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cr-connect-workflow
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Merge branch 'feature/improved_task_event_api' into feature/approvals_dashboard_prototype

This commit is contained in:
Aaron Louie 2020-07-22 09:34:52 -04:00
parent e82532aad8 3d9eeab502
commit 21d248cdc0
35 changed files with 174 additions and 210 deletions
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1
Pipfile
View File

@ -39,6 +39,7 @@ requests = "*"
sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
sphinx = "*"
spiffworkflow = {editable = true,git = "https://github.com/sartography/SpiffWorkflow.git",ref = "master"}
#spiffworkflow = {editable = true,path="/home/kelly/sartography/SpiffWorkflow/"}
swagger-ui-bundle = "*"
webtest = "*"
werkzeug = "*"

47
Pipfile.lock generated
View File

@ -322,7 +322,6 @@
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@ -412,12 +411,8 @@
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@ -510,11 +509,11 @@
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"index": "pypi",
"version": "==3.7.0"
"version": "==3.7.1"
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"marshmallow-enum": {
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@ -646,19 +645,8 @@
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"pyasn1": {
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@ -713,11 +701,9 @@
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"python-editor": {
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@ -900,7 +886,7 @@
"spiffworkflow": {
"editable": true,
"git": "https://github.com/sartography/SpiffWorkflow.git",
"ref": "c72ced41e323aa69fcb6f7708e1869e98add716d"
"ref": "161b3e2ac62a824c6b771e9b817a2bd477af0d17"
},
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@ -937,12 +923,11 @@
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},
"urllib3": {
"hashes": [

3
config/default.py
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@ -15,7 +15,8 @@ TEST_UID = environ.get('TEST_UID', default="dhf8r")
ADMIN_UIDS = re.split(r',\s*', environ.get('ADMIN_UIDS', default="dhf8r,ajl2j,cah3us,cl3wf"))
# Sentry flag
ENABLE_SENTRY = environ.get('ENABLE_SENTRY', default="false") == "true"
ENABLE_SENTRY = environ.get('ENABLE_SENTRY', default="false") == "true" # To be removed soon
SENTRY_ENVIRONMENT = environ.get('SENTRY_ENVIRONMENT', None)
# Add trailing slash to base path
APPLICATION_ROOT = re.sub(r'//', '/', '/%s/' % environ.get('APPLICATION_ROOT', default="/").strip('/'))

9
crc/__init__.py
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@ -52,8 +52,9 @@ origins_re = [r"^https?:\/\/%s(.*)" % o.replace('.', '\.') for o in app.config['
cors = CORS(connexion_app.app, origins=origins_re)
# Sentry error handling
if app.config['ENABLE_SENTRY']:
if app.config['SENTRY_ENVIRONMENT']:
sentry_sdk.init(
environment=app.config['SENTRY_ENVIRONMENT'],
dsn="https://25342ca4e2d443c6a5c49707d68e9f40@o401361.ingest.sentry.io/5260915",
integrations=[FlaskIntegration()]
)
@ -91,9 +92,3 @@ def clear_db():
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
@app.cli.command()
def rrt_data_fix():
"""Finds all the empty task event logs, and populates
them with good wholesome data."""
from crc.services.workflow_service import WorkflowService
WorkflowService.fix_legacy_data_model_for_rrt()

2
crc/api/common.py
View File

@ -25,6 +25,7 @@ class ApiError(Exception):
instance.task_name = task.task_spec.description or ""
instance.file_name = task.workflow.spec.file or ""
instance.task_data = task.data
app.logger.error(message, exc_info=True)
return instance
@classmethod
@ -35,6 +36,7 @@ class ApiError(Exception):
instance.task_name = task_spec.description or ""
if task_spec._wf_spec:
instance.file_name = task_spec._wf_spec.file
app.logger.error(message, exc_info=True)
return instance
@classmethod

7
crc/models/study.py
View File

@ -40,7 +40,7 @@ class StudyModel(db.Model):
class WorkflowMetadata(object):
def __init__(self, id, name, display_name, description, spec_version, category_id, state: WorkflowState, status: WorkflowStatus,
def __init__(self, id, name, display_name, description, spec_version, category_id, category_display_name, state: WorkflowState, status: WorkflowStatus,
total_tasks, completed_tasks, display_order):
self.id = id
self.name = name
@ -48,6 +48,7 @@ class WorkflowMetadata(object):
self.description = description
self.spec_version = spec_version
self.category_id = category_id
self.category_display_name = category_display_name
self.state = state
self.status = status
self.total_tasks = total_tasks
@ -64,6 +65,7 @@ class WorkflowMetadata(object):
description=workflow.workflow_spec.description,
spec_version=workflow.spec_version(),
category_id=workflow.workflow_spec.category_id,
category_display_name=workflow.workflow_spec.category.display_name,
state=WorkflowState.optional,
status=workflow.status,
total_tasks=workflow.total_tasks,
@ -79,7 +81,8 @@ class WorkflowMetadataSchema(ma.Schema):
class Meta:
model = WorkflowMetadata
additional = ["id", "name", "display_name", "description",
"total_tasks", "completed_tasks", "display_order"]
"total_tasks", "completed_tasks", "display_order",
"category_id", "category_display_name"]
unknown = INCLUDE

