Fb integration tests (#40)

* Add integration marker and integration test suite

* remove coverage from default pytest options

it prevents us from being able to use the Python Debugger in Intellij/PyCharm

* Fix typo

* Add option to disable CSRF to ServerContext

- Remove global DISABLE_CSRF_CHECK
- Explicitly define args/kwargs for ServerContext, effectively making create_server_context useless. Will deprecate and remove at a later date.

* Add dataset test fixture, create_dataset and create_dupicate_dataset tests

* Add container.py

Users can now create and delete containers with the python API

* Upper case constants

* Add study creation code to test_integration.py

* add unit tests for endpoint testing of qc states

* Clean up test_integration.py

* Use python naming conventions in query_examples.py

* Use python naming conventions in test_integration.py

* use python naming conventions in sample files

* Read properties file from TC during integration tests

* Fix copy/paste error

Co-authored-by: Alan Vezina <[email protected]>
Co-authored-by: Trey Chadick <[email protected]>

Author: 3 people

MANIFEST.in

@@ -1,2 +1,3 @@
 include *.txt
-recursive-include docs *.txt
+include pytest.ini
+recursive-include docs *.txt

README.md

@@ -125,5 +125,12 @@ Then, the tests can be run with
 $ pytest .
 ```
 
+The integration tests do not run by default. If you want to run the integration tests make sure you have a live server
+running, a netrc file, and run the following command:
+
+```bash
+$ pytest . -m "integration"
+```
+
 ### Maintainers
 Package maintainer's can reference the [Python Package Maintenance](https://docs.google.com/document/d/13nVxwyctH4YZ6gDhcrOu9Iz6qGFPAxicE1VHiVYpw9A/) document (requires permission) for updating releases.

labkey/container.py

@@ -0,0 +1,40 @@
+from labkey.utils import json_dumps, ServerContext
+
+
+def create(server_context, name, container_path=None, description=None, folderType=None, isWorkbook=None, title=None):
+    # type: (ServerContext, str, str, str, str, bool, str) -> dict
+    """
+    Create a container in LabKey.
+
+    :param server_context: A LabKey server context. See utils.create_server_context.
+    :param name: The name of the container.
+    :param container_path: the path of where you want to create the container.
+    :param description: a description for the container.
+    :param folderType: the desired folder type for the container.
+    :param isWorkbook: sets whether the container is a workbook.
+    :param title: the title for the container.
+    :return:
+    """
+    headers = {'Content-Type': 'application/json'}
+    url = server_context.build_url('core', 'createContainer.api', container_path)
+    payload = {
+        'description': description,
+        'folderType': folderType,
+        'isWorkbook': isWorkbook,
+        'name': name,
+        'title': title,
+    }
+    return server_context.make_request(url, json_dumps(payload), headers=headers)
+
+
+def delete(server_context, container_path=None):
+    # type: (ServerContext, str)
+    """
+    Deletes a container at the given container_path, or at the server_context's container path
+    :param server_context: A LabKey server context. See utils.create_server_context.
+    :param container_path: The path of the container to delete.
+    :return:
+    """
+    headers = {'Content-Type': 'application/json'}
+    url = server_context.build_url('core', 'deleteContainer.api', container_path)
+    return server_context.make_request(url, None, headers=headers)

labkey/security.py

@@ -15,8 +15,8 @@
 #
 from __future__ import unicode_literals
 
-security_controller = 'security'
-user_controller = 'user'
+SECURITY_CONTROLLER = 'security'
+USER_CONTROLLER = 'user'
 
 
 def activate_users(server_context, target_ids, container_path=None):
@@ -66,7 +66,7 @@ def create_user(server_context, email, container_path=None, send_email=False):
     :param send_email: true to send email notification to user
     :return:
     """
-    url = server_context.build_url(security_controller, 'createNewUser.api', container_path)
+    url = server_context.build_url(SECURITY_CONTROLLER, 'createNewUser.api', container_path)
