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cr-connect-workflow/tests/test_tasks_api.py
Dan Funk 11413838a7 Faster lookup fields. We were parsing the spec each time to get details about how to search. We're just grabbing the workflow id and task id now and building that straight into the full text search index for faster lookups. Should be peppy. 
Another speed improvement - data in the FileDataModel is deferred, and not queried until it is specifically used, as the new data structures need to use this model frequently.
2020-05-29 01:39:39 -04:00

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import json
import os
import random
from unittest.mock import patch
from tests.base_test import BaseTest
from crc import session, app
from crc.models.api_models import WorkflowApiSchema, MultiInstanceType, TaskSchema
from crc.models.file import FileModelSchema
from crc.models.stats import TaskEventModel
from crc.models.workflow import WorkflowStatus
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.workflow_service import WorkflowService
class TestTasksApi(BaseTest):
def get_workflow_api(self, workflow, soft_reset=False, hard_reset=False):
rv = self.app.get('/v1.0/workflow/%i?soft_reset=%s&hard_reset=%s' %
(workflow.id, str(soft_reset), str(hard_reset)),
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
workflow_api = WorkflowApiSchema().load(json_data)
self.assertEqual(workflow.workflow_spec_id, workflow_api.workflow_spec_id)
return workflow_api
def complete_form(self, workflow_in, task_in, dict_data, error_code = None):
prev_completed_task_count = workflow_in.completed_tasks
if isinstance(task_in, dict):
task_id = task_in["id"]
else:
task_id = task_in.id
rv = self.app.put('/v1.0/workflow/%i/task/%s/data' % (workflow_in.id, task_id),
headers=self.logged_in_headers(),
content_type="application/json",
data=json.dumps(dict_data))
if error_code:
self.assert_failure(rv, error_code=error_code)
return
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
# Assure stats are updated on the model
workflow = WorkflowApiSchema().load(json_data)
# The total number of tasks may change over time, as users move through gateways
# branches may be pruned. As we hit parallel Multi-Instance new tasks may be created...
self.assertIsNotNone(workflow.total_tasks)
self.assertEquals(prev_completed_task_count + 1, workflow.completed_tasks)
# Assure a record exists in the Task Events
task_events = session.query(TaskEventModel) \
.filter_by(workflow_id=workflow.id) \
.filter_by(task_id=task_id) \
.order_by(TaskEventModel.date.desc()).all()
self.assertGreater(len(task_events), 0)
event = task_events[0]
self.assertIsNotNone(event.study_id)
self.assertEquals("dhf8r", event.user_uid)
self.assertEquals(workflow.id, event.workflow_id)
self.assertEquals(workflow.workflow_spec_id, event.workflow_spec_id)
self.assertEquals(workflow.spec_version, event.spec_version)
self.assertEquals(WorkflowService.TASK_ACTION_COMPLETE, event.action)
self.assertEquals(task_in.id, task_id)
self.assertEquals(task_in.name, event.task_name)
self.assertEquals(task_in.title, event.task_title)
self.assertEquals(task_in.type, event.task_type)
self.assertEquals("COMPLETED", event.task_state)
# Not sure what vodoo is happening inside of marshmallow to get me in this state.
if isinstance(task_in.multi_instance_type, MultiInstanceType):
self.assertEquals(task_in.multi_instance_type.value, event.mi_type)
else:
self.assertEquals(task_in.multi_instance_type, event.mi_type)
self.assertEquals(task_in.multi_instance_count, event.mi_count)
self.assertEquals(task_in.multi_instance_index, event.mi_index)
self.assertEquals(task_in.process_name, event.process_name)
self.assertIsNotNone(event.date)
workflow = WorkflowApiSchema().load(json_data)
return workflow
def test_get_current_user_tasks(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
workflow = self.get_workflow_api(workflow)
task = workflow.next_task
self.assertEqual("Task_User_Select_Type", task.name)
self.assertEqual(3, len(task.form["fields"][0]["options"]))
self.assertIsNotNone(task.documentation)
expected_docs = """# h1 Heading 8-)
## h2 Heading
### h3 Heading
#### h4 Heading
##### h5 Heading
###### h6 Heading
"""
self.assertTrue(str.startswith(task.documentation, expected_docs))
def test_two_forms_task(self):
# Set up a new workflow
self.load_example_data()
workflow = self.create_workflow('two_forms')