1
crc/models/task_event.py
View File

@ -56,7 +56,6 @@ class TaskEventSchema(ma.Schema):
study = fields.Nested(StudySchema, dump_only=True)
workflow = fields.Nested(WorkflowMetadataSchema, dump_only=True)
class Meta:
model = TaskEvent
additional = ["id", "user_uid", "action", "task_id", "task_title",

29
crc/services/workflow_processor.py
View File

@ -17,12 +17,13 @@ from SpiffWorkflow.dmn.parser.BpmnDmnParser import BpmnDmnParser
from SpiffWorkflow.exceptions import WorkflowTaskExecException
from SpiffWorkflow.specs import WorkflowSpec
from crc import session
from crc import session, app
from crc.api.common import ApiError
from crc.models.file import FileDataModel, FileModel, FileType
from crc.models.workflow import WorkflowStatus, WorkflowModel, WorkflowSpecDependencyFile
from crc.scripts.script import Script
from crc.services.file_service import FileService
from crc import app
class CustomBpmnScriptEngine(BpmnScriptEngine):
@ -30,17 +31,29 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
Rather than execute arbitrary code, this assumes the script references a fully qualified python class
such as myapp.RandomFact. """
def execute(self, task: SpiffTask, script, **kwargs):
def execute(self, task: SpiffTask, script, data):
"""
Assume that the script read in from the BPMN file is a fully qualified python class. Instantiate
that class, pass in any data available to the current task so that it might act on it.
Assume that the class implements the "do_task" method.
This allows us to reference custom code from the BPMN diagram.
Functions in two modes.
1. If the command is proceeded by #! then this is assumed to be a python script, and will
attempt to load that python module and execute the do_task method on that script. Scripts
must be located in the scripts package and they must extend the script.py class.
2. If not proceeded by the #! this will attempt to execute the script directly and assumes it is
valid Python.
"""
# Shlex splits the whole string while respecting double quoted strings within
if not script.startswith('#!'):
try:
super().execute(task, script, data)
except SyntaxError as e:
raise ApiError.from_task('syntax_error',
f'If you are running a pre-defined script, please'
f' proceed the script with "#!", otherwise this is assumed to be'
f' pure python: {script}, {e.msg}', task=task)
else:
self.run_predefined_script(task, script[2:], data) # strip off the first two characters.
def run_predefined_script(self, task: SpiffTask, script, data):
commands = shlex.split(script)
printable_comms = commands
path_and_command = commands[0].rsplit(".", 1)
if len(path_and_command) == 1:
module_name = "crc.scripts." + self.camel_to_snake(path_and_command[0])

37
crc/services/workflow_service.py
View File

@ -376,7 +376,7 @@ class WorkflowService(object):
try:
task.title = spiff_task.workflow.script_engine.evaluate_expression(spiff_task, task.properties['display_name'])
except Exception as e:
app.logger.info("Failed to set title on task due to type error." + str(e))
app.logger.error("Failed to set title on task due to type error." + str(e), exc_info=True)
elif task.title and ' ' in task.title:
task.title = task.title.partition(' ')[2]
return task
@ -516,41 +516,6 @@ class WorkflowService(object):
db.session.add(task_event)
db.session.commit()
@staticmethod
def fix_legacy_data_model_for_rrt():
""" Remove this after use! This is just to fix RRT so the data is handled correctly.
Utility that is likely called via the flask command line, it will loop through all the
workflows in the system and attempt to add the right data into the task action log so that
users do not have to re fill out all of the forms if they start over or go back in the workflow.
Viciously inefficient, but should only have to run one time for RRT"""
workflows = db.session.query(WorkflowModel).all()
for workflow_model in workflows:
task_logs = db.session.query(TaskEventModel) \
.filter(TaskEventModel.workflow_id == workflow_model.id) \
.filter(TaskEventModel.action == WorkflowService.TASK_ACTION_COMPLETE) \
.order_by(TaskEventModel.date.desc()).all()
processor = WorkflowProcessor(workflow_model)
# Grab all the data from last task completed, which will be everything in this
# rrt situation because of how we were keeping all the data at the time.
latest_data = processor.next_task().data
# Move forward in the task spec tree, dropping any data that would have been
# added in subsequent tasks, just looking at form data, will not track the automated
# task data additions, hopefully this doesn't hang us.
for log in task_logs:
# if log.task_data is not None: # Only do this if the task event does not have data populated in it.
# continue
data = copy.deepcopy(latest_data) # Or you end up with insane crazy issues.
# In the simple case of RRT, there is exactly one task for the given task_spec
task = processor.bpmn_workflow.get_tasks_from_spec_name(log.task_name)[0]
data = WorkflowService.extract_form_data(data, task)
log.form_data = data
db.session.add(log)
db.session.commit()
@staticmethod
def extract_form_data(latest_data, task):
"""Removes data from latest_data that would be added by the child task or any of its children."""