     payload = {
         'email': email,
         'sendEmail': send_email
@@ -116,7 +116,7 @@ def get_roles(server_context, container_path=None):
     :param container_path:
     :return:
     """
-    url = server_context.build_url(security_controller, 'getRoles.api', container_path=container_path)
+    url = server_context.build_url(SECURITY_CONTROLLER, 'getRoles.api', container_path=container_path)
     return server_context.make_request(url, None)
 
 
@@ -127,7 +127,7 @@ def get_user_by_email(server_context, email):
     :param email:
     :return:
     """
-    url = server_context.build_url(user_controller, 'getUsers.api')
+    url = server_context.build_url(USER_CONTROLLER, 'getUsers.api')
     payload = dict(includeDeactivatedAccounts=True)
     result = server_context.make_request(url, payload)
 
@@ -142,7 +142,7 @@ def get_user_by_email(server_context, email):
 
 
 def list_groups(server_context, include_site_groups=False, container_path=None):
-    url = server_context.build_url(security_controller, 'listProjectGroups.api', container_path)
+    url = server_context.build_url(SECURITY_CONTROLLER, 'listProjectGroups.api', container_path)
 
     return server_context.make_request(url, {
         'includeSiteGroups': include_site_groups
@@ -184,7 +184,7 @@ def reset_password(server_context, email, container_path=None):
     :param container_path:
     :return:
     """
-    url = server_context.build_url(security_controller, 'adminRotatePassword.api', container_path)
+    url = server_context.build_url(SECURITY_CONTROLLER, 'adminRotatePassword.api', container_path)
 
     return server_context.make_request(url, {
         'email': email
@@ -201,7 +201,7 @@ 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 = server_context.build_url(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__"):
@@ -226,7 +226,7 @@ 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 = server_context.build_url(security_controller, api, container_path)
+    url = server_context.build_url(SECURITY_CONTROLLER, api, container_path)
 
     return server_context.make_request(url, {
         'roleClassName': role['uniqueName'],
@@ -244,7 +244,7 @@ def __make_user_api_request(server_context, target_ids, api, container_path=None
     :param container_path: container context
     :return: response json
     """
-    url = server_context.build_url(user_controller, api, container_path)
+    url = server_context.build_url(USER_CONTROLLER, api, container_path)
 
     return server_context.make_request(url, {
         'userId': target_ids

labkey/utils.py

@@ -27,19 +27,18 @@
 __default_timeout = 60 * 5  # 5 minutes
 API_KEY_TOKEN = 'apikey'
 CSRF_TOKEN = 'X-LABKEY-CSRF'
-DISABLE_CSRF_CHECK = False  # Used by tests to disable CSRF token check
 
 
 class ServerContext(object):
-
-    def __init__(self, **kwargs):
-        self._container_path = kwargs.pop('container_path', None)
-        self._context_path = kwargs.pop('context_path', None)
-        self._domain = kwargs.pop('domain', None)
-        self._use_ssl = kwargs.pop('use_ssl', True)
-        self._verify_ssl = kwargs.pop('verify_ssl', True)
-        self._api_key = kwargs.pop('api_key', None)
-
+    def __init__(self, domain, container_path, context_path=None, use_ssl=True, verify_ssl=True, api_key=None,
+                 disable_csrf=False):
+        self._container_path = container_path
+        self._context_path = context_path
+        self._domain = domain
+        self._use_ssl = use_ssl
+        self._verify_ssl = verify_ssl
+        self._api_key = api_key
+        self._disable_csrf = disable_csrf
         self._session = requests.Session()
 
         if self._use_ssl:
@@ -50,9 +49,7 @@ def __init__(self, **kwargs):
             self._scheme = 'http://'
 
     def __repr__(self):
-        return '<ServerContext [ {} | {} | {} ]>'.format(self._domain,
-                                                         self._context_path,
-                                                         self._container_path)
+        return '<ServerContext [ {} | {} | {} ]>'.format(self._domain, self._context_path, self._container_path)
 