# get the first form in the two form workflow.
workflow_api = self.get_workflow_api(workflow)
self.assertEqual('two_forms', workflow_api.workflow_spec_id)
self.assertEqual(2, len(workflow_api.navigation))
self.assertIsNotNone(workflow_api.next_task.form)
self.assertEqual("UserTask", workflow_api.next_task.type)
self.assertEqual("StepOne", workflow_api.next_task.name)
self.assertEqual(1, len(workflow_api.next_task.form['fields']))
# Complete the form for Step one and post it.
self.complete_form(workflow, workflow_api.next_task, {"color": "blue"})
# Get the next Task
workflow_api = self.get_workflow_api(workflow)
self.assertEqual("StepTwo", workflow_api.next_task.name)
# Get all user Tasks and check that the data have been saved
task = workflow_api.next_task
self.assertIsNotNone(task.data)
for val in task.data.values():
self.assertIsNotNone(val)
def test_error_message_on_bad_gateway_expression(self):
self.load_example_data()
workflow = self.create_workflow('exclusive_gateway')
# get the first form in the two form workflow.
task = self.get_workflow_api(workflow).next_task
self.complete_form(workflow, task, {"has_bananas": True})
def test_workflow_with_parallel_forms(self):
self.load_example_data()
workflow = self.create_workflow('exclusive_gateway')
# get the first form in the two form workflow.
task = self.get_workflow_api(workflow).next_task
self.complete_form(workflow, task, {"has_bananas": True})
# Get the next Task
workflow_api = self.get_workflow_api(workflow)
self.assertEqual("Task_Num_Bananas", workflow_api.next_task.name)
def test_navigation_with_parallel_forms(self):
self.load_example_data()
workflow = self.create_workflow('exclusive_gateway')
# get the first form in the two form workflow.
workflow_api = self.get_workflow_api(workflow)
self.assertIsNotNone(workflow_api.navigation)
nav = workflow_api.navigation
self.assertEquals(5, len(nav))
self.assertEquals("Do You Have Bananas", nav[0]['title'])
self.assertEquals("Bananas?", nav[1]['title'])
self.assertEquals("FUTURE", nav[1]['state'])
self.assertEquals("yes", nav[2]['title'])
self.assertEquals("NOOP", nav[2]['state'])
self.assertEquals("no", nav[3]['title'])
self.assertEquals("NOOP", nav[3]['state'])
def test_navigation_with_exclusive_gateway(self):
self.load_example_data()
workflow = self.create_workflow('exclusive_gateway_2')
# get the first form in the two form workflow.
workflow_api = self.get_workflow_api(workflow)
self.assertIsNotNone(workflow_api.navigation)
nav = workflow_api.navigation
self.assertEquals(7, len(nav))
self.assertEquals("Task 1", nav[0]['title'])
self.assertEquals("Which Branch?", nav[1]['title'])
self.assertEquals("a", nav[2]['title'])
self.assertEquals("Task 2a", nav[3]['title'])
self.assertEquals("b", nav[4]['title'])
self.assertEquals("Task 2b", nav[5]['title'])
self.assertEquals("Task 3", nav[6]['title'])
def test_document_added_to_workflow_shows_up_in_file_list(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('docx')
# get the first form in the two form workflow.
task = self.get_workflow_api(workflow).next_task
data = {
"full_name": "Buck of the Wild",
"date": "5/1/2020",
"title": "Leader of the Pack",
"company": "In the company of wolves",
"last_name": "Mr. Wolf"
}
workflow_api = self.complete_form(workflow, task, data)
self.assertIsNotNone(workflow_api.next_task)
self.assertEqual("EndEvent_0evb22x", workflow_api.next_task.name)
self.assertTrue(workflow_api.status == WorkflowStatus.complete)
rv = self.app.get('/v1.0/file?workflow_id=%i' % workflow.id, headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
files = FileModelSchema(many=True).load(json_data, session=session)
self.assertTrue(len(files) == 1)
# Assure we can still delete the study even when there is a file attached to a workflow.
rv = self.app.delete('/v1.0/study/%i' % workflow.study_id, headers=self.logged_in_headers())
self.assert_success(rv)
def test_get_documentation_populated_in_end(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task
self.assertEqual("Task_User_Select_Type", task.name)
self.assertEqual(3, len(task.form["fields"][0]["options"]))
self.assertIsNotNone(task.documentation)
self.complete_form(workflow, workflow_api.next_task, {"type": "norris"})
workflow_api = self.get_workflow_api(workflow)
self.assertEqual("EndEvent_0u1cgrf", workflow_api.next_task.name)
self.assertIsNotNone(workflow_api.next_task.documentation)
self.assertTrue("norris" in workflow_api.next_task.documentation)
def test_load_workflow_from_outdated_spec(self):