4
crc/static/bpmn/core_info/core_info.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_0be39yr" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_0be39yr" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_1cme33c" isExecutable="false">
<bpmn:parallelGateway id="ParallelGateway_0ecwf3g">
<bpmn:incoming>Flow_1wqp7vf</bpmn:incoming>
@ -212,7 +212,7 @@
<bpmn:scriptTask id="Activity_10nxpt2" name="Load Study Details">
<bpmn:incoming>SequenceFlow_1r3yrhy</bpmn:incoming>
<bpmn:outgoing>Flow_09h1imz</bpmn:outgoing>
<bpmn:script>StudyInfo details</bpmn:script>
<bpmn:script>#! StudyInfo details</bpmn:script>
</bpmn:scriptTask>
<bpmn:businessRuleTask id="Activity_PBMultiSiteCheckQ12" name="PB Multi-Site Check Q12" camunda:decisionRef="Decision_core_info_multi_site_q12">
<bpmn:incoming>Flow_09h1imz</bpmn:incoming>

4
crc/static/bpmn/data_security_plan/data_security_plan.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_1wv9t3c" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_1wv9t3c" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_19ej1y2" name="Data Securty Plan" isExecutable="true">
<bpmn:startEvent id="StartEvent_1co48s3">
<bpmn:outgoing>SequenceFlow_100w7co</bpmn:outgoing>
@ -453,7 +453,7 @@ Indicate all the possible formats in which you will transmit your data outside o
<bpmn:incoming>SequenceFlow_0k2r83n</bpmn:incoming>
<bpmn:incoming>SequenceFlow_0t6xl9i</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_16kyite</bpmn:outgoing>
<bpmn:script>CompleteTemplate NEW_DSP_template.docx Study_DataSecurityPlan</bpmn:script>
<bpmn:script>#! CompleteTemplate NEW_DSP_template.docx Study_DataSecurityPlan</bpmn:script>
</bpmn:scriptTask>
<bpmn:manualTask id="Task_0q6ir2l" name="View Instructions">
<bpmn:documentation>##### Instructions

7
crc/static/bpmn/documents_approvals/documents_approvals.bpmn
View File

@ -41,8 +41,7 @@
{%- else -%}
| {{doc.display_name}} | Not started | [?](/help/documents/{{doc.code}}) | No file yet |
{%- endif %}
{% endif %}{% endfor %}
</bpmn:documentation>
{% endif %}{% endfor %}</bpmn:documentation>
<bpmn:extensionElements>
<camunda:properties>
<camunda:property name="display_name" value="Documents and Approvals" />
@ -54,12 +53,12 @@
<bpmn:scriptTask id="Activity_0a14x7j" name="Load Approvals">
<bpmn:incoming>Flow_0c7ryff</bpmn:incoming>
<bpmn:outgoing>Flow_142jtxs</bpmn:outgoing>
<bpmn:script>StudyInfo approvals</bpmn:script>
<bpmn:script>#! StudyInfo approvals</bpmn:script>
</bpmn:scriptTask>
<bpmn:scriptTask id="Activity_1aju60t" name="Load Documents">
<bpmn:incoming>Flow_1k3su2q</bpmn:incoming>
<bpmn:outgoing>Flow_0c7ryff</bpmn:outgoing>
<bpmn:script>StudyInfo documents</bpmn:script>
<bpmn:script>#! StudyInfo documents</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_142jtxs" sourceRef="Activity_0a14x7j" targetRef="Activity_DisplayDocsAndApprovals" />
<bpmn:sequenceFlow id="Flow_0c7ryff" sourceRef="Activity_1aju60t" targetRef="Activity_0a14x7j" />

4
crc/static/bpmn/ide_supplement/ide_supplement.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_1e7871f" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_1e7871f" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_04jm0bm" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1dhb8f4</bpmn:outgoing>
@ -36,7 +36,7 @@
<bpmn:scriptTask id="ScriptTask_1fn00ox" name="Load IRB Details">
<bpmn:incoming>SequenceFlow_1dhb8f4</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1uzcl1f</bpmn:outgoing>
<bpmn:script>StudyInfo details</bpmn:script>
<bpmn:script>#! StudyInfo details</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1uzcl1f" sourceRef="ScriptTask_1fn00ox" targetRef="Task_SupplementIDE" />
<bpmn:exclusiveGateway id="ExclusiveGateway_1fib89p" name="IS_IDE = True and Number Provided?&#10;&#10;">

