Merge remote-tracking branch 'origin/master'

crc/api.yml

@@ -680,7 +680,21 @@ paths:
                 type: string
                 format: binary
                 example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
-
+  /list_scripts:
+    get:
+      operationId: crc.api.tools.list_scripts
+      summary: Returns an list of scripts, along with their descriptions
+      tags:
+        - Configurator Tools
+      responses:
+        '201':
+          description: The list of scripts
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/Script"
 components:
   schemas:
     User:
@@ -969,3 +983,12 @@ components:
         message:
           type: string
           example: "You do not have permission to view the requested study."
+    Script:
+      properties:
+        name:
+          type: string
+          format: string
+          example: "random_fact"
+        description:
+          type: string
+          example: "Returns a random fact about a topic.  Provide an argument of either 'cat', 'norris', or 'buzzword'"

crc/api/common.py

@@ -6,6 +6,7 @@ class ApiError(Exception):
         self.status_code = status_code
         self.code = code
         self.message = message
+        Exception.__init__(self, self.message)
 
 
 class ApiErrorSchema(ma.Schema):

crc/api/tools.py

@@ -1,18 +1,14 @@
 import io
 import json
-import uuid
-from io import BytesIO
 
 import connexion
-import jinja2
-from docxtpl import DocxTemplate
 from flask import send_file
 from jinja2 import Template, UndefinedError
 
-from crc.api.common import ApiError, ApiErrorSchema
-from crc.scripts.CompleteTemplate import CompleteTemplate
-from crc.services.file_service import FileService
-
+from crc.api.common import ApiError
+from crc.scripts.complete_template import CompleteTemplate
+from crc.scripts.script import Script
+import crc.scripts
 
 def render_markdown(data, template):
     """
@@ -48,3 +44,17 @@ def render_docx(data):
         raise ApiError(code="invalid", message=str(e))
     except Exception as e:
         raise ApiError(code="invalid", message=str(e))
+
+
+def list_scripts():
+    """Provides a list of scripts that can be called by a script task."""
+    scripts = Script.get_all_subclasses()
+    script_meta = []
+    for script_class in scripts:
+        script_meta.append(
+            {
+                "name": script_class.__name__,
+                "description": script_class().get_description()
+            })
+    return script_meta
+

crc/scripts/IRBDocAPI.py

@@ -1,9 +0,0 @@
-import requests
-
-
-class IRBDocAPI:
-    """Just your basic class that can pull in data from a few api endpoints and do a basic task."""
-
-    def do_task(self, task_data):
-        print('*** IRB_Doc_API > do_task ***')
-        print('task_data', task_data)

crc/scripts/LoadStudies.py

@@ -1,24 +0,0 @@
-import requests
-
-
-class LoadStudies:
-    """Just your basic class that can pull in data from a few api endpoints and do a basic task."""
-
-    def do_task(self, task_data):
-        print('*** LoadStudies > do_task ***')
-        print('task_data', task_data)
-
-class LoadStudy:
-    """Just your basic class that can pull in data from a few api endpoints and do a basic task."""
-
-    def do_task(self, task_data):
-        print('*** LoadStudies > do_task ***')
-        print('task_data', task_data)
-        irb_study = {
-            'tbd': 0,
-            'protocol_builder_available': True,
-            'irb_review_type': 'Full Board',
-            'irb_requires': True,
-        }
-
-        return irb_study

crc/scripts/complete_template.py

@@ -9,17 +9,18 @@ from crc.models.workflow import WorkflowSpecModel
 from docxtpl import DocxTemplate
 import jinja2
 
+from crc.scripts.script import Script
 from crc.services.file_service import FileService
 from crc.services.workflow_processor import WorkflowProcessor
 
 
-class CompleteTemplate(object):
-    """Completes a word template, using the data available in the current task. Heavy on the
-    error messages, because there is so much that can go wrong here, and we want to provide
-    as much feedback as possible.  Some of this might move up to a higher level object or be
-    passed into all tasks as we complete more work."""
+class CompleteTemplate(Script):
 
