Source code for camcops_server.cc_modules.cc_unittest

#!/usr/bin/env python



    Copyright (C) 2012, University of Cambridge, Department of Psychiatry.
    Created by Rudolf Cardinal (

    This file is part of CamCOPS.

    CamCOPS is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    CamCOPS is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with CamCOPS. If not, see <>.


**Framework and support functions for unit tests.**


import base64
import copy
import logging
import os
import sqlite3
from typing import Any, List, Type, TYPE_CHECKING
import unittest

from cardinal_pythonlib.classes import all_subclasses
from cardinal_pythonlib.dbfunc import get_fieldnames_from_cursor
from cardinal_pythonlib.httpconst import MimeType
from cardinal_pythonlib.logs import BraceStyleAdapter
import pendulum
import pytest
from sqlalchemy.engine.base import Engine

from camcops_server.cc_modules.cc_baseconstants import ENVVAR_CONFIG_FILE
from camcops_server.cc_modules.cc_constants import ERA_NOW
from camcops_server.cc_modules.cc_device import Device
from camcops_server.cc_modules.cc_exportrecipient import ExportRecipient
from camcops_server.cc_modules.cc_group import Group
from camcops_server.cc_modules.cc_idnumdef import IdNumDefinition
from camcops_server.cc_modules.cc_ipuse import IpUse
from camcops_server.cc_modules.cc_request import (
from camcops_server.cc_modules.cc_sqlalchemy import sql_from_sqlite_database
from camcops_server.cc_modules.cc_user import User
from camcops_server.cc_modules.cc_membership import UserGroupMembership
from camcops_server.cc_modules.cc_testfactories import (
from camcops_server.cc_modules.cc_version import CAMCOPS_SERVER_VERSION

    from sqlalchemy.orm import Session
    from camcops_server.cc_modules.cc_db import GenericTabletRecordMixin
    from camcops_server.cc_modules.cc_patient import Patient
    from camcops_server.cc_modules.cc_patientidnum import PatientIdNum
    from camcops_server.cc_modules.cc_task import Task

log = BraceStyleAdapter(logging.getLogger(__name__))

# =============================================================================
# Constants
# =============================================================================

DEMO_PNG_BYTES = base64.b64decode(
    # 1x1 pixel, black

# =============================================================================
# Unit testing
# =============================================================================

