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Adds Protocol Builder models and schemas. Reorganizes and cleans up some files.

This commit is contained in:
Aaron Louie 2020-02-27 09:54:46 -05:00
parent 3ef4860391
commit 27d7afb656
10 changed files with 311 additions and 82 deletions
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3
crc/api/study.py
View File

@ -7,7 +7,8 @@ from flask import g
from crc import session, auth
from crc.api.common import ApiError, ApiErrorSchema
from crc.api.workflow import __get_workflow_api_model
from crc.models.study import StudyModelSchema, StudyModel, ProtocolBuilderStudy, ProtocolBuilderStatus
from crc.models.study import StudyModelSchema, StudyModel
from models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
from crc.services import protocol_builder
from crc.services.workflow_processor import WorkflowProcessor

247
crc/models/protocol_builder.py Normal file
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@ -0,0 +1,247 @@
import enum
from marshmallow import INCLUDE
from crc import ma
class ProtocolBuilderInvestigatorType(enum.Enum):
PI = "Primary Investigator"
SI = "Sub Investigator"
DC = "Department Contact"
SC_I = "Study Coordinator 1"
SC_II = "Study Coordinator 2"
AS_C = "Additional Study Coordinators"
DEPT_CH = "Department Chair"
IRBC = "IRB Coordinator"
SCI = "Scientific Contact"
class ProtocolBuilderStatus(enum.Enum):
out_of_date = "out_of_date"
in_process = "in_process"
complete = "complete"
updating = "updating"
class ProtocolBuilderStudy(object):
def __init__(
self, STUDYID: int, HSRNUMBER: str, TITLE: str, NETBADGEID: str,
Q_COMPLETE: bool, DATE_MODIFIED: str
):
self.STUDYID = STUDYID
self.HSRNUMBER = HSRNUMBER
self.TITLE = TITLE
self.NETBADGEID = NETBADGEID
self.Q_COMPLETE = Q_COMPLETE
self.DATE_MODIFIED = DATE_MODIFIED
class ProtocolBuilderStudySchema(ma.Schema):
class Meta:
model = ProtocolBuilderStudy
unknown = INCLUDE
class ProtocolBuilderInvestigator(object):
def __init__(self, STUDYID: int, NETBADGEID: str, INVESTIGATORTYPE: str, INVESTIGATORTYPEFULL: str):
self.STUDYID = STUDYID
self.NETBADGEID = NETBADGEID
self.INVESTIGATORTYPE = INVESTIGATORTYPE
self.INVESTIGATORTYPEFULL = INVESTIGATORTYPEFULL
class ProtocolBuilderInvestigatorSchema(ma.Schema):
class Meta:
model = ProtocolBuilderInvestigator
unknown = INCLUDE
class ProtocolBuilderRequiredDocument(object):
DOC_TYPES = {
1: "Investigators Brochure",
6: "Cancer Center's PRC Approval Form",
8: "SOM CTO IND/IDE Review Letter",
9: "HIRE Approval",
10: "Cancer Center's PRC Approval Waiver",
12: "Certificate of Confidentiality Application",
