{}'.format(json_value))
+
+class TaskEventView(AdminModelView):
+ column_filters = ['workflow_id', 'action']
+ column_list = ['study_id', 'user_id', 'workflow_id', 'action', 'task_title', 'form_data', 'date']
+ column_formatters = {
+ 'form_data': json_formatter,
+ }
+
+admin = Admin(app)
+
+admin.add_view(StudyView(StudyModel, db.session))
+admin.add_view(ApprovalView(ApprovalModel, db.session))
+admin.add_view(UserView(UserModel, db.session))
+admin.add_view(WorkflowView(WorkflowModel, db.session))
+admin.add_view(FileView(FileModel, db.session))
+admin.add_view(TaskEventView(TaskEventModel, db.session))
diff --git a/crc/api/approval.py b/crc/api/approval.py
index b3ee0fed..fd01e221 100644
--- a/crc/api/approval.py
+++ b/crc/api/approval.py
@@ -1,9 +1,11 @@
+import csv
+import io
import json
import pickle
from base64 import b64decode
from datetime import datetime
-from flask import g
+from flask import g, make_response
from crc import db, session
from crc.api.common import ApiError
@@ -88,71 +90,25 @@ def get_approvals_for_study(study_id=None):
return results
+def get_health_attesting_csv():
+ records = ApprovalService.get_health_attesting_records()
+ si = io.StringIO()
+ cw = csv.writer(si)
+ cw.writerows(records)
+ output = make_response(si.getvalue())
+ output.headers["Content-Disposition"] = "attachment; filename=health_attesting.csv"
+ output.headers["Content-type"] = "text/csv"
+ return output
+
+
# ----- Begin descent into madness ---- #
def get_csv():
"""A damn lie, it's a json file. A huge bit of a one-off for RRT, but 3 weeks of midnight work can convince a
man to do just about anything"""
- approvals = ApprovalService.get_all_approvals(include_cancelled=False)
- output = []
- errors = []
- for approval in approvals:
- try:
- if approval.status != ApprovalStatus.APPROVED.value:
- continue
- for related_approval in approval.related_approvals:
- if related_approval.status != ApprovalStatus.APPROVED.value:
- continue
- workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == approval.workflow_id).first()
- data = json.loads(workflow.bpmn_workflow_json)
- last_task = find_task(data['last_task']['__uuid__'], data['task_tree'])
- personnel = extract_value(last_task, 'personnel')
- training_val = extract_value(last_task, 'RequiredTraining')
- pi_supervisor = extract_value(last_task, 'PISupervisor')['value']
- review_complete = 'AllRequiredTraining' in training_val
- pi_uid = workflow.study.primary_investigator_id
- pi_details = LdapService.user_info(pi_uid)
- details = []
- details.append(pi_details)
- for person in personnel:
- uid = person['PersonnelComputingID']['value']
- details.append(LdapService.user_info(uid))
+ content = ApprovalService.get_not_really_csv_content()
- for person in details:
- record = {
- "study_id": approval.study_id,
- "pi_uid": pi_details.uid,
- "pi": pi_details.display_name,
- "name": person.display_name,
- "uid": person.uid,
- "email": person.email_address,
- "supervisor": "",
- "review_complete": review_complete,
- }
- # We only know the PI's supervisor.
- if person.uid == pi_details.uid:
- record["supervisor"] = pi_supervisor
+ return content
- output.append(record)
-
- except Exception as e:
- errors.append("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
- return {"results": output, "errors": errors }
-
-
-def extract_value(task, key):
- if key in task['data']:
- return pickle.loads(b64decode(task['data'][key]['__bytes__']))
- else:
- return ""
-
-
-def find_task(uuid, task):
- if task['id']['__uuid__'] == uuid:
- return task
- for child in task['children']:
- task = find_task(uuid, child)
- if task:
- return task
# ----- come back to the world of the living ---- #
diff --git a/crc/api/common.py b/crc/api/common.py
index f8673a5b..cb527c73 100644
--- a/crc/api/common.py
+++ b/crc/api/common.py
@@ -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
diff --git a/crc/api/tools.py b/crc/api/tools.py
index d140e962..de30d10d 100644
--- a/crc/api/tools.py
+++ b/crc/api/tools.py
@@ -2,6 +2,7 @@ import io
import json
import connexion
+from SpiffWorkflow.bpmn.PythonScriptEngine import PythonScriptEngine
from flask import send_file
from jinja2 import Template, UndefinedError
@@ -10,11 +11,12 @@ from crc.scripts.complete_template import CompleteTemplate
from crc.scripts.script import Script
import crc.scripts
from crc.services.mails import send_test_email
+from crc.services.workflow_processor import WorkflowProcessor
def render_markdown(data, template):
"""
- Provides a quick way to very that a Jinja markdown template will work properly on a given json
+ Provides a quick way to very that a Jinja markdown template will work properly on a given json
data structure. Useful for folks that are building these markdown templates.
"""
try:
@@ -61,8 +63,22 @@ def list_scripts():
})
return script_meta
+
def send_email(address):
"""Just sends a quick test email to assure the system is working."""
if not address:
address = "dan@sartography.com"
- return send_test_email(address, [address])
\ No newline at end of file
+ return send_test_email(address, [address])
+
+
+def evaluate_python_expression(expression, body):
+ """Evaluate the given python expression, returning it's result. This is useful if the
+ front end application needs to do real-time processing on task data. If for instance
+ there is a hide expression that is based on a previous value in the same form."""
+ try:
+ # fixme: The script engine should be pulled from Workflow Processor,
+ # but the one it returns overwrites the evaluate expression making it uncallable.
+ script_engine = PythonScriptEngine()
+ return script_engine.evaluate(expression, **body)
+ except Exception as e:
+ raise ApiError("expression_error", str(e))
diff --git a/crc/api/workflow.py b/crc/api/workflow.py
index 655a85e7..a290d340 100644
--- a/crc/api/workflow.py
+++ b/crc/api/workflow.py
@@ -1,12 +1,13 @@
import uuid
+from SpiffWorkflow.util.deep_merge import DeepMerge
from flask import g
-
from crc import session, app
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.api_models import WorkflowApi, WorkflowApiSchema, NavigationItem, NavigationItemSchema
from crc.models.file import FileModel, LookupDataSchema
-from crc.models.stats import TaskEventModel
+from crc.models.study import StudyModel, WorkflowMetadata
+from crc.models.task_event import TaskEventModel, TaskEventModelSchema, TaskEvent, TaskEventSchema
from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel, WorkflowSpecCategoryModel, \
WorkflowSpecCategoryModelSchema
from crc.services.file_service import FileService
@@ -41,7 +42,6 @@ def get_workflow_specification(spec_id):
def validate_workflow_specification(spec_id):
-
errors = []
try:
WorkflowService.test_spec(spec_id)
@@ -57,7 +57,6 @@ def validate_workflow_specification(spec_id):
return ApiErrorSchema(many=True).dump(errors)
-
def update_workflow_specification(spec_id, body):
if spec_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.')
@@ -89,115 +88,95 @@ def delete_workflow_specification(spec_id):
session.query(TaskEventModel).filter(TaskEventModel.workflow_spec_id == spec_id).delete()
- # Delete all stats and workflow models related to this specification
+ # Delete all events and workflow models related to this specification
for workflow in session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id):
StudyService.delete_workflow(workflow)
session.query(WorkflowSpecModel).filter_by(id=spec_id).delete()
session.commit()
-def __get_workflow_api_model(processor: WorkflowProcessor, next_task = None):
- """Returns an API model representing the state of the current workflow, if requested, and
- possible, next_task is set to the current_task."""
-
- nav_dict = processor.bpmn_workflow.get_nav_list()
- navigation = []
- for nav_item in nav_dict:
- spiff_task = processor.bpmn_workflow.get_task(nav_item['task_id'])
- if 'description' in nav_item:
- nav_item['title'] = nav_item.pop('description')
- # fixme: duplicate code from the workflow_service. Should only do this in one place.
- if ' ' in nav_item['title']:
- nav_item['title'] = nav_item['title'].partition(' ')[2]
- else:
- nav_item['title'] = ""
- if spiff_task:
- nav_item['task'] = WorkflowService.spiff_task_to_api_task(spiff_task, add_docs_and_forms=False)
- nav_item['title'] = nav_item['task'].title # Prefer the task title.
- else:
- nav_item['task'] = None
- if not 'is_decision' in nav_item:
- nav_item['is_decision'] = False
-
- navigation.append(NavigationItem(**nav_item))
- NavigationItemSchema().dump(nav_item)
-
- spec = session.query(WorkflowSpecModel).filter_by(id=processor.workflow_spec_id).first()
- workflow_api = WorkflowApi(
- id=processor.get_workflow_id(),
- status=processor.get_status(),
- next_task=None,
- navigation=navigation,
- workflow_spec_id=processor.workflow_spec_id,
- spec_version=processor.get_version_string(),
- is_latest_spec=processor.is_latest_spec,
- total_tasks=len(navigation),
- completed_tasks=processor.workflow_model.completed_tasks,
- last_updated=processor.workflow_model.last_updated,
- title=spec.display_name
- )
- if not next_task: # The Next Task can be requested to be a certain task, useful for parallel tasks.
- # This may or may not work, sometimes there is no next task to complete.
- next_task = processor.next_task()
- if next_task:
- workflow_api.next_task = WorkflowService.spiff_task_to_api_task(next_task, add_docs_and_forms=True)
-
- return workflow_api
-
-
def get_workflow(workflow_id, soft_reset=False, hard_reset=False):
workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by(id=workflow_id).first()
processor = WorkflowProcessor(workflow_model, soft_reset=soft_reset, hard_reset=hard_reset)
- workflow_api_model = __get_workflow_api_model(processor)
+ workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
+ WorkflowService.update_task_assignments(processor)
return WorkflowApiSchema().dump(workflow_api_model)
+def get_task_events(action):
+ """Provides a way to see a history of what has happened, or get a list of tasks that need your attention."""
+ query = session.query(TaskEventModel).filter(TaskEventModel.user_uid == g.user.uid)
+ if action:
+ query = query.filter(TaskEventModel.action == action)
+ events = query.all()
+
+ # Turn the database records into something a little richer for the UI to use.
+ task_events = []
+ for event in events:
+ study = session.query(StudyModel).filter(StudyModel.id == event.study_id).first()
+ workflow = session.query(WorkflowModel).filter(WorkflowModel.id == event.workflow_id).first()
+ workflow_meta = WorkflowMetadata.from_workflow(workflow)
+ task_events.append(TaskEvent(event, study, workflow_meta))
+ return TaskEventSchema(many=True).dump(task_events)
+
+
def delete_workflow(workflow_id):
StudyService.delete_workflow(workflow_id)
def set_current_task(workflow_id, task_id):
workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
- user_uid = __get_user_uid(workflow_model.study.user_uid)
processor = WorkflowProcessor(workflow_model)
task_id = uuid.UUID(task_id)
- task = processor.bpmn_workflow.get_task(task_id)
- if task.state != task.COMPLETED and task.state != task.READY:
+ spiff_task = processor.bpmn_workflow.get_task(task_id)
+ _verify_user_and_role(processor, spiff_task)
+ user_uid = g.user.uid
+ if spiff_task.state != spiff_task.COMPLETED and spiff_task.state != spiff_task.READY:
raise ApiError("invalid_state", "You may not move the token to a task who's state is not "
"currently set to COMPLETE or READY.")
