Esempio n. 1
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def test_preview_scan(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 0
        }
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'preview_scan'
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200
    expected = '7d185cd48e077baefaf7bc216488ee49'

    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected
Esempio n. 2
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def test_preview_scan(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 0
        }
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({'id': id, 'method': 'preview_scan'})

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200
    expected = '1b9723cd7e9ecd54f28c7dae13e38511'

    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected
Esempio n. 3
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def test_describe(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'describe',
        'params': {
            'method': 'acquisition_params'
        }

    })
    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200
    assert response.json()['result'] \
        == ApiAdapter.acquisition_params.description

    # Try describing a method that doesn't exist
    request = jsonrpc_message({
        'id': id,
        'method': 'describe',
        'params': {
            'method': 'no_where_man'
        }

    })
    response = requests.post(acquisition_server.url, json=request)
    expected = {
        'message': 'Method no_where_man not found.',
        'code': -32000
    }
    assert response.status_code == 500
    error = response.json()['error']
    del error['data']
    assert error == expected
Esempio n. 4
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def test_stem_acquire(fei_acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
    })
    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'stem_rotation': 2.1
        }
    })

    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({'id': id, 'method': 'stem_acquire'})

    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200
    expected = '3b3d4b6163f48ec0f665fe114fac0d15'

    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected
Esempio n. 5
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def test_invalid_request(handler):
    request = {}
    response = handler.rpc(request)
    excepted = jsonrpc_message({
        'id': None,
        'error': {
            'message': 'Invalid request.',
            'code': -32600
        }
    })
    assert response == excepted

    id = 1234
    request = {'id': id}
    response = handler.rpc(request)
    excepted = jsonrpc_message({
        'id': id,
        'error': {
            'message': 'Invalid request.',
            'code': -32600
        }
    })
    assert response == excepted

    request = {'id': id, 'method': 'foo'}
    response = handler.rpc(request)
    excepted = jsonrpc_message({
        'id': id,
        'error': {
            'message': 'Invalid request.',
            'code': -32600
        }
    })
    assert response == excepted
Esempio n. 6
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def test_connected_missing_regex(passive_acquisition_server, tmpdir):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
        'params': {
            'path': tmpdir.strpath,
            'fileNameRegexGroups': ['angle'],
            'groupRegexSubstitutions': [{
                'n[': '-'
            }]
        }
    })

    response = requests.post(passive_acquisition_server.url, json=request)
    assert response.status_code == 500, response.content

    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
        'params': {
            'path': tmpdir.strpath,
            'fileNameRegex': '.*',
            'groupRegexSubstitutions': [{
                'n[': '-'
            }]
        }
    })

    response = requests.post(passive_acquisition_server.url, json=request)
    assert response.status_code == 500, response.content
Esempio n. 7
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def test_describe(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'describe',
        'params': {
            'method': 'acquisition_params'
        }
    })
    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200
    assert response.json()['result'] \
        == ApiAdapter.acquisition_params.description

    # Try describing a method that doesn't exist
    request = jsonrpc_message({
        'id': id,
        'method': 'describe',
        'params': {
            'method': 'no_where_man'
        }
    })
    response = requests.post(acquisition_server.url, json=request)
    expected = {'message': 'Method no_where_man not found.', 'code': -32000}
    assert response.status_code == 500
    error = response.json()['error']
    del error['data']
    assert error == expected
Esempio n. 8
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def test_stem_acquire(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 1
        }
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({'id': id, 'method': 'stem_acquire'})

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200
    expected = '2dbadcaa028e763a0a69efd371b48c9d'

    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected
Esempio n. 9
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def test_acquisition_params(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'acquisition_params',
    })
    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200
    expected = {
        'test': 1,
        'foo': 'foo'
    }
    assert response.status_code == 200
    assert response.json()['result'] == expected

    # Now update
    request = jsonrpc_message({
        'id': id,
        'method': 'acquisition_params',
        'params': {
            'foo': 'bar'
        }
    })
    response = requests.post(acquisition_server.url, json=request)
    expected = {
        'test': 1,
        'foo': 'bar'
    }
    assert response.status_code == 200
    assert response.json()['result'] == expected
Esempio n. 10
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def test_method_dict_params(handler):
    message = 'Hey!'

    def test(message=None):
        return {
            'data': message
        }

    handler.add_method('test', test)

