Merge pull request #42 from sartography/feature/new_script_engine

Updated to use the latest script engine / evaluation engine that crea…

Pipfile.lock

@@ -478,11 +478,11 @@
         },
         "marshmallow": {
             "hashes": [
-                "sha256:56663fa1d5385c14c6a1236badd166d6dee987a5f64d2b6cc099dadf96eb4f09",
+                "sha256:c2673233aa21dde264b84349dc2fd1dce5f30ed724a0a00e75426734de5b84ab",
-                "sha256:f12203bf8d94c410ab4b8d66edfde4f8a364892bde1f6747179765559f93d62a"
+                "sha256:f88fe96434b1f0f476d54224d59333eba8ca1a203a2695683c1855675c4049a7"
             ],
             "index": "pypi",
-            "version": "==3.5.2"
+            "version": "==3.6.0"
         },
         "marshmallow-enum": {
             "hashes": [
@@ -783,7 +783,7 @@
         "spiffworkflow": {
             "editable": true,
             "git": "https://github.com/sartography/SpiffWorkflow.git",
-            "ref": "6608bb1d9cc77b906bf668804470e850ec798414"
+            "ref": "f626ac6d4f035f3a65a058320efd8d33d1ec652a"
         },
         "sqlalchemy": {
             "hashes": [
@@ -938,11 +938,11 @@
         },
         "pytest": {
             "hashes": [
-                "sha256:0e5b30f5cb04e887b91b1ee519fa3d89049595f428c1db76e73bd7f17b09b172",
+                "sha256:95c710d0a72d91c13fae35dce195633c929c3792f54125919847fdcdf7caa0d3",
-                "sha256:84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970"
+                "sha256:eb2b5e935f6a019317e455b6da83dd8650ac9ffd2ee73a7b657a30873d67a698"
             ],
             "index": "pypi",
-            "version": "==5.4.1"
+            "version": "==5.4.2"
         },
         "six": {
             "hashes": [

crc/scripts/study_info.py

@@ -52,7 +52,12 @@ class StudyInfo(Script):
                         "NETBADGEID": "dhf8r"
                     },
                 "details":
-                    {},
+                    {
+                        "IS_IND": 0,
+                        "IS_IDE": 0,
+                        "IS_MULTI_SITE": 0,
+                        "IS_UVA_PI_MULTI": 0
+                    },
                 "approvals": {
                     "study_id": 12,
                     "workflow_id": 321,

crc/services/study_service.py

@@ -2,9 +2,10 @@ from datetime import datetime
 import json
 from typing import List
 
+import requests
 from SpiffWorkflow import WorkflowException
 
-from crc import db, session
+from crc import db, session, app
 from crc.api.common import ApiError
 from crc.models.file import FileModel, FileModelSchema
 from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
@@ -108,7 +109,11 @@ class StudyService(object):
         that is available.."""
 
         # Get PB required docs
-        pb_docs = ProtocolBuilderService.get_required_docs(study_id=study_id)
+        try:
+            pb_docs = ProtocolBuilderService.get_required_docs(study_id=study_id)
+        except requests.exceptions.ConnectionError as ce:
+            app.logger.error("Failed to connect to the Protocol Builder - %s" % str(ce))
+            pb_docs = []
 
         # Loop through all known document types, get the counts for those files, and use pb_docs to mark those required.
         doc_dictionary = FileService.get_file_reference_dictionary()

crc/services/workflow_processor.py

@@ -4,7 +4,7 @@ import string
 import xml.etree.ElementTree as ElementTree
 from datetime import datetime
 
-from SpiffWorkflow import Task as SpiffTask
+from SpiffWorkflow import Task as SpiffTask, WorkflowException
 from SpiffWorkflow.bpmn.BpmnScriptEngine import BpmnScriptEngine
 from SpiffWorkflow.bpmn.parser.ValidationException import ValidationException
 from SpiffWorkflow.bpmn.serializer.BpmnSerializer import BpmnSerializer
@@ -12,6 +12,7 @@ from SpiffWorkflow.bpmn.specs.EndEvent import EndEvent
 from SpiffWorkflow.bpmn.workflow import BpmnWorkflow
 from SpiffWorkflow.camunda.parser.CamundaParser import CamundaParser
 from SpiffWorkflow.dmn.parser.BpmnDmnParser import BpmnDmnParser
+from SpiffWorkflow.exceptions import WorkflowTaskExecException
 from SpiffWorkflow.operators import Operator
 from SpiffWorkflow.specs import WorkflowSpec
 
@@ -69,24 +70,6 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
         camel = camel.strip()
         return re.sub(r'(?<!^)(?=[A-Z])', '_', camel).lower()
 
-    def evaluate(self, task, expression):
-        """
-        Evaluate the given expression, within the context of the given task and
-        return the result.
-        """
-        if isinstance(expression, Operator):
-            return expression._matches(task)
-        else:
-            return self._eval(task, expression, **task.data)
-
-    def _eval(self, task, expression, **kwargs):
-        locals().update(kwargs)
-        try:
-            return eval(expression)
-        except NameError as ne:
-            raise ApiError.from_task('invalid_expression',
-                                     "The expression '%s' you provided has a missing value. % s" % (expression, str(ne)),
-                                     task=task)
 
 class MyCustomParser(BpmnDmnParser):
     """
@@ -282,13 +265,13 @@ class WorkflowProcessor(object):
 
 
     @staticmethod
-    def populate_form_with_random_data(task):
+    def populate_form_with_random_data(task, task_api):
         """populates a task with random data - useful for testing a spec."""
 
