Esempio n. 1
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def test_new_file():
    """ Test that new file are created correctly """
    os.environ['DATASERVICE_API'] = 'http://api.com/'
    mock = patch('service.requests')
    req = mock.start()
    mock_resp = MagicMock()
    mock_resp.status_code = 201
    mock_resp.json.return_value = {'results': {'kf_id': 'GF_00000000'}}
    req.post.return_value = mock_resp

    importer = service.FileImporter('http://api.com/', 'abc123')

    res = importer.new_file(BUCKET, OBJECT, 'd41d8cd98f00b204e9800998ecf8427e',
                            1024)

    expected = {
        'file_name': '60d33dec-98db-446c-ac64-f4d027588f26.cram',
        'file_format': 'cram',
        'data_type': 'Aligned Reads',
        'controlled_access': True,
        'availability': 'Immediate Download',
        'is_harmonized': True,
        'reference_genome': 'GRCh38',
        'hashes': {
            'etag': 'd41d8cd98f00b204e9800998ecf8427e'
        },
        'size': 1024,
        'urls': ['s3://{}/{}'.format(BUCKET, OBJECT)],
        'acl': []
    }

    req.post.assert_called_with('http://api.com/genomic-files', json=expected)
    assert req.post.call_count == 1
Esempio n. 2
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def test_no_biospecimen(event, obj):
    """ Test that nothing is done if the biospecimen does not exist """
    obj()
    s3 = boto3.client('s3')
    mock = patch('service.requests')
    req = mock.start()
    mock_resp = MagicMock()
    mock_resp.status_code = 404
    req.get.return_value = mock_resp

    importer = service.FileImporter('http://api.com/', 'abc123')
    with pytest.raises(service.ImportException):
        importer.import_harmonized(event['Records'][0])

    req.get.assert_any_call('http://api.com/biospecimens/BS_QV3Z0DZM')
    mock.stop()
Esempio n. 3
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def test_new_file_error():
    """ Test that new file with predefined kf_id """
    os.environ['DATASERVICE_API'] = 'http://api.com/'
    mock = patch('service.requests')
    req = mock.start()
    mock_resp = MagicMock()
    mock_resp.status_code = 400
    mock_resp.json.return_value = {'results': {'kf_id': 'GF_00000002'}}
    req.post.return_value = mock_resp

    importer = service.FileImporter('http://api.com/', 'abc123')

    with pytest.raises(service.DataServiceException):
        res = importer.new_file(BUCKET, OBJECT,
                                'd41d8cd98f00b204e9800998ecf8427e', 1024)

    assert req.post.call_count == 1
def test_get_gf_id_tag():
    """ Test that gf_id is returned from tags correctly """
    mock = patch('service.requests')
    req = mock.start()
    mock_resp = MagicMock()
    mock_resp.status_code = 404
    mock_resp.json.return_value = {'_status': {'code': 404}}
    req.post.return_value = mock_resp

    importer = service.FileImporter('http://api.com/', 'abc123')

    tags = {'gf_id': 'GF_00000003'}

    res = importer.get_gf_id_tag(tags)

    assert res == 'GF_00000003'
    assert req.get.call_count == 1

    mock.stop()
def test_get_gf_id_tag_exists():
    """ Test getting gf_id tag if it already exists """
    mock = patch('service.requests')
    req = mock.start()
    mock_resp = MagicMock()
    mock_resp.status_code = 200
    mock_resp.json.return_value = {'results': {'kf_id': 'GF_00000003'}}
    req.get.return_value = mock_resp

    importer = service.FileImporter('http://api.com/', 'abc123')

    tags = {'gf_id': 'GF_00000003'}

    with pytest.raises(service.ImportException):
        res = importer.get_gf_id_tag(tags)