    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'test',
        'params': {
            'message': message
        }
    })
    response = handler.rpc(request)
    expected = jsonrpc_message({
        'id': id,
        'result': {
            'data': message
        }
    })

    assert response == expected
Esempio n. 11
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def test_stem_acquire(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 0
        }
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({'id': id, 'method': 'stem_acquire'})

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200
    expected = '7d185cd48e077baefaf7bc216488ee49'

    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected

    # Try out of range
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 74
        }
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({'id': id, 'method': 'stem_acquire'})

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200

    expected = 'ac70e27a7db5710e1433393adeda4940'
    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected
Esempio n. 12
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def test_method_no_params(handler):
    def test():
        return {'data': 'big data!'}

    handler.add_method('test', test)

    id = 1234
    request = jsonrpc_message({'id': id, 'method': 'test'})
    response = handler.rpc(request)
    expected = jsonrpc_message({'id': id, 'result': {'data': 'big data!'}})

    assert response == expected
Esempio n. 13
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def test_connection(acquisition_server):
    id = 1234
    request = jsonrpc_message({'id': id, 'method': 'connect'})

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200
    assert response.json()['result']

    # Now disconnect
    request = jsonrpc_message({'id': id, 'method': 'disconnect'})
    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200
    assert not response.json()['result']
Esempio n. 14
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def test_method_not_found(handler):
    id = 1234
    request = jsonrpc_message({'id': id, 'method': 'foo'})
    response = handler.rpc(request)
    expected = jsonrpc_message({
        'id': id,
        'error': {
            'message': 'Method "foo" not found.',
            'code': -32601,
            'data': 'foo'
        }
    })

    assert response == expected
Esempio n. 15
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def test_tiff_stem_acquire(passive_acquisition_server, tmpdir,
                           mock_tiff_tiltseries_writer):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
        'params': {
            'path': tmpdir.strpath,
            'fileNameRegex': r'.*\.tif'
        }
    })
    response = requests.post(passive_acquisition_server.url, json=request)
    assert response.status_code == 200, response.content

    request = jsonrpc_message({
        'id': id,
        'method': 'stem_acquire'
    })

    tilt_series = []
    for _ in range(0, 1000):
        response = requests.post(passive_acquisition_server.url, json=request)
        assert response.status_code == 200, response.content
        # No images left to fetch
        result = response.json()['result']
        if result is None:
            continue

        url = result['imageUrl']
        response = requests.get(url)
        tilt_series.append(response.content)

        if len(tilt_series) == mock_tiff_tiltseries_writer.series_size:
            break

    # make sure we got all the images
    assert len(tilt_series) == mock_tiff_tiltseries_writer.series_size

    # Now check we got the write images
    with Image.open(test_image()) as image_stack:
        for i in range(0, image_stack.n_frames):
            md5 = hashlib.md5()
            md5.update(tilt_series[i])

            image_stack.seek(i)
            image_slice = tobytes(image_stack)
            expected_md5 = hashlib.md5()
            expected_md5.update(image_slice)
            assert md5.hexdigest() == expected_md5.hexdigest()
Esempio n. 16
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def test_tilt_params(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 23
        }
    })

    response = requests.post(acquisition_server.url, json=request)

    assert response.status_code == 200
    expected = jsonrpc_message({'id': id, 'result': 23})
    assert response.json() == expected
Esempio n. 17
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def test_method_not_found(handler):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'foo'
    })
    response = handler.rpc(request)
    expected = jsonrpc_message({
        'id': id,
        'error': {
            'message': 'Method "foo" not found.',
            'code': -32601,
            'data': 'foo'
        }
    })

    assert response == expected
Esempio n. 18
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def test_method_list_params(handler):
    message = 'Hey!'

    def test(message):
        return {'data': message}

    handler.add_method('test', test)

    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'test',
        'params': [message]
    })
    response = handler.rpc(request)
    expected = jsonrpc_message({'id': id, 'result': {'data': message}})

    assert response == expected
Esempio n. 19
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def test_tilt_params(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 23
        }
    })

    response = requests.post(acquisition_server.url, json=request)

    assert response.status_code == 200
    expected = jsonrpc_message({
        'id': id,
        'result': 23
    })
    assert response.json() == expected
Esempio n. 20
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def test_method_not_found(acquisition_server):
    source = 'test'

    id = 1234
    request = jsonrpc_message({'id': id, 'method': 'test', 'params': [source]})

    response = requests.post(acquisition_server.url, json=request)

    assert response.status_code == 404
    expected = jsonrpc_message({
        'id': id,
        'error': {
            'message': 'Method "test" not found.',
            'data': 'test',
            'code': -32601
        }
    })
    assert response.json() == expected
Esempio n. 21
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def test_connection(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect'
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200
    assert response.json()['result']

