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Merged
merged 1 commit into from
Apr 18, 2017
Merged

ServerContext, CSRF #8

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68 changes: 10 additions & 58 deletions labkey/experiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,40 +16,6 @@
from __future__ import unicode_literals
import json

from requests.exceptions import SSLError, ConnectionError
from labkey.utils import build_url, handle_response
from labkey.exceptions import ServerContextError, ServerNotFoundError


# EXAMPLE
# -------

# from utils import create_server_context
# from experiment import load_batch, save_batch
#
# print("Create a server context")
# server_context = create_server_context('localhost:8080', 'CDSTest Project', 'labkey', use_ssl=False)
#
# print("Load an Assay batch from the server")
# assay_id = # provide one from your server
# batch_id = # 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)
#
# print("Modify a property")
# batch_property_name = '' # provide one from your assay
# batch_property_value = '' # provide one
# run_group.properties[batch_property_name] = batch_property_value
#
# print("Save the batch")
# save_batch(server_context, assay_id, run_group)

# --------
# /EXAMPLE


# TODO Incorporate logging
def load_batch(server_context, assay_id, batch_id):
Expand All @@ -60,8 +26,7 @@ def load_batch(server_context, assay_id, batch_id):
:param batch_id:
:return:
"""
load_batch_url = build_url(server_context, 'assay', 'getAssayBatch.api')
session = server_context['session']
load_batch_url = server_context.build_url('assay', 'getAssayBatch.api')
loaded_batch = None

payload = {
Expand All @@ -74,15 +39,9 @@ def load_batch(server_context, assay_id, batch_id):
'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)
except ConnectionError as e:
raise ServerNotFoundError(e)
json_body = server_context.make_request(load_batch_url, json.dumps(payload, sort_keys=True), headers=headers)
if json_body is not None:
loaded_batch = Batch.from_data(json_body['batch'])

return loaded_batch

Expand Down Expand Up @@ -110,11 +69,9 @@ def save_batches(server_context, assay_id, batches):
:param batches: The Batch(es) to save.
:return:
"""

save_batch_url = build_url(server_context, 'assay', 'saveAssayBatch.api')
session = server_context['session']

save_batch_url = server_context.build_url('assay', 'saveAssayBatch.api')
json_batches = []

if batches is None:
return None # Nothing to save

Expand All @@ -133,15 +90,10 @@ def save_batches(server_context, assay_id, batches):
'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)
json_body = server_context.make_request(save_batch_url, json.dumps(payload, sort_keys=True), headers=headers)
if json_body is not None:
resp_batches = json_body['batches']
return [Batch.from_data(resp_batch) for resp_batch in resp_batches]

return None

Expand Down
31 changes: 12 additions & 19 deletions labkey/query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,9 +47,6 @@
from __future__ import unicode_literals
import json

from labkey.utils import build_url, make_request


_query_headers = {
'Content-Type': 'application/json'
}
Expand Down Expand Up @@ -79,17 +76,15 @@ def delete_rows(server_context, schema_name, query_name, rows, container_path=No
:param timeout: timeout of request in seconds (defaults to 30s)
:return:
"""
url = build_url(server_context, 'query', 'deleteRows.api', container_path=container_path)
url = server_context.build_url('query', 'deleteRows.api', container_path=container_path)

payload = {
'schemaName': schema_name,
'queryName': query_name,
'rows': rows
}

# explicit json payload and headers required for form generation
return make_request(server_context, url, json.dumps(payload, sort_keys=True), headers=_query_headers,
timeout=timeout)
return server_context.make_request(url, json.dumps(payload, sort_keys=True), headers=_query_headers, timeout=timeout)


def execute_sql(server_context, schema_name, sql, container_path=None,
Expand Down Expand Up @@ -119,7 +114,7 @@ def execute_sql(server_context, schema_name, sql, container_path=None,
:param timeout: timeout of request in seconds (defaults to 30s)
:return:
"""
url = build_url(server_context, 'query', 'executeSql.api', container_path=container_path)
url = server_context.build_url('query', 'executeSql.api', container_path=container_path)