[docs]class ExtendedTestCase(unittest.TestCase): """ A subclass of :class:`unittest.TestCase` that provides some additional functionality. """ # Logging in unit tests: # # noqa # # ... but actually, my code below is simpler and works fine.
[docs] @classmethod def announce(cls, msg: str) -> None: """ Logs a message to the Python log. """"{}.{}:{}", cls.__module__, cls.__name__, msg)
[docs] def assertIsInstanceOrNone( self, obj: object, cls: Type, msg: str = None ) -> None: """ Asserts that ``obj`` is an instance of ``cls`` or is None. The parameter ``msg`` is used as part of the failure message if it isn't. """ if obj is None: return self.assertIsInstance(obj, cls, msg)
[docs]@pytest.mark.usefixtures("setup") class DemoRequestTestCase(ExtendedTestCase): """ Test case that creates a demo Pyramid request that refers to a bare in-memory SQLite database. """ dbsession: "Session" config_file: str engine: Engine database_on_disk: bool db_filename: str
[docs] def setUp(self) -> None: for factory in all_subclasses(BaseFactory): factory._meta.sqlalchemy_session = self.dbsession # config file has already been set up for the session in os.environ[ENVVAR_CONFIG_FILE] = self.config_file self.req = get_unittest_request(self.dbsession) # request.config is a class property. We want to be able to override # config settings in a test by setting them directly on the config # object (e.g. = "bar"), then restore the defaults # afterwards. self.old_config = copy.copy(self.req.config) self.req.matched_route = unittest.mock.Mock() self.recipdef = ExportRecipient()
[docs] def tearDown(self) -> None: CamcopsRequest.config = self.old_config
[docs] def set_echo(self, echo: bool) -> None: """ Changes the database echo status. """ self.engine.echo = echo
[docs] def dump_database(self, loglevel: int = logging.INFO) -> None: """ Writes the test in-memory SQLite database to the logging stream. Args: loglevel: log level to use """ if not self.database_on_disk: log.warning("Cannot dump database (use database_on_disk for that)") return"Dumping database; please wait...") connection = sqlite3.connect(self.db_filename) sql_text = sql_from_sqlite_database(connection) connection.close() log.log(loglevel, "SQLite database:\n{}", sql_text)
[docs] def dump_table( self, tablename: str, column_names: List[str] = None, loglevel: int = logging.INFO, ) -> None: """ Writes one table of the in-memory SQLite database to the logging stream. Args: tablename: table to dump column_names: column names to dump, or ``None`` for all loglevel: log level to use """ if not self.database_on_disk: log.warning("Cannot dump database (use database_on_disk for that)") return connection = sqlite3.connect(self.db_filename) cursor = connection.cursor() columns = ",".join(column_names) if column_names else "*" sql = f"SELECT {columns} FROM {tablename}" cursor.execute(sql) # noinspection PyTypeChecker fieldnames = get_fieldnames_from_cursor(cursor) results = ( ",".join(fieldnames) + "\n" + "\n".join( ",".join(str(value) for value in row) for row in cursor.fetchall() ) ) connection.close() log.log(loglevel, "Contents of table {}:\n{}", tablename, results)
[docs]class BasicDatabaseTestCase(DemoRequestTestCase): """ Test case that sets up some useful database records for testing: ID numbers, user, group, devices etc and has helper methods for creating patients and tasks """
[docs] def setUp(self) -> None: super().setUp() self.set_era("2010-07-07T13:40+0100") # Set up groups, users, etc. # ... ID number definitions idnum_type_nhs = 1 idnum_type_rio = 2 idnum_type_study = 3 self.nhs_iddef = IdNumDefinition( which_idnum=idnum_type_nhs, description="NHS number", short_description="NHS#", hl7_assigning_authority="NHS", hl7_id_type="NHSN", ) self.dbsession.add(self.nhs_iddef) self.rio_iddef = IdNumDefinition( which_idnum=idnum_type_rio, description="RiO number", short_description="RiO", hl7_assigning_authority="CPFT", hl7_id_type="CPRiO", ) self.dbsession.add(self.rio_iddef) self.study_iddef = IdNumDefinition( which_idnum=idnum_type_study, description="Study number", short_description="Study", ) self.dbsession.add(self.study_iddef) # ... group = Group() = "testgroup" = "Test group" = "sex AND anyidnum" = "sex AND idnum1" = IpUse() self.dbsession.add( self.dbsession.flush() # sets PK fields GroupFactory.reset_sequence( + 1) # ... users self.user = User.get_system_user(self.dbsession) self.user.upload_group_id = self.req._debugging_user = self.user # improve our debugging user # ... devices self.server_device = Device.get_server_device(self.dbsession) DeviceFactory.reset_sequence( + 1) self.other_device = DeviceFactory( name="other_device", friendly_name="Test device that may upload", registered_by_user=self.user, when_registered_utc=self.era_time_utc, camcops_version=CAMCOPS_SERVER_VERSION, ) # ... export recipient definition (the minimum) self.recipdef.primary_idnum = idnum_type_nhs self.dbsession.flush() # sets PK fields UserFactory.reset_sequence( + 1) self.create_tasks()