# Only reset the token if the task doesn't already have it.
- if task.state == task.COMPLETED:
- task.reset_token(reset_data=False) # we could optionally clear the previous data.
+ if spiff_task.state == spiff_task.COMPLETED:
+ spiff_task.reset_token(reset_data=True) # Don't try to copy the existing data back into this task.
+
processor.save()
- WorkflowService.log_task_action(user_uid, processor, task, WorkflowService.TASK_ACTION_TOKEN_RESET)
- workflow_api_model = __get_workflow_api_model(processor, task)
+ WorkflowService.log_task_action(user_uid, processor, spiff_task, WorkflowService.TASK_ACTION_TOKEN_RESET)
+ WorkflowService.update_task_assignments(processor)
+
+ workflow_api_model = WorkflowService.processor_to_workflow_api(processor, spiff_task)
return WorkflowApiSchema().dump(workflow_api_model)
-def update_task(workflow_id, task_id, body):
+def update_task(workflow_id, task_id, body, terminate_loop=None):
workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
-
if workflow_model is None:
raise ApiError("invalid_workflow_id", "The given workflow id is not valid.", status_code=404)
elif workflow_model.study is None:
raise ApiError("invalid_study", "There is no study associated with the given workflow.", status_code=404)
- user_uid = __get_user_uid(workflow_model.study.user_uid)
processor = WorkflowProcessor(workflow_model)
task_id = uuid.UUID(task_id)
- task = processor.bpmn_workflow.get_task(task_id)
- if task.state != task.READY:
+ spiff_task = processor.bpmn_workflow.get_task(task_id)
+ _verify_user_and_role(processor, spiff_task)
+ if not spiff_task:
+ raise ApiError("empty_task", "Processor failed to obtain task.", status_code=404)
+ if spiff_task.state != spiff_task.READY:
raise ApiError("invalid_state", "You may not update a task unless it is in the READY state. "
"Consider calling a token reset to make this task Ready.")
- task.update_data(body)
- processor.complete_task(task)
+
+ if terminate_loop:
+ spiff_task.terminate_loop()
+ spiff_task.update_data(body)
+ processor.complete_task(spiff_task)
processor.do_engine_steps()
processor.save()
- WorkflowService.log_task_action(user_uid, processor, task, WorkflowService.TASK_ACTION_COMPLETE)
- workflow_api_model = __get_workflow_api_model(processor)
+ # Log the action, and any pending task assignments in the event of lanes in the workflow.
+ WorkflowService.log_task_action(g.user.uid, processor, spiff_task, WorkflowService.TASK_ACTION_COMPLETE)
+ WorkflowService.update_task_assignments(processor)
+
+ workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
return WorkflowApiSchema().dump(workflow_api_model)
@@ -240,7 +219,7 @@ def delete_workflow_spec_category(cat_id):
session.commit()
-def lookup(workflow_id, field_id, query, limit):
+def lookup(workflow_id, field_id, query=None, value=None, limit=10):
"""
given a field in a task, attempts to find the lookup table or function associated
with that field and runs a full-text query against it to locate the values and
@@ -248,16 +227,25 @@ def lookup(workflow_id, field_id, query, limit):
Tries to be fast, but first runs will be very slow.
"""
workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
- lookup_data = LookupService.lookup(workflow, field_id, query, limit)
+ lookup_data = LookupService.lookup(workflow, field_id, query, value, limit)
return LookupDataSchema(many=True).dump(lookup_data)
-def __get_user_uid(user_uid):
- if 'user' in g:
- if g.user.uid not in app.config['ADMIN_UIDS'] and user_uid != g.user.uid:
- raise ApiError("permission_denied", "You are not authorized to edit the task data for this workflow.", status_code=403)
- else:
- return g.user.uid
+def _verify_user_and_role(processor, spiff_task):
+ """Assures the currently logged in user can access the given workflow and task, or
+ raises an error.
+ Allow administrators to modify tasks, otherwise assure that the current user
+ is allowed to edit or update the task. Will raise the appropriate error if user
+ is not authorized. """
- else:
+ if 'user' not in g:
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
+
+ if g.user.uid in app.config['ADMIN_UIDS']:
+ return g.user.uid
+
+ allowed_users = WorkflowService.get_users_assigned_to_task(processor, spiff_task)
+ if g.user.uid not in allowed_users:
+ raise ApiError.from_task("permission_denied",
+ f"This task must be completed by '{allowed_users}', "
+ f"but you are {g.user.uid}", spiff_task)
diff --git a/crc/models/api_models.py b/crc/models/api_models.py
index 53706a75..843609e0 100644
--- a/crc/models/api_models.py
+++ b/crc/models/api_models.py
@@ -29,20 +29,44 @@ class NavigationItem(object):
self.state = state
self.is_decision = is_decision
self.task = task
+ self.lane = lane
class Task(object):
+ ##########################################################################
+ # Custom properties and validations defined in Camunda form fields #
+ ##########################################################################
+
+ # Repeating form section
PROP_OPTIONS_REPEAT = "repeat"
- PROP_OPTIONS_FILE = "spreadsheet.name"
- PROP_OPTIONS_VALUE_COLUMN = "spreadsheet.value.column"
- PROP_OPTIONS_LABEL_COL = "spreadsheet.label.column"
+
+ # Read-only field
+ PROP_OPTIONS_READ_ONLY = "read_only"
+
+ # LDAP lookup
PROP_LDAP_LOOKUP = "ldap.lookup"
- VALIDATION_REQUIRED = "required"
+
+ # Autocomplete field
FIELD_TYPE_AUTO_COMPLETE = "autocomplete"
+ # Required field
+ VALIDATION_REQUIRED = "required"
- def __init__(self, id, name, title, type, state, form, documentation, data,
- multi_instance_type, multi_instance_count, multi_instance_index, process_name, properties):
+ # Enum field options values pulled from a spreadsheet
+ PROP_OPTIONS_FILE_NAME = "spreadsheet.name"
+ PROP_OPTIONS_FILE_VALUE_COLUMN = "spreadsheet.value.column"
+ PROP_OPTIONS_FILE_LABEL_COLUMN = "spreadsheet.label.column"
+
+ # Enum field options values pulled from task data
+ PROP_OPTIONS_DATA_NAME = "data.name"
+ PROP_OPTIONS_DATA_VALUE_COLUMN = "data.value.column"
+ PROP_OPTIONS_DATA_LABEL_COLUMN = "data.label.column"
+
+ ##########################################################################
+
+ def __init__(self, id, name, title, type, state, lane, form, documentation, data,
+ multi_instance_type, multi_instance_count, multi_instance_index,
+ process_name, properties):
self.id = id
self.name = name
self.title = title
@@ -51,6 +75,7 @@ class Task(object):
self.form = form
self.documentation = documentation
self.data = data
+ self.lane = lane
self.multi_instance_type = multi_instance_type # Some tasks have a repeat behavior.
self.multi_instance_count = multi_instance_count # This is the number of times the task could repeat.
self.multi_instance_index = multi_instance_index # And the index of the currently repeating task.
@@ -60,7 +85,7 @@ class Task(object):
class OptionSchema(ma.Schema):
class Meta:
- fields = ["id", "name"]
+ fields = ["id", "name", "data"]
class ValidationSchema(ma.Schema):
@@ -70,15 +95,11 @@ class ValidationSchema(ma.Schema):
class FormFieldPropertySchema(ma.Schema):
class Meta:
- fields = [
- "id", "value"
- ]
+ fields = ["id", "value"]
class FormFieldSchema(ma.Schema):
class Meta:
- fields = [
- "id", "type", "label", "default_value", "options", "validation", "properties", "value"
- ]
+ fields = ["id", "type", "label", "default_value", "options", "validation", "properties", "value"]
default_value = marshmallow.fields.String(required=False, allow_none=True)
options = marshmallow.fields.List(marshmallow.fields.Nested(OptionSchema))
@@ -93,7 +114,7 @@ class FormSchema(ma.Schema):
class TaskSchema(ma.Schema):
class Meta:
- fields = ["id", "name", "title", "type", "state", "form", "documentation", "data", "multi_instance_type",
+ fields = ["id", "name", "title", "type", "state", "lane", "form", "documentation", "data", "multi_instance_type",
"multi_instance_count", "multi_instance_index", "process_name", "properties"]
multi_instance_type = EnumField(MultiInstanceType)
@@ -101,6 +122,7 @@ class TaskSchema(ma.Schema):
form = marshmallow.fields.Nested(FormSchema, required=False, allow_none=True)
title = marshmallow.fields.String(required=False, allow_none=True)
process_name = marshmallow.fields.String(required=False, allow_none=True)
+ lane = marshmallow.fields.String(required=False, allow_none=True)
@marshmallow.post_load
def make_task(self, data, **kwargs):
@@ -110,10 +132,11 @@ class TaskSchema(ma.Schema):
class NavigationItemSchema(ma.Schema):
class Meta:
fields = ["id", "task_id", "name", "title", "backtracks", "level", "indent", "child_count", "state",
- "is_decision", "task"]
+ "is_decision", "task", "lane"]
unknown = INCLUDE
task = marshmallow.fields.Nested(TaskSchema, dump_only=True, required=False, allow_none=True)
backtracks = marshmallow.fields.String(required=False, allow_none=True)
+ lane = marshmallow.fields.String(required=False, allow_none=True)
title = marshmallow.fields.String(required=False, allow_none=True)
task_id = marshmallow.fields.String(required=False, allow_none=True)
diff --git a/crc/models/approval.py b/crc/models/approval.py
index 0592fbd1..df433fac 100644
--- a/crc/models/approval.py
+++ b/crc/models/approval.py
@@ -57,28 +57,16 @@ class Approval(object):
@classmethod
def from_model(cls, model: ApprovalModel):
- # TODO: Reduce the code by iterating over model's dict keys
- instance = cls()
- instance.id = model.id
- instance.study_id = model.study_id
- instance.workflow_id = model.workflow_id
- instance.version = model.version
- instance.approver_uid = model.approver_uid
- instance.status = model.status
- instance.message = model.message
- instance.date_created = model.date_created
- instance.date_approved = model.date_approved
- instance.version = model.version
- instance.title = ''
+ args = dict((k, v) for k, v in model.__dict__.items() if not k.startswith('_'))
+ instance = cls(**args)
instance.related_approvals = []
+ instance.title = model.study.title if model.study else ''
- if model.study:
- instance.title = model.study.title
try:
instance.approver = LdapService.user_info(model.approver_uid)
instance.primary_investigator = LdapService.user_info(model.study.primary_investigator_id)
except ApiError as ae:
- app.logger.error("Ldap lookup failed for approval record %i" % model.id)
+ app.logger.error(f'Ldap lookup failed for approval record {model.id}', exc_info=True)
doc_dictionary = FileService.get_doc_dictionary()
instance.associated_files = []
diff --git a/crc/models/email.py b/crc/models/email.py
new file mode 100644
index 00000000..dc8c6834
--- /dev/null
+++ b/crc/models/email.py
@@ -0,0 +1,18 @@
+from flask_marshmallow.sqla import SQLAlchemyAutoSchema
+from marshmallow import EXCLUDE
+from sqlalchemy import func
+
+from crc import db
+from crc.models.study import StudyModel
+
+
+class EmailModel(db.Model):
+ __tablename__ = 'email'
+ id = db.Column(db.Integer, primary_key=True)
+ subject = db.Column(db.String)
+ sender = db.Column(db.String)
+ recipients = db.Column(db.String)
+ content = db.Column(db.String)
+ content_html = db.Column(db.String)
+ study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=True)
+ study = db.relationship(StudyModel)
diff --git a/crc/models/file.py b/crc/models/file.py
index 15a48709..8afed6cd 100644
--- a/crc/models/file.py
+++ b/crc/models/file.py
@@ -144,7 +144,6 @@ class LookupFileModel(db.Model):
"""Gives us a quick way to tell what kind of lookup is set on a form field.