    # Now disconnect
    request = jsonrpc_message({
        'id': id,
        'method': 'disconnect'
    })
    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200
    assert not response.json()['result']
Esempio n. 22
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def test_describe_adapter(acquisition_server):
    id = 1234
    request = jsonrpc_message({'id': id, 'method': 'describe'})
    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200, response.json()
    expected = {
        'name':
        '%s.%s' % (inspect.getmodule(ApiAdapter).__name__, ApiAdapter.__name__)
    }
    assert response.json()['result'] \
        == expected, response.json()
Esempio n. 23
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def test_not_connected(fei_acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'stem_rotation': 2.1
        }
    })

    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 500
Esempio n. 24
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def test_connected_invalid_path(passive_acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
        'params': {
            'path': '/bogus'
        }
    })

    response = requests.post(passive_acquisition_server.url, json=request)
    assert response.status_code == 500, response.content
Esempio n. 25
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def test_acquisition_params(fei_acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
    })
    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'acquisition_params',
    })
    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200
    expected = {
        'calX': 1.2e-08,
        'calY': 1.2e-08,
        'units': 'nm'
    }
    assert response.json()['result']['size'] == expected
Esempio n. 26
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def test_invalid_content_type(acquisition_server):
    response = requests.post(acquisition_server.url, data='test')

    expected = jsonrpc_message({
        'id': None,
        'error': {
            'message': 'Invalid content type.',
            'data': 'text/plain',
            'code': -32700
        }
    })
    assert response.json() == expected
Esempio n. 27
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def test_tilt_params(fei_acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
    })
    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 2.1
        }
    })

    response = requests.post(fei_acquisition_server.url, json=request)

    assert response.status_code == 200
    assert response.json()['result'] == 2.1
Esempio n. 28
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def test_invalid_content_type(acquisition_server):
    response = requests.post(acquisition_server.url, data='test')

    expected = jsonrpc_message({
        'id': None,
        'error': {
            'message': 'Invalid content type.',
            'data': 'text/plain',
            'code': -32700
        }
    })
    assert response.json() == expected
Esempio n. 29
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def test_method_not_found(acquisition_server):
    source = 'test'

    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'test',
        'params': [source]
    })

    response = requests.post(acquisition_server.url, json=request)

    assert response.status_code == 404
    expected = jsonrpc_message({
        'id': id,
        'error': {
            'message':  'Method "test" not found.',
            'data': 'test',
            'code': -32601
        }
    })
    assert response.json() == expected
Esempio n. 30
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def test_invalid_request(handler):
    request = {}
    response = handler.rpc(request)
    excepted = jsonrpc_message({
        'id': None,
        'error': {
            'message': 'Invalid request.',
            'code': -32600
        }
    })
    assert response == excepted

    id = 1234
    request = {
        'id': id
    }
    response = handler.rpc(request)
    excepted = jsonrpc_message({
        'id': id,
        'error': {
            'message': 'Invalid request.',
            'code': -32600
        }
    })
    assert response == excepted

    request = {
        'id': id,
        'method': 'foo'
    }
    response = handler.rpc(request)
    excepted = jsonrpc_message({
        'id': id,
        'error': {
            'message': 'Invalid request.',
            'code': -32600
        }
    })
    assert response == excepted
Esempio n. 31
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def test_stem_acquire(fei_acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
    })
    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 2.1
        }
    })

    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'stem_acquire'
    })

    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200
    expected = '0cdcc5139186b0cbb84042eacfca1a13'

    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected
Esempio n. 32
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def test_method_no_params(handler):

    def test():
        return {
            'data': 'big data!'
        }

    handler.add_method('test', test)

