def test_map_object_with_non_existent_anchor(self):
# given:
json_object = json.loads('''{
"description": "test"
}''')
mapper = JsonMapper(json_object)
# when:
flat_result = mapper.map({
'$on': 'non.existent.node',
'name': ['text']
})
# and:
nested_result = mapper.map({
'text': ['description'],
'optional': {
'$on': 'non.existent.node',
'field': ['field']
}
})
# then:
self.assertIsNone(flat_result)
self.assertEqual({'text': 'test'}, nested_result)
def test_map_list_of_objects_with_nested_anchoring(self):
# given:
json_object = json.loads('''{
"social_network": {
"friends": [
{
"name": "Carl",
"age": 24
},
{
"name": "Tina",
"age": 22
},
{
"name": "Oscar",
"age": 22
}
]
}
}''')
# when:
people_json = JsonMapper(json_object).map({
'$on': 'social_network',
'people': {
'$on': 'friends',
'person_name': ['name'],
'person_age': ['age']
}
})
# then:
people = people_json.get('people')
self.assertIsNotNone(people)
self.assertEqual(3, len(people))
def test_map_object_with_invalid_spec(self):
# given:
json_object = json.loads('''{
"description": "this is a test"
}''')
# expect: main spec
with self.assertRaises(UnreadableSpecification):
JsonMapper(json_object).map('spec')
# and: field spec
with self.assertRaises(UnreadableSpecification):
JsonMapper(json_object).map({'d': 'specification'})
# and: empty dict as spec
with self.assertRaises(UnreadableSpecification):
JsonMapper(json_object).map({})
# and: empty field specification
with self.assertRaises(UnreadableSpecification):
JsonMapper(json_object).map({'field': []})
# and: None field specification
with self.assertRaises(UnreadableSpecification):
JsonMapper(json_object).map({'field': None})
def test_map_object_with_filter(self):
# given:
json_template = Template('''{
"name": "$name",
"age": $age
}''')
# and:
filtered_out_json = json.loads(json_template.substitute({'name': 'Charlie', 'age': 10}))
passing_json = json.loads(json_template.substitute({'name': 'Mary', 'age': 27}))
# and:
def is_adult(*args):
age = args[0]
return age >= 18
# and:
filtered_spec = {
'$filter': ['age', is_adult],
'known_by': ['name']
}
# when:
under_age_result = JsonMapper(filtered_out_json).map(filtered_spec)
adult_result = JsonMapper(passing_json).map(filtered_spec)
# then:
self.assertEqual({}, under_age_result)
self.assertEqual({'known_by': 'Mary'}, adult_result)
def test_map_object_with_non_node_anchor(self):
# given:
json_object = json.loads('''{
"name": "Boaty McBoatface"
}''')
mapper = JsonMapper(json_object)
# expect:
with self.assertRaises(InvalidNode):
mapper.map({
'known_as': ['name']
}, on='name')
def test_map_with_array_literal(self):
# given:
json_mapper = JsonMapper({})
# when:
values = ['list', 'of', 'values']
result = json_mapper.map({
'metadata': ['$array', values],
'empty': ['$array', []]
})
# then:
self.assertEqual(values, result.get('metadata'))
self.assertFalse('empty' in result.keys())
def test_map_list_of_objects(self):
# given:
json_object = json.loads('''{
"contacts": [
{
"name": "James",
"phone": "55556161"
},
{
"name": "Ana",
"phone": "55510103"
}
]
}''')
# when:
people = JsonMapper(json_object).map(on='contacts', using={
'known_by': ['name']
})
# then:
self.assertEqual(2, len(people))
names = [person.get('known_by') for person in people]
self.assertTrue('Ana' in names)
self.assertTrue('James' in names)
def test_map_object_with_custom_processing(self):
# given:
json_object = json.loads('''{
"name": "Pedro,Catapang,de Guzman",
"age": 44
}''')
# and:
def parse_name(*args):
name = args[0]
index = args[1]
return name.split(',')[index]
# and:
def fake_age(*args):
age = args[0]
return age - 10
# when:
resulting_json = JsonMapper(json_object).map({
'first_name': ['name', parse_name, 0],
'middle_name': ['name', parse_name, 1],
'last_name': ['name', parse_name, 2],
'fake_age': ['age', fake_age]
})
# then:
self.assertEqual('Pedro', resulting_json['first_name'])
self.assertEqual('Catapang', resulting_json['middle_name'])
self.assertEqual('de Guzman', resulting_json['last_name'])
self.assertEqual(34, resulting_json['fake_age'])
def test_map_object_allow_empty_strings(self):
# given:
json_object = json.loads('''{