Connected to the file data model, so that if a new version of the same file is
created, we can update the listing."""
- #fixme: What happens if they change the file associated with a lookup field?
__tablename__ = 'lookup_file'
id = db.Column(db.Integer, primary_key=True)
workflow_spec_id = db.Column(db.String)
@@ -153,6 +152,7 @@ class LookupFileModel(db.Model):
file_data_model_id = db.Column(db.Integer, db.ForeignKey('file_data.id'))
dependencies = db.relationship("LookupDataModel", lazy="select", backref="lookup_file_model", cascade="all, delete, delete-orphan")
+
class LookupDataModel(db.Model):
__tablename__ = 'lookup_data'
id = db.Column(db.Integer, primary_key=True)
@@ -181,6 +181,7 @@ class LookupDataSchema(SQLAlchemyAutoSchema):
load_instance = True
include_relationships = False
include_fk = False # Includes foreign keys
+ exclude = ['id'] # Do not include the id field, it should never be used via the API.
class SimpleFileSchema(ma.Schema):
diff --git a/crc/models/ldap.py b/crc/models/ldap.py
index 7e05eccd..802e0d36 100644
--- a/crc/models/ldap.py
+++ b/crc/models/ldap.py
@@ -29,6 +29,9 @@ class LdapModel(db.Model):
affiliation=", ".join(entry.uvaPersonIAMAffiliation),
sponsor_type=", ".join(entry.uvaPersonSponsoredType))
+ def proper_name(self):
+ return f'{self.display_name} - ({self.uid})'
+
class LdapSchema(SQLAlchemyAutoSchema):
class Meta:
diff --git a/crc/models/stats.py b/crc/models/stats.py
deleted file mode 100644
index c72df7d4..00000000
--- a/crc/models/stats.py
+++ /dev/null
@@ -1,32 +0,0 @@
-from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
-
-from crc import db
-
-
-class TaskEventModel(db.Model):
- __tablename__ = 'task_event'
- id = db.Column(db.Integer, primary_key=True)
- study_id = db.Column(db.Integer, db.ForeignKey('study.id'), nullable=False)
- user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=False)
- workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=False)
- workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'))
- spec_version = db.Column(db.String)
- action = db.Column(db.String)
- task_id = db.Column(db.String)
- task_name = db.Column(db.String)
- task_title = db.Column(db.String)
- task_type = db.Column(db.String)
- task_state = db.Column(db.String)
- mi_type = db.Column(db.String)
- mi_count = db.Column(db.Integer)
- mi_index = db.Column(db.Integer)
- process_name = db.Column(db.String)
- date = db.Column(db.DateTime)
-
-
-class TaskEventModelSchema(SQLAlchemyAutoSchema):
- class Meta:
- model = TaskEventModel
- load_instance = True
- include_relationships = True
- include_fk = True # Includes foreign keys
diff --git a/crc/models/study.py b/crc/models/study.py
index 540ee018..47d4eb8f 100644
--- a/crc/models/study.py
+++ b/crc/models/study.py
@@ -31,10 +31,8 @@ class StudyModel(db.Model):
self.title = pbs.TITLE
self.user_uid = pbs.NETBADGEID
self.last_updated = pbs.DATE_MODIFIED
- self.protocol_builder_status = ProtocolBuilderStatus.INCOMPLETE
- if pbs.Q_COMPLETE:
- self.protocol_builder_status = ProtocolBuilderStatus.ACTIVE
+ self.protocol_builder_status = ProtocolBuilderStatus.ACTIVE
if pbs.HSRNUMBER:
self.protocol_builder_status = ProtocolBuilderStatus.OPEN
if self.on_hold:
diff --git a/crc/models/task_event.py b/crc/models/task_event.py
new file mode 100644
index 00000000..a6cb1a2d
--- /dev/null
+++ b/crc/models/task_event.py
@@ -0,0 +1,64 @@
+from marshmallow import INCLUDE, fields
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
+
+from crc import db, ma
+from crc.models.study import StudyModel, StudySchema, WorkflowMetadataSchema, WorkflowMetadata
+from crc.models.workflow import WorkflowModel
+
+
+class TaskEventModel(db.Model):
+ __tablename__ = 'task_event'
+ id = db.Column(db.Integer, primary_key=True)
+ study_id = db.Column(db.Integer, db.ForeignKey('study.id'), nullable=False)
+ user_uid = db.Column(db.String, nullable=False) # In some cases the unique user id may not exist in the db yet.
+ workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=False)
+ workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'))
+ spec_version = db.Column(db.String)
+ action = db.Column(db.String)
+ task_id = db.Column(db.String)
+ task_name = db.Column(db.String)
+ task_title = db.Column(db.String)
+ task_type = db.Column(db.String)
+ task_state = db.Column(db.String)
+ task_lane = db.Column(db.String)
+ form_data = db.Column(db.JSON) # And form data submitted when the task was completed.
+ mi_type = db.Column(db.String)
+ mi_count = db.Column(db.Integer)
+ mi_index = db.Column(db.Integer)
+ process_name = db.Column(db.String)
+ date = db.Column(db.DateTime)
+
+
+class TaskEventModelSchema(SQLAlchemyAutoSchema):
+ class Meta:
+ model = TaskEventModel
+ load_instance = True
+ include_relationships = True
+ include_fk = True # Includes foreign keys
+
+
+class TaskEvent(object):
+ def __init__(self, model: TaskEventModel, study: StudyModel, workflow: WorkflowMetadata):
+ self.id = model.id
+ self.study = study
+ self.workflow = workflow
+ self.user_uid = model.user_uid
+ self.action = model.action
+ self.task_id = model.task_id
+ self.task_title = model.task_title
+ self.task_name = model.task_name
+ self.task_type = model.task_type
+ self.task_state = model.task_state
+ self.task_lane = model.task_lane
+
+
+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",
+ "task_name", "task_type", "task_state", "task_lane"]
+ unknown = INCLUDE
diff --git a/crc/models/user.py b/crc/models/user.py
index 55bba35f..221176bc 100644
--- a/crc/models/user.py
+++ b/crc/models/user.py
@@ -35,7 +35,7 @@ class UserModel(db.Model):
}
return jwt.encode(
payload,
- app.config.get('TOKEN_AUTH_SECRET_KEY'),
+ app.config.get('SECRET_KEY'),
algorithm='HS256',
)
@@ -47,7 +47,7 @@ class UserModel(db.Model):
:return: integer|string
"""
try:
- payload = jwt.decode(auth_token, app.config.get('TOKEN_AUTH_SECRET_KEY'), algorithms='HS256')
+ payload = jwt.decode(auth_token, app.config.get('SECRET_KEY'), algorithms='HS256')
return payload
except jwt.ExpiredSignatureError:
raise ApiError('token_expired', 'The Authentication token you provided expired and must be renewed.')
diff --git a/crc/scripts/email.py b/crc/scripts/email.py
new file mode 100644
index 00000000..855ec8a4
--- /dev/null
+++ b/crc/scripts/email.py
@@ -0,0 +1,90 @@
+import markdown
+from jinja2 import Template
+
+from crc import app
+from crc.api.common import ApiError
+from crc.scripts.script import Script
+from crc.services.ldap_service import LdapService
+from crc.services.mails import send_mail
+
+
+class Email(Script):
+ """This Script allows to be introduced as part of a workflow and called from there, specifying
+ recipients and content """
+
+ def get_description(self):
+ return """
+Creates an email, using the provided arguments (a list of UIDs)"
+Each argument will be used to look up personal information needed for
+the email creation.
+
+Example:
+Email Subject ApprvlApprvr1 PIComputingID
+"""
+
+ def do_task_validate_only(self, task, *args, **kwargs):
+ self.get_subject(task, args)
+ self.get_users_info(task, args)
+ self.get_content(task)
+
+ def do_task(self, task, *args, **kwargs):
+ args = [arg for arg in args if type(arg) == str]
+ subject = self.get_subject(task, args)
+ recipients = self.get_users_info(task, args)
+ content, content_html = self.get_content(task)
+ if recipients:
+ send_mail(
+ subject=subject,
+ sender=app.config['DEFAULT_SENDER'],
+ recipients=recipients,
+ content=content,
+ content_html=content_html
+ )
+
+ def get_users_info(self, task, args):
+ if len(args) < 1:
+ raise ApiError(code="missing_argument",
+ message="Email script requires at least one argument. The "
+ "name of the variable in the task data that contains user"
+ "id to process. Multiple arguments are accepted.")
+ emails = []
+ for arg in args:
+ try:
+ uid = task.workflow.script_engine.evaluate_expression(task, arg)
+ except Exception as e:
+ app.logger.error(f'Workflow engines could not parse {arg}', exc_info=True)
+ continue
+ user_info = LdapService.user_info(uid)
+ email = user_info.email_address
+ emails.append(user_info.email_address)
+ if not isinstance(email, str):
+ raise ApiError(code="invalid_argument",
+ message="The Email script requires at least 1 UID argument. The "
+ "name of the variable in the task data that contains subject and"
+ " user ids to process. This must point to an array or a string, but "
+ "it currently points to a %s " % emails.__class__.__name__)
+
+ return emails
+
+ def get_subject(self, task, args):
+ if len(args) < 1:
+ raise ApiError(code="missing_argument",
+ message="Email script requires at least one subject argument. The "
+ "name of the variable in the task data that contains subject"
+ " to process. Multiple arguments are accepted.")