    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'test'
    })
    response = handler.rpc(request)
    expected = jsonrpc_message({
        'id': id,
        'result': {
            'data': 'big data!'
        }
    })

    assert response == expected
Esempio n. 33
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def test_describe_adapter(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'describe'
    })
    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200, response.json()
    expected = {
        'name': '%s.%s' % (inspect.getmodule(ApiAdapter).__name__,
                           ApiAdapter.__name__)
    }
    assert response.json()['result'] \
        == expected, response.json()
Esempio n. 34
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def test_invalid_json(acquisition_server):
    headers = {'content-type': 'application/json'}
    response = requests.post(acquisition_server.url, headers=headers,
                             data='test')

    expected = jsonrpc_message({
        'id': None,
        'error': {
            'message': 'Invalid JSON.',
            'code': -32700
        }
    })
    response_json = response.json()
    del response_json['error']['data']
    assert response_json == expected
Esempio n. 35
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def test_acquisition_params(fei_acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
    })
    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'acquisition_params',
    })
    response = requests.post(fei_acquisition_server.url, json=request)
    assert response.status_code == 200
    expected = {'dwell_time': 3.1, 'binning': 10, 'image_size': 'FULL'}
    assert response.json()['result'] == expected

    # Now update
    request = jsonrpc_message({
        'id': id,
        'method': 'acquisition_params',
        'params': {
            'dwell_time': 5.2,
            'binning': 100,
            'image_size': 1
        }
    })
    response = requests.post(fei_acquisition_server.url, json=request)
    expected = {
        'dwell_time': 5.2,
        'binning': 100,
        'image_size': 'ACQIMAGESIZE_HALF'
    }
    assert response.status_code == 200
    assert response.json()['result'] == expected
Esempio n. 36
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def test_connected(passive_acquisition_server, tmpdir):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
        'params': {
            'path': tmpdir.strpath
        }
    })

    response = requests.post(passive_acquisition_server.url, json=request)
    assert response.status_code == 200, response.content

    # As we haven't started a mock tilt series write calls to should
    # return noting
    response = requests.post(passive_acquisition_server.url, json=request)
    assert response.status_code == 200

    result = response.json()['result']
    assert result is None
Esempio n. 37
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def test_stem_acquire(acquisition_server):
    id = 1234
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 0
        }
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'stem_acquire'
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200
    expected = '7d185cd48e077baefaf7bc216488ee49'

    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected

    # Try out of range
    request = jsonrpc_message({
        'id': id,
        'method': 'tilt_params',
        'params': {
            'angle': 74
        }
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    request = jsonrpc_message({
        'id': id,
        'method': 'stem_acquire'
    })

    response = requests.post(acquisition_server.url, json=request)
    assert response.status_code == 200

    # Now fetch the image
    url = response.json()['result']
    response = requests.get(url)

    assert response.status_code == 200

    expected = 'ac70e27a7db5710e1433393adeda4940'
    md5 = hashlib.md5()
    md5.update(response.content)
    assert md5.hexdigest() == expected
Esempio n. 38
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def test_deploy(acquisition_dev_server, sentinel_path1, sentinel_path2):
    adapter_path = os.path.join(os.path.dirname(__file__), 'fixtures',
                                'source1.py')
    with open(adapter_path) as fp:
        src = fp.read()

    request = jsonrpc_message({
        'id': 1234,
        'method': 'deploy_adapter',
        'params': ['foo', 'ApiAdapter1', src]
    })

    url = '%s/dev' % acquisition_dev_server.base_url
    response = requests.post(url, json=request)
    assert response.status_code == 200

    magic = '299792458'
    # Call connect and make sure it writes out a file
    request = jsonrpc_message({
        'id': 1234,
        'method': 'connect',
        'params': {
            'magic': magic
        }
    })

    assert not os.path.exists(sentinel_path1)

    response = requests.post(acquisition_dev_server.url, json=request)
    assert response.status_code == 200

    assert os.path.exists(sentinel_path1)
    with open(sentinel_path1) as fp:
        assert fp.read() == magic

    # Now redeploy
    adapter_path = os.path.join(os.path.dirname(__file__), 'fixtures',
                                'source2.py')
    with open(adapter_path) as fp:
        src = fp.read()

    request = jsonrpc_message({
        'id': 1234,
        'method': 'deploy_adapter',
        'params': ['foo', 'ApiAdapter2', src]
    })

    url = '%s/dev' % acquisition_dev_server.base_url
    response = requests.post(url, json=request)
    assert response.status_code == 200

    magic = '299792458'
    # Call connect and make sure it writes out a file
    request = jsonrpc_message({
        'id': 1234,
        'method': 'connect',
        'params': {
            'magic': magic
        }
    })

    assert not os.path.exists(sentinel_path2)

    response = requests.post(acquisition_dev_server.url, json=request)
    assert response.status_code == 200