-    def do_task(self, task, *args, **kwargs):
+    def get_description(self):
+        return """Takes one argument, which is the name of a MS Word docx file to use as a template.
+        All data currently collected up to this Task will be available for use in the template."""
+
+    def do_task(self, task, study_id, *args, **kwargs):
         """Entry point, mostly worried about wiring it all up."""
         if len(args) != 1:
             raise ApiError(code="missing_argument",

crc/scripts/fact_service.py

@@ -1,8 +1,12 @@
 import requests
 
+from crc.scripts.script import Script
 
-class FactService:
-    """Just your basic class that can pull in data from a few api endpoints and do a basic task."""
+
+class FactService(Script):
+    def get_description(self):
+        return """Just your basic class that can pull in data from a few api endpoints and 
+        do a basic task."""
 
     def get_cat(self):
         response = requests.get('https://cat-fact.herokuapp.com/facts/random')
@@ -16,7 +20,7 @@ class FactService:
         response = requests.get('https://api.chucknorris.io/jokes/random')
         return response.json()['value']
 
-    def do_task(self, task, **kwargs):
+    def do_task(self, task, study_id, **kwargs):
         print(task.data)
 
         if "type" not in task.data:

crc/scripts/script.py

@@ -0,0 +1,41 @@
+import importlib
+import os
+import pkgutil
+
+from crc.api.common import ApiError
+
+
+class Script:
+    """ Provides an abstract class that defines how scripts should work, this
+    must be extended in all Script Tasks."""
+
+    def get_description(self):
+        raise ApiError("invalid_script",
+                       "This script does not supply a description.")
+
+    def do_task(self, task, study_id, **kwargs):
+        raise ApiError("invalid_script",
+                       "This is an internal error. The script you are trying to execute " +
+                       "does not properly implement the do_task function.")
+
+    @staticmethod
+    def get_all_subclasses():
+        return Script._get_all_subclasses(Script)
+
+    @staticmethod
+    def _get_all_subclasses(cls):
+
+        # hackish mess to make sure we have all the modules loaded for the scripts
+        pkg_dir = os.path.dirname(__file__)
+        for (module_loader, name, ispkg) in pkgutil.iter_modules([pkg_dir]):
+            importlib.import_module('.' + name, __package__)
+
+
+        """Returns a list of all classes that extend this class."""
+        all_subclasses = []
+
+        for subclass in cls.__subclasses__():
+            all_subclasses.append(subclass)
+            all_subclasses.extend(Script._get_all_subclasses(subclass))
+
+        return all_subclasses

crc/scripts/study_info.py

@@ -0,0 +1,45 @@
+import requests
+
+from crc import session
+from crc.api.common import ApiError
+from crc.models.study import StudyModel, StudyModelSchema
+from crc.scripts.script import Script
+from crc.services.protocol_builder import ProtocolBuilderService
+
+
+class StudyInfo(Script):
+    """Just your basic class that can pull in data from a few api endpoints and do a basic task."""
+    pb = ProtocolBuilderService()
+    type_options = ['info', 'investigators', 'required_docs', 'details']
+
+    def get_description(self):
+        return """StudyInfo [TYPE], where TYPE is one of 'info', 'investigators','required_docs', or 'details'
+            Adds details about the current study to the Task Data.  The type of information required should be 
+            provided as an argument.  Basic returns the basic information such as the title.  Investigators provides
+            detailed information about each investigator in th study.  Details provides a large number
+            of details about the study, as gathered within the protocol builder, and 'required_docs', 
+            lists all the documents the Protocol Builder has determined will be required as a part of
+            this study. 
+        """
+
+    def do_task(self, task, study_id, *args, **kwargs):
+        if len(args) != 1 or (args[0] not in StudyInfo.type_options):
+            raise ApiError(code="missing_argument",
+                           message="The StudyInfo script requires a single argument which must be "
+                                   "one of %s" % ",".join(StudyInfo.type_options))
+        cmd = args[0]
+        if cmd == 'info':
+            study = session.query(StudyModel).filter_by(id=study_id).first()
+            schema = StudyModelSchema()
+            details = {"study": {"info": schema.dump(study)}}
+            task.data.update(details)
+        if cmd == 'investigators':
+            details = {"study": {"investigators": self.pb.get_investigators(study_id)}}
+            task.data.update(details)
+        if cmd == 'required_docs':
+            details = {"study": {"required_docs": self.pb.get_required_docs(study_id)}}
+            task.data.update(details)
+        if cmd == 'details':
+            details = {"study": {"details": self.pb.get_study_details(study_id)}}
+            task.data.update(details)
+