+ subject = args[0]
+ if not isinstance(subject, str):
+ raise ApiError(code="invalid_argument",
+ message="The Email script requires 1 argument. The "
+ "the name of the variable in the task data that contains user"
+ "ids to process. This must point to an array or a string, but "
+ "it currently points to a %s " % subject.__class__.__name__)
+
+ return subject
+
+ def get_content(self, task):
+ content = task.task_spec.documentation
+ template = Template(content)
+ rendered = template.render(task.data)
+ rendered_markdown = markdown.markdown(rendered).replace('\n', 'Hypertext Markup Language content for this email
' + + EmailService.add_email(subject=subject, sender=sender, recipients=recipients, + content=content, content_html=content_html, study_id=study.id) + + email_model = EmailModel.query.first() + + self.assertEqual(email_model.subject, subject) + self.assertEqual(email_model.sender, sender) + self.assertEqual(email_model.recipients, str(recipients)) + self.assertEqual(email_model.content, content) + self.assertEqual(email_model.content_html, content_html) + self.assertEqual(email_model.study, study) + + subject = 'Email Subject - Empty study' + EmailService.add_email(subject=subject, sender=sender, recipients=recipients, + content=content, content_html=content_html) + + email_model = EmailModel.query.order_by(EmailModel.id.desc()).first() + + self.assertEqual(email_model.subject, subject) + self.assertEqual(email_model.sender, sender) + self.assertEqual(email_model.recipients, str(recipients)) + self.assertEqual(email_model.content, content) + self.assertEqual(email_model.content_html, content_html) + self.assertEqual(email_model.study, None) diff --git a/tests/emails/test_mails.py b/tests/emails/test_mails.py new file mode 100644 index 00000000..e9320f4d --- /dev/null +++ b/tests/emails/test_mails.py @@ -0,0 +1,113 @@ +from crc import mail +from crc.models.email import EmailModel +from crc.services.mails import ( + send_ramp_up_submission_email, + send_ramp_up_approval_request_email, + send_ramp_up_approval_request_first_review_email, + send_ramp_up_approved_email, + send_ramp_up_denied_email, + send_ramp_up_denied_email_to_approver +) +from tests.base_test import BaseTest + + +class TestMails(BaseTest): + + def setUp(self): + """Initial setup shared by all TestApprovals tests""" + self.load_example_data() + self.study = self.create_study() + self.workflow = self.create_workflow('random_fact') + + self.sender = 'sender@sartography.com' + self.recipients = ['recipient@sartography.com'] + self.primary_investigator = 'Dr. Bartlett' + self.approver_1 = 'Max Approver' + self.approver_2 = 'Close Reviewer' + + def test_send_ramp_up_submission_email(self): + with mail.record_messages() as outbox: + send_ramp_up_submission_email(self.sender, self.recipients, self.approver_1) + self.assertEqual(len(outbox), 1) + self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Submitted') + self.assertIn(self.approver_1, outbox[0].body) + self.assertIn(self.approver_1, outbox[0].html) + + send_ramp_up_submission_email(self.sender, self.recipients, self.approver_1, self.approver_2) + self.assertEqual(len(outbox), 2) + self.assertIn(self.approver_1, outbox[1].body) + self.assertIn(self.approver_1, outbox[1].html) + self.assertIn(self.approver_2, outbox[1].body) + self.assertIn(self.approver_2, outbox[1].html) + + db_emails = EmailModel.query.count() + self.assertEqual(db_emails, 2) + + def test_send_ramp_up_approval_request_email(self): + with mail.record_messages() as outbox: + send_ramp_up_approval_request_email(self.sender, self.recipients, self.primary_investigator) + + self.assertEqual(len(outbox), 1) + self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Approval Request') + self.assertIn(self.primary_investigator, outbox[0].body) + self.assertIn(self.primary_investigator, outbox[0].html) + + db_emails = EmailModel.query.count() + self.assertEqual(db_emails, 1) + + def test_send_ramp_up_approval_request_first_review_email(self): + with mail.record_messages() as outbox: + send_ramp_up_approval_request_first_review_email( + self.sender, self.recipients, self.primary_investigator + ) + + self.assertEqual(len(outbox), 1) + self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Approval Request') + self.assertIn(self.primary_investigator, outbox[0].body) + self.assertIn(self.primary_investigator, outbox[0].html) + + db_emails = EmailModel.query.count() + self.assertEqual(db_emails, 1) + + def test_send_ramp_up_approved_email(self): + with mail.record_messages() as outbox: + send_ramp_up_approved_email(self.sender, self.recipients, self.approver_1) + self.assertEqual(len(outbox), 1) + self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Approved') + self.assertIn(self.approver_1, outbox[0].body) + self.assertIn(self.approver_1, outbox[0].html) + + send_ramp_up_approved_email(self.sender, self.recipients, self.approver_1, self.approver_2) + self.assertEqual(len(outbox), 2) + self.assertIn(self.approver_1, outbox[1].body) + self.assertIn(self.approver_1, outbox[1].html) + self.assertIn(self.approver_2, outbox[1].body) + self.assertIn(self.approver_2, outbox[1].html) + + db_emails = EmailModel.query.count() + self.assertEqual(db_emails, 2) + + def test_send_ramp_up_denied_email(self): + with mail.record_messages() as outbox: + send_ramp_up_denied_email(self.sender, self.recipients, self.approver_1) + self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Denied') + self.assertIn(self.approver_1, outbox[0].body) + self.assertIn(self.approver_1, outbox[0].html) + + db_emails = EmailModel.query.count() + self.assertEqual(db_emails, 1) + + def test_send_send_ramp_up_denied_email_to_approver(self): + with mail.record_messages() as outbox: + send_ramp_up_denied_email_to_approver( + self.sender, self.recipients, self.primary_investigator, self.approver_2 + ) + + self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Denied') + self.assertIn(self.primary_investigator, outbox[0].body) + self.assertIn(self.primary_investigator, outbox[0].html) + self.assertIn(self.approver_2, outbox[0].body) + self.assertIn(self.approver_2, outbox[0].html) + + db_emails = EmailModel.query.count() + self.assertEqual(db_emails, 1) diff --git a/tests/test_file_service.py b/tests/files/test_file_service.py similarity index 98% rename from tests/test_file_service.py rename to tests/files/test_file_service.py index 1dea810c..dd95e458 100644 --- a/tests/test_file_service.py +++ b/tests/files/test_file_service.py @@ -61,14 +61,14 @@ class TestFileService(BaseTest): # Archive the file file_models = FileService.get_workflow_files(workflow_id=workflow.id) - self.assertEquals(1, len(file_models)) + self.assertEqual(1, len(file_models)) file_model = file_models[0] file_model.archived = True db.session.add(file_model) # Assure that the file no longer comes back. file_models = FileService.get_workflow_files(workflow_id=workflow.id) - self.assertEquals(0, len(file_models)) + self.assertEqual(0, len(file_models)) # Add the file again with different data FileService.add_workflow_file(workflow_id=workflow.id, diff --git a/tests/test_files_api.py b/tests/files/test_files_api.py similarity index 98% rename from tests/test_files_api.py rename to tests/files/test_files_api.py index 2d14a8b5..59e6c1f6 100644 --- a/tests/test_files_api.py +++ b/tests/files/test_files_api.py @@ -91,7 +91,6 @@ class TestFilesApi(BaseTest): content_type='multipart/form-data', headers=self.logged_in_headers()) self.assert_success(rv) - def test_archive_file_no_longer_shows_up(self): self.load_example_data() self.create_reference_document() @@ -109,21 +108,16 @@ class TestFilesApi(BaseTest): self.assert_success(rv) rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id, headers=self.logged_in_headers()) self.assert_success(rv) - self.assertEquals(1, len(json.loads(rv.get_data(as_text=True)))) + self.assertEqual(1, len(json.loads(rv.get_data(as_text=True)))) file_model = db.session.query(FileModel).filter(FileModel.workflow_id == workflow.id).all() - self.assertEquals(1, len(file_model)) + self.assertEqual(1, len(file_model)) file_model[0].archived = True db.session.commit() rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id, headers=self.logged_in_headers()) self.assert_success(rv) - self.assertEquals(0, len(json.loads(rv.get_data(as_text=True)))) - - - - - + self.assertEqual(0, len(json.loads(rv.get_data(as_text=True)))) def test_set_reference_file(self): file_name = "irb_document_types.xls" @@ -285,8 +279,8 @@ class TestFilesApi(BaseTest): .filter(ApprovalModel.status == ApprovalStatus.PENDING.value)\ .filter(ApprovalModel.study_id == workflow.study_id).all() - self.assertEquals(1, len(approvals)) - self.assertEquals(1, len(approvals[0].approval_files)) + self.assertEqual(1, len(approvals)) + self.assertEqual(1, len(approvals[0].approval_files)) def test_change_primary_bpmn(self): diff --git a/tests/test_study_api.py b/tests/study/test_study_api.py similarity index 94% rename from tests/test_study_api.py rename to tests/study/test_study_api.py index cdae21c5..3b781f50 100644 --- a/tests/test_study_api.py +++ b/tests/study/test_study_api.py @@ -7,7 +7,8 @@ from unittest.mock import patch from crc import session, app from crc.models.protocol_builder import ProtocolBuilderStatus, \ ProtocolBuilderStudySchema -from crc.models.stats import TaskEventModel +from crc.models.approval import ApprovalStatus +from crc.models.task_event import TaskEventModel from crc.models.study import StudyModel, StudySchema from crc.models.workflow import WorkflowSpecModel, WorkflowModel from crc.services.file_service import FileService @@ -95,8 +96,21 @@ class TestStudyApi(BaseTest): # TODO: WRITE A TEST FOR STUDY FILES def test_get_study_has_details_about_approvals(self): - # TODO: WRITE A TEST FOR STUDY APPROVALS - pass + self.load_example_data() + full_study = self._create_study_workflow_approvals( + user_uid="dhf8r", title="first study", primary_investigator_id="lb3dp", + approver_uids=["lb3dp", "dhf8r"], statuses=[ApprovalStatus.PENDING.value, ApprovalStatus.PENDING.value] + ) + + api_response = self.app.get('/v1.0/study/%i' % full_study['study'].id, + headers=self.logged_in_headers(), content_type="application/json") + self.assert_success(api_response) + study = StudySchema().loads(api_response.get_data(as_text=True)) + + self.assertEqual(len(study.approvals), 2) + + for approval in study.approvals: + self.assertEqual(full_study['study'].title, approval['title']) def test_add_study(self): self.load_example_data() @@ -168,8 +182,6 @@ class TestStudyApi(BaseTest): num_open = 0 for study in json_data: - if study['protocol_builder_status'] == 'INCOMPLETE': # One study in user_studies.json is not q_complete - num_incomplete += 1 if study['protocol_builder_status'] == 'ABANDONED': # One study does not exist in user_studies.json num_abandoned += 1 if study['protocol_builder_status'] == 'ACTIVE': # One