14: "Institutional Biosafety Committee Approval",
18: "SOM CTO Approval Letter - UVA PI Multisite Trial",
20: "IRB Approval or Letter of Approval from Administration: Study Conducted at non- UVA Facilities ",
21: "New Medical Device Form",
22: "SOM CTO Review regarding need for IDE",
23: "SOM CTO Review regarding need for IND",
24: "InfoSec Approval",
25: "Scientific Pre-review Documentation",
26: "IBC Number",
32: "IDS - Investigational Drug Service Approval",
36: "RDRC Approval ",
40: "SBS/IRB Approval-FERPA",
41: "HIRE Standard Radiation Language",
42: "COI Management Plan ",
43: "SOM CTO Approval Letter-Non UVA, Non Industry PI MultiSite Study",
44: "GRIME Approval",
45: "GMEC Approval",
46: "IRB Reliance Agreement Request Form- IRB-HSR is IRB of Record",
47: "Non UVA IRB Approval - Initial and Last Continuation",
48: "MR Physicist Approval- Use of Gadolinium",
49: "SOM CTO Approval- Non- UVA Academia PI of IDE",
51: "IDS Waiver",
52: "Package Inserts",
53: "IRB Reliance Agreement Request Form- IRB-HSR Not IRB of Record",
54: "ESCRO Approval",
57: "Laser Safety Officer Approval",
}
def __init__(self, AUXDOCID: str, AUXDOC: str):
self.AUXDOCID = AUXDOCID
self.AUXDOC = AUXDOC
class ProtocolBuilderRequiredDocumentSchema(ma.Schema):
class Meta:
model = ProtocolBuilderRequiredDocument
unknown = INCLUDE
class ProtocolBuilderStudyDetails(object):
def __init__(
self,
STUDYID: int,
IS_IND: int,
IND_1: str,
IND_2: str,
IND_3: str,
IS_UVA_IND: int,
IS_IDE: int,
IS_UVA_IDE: int,
IDE: str,
IS_CHART_REVIEW: int,
IS_RADIATION: int,
GCRC_NUMBER: str,
IS_GCRC: int,
IS_PRC_DSMP: int,
IS_PRC: int,
PRC_NUMBER: str,
IS_IBC: int,
IBC_NUMBER: str,
SPONSORS_PROTOCOL_REVISION_DATE: int,
IS_SPONSOR_MONITORING: int,
IS_AUX: int,
IS_SPONSOR: int,
IS_GRANT: int,
IS_COMMITTEE_CONFLICT: int,
DSMB: int,
DSMB_FREQUENCY: int,
IS_DB: int,
IS_UVA_DB: int,
IS_CENTRAL_REG_DB: int,
IS_CONSENT_WAIVER: int,
IS_HGT: int,
IS_GENE_TRANSFER: int,
IS_TISSUE_BANKING: int,
IS_SURROGATE_CONSENT: int,
IS_ADULT_PARTICIPANT: int,
IS_MINOR_PARTICIPANT: int,
IS_MINOR: int,
IS_BIOMEDICAL: int,
IS_QUALITATIVE: int,
IS_PI_SCHOOL: int,
IS_PRISONERS_POP: int,
IS_PREGNANT_POP: int,
IS_FETUS_POP: int,
IS_MENTAL_IMPAIRMENT_POP: int,
IS_ELDERLY_POP: int,
IS_OTHER_VULNERABLE_POP: int,
OTHER_VULNERABLE_DESC: str,
IS_MULTI_SITE: int,
IS_UVA_LOCATION: int,
NON_UVA_LOCATION: str,
MULTI_SITE_LOCATIONS: str,
IS_OUTSIDE_CONTRACT: int,
IS_UVA_PI_MULTI: int,
IS_NOT_PRC_WAIVER: int,
IS_CANCER_PATIENT: int,
UPLOAD_COMPLETE: int,
IS_FUNDING_SOURCE: int,
IS_PI_INITIATED: int,
IS_ENGAGED_RESEARCH: int,
IS_APPROVED_DEVICE: int,
IS_FINANCIAL_CONFLICT: int,