# Start the basic two_forms workflow and complete a task.
self.load_example_data()
workflow = self.create_workflow('two_forms')
workflow_api = self.get_workflow_api(workflow)
self.complete_form(workflow, workflow_api.next_task, {"color": "blue"})
self.assertTrue(workflow_api.is_latest_spec)
# Modify the specification, with a major change that alters the flow and can't be deserialized
# effectively, if it uses the latest spec files.
file_path = os.path.join(app.root_path, '..', 'tests', 'data', 'two_forms', 'mods', 'two_forms_struc_mod.bpmn')
self.replace_file("two_forms.bpmn", file_path)
workflow_api = self.get_workflow_api(workflow)
self.assertTrue(workflow_api.spec_version.startswith("v1 "))
self.assertFalse(workflow_api.is_latest_spec)
workflow_api = self.get_workflow_api(workflow, hard_reset=True)
self.assertTrue(workflow_api.spec_version.startswith("v2 "))
self.assertTrue(workflow_api.is_latest_spec)
# Assure this hard_reset sticks (added this after a bug was found)
workflow_api = self.get_workflow_api(workflow)
self.assertTrue(workflow_api.spec_version.startswith("v2 "))
self.assertTrue(workflow_api.is_latest_spec)
def test_soft_reset_errors_out_and_next_result_is_on_original_version(self):
# Start the basic two_forms workflow and complete a task.
self.load_example_data()
workflow = self.create_workflow('two_forms')
workflow_api = self.get_workflow_api(workflow)
self.complete_form(workflow, workflow_api.next_task, {"color": "blue"})
self.assertTrue(workflow_api.is_latest_spec)
# Modify the specification, with a major change that alters the flow and can't be deserialized
# effectively, if it uses the latest spec files.
file_path = os.path.join(app.root_path, '..', 'tests', 'data', 'two_forms', 'mods', 'two_forms_struc_mod.bpmn')
self.replace_file("two_forms.bpmn", file_path)
# perform a soft reset returns an error
rv = self.app.get('/v1.0/workflow/%i?soft_reset=%s&hard_reset=%s' %
(workflow.id, "true", "false"),
content_type="application/json",
headers=self.logged_in_headers())
self.assert_failure(rv, error_code="unexpected_workflow_structure")
# Try again without a soft reset, and we are still ok, and on the original version.
workflow_api = self.get_workflow_api(workflow)
self.assertTrue(workflow_api.spec_version.startswith("v1 "))
self.assertFalse(workflow_api.is_latest_spec)
def test_manual_task_with_external_documentation(self):
self.load_example_data()
workflow = self.create_workflow('manual_task_with_external_documentation')
# get the first form in the two form workflow.
task = self.get_workflow_api(workflow).next_task
workflow_api = self.complete_form(workflow, task, {"name": "Dan"})
workflow = self.get_workflow_api(workflow)
self.assertEquals('Task_Manual_One', workflow.next_task.name)
self.assertEquals('ManualTask', workflow_api.next_task.type)
self.assertTrue('Markdown' in workflow_api.next_task.documentation)
self.assertTrue('Dan' in workflow_api.next_task.documentation)
def test_bpmn_extension_properties_are_populated(self):
self.load_example_data()
workflow = self.create_workflow('manual_task_with_external_documentation')
# get the first form in the two form workflow.
task = self.get_workflow_api(workflow).next_task
self.assertEquals("JustAValue", task.properties['JustAKey'])
@patch('crc.services.protocol_builder.requests.get')
def test_multi_instance_task(self, mock_get):
self.load_example_data()
# Enable the protocol builder.
app.config['PB_ENABLED'] = True
# This depends on getting a list of investigators back from the protocol builder.
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('investigators.json')
workflow = self.create_workflow('multi_instance')
# get the first form in the two form workflow.
workflow = self.get_workflow_api(workflow)
navigation = self.get_workflow_api(workflow).navigation
self.assertEquals(4, len(navigation)) # Start task, form_task, multi_task, end task
self.assertEquals("UserTask", workflow.next_task.type)
self.assertEquals(MultiInstanceType.sequential.value, workflow.next_task.multi_instance_type)
self.assertEquals(9, workflow.next_task.multi_instance_count)
# Assure that the names for each task are properly updated, so they aren't all the same.
self.assertEquals("Primary Investigator", workflow.next_task.properties['display_name'])
def test_lookup_endpoint_for_task_field_enumerations(self):
self.load_example_data()
workflow = self.create_workflow('enum_options_with_search')