"pet_name": "Champ",
"favourite_food": ""
}''')
# when:
pet_json = JsonMapper(json_object).map({
'name': ['pet_name'],
'fav_food': ['favourite_food']
})
# then:
self.assertEqual('Champ', pet_json.get('name'))
self.assertEqual('', pet_json.get('fav_food'))
def test_map_object_list_with_filter(self):
# given:
json_object = json.loads('''{
"product_list": [
{
"name": "eggs",
"price": 1.25
},
{
"name": "milk",
"price": 0.50
},
{
"name": "loaf",
"price": 2.25
}
]
}''')
# and:
def price_filter(*args):
price = args[0]
return price >= 1
# when:
products = JsonMapper(json_object).map({
'$on': 'product_list',
'$filter': ['price', price_filter],
'item': ['name']
})
# then:
self.assertEqual(2, len(products))
item_names = [item.get('item') for item in products]
self.assertTrue('eggs' in item_names and 'loaf' in item_names)
def test_map_with_object_literal(self):
# given:
json_object = json.loads('''{
"description": "test"
}''')
# when:
metadata = {'authored_by': 'me'}
result = JsonMapper(json_object).map({
'text': ['description'],
'metadata': ['$object', metadata],
'empty': ['$object', {}]
})
# then:
self.assertEqual(metadata, result.get('metadata'))
self.assertFalse('empty' in result.keys())
def test_map_object_ignore_missing_fields(self):
# given:
json_object = json.loads('''{
"first_name": "Juan",
"last_name": "dela Cruz"
}''')
# when:
person_json = JsonMapper(json_object).map({
'fname': ['first_name'],
'mname': ['middle_name'],
'lname': ['last_name']
})
# then:
self.assertEqual('Juan', person_json.get('fname'))
self.assertEqual('dela Cruz', person_json.get('lname'))
self.assertTrue('mname' not in person_json)
def test_map_object_using_spec_based_anchor(self):
# given:
json_object = json.loads('''{
"shipping_info": {
"recipient": "Kamado Tanjiro",
"address": "Tokyo, Japan"
}
}''')
# when:
delivery_json = JsonMapper(json_object).map({
'$on': 'shipping_info',
'name': ['recipient'],
'location': ['address']
})
# then:
self.assertEqual('Kamado Tanjiro', delivery_json.get('name'))
self.assertEqual('Tokyo, Japan', delivery_json.get('location'))
def test_map_object_with_nested_spec(self):
# given:
json_object = json.loads('''{
"first_name": "Vanessa",
"last_name": "Doofenshmirtz"
}''')
# when:
profile_json = JsonMapper(json_object).map({
'profile': {
'first_name': ['first_name'],
'last_name': ['last_name']
}
})
# then:
profile = profile_json.get('profile')
self.assertIsNotNone(profile)
self.assertEqual('Vanessa', profile.get('first_name'))
self.assertEqual('Doofenshmirtz', profile.get('last_name'))
def test_map_object_using_chained_spec_based_anchors(self):
# given:
json_object = json.loads('''{
"user": {
"profile": {
"name": "Kamado Nezuko",
"location": "hako no naka"
}
}
}''')
# when:
person_json = JsonMapper(json_object).map({
'$on': 'user',
'person': {
'$on': 'profile',
'known_by': ['name']
}
})
# then:
self.assertEqual('Kamado Nezuko', person_json.get('person', {}).get('known_by'))
def test_map_object_using_field_chaining(self):
# given:
json_object = json.loads('''{
"name": "John Doe",
"address": {
"city": "London",
"country": "UK"
}
}''')
# when:
profile_json = JsonMapper(json_object).map({
'user.profile': ['name'],
'user.address_city': ['address.city'],
'user.address_country': ['address.country']
})
# then:
self.assertIsNotNone(profile_json)
self.assertEqual('John Doe', profile_json.get('user', {}).get('profile'))
self.assertEqual('London', profile_json.get('user', {}).get('address_city'))
self.assertEqual('UK', profile_json.get('user', {}).get('address_country'))
def test_map_object(self):
# given:
json_object = json.loads('''{
"user_name": "jdelacruz",
"user_age": 31
}''')
# when:
converted_json = JsonMapper(json_object).map({
'name': ['user_name'],
'age': ['user_age']
})
# then:
self.assertIsNotNone(converted_json)
self.assertEqual('jdelacruz', converted_json['name'])
self.assertEqual(31, converted_json['age'])
def test_map_with_invalid_object_literal(self):
# given:
json_mapper = JsonMapper({})
# expect: non dict as object literal
with self.assertRaises(UnreadableSpecification):
json_mapper.map({
'field': ['$object', 'testing!']
