def load_batch(server_context, assay_id, batch_id):
"""
Loads a batch from the server.
:param server_context: A LabKey server context. See utils.create_server_context.
:param assay_id: The protocol id of the assay from which to load a batch.
:param batch_id:
:return:
"""
load_batch_url = build_url(server_context, 'assay', 'getAssayBatch.api')
session = server_context['session']
loaded_batch = None
payload = {'assayId': assay_id, 'batchId': batch_id}
headers = {'Content-type': 'application/json', 'Accept': 'text/plain'}
try:
response = session.post(load_batch_url,
data=json.dumps(payload, sort_keys=True),
headers=headers)
json_body = handle_response(response)
if json_body is not None:
loaded_batch = Batch.from_data(json_body['batch'])
except SSLError as e:
raise ServerContextError(e)
return loaded_batch
def load_batch(server_context, assay_id, batch_id):
"""
Loads a batch from the server.
:param server_context: A LabKey server context. See utils.create_server_context.
:param assay_id: The protocol id of the assay from which to load a batch.
:param batch_id:
:return:
"""
load_batch_url = build_url(server_context, 'assay', 'getAssayBatch.api')
session = server_context['session']
loaded_batch = None
payload = {
'assayId': assay_id,
'batchId': batch_id
}
headers = {
'Content-type': 'application/json',
'Accept': 'text/plain'
}
try:
response = session.post(load_batch_url, data=json.dumps(payload, sort_keys=True), headers=headers)
json_body = handle_response(response)
if json_body is not None:
loaded_batch = Batch.from_data(json_body['batch'])
except SSLError as e:
raise ServerContextError(e)
return loaded_batch
def _make_request(server_context, url, payload, headers=None, timeout=_default_timeout):
try:
session = server_context['session']
raw_response = session.post(url, data=payload, headers=headers, timeout=timeout)
return handle_response(raw_response)
except SSLError as e:
raise ServerContextError(e)
def _make_request(server_context,
url,
payload,
headers=None,
timeout=_default_timeout):
try:
session = server_context['session']
raw_response = session.post(url,
data=payload,
headers=headers,
timeout=timeout)
return handle_response(raw_response)
except SSLError as e:
raise ServerContextError(e)
def save_batches(server_context, assay_id, batches):
"""
Saves a modified batches.
:param server_context: A LabKey server context. See utils.create_server_context.
:param assay_id: The assay protocol id.
:param batches: The Batch(es) to save.
:return:
"""
save_batch_url = build_url(server_context, 'assay', 'saveAssayBatch.api')
session = server_context['session']
json_batches = []
if batches is None:
return None # Nothing to save
for batch in batches:
if isinstance(batch, Batch):
json_batches.append(batch.to_json())
else:
raise Exception('save_batch() "batches" expected to be a set Batch instances')
payload = {
'assayId': assay_id,
'batches': json_batches
}
headers = {
'Content-type': 'application/json',
'Accept': 'text/plain'
}
try:
# print(payload)
response = session.post(save_batch_url, data=json.dumps(payload, sort_keys=True), headers=headers)
json_body = handle_response(response)
if json_body is not None:
resp_batches = json_body['batches']
return [Batch.from_data(resp_batch) for resp_batch in resp_batches]
except SSLError as e:
raise ServerContextError(e)
return None
def save_batches(server_context, assay_id, batches):
"""
Saves a modified batches.
:param server_context: A LabKey server context. See utils.create_server_context.
:param assay_id: The assay protocol id.
:param batches: The Batch(es) to save.