4
crc/static/bpmn/ids_full_submission/ids_full_submission.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_07f7kut" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.0.0">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_07f7kut" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_IDS" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1dexemq</bpmn:outgoing>
@ -217,7 +217,7 @@ Protocol Owner: **(need to insert value here)**</bpmn:documentation>
<bpmn:scriptTask id="Activity_LoadDocuments" name="Load Documents">
<bpmn:incoming>SequenceFlow_1dexemq</bpmn:incoming>
<bpmn:outgoing>Flow_1x9d2mo</bpmn:outgoing>
<bpmn:script>StudyInfo documents</bpmn:script>
<bpmn:script>#! StudyInfo documents</bpmn:script>
</bpmn:scriptTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">

2
crc/static/bpmn/ind_update/ind_update.bpmn
View File

@ -12,7 +12,7 @@
<bpmn:scriptTask id="ScriptTask_LoadIRBDetails" name="Load IRB Details">
<bpmn:incoming>SequenceFlow_1dhb8f4</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1uzcl1f</bpmn:outgoing>
<bpmn:script>StudyInfo details</bpmn:script>
<bpmn:script>#! StudyInfo details</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1uzcl1f" sourceRef="ScriptTask_LoadIRBDetails" targetRef="Task_SupplementIDE" />
<bpmn:businessRuleTask id="Task_SupplementIDE" name="Current IND Status" camunda:decisionRef="decision_ind_check">

4
crc/static/bpmn/irb_api_details/irb_api_details.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_00j2iu5" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_00j2iu5" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_1gmf4la" isExecutable="true">
<bpmn:documentation />
<bpmn:startEvent id="StartEvent_1">
@ -8,7 +8,7 @@
<bpmn:scriptTask id="ScriptTask_02924vs" name="Load IRB Details">
<bpmn:incoming>SequenceFlow_1fmyo77</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_18nr0gf</bpmn:outgoing>
<bpmn:script>StudyInfo details</bpmn:script>
<bpmn:script>#! StudyInfo details</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1fmyo77" sourceRef="StartEvent_1" targetRef="ScriptTask_02924vs" />
<bpmn:sequenceFlow id="SequenceFlow_18nr0gf" sourceRef="ScriptTask_02924vs" targetRef="Activity_FromIRB-API" />

24
crc/static/bpmn/irb_api_personnel/irb_api_personnel.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_06pyjz2" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_06pyjz2" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_01143nb" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>Flow_0kcrx5l</bpmn:outgoing>
@ -7,7 +7,7 @@
<bpmn:scriptTask id="ScriptTask_LoadPersonnel" name="Load IRB Personnel">
<bpmn:incoming>Flow_0kcrx5l</bpmn:incoming>
<bpmn:outgoing>Flow_1dcsioh</bpmn:outgoing>
<bpmn:script>StudyInfo investigators</bpmn:script>
<bpmn:script>#! StudyInfo investigators</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_1qor16n">
<bpmn:documentation>## The following information was gathered:
@ -54,28 +54,28 @@
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_01143nb">
<bpmndi:BPMNEdge id="Flow_1dcsioh_di" bpmnElement="Flow_1dcsioh">
<di:waypoint x="480" y="120" />
<di:waypoint x="540" y="120" />
<di:waypoint x="360" y="120" />
<di:waypoint x="420" y="120" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1mplloa_di" bpmnElement="Flow_1mplloa">
<di:waypoint x="640" y="120" />
<di:waypoint x="722" y="120" />
<di:waypoint x="520" y="120" />
<di:waypoint x="602" y="120" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0kcrx5l_di" bpmnElement="Flow_0kcrx5l">
<di:waypoint x="308" y="120" />
<di:waypoint x="380" y="120" />
<di:waypoint x="188" y="120" />
<di:waypoint x="260" y="120" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="272" y="102" width="36" height="36" />
<dc:Bounds x="152" y="102" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_0h49cmf_di" bpmnElement="ScriptTask_LoadPersonnel">
<dc:Bounds x="380" y="80" width="100" height="80" />
<dc:Bounds x="260" y="80" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0d622qi_di" bpmnElement="Activity_EditOtherPersonnel">
<dc:Bounds x="540" y="80" width="100" height="80" />
<dc:Bounds x="420" y="80" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_1qor16n_di" bpmnElement="EndEvent_1qor16n">
<dc:Bounds x="722" y="102" width="36" height="36" />
<dc:Bounds x="602" y="102" width="36" height="36" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>