})
# and: no specified literal
with self.assertRaises(UnreadableSpecification):
json_mapper.map({
'field': ['$object']
})
def convert(hca_data: dict):
spec = {
'$on': 'project',
'alias': ['uuid.uuid', prefix_with, ALIAS_PREFIX],
'attributes': {
'Project Core - Project Short Name':
['content.project_core.project_short_name', dsp_attribute],
'HCA Project UUID': ['uuid.uuid', dsp_attribute]
},
'releaseDate': ['submissionDate', format_date],
# TODO title probably needs padding? (len < 25)
'title': ['content.project_core.project_title'],
'description': ['content.project_core.project_description'],
'contacts': {
'$on': 'content.contributors',
'$filter': ['project_role', _is_not_wrangler],
'firstName': ['name', _parse_name, 0],
'middleInitials': ['name', _parse_name, 1],
'lastName': ['name', _parse_name, 2],
'email': ['email', default_to, ''],
'affiliation': ['institution', default_to, ''],
'phone': ['phone', default_to, ''],
'address': ['address', default_to, ''],
'orcid': ['orcid', default_to, '']
},
'publications': {
'$on': 'content.publications',
'authors': ['authors', concatenate_list],
'doi': ['doi', default_to, ''],
'articleTitle': ['title', default_to, ''],
'pubmedId': ['pmid', default_to, '']
},
'funders': {
'$on': 'content.funders',
'grantId': ['grant_id', default_to, ''],
'grantTitle': ['grant_title', default_to, ''],
'organization': ['organization', default_to, '']
}
}
return JsonMapper(hca_data).map(spec)
def test_map_object_with_anchored_key(self):
# given:
json_object = json.loads('''{
"user": {
"name": "Jane Doe"
},
"address": {
"city": "Cambridge",
"country": "UK"
}
}''')
# when:
address_json = JsonMapper(json_object).map(
on='address',
using={
'address_city': ['city'],
'address_country': ['country']
})
# then:
self.assertIsNotNone(address_json)
self.assertEqual('Cambridge', address_json['address_city'])
self.assertEqual('UK', address_json['address_country'])
def convert(hca_data: dict):
# added these for easier typing
sp = 'sequencing_protocol'
lp = 'library_preparation_protocol'
ib = 'input_biomaterial'
spec = {
'alias': [f'{sp}.content.protocol_core.protocol_id'],
'title': [f'{sp}.content.protocol_core.protocol_name'],
'description': [f'{sp}.content.protocol_core.protocol_description'],
'sampleUses':
json_array({'sampleRef': {
'alias': '{sampleAlias.placeholder}'
}}),
'studyRef':
json_object({'alias': '{studyAlias.placeholder}'}),
'attributes': {
'HCA Input Biomaterial UUID': [f'{ib}.uuid.uuid', dsp_attribute],
'HCA Library Preparation Protocol UUID':
[f'{lp}.uuid.uuid', dsp_attribute],
'HCA Process UUID': ['process.uuid.uuid', dsp_attribute],
'HCA Sequencing Protocol UUID': [f'{sp}.uuid.uuid', dsp_attribute],
'Input Biomaterial - Biomaterial Core - Biomaterial Id':
[f'{ib}.content.biomaterial_core.biomaterial_id', dsp_attribute],
'Input Biomaterial - Biomaterial Core - Ncbi Taxon Id - 0': [
f'{ib}.content.biomaterial_core.ncbi_taxon_id',
taxon_id_attribute
],
'Library Preparation Protocol - End Bias':
[f'{lp}.content.end_bias', dsp_attribute],
'Library Preparation Protocol - Library Construction Method': [
f'{lp}.content.library_construction_method.ontology_label',
ontology_term
],
'Library Preparation Protocol - Nucleic Acid Source':
[f'{lp}.content.nucleic_acid_source', dsp_attribute],
'Library Preparation Protocol - Primer':
[f'{lp}.content.primer', dsp_attribute],
'Library Preparation Protocol - Protocol Core - Protocol Id':
[f'{lp}.content.protocol_core.protocol_id', dsp_attribute],
'Library Preparation Protocol - Strand':
[f'{lp}.content.strand', dsp_attribute],
'Process - Process Core - Process Id':
['process.content.process_core.process_id', dsp_attribute],
'Sequencing Protocol - Paired End':
[f'{sp}.content.paired_end', dsp_attribute],
'Sequencing Protocol - Protocol Core - Protocol Id':
[f'{sp}.content.protocol_core.protocol_id', dsp_attribute],
'Sequencing Protocol - Sequencing Approach':
[f'{sp}.content.sequencing_approach.text', ontology_term],
'library_strategy': ['', fixed_dsp_attribute, 'OTHER'],
'library_source':
['', fixed_dsp_attribute, 'TRANSCRIPTOMIC SINGLE CELL'],
'library_selection': [f'{lp}.content.primer', map_primer],
'library_layout': [
f'{sp}.content.paired_end', library_layout_attribute
],
'library_name': [
f'{ib}.content.biomaterial_core.biomaterial_id', dsp_attribute
],
'instrument_model': [
f'{sp}.content.instrument_manufacturer_model.text',
instrument_model
],
'platform_type': ['', fixed_dsp_attribute, 'ILLUMINA'],
'design_description': ['', fixed_dsp_attribute, 'unspecified'],
# TODO if library_layout is SINGLE, this is "0"
'nominal_length': [f'{lp}.content.nominal_length', nominal_value],
'nominal_sdev': [f'{lp}.content.nominal_sdev', nominal_value]
}
}
return JsonMapper(hca_data).map(spec)
def convert_project(hca_data: dict):
return JsonMapper(hca_data).map(project_spec)
def convert(hca_data: dict):
project = hca_data.get('project')
use_spec = spec if project and project.get(
'releaseDate') else no_release_date_spec
return JsonMapper(hca_data).map(use_spec)