IS_NOT_CONSENT_WAIVER: int,
IS_FOR_CANCER_CENTER: int,
IS_REVIEW_BY_CENTRAL_IRB: int,
IRBREVIEWERADMIN: str
):
self.STUDYID = STUDYID
self.IS_IND = IS_IND
self.IND_1 = IND_1
self.IND_2 = IND_2
self.IND_3 = IND_3
self.IS_UVA_IND = IS_UVA_IND
self.IS_IDE = IS_IDE
self.IS_UVA_IDE = IS_UVA_IDE
self.IDE = IDE
self.IS_CHART_REVIEW = IS_CHART_REVIEW
self.IS_RADIATION = IS_RADIATION
self.GCRC_NUMBER = GCRC_NUMBER
self.IS_GCRC = IS_GCRC
self.IS_PRC_DSMP = IS_PRC_DSMP
self.IS_PRC = IS_PRC
self.PRC_NUMBER = PRC_NUMBER
self.IS_IBC = IS_IBC
self.IBC_NUMBER = IBC_NUMBER
self.SPONSORS_PROTOCOL_REVISION_DATE = SPONSORS_PROTOCOL_REVISION_DATE
self.IS_SPONSOR_MONITORING = IS_SPONSOR_MONITORING
self.IS_AUX = IS_AUX
self.IS_SPONSOR = IS_SPONSOR
self.IS_GRANT = IS_GRANT
self.IS_COMMITTEE_CONFLICT = IS_COMMITTEE_CONFLICT
self.DSMB = DSMB
self.DSMB_FREQUENCY = DSMB_FREQUENCY
self.IS_DB = IS_DB
self.IS_UVA_DB = IS_UVA_DB
self.IS_CENTRAL_REG_DB = IS_CENTRAL_REG_DB
self.IS_CONSENT_WAIVER = IS_CONSENT_WAIVER
self.IS_HGT = IS_HGT
self.IS_GENE_TRANSFER = IS_GENE_TRANSFER
self.IS_TISSUE_BANKING = IS_TISSUE_BANKING
self.IS_SURROGATE_CONSENT = IS_SURROGATE_CONSENT
self.IS_ADULT_PARTICIPANT = IS_ADULT_PARTICIPANT
self.IS_MINOR_PARTICIPANT = IS_MINOR_PARTICIPANT
self.IS_MINOR = IS_MINOR
self.IS_BIOMEDICAL = IS_BIOMEDICAL
self.IS_QUALITATIVE = IS_QUALITATIVE
self.IS_PI_SCHOOL = IS_PI_SCHOOL
self.IS_PRISONERS_POP = IS_PRISONERS_POP
self.IS_PREGNANT_POP = IS_PREGNANT_POP
self.IS_FETUS_POP = IS_FETUS_POP
self.IS_MENTAL_IMPAIRMENT_POP = IS_MENTAL_IMPAIRMENT_POP
self.IS_ELDERLY_POP = IS_ELDERLY_POP
self.IS_OTHER_VULNERABLE_POP = IS_OTHER_VULNERABLE_POP
self.OTHER_VULNERABLE_DESC = OTHER_VULNERABLE_DESC
self.IS_MULTI_SITE = IS_MULTI_SITE
self.IS_UVA_LOCATION = IS_UVA_LOCATION
self.NON_UVA_LOCATION = NON_UVA_LOCATION
self.MULTI_SITE_LOCATIONS = MULTI_SITE_LOCATIONS
self.IS_OUTSIDE_CONTRACT = IS_OUTSIDE_CONTRACT
self.IS_UVA_PI_MULTI = IS_UVA_PI_MULTI
self.IS_NOT_PRC_WAIVER = IS_NOT_PRC_WAIVER
self.IS_CANCER_PATIENT = IS_CANCER_PATIENT
self.UPLOAD_COMPLETE = UPLOAD_COMPLETE
self.IS_FUNDING_SOURCE = IS_FUNDING_SOURCE
self.IS_PI_INITIATED = IS_PI_INITIATED
self.IS_ENGAGED_RESEARCH = IS_ENGAGED_RESEARCH
self.IS_APPROVED_DEVICE = IS_APPROVED_DEVICE
self.IS_FINANCIAL_CONFLICT = IS_FINANCIAL_CONFLICT
self.IS_NOT_CONSENT_WAIVER = IS_NOT_CONSENT_WAIVER
self.IS_FOR_CANCER_CENTER = IS_FOR_CANCER_CENTER
self.IS_REVIEW_BY_CENTRAL_IRB = IS_REVIEW_BY_CENTRAL_IRB
self.IRBREVIEWERADMIN = IRBREVIEWERADMIN
class ProtocolBuilderStudyDetailsSchema(ma.Schema):
class Meta:
model = ProtocolBuilderStudyDetails
unknown = INCLUDE

