Merge pull request #147 from sartography/dev

Dev to Test
2020-07-10 09:12:46 -04:00 · 2020-07-10 09:12:46 -04:00 · 8976ad70ed
parent 3d6ed3bb48 ff7c30b879
commit 8976ad70ed
18 changed files with 235 additions and 151 deletions
--- a/Pipfile.lock
+++ b/Pipfile.lock
@ -197,40 +197,43 @@
        },
        "coverage": {
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            ],
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-            "version": "==5.1"
+            "version": "==5.2"
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        "docutils": {
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@ -565,7 +568,8 @@
        },
        "openpyxl": {
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            ],
            "index": "pypi",
            "version": "==3.0.4"
@ -827,11 +831,11 @@
        },
        "sphinx": {
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+            "version": "==3.1.2"
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        "sphinxcontrib-applehelp": {
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@ -878,7 +882,7 @@
        "spiffworkflow": {
            "editable": true,
            "git": "https://github.com/sartography/SpiffWorkflow.git",
-            "ref": "4d16fe9727bf2033d6f651ed0dece20693d54025"
+            "ref": "e47dbce4147f2475f50ef705eab32a1426540613"
        },
        "sqlalchemy": {
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@ -1007,40 +1011,43 @@
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--- a/crc/models/approval.py
+++ b/crc/models/approval.py
@ -57,23 +57,11 @@ 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)
--- a/crc/services/approval_service.py
+++ b/crc/services/approval_service.py
@ -287,7 +287,7 @@ class ApprovalService(object):
                    )
                    if mail_result:
                        app.logger.error(mail_result, exc_info=True)
-        # TODO: Log update action by approver_uid - maybe ?
+
        return db_approval

    @staticmethod
@ -299,11 +299,12 @@ class ApprovalService(object):
            pending approvals and create a new approval for the latest version
            of the workflow."""

-        # Find any existing approvals for this workflow and approver.
-        latest_approval_request = db.session.query(ApprovalModel). \
+        # Find any existing approvals for this workflow.
+        latest_approval_requests = db.session.query(ApprovalModel). \
            filter(ApprovalModel.workflow_id == workflow_id). \
-            filter(ApprovalModel.approver_uid == approver_uid). \
-            order_by(desc(ApprovalModel.version)).first()
+            order_by(desc(ApprovalModel.version))
+
+        latest_approver_request = latest_approval_requests.filter(ApprovalModel.approver_uid == approver_uid).first()

        # Construct as hash of the latest files to see if things have changed since
        # the last approval.
@ -318,16 +319,20 @@ class ApprovalService(object):
        # If an existing approval request exists and no changes were made, do nothing.
        # If there is an existing approval request for a previous version of the workflow
        # then add a new request, and cancel any waiting/pending requests.
-        if latest_approval_request:
-            request_file_ids = list(file.file_data_id for file in latest_approval_request.approval_files)
+        if latest_approver_request:
+            request_file_ids = list(file.file_data_id for file in latest_approver_request.approval_files)
            current_data_file_ids.sort()
            request_file_ids.sort()
+            other_approver = latest_approval_requests.filter(ApprovalModel.approver_uid != approver_uid).first()
            if current_data_file_ids == request_file_ids:
-                return  # This approval already exists.
+                return  # This approval already exists or we're updating other approver.
            else:
-                latest_approval_request.status = ApprovalStatus.CANCELED.value
-                db.session.add(latest_approval_request)
-                version = latest_approval_request.version + 1
+                for approval_request in latest_approval_requests:
+                    if (approval_request.version == latest_approver_request.version and
+                        approval_request.status != ApprovalStatus.CANCELED.value):
+                        approval_request.status = ApprovalStatus.CANCELED.value
+                        db.session.add(approval_request)
+                version = latest_approver_request.version + 1
        else:
            version = 1

--- a/crc/services/email_service.py
+++ b/crc/services/email_service.py
@ -13,7 +13,7 @@ class EmailService(object):
    """Provides common tools for working with an Email"""

    @staticmethod
-    def add_email(subject, sender, recipients, content, content_html, study_id):
+    def add_email(subject, sender, recipients, content, content_html, study_id=None):
        """We will receive all data related to an email and store it"""