    assert os.path.exists(sentinel_path2)
    with open(sentinel_path2) as fp:
        assert fp.read() == '%sx2' % magic
Esempio n. 39
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def test_dm3_stem_acquire(passive_acquisition_server, tmpdir,
                          mock_dm3_tiltseries_writer):
    id = 1234
    angle_regex = r'.*_([n,p]{1}[\d,\.]+)degree.*\.dm3'
    request = jsonrpc_message({
        'id': id,
        'method': 'connect',
        'params': {
            'path': tmpdir.strpath,
            'fileNameRegex': angle_regex,
            'fileNameRegexGroups': ['angle'],
            'groupRegexSubstitutions': {
                'angle': [{
                    'n': '-',
                    'p': '+'
                }]
            }
        }
    })
    response = requests.post(passive_acquisition_server.url, json=request)
    assert response.status_code == 200, response.content

    request = jsonrpc_message({
        'id': id,
        'method': 'stem_acquire'
    })

    tilt_series = []
    tilt_series_metadata = []
    for _ in range(0, 1000):
        response = requests.post(passive_acquisition_server.url, json=request)
        assert response.status_code == 200, response.content
        # No images left to fetch
        result = response.json()['result']
        if result is None:
            continue

        url = result['imageUrl']
        response = requests.get(url)
        tilt_series.append(response.content)
        if 'meta' in result:
            tilt_series_metadata.append(result['meta'])

        if len(tilt_series) == mock_dm3_tiltseries_writer.series_size:
            break

    # make sure we got all the images
    assert len(tilt_series) == mock_dm3_tiltseries_writer.series_size

    # Now check we got the write images
    for (i, (filename, fp)) in enumerate(test_dm3_tilt_series()):
        dm3_file = dm3.DM3(fp)
        expected_metadata \
            = {k: v.decode('utf8') for k, v in dm3_file.info.items()}
        expected_metadata['fileName'] = filename
        angle = re.match(angle_regex, filename).group(1)
        angle = angle.replace('n', '-')
        angle = angle.replace('p', '+')
        expected_metadata['angle'] = angle
        assert tilt_series_metadata[i] == expected_metadata

        md5 = hashlib.md5()
        md5.update(tilt_series[i])

        image = Image.fromarray(dm3_file.imagedata)
        tiff_image_data = tobytes(image)
        expected_md5 = hashlib.md5()
        expected_md5.update(tiff_image_data)

        assert md5.hexdigest() == expected_md5.hexdigest()
Esempio n. 40
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def test_deploy(acquisition_dev_server, sentinel_path1, sentinel_path2):
    adapter_path = os.path.join(os.path.dirname(__file__), 'fixtures',
                                'source1.py')
    with open(adapter_path) as fp:
        src = fp.read()

    request = jsonrpc_message({
        'id': 1234,
        'method': 'deploy_adapter',
        'params': ['foo', 'ApiAdapter1', src]
    })

    url = '%s/dev' % acquisition_dev_server.base_url
    response = requests.post(url, json=request)
    assert response.status_code == 200

    magic = '299792458'
    # Call connect and make sure it writes out a file
    request = jsonrpc_message({
        'id': 1234,
        'method': 'connect',
        'params': {
            'magic': magic
        }
    })

    assert not os.path.exists(sentinel_path1)

    response = requests.post(acquisition_dev_server.url, json=request)
    assert response.status_code == 200

    assert os.path.exists(sentinel_path1)
    with open(sentinel_path1) as fp:
        assert fp.read() == magic

    # Now redeploy
    adapter_path = os.path.join(os.path.dirname(__file__), 'fixtures',
                                'source2.py')
    with open(adapter_path) as fp:
        src = fp.read()

    request = jsonrpc_message({
        'id': 1234,
        'method': 'deploy_adapter',
        'params': ['foo', 'ApiAdapter2', src]
    })

    url = '%s/dev' % acquisition_dev_server.base_url
    response = requests.post(url, json=request)
    assert response.status_code == 200

    magic = '299792458'
    # Call connect and make sure it writes out a file
    request = jsonrpc_message({
        'id': 1234,
        'method': 'connect',
        'params': {
            'magic': magic
        }
    })

    assert not os.path.exists(sentinel_path2)

    response = requests.post(acquisition_dev_server.url, json=request)
    assert response.status_code == 200

    assert os.path.exists(sentinel_path2)
    with open(sentinel_path2) as fp:
        assert fp.read() == '%sx2' % magic