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