8
crc/static/bpmn/research_rampup/research_rampup.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_1oogn9j" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_1oogn9j" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_0ssahs9" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_05ja25w</bpmn:outgoing>
@ -598,7 +598,7 @@ Use the EHS [Lab Safety Plan During COVID 19 template](https://www.google.com/ur
This step is internal to the system and do not require and user interaction</bpmn:documentation>
<bpmn:incoming>Flow_11uqavk</bpmn:incoming>
<bpmn:outgoing>Flow_0aqgwvu</bpmn:outgoing>
<bpmn:script>CompleteTemplate ResearchRampUpPlan.docx RESEARCH_RAMPUP</bpmn:script>
<bpmn:script>#! CompleteTemplate ResearchRampUpPlan.docx RESEARCH_RAMPUP</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_0aqgwvu" sourceRef="Activity_GenerateRRP" targetRef="Activity_AcknowledgePlanReview" />
<bpmn:sequenceFlow id="Flow_0j4rs82" sourceRef="Activity_SubmitPlan" targetRef="Activity_0absozl" />
@ -755,7 +755,7 @@ Notify the Area Monitor for
This step is internal to the system and do not require and user interaction</bpmn:documentation>
<bpmn:incoming>Flow_0j4rs82</bpmn:incoming>
<bpmn:outgoing>Flow_07ge8uf</bpmn:outgoing>
<bpmn:script>RequestApproval ApprvlApprvr1 ApprvlApprvr2</bpmn:script>
<bpmn:script>#!RequestApproval ApprvlApprvr1 ApprvlApprvr2</bpmn:script>
</bpmn:scriptTask>
<bpmn:scriptTask id="Activity_1u58hox" name="Update Request">
<bpmn:documentation>#### Script Task
@ -764,7 +764,7 @@ This step is internal to the system and do not require and user interaction</bpm
This step is internal to the system and do not require and user interaction</bpmn:documentation>
<bpmn:incoming>Flow_16y8glw</bpmn:incoming>
<bpmn:outgoing>Flow_0uc4o6c</bpmn:outgoing>
<bpmn:script>UpdateStudy title:PIComputingID.label pi:PIComputingID.value</bpmn:script>
<bpmn:script>#! UpdateStudy title:PIComputingID.label pi:PIComputingID.value</bpmn:script>
</bpmn:scriptTask>
<bpmn:userTask id="PersonnelSchedule" name="Upload Weekly Personnel Schedule(s)" camunda:formKey="Personnel Weekly Schedule">
<bpmn:documentation>#### Weekly Personnel Schedule(s)

6
crc/static/bpmn/top_level_workflow/top_level_workflow.bpmn
View File

@ -11,7 +11,7 @@
<bpmn:scriptTask id="Task_Load_Requirements" name="Load Documents From PB">
<bpmn:incoming>SequenceFlow_1ees8ka</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_17ct47v</bpmn:outgoing>
<bpmn:script>StudyInfo documents</bpmn:script>
<bpmn:script>#! StudyInfo documents</bpmn:script>
</bpmn:scriptTask>
<bpmn:businessRuleTask id="Activity_1yqy50i" name="Enter Core Info&#10;" camunda:decisionRef="enter_core_info">
<bpmn:incoming>Flow_1m8285h</bpmn:incoming>
@ -62,7 +62,7 @@
<bpmn:scriptTask id="Activity_0f295la" name="Load Details from PB">
<bpmn:incoming>Flow_0pwtiqm</bpmn:incoming>
<bpmn:outgoing>Flow_0eq6px2</bpmn:outgoing>
<bpmn:script>StudyInfo details</bpmn:script>
<bpmn:script>#! StudyInfo details</bpmn:script>
</bpmn:scriptTask>
<bpmn:businessRuleTask id="Activity_0ahlc3u" name="IDE Supplement" camunda:decisionRef="decision_ide_menu_check">
<bpmn:incoming>Flow_14ce1d7</bpmn:incoming>
@ -91,7 +91,7 @@
<bpmn:scriptTask id="Activity_0g3qa1c" name="Load Personnel from PB">
<bpmn:incoming>Flow_1qyrmzn</bpmn:incoming>
<bpmn:outgoing>Flow_0vo6ul1</bpmn:outgoing>
<bpmn:script>StudyInfo investigators</bpmn:script>
<bpmn:script>#! StudyInfo investigators</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_1ybicki" sourceRef="Activity_13ep6ar" targetRef="Event_135x8jg" />
<bpmn:businessRuleTask id="Activity_13ep6ar" name="Personnel" camunda:decisionRef="personnel">

6
docker_run.sh
View File

@ -23,12 +23,6 @@ if [ "$RESET_DB_RRT" = "true" ]; then
pipenv run flask load-example-rrt-data
fi
if [ "$FIX_RRT_DATA" = "true" ]; then
echo 'Fixing RRT data...'
pipenv run flask rrt-data-fix
fi
# THIS MUST BE THE LAST COMMAND!
if [ "$APPLICATION_ROOT" = "/" ]; then
pipenv run gunicorn --bind 0.0.0.0:$PORT0 wsgi:app

1
example_data.py
View File

@ -251,7 +251,6 @@ class ExampleDataLoader:
master_spec=False,
from_tests=True)
def create_spec(self, id, name, display_name="", description="", filepath=None, master_spec=False,
category_id=None, display_order=None, from_tests=False):
"""Assumes that a directory exists in static/bpmn with the same name as the given id.