         if not hasattr(task.task_spec, 'form'): return
 
         form_data = {}
-        for field in task.task_spec.form.fields:
+        for field in task_api.form.fields:
             if field.type == "enum":
                 if len(field.options) > 0:
                     form_data[field.id] = random.choice(field.options)
@@ -346,7 +329,10 @@ class WorkflowProcessor(object):
         return self.workflow_model.spec_version
 
     def do_engine_steps(self):
-        self.bpmn_workflow.do_engine_steps()
+        try:
+            self.bpmn_workflow.do_engine_steps()
+        except WorkflowTaskExecException as we:
+            raise ApiError.from_task("task_error", str(we), we.task)
 
     def serialize(self):
         return self._serializer.serialize_workflow(self.bpmn_workflow)

crc/services/workflow_service.py

@@ -54,8 +54,8 @@ class WorkflowService(object):
                 tasks = bpmn_workflow.get_tasks(SpiffTask.READY)
                 for task in tasks:
                     task_api = WorkflowService.spiff_task_to_api_task(
-                        task)  # Assure we try to process the documenation, and raise those errors.
+                        task, add_docs_and_forms=True)  # Assure we try to process the documenation, and raise those errors.
-                    WorkflowProcessor.populate_form_with_random_data(task)
+                    WorkflowProcessor.populate_form_with_random_data(task, task_api)
                     task.complete()
             except WorkflowException as we:
                 raise ApiError.from_task_spec("workflow_execution_exception", str(we),
@@ -151,13 +151,15 @@ class WorkflowService(object):
 
     @staticmethod
     def process_options(spiff_task, field):
-        lookup_model = WorkflowService.get_lookup_table(spiff_task, field);
+        lookup_model = WorkflowService.get_lookup_table(spiff_task, field)
 
         # If lookup is set to true, do not populate options, a lookup will happen later.
         if field.has_property(Task.EMUM_OPTIONS_AS_LOOKUP) and field.get_property(Task.EMUM_OPTIONS_AS_LOOKUP):
             pass
         else:
             data = db.session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_model).all()
+            if not hasattr(field, 'options'):
+                field.options = []
             for d in data:
                 field.options.append({"id": d.value, "name": d.label})
 

crc/static/bpmn/ids_full_submission/pharmacy_manual.dmn

@@ -7,7 +7,7 @@
     <decisionTable id="decisionTable_1">
       <input id="input_1" label="Pharmacy Manual Upload Count">
         <inputExpression id="inputExpression_1" typeRef="integer">
-          <text>StudyInfo.documents["DrugDevDoc_PharmManual"]["count"]</text>
+          <text>StudyInfo.documents.DrugDevDoc_PharmManual.count</text>
         </inputExpression>
       </input>
       <output id="output_1" label="Pharmacy Manual(s) Uploaded?" name="isPharmacyManual" typeRef="boolean" />

tests/test_tasks_api.py

@@ -315,6 +315,7 @@ class TestTasksApi(BaseTest):
         results = json.loads(rv.get_data(as_text=True))
         self.assertEqual(5, len(results))
 
+
     def test_sub_process(self):
         self.load_example_data()
         workflow = self.create_workflow('subprocess')

tests/test_workflow_processor.py

@@ -19,6 +19,7 @@ from crc.services.file_service import FileService
 from crc.services.study_service import StudyService
 from crc.models.protocol_builder import ProtocolBuilderStudySchema, ProtocolBuilderInvestigatorSchema, \
     ProtocolBuilderRequiredDocumentSchema
+from crc.services.workflow_service import WorkflowService
 from tests.base_test import BaseTest
 from crc.services.workflow_processor import WorkflowProcessor
 
@@ -26,7 +27,8 @@ from crc.services.workflow_processor import WorkflowProcessor
 class TestWorkflowProcessor(BaseTest):
 
     def _populate_form_with_random_data(self, task):
-        WorkflowProcessor.populate_form_with_random_data(task)
+        api_task = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
+        WorkflowProcessor.populate_form_with_random_data(task, api_task)
 
     def get_processor(self, study_model, spec_model):
         workflow_model = StudyService._create_workflow_model(study_model, spec_model)
@@ -206,7 +208,7 @@ class TestWorkflowProcessor(BaseTest):
         processor.complete_task(next_user_tasks[0])
         with self.assertRaises(ApiError) as context:
             processor.do_engine_steps()
-        self.assertEqual("invalid_expression", context.exception.code)
+        self.assertEqual("task_error", context.exception.code)
 
     def test_workflow_with_docx_template(self):
         self.load_example_data()
@@ -417,4 +419,4 @@ class TestWorkflowProcessor(BaseTest):
         task.task_spec.form.fields.append(field)
 
         with self.assertRaises(ApiError):
-            processor.populate_form_with_random_data(task)
+            self._populate_form_with_random_data(task)

tests/test_workflow_spec_validation_api.py

@@ -43,12 +43,12 @@ class TestWorkflowSpecValidation(BaseTest):
     def test_invalid_expression(self):
         errors = self.validate_workflow("invalid_expression")
         self.assertEqual(1, len(errors))
-        self.assertEqual("invalid_expression", errors[0]['code'])
+        self.assertEqual("workflow_execution_exception", errors[0]['code'])
         self.assertEqual("ExclusiveGateway_003amsm", errors[0]['task_id'])
         self.assertEqual("Has Bananas Gateway", errors[0]['task_name'])
         self.assertEqual("invalid_expression.bpmn", errors[0]['file_name'])
-        self.assertEqual("The expression 'this_value_does_not_exist==true' you provided has a missing value."
+        self.assertEqual('ExclusiveGateway_003amsm: Error evaluating expression \'this_value_does_not_exist==true\', '
-                         " name 'this_value_does_not_exist' is not defined", errors[0]["message"])
+                         'name \'this_value_does_not_exist\' is not defined', errors[0]["message"])
 
     def test_validation_error(self):
         errors = self.validate_workflow("invalid_spec")