crc/services/protocol_builder.py

@@ -4,6 +4,7 @@ from typing import List, Optional
 import requests
 
 from crc import app
+from crc.api.common import ApiError
 from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStudySchema, ProtocolBuilderInvestigator, \
     ProtocolBuilderRequiredDocument, ProtocolBuilderStudyDetails, ProtocolBuilderInvestigatorSchema, \
     ProtocolBuilderRequiredDocumentSchema, ProtocolBuilderStudyDetailsSchema
@@ -17,36 +18,54 @@ class ProtocolBuilderService(object):
 
     @staticmethod
     def get_studies(user_id) -> Optional[List[ProtocolBuilderStudy]]:
+        if not isinstance(user_id, str):
+            raise ApiError("invalid_user_id", "This user id is invalid: " + str(user_id))
         response = requests.get(ProtocolBuilderService.STUDY_URL % user_id)
         if response.ok and response.text:
             pb_studies = ProtocolBuilderStudySchema(many=True).loads(response.text)
             return pb_studies
         else:
-            return None
+            raise ApiError("protocol_builder_error",
+                           "Received an invalid response from the protocol builder (status %s): %s" %
+                           (response.status_code, response.text))
 
     @staticmethod
     def get_investigators(study_id) -> Optional[List[ProtocolBuilderInvestigator]]:
+        ProtocolBuilderService.check_args(study_id)
         response = requests.get(ProtocolBuilderService.INVESTIGATOR_URL % study_id)
         if response.ok and response.text:
             pb_studies = ProtocolBuilderInvestigatorSchema(many=True).loads(response.text)
             return pb_studies
         else:
-            return None
+            raise ApiError("protocol_builder_error",
+                           "Received an invalid response from the protocol builder (status %s): %s" %
+                           (response.status_code, response.text))
 
     @staticmethod
     def get_required_docs(study_id) -> Optional[List[ProtocolBuilderRequiredDocument]]:
+        ProtocolBuilderService.check_args(study_id)
         response = requests.get(ProtocolBuilderService.REQUIRED_DOCS_URL % study_id)
         if response.ok and response.text:
             pb_studies = ProtocolBuilderRequiredDocumentSchema(many=True).loads(response.text)
             return pb_studies
         else:
-            return None
+            raise ApiError("protocol_builder_error",
+                           "Received an invalid response from the protocol builder (status %s): %s" %
+                           (response.status_code, response.text))
 