# get the first form in the two form workflow.
workflow = self.get_workflow_api(workflow)
task = workflow.next_task
field_id = task.form['fields'][0]['id']
rv = self.app.get('/v1.0/workflow/%i/lookup/%s?query=%s&limit=5' %
(workflow.id, field_id, 'c'), # All records with a word that starts with 'c'
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(rv)
results = json.loads(rv.get_data(as_text=True))
self.assertEqual(5, len(results))
def test_lookup_endpoint_for_task_ldap_field_lookup(self):
self.load_example_data()
workflow = self.create_workflow('ldap_lookup')
# get the first form
workflow = self.get_workflow_api(workflow)
task = workflow.next_task
field_id = task.form['fields'][0]['id']
# lb3dp is a user record in the mock ldap responses for tests.
rv = self.app.get('/v1.0/workflow/%s/lookup/%s?query=%s&limit=5' %
(workflow.id, field_id, 'lb3dp'),
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(rv)
results = json.loads(rv.get_data(as_text=True))
self.assertEqual(1, len(results))
def test_sub_process(self):
self.load_example_data()
workflow = self.create_workflow('subprocess')
workflow_api = self.get_workflow_api(workflow)
navigation = workflow_api.navigation
task = workflow_api.next_task
self.assertEquals(2, len(navigation))
self.assertEquals("UserTask", task.type)
self.assertEquals("Activity_A", task.name)
self.assertEquals("My Sub Process", task.process_name)
workflow_api = self.complete_form(workflow, task, {"name": "Dan"})
task = workflow_api.next_task
self.assertIsNotNone(task)
self.assertEquals("Activity_B", task.name)
self.assertEquals("Sub Workflow Example", task.process_name)
workflow_api = self.complete_form(workflow, task, {"name": "Dan"})
self.assertEquals(WorkflowStatus.complete, workflow_api.status)
def test_update_task_resets_token(self):
self.load_example_data()
workflow = self.create_workflow('exclusive_gateway')
# Start the workflow.
first_task = self.get_workflow_api(workflow).next_task
self.complete_form(workflow, first_task, {"has_bananas": True})
workflow = self.get_workflow_api(workflow)
self.assertEquals('Task_Num_Bananas', workflow.next_task.name)
# Trying to re-submit the initial task, and answer differently, should result in an error.
self.complete_form(workflow, first_task, {"has_bananas": False}, error_code="invalid_state")
# Go ahead and set the number of bananas.
workflow = self.get_workflow_api(workflow)
task = workflow.next_task
self.complete_form(workflow, task, {"num_bananas": 4})
# We are now at the end of the workflow.
# Make the old task the current task.
rv = self.app.put('/v1.0/workflow/%i/task/%s/set_token' % (workflow.id, first_task.id),
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
workflow = WorkflowApiSchema().load(json_data)
# Assure the Next Task is the one we just reset the token to be on.
self.assertEquals("Task_Has_Bananas", workflow.next_task.name)
# Go ahead and get that workflow one more time, it should still be right.
workflow = self.get_workflow_api(workflow)
# Assure the Next Task is the one we just reset the token to be on.
self.assertEquals("Task_Has_Bananas", workflow.next_task.name)
# The next task should be a different value.
self.complete_form(workflow, workflow.next_task, {"has_bananas": False})
workflow = self.get_workflow_api(workflow)
self.assertEquals('Task_Why_No_Bananas', workflow.next_task.name)
@patch('crc.services.protocol_builder.requests.get')
def test_parallel_multi_instance(self, mock_get):
# Assure we get nine investigators back from the API Call, as set in the investigators.json file.
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('investigators.json')
self.load_example_data()
workflow = self.create_workflow('multi_instance_parallel')
workflow_api = self.get_workflow_api(workflow)
self.assertEquals(12, len(workflow_api.navigation))
ready_items = [nav for nav in workflow_api.navigation if nav['state'] == "READY"]
self.assertEquals(9, len(ready_items))
self.assertEquals("UserTask", workflow_api.next_task.type)
self.assertEquals("MutiInstanceTask",workflow_api.next_task.name)
self.assertEquals("more information", workflow_api.next_task.title)
for i in random.sample(range(9), 9):
task = TaskSchema().load(ready_items[i]['task'])
self.complete_form(workflow, task, {"investigator":{"email": "dhf8r@virginia.edu"}})
#tasks = self.get_workflow_api(workflow).user_tasks
workflow = self.get_workflow_api(workflow)
self.assertEquals(WorkflowStatus.complete, workflow.status)
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