igvf-python-client/test/e2e/test_endpoints.py at main · IGVF-DACC/igvf-python-client · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
import pytest


def test_endpoints_test_search_simple():
    from igvf_client import IgvfApi
    from igvf_client.models.software import Software
    api = IgvfApi()
    r = api.search(query='abc')
    assert r.total > 2
    r = api.search(query='abc', limit=1)
    assert len(r.graph) == 1
    r = api.search(query='abc', type=['Software'], limit=1)
    assert len(r.graph) == 1
    item = r.graph[0].actual_instance
    assert isinstance(item, Software)
    assert item.type == ['Software', 'Item']
    assert 'software' in item.id
    assert 'lab' in item.lab
    assert 'award' in item.award
    assert item.status == 'released'
    assert item.uuid is not None
    assert item.title is not None


def test_endpoints_test_search_filters():
    from igvf_client import IgvfApi
    from igvf_client.models.software import Software
    api = IgvfApi()
    all_users = api.search(type=['User'], limit=0)
    cherry_lab_users = api.search(
        type=['User'],
        limit=0,
        field_filters={
            'lab': '/labs/j-michael-cherry/'
        }
    )
    assert cherry_lab_users.total > 10
    assert all_users.total > cherry_lab_users.total


def test_endpoints_test_collections():
    from igvf_client import IgvfApi
    api = IgvfApi()
    file_id = '/sequence-files/IGVFFI4531KBUU/'
    files = api.measurement_sets(files_id=[file_id]).graph[0].files
    assert len(files) >= 1
    assert file_id in files
    users = api.users(lab=['/labs/j-michael-cherry/'])
    assert users.total > 10
    assert users.graph[0].lab == '/labs/j-michael-cherry/'


def test_endpoints_test_schemas():
    from igvf_client import IgvfApi
    api = IgvfApi()
    schemas = api.schemas()
    assert len(schemas) > 50
    assert 'AccessKey' in schemas
    assert 'User' in schemas
    user_schema = api.schema_for_item_type('User')
    assert schemas['User'] == user_schema


def test_endpoints_test_user_collection():
    from igvf_client import IgvfApi
    api = IgvfApi()
    users = api.users(title=['Indexing Service'])
    assert users.total == 1
    assert users.id == '/users/@@listing?title=Indexing%20Service&frame=object'
    assert users.graph[0].id == '/users/1ac5c055-d3e8-4290-a4bb-d5e2f508e54a/'
    assert users.graph[0].uuid == '1ac5c055-d3e8-4290-a4bb-d5e2f508e54a'
    assert users.graph[0].lab == '/labs/j-michael-cherry/'
    assert users.graph[0].title == 'Indexing Service'
    assert users.graph[0].type == ['User', 'Item']
    user = api.get_by_id(users.graph[0].uuid)
    assert user.actual_instance == users.graph[0]


def test_endpoints_test_report():
    from igvf_client import IgvfApi
    api = IgvfApi()
    r = api.report(type=['User'], field_filters={'lab': '/labs/j-michael-cherry/'})
    assert 'Indexing Service' in r
    assert 'J. Michael Cherry' in r
    assert 'ID' in r
    assert 'UUID' in r
    assert 'Title' in r
    assert 'Lab' in r
    assert 'Status' in r


def test_endpoints_test_curated_set_collection():
    from igvf_client import IgvfApi
    api = IgvfApi()
    curated_sets = api.curated_sets(files_file_format=['tsv'])
    assert curated_sets.total > 10


def test_endpoints_test_download_tsv_file():
    from igvf_client import IgvfApi
    api = IgvfApi()
    r = api.search(field_filters={'file_format': 'tsv'})
    raw_tsv = api.download(r.graph[0].uuid)
    assert isinstance(raw_tsv, bytes)
    assert len(raw_tsv) > 1


def test_endpoints_test_search_facets():
    from igvf_client import IgvfApi
    api = IgvfApi()
    actual_types = [x['key'] for x in api.search(field_filters={'files.file_format': 'tsv'}).facets[0].terms]
    expected_types = ['FileSet', 'AuxiliarySet', 'CuratedSet']
    for type_ in expected_types:
        assert type_ in actual_types


def test_endpoints_test_search_field_filters():
    from igvf_client import IgvfApi
    api = IgvfApi()
    r = api.search(type=['Item'], field_filters={'status': 'current'})
    assert r.total > 100
    r2 = api.search(type=['Item'], field_filters={'status': ['current', 'released']})
    assert r2.total > r.total


def test_endpoints_test_sequence_file_int_coercion():
    from igvf_client import IgvfApi
    api = IgvfApi()
    api.sequence_files()