payload = {
'schemaName': schema_name,
Expand Down Expand Up @@ -148,7 +143,7 @@ def execute_sql(server_context, schema_name, sql, container_path=None,
if required_version is not None:
payload['apiVersion'] = required_version

return make_request(server_context, url, payload, timeout=timeout)
return server_context.make_request(url, payload, timeout=timeout)


def insert_rows(server_context, schema_name, query_name, rows, container_path=None, timeout=_default_timeout):
Expand All @@ -162,17 +157,16 @@ def insert_rows(server_context, schema_name, query_name, rows, container_path=No
:param timeout: timeout of request in seconds (defaults to 30s)
:return:
"""
url = build_url(server_context, 'query', 'insertRows.api', container_path=container_path)
url = server_context.build_url('query', 'insertRows.api', container_path=container_path)

payload = {
'schemaName': schema_name,
'queryName': query_name,
'rows': rows
}

# explicit json payload and headers required for form generation
return make_request(server_context, url, json.dumps(payload, sort_keys=True), headers=_query_headers,
timeout=timeout)
return server_context.make_request(url, json.dumps(payload, sort_keys=True), headers=_query_headers,
timeout=timeout)


def select_rows(server_context, schema_name, query_name, view_name=None,
Expand Down Expand Up @@ -216,7 +210,7 @@ def select_rows(server_context, schema_name, query_name, view_name=None,
:param timeout: Request timeout in seconds (defaults to 30s)
:return:
"""
url = build_url(server_context, 'query', 'getQuery.api', container_path=container_path)
url = server_context.build_url('query', 'getQuery.api', container_path=container_path)

payload = {
'schemaName': schema_name,
Expand Down Expand Up @@ -268,7 +262,7 @@ def select_rows(server_context, schema_name, query_name, view_name=None,
if required_version is not None:
payload['apiVersion'] = required_version

return make_request(server_context, url, payload, timeout=timeout)
return server_context.make_request(url, payload, timeout=timeout)


def update_rows(server_context, schema_name, query_name, rows, container_path=None, timeout=_default_timeout):
Expand All @@ -283,17 +277,16 @@ def update_rows(server_context, schema_name, query_name, rows, container_path=No
:param timeout: timeout of request in seconds (defaults to 30s)
:return:
"""
url = build_url(server_context, 'query', 'updateRows.api', container_path=container_path)
url = server_context.build_url('query', 'updateRows.api', container_path=container_path)

payload = {
'schemaName': schema_name,
'queryName': query_name,
'rows': rows
}

# explicit json payload and headers required for form generation
return make_request(server_context, url, json.dumps(payload, sort_keys=True), headers=_query_headers,
timeout=timeout)
return server_context.make_request(url, json.dumps(payload, sort_keys=True), headers=_query_headers,
timeout=timeout)


# TODO: Provide filter generators.
Expand Down
55 changes: 22 additions & 33 deletions labkey/security.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,6 @@
#
from __future__ import unicode_literals

from labkey.utils import build_url, make_request

security_controller = 'security'
user_controller = 'user'

Expand Down Expand Up @@ -68,13 +66,13 @@ def create_user(server_context, email, container_path=None, send_email=False):
:param send_email: true to send email notification to user
:return:
"""
url = build_url(server_context, security_controller, 'createNewUser.api', container_path)
url = server_context.build_url(security_controller, 'createNewUser.api', container_path)
payload = {
'email': email,
'sendEmail': send_email
}

return make_request(server_context, url, payload)
return server_context.make_request(url, payload)


def deactivate_users(server_context, target_ids, container_path=None):
Expand Down Expand Up @@ -118,8 +116,8 @@ def get_roles(server_context, container_path=None):
:param container_path:
:return:
"""
url = build_url(server_context, security_controller, 'getRoles.api', container_path=container_path)
return make_request(server_context, url, None)
url = server_context.build_url(security_controller, 'getRoles.api', container_path=container_path)
return server_context.make_request(url, None)