     @staticmethod
     def get_study_details(study_id) -> Optional[ProtocolBuilderStudyDetails]:
+        ProtocolBuilderService.check_args(study_id)
         response = requests.get(ProtocolBuilderService.STUDY_DETAILS_URL % study_id)
         if response.ok and response.text:
             pb_study_details = ProtocolBuilderStudyDetailsSchema().loads(response.text)
             return pb_study_details
         else:
-            return None
+            raise ApiError("protocol_builder_error",
+                           "Received an invalid response from the protocol builder (status %s): %s" %
+                           (response.status_code, response.text))
+
+    @staticmethod
+    def check_args(study_id):
+        if not isinstance(study_id, int):
+            raise ApiError("invalid_study_id", "This study id is invalid: " + str(study_id))

crc/services/workflow_processor.py

@@ -1,3 +1,4 @@
+import re
 import xml.etree.ElementTree as ElementTree
 
 from SpiffWorkflow import Task as SpiffTask, Workflow
@@ -13,6 +14,7 @@ from crc import session
 from crc.api.common import ApiError
 from crc.models.file import FileDataModel, FileModel, FileType
 from crc.models.workflow import WorkflowStatus, WorkflowModel
+from crc.scripts.script import Script
 
 
 class CustomBpmnScriptEngine(BpmnScriptEngine):
@@ -20,7 +22,7 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
     Rather than execute arbitrary code, this assumes the script references a fully qualified python class
     such as myapp.RandomFact. """
 
-    def execute(self, task, script, **kwargs):
+    def execute(self, task:SpiffTask, script, **kwargs):
         """
         Assume that the script read in from the BPMN file is a fully qualified python class. Instantiate
         that class, pass in any data available to the current task so that it might act on it.
@@ -29,11 +31,31 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
         This allows us to reference custom code from the BPMN diagram.
         """
         commands = script.split(" ")
-        module_name = "crc." + commands[0]
-        class_name = module_name.split(".")[-1]
+        path_and_command = commands[0].rsplit(".", 1)
+        if len(path_and_command) == 1:
+            module_name = "crc.scripts." + self.camel_to_snake(path_and_command[0])
+            class_name = path_and_command[0]
+        else:
+            module_name = "crc.scripts." + path_and_command[0] + "." + self.camel_to_snake(path_and_command[1])
+            class_name = path_and_command[1]
+        try:
             mod = __import__(module_name, fromlist=[class_name])
             klass = getattr(mod, class_name)
-        klass().do_task(task, *commands[1:])
+            study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
+            if not isinstance(klass(), Script):
+                raise ApiError("invalid_script",
+                               "This is an internal error. The script '%s:%s' you called  "
+                               "does not properly implement the CRC Script class." %
+                               (module_name, class_name))
+            klass().do_task(task, study_id, *commands[1:])
+        except ModuleNotFoundError as mnfe:
+            raise ApiError("invalid_script",
+                           "Unable to locate Script: '%s:%s'" % (module_name, class_name), 400)
+
+    @staticmethod
+    def camel_to_snake(camel):
+        camel = camel.strip()
+        return re.sub(r'(?<!^)(?=[A-Z])', '_', camel).lower()
 
     def evaluate(self, task, expression):
         """
@@ -66,7 +88,7 @@ class WorkflowProcessor(object):
     _script_engine = CustomBpmnScriptEngine()
     _serializer = BpmnSerializer()
     WORKFLOW_ID_KEY = "workflow_id"
-    STUDY_ID_KEY = "session_id"
+    STUDY_ID_KEY = "study_id"
 
     def __init__(self, workflow_spec_id, bpmn_json):
         wf_spec = self.get_spec(workflow_spec_id)
@@ -104,6 +126,7 @@ class WorkflowProcessor(object):
     def create(cls,  study_id, workflow_spec_id):
         spec = WorkflowProcessor.get_spec(workflow_spec_id)
         bpmn_workflow = BpmnWorkflow(spec, script_engine=cls._script_engine)
+        bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY] = study_id
         bpmn_workflow.do_engine_steps()
         json = cls._serializer.serialize_workflow(bpmn_workflow)
         processor = cls(workflow_spec_id, json)
@@ -116,7 +139,6 @@ class WorkflowProcessor(object):
         # a second time to store the serilaization so we can maintain this link within
         # the spiff-workflow process.
         processor.bpmn_workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY] = workflow_model.id
-        processor.bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY] = study_id
         workflow_model.bpmn_workflow_json = processor.serialize()
         session.add(workflow_model)
         session.commit()

