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NES-991 Expands testing for 'full' and 'abbreviated' header types; so…
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…lves TODO's; expands testing with goodtables
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@caco13
caco13 committed Oct 24, 2019
1 parent 8107b01 commit d679d78
Showing 1 changed file with 60 additions and 55 deletions.
115 changes: 60 additions & 55 deletions patientregistrationsystem/qdc/export/tests/test_views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2108,17 +2108,18 @@ def test_export_per_experiment_adds_basic_experiment_data_file_info_to_datapacka
json_data = self.get_datapackage_json_data(temp_dir, response)
experiment_resource = next(item for item in json_data['resources'] if item['name'] == 'Experiment')

# As Experiment.csv/tsv resource has 'schema' key, that is
# itself a dict with other data, we test key/value pairs for all
# keys except 'schema'.
# Remove schema field if it exists. The test was written before the
# test that drives adding schema field to datapackage.json
if 'schema' in experiment_resource:
experiment_resource.pop('schema')
test_dict = {
'name': 'Experiment', 'title': 'Experiment', 'path': 'data/Experiment_data/Experiment.csv',
'format': 'csv', 'mediatype': 'text/csv', 'encoding': 'UTF-8',
'profile': 'tabular-data-resource'
}
self.assertTrue(all(
item in experiment_resource.items() for item in test_dict.items()),
str(test_dict) + ' is not subdict of ' + str(experiment_resource))
self.assertEqual(
test_dict, experiment_resource,
str(test_dict) + ' not equal ' + str(experiment_resource))

shutil.rmtree(temp_dir)

Expand Down Expand Up @@ -2217,16 +2218,10 @@ def test_export_per_experiment_adds_participants_diagnosis_file_info_to_datapack
self.append_session_variable('license', '0')

data = self._set_post_data()
# Add selected diagnosis (all here)
data['diagnosis_selected'] = [
'medicalrecorddata__diagnosis__date*diagnosis_date',
'medicalrecorddata__diagnosis__description*diagnosis_description',
'medicalrecorddata__diagnosis__classification_of_diseases__code*classification_of_diseases_code',
'medicalrecorddata__diagnosis__classification_of_diseases__description'
'*classification_of_diseases_description',
'medicalrecorddata__diagnosis__classification_of_diseases__abbreviated_description'
'*classification_of_diseases_description'
]
data['diagnosis_selected'] = []
# Append al possible diagnosis attributes in POST data
for field in DIAGNOSIS_FIELDS:
data['diagnosis_selected'].append(field['field'] + '*' + field['header'])

response = self.client.post(reverse('export_view'), data)

Expand Down Expand Up @@ -2258,7 +2253,7 @@ def test_export_per_experiment_adds_participants_diagnosis_table_schema_info_to_
data = self._set_post_data()
data['diagnosis_selected'] = []
# Append al possible diagnosis attributes in POST data
for field in DIAGNOSIS_FIELDS: # TODO (NES-987): do the same in the other diagnosis test
for field in DIAGNOSIS_FIELDS:
data['diagnosis_selected'].append(field['field'] + '*' + field['header'])

