def test_server(setup):
"""
Test the server properly handle /location resources
"""
user = setup.user
# create a location
location = api.create_resource('/location', {'code': api.get_random_name()[0:9]}, user)
assert 'id' in location # created
location_id = location['id']
location['code'] = api.get_random_name()[0:9]
location = api.update_resource('/location/{}'.format(location_id), location, user)
assert location['id'] == location_id
# get the location
location = api.get_resource('/location/{}'.format(location['id']), user=user)
# query for locations
locations = api.query_resource('/location', q=location['code'], user=user)
assert location['id'] in [location['id'] for location in locations]
# delete the created resources
api.delete_resource('/location/{}'.format(location['id']), user)
def test_route(setup):
"""
Test the server properly handle /taxon resources
"""
user = setup.user
source_detail = SourceDetail(name=test.get_random_name(), description="the description")
setup.session.add(source_detail)
setup.session.commit()
# TODO: test that POST with taxon and taxon_id both work, same with source_detail
# create an accession
first_accession = test.create_resource('/accession', {
'taxon_id': setup.taxon.id,
'code': test.get_random_name(),
'source': {
'id': source_detail.id,
'sources_code': test.get_random_name(),
'collection': {
"locale": test.get_random_name()
},
'propagation': {
'prop_type': 'UnrootedCutting',
'media': "Fafard 3B"
}
},
# TODO: setting the plant propagation id would require us to create a second
# accession, plant and plant propagation record and set that record
# here
'plant_propagation': {}
}, user)
# create another accession and use the first as a synonym
data = {'taxon_id': setup.taxon.id, 'code': test.get_random_name()}
notes = [{'user': '******', 'category': 'test', 'date': '1/1/2001', 'note': 'test note'},
{'user': '******', 'category': 'test', 'date': '2/2/2001', 'note': 'test note2'}],
synonyms = [{'synonym': first_accession}]
second_accession = test.create_resource('/accession', data, user)
assert 'id' in second_accession # created
# update the accession
second_accession['accession'] = test.get_random_name()
second_accession['source'] = first_accession['source']
second_id = second_accession['id']
second_accession = test.update_resource('/accession/' + str(second_id), second_accession, user)
assert second_accession['id'] == second_id # make sure they have the same ref after the update
# get the accession
first_accession = test.get_resource('/accession/' + str(first_accession['id']), user=user)
# query for taxa
accessions = test.query_resource('/accession', q=second_accession['code'], user=user)
assert second_accession['id'] in [accession['id'] for accession in accessions]
# delete the created resources
test.delete_resource('/accession/' + str(first_accession['id']), user)
test.delete_resource('/accession/' + str(second_accession['id']), user)
def test_search(setup):
user = setup.user
family_name = api.get_random_name()
family = api.create_resource('/family', {'family': family_name}, user=user)
family2 = api.create_resource('/family', {'family': api.get_random_name()}, user=user)
# return $http({method: 'GET', url: globals.apiRoot + '/search', params: {'q': value}})
# .then(callback);
response = requests.get(api.api_root + "/search", params={'q': family_name},
headers=get_headers(), auth=(user.email, user.access_token))
assert response.status_code == 200
response_json = json.loads(response.text)
assert 'families' in response_json
families = response_json['families']
assert len(families) == 1
assert families[0]['id'] == family['id']
api.delete_resource('/family/{}'.format(family['id']), user=user)
api.delete_resource('/family/{}'.format(family2['id']), user=user)
def test_distribution(setup):
# create a taxon taxon
taxon = Taxon(genus=setup.genus, sp=api.get_random_name())
setup.session.add(taxon)
geography = Geography(name="Test")
setup.session.add(geography)
setup.session.commit()
dist_route = "/taxon/{}/distributions".format(taxon.id)
# get a geogrpahy
# geography = setup.session.query(Geography).get(1)
# assert geography is not None
# add the geography to the taxon
# create a vernacular name using the route
dist_json = api.create_resource(dist_route, geography.json(), user=setup.user)