def set_era(self, iso_datetime: str) -> None: from cardinal_pythonlib.datetimefunc import ( convert_datetime_to_utc, format_datetime, ) from camcops_server.cc_modules.cc_constants import DateFormat self.era_time = pendulum.parse(iso_datetime) self.era_time_utc = convert_datetime_to_utc(self.era_time) self.era = format_datetime(self.era_time, DateFormat.ISO8601) def create_patient_with_two_idnums(self) -> "Patient": from camcops_server.cc_modules.cc_patient import Patient from camcops_server.cc_modules.cc_patientidnum import PatientIdNum # Populate database with two of everything patient = Patient() = 1 self.apply_standard_db_fields(patient) patient.forename = "Forename1" patient.surname = "Surname1" patient.dob = pendulum.parse("1950-01-01") self.dbsession.add(patient) patient_idnum1 = PatientIdNum() = 1 self.apply_standard_db_fields(patient_idnum1) patient_idnum1.patient_id = patient_idnum1.which_idnum = self.nhs_iddef.which_idnum patient_idnum1.idnum_value = 333 self.dbsession.add(patient_idnum1) patient_idnum2 = PatientIdNum() = 2 self.apply_standard_db_fields(patient_idnum2) patient_idnum2.patient_id = patient_idnum2.which_idnum = self.rio_iddef.which_idnum patient_idnum2.idnum_value = 444 self.dbsession.add(patient_idnum2) self.dbsession.commit() return patient def create_patient_with_one_idnum(self) -> "Patient": from camcops_server.cc_modules.cc_patient import Patient patient = Patient() = 2 self.apply_standard_db_fields(patient) patient.forename = "Forename2" patient.surname = "Surname2" patient.dob = pendulum.parse("1975-12-12") self.dbsession.add(patient) self.create_patient_idnum( id=3,, which_idnum=self.nhs_iddef.which_idnum, idnum_value=555, ) return patient def create_patient_idnum( self, as_server_patient: bool = False, **kwargs: Any ) -> "PatientIdNum": from camcops_server.cc_modules.cc_patientidnum import PatientIdNum patient_idnum = PatientIdNum() self.apply_standard_db_fields(patient_idnum, era_now=as_server_patient) for key, value in kwargs.items(): setattr(patient_idnum, key, value) if "id" not in kwargs: patient_idnum.save_with_next_available_id( self.req, patient_idnum._device_id ) else: self.dbsession.add(patient_idnum) self.dbsession.commit() return patient_idnum def create_patient( self, as_server_patient: bool = False, **kwargs: Any ) -> "Patient": from camcops_server.cc_modules.cc_patient import Patient patient = Patient() self.apply_standard_db_fields(patient, era_now=as_server_patient) for key, value in kwargs.items(): setattr(patient, key, value) if "id" not in kwargs: patient.save_with_next_available_id(self.req, patient._device_id) else: self.dbsession.add(patient) self.dbsession.commit() return patient def create_tasks(self) -> None: # Override in subclass pass
[docs] def apply_standard_task_fields(self, task: "Task") -> None: """ Writes some default values to an SQLAlchemy ORM object representing a task. """ self.apply_standard_db_fields(task) task.when_created = self.era_time
[docs] def apply_standard_db_fields( self, obj: "GenericTabletRecordMixin", era_now: bool = False ) -> None: """ Writes some default values to an SQLAlchemy ORM object representing a record uploaded from a client (tablet) device. Though we use the server device ID. """ obj._device_id = obj._era = ERA_NOW if era_now else self.era obj._group_id = obj._current = True obj._adding_user_id = obj._when_added_batch_utc = self.era_time_utc
def create_user(self, **kwargs) -> User: user = User() user.hashedpw = "" for key, value in kwargs.items(): setattr(user, key, value) self.dbsession.add(user) return user def create_group(self, name: str, **kwargs) -> Group: group = Group() = name for key, value in kwargs.items(): setattr(group, key, value) self.dbsession.add(group) return group def create_membership( self, user: User, group: Group, **kwargs ) -> UserGroupMembership: ugm = UserGroupMembership(, for key, value in kwargs.items(): setattr(ugm, key, value) self.dbsession.add(ugm) return ugm
[docs] def tearDown(self) -> None: pass
[docs]class DemoDatabaseTestCase(BasicDatabaseTestCase): """ Test case that sets up a demonstration CamCOPS database with two tasks of each type """ def create_tasks(self) -> None: from camcops_server.cc_modules.cc_blob import Blob from import Photo from camcops_server.cc_modules.cc_task import Task patient_with_two_idnums = self.create_patient_with_two_idnums() patient_with_one_idnum = self.create_patient_with_one_idnum() for cls in Task.all_subclasses_by_tablename(): t1 = cls() = 1 self.apply_standard_task_fields(t1) if t1.has_patient: t1.patient_id = if isinstance(t1, Photo): b = Blob() = 1 self.apply_standard_db_fields(b) b.tablename = t1.tablename b.tablepk = b.fieldname = "photo_blobid" b.filename = "some_picture.png" b.mimetype = MimeType.PNG b.image_rotation_deg_cw = 0 b.theblob = DEMO_PNG_BYTES self.dbsession.add(b) t1.photo_blobid = self.dbsession.add(t1) t2 = cls() = 2 self.apply_standard_task_fields(t2) if t2.has_patient: t2.patient_id = self.dbsession.add(t2) self.dbsession.commit()