# Test for code, full and abbreviated question texts
Expand Down Expand Up @@ -3092,7 +3087,6 @@ def test_export_per_experiment_adds_questionnaire_responses_file_to_datapackage_
update_mocks7_abbreviated(mockServer)
data = {
'per_participant': ['on'], 'action': ['run'], 'per_questionnaire': ['on'],
# TODO (NES-991): do for 'full' and 'abbreviated'
'headings': [heading_type],
'to_experiment[]': to_experiment,
'patient_selected': ['age*age'], 'responses': ['short']
Expand All @@ -3110,7 +3104,6 @@ def test_export_per_experiment_adds_questionnaire_responses_file_to_datapackage_
item for item in json_data['resources'] if item['name'] == unique_name)
# Remove schema field if it exists. The test was written before the
# test that drives adding schema field to datapackage.json
# TODO (NES-991): do this way for the other tests
if 'schema' in questionnaire_response_resource:
questionnaire_response_resource.pop('schema')
test_dict = {
Expand Down Expand Up @@ -3267,7 +3260,6 @@ def test_export_per_experiment_adds_entrance_questionnaire_metadata_file_to_data
item for item in json_data['resources'] if item['title'] == filename)
# Remove schema field if it exists. The test was written before the
# test that drives adding schema field to datapackage.json
# TODO (NES-991): do this way for the other tests
if 'schema' in questionnaire_response_resource:
questionnaire_response_resource.pop('schema')
test_dict = {
Expand Down Expand Up @@ -3371,7 +3363,6 @@ def test_export_per_experiment_adds_entrance_questionnaire_responses_file_to_dat
item for item in json_data['resources'] if item['title'] == filename)
# Remove schema field if it exists. The test was written before the
# test that drives adding schema field to datapackage.json
# TODO (NES-991): do this way for the other tests
if 'schema' in questionnaire_response_resource:
questionnaire_response_resource.pop('schema')
test_dict = {
Expand Down Expand Up @@ -3434,7 +3425,6 @@ def test_export_per_experiment_adds_entrance_questionnaire_responses_file_to_dat
item for item in json_data['resources'] if item['title'] == filename)
# Remove schema field if it exists. The test was written before the
# test that drives adding schema field to datapackage.json
# TODO (NES-991): do this way for the other tests
if 'schema' in questionnaire_response_resource:
questionnaire_response_resource.pop('schema')
test_dict = {
Expand Down Expand Up @@ -3889,18 +3879,14 @@ def test_export_per_participant_adds_participants_diagnosis_file_info_to_datapac
'1*' + str(LIMESURVEY_SURVEY_ID_2) + '*' + survey2.en_title + '*acquisitiondate*acquisitiondate',
'1*' + str(LIMESURVEY_SURVEY_ID_2) + '*' + survey2.en_title + '*textfragezwei*textfragezwei'
]
data = {'headings': ['code'], 'per_participant': ['on'], 'per_questionnaire': ['on'], 'files_format': ['csv'],
'action': ['run'], 'responses': ['short'], 'patient_selected': ['age*age'], 'license': '0', 'to[]': to,
# Add selected diagnosis (all here)
'diagnosis_selected': [
'medicalrecorddata__diagnosis__date*diagnosis_date',
'medicalrecorddata__diagnosis__description*diagnosis_description',
'medicalrecorddata__diagnosis__classification_of_diseases__code*classification_of_diseases_code',
'medicalrecorddata__diagnosis__classification_of_diseases__description'
'*classification_of_diseases_description',
'medicalrecorddata__diagnosis__classification_of_diseases__abbreviated_description'
'*classification_of_diseases_description'
]}
data = {
'headings': ['code'], 'per_participant': ['on'], 'per_questionnaire': ['on'], 'files_format': ['csv'],
'action': ['run'], 'responses': ['short'], 'patient_selected': ['age*age'], 'license': '0', 'to[]': to,
'diagnosis_selected': []
}
# Append al possible diagnosis attributes in POST data
for field in DIAGNOSIS_FIELDS:
data['diagnosis_selected'].append(field['field'] + '*' + field['header'])

response = self.client.post(reverse('export_view'), data)

Expand Down Expand Up @@ -3951,7 +3937,7 @@ def test_export_per_participant_adds_participants_diagnosis_table_schema_info_to
'diagnosis_selected': []
}
# Append all possible diagnosis attributes in POST data
for field in DIAGNOSIS_FIELDS: # TODO (NES-991): do the same in the other diagnosis test
for field in DIAGNOSIS_FIELDS:
data['diagnosis_selected'].append(field['field'] + '*' + field['header'])

for heading_type in 'code', 'full', 'abbreviated':
Expand All @@ -3968,7 +3954,11 @@ def test_export_per_participant_adds_participants_diagnosis_table_schema_info_to
diagnosis_resource = next(item for item in json_data['resources'] if item['name'] == 'diagnosis')
self.assertIn('schema', diagnosis_resource)
self.assertIn('fields', diagnosis_resource['schema'])
self._assert_participants_related_fields_table_schema(diagnosis_resource['schema'], heading_type, DIAGNOSIS_FIELDS)
self._assert_participants_related_fields_table_schema(
diagnosis_resource['schema'], heading_type, DIAGNOSIS_FIELDS)

report = validate(os.path.join(temp_dir, 'datapackage.json'))
self._assert_goodtables(report, heading_type)

shutil.rmtree(temp_dir)

Expand Down Expand Up @@ -4010,6 +4000,10 @@ def test_export_per_participant_adds_questionnaire_metadata_file_to_datapackage_
title = 'Fields_' + str(survey.lime_survey_id) + '_' + 'en'

questionnaire_metadata_resource = next(item for item in json_data['resources'] if item['title'] == title)
# Remove schema field if it exists. The test was written before the
# test that drives adding schema field to datapackage.json
if 'schema' in questionnaire_metadata_resource:
questionnaire_metadata_resource.pop('schema')
test_dict = {
'name': unique_name, 'title': title,
'path': os.path.join(
Expand All @@ -4018,10 +4012,12 @@ def test_export_per_participant_adds_questionnaire_metadata_file_to_datapackage_
'format': 'csv', 'mediatype': 'text/csv', 'description': 'Questionnaire metadata',
'profile': 'tabular-data-resource',
}
self.assertEqual(
test_dict, questionnaire_metadata_resource,
str(test_dict) + ' not equal ' + str(questionnaire_metadata_resource)
)

self.assertTrue(all(
item in questionnaire_metadata_resource.items() for item in test_dict.items()),
str(test_dict) + ' is not subdict of ' + str(questionnaire_metadata_resource))
shutil.rmtree(temp_dir)

