from labkey.utils import create_server_context
from labkey.query import select_rows, QueryFilter
print("Create a server context")
server_context = create_server_context('idri.labkey.com', 'Formulations')
ssr = select_rows(server_context, 'Samples', 'Formulations')
print("select_rows: There are " + str(len(ssr['rows'])) + " rows.")
ssr = select_rows(server_context, 'Samples', 'Formulations', filter_array=[
QueryFilter('Batch', 'QF', filter_type=QueryFilter.Types.CONTAINS)
])
print("select_rows: There are " + str(len(ssr['rows'])) + " filtered rows.")
# validate call is made as expected
expected_args = expected_kwargs.pop('expected_args')
mock_post.assert_called_once_with(*expected_args, **expected_kwargs)
configs = {
'protocol': 'https://'
, 'server': 'my_testServer:8080'
, 'context_path': 'testPath'
, 'project_path': 'testProject/subfolder'
}
schema = 'testSchema'
query = 'testQuery'
server_context = create_server_context(configs['server'], configs['project_path'], configs['context_path'])
class TestDeleteRows(unittest.TestCase):
def setUp(self):
self.configs = configs.copy()
self.service = MockDeleteRows(**self.configs)
self.expected_kwargs = {
'expected_args': [self.service.get_server_url()]
, 'data': '{"queryName": "' + query + '", "rows": "{id:1234}", "schemaName": "' + schema + '"}'
, 'headers': {u'Content-Type': u'application/json'}
, 'timeout': 30
}
rows = '{id:1234}'
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# 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.
#
# Sample to get a batch
from labkey.utils import create_server_context
from labkey.experiment import load_batch
print("Create a server context")
project_name = 'ModuleAssayTest' # Project folder name
server_context = create_server_context('localhost:8080', project_name, 'labkey', use_ssl=False)
print("Load an Assay batch from the server")
assay_id = 2809 # provide one from your server
batch_id = 120 # provide one from your server
run_group = load_batch(server_context, assay_id, batch_id)
if run_group is not None:
print("Batch Id: " + str(run_group.id))
print("Created By: " + run_group.created_by)
from __future__ import unicode_literals
from labkey.utils import create_server_context
from labkey.exceptions import RequestError, QueryNotFoundError, ServerContextError, ServerNotFoundError
from labkey.query import select_rows, update_rows, Pagination, QueryFilter, \
insert_rows, delete_rows, execute_sql
from requests.exceptions import Timeout
import copy
print("Create a server context")
labkey_server = 'localhost:8080'
project_name = 'moduleAssayTest' # Project folder name
contextPath = 'labkey'
server_context = create_server_context(labkey_server, project_name, contextPath, use_ssl=False)
schema = 'lists'
table = 'Demographics'
column1 = 'Group Assignment'
column2 = 'Participant ID'
###################
# Test basic select_rows
###################
result = select_rows(server_context, schema, table)
if result is not None:
print(result['rows'][0])
print("select_rows: There are " + str(result['rowCount']) + " rows.")
else:
from __future__ import unicode_literals
from labkey.utils import create_server_context
from labkey.exceptions import RequestError, QueryNotFoundError, ServerContextError, ServerNotFoundError
from labkey.query import select_rows, update_rows, Pagination, QueryFilter, \
insert_rows, delete_rows, truncate_table, execute_sql
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'
server_context = create_server_context(labkey_server,
project_name,
context_path,
use_ssl=False)
schema = 'lists'
table = 'Demographics'
column1 = 'Group Assignment'
column2 = 'Participant ID'
###################
# Test basic select_rows
###################
result = select_rows(server_context, schema, table)
if result is not None:
print(result['rows'][0])
print("select_rows: There are " + str(result['rowCount']) + " rows.")
else:
"""
Examples using the Experiment.py API
Sample code to submit a single batch of Assay data containing a run with three rows of data
"""
from labkey.utils import create_server_context
from labkey.experiment import save_batch, Batch, Run
assay_id = 2809 # provide one from your server. rowid from the URL query parameters
print("Create a server context")
project_name = 'ModuleAssayTest'
server_context = create_server_context('localhost:8080',
project_name,
'labkey',
use_ssl=False)
# Run data rows
dataRows = [
{
# ColumnName : Value
"SampleId": "Monkey 1",
"TimePoint": "2008/11/02 11:22:33",
"DoubleData": 4.5,
"HiddenData": "another data point"
},
{
"SampleId": "Monkey 2",
"TimePoint": "2008/11/02 14:00:01",
"DoubleData": 3.1,
context = SSL.Context(SSL.SSLv23_METHOD)
# Get REDCap params from config file
rc_api_url = config.rcparams['rc_api_url']
rc_base_url = config.rcparams['rc_base_url']
rc_refer_pid = config.rcparams['ndd_rc_refer_pid']
rc_refer_apikey = config.rcparams['ndd_rc_refer_apikey']
rc_data_pid = config.rcparams['ndd_rc_data_pid']
rc_data_apikey = config.rcparams['ndd_rc_data_apikey']
rc_sample_pid = config.rcparams['ndd_rc_sample_pid']
rc_sample_apikey = config.rcparams['ndd_rc_sample_apikey']
# Initialize LK properties from config file and create server context where queries will be executed
labkey_server = config.lkparams['labkey_server']
project_name = config.lkparams['project_name']
context_path = config.lkparams['context_path']
use_ssl = config.lkparams['use_ssl']
server_context = create_server_context(labkey_server, project_name, context_path, use_ssl)
app = Flask(__name__)
app.config['SERVER_NAME']=config.flaskparams['servname']
app.config['PREFERRRED_URL_SCHEME']='https'
cors = CORS(app, resources={r'/*': {'origins': originspermitted}})
# Pull RedCap metadata that will be used in various routes
dd_refer = NDDdb.getMetaData(rc_api_url, rc_refer_apikey, 'family_members')
dd_data = NDDdb.getMetaData(rc_api_url, rc_data_apikey, 'family_members')
dd_refer.set_index(keys='field_name', drop = False, inplace = True, verify_integrity = True)
dd_data.set_index(keys='field_name', drop = False, inplace = True, verify_integrity = True)
# Relation map for LabKey updates
reln_map = NDDdb.parseChoiceMap(dd_data.loc['demo_relation','select_choices_or_calculations'], CHOICEPATTERN, ALTPATTERN)
