def test_part_parameter_values():
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_auth.yml'))
part_id = 1
ice.set_part_custom_field(part_id, "TEST_PARAM", "TEST_VALUE")
assert ice.get_part_custom_field(part_id, "TEST_PARAM") == "TEST_VALUE"
parts = ice.find_parts_by_custom_field_value("TEST_PARAM", "TEST_VALUE")
assert len(parts) == 1
fields = ice.get_part_custom_fields_list(part_id)
assert len(fields) == 1
for field in fields:
response = ice.delete_custom_field(field['id'])
assert response.ok
def test_file_attachments():
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_auth.yml'))
record = load_record(os.path.join('tests', 'data', 'example_record.gb'))
part_id = 1
try:
ice.delete_part_record(part_id)
except:
pass
ice.attach_record_to_part(ice_part_id=part_id, record=record)
new_record = ice.get_record(part_id)
assert len(new_record) == 150
ice.delete_part_record(part_id)
def test_folder_methods():
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_token.yml'))
folders = ice.get_collection_folders('PERSONAL')
assert (len(folders) == 1) and (folders[0]['folderName'] == 'test_folder')
def test_search_methods():
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_auth.yml'))
test1_part, errors = ice.find_entry_by_name("Test1")
assert (errors is None)
assert test1_part["id"] == 1
def test_auth():
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_token.yml'))
assert (len(ice.get_collection_folders('PERSONAL')) > 0)
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_auth.yml'))
assert ice.session_infos['description'] == 'I am John'
import os
import time
import icebreaker
from icebreaker.tools import load_record
conf_folder = os.path.join('tests', 'configs')
ice_admin = icebreaker.IceClient(os.path.join(conf_folder, 'admin_auth.yml'))
result = ice_admin.rebuild_search_indexes()
assert result.ok
time.sleep(5)
def test_auth():
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_token.yml'))
assert (len(ice.get_collection_folders('PERSONAL')) > 0)
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_auth.yml'))
assert ice.session_infos['description'] == 'I am John'
def test_search_methods():
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_auth.yml'))
test1_part, errors = ice.find_entry_by_name("Test1")
assert (errors is None)
assert test1_part["id"] == 1
def test_folder_methods():
ice = icebreaker.IceClient(os.path.join(conf_folder, 'john_doe_token.yml'))
folders = ice.get_collection_folders('PERSONAL')
assert (len(folders) == 1) and (folders[0]['folderName'] == 'test_folder')
from Bio import SeqIO
import os
import pandas
import json
import icebreaker
new_ice = icebreaker.IceClient("../api_tokens/local_update.yaml")
new_ice_folders = new_ice.get_collection_folders("PERSONAL")
root_data_folder = "local_data"
collection_folders = os.listdir(root_data_folder)
for folder in collection_folders:
print("Processing folder", folder)
if folder not in new_ice_folders:
folder_infos = new_ice.create_folder(folder)
new_ice_folders.append(folder)
folder_id = folder_infos["id"]
else:
folder_id = new_ice.get_folder_id(folder)
data_folder = os.path.join(root_data_folder, folder, "data")
genbank_folder = os.path.join(root_data_folder, folder, "records")
parts_ids = []
for data_file in os.listdir(data_folder):
part_id = ".".join(data_file.split(".")[:-1])
print("... entry", part_id)
data_file_path = os.path.join(root_data_folder, folder, "data",
data_file)
with open(data_file_path, "r") as f:
part_infos = json.load(f)
genbank_file_path = os.path.join(root_data_folder, folder, "records",
from Bio import SeqIO
import os
import pandas
import json
import icebreaker
# LOAD ALL "SHARED" FOLDERS DATA ON YOUR COMPUTER
ice = icebreaker.IceClient("../api_tokens/admin.yaml")
folders = ice.get_collection_folders("SHARED")
# folders = folders[:4] # test with a small part
local_data_folder = "local_data"
os.mkdir(local_data_folder)
for folder in folders:
print("Processing folder", folder["folderName"])
local_folder_path = os.path.join(local_data_folder, folder["folderName"])
if not os.path.exists(local_folder_path):
os.mkdir(local_folder_path)
parts_in_folder = ice.get_folder_entries(folder_id=folder["id"])
genbanks_path = os.path.join(local_folder_path, "records")
if not os.path.exists(genbanks_path):
os.mkdir(genbanks_path)
parts_data_path = os.path.join(local_folder_path, "data")
if not os.path.exists(parts_data_path):
os.mkdir(parts_data_path)
parts_infos_list = []
for part in parts_in_folder:
print("... entry", part["name"])
part_infos = ice.get_part_infos(part["id"])
parts_infos_list.append(part_infos)