        # Find corresponding study - if any
--- a/crc/services/study_service.py
+++ b/crc/services/study_service.py
@ -1,3 +1,4 @@
+from copy import copy
 from datetime import datetime
 import json
 from typing import List
@ -64,13 +65,15 @@ class StudyService(object):
        study.files = list(files)

        # Calling this line repeatedly is very very slow.  It creates the
-        # master spec and runs it.
-        status = StudyService.__get_study_status(study_model)
-        study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)
+        # master spec and runs it.  Don't execute this for Abandoned studies, as
+        # we don't have the information to process them.
+        if study.protocol_builder_status != ProtocolBuilderStatus.ABANDONED:
+            status = StudyService.__get_study_status(study_model)
+            study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)

-        # Group the workflows into their categories.
-        for category in study.categories:
-            category.workflows = {w for w in workflow_metas if w.category_id == category.id}
+            # Group the workflows into their categories.
+            for category in study.categories:
+                category.workflows = {w for w in workflow_metas if w.category_id == category.id}

        return study

@ -183,6 +186,7 @@ class StudyService(object):

    @staticmethod
    def get_investigators(study_id, all=False):
+        """Convert array of investigators from protocol builder into a dictionary keyed on the type. """

        # Loop through all known investigator types as set in the reference file
        inv_dictionary = FileService.get_reference_data(FileService.INVESTIGATOR_LIST, 'code')
@ -190,18 +194,26 @@ class StudyService(object):
        # Get PB required docs
        pb_investigators = ProtocolBuilderService.get_investigators(study_id=study_id)

-        """Convert array of investigators from protocol builder into a dictionary keyed on the type"""
+        # It is possible for the same type to show up more than once in some circumstances, in those events
+        # append a counter to the name.
+        investigators = {}
        for i_type in inv_dictionary:
-            pb_data = next((item for item in pb_investigators if item['INVESTIGATORTYPE'] == i_type), None)
-            if pb_data:
-                inv_dictionary[i_type]['user_id'] = pb_data["NETBADGEID"]
-                inv_dictionary[i_type].update(StudyService.get_ldap_dict_if_available(pb_data["NETBADGEID"]))
-            else:
-                inv_dictionary[i_type]['user_id'] = None
-
+            pb_data_entries = list(item for item in pb_investigators if item['INVESTIGATORTYPE'] == i_type)
+            entry_count = 0
+            investigators[i_type] = copy(inv_dictionary[i_type])
+            investigators[i_type]['user_id'] = None
+            for pb_data in pb_data_entries:
+                entry_count += 1
+                if entry_count == 1:
+                    t = i_type
+                else:
+                    t = i_type + "_" + str(entry_count)
+                investigators[t] = copy(inv_dictionary[i_type])
+                investigators[t]['user_id'] = pb_data["NETBADGEID"]
+                investigators[t].update(StudyService.get_ldap_dict_if_available(pb_data["NETBADGEID"]))
        if not all:
-            inv_dictionary = dict(filter(lambda elem: elem[1]['user_id'] is not None, inv_dictionary.items()))
-        return inv_dictionary
+            investigators = dict(filter(lambda elem: elem[1]['user_id'] is not None, investigators.items()))
+        return investigators

    @staticmethod
    def get_ldap_dict_if_available(user_id):
--- a/crc/services/workflow_processor.py
+++ b/crc/services/workflow_processor.py
@ -1,4 +1,6 @@
 import re
+
+from SpiffWorkflow.serializer.exceptions import MissingSpecError
 from lxml import etree
 import shlex
 from datetime import datetime
@ -138,7 +140,7 @@ class WorkflowProcessor(object):
                workflow_model.bpmn_workflow_json = WorkflowProcessor._serializer.serialize_workflow(self.bpmn_workflow)
                self.save()

-        except KeyError as ke:
+        except MissingSpecError as ke:
            raise ApiError(code="unexpected_workflow_structure",
                           message="Failed to deserialize workflow"
                                   " '%s' version %s, due to a mis-placed or missing task '%s'" %
--- a/crc/services/workflow_service.py
+++ b/crc/services/workflow_service.py
@ -384,7 +384,8 @@ class WorkflowService(object):
        except TypeError as te:
            raise ApiError.from_task(code="template_error", message="Error processing template for task %s: %s" %
                                                          (spiff_task.task_spec.name, str(te)), task=spiff_task)
-        # TODO:  Catch additional errors and report back.
+        except Exception as e:
+            app.logger.error(str(e), exc_info=True)

