validation.tests.test_helpers

Complexity

Total Complexity

22

Size/Duplication

Total Lines	452
Duplicated Lines	0 %

Importance

Changes

0

22 Methods

Rating	Name	Duplication	Size	Complexity
A	MetaDataValidationTestCase.test_issues_with_ebi()	0	15	1
A	MetaDataValidationTestCase.test_issues_with_ruleset()	0	15	1
A	SubmissionMixin.setUpClass()	0	9	1
A	SubmissionTestCase.test_sample_relationship_issue()	0	26	1
A	MetaDataValidationTestCase.check_biosample_id()	0	28	1
A	SubmissionTestCase.test_sample_issue_organism_part()	0	31	1
A	SubmissionMixin.setUp()	0	5	1
A	SampleUpdateTestCase.setUp()	0	17	1
A	SubmissionTestCase.test_submission()	0	19	1
A	SampleUpdateTestCase.test_sample_update()	0	18	1
A	RulesTestCase.test_check_ruleset()	0	9	1
A	SubmissionTestCase.test_animal_relationship()	0	26	1
A	SubmissionTestCase.test_sample()	0	21	1
A	MetaDataValidationTestCase.test_check_biosample_id_issue()	0	9	1
A	RulesTestCase.setUp()	0	2	1
A	SubmissionTestCase.setUp()	0	11	1
A	SubmissionTestCase.test_animal()	0	22	1
A	SubmissionTestCase.test_wrong_json_structure()	0	15	1
A	MetaDataValidationTestCase.test_check_biosample_id_target()	0	9	1
A	ValidationSummaryTestCase.setUp()	0	13	1
A	ValidationSummaryTestCase.test_initialization()	0	8	1
A	ValidationSummaryTestCase.test_after_data_deletion()	0	19	1

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 22 14:28:16 2019

@author: Paolo Cozzi <cozzi@ibba.cnr.it>
"""

import json

from image_validation.ValidationResult import ValidationResultRecord
from unittest.mock import patch, Mock

from django.test import TestCase

from image_app.models import Animal, Sample, Submission, Person, Name

from common.tests import PersonMixinTestCase

from ..helpers import (
    MetaDataValidation, OntologyCacheError, RulesetError)

from ..models import ValidationResult, ValidationSummary


class MetaDataValidationTestCase(TestCase):
    @patch("validation.helpers.validation.read_in_ruleset",
           side_effect=json.JSONDecodeError("meow", "woof", 42))
    def test_issues_with_ebi(self, my_issue):
        """
        Test temporary issues related with OLS EBI server during
        image_validation.use_ontology.OntologyCache loading"""

        # assert issues from validation.helpers.validation.read_in_ruleset
        self.assertRaisesMessage(
            OntologyCacheError,
            "Issue with 'https://www.ebi.ac.uk/ols/api/'",
            MetaDataValidation)

        # test mocked function called
        self.assertTrue(my_issue.called)

    @patch("validation.helpers.validation.check_ruleset",
           return_value=["Test for ruleset errors"])
    def test_issues_with_ruleset(self, my_issue):
        """
        Test errors regarding ruleset
        """

        # assert issues from validation.helpers.validation.read_in_ruleset
        self.assertRaisesMessage(
            RulesetError,
            "Test for ruleset errors",
            MetaDataValidation)

        # test mocked function called
        self.assertTrue(my_issue.called)

    @patch("requests.get")
    @patch("validation.helpers.validation.read_in_ruleset")
    @patch("validation.helpers.validation.check_ruleset",
           return_value=[])
    def check_biosample_id(self, my_check, my_read, mock_get, status_code):
        """Base method for checking biosample id"""

        # paching response
        response = Mock()
        response.status_code = status_code
        mock_get.return_value = response

        # create a fake ValidationResultRecord
        record_result = ValidationResultRecord(record_id="test")

        # get a metadata object
        metadata = MetaDataValidation()

        # check biosample object
        record_result = metadata.check_biosample_id_target(
            "FAKEA123456", "test", record_result)

        # assert my methods called
        self.assertTrue(my_check.called)
        self.assertTrue(my_read.called)
        self.assertTrue(mock_get.called)

        return record_result

    def test_check_biosample_id_target(self):
        """Test fecthing biosample ids from MetaDataValidation"""

        # pacthing response
        record_result = self.check_biosample_id(status_code=200)

        # test pass status and no messages
        self.assertEqual(record_result.get_overall_status(), 'Pass')
        self.assertEqual(record_result.get_messages(), [])

    def test_check_biosample_id_issue(self):
        """No valid biosample is found for this object"""