study is marked complete without HSR Number @@ -182,8 +194,8 @@ class TestStudyApi(BaseTest): self.assertGreater(num_db_studies_after, num_db_studies_before) self.assertEqual(num_abandoned, 1) self.assertEqual(num_open, 1) - self.assertEqual(num_active, 1) - self.assertEqual(num_incomplete, 1) + self.assertEqual(num_active, 2) + self.assertEqual(num_incomplete, 0) self.assertEqual(len(json_data), num_db_studies_after) self.assertEqual(num_open + num_active + num_incomplete + num_abandoned, num_db_studies_after) diff --git a/tests/test_study_details_documents.py b/tests/study/test_study_details_documents.py similarity index 100% rename from tests/test_study_details_documents.py rename to tests/study/test_study_details_documents.py diff --git a/tests/test_study_service.py b/tests/study/test_study_service.py similarity index 88% rename from tests/test_study_service.py rename to tests/study/test_study_service.py index 1c482bcb..b436835f 100644 --- a/tests/test_study_service.py +++ b/tests/study/test_study_service.py @@ -183,7 +183,7 @@ class TestStudyService(BaseTest): @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_docs - def test_get_personnel(self, mock_docs): + def test_get_personnel_roles(self, mock_docs): self.load_example_data() # mock out the protocol builder @@ -191,9 +191,9 @@ class TestStudyService(BaseTest): mock_docs.return_value = json.loads(docs_response) workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case. - investigators = StudyService().get_investigators(workflow.study_id) + investigators = StudyService().get_investigators(workflow.study_id, all=True) - self.assertEqual(9, len(investigators)) + self.assertEqual(10, len(investigators)) # dhf8r is in the ldap mock data. self.assertEqual("dhf8r", investigators['PI']['user_id']) @@ -207,3 +207,26 @@ class TestStudyService(BaseTest): # No value is provided for Department Chair self.assertIsNone(investigators['DEPT_CH']['user_id']) + + @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_docs + def test_get_study_personnel(self, mock_docs): + self.load_example_data() + + # mock out the protocol builder + docs_response = self.protocol_builder_response('investigators.json') + mock_docs.return_value = json.loads(docs_response) + + workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case. + investigators = StudyService().get_investigators(workflow.study_id, all=False) + + self.assertEqual(5, len(investigators)) + + # dhf8r is in the ldap mock data. + self.assertEqual("dhf8r", investigators['PI']['user_id']) + self.assertEqual("Dan Funk", investigators['PI']['display_name']) # Data from ldap + self.assertEqual("Primary Investigator", investigators['PI']['label']) # Data from xls file. + self.assertEqual("Always", investigators['PI']['display']) # Data from xls file. + + # Both Alex and Aaron are SI, and both should be returned. + self.assertEqual("ajl2j", investigators['SI']['user_id']) + self.assertEqual("cah3us", investigators['SI_2']['user_id']) diff --git a/tests/test_update_study_script.py b/tests/study/test_update_study_script.py similarity index 100% rename from tests/test_update_study_script.py rename to tests/study/test_update_study_script.py diff --git a/tests/test_lookup_service.py b/tests/test_lookup_service.py index b61e20e2..a27427f4 100644 --- a/tests/test_lookup_service.py +++ b/tests/test_lookup_service.py @@ -61,6 +61,15 @@ class TestLookupService(BaseTest): lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all() self.assertEqual(4, len(lookup_data)) + def test_lookup_based_on_id(self): + spec = BaseTest.load_test_spec('enum_options_from_file') + workflow = self.create_workflow('enum_options_from_file') + processor = WorkflowProcessor(workflow) + processor.do_engine_steps() + results = LookupService.lookup(workflow, "AllTheNames", "", value="1000", limit=10) + self.assertEqual(1, len(results), "It is possible to find an item based on the id, rather than as a search") + self.assertIsNotNone(results[0].data) + self.assertIsInstance(results[0].data, dict) def test_some_full_text_queries(self): @@ -114,6 +123,9 @@ class TestLookupService(BaseTest): results = LookupService.lookup(workflow, "AllTheNames", "1 (!-Something", limit=10) self.assertEqual("1 Something", results[0].label, "special characters don't flake out") + results = LookupService.lookup(workflow, "AllTheNames", "1 Something", limit=10) + self.assertEqual("1 Something", results[0].label, "double spaces should not be an issue.") + # 1018 10000 Something Industry diff --git a/tests/test_looping_task.py b/tests/test_looping_task.py new file mode 100644 index 00000000..e56e0877 --- /dev/null +++ b/tests/test_looping_task.py @@ -0,0 +1,54 @@ +from unittest.mock import patch + +from crc import session +from crc.models.api_models import MultiInstanceType +from crc.models.study import StudyModel +from crc.models.workflow import WorkflowStatus +from crc.services.study_service import StudyService +from crc.services.workflow_processor import WorkflowProcessor +from crc.services.workflow_service import WorkflowService +from tests.base_test import BaseTest + + +class TestWorkflowProcessorLoopingTask(BaseTest): + """Tests the Workflow Processor as it deals with a Looping task""" + + def _populate_form_with_random_data(self, task): + api_task = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True) + WorkflowService.populate_form_with_random_data(task, api_task, required_only=False) + + def get_processor(self, study_model, spec_model): + workflow_model = StudyService._create_workflow_model(study_model, spec_model) + return WorkflowProcessor(workflow_model) + + def test_create_and_complete_workflow(self): + # This depends on getting a list of investigators back from the protocol builder. + + workflow = self.create_workflow('looping_task') + task = self.get_workflow_api(workflow).next_task + + self.assertEqual("GetNames", task.name) + + self.assertEqual(task.multi_instance_type, 'looping') + self.assertEqual(1, task.multi_instance_index) + self.complete_form(workflow,task,{'GetNames_CurrentVar':{'Name': 'Peter Norvig', 'Nickname': 'Pete'}}) + task = self.get_workflow_api(workflow).next_task + + self.assertEqual(task.multi_instance_type,'looping') + self.assertEqual(2, task.multi_instance_index) + self.complete_form(workflow, + task, + {'GetNames_CurrentVar':{'Name': 'Stuart Russell', 'Nickname': 'Stu'}}, + terminate_loop=True) + + task = self.get_workflow_api(workflow).next_task + self.assertEqual(task.name,'Event_End') + self.assertEqual(workflow.completed_tasks,workflow.total_tasks) + self.assertEqual(task.data, {'GetNames_CurrentVar': 2, + 'GetNames': {'1': {'Name': 'Peter Norvig', + 'Nickname': 'Pete'}, + '2': {'Name': 'Stuart Russell', + 'Nickname': 'Stu'}}}) + + + diff --git a/tests/test_mails.py b/tests/test_mails.py deleted file mode 100644 index 15a01583..00000000 --- a/tests/test_mails.py +++ /dev/null @@ -1,55 +0,0 @@ - -from tests.base_test import BaseTest - -from crc.services.mails import ( - send_ramp_up_submission_email, - send_ramp_up_approval_request_email, - send_ramp_up_approval_request_first_review_email, - send_ramp_up_approved_email, - send_ramp_up_denied_email, - send_ramp_up_denied_email_to_approver -) - - -class TestMails(BaseTest): - - def setUp(self): - self.sender = 'sender@sartography.com' - self.recipients = ['recipient@sartography.com'] - self.primary_investigator = 'Dr. Bartlett' - self.approver_1 = 'Max Approver' - self.approver_2 = 'Close Reviewer' - - def test_send_ramp_up_submission_email(self): - send_ramp_up_submission_email(self.sender, self.recipients, self.approver_1) - self.assertTrue(True) - - send_ramp_up_submission_email(self.sender, self.recipients, self.approver_1, self.approver_2) - self.assertTrue(True) - - def test_send_ramp_up_approval_request_email(self): - send_ramp_up_approval_request_email(self.sender, self.recipients, self.primary_investigator) - self.assertTrue(True) - - def test_send_ramp_up_approval_request_first_review_email(self): - send_ramp_up_approval_request_first_review_email( - self.sender, self.recipients, self.primary_investigator - ) - self.assertTrue(True) - - def test_send_ramp_up_approved_email(self): - send_ramp_up_approved_email(self.sender, self.recipients, self.approver_1) - self.assertTrue(True) - - send_ramp_up_approved_email(self.sender, self.recipients, self.approver_1, self.approver_2) - self.assertTrue(True) - - def test_send_ramp_up_denied_email(self): - send_ramp_up_denied_email(self.sender, self.recipients, self.approver_1) - self.assertTrue(True) - - def test_send_send_ramp_up_denied_email_to_approver(self): - send_ramp_up_denied_email_to_approver( - self.sender, self.recipients, self.primary_investigator, self.approver_2 - ) - self.assertTrue(True) diff --git a/tests/test_protocol_builder.py b/tests/test_protocol_builder.py index e5b75632..2a77ec05 100644 --- a/tests/test_protocol_builder.py +++ b/tests/test_protocol_builder.py @@ -24,7 +24,7 @@ class TestProtocolBuilder(BaseTest): mock_get.return_value.text = self.protocol_builder_response('investigators.json') response = ProtocolBuilderService.get_investigators(self.test_study_id) self.assertIsNotNone(response) - self.assertEqual(3, len(response)) + self.assertEqual(5, len(response)) self.assertEqual("DC", response[0]["INVESTIGATORTYPE"]) self.assertEqual("Department Contact", response[0]["INVESTIGATORTYPEFULL"]) self.assertEqual("asd3v", response[0]["NETBADGEID"]) diff --git a/tests/test_tasks_api.py b/tests/test_tasks_api.py index 654b777e..8284313d 100644 --- a/tests/test_tasks_api.py +++ b/tests/test_tasks_api.py @@ -4,6 +4,7 @@ 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 @@ -12,6 +13,18 @@ from crc.models.workflow import WorkflowStatus class TestTasksApi(BaseTest): + def assert_options_populated(self, results, lookup_data_keys): + option_keys = ['value', 'label', 'data'] + self.assertIsInstance(results, list) + for result in results: + for option_key in option_keys: + self.assertTrue(option_key in result, 'should have value, label, and data properties populated') + self.assertIsNotNone(result[option_key], '%s should not be None' % option_key) + + self.assertIsInstance(result['data'], dict) + for lookup_data_key in lookup_data_keys: + self.assertTrue(lookup_data_key in result['data'], 'should have all lookup data columns populated') + def test_get_current_user_tasks(self): self.load_example_data() workflow = self.create_workflow('random_fact') @@ -250,7 +263,7 @@ class TestTasksApi(BaseTest): self.assertEqual(4, len(navigation)) # Start task, form_task, multi_task, end task self.assertEqual("UserTask", workflow.next_task.type) self.assertEqual(MultiInstanceType.sequential.value, workflow.next_task.multi_instance_type) - self.assertEqual(9, workflow.next_task.multi_instance_count) + self.assertEqual(5, workflow.next_task.multi_instance_count) # Assure that the names for each task are properly updated, so they