# check the geography is in the distribution list
dists = api.get_resource(dist_route, user=setup.user)
assert isinstance(dists, list)
assert geography.id in [dist["id"] for dist in dists]
# delete the name via the route
api.delete_resource(dist_route + "/{}".format(dist_json["id"]), user=setup.user)
setup.session.delete(taxon)
setup.session.commit()
def test_names(setup):
# create a taxon taxon
taxon = Taxon(genus=setup.genus, sp=api.get_random_name())
setup.session.add(taxon)
setup.session.commit()
names_route = "/taxon/{}/names".format(taxon.id)
# create a vernacular name using the route
name_json = api.create_resource(
names_route, {"name": api.get_random_name(), "language": api.get_random_name()}, user=setup.user
)
assert "id" in name_json
# check the name is in the list of names
names = api.get_resource(names_route, user=setup.user)
assert isinstance(names, list)
assert name_json["id"] in [name["id"] for name in names]
# delete the name via the route
api.delete_resource(names_route + "/{}".format(name_json["id"]), user=setup.user)
setup.session.delete(taxon)
setup.session.commit()
def test_parser(setup):
"""
Test the bauble.search.SearchParser
"""
user = setup.user
family = api.create_resource('/family', {'family': api.get_random_name()}, user=user)
parser = bauble.search.SearchParser()
parser.statement.parseString(family['family'])
api.delete_resource('/family/{}'.format(family['id']), user)
def test_delete(setup):
session = setup.session
report = Report(name=api.get_random_name())
session.add(report)
session.commit()
api.delete_resource('/report/{}'.format(report.id), setup.user)
report_id = report.id
session.expunge(report)
assert session.query(Report).get(report_id) is None
def test_route(setup):
"""
Test the /family resource.
"""
session = setup.session
user = setup.user
# create a family family
first_family = api.create_resource('/family', {'family': api.get_random_name()}, user)
# create another family and use the first as a synonym
data = {'family': api.get_random_name(),
'notes': [{'user': '******', 'category': 'test', 'date': '2001/1/1', 'note': 'test note'},
{'user': '******', 'category': 'test', 'date': '2002/2/2', 'note': 'test note2'}],
'synonyms': [first_family]
}
second_family = api.create_resource('/family', data, user)
assert 'id' in second_family # created
# update the family
second_family['family'] = api.get_random_name()
second_id = second_family['id']
second_family = api.update_resource('/family/{}'.format(second_id), second_family, user)
assert second_family['id'] == second_id # make sure they have the same ref after the update
# get the family
first_family = api.get_resource('/family/{}'.format(first_family['id']), user=user)
# query for families
#response_json = api.query_resource('/family', q=second_family['family'], user=user)
filter_by = json.dumps({'family': second_family['family'][0:4] + '%'})
response_json = api.get_resource('/family', {'filter': filter_by}, user=user)
assert len(response_json) == 1
second_family = response_json[0] # we're assuming there's only one
assert second_family['id'] == second_id
# make sure filtering against properties that aren't columns doesn't work
filter_by = json.dumps({'something': 'test'})
response_json = api.get_resource('/family', {'filter': filter_by}, user=user)
assert len(response_json) > 1
# delete the created resources
api.delete_resource('/family/{}'.format(first_family['id']), user)
api.delete_resource('/family/{}'.format(second_family['id']), user)
def test_route(setup):
"""
Test the server properly handle /taxon resources
"""
# create a taxon taxon
first_taxon = api.create_resource(
"/taxon", {"sp": api.get_random_name(), "genus_id": setup.genus.id}, user=setup.user
)
second_taxon = api.create_resource(
"/taxon", {"sp": api.get_random_name(), "genus_id": setup.genus.id}, user=setup.user
)
assert "id" in second_taxon # created
# update the taxon
second_taxon["sp"] = api.get_random_name()
second_id = second_taxon["id"]
second_taxon = api.update_resource("/taxon/" + str(second_id), second_taxon, user=setup.user)
