cr-connect-workflow/tests/test_workflow_service.py

180 lines
9.1 KiB
Python

import json
import os
from sqlalchemy import func
from crc import session, app
from crc.models.api_models import WorkflowApiSchema, Task
from crc.models.file import FileModelSchema, FileDataModel, FileModel, LookupFileModel, LookupDataModel
from crc.models.stats import WorkflowStatsModel, TaskEventModel
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
from tests.base_test import BaseTest
class TestWorkflowService(BaseTest):
def test_documentation_processing_handles_replacements(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
task.task_spec.documentation = "Some simple docs"
docs = WorkflowService._process_documentation(task)
self.assertEqual("Some simple docs", docs)
task.data = {"replace_me": "new_thing"}
task.task_spec.documentation = "{{replace_me}}"
docs = WorkflowService._process_documentation(task)
self.assertEqual("new_thing", docs)
documentation = """
# Bigger Test
* bullet one
* bullet two has {{replace_me}}
# other stuff.
"""
expected = """
# Bigger Test
* bullet one
* bullet two has new_thing
# other stuff.
"""
task.task_spec.documentation = documentation
result = WorkflowService._process_documentation(task)
self.assertEqual(expected, result)
def test_documentation_processing_handles_conditionals(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
task.task_spec.documentation = "This test {% if works == 'yes' %}works{% endif %}"
docs = WorkflowService._process_documentation(task)
self.assertEqual("This test ", docs)
task.data = {"works": 'yes'}
docs = WorkflowService._process_documentation(task)
self.assertEqual("This test works", docs)
def test_enum_options_from_file(self):
self.load_example_data()
workflow = self.create_workflow('enum_options_from_file')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
WorkflowService.process_options(task, task.task_spec.form.fields[0])
options = task.task_spec.form.fields[0].options
self.assertEquals(19, len(options))
self.assertEquals('1000', options[0]['id'])
self.assertEquals("UVA - INTERNAL - GM USE ONLY", options[0]['name'])
def test_create_lookup_file(self):
spec = self.load_test_spec('enum_options_from_file')
file_model = session.query(FileModel).filter(FileModel.name == "customer_list.xls").first()
file_data_model = session.query(FileDataModel).filter(FileDataModel.file_model == file_model).first()
WorkflowService._get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
lookup_records = session.query(LookupFileModel).all()
self.assertIsNotNone(lookup_records)
self.assertEqual(1, len(lookup_records))
lookup_record = lookup_records[0]
self.assertIsNotNone(lookup_record)
self.assertEquals("CUSTOMER_NUMBER", lookup_record.value_column)
self.assertEquals("CUSTOMER_NAME", lookup_record.label_column)
self.assertEquals("CUSTOMER_NAME", lookup_record.label_column)
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(19, len(lookup_data))
self.assertEquals("1000", lookup_data[0].value)
self.assertEquals("UVA - INTERNAL - GM USE ONLY", lookup_data[0].label)
# search_results = session.query(LookupDataModel).\
# filter(LookupDataModel.lookup_file_model_id == lookup_record.id).\
# filter(LookupDataModel.__ts_vector__.op('@@')(func.plainto_tsquery('INTERNAL'))).all()
search_results = LookupDataModel.query.filter(LookupDataModel.label.match("INTERNAL")).all()
self.assertEquals(1, len(search_results))
search_results = LookupDataModel.query.filter(LookupDataModel.label.match("internal")).all()
self.assertEquals(1, len(search_results))
# This query finds results where a word starts with "bio"
search_results = LookupDataModel.query.filter(LookupDataModel.label.match("bio:*")).all()
self.assertEquals(2, len(search_results))
def test_create_lookup_file_multiple_times_does_not_update_database(self):
spec = self.load_test_spec('enum_options_from_file')
file_model = session.query(FileModel).filter(FileModel.name == "customer_list.xls").first()
file_data_model = session.query(FileDataModel).filter(FileDataModel.file_model == file_model).first()
WorkflowService._get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
WorkflowService._get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
WorkflowService._get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
lookup_records = session.query(LookupFileModel).all()
self.assertIsNotNone(lookup_records)
self.assertEqual(1, len(lookup_records))
lookup_record = lookup_records[0]
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(19, len(lookup_data))
# Using the same table with different lookup lable or value, does create additional records.
WorkflowService._get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NAME", "CUSTOMER_NUMBER")
lookup_records = session.query(LookupFileModel).all()
self.assertIsNotNone(lookup_records)
self.assertEqual(2, len(lookup_records))
def test_some_full_text_queries(self):
self.load_test_spec('enum_options_from_file')
file_model = session.query(FileModel).filter(FileModel.name == "customer_list.xls").first()
file_data_model = session.query(FileDataModel).filter(FileDataModel.file_model == file_model).first()
lookup_table = WorkflowService._get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_table).all()
results = WorkflowService.run_lookup_query(lookup_table.id, "medicines", limit=10)
self.assertEquals(1, len(results), "words in the middle of label are detected.")
self.assertEquals("The Medicines Company", results[0].label)
results = WorkflowService.run_lookup_query(lookup_table.id, "", limit=10)
self.assertEquals(10, len(results), "Blank queries return everything, to the limit")
results = WorkflowService.run_lookup_query(lookup_table.id, "UVA", limit=10)
self.assertEquals(1, len(results), "Beginning of label is found.")
self.assertEquals("UVA - INTERNAL - GM USE ONLY", results[0].label)
results = WorkflowService.run_lookup_query(lookup_table.id, "uva", limit=10)
self.assertEquals(1, len(results), "case does not matter.")
self.assertEquals("UVA - INTERNAL - GM USE ONLY", results[0].label)
results = WorkflowService.run_lookup_query(lookup_table.id, "medici", limit=10)
self.assertEquals(1, len(results), "partial words are picked up.")
self.assertEquals("The Medicines Company", results[0].label)
results = WorkflowService.run_lookup_query(lookup_table.id, "Genetics Savings", limit=10)
self.assertEquals(1, len(results), "multiple terms are picked up..")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
results = WorkflowService.run_lookup_query(lookup_table.id, "Genetics Sav", limit=10)
self.assertEquals(1, len(results), "prefix queries still work with partial terms")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
results = WorkflowService.run_lookup_query(lookup_table.id, "Gen Sav", limit=10)
self.assertEquals(1, len(results), "prefix queries still work with ALL the partial terms")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
results = WorkflowService.run_lookup_query(lookup_table.id, "Inc", limit=10)
self.assertEquals(7, len(results), "short terms get multiple correct results.")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
# Fixme: Stop words are taken into account on the query side, and haven't found a fix yet.
#results = WorkflowService.run_lookup_query(lookup_table.id, "in", limit=10)
#self.assertEquals(7, len(results), "stop words are not removed.")
#self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)