22
crc/models/study.py
View File

@ -1,18 +1,9 @@
from datetime import datetime
import enum
from marshmallow_enum import EnumField
from marshmallow_sqlalchemy import ModelSchema
from sqlalchemy import func
from crc import db
class ProtocolBuilderStatus(enum.Enum):
out_of_date = "out_of_date"
in_process = "in_process"
complete = "complete"
updating = "updating"
from models.protocol_builder import ProtocolBuilderStatus
class StudyModel(db.Model):
@ -36,14 +27,3 @@ class StudyModelSchema(ModelSchema):
protocol_builder_status = EnumField(ProtocolBuilderStatus)
class ProtocolBuilderStudy(object):
def __init__(
self, STUDYID: int, HSRNUMBER: str, TITLE: str, NETBADGEID: str,
Q_COMPLETE: bool, DATE_MODIFIED: str
):
self.STUDYID = STUDYID
self.HSRNUMBER = HSRNUMBER
self.TITLE = TITLE
self.NETBADGEID = NETBADGEID
self.Q_COMPLETE = Q_COMPLETE
self.DATE_MODIFIED = DATE_MODIFIED

2
crc/scripts/CompleteTemplate.py
View File

@ -19,7 +19,6 @@ class CompleteTemplate(object):
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."""
def do_task(self, task, *args, **kwargs):
"""Entry point, mostly worried about wiring it all up."""
if len(args) != 1:
@ -38,7 +37,6 @@ class CompleteTemplate(object):
.filter(FileModel.name == file_name) \
.filter(FileModel.workflow_spec_id == workflow_spec_model.id).first()
if file_data_model is None:
raise ApiError(code="file_missing",
message="Can not find a file called '%s' "

1
crc/services/FileService.py
View File

@ -11,7 +11,6 @@ class FileService(object):
DOCX_MIME = "application/vnd.openxmlformats-officedocument.wordprocessingml.document"
@staticmethod
def add_workflow_spec_file(workflow_spec_id, name, content_type, binary_data):
"""Create a new file and associate it with a workflow spec."""

74
crc/services/protocol_builder.py
View File

@ -1,44 +1,52 @@
import json
from typing import List, Optional
import requests
from crc import app
STUDY_URL = app.config['PB_USER_STUDIES_URL']
INVESTIGATOR_URL = app.config['PB_INVESTIGATORS_URL']
REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
from models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStudySchema, ProtocolBuilderInvestigator, \
ProtocolBuilderRequiredDocument, ProtocolBuilderStudyDetails, ProtocolBuilderInvestigatorSchema, \
ProtocolBuilderRequiredDocumentSchema, ProtocolBuilderStudyDetailsSchema
class ProtocolBuilderService(object):
STUDY_URL = app.config['PB_USER_STUDIES_URL']
INVESTIGATOR_URL = app.config['PB_INVESTIGATORS_URL']
REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
@staticmethod
def get_studies(user_id) -> Optional[List[ProtocolBuilderStudy]]:
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
def get_studies(user_id):
response = requests.get(STUDY_URL % user_id)
if response.ok:
return json.loads(response.text)
else:
return None
@staticmethod
def get_investigators(study_id) -> Optional[List[ProtocolBuilderInvestigator]]:
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
@staticmethod
def get_required_docs(study_id) -> Optional[List[ProtocolBuilderRequiredDocument]]:
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
def get_investigators(study_id):
response = requests.get(INVESTIGATOR_URL % study_id)
if response.ok:
return json.loads(response.text)
else:
return None
def get_required_docs(study_id):
response = requests.get(REQUIRED_DOCS_URL % study_id)
if response.ok:
return json.loads(response.text)
else:
return None
def get_study_details(study_id):
response = requests.get(STUDY_DETAILS_URL % study_id)
if response.ok:
return json.loads(response.text)
else:
return None
@staticmethod
def get_study_details(study_id) -> Optional[ProtocolBuilderStudyDetails]:
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