crc/static/bpmn/docx/docx.bpmn

@@ -1,65 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_96a17d9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
-  <bpmn:process id="Process_93a29b3" isExecutable="true">
-    <bpmn:startEvent id="StartEvent_1">
-      <bpmn:outgoing>SequenceFlow_0637d8i</bpmn:outgoing>
-    </bpmn:startEvent>
-    <bpmn:sequenceFlow id="SequenceFlow_0637d8i" sourceRef="StartEvent_1" targetRef="task_gather_information" />
-    <bpmn:userTask id="task_gather_information" name="Gather Information" camunda:formKey="example_document_form">
-      <bpmn:extensionElements>
-        <camunda:formData>
-          <camunda:formField id="full_name" label="What is your name?" type="string" />
-          <camunda:formField id="date" label="date" type="string" />
-          <camunda:formField id="title" label="Title" type="string" />
-          <camunda:formField id="company" label="Company" type="string" />
-          <camunda:formField id="last_name" label="Last Name" type="string" />
-        </camunda:formData>
-      </bpmn:extensionElements>
-      <bpmn:incoming>SequenceFlow_0637d8i</bpmn:incoming>
-      <bpmn:outgoing>SequenceFlow_1i7hk1a</bpmn:outgoing>
-    </bpmn:userTask>
-    <bpmn:sequenceFlow id="SequenceFlow_1i7hk1a" sourceRef="task_gather_information" targetRef="task_generate_document" />
-    <bpmn:scriptTask id="task_generate_document" name="Generate Document">
-      <bpmn:extensionElements>
-        <camunda:properties>
-          <camunda:property name="template" />
-        </camunda:properties>
-      </bpmn:extensionElements>
-      <bpmn:incoming>SequenceFlow_1i7hk1a</bpmn:incoming>
-      <bpmn:outgoing>SequenceFlow_11c35oq</bpmn:outgoing>
-      <bpmn:script>scripts.CompleteTemplate Letter.docx</bpmn:script>
-    </bpmn:scriptTask>
-    <bpmn:endEvent id="EndEvent_0evb22x">
-      <bpmn:incoming>SequenceFlow_11c35oq</bpmn:incoming>
-    </bpmn:endEvent>
-    <bpmn:sequenceFlow id="SequenceFlow_11c35oq" sourceRef="task_generate_document" targetRef="EndEvent_0evb22x" />
-  </bpmn:process>
-  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
-    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_93a29b3">
-      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
-        <dc:Bounds x="179" y="99" width="36" height="36" />
-      </bpmndi:BPMNShape>
-      <bpmndi:BPMNEdge id="SequenceFlow_0637d8i_di" bpmnElement="SequenceFlow_0637d8i">
-        <di:waypoint x="215" y="117" />
-        <di:waypoint x="265" y="117" />
-      </bpmndi:BPMNEdge>
-      <bpmndi:BPMNShape id="UserTask_02o51o8_di" bpmnElement="task_gather_information">
-        <dc:Bounds x="265" y="77" width="100" height="80" />
-      </bpmndi:BPMNShape>
-      <bpmndi:BPMNEdge id="SequenceFlow_1i7hk1a_di" bpmnElement="SequenceFlow_1i7hk1a">
-        <di:waypoint x="365" y="117" />
-        <di:waypoint x="465" y="117" />
-      </bpmndi:BPMNEdge>
-      <bpmndi:BPMNShape id="ScriptTask_0xjh8x4_di" bpmnElement="task_generate_document">
-        <dc:Bounds x="465" y="77" width="100" height="80" />
-      </bpmndi:BPMNShape>
-      <bpmndi:BPMNShape id="EndEvent_0evb22x_di" bpmnElement="EndEvent_0evb22x">
-        <dc:Bounds x="665" y="99" width="36" height="36" />
-      </bpmndi:BPMNShape>
-      <bpmndi:BPMNEdge id="SequenceFlow_11c35oq_di" bpmnElement="SequenceFlow_11c35oq">
-        <di:waypoint x="565" y="117" />
-        <di:waypoint x="665" y="117" />
-      </bpmndi:BPMNEdge>
-    </bpmndi:BPMNPlane>
-  </bpmndi:BPMNDiagram>
-</bpmn:definitions>

