cr-connect-workflow/tests/test_required_docs_script.py

import io
import os
from unittest.mock import patch

from crc import app, db
from crc.models.file import CONTENT_TYPES, FileDataModel, FileModel
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowSpecModel, WorkflowModel
from crc.scripts.required_docs import RequiredDocs
from crc.scripts.study_info import StudyInfo
from crc.services.file_service import FileService
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.workflow_processor import WorkflowProcessor
from tests.base_test import BaseTest


class TestRequiredDocsScript(BaseTest):
    test_uid = "dhf8r"
    test_study_id = 1

    """
            1. get a list of only the required documents for the study.
            2. For this study, is this document required accroding to the protocol builder? 
            3. For ALL uploaded documents, what the total number of files that were uploaded? per instance of this document naming
            convention that we are implementing for the IRB.
    """

    def test_validate_returns_error_if_reference_files_do_not_exist(self):
        file_model = db.session.query(FileModel). \
            filter(FileModel.is_reference == True). \
            filter(FileModel.name == FileService.IRB_PRO_CATEGORIES_FILE).first()
        if file_model:
            db.session.query(FileDataModel).filter(FileDataModel.file_model_id == file_model.id).delete()
            db.session.query(FileModel).filter(FileModel.id == file_model.id).delete()
        db.session.commit()
        db.session.flush()
        errors = RequiredDocs.validate()
        self.assertTrue(len(errors) > 0)
        self.assertEquals("file_not_found", errors[0].code)

    def test_no_validation_error_when_correct_file_exists(self):
        self.create_reference_document()
        errors = RequiredDocs.validate()
        self.assertTrue(len(errors) == 0)

    def test_load_lookup_data(self):
        self.create_reference_document()
        dict = FileService.get_file_reference_dictionary()
        self.assertIsNotNone(dict)

    @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.text = self.protocol_builder_response('required_docs.json')
        self.create_reference_document()
        script = RequiredDocs()
        required_docs = script.get_required_docs(12)
        self.assertIsNotNone(required_docs)
        self.assertTrue(len(required_docs) == 5)
        self.assertEquals(6, required_docs[0]['id'])
        self.assertEquals("Cancer Center's PRC Approval Form", required_docs[0]['name'])
        self.assertEquals("UVA Compliance", required_docs[0]['category1'])
        self.assertEquals("PRC Approval", required_docs[0]['category2'])
        self.assertEquals("CRC", required_docs[0]['Who Uploads?'])
        self.assertEquals(0, required_docs[0]['count'])

    @patch('crc.services.protocol_builder.requests.get')
    def test_get_required_docs_has_correct_count_when_a_file_exists(self, mock_get):

        self.load_example_data()

        # Mock out the protocol builder
        mock_get.return_value.ok = True
        mock_get.return_value.text = self.protocol_builder_response('required_docs.json')

        # Make sure the xslt refernce document is in place.
        self.create_reference_document()
        script = RequiredDocs()

        # Add a document to the study with the correct code.
        workflow = self.create_workflow('docx')
        irb_code = "UVACompliance.PRCApproval" # The first file referenced in pb required docs.
        FileService.add_task_file(study_id = workflow.study_id, workflow_id = workflow.id,
                                  task_id ="fakingthisout",
                                  name="anything.png", content_type="text",
                                  binary_data=b'1234', irb_doc_code=irb_code)

        required_docs = script.get_required_docs(workflow.study_id)
        self.assertIsNotNone(required_docs)
        self.assertEquals(1, required_docs[0]['count'])