def get_report_api_wrapper():
global __api_wrapper, __report_config
if __api_wrapper is None:
__report_config_init()
__api_wrapper = APIWrapper(__report_config['domain'],
__report_config['containerPath'],
__report_config['contextPath'],
__report_config['useSsl'],
api_key=__api_key)
return __api_wrapper
def __init__(self):
with open("../config/keys.json", "r") as file:
config = json.load(file)
self.labkey_server = "https://immunespace.org"
self.project_name = "Studies" # Studies # container_path
self.context_path = "study" # study ?
self.api_key = config.get("apiKey", False)
if not self.api_key:
raise Exception
self.api = APIWrapper(self.labkey_server, self.project_name,
self.context_path, self.api_key)
def api(server_context_vars):
server, context_path = server_context_vars
api = APIWrapper(server, PROJECT_NAME, context_path, use_ssl=False)
api.security.stop_impersonating(
) # Call stop impersonating incase previous test run failed while impersonating a user.
return api
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
from labkey.api_wrapper import APIWrapper
from labkey.experiment import Batch, Run
labkey_server = "localhost:8080"
project_name = "ModulesAssayTest" # Project folder name
context_path = "labkey"
api = APIWrapper(labkey_server, project_name, context_path, use_ssl=False)
assay_id = 3315 # provide one from your server
###################
# Save an Assay batch
###################
# Generate the Run object(s)
run_test = Run()
run_test.name = "python upload"
run_test.data_rows = [
{
# ColumnName: Value
"SampleId": "Monkey 1",
"TimePoint": "2008/11/02 11:22:33",
from labkey.exceptions import (
RequestError,
QueryNotFoundError,
ServerContextError,
ServerNotFoundError,
)
from labkey.query import Pagination, QueryFilter
from requests.exceptions import Timeout
import copy
print("Create a server context")
labkey_server = "localhost:8080"
project_name = "ModuleAssayTest" # Project folder name
context_path = "labkey"
api = APIWrapper(labkey_server, project_name, context_path, use_ssl=False)
schema = "lists"
table = "Demographics"
column1 = "Group Assignment"
column2 = "Participant ID"
###################
# Test basic select_rows
###################
result = api.query.select_rows(schema, table)
if result is not None:
print(result["rows"][0])
print("select_rows: There are " + str(result["rowCount"]) + " rows.")
else:
import os
import subprocess
import argparse
import labkey as lk
import pandas as pd
from labkey.api_wrapper import APIWrapper
import glob as glob
key_file = '/global/cfs/cdirs/metatlas/labkey_user.txt'
with open(key_file,'r') as fid:
api_key = fid.read().strip()
labkey_server='metatlas.nersc.gov'
project_name='LIMS/'
api = APIWrapper(labkey_server, project_name, use_ssl=True,api_key=api_key)
def get_tasks_from_lims():
sql = """SELECT input_file,output_file FROM file_conversion_task WHERE task='raw_to_mzml';"""
# context_path = "labkey"
sql_result = api.query.execute_sql('lists', sql,max_rows=1e6)
if sql_result is None:
print(('execute_sql: Failed to load results from ' + schema + '.' + table))
return None
else:
df = pd.DataFrame(sql_result['rows'])
df = df[[c for c in df.columns if not c.startswith('_')]]
return df