aren't all the same. self.assertEqual("Primary Investigator", workflow.next_task.properties['display_name']) @@ -270,6 +283,80 @@ class TestTasksApi(BaseTest): self.assert_success(rv) results = json.loads(rv.get_data(as_text=True)) self.assertEqual(5, len(results)) + self.assert_options_populated(results, ['CUSTOMER_NUMBER', 'CUSTOMER_NAME', 'CUSTOMER_CLASS_MEANING']) + + def test_lookup_endpoint_for_task_field_using_lookup_entry_id(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)) + self.assert_options_populated(results, ['CUSTOMER_NUMBER', 'CUSTOMER_NAME', 'CUSTOMER_CLASS_MEANING']) + + rv = self.app.get('/v1.0/workflow/%i/lookup/%s?value=%s' % + (workflow.id, field_id, results[0]['value']), # All records with a word that starts with 'c' + headers=self.logged_in_headers(), + content_type="application/json") + results = json.loads(rv.get_data(as_text=True)) + self.assertEqual(1, len(results)) + self.assert_options_populated(results, ['CUSTOMER_NUMBER', 'CUSTOMER_NAME', 'CUSTOMER_CLASS_MEANING']) + self.assertNotIn('id', results[0], "Don't include the internal id, that can be very confusing, and should not be used.") + + def test_lookup_endpoint_also_works_for_enum(self): + # Naming here get's a little confusing. fields can be marked as enum or autocomplete. + # In the event of an auto-complete it's a type-ahead search field, for an enum the + # the key/values from the spreadsheet are added directly to the form and it shows up as + # a dropdown. This tests the case of wanting to get additional data when a user selects + # something from a dropdown. + self.load_example_data() + workflow = self.create_workflow('enum_options_from_file') + # 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'] + option_id = task.form['fields'][0]['options'][0]['id'] + rv = self.app.get('/v1.0/workflow/%i/lookup/%s?value=%s' % + (workflow.id, field_id, option_id), # 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(1, len(results)) + self.assert_options_populated(results, ['CUSTOMER_NUMBER', 'CUSTOMER_NAME', 'CUSTOMER_CLASS_MEANING']) + self.assertIsInstance(results[0]['data'], dict) + + def test_enum_from_task_data(self): + self.load_example_data() + workflow = self.create_workflow('enum_options_from_task_data') + # get the first form in the two form workflow. + workflow_api = self.get_workflow_api(workflow) + task = workflow_api.next_task + + workflow_api = self.complete_form(workflow, task, {'invitees': [ + {'first_name': 'Alistair', 'last_name': 'Aardvark', 'age': 43, 'likes_pie': True, 'num_lumps': 21, 'secret_id': 'Antimony', 'display_name': 'Professor Alistair A. Aardvark'}, + {'first_name': 'Berthilda', 'last_name': 'Binturong', 'age': 12, 'likes_pie': False, 'num_lumps': 34, 'secret_id': 'Beryllium', 'display_name': 'Dr. Berthilda B. Binturong'}, + {'first_name': 'Chesterfield', 'last_name': 'Capybara', 'age': 32, 'likes_pie': True, 'num_lumps': 1, 'secret_id': 'Cadmium', 'display_name': 'The Honorable C. C. Capybara'}, + ]}) + task = workflow_api.next_task + + field_id = task.form['fields'][0]['id'] + options = task.form['fields'][0]['options'] + self.assertEqual(3, len(options)) + option_id = options[0]['id'] + self.assertEqual('Professor Alistair A. Aardvark', options[0]['name']) + self.assertEqual('Dr. Berthilda B. Binturong', options[1]['name']) + self.assertEqual('The Honorable C. C. Capybara', options[2]['name']) + self.assertEqual('Alistair', options[0]['data']['first_name']) + self.assertEqual('Berthilda', options[1]['data']['first_name']) + self.assertEqual('Chesterfield', options[2]['data']['first_name']) def test_lookup_endpoint_for_task_ldap_field_lookup(self): self.load_example_data() @@ -285,6 +372,9 @@ class TestTasksApi(BaseTest): content_type="application/json") self.assert_success(rv) results = json.loads(rv.get_data(as_text=True)) + self.assert_options_populated(results, ['telephone_number', 'affiliation', 'uid', 'title', + 'given_name', 'department', 'date_cached', 'sponsor_type', + 'display_name', 'email_address']) self.assertEqual(1, len(results)) def test_sub_process(self): @@ -299,13 +389,13 @@ class TestTasksApi(BaseTest): self.assertEqual("UserTask", task.type) self.assertEqual("Activity_A", task.name) self.assertEqual("My Sub Process", task.process_name) - workflow_api = self.complete_form(workflow, task, {"name": "Dan"}) + workflow_api = self.complete_form(workflow, task, {"FieldA": "Dan"}) task = workflow_api.next_task self.assertIsNotNone(task) self.assertEqual("Activity_B", task.name) self.assertEqual("Sub Workflow Example", task.process_name) - workflow_api = self.complete_form(workflow, task, {"name": "Dan"}) + workflow_api = self.complete_form(workflow, task, {"FieldB": "Dan"}) self.assertEqual(WorkflowStatus.complete, workflow_api.status) def test_update_task_resets_token(self): @@ -363,17 +453,25 @@ class TestTasksApi(BaseTest): workflow = self.create_workflow('multi_instance_parallel') workflow_api = self.get_workflow_api(workflow) - self.assertEqual(12, len(workflow_api.navigation)) + self.assertEqual(8, len(workflow_api.navigation)) ready_items = [nav for nav in workflow_api.navigation if nav['state'] == "READY"] - self.assertEqual(9, len(ready_items)) + self.assertEqual(5, len(ready_items)) self.assertEqual("UserTask", workflow_api.next_task.type) - self.assertEqual("MutiInstanceTask",workflow_api.next_task.name) - self.assertEqual("more information", workflow_api.next_task.title) + self.assertEqual("MultiInstanceTask",workflow_api.next_task.name) + self.assertEqual("Primary Investigator", workflow_api.next_task.title) - for i in random.sample(range(9), 9): + for i in random.sample(range(5), 5): task = TaskSchema().load(ready_items[i]['task']) - self.complete_form(workflow, task, {"investigator":{"email": "dhf8r@virginia.edu"}}) + rv = self.app.put('/v1.0/workflow/%i/task/%s/set_token' % (workflow.id, 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) + data = workflow.next_task.data + data['investigator']['email'] = "dhf8r@virginia.edu" + self.complete_form(workflow, task, data) #tasks = self.get_workflow_api(workflow).user_tasks workflow = self.get_workflow_api(workflow) diff --git a/tests/test_tools_api.py b/tests/test_tools_api.py index c6f543c1..3ddf9fea 100644 --- a/tests/test_tools_api.py +++ b/tests/test_tools_api.py @@ -37,3 +37,12 @@ class TestStudyApi(BaseTest): self.assertTrue(len(scripts) > 1) self.assertIsNotNone(scripts[0]['name']) self.assertIsNotNone(scripts[0]['description']) + + def test_eval_hide_expression(self): + """Assures we can use python to process a hide expression fron the front end""" + rv = self.app.put('/v1.0/eval?expression=x.y==2', + data='{"x":{"y":2}}', follow_redirects=True, + content_type='application/json', + headers=self.logged_in_headers()) + self.assert_success(rv) + self.assertEqual("true", rv.get_data(as_text=True).strip()) diff --git a/tests/test_user_roles.py b/tests/test_user_roles.py new file mode 100644 index 00000000..6104641c --- /dev/null +++ b/tests/test_user_roles.py @@ -0,0 +1,202 @@ +import json + +from tests.base_test import BaseTest +from crc.models.workflow import WorkflowStatus +from crc import db +from crc.api.common import ApiError +from crc.models.task_event import TaskEventModel, TaskEventSchema +from crc.services.workflow_service import WorkflowService + + +class TestTasksApi(BaseTest): + + def test_raise_error_if_role_does_not_exist_in_data(self): + workflow = self.create_workflow('roles', as_user="lje5u") + workflow_api = self.get_workflow_api(workflow, user_uid="lje5u") + data = workflow_api.next_task.data + # User lje5u can complete the first task + self.complete_form(workflow, workflow_api.next_task, data, user_uid="lje5u") + + # The next task is a supervisor task, and should raise an error if the role + # information is not in the task data. + workflow_api = self.get_workflow_api(workflow, user_uid="lje5u") + data = workflow_api.next_task.data + data["approved"] = True + result = self.complete_form(workflow, workflow_api.next_task, data, user_uid="lje5u", + error_code="permission_denied") + + def test_validation_of_workflow_fails_if_workflow_does_not_define_user_for_lane(self): + error = None + try: + workflow = self.create_workflow('invalid_roles', as_user="lje5u") + WorkflowService.test_spec(workflow.workflow_spec_id) + except ApiError as ae: + error = ae + self.assertIsNotNone(error, "An error should be raised.") + self.assertEquals("invalid_role", error.code) + + def test_raise_error_if_user_does_not_have_the_correct_role(self): + submitter = self.create_user(uid='lje5u') + supervisor = self.create_user(uid='lb3dp') + workflow = self.create_workflow('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 + data = workflow_api.next_task.data + data['supervisor'] = supervisor.uid + self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid) + + # But she can not complete the supervisor role. + workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid) + data = workflow_api.next_task.data + data["approval"] = True + result = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid, + error_code="permission_denied") + + # Only her supervisor can do that. + self.complete_form(workflow, workflow_api.next_task, data, user_uid=supervisor.uid) + + def test_nav_includes_lanes(self): + submitter = self.create_user(uid='lje5u') + workflow = self.create_workflow('roles', as_user=submitter.uid) + workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid) + + nav = workflow_api.navigation + self.assertEquals(5, len(nav)) + self.assertEquals("supervisor", nav[1]['lane']) + + 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_api = self.get_workflow_api(workflow, user_uid=submitter.uid) + + # User lje5u can complete the first task, and set her supervisor + data = workflow_api.next_task.data + data['supervisor'] = supervisor.uid + workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid) + + # At this point there should be a task_log with an action of Lane Change on it for + # the supervisor. + task_logs = db.session.query(TaskEventModel). \ + filter(TaskEventModel.user_uid == supervisor.uid). \ + filter(TaskEventModel.action == WorkflowService.TASK_ACTION_ASSIGNMENT).all() + self.assertEquals(1, len(task_logs)) + + # A call to the /task endpoint as the supervisor user should return a list of + # tasks that need their attention. + rv = self.app.get('/v1.0/task_events?action=ASSIGNMENT', + headers=self.logged_in_headers(supervisor), + content_type="application/json") + self.assert_success(rv) + json_data = json.loads(rv.get_data(as_text=True)) + tasks = TaskEventSchema(many=True).load(json_data) + self.assertEquals(1, len(tasks)) + self.assertEquals(workflow.id, tasks[0]['workflow']['id']) + self.assertEquals(workflow.study.id, tasks[0]['study']['id']) + + # Assure we can say something sensible like: + # You have a task called "Approval" to be completed in the "Supervisor Approval" workflow + # for the