@override_settings(MEDIA_ROOT=TEMP_MEDIA_ROOT)
@patch('survey.abc_search_engine.Server')
Expand All @@ -4045,10 +4041,6 @@ def test_export_per_participant_adds_questionnaire_metadata_table_schema_to_ques
'1*' + str(LIMESURVEY_SURVEY_ID_2) + '*' + survey2.en_title + '*acquisitiondate*acquisitiondate',
'1*' + str(LIMESURVEY_SURVEY_ID_2) + '*' + survey2.en_title + '*textfragezwei*textfragezwei'
]
# TODO (NES-991): tests for 'full' and 'abbreviated'.
# Obs.: By now NES exports by code only even if the user
# selects 'full' or 'abbreviated' for headings. Besides that
# the codes are in English too, even for questionnaires in pt-BR.
data = {
'headings': ['code'], 'per_participant': ['on'], 'per_questionnaire': ['on'],
'files_format': ['csv'], 'action': ['run'], 'responses': ['short'],
Expand All @@ -4069,6 +4061,11 @@ def test_export_per_participant_adds_questionnaire_metadata_table_schema_to_ques
{'name': item[0], 'title': item[0], 'type': item[1], 'format': 'default'},
questionnaire_metadata_resource['schema']['fields'])

report = validate(os.path.join(temp_dir, 'datapackage.json'))
self._assert_goodtables(report, 'code')

shutil.rmtree(temp_dir)

@override_settings(MEDIA_ROOT=TEMP_MEDIA_ROOT)
@patch('survey.abc_search_engine.Server')
def test_export_per_participant_adds_questionnaire_response_file_to_datapackage_json_file1(self, mockServer):
Expand Down Expand Up @@ -4109,9 +4106,10 @@ def test_export_per_participant_adds_questionnaire_response_file_to_datapackage_

questionnaire_response_resource = next(
item for item in json_data['resources'] if item['title'] == filename)
# As this resource has 'schema' key, that is
# itself a dict with other data, we test key/value pairs for all
# keys except 'schema'.
# Remove schema field if it exists. The test was written before the
# test that drives adding schema field to datapackage.json
if 'schema' in questionnaire_response_resource:
questionnaire_response_resource.pop('schema')
test_dict = {
'name': slugify(filename), 'title': filename,
'path': os.path.join(
Expand All @@ -4121,9 +4119,9 @@ def test_export_per_participant_adds_questionnaire_response_file_to_datapackage_
'format': 'csv', 'mediatype': 'text/csv', 'description': 'Questionnaire response',
'profile': 'tabular-data-resource',
}
self.assertTrue(all(
item in questionnaire_response_resource.items() for item in test_dict.items()),
str(test_dict) + ' is not subdict of ' + str(questionnaire_response_resource))
self.assertEqual(
test_dict, questionnaire_response_resource,
str(test_dict) + ' not equal ' + str(questionnaire_response_resource))

shutil.rmtree(temp_dir)

Expand Down Expand Up @@ -4189,6 +4187,9 @@ def test_export_per_participant_adds_questionnaire_responses_table_schema_info_t
}, questionnaire_response_resource['schema']['fields']
)

report = self._set_validation_for_goodtables(os.path.join(temp_dir, 'datapackage.json'), heading_type)
self._assert_goodtables(report, heading_type)

shutil.rmtree(temp_dir)

@override_settings(MEDIA_ROOT=TEMP_MEDIA_ROOT)
Expand Down Expand Up @@ -4234,9 +4235,10 @@ def test_export_per_participant_adds_questionnaire_response_file_to_datapackage_
survey.code + '_' + slugify(survey.en_title), filename + extension)
questionnaire_response_resource = next(
item for item in json_data['resources'] if item['path'] == path_resource)
# As this resource has 'schema' key, that is
# itself a dict with other data, we test key/value pairs for all
# keys except 'schema'.
# Remove schema field if it exists. The test was written before the
# test that drives adding schema field to datapackage.json
if 'schema' in questionnaire_response_resource:
questionnaire_response_resource.pop('schema')
test_dict = {
'name': slugify(filename), 'title': filename,
'path': os.path.join(
Expand All @@ -4245,9 +4247,9 @@ def test_export_per_participant_adds_questionnaire_response_file_to_datapackage_
'format': 'csv', 'mediatype': 'text/csv', 'description': 'Questionnaire response',
'profile': 'tabular-data-resource',
}
self.assertTrue(all(
item in questionnaire_response_resource.items() for item in test_dict.items()),
str(test_dict) + ' is not subdict of ' + str(questionnaire_response_resource))
self.assertEqual(
test_dict, questionnaire_response_resource,
str(test_dict) + ' not equal ' + str(questionnaire_response_resource))

shutil.rmtree(temp_dir)

Expand Down Expand Up @@ -4318,6 +4320,9 @@ def test_export_per_participant_adds_questionnaire_responses_table_schema_info_t
}, questionnaire_response_resource['schema']['fields']
)

report = self._set_validation_for_goodtables(os.path.join(temp_dir, 'datapackage.json'), heading_type)
self._assert_goodtables(report, heading_type)

shutil.rmtree(temp_dir)

def test_export_adds_resource_has_already_resource_with_same_name_adds_hash(self):
Expand Down

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