assert second_taxon["id"] == second_id # make sure they have the same ref after the update
# get the taxon
first_taxon = api.get_resource("/taxon/" + str(first_taxon["id"]), user=setup.user)
# query for taxa
# print('data[sp]: ' + str(data['sp']))
# print('second_taxon', second_taxon)
# response_json = api.query_resource('/taxon', q=data['sp'])
# print(response_json)
# second_taxon = response_json['results'][0] # we're assuming there's only one
# assert second_taxon['ref'] == second_ref
# test getting the taxon relative to its family
# ** TODO: now we just embed the relation in the /taxon/:id
# ** request....need to create a test to make sure it's happening
# taxa = api.get_resource('/family/{}/genera/taxa'.format(family['id']), user=user)
# assert first_taxon['id'] in [taxon['id'] for taxon in taxa]
# delete the created resources
api.delete_resource("/taxon/" + str(first_taxon["id"]), user=setup.user)
api.delete_resource("/taxon/" + str(second_taxon["id"]), user=setup.user)
def test_organization(setup):
org_json = api.create_resource("/organization", {
'name': 'Test BG'
}, user=setup.user)
# make sure we can get the organization resource
org_json = api.get_resource('/organization/{}'.format(org_json['id']), user=setup.user)
owner_id = org_json['owners'][0]
user_json = api.get_resource('/user/{}'.format(owner_id), user=setup.user)
assert user_json['id'] == owner_id
# add another user to the organization
#user2_data = organization.owners[0].json()
user2_data = setup.user.json()
user2_data['username'] = api.get_random_name()
user2_data['email'] = api.get_random_name()
user2_data['organization'] = org_json
user2 = api.create_resource("/user", user2_data, user=setup.user)
assert user2 is not None
# TODO delete all the tables and schema for the organization
api.delete_resource('/organization/{}'.format(org_json['id']), user=setup.user)
def xtest_resource(session):
"""
Test the server properly /family resources
"""
return
db.set_session_schema(session, session.merge(organization).pg_schema)
families = session.query(Family)
# create a family family
first_family = api.create_resource('/family', {'family': api.get_random_name()})
# get the family
first_family = api.get_resource(first_family['ref'])
# query for families
response_json = api.query_resource('/family', q=second_family['family'])
second_family = response_json[0] # we're assuming there's only one
assert second_family['ref'] == second_ref
# delete the created resources
api.delete_resource(first_family['ref'])
api.delete_resource(second_family['ref'])
def test_server(setup):
"""
Test the server properly handle /genus resources
"""
user = setup.user
family = api.create_resource('/family', {'family': api.get_random_name()}, user)
# create a genus
first_genus = api.create_resource('/genus', {'genus': api.get_random_name(), 'family': family},
user)
# create another genus and use the first as a synonym
data = {'genus': api.get_random_name(),
'family': family,
'notes': [{'user': '******', 'category': 'test', 'date': '2001-1-1',
'note': 'test note'},
{'user': '******', 'category': 'test', 'date': '2002-2-2',
'note': 'test note2'}],
'synonyms': [first_genus]
#'synonyms': [{'synonym': first_genus}]
}
second_genus = api.create_resource('/genus', data, user)
assert 'id' in second_genus # created
# update the genus
second_genus['genus'] = api.get_random_name()
second_id = second_genus['id']
second_genus = api.update_resource('/genus/' + str(second_id), second_genus, user=user)
assert second_genus['id'] == second_id # make sure they have the same id after the update
# get the genus
first_genus = api.get_resource('/genus/' + str(first_genus['id']), user=user)
# query for genera and make sure the second genus is in the results
genera = api.query_resource('/genus', q=second_genus['genus'], user=user)
# TODO: ** shouldn't len(genera) be 1 since the name should be unique
#assert second_genus['ref'] in [genus['ref'] for genus in genera]
assert second_genus['id'] in [genus['id'] for genus in genera]