study 'Why dogs are stinky' managed by user "Jane Smith (js42x)", + # please check here to complete the task. + # Display name isn't set in the tests, so just checking name, but the full workflow details are included. + # I didn't delve into the full user details to keep things decoupled from ldap, so you just get the + # uid back, but could query to get the full entry. + self.assertEquals("roles", tasks[0]['workflow']['name']) + self.assertEquals("Beer consumption in the bipedal software engineer", tasks[0]['study']['title']) + self.assertEquals("lje5u", tasks[0]['study']['user_uid']) + + # Completing the next step of the workflow will close the task. + data['approval'] = True + self.complete_form(workflow, workflow_api.next_task, data, user_uid=supervisor.uid) + + def test_navigation_and_current_task_updates_through_workflow(self): + + submitter = self.create_user(uid='lje5u') + supervisor = self.create_user(uid='lb3dp') + workflow = self.create_workflow('roles', as_user=submitter.uid) + + # Navigation as Submitter with ready task. + workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid) + nav = workflow_api.navigation + self.assertEquals(5, len(nav)) + self.assertEquals('READY', nav[0]['state']) # First item is ready, no progress yet. + self.assertEquals('LOCKED', nav[1]['state']) # Second item is locked, it is the review and doesn't belong to this user. + self.assertEquals('LOCKED', nav[2]['state']) # third item is a gateway, and belongs to no one, and is locked. + self.assertEquals('NOOP', nav[3]['state']) # Approved Path, has no operation + self.assertEquals('NOOP', nav[4]['state']) # Rejected Path, has no operation. + self.assertEquals('READY', workflow_api.next_task.state) + + # Navigation as Submitter after handoff to supervisor + data = workflow_api.next_task.data + data['supervisor'] = supervisor.uid + workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid) + nav = workflow_api.navigation + self.assertEquals('COMPLETED', nav[0]['state']) # First item is ready, no progress yet. + self.assertEquals('LOCKED', nav[1]['state']) # Second item is locked, it is the review and doesn't belong to this user. + self.assertEquals('LOCKED', nav[2]['state']) # third item is a gateway, and belongs to no one, and is locked. + self.assertEquals('LOCKED', workflow_api.next_task.state) + # In the event the next task is locked, we should say something sensible here. + # It is possible to look at the role of the task, and say The next task "TASK TITLE" will + # be handled by 'dhf8r', who is full-filling the role of supervisor. the Task Data + # is guaranteed to have a supervisor attribute in it that will contain the users uid, which + # could be looked up through an ldap service. + self.assertEquals('supervisor', workflow_api.next_task.lane) + + + # Navigation as Supervisor + workflow_api = self.get_workflow_api(workflow, user_uid=supervisor.uid) + nav = workflow_api.navigation + self.assertEquals(5, len(nav)) + self.assertEquals('LOCKED', nav[0]['state']) # First item belongs to the submitter, and is locked. + self.assertEquals('READY', nav[1]['state']) # Second item is locked, it is the review and doesn't belong to this user. + self.assertEquals('LOCKED', nav[2]['state']) # third item is a gateway, and belongs to no one, and is locked. + self.assertEquals('READY', workflow_api.next_task.state) + + data = workflow_api.next_task.data + data["approval"] = False + workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=supervisor.uid) + + # Navigation as Supervisor, after completing task. + nav = workflow_api.navigation + self.assertEquals(5, len(nav)) + self.assertEquals('LOCKED', nav[0]['state']) # First item belongs to the submitter, and is locked. + self.assertEquals('COMPLETED', nav[1]['state']) # Second item is locked, it is the review and doesn't belong to this user. + self.assertEquals('COMPLETED', nav[2]['state']) # third item is a gateway, and is now complete. + self.assertEquals('LOCKED', workflow_api.next_task.state) + + # Navigation as Submitter, coming back in to a rejected workflow to view the rejection message. + workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid) + nav = workflow_api.navigation + self.assertEquals(5, len(nav)) + self.assertEquals('COMPLETED', nav[0]['state']) # First item belongs to the submitter, and is locked. + self.assertEquals('LOCKED', nav[1]['state']) # Second item is locked, it is the review and doesn't belong to this user. + self.assertEquals('LOCKED', nav[2]['state']) # third item is a gateway belonging to the supervisor, and is locked. + self.assertEquals('READY', workflow_api.next_task.state) + + # Navigation as Submitter, re-completing the original request a second time, and sending it for review. + workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid) + nav = workflow_api.navigation + self.assertEquals(5, len(nav)) + self.assertEquals('COMPLETED', nav[0]['state']) # We still have some issues here, the navigation will be off when looping back. + self.assertEquals('LOCKED', nav[1]['state']) # Second item is locked, it is the review and doesn't belong to this user. + self.assertEquals('LOCKED', nav[2]['state']) # third item is a gateway belonging to the supervisor, and is locked. + self.assertEquals('READY', workflow_api.next_task.state) + + data["favorite_color"] = "blue" + data["quest"] = "to seek the holy grail" + workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid) + self.assertEquals('LOCKED', workflow_api.next_task.state) + + workflow_api = self.get_workflow_api(workflow, user_uid=supervisor.uid) + self.assertEquals('READY', workflow_api.next_task.state) + + data = workflow_api.next_task.data + data["approval"] = True + workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=supervisor.uid) + self.assertEquals('LOCKED', workflow_api.next_task.state) + + workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid) + self.assertEquals('COMPLETED', workflow_api.next_task.state) + self.assertEquals('EndEvent', workflow_api.next_task.type) # Are are at the end. + self.assertEquals(WorkflowStatus.complete, workflow_api.status) \ No newline at end of file diff --git a/tests/test_workflow_processor.py b/tests/workflow/test_workflow_processor.py similarity index 88% rename from tests/test_workflow_processor.py rename to tests/workflow/test_workflow_processor.py index b3f6c374..a51f029d 100644 --- a/tests/test_workflow_processor.py +++ b/tests/workflow/test_workflow_processor.py @@ -187,7 +187,7 @@ class TestWorkflowProcessor(BaseTest): 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) - # Attemping a soft update on a structural change should raise a sensible error. + # Attempting a soft update on a structural change should raise a sensible error. with self.assertRaises(ApiError) as context: processor3 = WorkflowProcessor(processor.workflow_model, soft_reset=True) self.assertEqual("unexpected_workflow_structure", context.exception.code) @@ -270,53 +270,6 @@ class TestWorkflowProcessor(BaseTest): processor = self.get_processor(study, workflow_spec_model) self.assertTrue(processor.get_version_string().startswith('v2.1.1')) - def test_restart_workflow(self): - self.load_example_data() - study = session.query(StudyModel).first() - workflow_spec_model = self.load_test_spec("two_forms") - processor = self.get_processor(study, workflow_spec_model) - self.assertEqual(processor.workflow_model.workflow_spec_id, workflow_spec_model.id) - task = processor.next_task() - task.data = {"key": "Value"} - processor.complete_task(task) - task_before_restart = processor.next_task() - processor.hard_reset() - task_after_restart = processor.next_task() - - self.assertNotEqual(task.get_name(), task_before_restart.get_name()) - self.assertEqual(task.get_name(), task_after_restart.get_name()) - self.assertEqual(task.data, task_after_restart.data) - - def test_soft_reset(self): - self.load_example_data() - - # Start the two_forms workflow, and enter some data in the first form. - study = session.query(StudyModel).first() - workflow_spec_model = self.load_test_spec("two_forms") - processor = self.get_processor(study, workflow_spec_model) - self.assertEqual(processor.workflow_model.workflow_spec_id, workflow_spec_model.id) - task = processor.next_task() - task.data = {"color": "blue"} - processor.complete_task(task) - - # Modify the specification, with a minor text change. - file_path = os.path.join(app.root_path, '..', 'tests', 'data', 'two_forms', 'mods', 'two_forms_text_mod.bpmn') - self.replace_file("two_forms.bpmn", file_path) - - # Setting up another processor should not error out, but doesn't pick up the update. - processor.workflow_model.bpmn_workflow_json = processor.serialize() - processor2 = WorkflowProcessor(processor.workflow_model) - self.assertEqual("Step 1", processor2.bpmn_workflow.last_task.task_spec.description) - self.assertNotEqual("# This is some documentation I wanted to add.", - processor2.bpmn_workflow.last_task.task_spec.documentation) - - # You can do a soft update and get the right response. - processor3 = WorkflowProcessor(processor.workflow_model, soft_reset=True) - self.assertEqual("Step 1", processor3.bpmn_workflow.last_task.task_spec.description) - self.assertEqual("# This is some documentation I wanted to add.", - processor3.bpmn_workflow.last_task.task_spec.documentation) - - def test_hard_reset(self): self.load_example_data() @@ -344,8 +297,10 @@ class TestWorkflowProcessor(BaseTest): # Do a hard reset, which should bring us back to the beginning, but retain the data. processor3 = WorkflowProcessor(processor.workflow_model, hard_reset=True) self.assertEqual("Step 1", processor3.next_task().task_spec.description) - self.assertEqual({"color": "blue"}, processor3.next_task().data) - processor3.complete_task(processor3.next_task()) + self.assertTrue(processor3.is_latest_spec) # Now at version 2. + task = processor3.next_task() + task.data = {"color": "blue"} + processor3.complete_task(task) self.assertEqual("New Step", processor3.next_task().task_spec.description) self.assertEqual("blue", processor3.next_task().data["color"]) @@ -413,4 +368,19 @@ class TestWorkflowProcessor(BaseTest): task.task_spec.form.fields.append(field) with self.assertRaises(ApiError): - self._populate_form_with_random_data(task) \ No newline at end of file + self._populate_form_with_random_data(task) + + + def test_get_role_by_name(self): + self.load_example_data() + workflow_spec_model = self.load_test_spec("roles") + study = session.query(StudyModel).first() + processor = self.get_processor(study, workflow_spec_model) + processor.do_engine_steps() + tasks = processor.next_user_tasks() + task = tasks[0] + self._populate_form_with_random_data(task) + processor.complete_task(task) + supervisor_task = processor.next_user_tasks()[0] + self.assertEquals("supervisor", supervisor_task.task_spec.lane) + diff --git a/tests/test_workflow_processor_multi_instance.py