:return:
"""
save_batch_url = build_url(server_context, 'assay', 'saveAssayBatch.api')
session = server_context['session']
json_batches = []
if batches is None:
return None # Nothing to save
for batch in batches:
if isinstance(batch, Batch):
json_batches.append(batch.to_json())
else:
raise Exception(
'save_batch() "batches" expected to be a set Batch instances')
payload = {'assayId': assay_id, 'batches': json_batches}
headers = {'Content-type': 'application/json', 'Accept': 'text/plain'}
try:
# print(payload)
response = session.post(save_batch_url,
data=json.dumps(payload, sort_keys=True),
headers=headers)
json_body = handle_response(response)
if json_body is not None:
resp_batches = json_body['batches']
return [Batch.from_data(resp_batch) for resp_batch in resp_batches]
except SSLError as e:
raise ServerContextError(e)
return None
def update_wiki(server_context, wiki_name, wiki_body, container_path=None):
"""
Used to update an existing wiki page
:param server_context: A LabKey server context. See labkey.utils.create_server_context.
:param wiki_name: The name of the wiki.
:param wiki_body: The body of the wiki.
:param container_path: Optional container path that can be used to override the server_context container path
:return: returns a dictionary containing the response from the server. The 'success' key
in the dictionary will be true when the wiki was successfully updated. It will be false
in the case of a failure. In the case of a failure, the 'error' key contains the error
message returned by the server.
"""
# Build the URL for reading the wiki page
read_wiki_url = build_url(server_context,
'wiki',
'editWiki.api',
container_path=container_path)
payload = {'name': wiki_name}
headers = {'Content-type': 'application/json'}
session = server_context['session']
try:
read_response = session.get(read_wiki_url,
params=payload,
headers=headers)
except SSLError as e:
print(
"There was a problem while attempting to submit the read for the wiki page "
+ str(wiki_name) + " via the URL " + str(e.geturl()) +
". The HTTP response code was " + str(e.getcode()))
print("The HTTP client error was: " + format(e))
return 1 # TODO: this is incorrect, should return 'success'/'error' properly like the docs say
data = read_response.text
# Search HTML response for required information on wiki. This is stored in the javascript
# variable named
# - _wikiProps: for 14.3 and earlier
# - LABKEY._wiki.setProps for 15.1 and later
data_list = data.split('\n')
# If LabKey Server is v14.3 or earlier find line containing '_wikiProp'
v = next((i for i in range(len(data_list)) if '_wikiProp' in data_list[i]),
None)
# If v = None, then server is running 15.1 or later and find the line
# containing 'LABKEY._wiki.setProps'
if v is None:
v = next((i for i in range(len(data_list))
if 'LABKEY._wiki.setProps' in data_list[i]), None)
# Verify that we found the variable in the HTML response. If not
# do not proceed
if v is None:
print(
"There was a problem while attempting to read the data for the wiki page '"
+ str(wiki_name) + "'.")
print(
"The script is unable to find the wiki properties in the HTML response"
)
return 1 # TODO: this is incorrect, should return 'success'/'error' properly like the docs say
wiki_vars = {}
for j in range(100):
# Read each line, until find a javascript closing bracket.
if '};' in data_list[v + j + 1]:
break
if '});' in data_list[v + j + 1]:
break
wvar = data_list[v + j + 1].rstrip().lstrip().replace('\'',
'').replace(
',', '')
wiki_vars[wvar.split(':')[0]] = wvar.split(':')[1]
# Build the URL for updating the wiki page
update_wiki_url = build_url(server_context,
'wiki',
'saveWiki.api',
container_path=container_path)
headers = {'Content-type': 'application/json'}
# Update wiki_vars to use the new wiki content.
wiki_vars['name'] = wiki_name
wiki_vars['body'] = wiki_body
try:
response = session.post(update_wiki_url,
data=json.dumps(wiki_vars, sort_keys=True),
headers=headers)
data = handle_response(response)
except SSLError as e:
print(
"There was a problem while attempting to submit the read for the wiki page '"
+ str(wiki_name) + "' via the URL " + str(e.geturl()) +
". The HTTP response code was " + str(e.getcode()))
print("The HTTP client error was: " + format(e))
return 1 # TODO: this is incorrect, should return 'success'/'error' properly like the docs say
return data