5
crc/services/workflow_processor.py
View File

@ -54,7 +54,6 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
'The expression you provided does not exist:' + expression)
class MyCustomParser(BpmnDmnParser):
"""
A BPMN and DMN parser that can also parse Camunda forms.
@ -62,6 +61,7 @@ class MyCustomParser(BpmnDmnParser):
OVERRIDE_PARSER_CLASSES = BpmnDmnParser.OVERRIDE_PARSER_CLASSES
OVERRIDE_PARSER_CLASSES.update(CamundaParser.OVERRIDE_PARSER_CLASSES)
class WorkflowProcessor(object):
_script_engine = CustomBpmnScriptEngine()
_serializer = BpmnSerializer()
@ -171,9 +171,6 @@ class WorkflowProcessor(object):
next_task = task
return next_task
def complete_task(self, task):
self.bpmn_workflow.complete_task_from_id(task.id)

33
tests/test_protocol_builder.py
View File

@ -1,40 +1,37 @@
from unittest.mock import patch
from crc import db
from crc.models.user import UserModel
from crc.services import protocol_builder
from crc.services.protocol_builder import ProtocolBuilderService
from tests.base_test import BaseTest
class TestProtocolBuilder(BaseTest):
test_uid = "dhf8r"
test_study_id = 1
@patch('crc.services.protocol_builder.requests.get')
def test_get_studies(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.json.return_value = self.protocol_builder_response('study_details.json')
response = protocol_builder.get_studies(self.test_uid)
mock_get.return_value.text = self.protocol_builder_response('user_studies.json')
response = ProtocolBuilderService.get_studies(self.test_uid)
self.assertIsNotNone(response)
@patch('crc.services.protocol_builder.requests.get')
def test_get_investigators(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.json.return_value = self.protocol_builder_response('investigators.json')
response = protocol_builder.get_studies(self.test_study_id)
self.assertIsNotNone(response)
@patch('crc.services.protocol_builder.requests.get')
def test_get_details(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.json.return_value = self.protocol_builder_response('study_details.json')
response = protocol_builder.get_studies(self.test_study_id)
mock_get.return_value.text = self.protocol_builder_response('investigators.json')
response = ProtocolBuilderService.get_investigators(self.test_study_id)
self.assertIsNotNone(response)
@patch('crc.services.protocol_builder.requests.get')
def test_get_required_docs(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.json.return_value = self.protocol_builder_response('required_docs.json')
response = protocol_builder.get_studies(self.test_study_id)
self.assertIsNotNone(response)
mock_get.return_value.text = self.protocol_builder_response('required_docs.json')
response = ProtocolBuilderService.get_required_docs(self.test_study_id)
self.assertIsNotNone(response)
@patch('crc.services.protocol_builder.requests.get')
def test_get_details(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('study_details.json')
response = ProtocolBuilderService.get_study_details(self.test_study_id)
self.assertIsNotNone(response)

3
tests/test_study_api.py
View File

@ -3,7 +3,8 @@ from datetime import datetime, tzinfo, timezone
from crc import session
from crc.models.file import FileModel
from crc.models.study import StudyModel, StudyModelSchema, ProtocolBuilderStatus
from crc.models.study import StudyModel, StudyModelSchema
from models.protocol_builder import ProtocolBuilderStatus
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
WorkflowApiSchema
from tests.base_test import BaseTest

3
tests/test_workflow_spec_api.py
View File

@ -3,7 +3,8 @@ from datetime import datetime, tzinfo, timezone
from crc import session
from crc.models.file import FileModel
from crc.models.study import StudyModel, StudyModelSchema, ProtocolBuilderStatus
from crc.models.study import StudyModel, StudyModelSchema
from models.protocol_builder import ProtocolBuilderStatus
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
WorkflowApiSchema
from tests.base_test import BaseTest