        # pacthing response
        record_result = self.check_biosample_id(status_code=404)

        # test Warning status and one message
        self.assertEqual(record_result.get_overall_status(), 'Warning')
        self.assertEqual(len(record_result.get_messages()), 1)


class SubmissionMixin(PersonMixinTestCase):
    # an attribute for PersonMixinTestCase
    person = Person

    fixtures = [
        'image_app/animal',
        'image_app/dictbreed',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/dictsex',
        'image_app/dictspecie',
        'image_app/dictstage',
        'image_app/dictuberon',
        'image_app/name',
        'image_app/ontology',
        'image_app/organization',
        'image_app/publication',
        'image_app/sample',
        'image_app/submission',
        'image_app/user'
    ]

    @classmethod
    def setUpClass(cls):
        # calling my base class setup
        super().setUpClass()

        # drop publication for semplicity
        name = Name.objects.get(pk=3)
        publication = name.publication
        publication.delete()

    def setUp(self):
        # calling my base class setup
        super().setUp()

        self.metadata = MetaDataValidation()


class SubmissionTestCase(SubmissionMixin, TestCase):
    """Deal real tests using image_validation library: this want to ensure
    that InjectTools can work with image_validation"""

    def setUp(self):
        # calling my base class setup
        super().setUp()

        # get an animal object
        self.animal = Animal.objects.get(pk=1)
        self.animal_record = self.animal.to_biosample()

        # get a sample object
        self.sample = Sample.objects.get(pk=1)
        self.sample_record = self.sample.to_biosample()

    def test_animal(self):
        """Testing an animal submission"""

        # at the time of writing this reference data raise one warning
        reference = ("Pass", "")

        # check for usi structure
        usi_result = self.metadata.check_usi_structure([self.animal_record])
        self.assertEqual(usi_result, [])

        # validate record
        result = self.metadata.validate(self.animal_record)

        # assert result type
        self.assertIsInstance(result, ValidationResultRecord)
        self.assertEqual(result.get_overall_status(), reference[0])

        def search(y):
            return reference[1] in y

        matches = [search(message) for message in result.get_messages()]
        self.assertNotIn(False, matches)

    def test_animal_relationship(self):
        """Testing an animal with a relationship"""

        # at the time of writing this reference data raise one warning
        reference = ("Pass", "")

        # get a to_biosample record
        animal = Animal.objects.get(pk=3)
        animal_record = animal.to_biosample()

        # check for usi structure
        usi_result = self.metadata.check_usi_structure([animal_record])
        self.assertEqual(usi_result, [])

        # validate record
        result = self.metadata.validate(animal_record)

        # assert result type
        self.assertIsInstance(result, ValidationResultRecord)
        self.assertEqual(result.get_overall_status(), reference[0])

        def search(y):
            return reference[1] in y

        matches = [search(message) for message in result.get_messages()]
        self.assertNotIn(False, matches)

    def test_sample(self):
        """Test a sample submission"""

        # at the time of writing this reference pass without problems
        reference = ("Pass", "")

        # check for usi structure
        usi_result = self.metadata.check_usi_structure([self.sample_record])
        self.assertEqual(usi_result, [])

        result = self.metadata.validate(self.sample_record)

        # assert result type
        self.assertIsInstance(result, ValidationResultRecord)
        self.assertEqual(result.get_overall_status(), reference[0])

        def search(y):
            return reference[1] == y

        matches = [search(message) for message in result.get_messages()]
        self.assertNotIn(False, matches)

    def test_sample_relationship_issue(self):
        """Testing an error with related alias. Not sure if it can happen or
        not"""

        # get record from sample
        record = self.sample_record

        # change alias in relationship in order to have no a related obj
        record["sampleRelationships"] = [{
            "alias": "IMAGEA999999999",
            "relationshipNature": "derived from"
        }]

        # create a fake ValidationResultRecord
        record_result = ValidationResultRecord(record_id=record['title'])

        # check relationship method
        related, result = self.metadata.check_relationship(
            record, record_result)

        # this is an error in results
        self.assertEqual(related, [])
        self.assertEqual(result.get_overall_status(), 'Error')
        self.assertIn(
            "Could not locate the referenced record",
            result.get_messages()[0])

    def test_sample_issue_organism_part(self):
        """Testing a problem in metadata: organism_part lacks of term"""

        # at the time of writing, this will have Errors
        reference = (
            "Error", (
                "Error: No url found for the field Organism part which has "
                "the type of ontology_id")
        )

        sample_record = self.sample.to_biosample()

        # set an attribute without ontology
        sample_record['attributes']['Organism part'] = [{'value': 'hair'}]

        # check for usi structure
        usi_result = self.metadata.check_usi_structure([sample_record])
        self.assertEqual(usi_result, [])