19
tests/base_test.py
View File

@ -19,7 +19,7 @@ from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.task_event import TaskEventModel
from crc.models.study import StudyModel
from crc.models.user import UserModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.services.workflow_service import WorkflowService
@ -164,14 +164,21 @@ class BaseTest(unittest.TestCase):
self.assertGreater(len(file_data), 0)
@staticmethod
def load_test_spec(dir_name, master_spec=False, category_id=None):
def load_test_spec(dir_name, display_name=None, master_spec=False, category_id=None):
"""Loads a spec into the database based on a directory in /tests/data"""
if category_id is None:
category = WorkflowSpecCategoryModel(name="test", display_name="Test Workflows", display_order=0)
db.session.add(category)
db.session.commit()
category_id = category.id
if session.query(WorkflowSpecModel).filter_by(id=dir_name).count() > 0:
return session.query(WorkflowSpecModel).filter_by(id=dir_name).first()
filepath = os.path.join(app.root_path, '..', 'tests', 'data', dir_name, "*")
if display_name is None:
display_name = dir_name
return ExampleDataLoader().create_spec(id=dir_name, name=dir_name, filepath=filepath, master_spec=master_spec,
category_id=category_id)
display_name=display_name, category_id=category_id)
@staticmethod
def protocol_builder_response(file_name):
@ -263,11 +270,13 @@ class BaseTest(unittest.TestCase):
return full_study
def create_workflow(self, workflow_name, study=None, category_id=None, as_user="dhf8r"):
def create_workflow(self, workflow_name, display_name=None, study=None, category_id=None, as_user="dhf8r"):
db.session.flush()
spec = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
if spec is None:
spec = self.load_test_spec(workflow_name, category_id=category_id)
if display_name is None:
display_name = workflow_name
spec = self.load_test_spec(workflow_name, display_name, category_id=category_id)
if study is None:
study = self.create_study(uid=as_user)
workflow_model = StudyService._create_workflow_model(study, spec)

4
tests/data/docx/docx.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_96a17d9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_96a17d9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_93a29b3" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0637d8i</bpmn:outgoing>
@ -27,7 +27,7 @@
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_1i7hk1a</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_11c35oq</bpmn:outgoing>
<bpmn:script>CompleteTemplate Letter.docx AD_CoCApp</bpmn:script>
<bpmn:script>#! CompleteTemplate Letter.docx AD_CoCApp</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_0evb22x">
<bpmn:incoming>SequenceFlow_11c35oq</bpmn:incoming>

4
tests/data/email/email.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0y2dq4f" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0y2dq4f" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_0tad5ma" name="Set Recipients" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>Flow_1synsig</bpmn:outgoing>
@ -20,7 +20,7 @@ Email content to be delivered to {{ ApprvlApprvr1 }}
---</bpmn:documentation>
<bpmn:incoming>Flow_08n2npe</bpmn:incoming>
<bpmn:outgoing>Flow_1xlrgne</bpmn:outgoing>
<bpmn:script>Email "Camunda Email Subject" ApprvlApprvr1 PIComputingID</bpmn:script>
<bpmn:script>#! Email "Camunda Email Subject" ApprvlApprvr1 PIComputingID</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_1synsig" sourceRef="StartEvent_1" targetRef="Activity_1l9vih3" />
<bpmn:sequenceFlow id="Flow_1xlrgne" sourceRef="Activity_0s5v97n" targetRef="Event_0izrcj4" />

4
tests/data/invalid_script/invalid_script.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1j7idla" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1j7idla" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_18biih5" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1pnq3kg</bpmn:outgoing>
@ -11,7 +11,7 @@
<bpmn:scriptTask id="Invalid_Script_Task" name="An Invalid Script Reference">
<bpmn:incoming>SequenceFlow_1pnq3kg</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_12pf6um</bpmn:outgoing>
<bpmn:script>NoSuchScript withArg1</bpmn:script>
<bpmn:script>#! NoSuchScript withArg1</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_12pf6um" sourceRef="Invalid_Script_Task" targetRef="EndEvent_063bpg6" />
</bpmn:process>

39
tests/data/invalid_script2/invalid_script2.bpmn Normal file
View File

@ -0,0 +1,39 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1j7idla" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_18biih5" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1pnq3kg</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="SequenceFlow_1pnq3kg" sourceRef="StartEvent_1" targetRef="Invalid_Script_Task" />
<bpmn:endEvent id="EndEvent_063bpg6">
<bpmn:incoming>SequenceFlow_12pf6um</bpmn:incoming>
</bpmn:endEvent>
<bpmn:scriptTask id="Invalid_Script_Task" name="An Invalid Script Reference">
<bpmn:incoming>SequenceFlow_1pnq3kg</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_12pf6um</bpmn:outgoing>
<bpmn:script>a really bad error that should fail</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_12pf6um" sourceRef="Invalid_Script_Task" targetRef="EndEvent_063bpg6" />
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_18biih5">
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_1pnq3kg_di" bpmnElement="SequenceFlow_1pnq3kg">
<di:waypoint x="215" y="117" />
<di:waypoint x="290" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="EndEvent_063bpg6_di" bpmnElement="EndEvent_063bpg6">
<dc:Bounds x="442" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_1imeym0_di" bpmnElement="Invalid_Script_Task">
<dc:Bounds x="290" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_12pf6um_di" bpmnElement="SequenceFlow_12pf6um">
<di:waypoint x="390" y="117" />
<di:waypoint x="442" y="117" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