example_data.py

@@ -74,37 +74,6 @@ class ExampleDataLoader:
         #                      name="crc_study_workflow",
         #                      display_name="CR Connect Study Workflow",
         #                      description='Draft workflow for CR Connect studies.')
-        workflow_specifications += \
-            self.create_spec(id="random_fact",
-                             name="random_fact",
-                             display_name="Random Fact Generator",
-                             description='Displays a random fact about a topic of your choosing.')
-        workflow_specifications += \
-            self.create_spec(id="two_forms",
-                             name="two_forms",
-                             display_name="Two dump questions on two separate tasks",
-                             description='the name says it all')
-        workflow_specifications += \
-            self.create_spec(id="decision_table",
-                             name="decision_table",
-                             display_name="Form with Decision Table",
-                             description='the name says it all')
-        workflow_specifications += \
-            self.create_spec(id="parallel_tasks",
-                             name="parallel_tasks",
-                             display_name="Parallel tasks",
-                             description='Four tasks that can happen simultaneously')
-        workflow_specifications += \
-            self.create_spec(id="exclusive_gateway",
-                             name="exclusive_gateway",
-                             display_name="Exclusive Gateway Example",
-                             description='How to take different paths based on input.')
-        workflow_specifications += \
-            self.create_spec(id="docx",
-                             name="docx",
-                             display_name="Form with document generation",
-                             description='the name says it all')
-
         all_data = users + studies + workflow_specifications
         return all_data
 

tests/data/docx/docx.bpmn

@@ -27,7 +27,7 @@
       </bpmn:extensionElements>
       <bpmn:incoming>SequenceFlow_1i7hk1a</bpmn:incoming>
       <bpmn:outgoing>SequenceFlow_11c35oq</bpmn:outgoing>
-      <bpmn:script>scripts.CompleteTemplate Letter.docx</bpmn:script>
+      <bpmn:script>CompleteTemplate Letter.docx</bpmn:script>
     </bpmn:scriptTask>
     <bpmn:endEvent id="EndEvent_0evb22x">
       <bpmn:incoming>SequenceFlow_11c35oq</bpmn:incoming>

tests/data/random_fact/random_fact.bpmn

@@ -130,7 +130,7 @@ Autoconverted link https://github.com/nodeca/pica (enable linkify to see)
       </bpmn:extensionElements>
       <bpmn:incoming>SequenceFlow_0641sh6</bpmn:incoming>
       <bpmn:outgoing>SequenceFlow_0t29gjo</bpmn:outgoing>
-      <bpmn:script>scripts.FactService</bpmn:script>
+      <bpmn:script>FactService</bpmn:script>
     </bpmn:scriptTask>
     <bpmn:endEvent id="EndEvent_0u1cgrf">
       <bpmn:documentation># Great Job!

tests/data/study_details/study_details.bpmn

@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
+  <bpmn:process id="Process_0exnnpv" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="SequenceFlow_1nfe5m9" sourceRef="StartEvent_1" targetRef="Task_Script_Load_Study_Details" />
+    <bpmn:scriptTask id="Task_Script_Load_Study_Details" name="Load Study Info">
+      <bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
+      <bpmn:script>StudyInfo info</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Details" targetRef="EndEvent_171dj09" />
+    <bpmn:endEvent id="EndEvent_171dj09">
+      <bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
+    </bpmn:endEvent>
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
+      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
+        <dc:Bounds x="179" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_1nfe5m9_di" bpmnElement="SequenceFlow_1nfe5m9">
+        <di:waypoint x="215" y="117" />
+        <di:waypoint x="270" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="ScriptTask_1mp6xid_di" bpmnElement="Task_Script_Load_Study_Details">
+        <dc:Bounds x="270" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
+        <di:waypoint x="370" y="117" />
+        <di:waypoint x="402" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="EndEvent_171dj09_di" bpmnElement="EndEvent_171dj09">
+        <dc:Bounds x="402" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/test_study_api.py