def get_user_by_email(server_context, email):
Expand All @@ -129,9 +127,9 @@ def get_user_by_email(server_context, email):
:param email:
:return:
"""
url = build_url(server_context, user_controller, 'getUsers.api')
url = server_context.build_url(user_controller, 'getUsers.api')
payload = dict(includeDeactivatedAccounts=True)
result = make_request(server_context, url, payload)
result = server_context.make_request(url, payload)

if result is None or result['users'] is None:
raise ValueError("No Users in container" + email)
Expand All @@ -144,13 +142,11 @@ def get_user_by_email(server_context, email):


def list_groups(server_context, include_site_groups=False, container_path=None):
url = build_url(server_context, security_controller, 'listProjectGroups.api', container_path)
url = server_context.build_url(security_controller, 'listProjectGroups.api', container_path)

payload = {
return server_context.make_request(url, {
'includeSiteGroups': include_site_groups
}

return make_request(server_context, url, payload)
})


def remove_from_group(server_context, user_ids, group_id, container_path=None):
Expand Down Expand Up @@ -188,13 +184,11 @@ def reset_password(server_context, email, container_path=None):
:param container_path:
:return:
"""
url = build_url(server_context, security_controller, 'adminRotatePassword.api', container_path)
url = server_context.build_url(security_controller, 'adminRotatePassword.api', container_path)

payload = {
return server_context.make_request(url, {
'email': email
}

return make_request(server_context, url, payload)
})


def __make_security_group_api_request(server_context, api, user_ids, group_id, container_path):
Expand All @@ -207,18 +201,16 @@ def __make_security_group_api_request(server_context, api, user_ids, group_id, c
:param container_path: Additional container context path
:return: Request json object
"""
url = build_url(server_context, security_controller, api, container_path)
url = server_context.build_url(security_controller, api, container_path)

# if user_ids is only a single scalar make it an array
if not hasattr(user_ids, "__iter__"):
user_ids = [user_ids]

payload = {
return server_context.make_request(url, {
'groupId': group_id,
'principalIds': user_ids
}

return make_request(server_context, url, payload)
})


def __make_security_role_api_request(server_context, api, role, email=None, user_id=None, container_path=None):
Expand All @@ -234,15 +226,13 @@ def __make_security_role_api_request(server_context, api, role, email=None, user
if email is None and user_id is None:
raise ValueError("Must supply either/both [email] or [user_id]")

url = build_url(server_context, security_controller, api, container_path)
url = server_context.build_url(security_controller, api, container_path)

payload = {
return server_context.make_request(url, {
'roleClassName': role['uniqueName'],
'principalId': user_id,
'email': email
}

return make_request(server_context, url, payload)
})


def __make_user_api_request(server_context, target_ids, api, container_path=None):
Expand All @@ -254,9 +244,8 @@ def __make_user_api_request(server_context, target_ids, api, container_path=None
:param container_path: container context
:return: response json
"""
url = build_url(server_context, user_controller, api, container_path)
payload = {
'userId': target_ids
}
url = server_context.build_url(user_controller, api, container_path)

return make_request(server_context, url, payload)
return server_context.make_request(url, {
'userId': target_ids
})
8 changes: 2 additions & 6 deletions labkey/unsupported/messageboard.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
"""
from __future__ import unicode_literals
from requests.exceptions import SSLError
from labkey.utils import build_url


def post_message(server_context, message_title, message_body, render_as, container_path=None):
Expand All @@ -36,19 +35,16 @@ def post_message(server_context, message_title, message_body, render_as, contain
:param container_path: Optional container path that can be used to override the server_context container path
:return: Returns 1 if successful, 0 is post failed.
"""
# Build the URL for querying LabKey Server
message_url = build_url(server_context, 'announcements', 'insert.api', container_path=container_path)
message_url = server_context.build_url('announcements', 'insert.api', container_path=container_path)

message_data = {
'title': message_title,
'body': message_body,
'rendererType': render_as
}

session = server_context['session']

try:
message_response = session.post(message_url, message_data)
server_context.make_request(message_url, message_data)
except SSLError as e:
print("There was problem while attempting to submit the message to " + str(e.geturl()) + ". The HTTP response code was " + str(e.getcode()))
print("The HTTP client error was: " + format(e))
Expand Down
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