4
tests/data/multi_instance/multi_instance.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_17fwemw" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_17fwemw" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="MultiInstance" isExecutable="true">
<bpmn:startEvent id="StartEvent_1" name="StartEvent_1">
<bpmn:outgoing>Flow_0t6p1sb</bpmn:outgoing>
@ -29,7 +29,7 @@
<bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
<bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
<bpmn:script>StudyInfo investigators</bpmn:script>
<bpmn:script>#! StudyInfo investigators</bpmn:script>
</bpmn:scriptTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">

4
tests/data/multi_instance_parallel/multi_instance_parallel.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_17fwemw" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_17fwemw" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="MultiInstance" isExecutable="true">
<bpmn:startEvent id="StartEvent_1" name="StartEvent_1">
<bpmn:outgoing>Flow_0t6p1sb</bpmn:outgoing>
@ -29,7 +29,7 @@
<bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
<bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
<bpmn:script>StudyInfo investigators</bpmn:script>
<bpmn:script>#! StudyInfo investigators</bpmn:script>
</bpmn:scriptTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">

4
tests/data/random_fact/random_fact.bpmn
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@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1gjhqt9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1gjhqt9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_1ds61df" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0c7wlth</bpmn:outgoing>
@ -132,7 +132,7 @@ Autoconverted link https://github.com/nodeca/pica (enable linkify to see)
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0641sh6</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_0t29gjo</bpmn:outgoing>
<bpmn:script>FactService</bpmn:script>
<bpmn:script>#! FactService</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_0u1cgrf">
<bpmn:documentation># Great Job!

4
tests/data/study_details/study_details.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_0exnnpv" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
@ -8,7 +8,7 @@
<bpmn:scriptTask id="Task_Script_Load_Study_Details" name="Load Study Info">
<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
<bpmn:script>StudyInfo info</bpmn:script>
<bpmn:script>#! StudyInfo info</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Details" targetRef="EndEvent_171dj09" />
<bpmn:endEvent id="EndEvent_171dj09">

4
tests/data/top_level_workflow/top_level_workflow.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1kudwnk" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1kudwnk" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_0jhpidf" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1ees8ka</bpmn:outgoing>
@ -11,7 +11,7 @@
<bpmn:scriptTask id="Task_Load_Requirements" name="Load Required Documents From PM">
<bpmn:incoming>SequenceFlow_1ees8ka</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_17ct47v</bpmn:outgoing>
<bpmn:script>StudyInfo documents</bpmn:script>
<bpmn:script>#! StudyInfo documents</bpmn:script>
</bpmn:scriptTask>
<bpmn:businessRuleTask id="Activity_1yqy50i" name="Enter Core Info&#10;" camunda:decisionRef="enter_core_info">
<bpmn:incoming>Flow_1m8285h</bpmn:incoming>

9
tests/study/test_study_service.py
View File

@ -27,7 +27,10 @@ class TestStudyService(BaseTest):
# Assure some basic models are in place, This is a damn mess. Our database models need an overhaul to make
# this easier - better relationship modeling is now critical.
self.load_test_spec("top_level_workflow", master_spec=True)
cat = WorkflowSpecCategoryModel(name="approvals", display_name="Approvals", display_order=0)
db.session.add(cat)
db.session.commit()
self.load_test_spec("top_level_workflow", master_spec=True, category_id=cat.id)
user = db.session.query(UserModel).filter(UserModel.uid == "dhf8r").first()
if not user:
user = UserModel(uid="dhf8r", email_address="whatever@stuff.com", display_name="Stayathome Smellalots")
@ -39,11 +42,7 @@ class TestStudyService(BaseTest):
study = StudyModel(title="My title", protocol_builder_status=ProtocolBuilderStatus.ACTIVE, user_uid=user.uid)
db.session.add(study)
cat = WorkflowSpecCategoryModel(name="approvals", display_name="Approvals", display_order=0)
db.session.add(cat)
db.session.commit()
self.assertIsNotNone(cat.id)
self.load_test_spec("random_fact", category_id=cat.id)
self.assertIsNotNone(study.id)