@@ -7,7 +7,6 @@ from crc.models.study import StudyModel, StudyModelSchema
 from crc.models.protocol_builder import ProtocolBuilderStatus
 from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
     WorkflowApiSchema
-from services.protocol_builder import ProtocolBuilderService
 from tests.base_test import BaseTest
 
 

tests/test_tasks_api.py

@@ -1,10 +1,12 @@
 import json
+from unittest.mock import patch
 
 from crc import session
 from crc.models.file import FileModelSchema
 from crc.models.study import StudyModel
 from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, \
     WorkflowApiSchema, WorkflowStatus, Task
+from crc.services.workflow_processor import WorkflowProcessor
 from tests.base_test import BaseTest
 
 
@@ -12,7 +14,8 @@ class TestTasksApi(BaseTest):
 
     def create_workflow(self, workflow_name):
         study = session.query(StudyModel).first()
-        spec = session.query(WorkflowSpecModel).filter_by(id=workflow_name).first()
+        spec = self.load_test_spec(workflow_name)
+        processor = WorkflowProcessor.create(study.id, spec.id)
         rv = self.app.post(
             '/v1.0/study/%i/workflows' % study.id,
             headers=self.logged_in_headers(),
@@ -186,8 +189,6 @@ class TestTasksApi(BaseTest):
         task.process_documentation(docs)
         self.assertEqual("This test works", task.documentation)
 
-
-
     def test_get_documentation_populated_in_end(self):
         self.load_example_data()
         workflow = self.create_workflow('random_fact')
@@ -201,3 +202,7 @@ class TestTasksApi(BaseTest):
         self.assertEqual("EndEvent_0u1cgrf", workflow_api.next_task['name'])
         self.assertIsNotNone(workflow_api.next_task['documentation'])
         self.assertTrue("norris" in workflow_api.next_task['documentation'])
+
+
+
+ #       response = ProtocolBuilderService.get_study_details(self.test_study_id)

tests/test_tools_api.py

@@ -22,7 +22,8 @@ class TestStudyApi(BaseTest):
 
     def test_render_docx(self):
         filepath = os.path.join(app.root_path, '..', 'tests', 'data', 'table.docx')
-        template_data = {"hippa": [{"option": "Name", "selected": True, "stored": ["Record at UVA", "Stored Long Term"]},
+        template_data = {"hippa": [
+                   {"option": "Name", "selected": True, "stored": ["Record at UVA", "Stored Long Term"]},
                    {"option": "Address", "selected": False},
                    {"option": "Phone", "selected": True, "stored": ["Send or Transmit outside of UVA"]}]}
         with open(filepath, 'rb') as f:
@@ -31,3 +32,11 @@ class TestStudyApi(BaseTest):
                               data=file_data, follow_redirects=True,
                               content_type='multipart/form-data')
             self.assert_success(rv)
+
+    def test_list_scripts(self):
+        rv = self.app.get('/v1.0/list_scripts')
+        self.assert_success(rv)
+        scripts = json.loads(rv.get_data(as_text=True))
+        self.assertTrue(len(scripts) > 1)
+        self.assertIsNotNone(scripts[0]['name'])
+        self.assertIsNotNone(scripts[0]['description'])