        # validate record. This will result in an error object
        result = self.metadata.validate(sample_record)

        # assert result type
        self.assertIsInstance(result, ValidationResultRecord)
        self.assertEqual(result.get_overall_status(), reference[0])

        def search(y):
            return reference[1] in y

        matches = [search(message) for message in result.get_messages()]
        self.assertNotIn(False, matches)

    def test_submission(self):
        """Testing usi_structure and duplicates in a submission"""

        # get all biosample data in a list
        data = [self.animal_record, self.sample_record]

        # test for usi structure
        usi_result = self.metadata.check_usi_structure(data)

        # no errors for check usi_structure
        self.assertIsInstance(usi_result, list)
        self.assertEqual(len(usi_result), 0)

        # test for duplicated data
        dup_result = self.metadata.check_duplicates(data)

        # no errors for check_duplicates
        self.assertIsInstance(dup_result, list)
        self.assertEqual(len(dup_result), 0)

    def test_wrong_json_structure(self):
        """Test that json structure is ok"""

        reference = [
            ('Wrong JSON structure: no title field for record with '
             'alias as IMAGEA000000001'),
        ]

        # delete some attributes from animal data
        del(self.animal_record['title'])

        # test for Json structure
        test = self.metadata.check_usi_structure([self.animal_record])

        self.assertEqual(reference, test)


class SampleUpdateTestCase(SubmissionMixin, TestCase):
    """Testing validation for a sample update"""

    def setUp(self):
        # calling my base class setup
        super().setUp()

        # get a samlple
        self.sample = Sample.objects.get(pk=1)

        # modify animal and sample
        self.animal_reference = "SAMEA4450079"
        self.sample.animal.name.biosample_id = self.animal_reference
        self.sample.animal.name.save()

        self.sample_reference = "SAMEA4450075"
        self.sample.name.biosample_id = self.sample_reference
        self.sample.name.save()

        self.record = self.sample.to_biosample()

    def test_sample_update(self):
        """Simulate a validation for an already submitted sample"""

        # at the time of writing this reference pass without problems
        reference = ("Pass", "")

        # check object
        result = self.metadata.validate(self.record)

        # assert result type
        self.assertIsInstance(result, ValidationResultRecord)
        self.assertEqual(result.get_overall_status(), reference[0])

        def search(y):
            return reference[1] == y

        matches = [search(message) for message in result.get_messages()]
        self.assertNotIn(False, matches)


class RulesTestCase(TestCase):
    """Assert that image rules are valid"""

    def setUp(self):
        self.metadata = MetaDataValidation()

    def test_check_ruleset(self):
        """Assert that rules are valid"""

        # get validation results
        ruleset_check = self.metadata.check_ruleset()

        # test image metadata rules
        self.assertIsInstance(ruleset_check, list)
        self.assertEqual(len(ruleset_check), 0)


class ValidationSummaryTestCase(TestCase):
    fixtures = [
        'image_app/animal',
        'image_app/dictbreed',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/dictsex',
        'image_app/dictspecie',
        'image_app/dictstage',
        'image_app/dictuberon',
        'image_app/name',
        'image_app/organization',
        'image_app/publication',
        'image_app/submission',
        'image_app/user',
        'image_app/sample',
        'validation/validationresult',
        'validation/validationsummary'
    ]

    def setUp(self):
        self.submission = Submission.objects.get(pk=1)
        self.validationsummary_animal = ValidationSummary.objects.get(
            submission=self.submission, type="animal")
        self.validationsummary_sample = ValidationSummary.objects.get(
            submission=self.submission, type="sample")

        # set names
        self.animal_name = Name.objects.get(pk=3)
        self.sample_name = Name.objects.get(pk=4)

        # track validationresult object
        self.validationresult = ValidationResult.objects.get(pk=1)

    def test_initialization(self):
        """Test that ValidationSummary is correctly initialized"""

        self.assertEqual(self.validationsummary_animal.all_count, 3)
        self.assertEqual(self.validationsummary_animal.issues_count, 0)

        self.assertEqual(self.validationsummary_sample.all_count, 1)
        self.assertEqual(self.validationsummary_sample.issues_count, 0)

    def test_after_data_deletion(self):
        """Ensure that all count changes after data deletion"""

        # drop one animal and one sample
        Animal.objects.get(pk=3).delete()
        Sample.objects.get(pk=1).delete()

        # call a method which updates animals and samples total count
        # HINT: should this number be updated when deleting animal and
        # samples in views?
        self.validationsummary_animal.reset_all_count()
        self.validationsummary_sample.reset_all_count()

        # test for counts
        self.assertEqual(self.validationsummary_animal.all_count, 2)
        self.assertEqual(self.validationsummary_animal.issues_count, 0)

        self.assertEqual(self.validationsummary_sample.all_count, 0)
        self.assertEqual(self.validationsummary_sample.issues_count, 0)