     def build_url(self, controller, action, container_path=None):
         # type: (self, str, str, str) -> str
@@ -83,7 +80,7 @@ def make_request(self, url, payload, headers=None, timeout=300, method='POST',
                     API_KEY_TOKEN: self._api_key
                 })
 
-        if not DISABLE_CSRF_CHECK:
+        if not self._disable_csrf:
             global CSRF_TOKEN
 
             # CSRF check
@@ -111,8 +108,9 @@ def make_request(self, url, payload, headers=None, timeout=300, method='POST',
             handle_request_exception(e, server_context=self)
 
 
-def create_server_context(domain, container_path, context_path=None, use_ssl=True, verify_ssl=True, api_key=None):
-    # type: (str, str, str, bool, bool, str) -> ServerContext
+def create_server_context(domain, container_path, context_path=None, use_ssl=True, verify_ssl=True, api_key=None,
+                          disable_csrf=False):
+    # type: (str, str, str, bool, bool, str, bool) -> ServerContext
     """
     Create a LabKey server context. This context is used to encapsulate properties
     about the LabKey server that is being requested against. This includes, but is not limited to,
@@ -123,19 +121,19 @@ def create_server_context(domain, container_path, context_path=None, use_ssl=Tru
     :param use_ssl:
     :param verify_ssl:
     :param api_key:
+    :param disable_csrf:
     :return:
     """
-    config = dict(
+    return ServerContext(
         domain=domain,
         container_path=container_path,
         context_path=context_path,
         use_ssl=use_ssl,
         verify_ssl=verify_ssl,
-        api_key=api_key
+        api_key=api_key,
+        disable_csrf=disable_csrf,
     )
 
-    return ServerContext(**config)
-
 
 def build_url(server_context, controller, action, container_path=None):
     # type: (ServerContext, str, str, str) -> str

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+addopts = -v -m "not integration"
+markers =
+    integration: mark tests as integration, they will not be run by default (to run add '-m "integration"')

samples/experiment_example.py

@@ -30,9 +30,9 @@
 ###################
 
 # Generate the Run object(s)
-runTest = Run()
-runTest.name = 'python upload'
-runTest.data_rows = [{
+run_test = Run()
+run_test.name = 'python upload'
+run_test.data_rows = [{
     # ColumnName: Value
     'SampleId': 'Monkey 1',
     'TimePoint': '2008/11/02 11:22:33',
@@ -49,11 +49,11 @@
     'DoubleData': 1.5,
     'HiddenData': 'jimbo'
 }]
-runTest.properties['RunFieldName'] = 'Run Field Value'
+run_test.properties['RunFieldName'] = 'Run Field Value'
 
 # Generate the Batch object(s)
 batch = Batch()
-batch.runs = [runTest]
+batch.runs = [run_test]
 batch.name = 'python batch'
 batch.properties['PropertyName'] = 'Property Value'
 

samples/experiment_platemetadata_example.py

@@ -30,9 +30,9 @@
 ###################
 
 # Generate the Run object(s)
-runTest = Run()
-runTest.name = 'python upload'
-runTest.data_rows = [{
+run_test = Run()
+run_test.name = 'python upload'
+run_test.data_rows = [{
     # ColumnName: Value
     'ParticipantId' : '1234',
     'VisitId' : 111,
@@ -47,11 +47,12 @@
     'WellLocation' : 'F12'
 }]
 
-# Assays that are configured for plate support have a required run property for the plate template, this is the plate template lsid
-runTest.properties['PlateTemplate'] = 'urn:lsid:labkey.com:PlateTemplate.Folder-6:d8bbec7d-34cd-1038-bd67-b3bd777822f8'
+# Assays that are configured for plate support have a required run property for the plate template, this is the plate
+# template lsid
+run_test.properties['PlateTemplate'] = 'urn:lsid:labkey.com:PlateTemplate.Folder-6:d8bbec7d-34cd-1038-bd67-b3bd777822f8'
 
 # The assay plate metadata is a specially formatted JSON object to map properties to the well groups
-runTest.plate_metadata = {
+run_test.plate_metadata = {
     'control' : {
       'positive' : {'dilution':  0.005},
       'negative' : {'dilution':  1.0}
@@ -66,7 +67,7 @@
 
 # Generate the Batch object(s)
 batch = Batch()
-batch.runs = [runTest]
+batch.runs = [run_test]
 batch.name = 'python batch'
 batch.properties['PropertyName'] = 'Property Value'