# test getting the genus relative to its family
# ** TODO: now we just embed the relation in the /genera/:id
# ** request....need to create a test to make sure it's happening
# genera = api.get_resource('/family/' + str(family['id']) + "/genera", user=user)
# assert first_genus['id'] in [genus['id'] for genus in genera]
# test getting a family with its genera relations
# ** TODO: now we just embed the relation in the /genera/:id
# ** request....need to create a test to make sure it's happening
#response_json = api.query_resource('/family', q=family['family'], relations="genera,notes", user=user)
#families = response_json
# TODO: *** i don't know if we still support returning relations like this...do
# we need to
# print(families[0]['genera'])
# assert first_genus['ref'] in [genus['ref'] for genus in families[0]['genera']]
# count the number of genera on a family
# TODO: ** count is temporarily disabled
# count = api.count_resource(family['ref'] + "/genera")
# assert count == "2"
# delete the created resources
api.delete_resource('/genus/' + str(first_genus['id']), user)
api.delete_resource('/genus/' + str(second_genus['id']), user)
api.delete_resource('/family/' + str(family['id']), user)
def test_server(setup):
"""
Test the server properly handle /taxon resources
"""
user = setup.user
family = api.create_resource('/family', {'family': api.get_random_name()}, user)
genus = api.create_resource('/genus', {'genus': api.get_random_name(),
'family': family}, user)
taxon = api.create_resource('/taxon', {'genus': genus, 'sp': api.get_random_name()}, user)
accession = api.create_resource('/accession',
{'taxon': taxon, 'code': api.get_random_name()}, user)
location = api.create_resource('/location', {'code': api.get_random_name()[0:9]}, user)
location2 = api.create_resource('/location', {'code': api.get_random_name()[0:9]}, user)
plant = api.create_resource('/plant', {
'accession': accession, 'location': location,
'code': api.get_random_name()[0:5],
'quantity': 10}, user)
# update the plant, add 2
assert 'id' in plant # created
plant_id = plant['id']
plant['code'] = api.get_random_name()[0:5]
plant['quantity'] = plant['quantity'] + 2
plant['change'] = {
#'reason': 'No reason really.',
'date': datetime.now().isoformat()
}
plant = api.update_resource(plant_ref(plant_id), plant, user)
assert plant['id'] == plant_id
plant = api.get_resource(plant_ref(plant['id']), user=user)
assert isinstance(plant['changes'], list)
assert plant['changes'][-1]['quantity'] == 2
assert plant['changes'][-1]['from_location_id'] == location['id']
assert plant['changes'][-1]['to_location_id'] is None
# update the plant and remove 3
plant['quantity'] = plant['quantity'] - 3
plant['change'] = {
#'reason': 'No reason really.',
'date': datetime.now().isoformat()
}
plant = api.update_resource(plant_ref(plant_id), plant, user)
assert plant['id'] == plant_id
plant = api.get_resource(plant_ref(plant['id']), user=user)
assert isinstance(plant['changes'], list)
assert plant['changes'][-1]['quantity'] == -3
assert plant['changes'][-1]['from_location_id'] == location['id']
assert plant['changes'][-1]['to_location_id'] is None
# move some of the plants to a new location
change_quantity = plant['quantity'] - 4
plant['quantity'] = change_quantity
plant['location_id'] = location2['id']
plant['change'] = {
'reason': 'No reason really.',
'date': datetime.now().isoformat()
}
plant = api.update_resource(plant_ref(plant_id), plant, user)
assert plant['id'] == plant_id
plant = api.get_resource(plant_ref(plant['id']), user=user)
assert isinstance(plant['changes'], list)
assert plant['changes'][-1]['quantity'] == change_quantity
assert plant['changes'][-1]['from_location_id'] == location['id']
assert plant['changes'][-1]['to_location_id'] == location2['id']
# query for plants
plants = api.query_resource('/plant', q=plant['code'], user=user)
assert plant['id'] in [plant['id'] for plant in plants]
# delete the created resources
api.delete_resource('/plant/' + str(plant['id']), user)
api.delete_resource('/location/' + str(location['id']), user)
api.delete_resource('/location/' + str(location2['id']), user)
api.delete_resource('/accession/' + str(accession['id']), user)
api.delete_resource('/taxon/' + str(taxon['id']), user)
api.delete_resource('/genus/' + str(genus['id']), user)
api.delete_resource('/family/' + str(family['id']), user)