    @staticmethod
    def process_options(spiff_task, field):
--- a/tests/approval/test_approvals_api.py
+++ b/tests/approval/test_approvals_api.py
@ -217,27 +217,6 @@ class TestApprovals(BaseTest):
        total_counts = sum(counts[status] for status in statuses)
        self.assertEqual(total_counts, len(approvals), 'Total approval counts for user should match number of approvals for user')

-    def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
-                                         workflow_spec_name="random_fact"):
-        study = self.create_study(uid=user_uid, title=title, primary_investigator_id=primary_investigator_id)
-        workflow = self.create_workflow(workflow_name=workflow_spec_name, study=study)
-        approvals = []
-
-        for i in range(len(approver_uids)):
-            approvals.append(self.create_approval(
-                study=study,
-                workflow=workflow,
-                approver_uid=approver_uids[i],
-                status=statuses[i],
-                version=1
-            ))
-
-        return {
-            'study': study,
-            'workflow': workflow,
-            'approvals': approvals,
-        }
-
    def _add_lots_of_random_approvals(self, n=100, workflow_spec_name="random_fact"):
        num_studies_before = db.session.query(StudyModel).count()
        statuses = [name for name, value in ApprovalStatus.__members__.items()]
--- a/tests/approval/test_approvals_service.py
+++ b/tests/approval/test_approvals_service.py
@ -1,7 +1,7 @@
 from tests.base_test import BaseTest
 from crc import db
 from crc.models.approval import ApprovalModel
-from crc.services.approval_service import ApprovalService
+from crc.services.approval_service import ApprovalService, ApprovalStatus
 from crc.services.file_service import FileService
 from crc.services.workflow_processor import WorkflowProcessor

@ -83,6 +83,34 @@ class TestApprovalsService(BaseTest):

        self.assertEqual(len(records), 2)

+    def test_new_approval_cancels_all_previous_approvals(self):
+        self.create_reference_document()
+        workflow = self.create_workflow("empty_workflow")
+        FileService.add_workflow_file(workflow_id=workflow.id,
+                                      name="anything.png", content_type="text",
+                                      binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
+        ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
+        ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="lb3dp")
+
+        current_count = ApprovalModel.query.count()
+        self.assertTrue(current_count, 2)
+
+        FileService.add_workflow_file(workflow_id=workflow.id,
+                                      name="borderline.png", content_type="text",
+                                      binary_data=b'906090', irb_doc_code="AD_CoCAppr" )
+
+        ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
+
+        current_count = ApprovalModel.query.count()
+        canceled_count = ApprovalModel.query.filter(ApprovalModel.status == ApprovalStatus.CANCELED.value)
+        self.assertTrue(current_count, 2)
+        self.assertTrue(current_count, 3)
+
+        ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="lb3dp")
+
+        current_count = ApprovalModel.query.count()
+        self.assertTrue(current_count, 4)
+
    def test_new_approval_sends_proper_emails(self):
        self.assertEqual(1, 1)

--- a/tests/base_test.py
+++ b/tests/base_test.py
@ -240,6 +240,29 @@ class BaseTest(unittest.TestCase):
            db.session.commit()
        return study

