won't work!
password = "******"
spreadname = 'Import Test Sheet'
rowsize = 2
colsize = 52
# load object SHOULD HANDLE ERRORS GRACEFULLY
print('Opening ' + data_file)
object_list = ReadJSON(data_file)
# find out what types of objects you have. use as worksheet names.
# also, change all json object values to strings
typelist = []
for json_object in object_list:
json_object = FlatJSON(json_object, keys)
typetemp = str(json_object['@type'][0])
typelist.append(typetemp)
for name, value in json_object.items():
if type(value) is list:
if value == []:
json_object[name] = ''
elif type(value[0]) is dict:
json_object[name] = str(value)
else:
json_object[name] = ', '.join(value)
elif (type(value) is int) | (type(value) is float):
json_object[name] = str(value)
typelist = list(set(typelist))
typelist.sort()
#if '.json' in object_filename:
# load object SHOULD HANDLE ERRORS GRACEFULLY
print('Opening ' + data_file)
json_object = ReadJSON('objects/' + data_file)
# if the returned json object is not a list, put it in one
if type(json_object) is dict:
object_list = []
object_list.append(json_object)
elif type(json_object) is list:
object_list = json_object
for new_object in object_list:
new_object = FlatJSON(new_object,keys)
# define object parameters. NEEDS TO RUN A CHECK TO CONFIRM THESE EXIST FIRST.
object_type = str(new_object[u'@type'][0])
object_id = str(new_object[u'@id'])
object_uuid = str(new_object[u'uuid'])
object_name = str(new_object[u'accession'])
# check to see if object already exists
# PROBLEM: SHOULD CHECK UUID AND NOT USE ANY SHORTCUT METADATA THAT MIGHT NEED TO CHANGE
# BUT CAN'T USE UUID IF NEW... HENCE PROBLEM
old_object = FlatJSON(get_ENCODE(object_id,keys),keys)
# # test the validity of new object
# if not ValidJSON(object_type,object_id,new_object):
# # get relevant schema
#if '.json' in object_filename:
# load object SHOULD HANDLE ERRORS GRACEFULLY
print('Opening ' + data_file)
json_object = ReadJSON('objects/' + data_file)
# if the returned json object is not a list, put it in one
if type(json_object) is dict:
object_list = []
object_list.append(json_object)
elif type(json_object) is list:
object_list = json_object
for new_object in object_list:
new_object = FlatJSON(new_object, keys)
# define object parameters. NEEDS TO RUN A CHECK TO CONFIRM THESE EXIST FIRST.
object_type = str(new_object[u'@type'][0])
object_id = str(new_object[u'@id'])
object_uuid = str(new_object[u'uuid'])
object_name = str(new_object[u'accession'])
# check to see if object already exists
# PROBLEM: SHOULD CHECK UUID AND NOT USE ANY SHORTCUT METADATA THAT MIGHT NEED TO CHANGE
# BUT CAN'T USE UUID IF NEW... HENCE PROBLEM
old_object = FlatJSON(get_ENCODE(object_id, keys), keys)
# # test the validity of new object
# if not ValidJSON(object_type,object_id,new_object):
# # get relevant schema
# search criteria
search_value_string = 'GM12893'
search_key_string = 'biosample_term_name'
# file name for saved objects
find_file = 'find.json'
# retrieve the relevant objects
master_objects = ElasticSearchJSON(server,query,object_type,hitnum)
# flatten objects and select based on search criteria
object_list = []
for master_object in master_objects:
master_object = FlatJSON(master_object,keys)
for key,value in master_object.items():
if search_key_string in str(key):
#print(key)
if type(value) is unicode:
if search_value_string in str(value):
print('Object ' + master_object[u'accession'] + ' Selected. ' + str(key) + ' - ' + value)
object_list.append(master_object)
break
if type(value) is list:
for entry in value:
if search_value_string in str(entry):
print('Object ' + master_object[u'accession'] + ' Selected. ' + str(key) + ' - ' + entry)
object_list.append(master_object)
break
email = "*****@*****.**" # Stanford accounts won't work!
password = "******"
spreadname = 'Import Test Sheet'
rowsize = 2
colsize = 52
# load object SHOULD HANDLE ERRORS GRACEFULLY
print('Opening ' + data_file)
object_list = ReadJSON(data_file)
# find out what types of objects you have. use as worksheet names.
# also, change all json object values to strings
typelist = []
for json_object in object_list:
json_object = FlatJSON(json_object,keys)
typetemp = str(json_object['@type'][0])
typelist.append(typetemp)
for name,value in json_object.items():
if type(value) is list:
if value == []:
json_object[name] = ''
elif type(value[0]) is dict:
json_object[name] = str(value)
else:
json_object[name] = ', '.join(value)
elif (type(value) is int) | (type(value) is float):
json_object[name] = str(value)
typelist = list(set(typelist))
typelist.sort()