3
tests/test_user_roles.py
View File

@ -68,7 +68,7 @@ class TestTasksApi(BaseTest):
def test_get_outstanding_tasks_awaiting_current_user(self):
submitter = self.create_user(uid='lje5u')
supervisor = self.create_user(uid='lb3dp')
workflow = self.create_workflow('roles', as_user=submitter.uid)
workflow = self.create_workflow('roles', display_name="Roles", as_user=submitter.uid)
workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid)
# User lje5u can complete the first task, and set her supervisor
@ -94,6 +94,7 @@ class TestTasksApi(BaseTest):
self.assertEquals(1, len(tasks))
self.assertEquals(workflow.id, tasks[0]['workflow']['id'])
self.assertEquals(workflow.study.id, tasks[0]['study']['id'])
self.assertEquals("Test Workflows", tasks[0]['workflow']['category_display_name'])
# Assure we can say something sensible like:
# You have a task called "Approval" to be completed in the "Supervisor Approval" workflow

44
tests/workflow/test_workflow_service.py
View File

@ -89,50 +89,6 @@ class TestWorkflowService(BaseTest):
WorkflowService.populate_form_with_random_data(task, task_api, required_only=False)
self.assertTrue(isinstance(task.data["sponsor"], dict))
@unittest.skip("RRT no longer needs to be supported")
def test_fix_legacy_data_model_for_rrt(self):
ExampleDataLoader().load_rrt() # Make sure the research_rampup is loaded, as it's not a test spec.
workflow = self.create_workflow('research_rampup')
processor = WorkflowProcessor(workflow, validate_only=True)
# Use the test spec code to complete the workflow of research rampup.
while not processor.bpmn_workflow.is_completed():
processor.bpmn_workflow.do_engine_steps()
tasks = processor.bpmn_workflow.get_tasks(SpiffTask.READY)
for task in tasks:
task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
WorkflowService.populate_form_with_random_data(task, task_api, False)
task.complete()
# create the task events
WorkflowService.log_task_action('dhf8r', processor, task,
WorkflowService.TASK_ACTION_COMPLETE)
processor.save()
db.session.commit()
WorkflowService.fix_legacy_data_model_for_rrt()
# All tasks should now have data associated with them.
task_logs = db.session.query(TaskEventModel) \
.filter(TaskEventModel.workflow_id == workflow.id) \
.filter(TaskEventModel.action == WorkflowService.TASK_ACTION_COMPLETE) \
.order_by(TaskEventModel.date).all() # Get them back in order.
self.assertEqual(17, len(task_logs))
for log in task_logs:
task = processor.bpmn_workflow.get_tasks_from_spec_name(log.task_name)[0]
self.assertIsNotNone(log.form_data)
# Each task should have the data in the form for that task in the task event.
if hasattr(task.task_spec, 'form'):
for field in task.task_spec.form.fields:
if field.has_property(Task.PROP_OPTIONS_REPEAT):
self.assertIn(field.get_property(Task.PROP_OPTIONS_REPEAT), log.form_data)
else:
self.assertIn(field.id, log.form_data)
# Some spot checks:
# The first task should be empty, with all the data removed.
self.assertEqual({}, task_logs[0].form_data)
def test_dmn_evaluation_errors_in_oncomplete_raise_api_errors_during_validation(self):
workflow_spec_model = self.load_test_spec("decision_table_invalid")
with self.assertRaises(ApiError):

14
tests/workflow/test_workflow_spec_validation_api.py
View File

@ -52,10 +52,6 @@ class TestWorkflowSpecValidation(BaseTest):
app.config['PB_ENABLED'] = True
self.validate_all_loaded_workflows()
@unittest.skip("RRT no longer needs to be supported")
def test_successful_validation_of_rrt_workflows(self):
self.load_example_data(use_rrt_data=True)
self.validate_all_loaded_workflows()
def validate_all_loaded_workflows(self):
workflows = session.query(WorkflowSpecModel).all()
@ -68,7 +64,6 @@ class TestWorkflowSpecValidation(BaseTest):
errors.extend(ApiErrorSchema(many=True).load(json_data))
self.assertEqual(0, len(errors), json.dumps(errors))
def test_invalid_expression(self):
self.load_example_data()
errors = self.validate_workflow("invalid_expression")
@ -100,6 +95,15 @@ class TestWorkflowSpecValidation(BaseTest):
self.assertEqual("An Invalid Script Reference", errors[0]['task_name'])
self.assertEqual("invalid_script.bpmn", errors[0]['file_name'])
def test_invalid_script2(self):
self.load_example_data()
errors = self.validate_workflow("invalid_script2")
self.assertEqual(2, len(errors))
self.assertEqual("error_loading_workflow", errors[0]['code'])
self.assertEqual("Invalid_Script_Task", errors[0]['task_id'])
self.assertEqual("An Invalid Script Reference", errors[0]['task_name'])
self.assertEqual("invalid_script2.bpmn", errors[0]['file_name'])
def test_repeating_sections_correctly_populated(self):
self.load_example_data()
spec_model = self.load_test_spec('repeat_form')