b/tests/workflow/test_workflow_processor_multi_instance.py similarity index 62% rename from tests/test_workflow_processor_multi_instance.py rename to tests/workflow/test_workflow_processor_multi_instance.py index aefb73f1..a67cae7f 100644 --- a/tests/test_workflow_processor_multi_instance.py +++ b/tests/workflow/test_workflow_processor_multi_instance.py @@ -1,13 +1,13 @@ from unittest.mock import patch +from tests.base_test import BaseTest -from crc import session +from crc import session, db from crc.models.api_models import MultiInstanceType from crc.models.study import StudyModel -from crc.models.workflow import WorkflowStatus +from crc.models.workflow import WorkflowStatus, WorkflowModel from crc.services.study_service import StudyService from crc.services.workflow_processor import WorkflowProcessor from crc.services.workflow_service import WorkflowService -from tests.base_test import BaseTest class TestWorkflowProcessorMultiInstance(BaseTest): @@ -32,7 +32,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest): 'error': 'Unable to locate a user with id asd3v in LDAP'}} def _populate_form_with_random_data(self, task): - WorkflowProcessor.populate_form_with_random_data(task) + WorkflowService.populate_form_with_random_data(task) def get_processor(self, study_model, spec_model): workflow_model = StudyService._create_workflow_model(study_model, spec_model) @@ -51,51 +51,72 @@ class TestWorkflowProcessorMultiInstance(BaseTest): self.assertIsNotNone(processor) self.assertEqual(WorkflowStatus.user_input_required, processor.get_status()) processor.bpmn_workflow.do_engine_steps() - next_user_tasks = processor.next_user_tasks() - self.assertEqual(1, len(next_user_tasks)) - - task = next_user_tasks[0] + workflow_api = WorkflowService.processor_to_workflow_api(processor) + self.assertIsNotNone(workflow_api) + self.assertIsNotNone(workflow_api.next_task) + # 1st investigator + api_task = workflow_api.next_task self.assertEqual(WorkflowStatus.user_input_required, processor.get_status()) - self.assertEqual("dhf8r", task.data["investigator"]["user_id"]) - - self.assertEqual("MutiInstanceTask", task.get_name()) - api_task = WorkflowService.spiff_task_to_api_task(task) - self.assertEqual(MultiInstanceType.sequential, api_task.multi_instance_type) + self.assertEqual("dhf8r", api_task.data["investigator"]["user_id"]) + self.assertTrue(api_task.name.startswith("MultiInstanceTask")) self.assertEqual(3, api_task.multi_instance_count) self.assertEqual(1, api_task.multi_instance_index) - task.update_data({"investigator":{"email":"asd3v@virginia.edu"}}) + + task = processor.get_current_user_tasks()[0] + self.assertEqual(task.id, api_task.id) + task.update_data({"investigator": {"email": "asd3v@virginia.edu"}}) processor.complete_task(task) processor.do_engine_steps() + workflow_api = WorkflowService.processor_to_workflow_api(processor) - task = next_user_tasks[0] - api_task = WorkflowService.spiff_task_to_api_task(task) - self.assertEqual("MutiInstanceTask", api_task.name) - task.update_data({"investigator":{"email":"asdf32@virginia.edu"}}) + # 2nd investigator + api_task = workflow_api.next_task + self.assertEqual(WorkflowStatus.user_input_required, processor.get_status()) + self.assertEqual(None, api_task.data["investigator"]["user_id"]) + self.assertTrue(api_task.name.startswith("MultiInstanceTask")) self.assertEqual(3, api_task.multi_instance_count) self.assertEqual(2, api_task.multi_instance_index) + + task = processor.get_current_user_tasks()[0] + self.assertEqual(task.id, api_task.id) + task.update_data({"investigator": {"email": "asdf32@virginia.edu"}}) processor.complete_task(task) processor.do_engine_steps() + workflow_api = WorkflowService.processor_to_workflow_api(processor) - task = next_user_tasks[0] - api_task = WorkflowService.spiff_task_to_api_task(task) - self.assertEqual("MutiInstanceTask", task.get_name()) - task.update_data({"investigator":{"email":"dhf8r@virginia.edu"}}) + # 3rd investigator + api_task = workflow_api.next_task + self.assertEqual(WorkflowStatus.user_input_required, processor.get_status()) + self.assertEqual("asd3v", api_task.data["investigator"]["user_id"]) + self.assertTrue(api_task.name.startswith("MultiInstanceTask")) self.assertEqual(3, api_task.multi_instance_count) self.assertEqual(3, api_task.multi_instance_index) + + task = processor.get_current_user_tasks()[0] + self.assertEqual(task.id, api_task.id) + task.update_data({"investigator": {"email": "dhf8r@virginia.edu"}}) processor.complete_task(task) processor.do_engine_steps() - task = processor.bpmn_workflow.last_task + workflow_api = WorkflowService.processor_to_workflow_api(processor) + + # Last task + api_task = workflow_api.next_task expected = self.mock_investigator_response expected['PI']['email'] = "asd3v@virginia.edu" expected['SC_I']['email'] = "asdf32@virginia.edu" expected['DC']['email'] = "dhf8r@virginia.edu" - self.assertEqual(expected, - task.data['StudyInfo']['investigators']) + self.assertEqual(expected, api_task.data['StudyInfo']['investigators']) self.assertEqual(WorkflowStatus.complete, processor.get_status()) + def refresh_processor(self, processor): + """Saves the processor, and returns a new one read in from the database""" + processor.save() + processor = WorkflowProcessor(processor.workflow_model) + return processor + @patch('crc.services.study_service.StudyService.get_investigators') def test_create_and_complete_workflow_parallel(self, mock_study_service): """Unlike the test above, the parallel task allows us to complete the items in any order.""" @@ -107,11 +128,15 @@ class TestWorkflowProcessorMultiInstance(BaseTest): workflow_spec_model = self.load_test_spec("multi_instance_parallel") study = session.query(StudyModel).first() processor = self.get_processor(study, workflow_spec_model) + processor = self.refresh_processor(processor) processor.bpmn_workflow.do_engine_steps() # In the Parallel instance, there should be three tasks, all of them in the ready state. next_user_tasks = processor.next_user_tasks() self.assertEqual(3, len(next_user_tasks)) + # There should be six tasks in the navigation: start event, the script task, end event, and three tasks + # for the three executions of hte multi-instance. + self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list())) # We can complete the tasks out of order. task = next_user_tasks[2] @@ -121,23 +146,31 @@ class TestWorkflowProcessorMultiInstance(BaseTest): api_task = WorkflowService.spiff_task_to_api_task(task) self.assertEqual(MultiInstanceType.parallel, api_task.multi_instance_type) - task.update_data({"investigator":{"email":"dhf8r@virginia.edu"}}) + + # Assure navigation picks up the label of the current element variable. + nav = WorkflowService.processor_to_workflow_api(processor, task).navigation + self.assertEquals("Primary Investigator", nav[2].title) + + task.update_data({"investigator": {"email": "dhf8r@virginia.edu"}}) processor.complete_task(task) processor.do_engine_steps() + self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list())) task = next_user_tasks[0] api_task = WorkflowService.spiff_task_to_api_task(task) - self.assertEqual("MutiInstanceTask", api_task.name) + self.assertEqual("MultiInstanceTask", api_task.name) task.update_data({"investigator":{"email":"asd3v@virginia.edu"}}) processor.complete_task(task) processor.do_engine_steps() + self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list())) task = next_user_tasks[1] api_task = WorkflowService.spiff_task_to_api_task(task) - self.assertEqual("MutiInstanceTask", task.get_name()) + self.assertEqual("MultiInstanceTask", task.get_name()) task.update_data({"investigator":{"email":"asdf32@virginia.edu"}}) processor.complete_task(task) processor.do_engine_steps() + self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list())) # Completing the tasks out of order, still provides the correct information. expected = self.mock_investigator_response @@ -148,3 +181,4 @@ class TestWorkflowProcessorMultiInstance(BaseTest): task.data['StudyInfo']['investigators']) self.assertEqual(WorkflowStatus.complete, processor.get_status()) + self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list())) diff --git a/tests/test_workflow_service.py b/tests/workflow/test_workflow_service.py similarity index 82% rename from tests/test_workflow_service.py rename to tests/workflow/test_workflow_service.py index 9f3ceda1..9ae49b5a 100644 --- a/tests/test_workflow_service.py +++ b/tests/workflow/test_workflow_service.py @@ -1,7 +1,16 @@ +import json +import unittest + from tests.base_test import BaseTest from crc.services.workflow_processor import WorkflowProcessor from crc.services.workflow_service import WorkflowService +from SpiffWorkflow import Task as SpiffTask, WorkflowException +from example_data import ExampleDataLoader +from crc import db +from crc.models.task_event import TaskEventModel +from crc.models.api_models import Task +from crc.api.common import ApiError class TestWorkflowService(BaseTest): @@ -78,4 +87,9 @@ class TestWorkflowService(BaseTest): task = processor.next_task() task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True) WorkflowService.populate_form_with_random_data(task, task_api, required_only=False) - self.assertTrue(isinstance(task.data["sponsor"], dict)) \ No newline at end of file + self.assertTrue(isinstance(task.data["sponsor"], dict)) + + 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): + WorkflowService.test_spec(workflow_spec_model.id) diff --git a/tests/test_workflow_spec_api.py b/tests/workflow/test_workflow_spec_api.py similarity index 100% rename from tests/test_workflow_spec_api.py rename to tests/workflow/test_workflow_spec_api.py diff --git a/tests/test_workflow_spec_validation_api.py b/tests/workflow/test_workflow_spec_validation_api.py similarity index 91% rename from tests/test_workflow_spec_validation_api.py rename to tests/workflow/test_workflow_spec_validation_api.py index cb9b6b77..0c17892e 100644 --- a/tests/test_workflow_spec_validation_api.py +++ b/tests/workflow/test_workflow_spec_validation_api.py @@ -1,4 +1,5 @@ import json +import unittest from unittest.mock import patch from tests.base_test import BaseTest @@ -51,9 +52,6 @@ class TestWorkflowSpecValidation(BaseTest): app.config['PB_ENABLED'] = True self.validate_all_loaded_workflows() - 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() @@ -66,7 +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") @@ -92,12 +89,21 @@ class TestWorkflowSpecValidation(BaseTest): self.load_example_data() errors = self.validate_workflow("invalid_script") self.assertEqual(2, len(errors)) - self.assertEqual("workflow_validation_exception", errors[0]['code']) + self.assertEqual("error_loading_workflow", errors[0]['code']) self.assertTrue("NoSuchScript" in errors[0]['message']) self.assertEqual("Invalid_Script_Task", errors[0]['task_id']) 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')