+    def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
+                                         workflow_spec_name="random_fact"):
+        study = self.create_study(uid=user_uid, title=title, primary_investigator_id=primary_investigator_id)
+        workflow = self.create_workflow(workflow_name=workflow_spec_name, study=study)
+        approvals = []
+
+        for i in range(len(approver_uids)):
+            approvals.append(self.create_approval(
+                study=study,
+                workflow=workflow,
+                approver_uid=approver_uids[i],
+                status=statuses[i],
+                version=1
+            ))
+
+        full_study = {
+            'study': study,
+            'workflow': workflow,
+            'approvals': approvals,
+        }
+
+        return full_study
+
    def create_workflow(self, workflow_name, study=None, category_id=None):
        db.session.flush()
        spec = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
--- a/tests/data/pb_responses/investigators.json
+++ b/tests/data/pb_responses/investigators.json
@ -13,5 +13,15 @@
    "INVESTIGATORTYPE": "PI",
    "INVESTIGATORTYPEFULL": "Primary Investigator",
    "NETBADGEID": "dhf8r"
+  },
+    {
+    "INVESTIGATORTYPE": "SI",
+    "INVESTIGATORTYPEFULL": "Sub Investigator",
+    "NETBADGEID": "ajl2j"
+  },
+  {
+    "INVESTIGATORTYPE": "SI",
+    "INVESTIGATORTYPEFULL": "Sub Investigator",
+    "NETBADGEID": "cah3us"
  }
-]
+]
--- a/tests/emails/test_email_service.py
+++ b/tests/emails/test_email_service.py
@ -31,4 +31,15 @@ class TestEmailService(BaseTest):
        self.assertEqual(email_model.content_html, content_html)
        self.assertEqual(email_model.study, study)

-        # TODO: Create email model without 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)
--- a/tests/study/test_study_api.py
+++ b/tests/study/test_study_api.py
@ -7,6 +7,7 @@ from unittest.mock import patch
 from crc import session, app
 from crc.models.protocol_builder import ProtocolBuilderStatus, \
    ProtocolBuilderStudySchema
+from crc.models.approval import ApprovalStatus
 from crc.models.stats import TaskEventModel
 from crc.models.study import StudyModel, StudySchema
 from crc.models.workflow import WorkflowSpecModel, WorkflowModel
@ -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()
--- a/tests/study/test_study_service.py
+++ b/tests/study/test_study_service.py
@ -193,7 +193,7 @@ class TestStudyService(BaseTest):
        workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
        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'])
@ -219,10 +219,14 @@ class TestStudyService(BaseTest):
        workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
        investigators = StudyService().get_investigators(workflow.study_id, all=False)

-        self.assertEqual(3, len(investigators))
+        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'])
--- 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"])
--- a/tests/test_tasks_api.py
+++ b/tests/test_tasks_api.py
@ -322,7 +322,7 @@ 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(3, 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'])
@ -480,15 +480,15 @@ class TestTasksApi(BaseTest):
        workflow = self.create_workflow('multi_instance_parallel')

        workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual(6, 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(3, len(ready_items))
+        self.assertEqual(5, len(ready_items))

        self.assertEqual("UserTask", workflow_api.next_task.type)
        self.assertEqual("MultiInstanceTask",workflow_api.next_task.name)
        self.assertEqual("Primary Investigator", workflow_api.next_task.title)

-        for i in random.sample(range(3), 3):
+        for i in random.sample(range(5), 5):
            task = TaskSchema().load(ready_items[i]['task'])
            rv = self.app.put('/v1.0/workflow/%i/task/%s/set_token' % (workflow.id, task.id),
                              headers=self.logged_in_headers(),
--- a/tests/workflow/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)
--- a/tests/workflow/test_workflow_processor_multi_instance.py
+++ b/tests/workflow/test_workflow_processor_multi_instance.py
@ -59,7 +59,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
        api_task = workflow_api.next_task
        self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
        self.assertEqual("dhf8r", api_task.data["investigator"]["user_id"])
-        self.assertEqual("MultiInstanceTask", api_task.name)
+        self.assertTrue(api_task.name.startswith("MultiInstanceTask"))
        self.assertEqual(3, api_task.multi_instance_count)
        self.assertEqual(1, api_task.multi_instance_index)

@ -74,7 +74,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
        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.assertEqual("MultiInstanceTask", api_task.name)
+        self.assertTrue(api_task.name.startswith("MultiInstanceTask"))
        self.assertEqual(3, api_task.multi_instance_count)
        self.assertEqual(2, api_task.multi_instance_index)

@ -89,7 +89,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
        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.assertEqual("MultiInstanceTask", api_task.name)
+        self.assertTrue(api_task.name.startswith("MultiInstanceTask"))
        self.assertEqual(3, api_task.multi_instance_count)
        self.assertEqual(3, api_task.multi_instance_index)