tests/test_workflow_processor.py

@@ -1,5 +1,6 @@
 import string
 import random
+from unittest.mock import patch
 
 from SpiffWorkflow.bpmn.specs.EndEvent import EndEvent
 
@@ -29,7 +30,7 @@ class TestWorkflowProcessor(BaseTest):
 
     def test_create_and_complete_workflow(self):
         self.load_example_data()
-        workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id="random_fact").first()
+        workflow_spec_model = self.load_test_spec("random_fact")
         study = session.query(StudyModel).first()
         processor = WorkflowProcessor.create(study.id, workflow_spec_model.id)
         self.assertEqual(study.id, processor.bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY])
@@ -54,9 +55,9 @@ class TestWorkflowProcessor(BaseTest):
     def test_workflow_with_dmn(self):
         self.load_example_data()
         study = session.query(StudyModel).first()
+        workflow_spec_model = self.load_test_spec("decision_table")
         files = session.query(FileModel).filter_by(workflow_spec_id='decision_table').all()
         self.assertEqual(2, len(files))
-        workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id="decision_table").first()
         processor = WorkflowProcessor.create(study.id, workflow_spec_model.id)
         self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
         next_user_tasks = processor.next_user_tasks()
@@ -79,7 +80,7 @@ class TestWorkflowProcessor(BaseTest):
 
     def test_workflow_with_parallel_forms(self):
         self.load_example_data()
-        workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id="parallel_tasks").first()
+        workflow_spec_model = self.load_test_spec("parallel_tasks")
         study = session.query(StudyModel).first()
         processor = WorkflowProcessor.create(study.id, workflow_spec_model.id)
         self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
@@ -121,7 +122,7 @@ class TestWorkflowProcessor(BaseTest):
     def test_workflow_processor_knows_the_text_task_even_when_parallel(self):
         self.load_example_data()
         study = session.query(StudyModel).first()
-        workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id="parallel_tasks").first()
+        workflow_spec_model = self.load_test_spec("parallel_tasks")
         processor = WorkflowProcessor.create(study.id, workflow_spec_model.id)
         self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
         next_user_tasks = processor.next_user_tasks()
@@ -141,7 +142,7 @@ class TestWorkflowProcessor(BaseTest):
 
     def test_workflow_processor_returns_next_task_as_end_task_if_complete(self):
         self.load_example_data()
-        workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id="random_fact").first()
+        workflow_spec_model = self.load_test_spec("random_fact")
         study = session.query(StudyModel).first()
         processor = WorkflowProcessor.create(study.id, workflow_spec_model.id)
         processor.do_engine_steps()
@@ -196,3 +197,20 @@ class TestWorkflowProcessor(BaseTest):
         self.assertIsNotNone(file_data.data)
         self.assertTrue(len(file_data.data) > 0)
         # Not going any farther here, assuming this is tested in libraries correctly.
+
+    def test_load_study_information(self):
+        """ Test a workflow that includes requests to pull in Study Details."""
+
+        self.load_example_data()
+        study = session.query(StudyModel).first()
+        workflow_spec_model = self.load_test_spec("study_details")
+        processor = WorkflowProcessor.create(study.id, workflow_spec_model.id)
+        processor.do_engine_steps()
+        task = processor.bpmn_workflow.last_task
+        self.assertIsNotNone(task.data)
+        self.assertIn("study", task.data)
+        self.assertIn("info", task.data["study"])
+        self.assertIn("title", task.data["study"]["info"])
+        self.assertIn("last_updated", task.data["study"]["info"])
+        self.assertIn("sponsor", task.data["study"]["info"])
+

tests/test_workflow_spec_api.py

@@ -47,7 +47,7 @@ class TestWorkflowSpec(BaseTest):
     def test_delete_workflow_specification(self):
         self.load_example_data()
         spec_id = 'random_fact'
-
+        self.load_test_spec(spec_id)
         num_specs_before = session.query(WorkflowSpecModel).filter_by(id=spec_id).count()
         self.assertEqual(num_specs_before, 1)