    assert req.get.call_count == 1

    mock.stop()
Esempio n. 6
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def test_req_tags(event, obj):
    """ Test that error is raised for missing tags """
    obj()
    s3 = boto3.client('s3')
    # Add a gf_id
    tags = TAGS.copy()
    tags['TagSet'] = tags['TagSet'][:4]
    response = s3.put_object_tagging(Bucket=BUCKET, Key=OBJECT, Tagging=tags)

    mock = patch('service.requests')
    req = mock.start()
    mock_resp = MagicMock()
    mock_resp.status_code = 404
    req.get.return_value = mock_resp

    importer = service.FileImporter('http://api.com/', 'abc123')
    with pytest.raises(service.ImportException):
        importer.import_harmonized(event['Records'][0])

    mock.stop()
Esempio n. 7
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def test_file_formats(filename, file_format, data_type):
    """ Test that file formats and data types are discovered correctly """
    mock = patch('service.requests')
    req = mock.start()
    mock_resp = MagicMock()
    mock_resp.status_code = 201
    mock_resp.json.return_value = {'results': {'kf_id': 'GF_00000001'}}
    req.post.return_value = mock_resp

    importer = service.FileImporter('http://api.com/', 'abc123')

    res = importer.new_file(SOURCE_BUCKET,
                            filename,
                            'd41d8cd98f00b204e9800998ecf8427e',
                            1024,
                            gf_id='GF_00000001',
                            bs_id='BS_00000000',
                            study_id='SD_00000000')

    expected = {
        'kf_id': 'GF_00000001',
        'file_name': filename,
        'file_format': file_format,
        'acl': ['SD_00000000'],
        'data_type': data_type,
        'controlled_access': True,
        'availability': 'Immediate Download',
        'is_harmonized': False,
        'biospecimen_id': 'BS_00000000',
        'hashes': {
            'etag': 'd41d8cd98f00b204e9800998ecf8427e'
        },
        'size': 1024,
        'urls': ['s3://{}/{}'.format(SOURCE_BUCKET, SOURCE_OBJECT)]
    }

    assert req.post.call_count == 1
    called_with = req.post.call_args_list[0][1]['json']
    assert called_with['file_format'] == file_format
    assert called_with['data_type'] == data_type
Esempio n. 8
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def test_new_file_bs_id():
    """ Test that new source file registers with a biospecimen """
    mock = patch('service.requests')
    req = mock.start()
    mock_resp = MagicMock()
    mock_resp.status_code = 201
    mock_resp.json.return_value = {'results': {'kf_id': 'GF_00000001'}}
    req.post.return_value = mock_resp

    importer = service.FileImporter('http://api.com/', 'abc123')

    res = importer.new_file(SOURCE_BUCKET,
                            SOURCE_OBJECT,
                            'd41d8cd98f00b204e9800998ecf8427e',
                            1024,
                            gf_id='GF_00000001',
                            bs_id='BS_00000000',
                            study_id='SD_00000000')

    expected = {
        'kf_id': 'GF_00000001',
        'file_name': 'bd042b24ae844a57ace28cf70cb3c852.bam.bai',
        'file_format': 'bai',
        'acl': ['SD_00000000'],
        'data_type': 'Aligned Reads Index',
        'controlled_access': True,
        'availability': 'Immediate Download',
        'is_harmonized': False,
        'biospecimen_id': 'BS_00000000',
        'hashes': {
            'etag': 'd41d8cd98f00b204e9800998ecf8427e'
        },
        'size': 1024,
        'urls': ['s3://{}/{}'.format(SOURCE_BUCKET, SOURCE_OBJECT)]
    }

    req.post.assert_called_with('http://api.com/genomic-files', json=expected)
    assert req.post.call_count == 1
def test_get_gf_id_tag_no_tag():
    """ Test getting gf_id tag if its not in the tags """
    importer = service.FileImporter('http://api.com/', 'abc123')
    tags = {'fake': 'tag'}
    res = importer.get_gf_id_tag(tags)
    assert res == None