def test_cacheable_pageable_json(os_makedirs, pj_read_json, ju_read,
cache_style, safe_read_url_get_msg5):
with patch("allensdk.core.json_utilities.read_url_get",
side_effect=safe_read_url_get_msg5) as ju_read_url_get:
archive_templates = \
{"cam_cell_queries": [
{'name': 'cam_cell_metric',
'description': 'see name',
'model': 'ApiCamCellMetric',
'num_rows': 1000,
'count': False
} ] }
rmat = RmaTemplate(query_manifest=archive_templates)
@cacheable()
@pageable(num_rows=2000)
def get_cam_cell_metrics(*args, **kwargs):
return rmat.template_query("cam_cell_queries", 'cam_cell_metric',
*args, **kwargs)
with patch(builtins.__name__ + '.open', mock_open(),
create=True) as open_mock:
open_mock.return_value.read = \
MagicMock(name='read',
return_value=[{'whatever': True},
{'whatever': True},
{'whatever': True},
{'whatever': True},
{'whatever': True}])
cam_cell_metrics = \
get_cam_cell_metrics(strategy='create',
path='/path/to/cam_cell_metrics.json',
num_rows=1,
total_rows='all',
**cache_style())
os_makedirs.assert_called_once_with('/path/to')
base_query = \
('http://api.brain-map.org/api/v2/data/query.json?'
'q=model::ApiCamCellMetric,'
'rma::options%5Bnum_rows$eq1%5D%5Bstart_row$eq{}%5D'
'%5Bcount$eqfalse%5D')
expected_calls = map(lambda c: call(base_query.format(c)),
[0, 1, 2, 3, 4, 5])
open_mock.assert_called_once_with('/path/to/cam_cell_metrics.json',
'wb')
open_mock.return_value.write.assert_called_once_with(
'[\n {\n "whatever": true\n },\n {\n "whatever": true\n },\n {\n "whatever": true\n },\n {\n "whatever": true\n },\n {\n "whatever": true\n }\n]'
)
assert ju_read_url_get.call_args_list == list(expected_calls)
assert len(cam_cell_metrics) == 5
def test_cacheable_pageable_csv(os_makedirs, read_csv, cache_style,
safe_read_url_get_msg5):
with patch("allensdk.core.json_utilities.read_url_get",
side_effect=safe_read_url_get_msg5) as ju_read_url_get:
archive_templates = \
{"cam_cell_queries": [
{'name': 'cam_cell_metric',
'description': 'see name',
'model': 'ApiCamCellMetric',
'num_rows': 1000,
'count': False
} ] }
rmat = RmaTemplate(query_manifest=archive_templates)
@cacheable()
@pageable(num_rows=2000)
def get_cam_cell_metrics(*args, **kwargs):
return rmat.template_query("cam_cell_queries", 'cam_cell_metric',
*args, **kwargs)
with patch(builtins.__name__ + '.open', mock_open(),
create=True) as open_mock:
with patch('csv.DictWriter.writerow') as csv_writerow:
cam_cell_metrics = \
get_cam_cell_metrics(strategy='create',
path='/path/to/cam_cell_metrics.csv',
num_rows=1,
total_rows='all',
**cache_style())
os_makedirs.assert_called_once_with('/path/to')
base_query = ('http://api.brain-map.org/api/v2/data/query.json?'
'q=model::ApiCamCellMetric,'
'rma::options%5Bnum_rows$eq1%5D%5Bstart_row$eq{}%5D'
'%5Bcount$eqfalse%5D')
expected_calls = map(lambda c: call(base_query.format(c)),
[0, 1, 2, 3, 4, 5])
assert ju_read_url_get.call_args_list == list(expected_calls)
read_csv.assert_called_once_with('/path/to/cam_cell_metrics.csv',
parse_dates=True)
assert csv_writerow.call_args_list == [
call({'whatever': 'whatever'}),
call({'whatever': True}),
call({'whatever': True}),
call({'whatever': True}),
call({'whatever': True}),
call({'whatever': True})
]
class ApiTemplateTests(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(ApiTemplateTests, self).__init__(*args, **kwargs)
self.templates = None
def setUp(self):
self.templates = \
{"ontology_queries": [
{'name': 'structures_by_graph_ids',
'description': 'see name',
'model': 'Structure',
'criteria': '[graph_id$in{{ graph_ids }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_ids']
},
{'name': 'structures_by_graph_names',
'description': 'see name',
'model': 'Structure',
'criteria': 'graph[structure_graphs.name$in{{ graph_names }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_names']
},
{'name': 'structures_by_set_ids',
'description': 'see name',
'model': 'Structure',
'criteria': '[structure_set_id$in{{ set_ids }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['set_ids']
},
{'name': 'structures_by_set_names',
'description': 'see name',
'model': 'Structure',
'criteria': 'structure_sets[name$in{{ set_names }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['set_names']
},
{'name': 'structure_graphs_list',
'description': 'see name',
'model': 'StructureGraph',
'num_rows': 'all',
'count': False
},
{'name': 'structure_sets_list',
'description': 'see name',
'model': 'StructureSet',
'num_rows': 'all',
'count': False
},
{'name': 'atlases_list',
'description': 'see name',
'model': 'Atlas',
'num_rows': 'all',
'count': False
},
{'name': 'atlases_table',
'description': 'see name',
'model': 'Atlas',
'criteria': '{% if graph_ids is defined %}[graph_id$in{{ graph_ids }}],{% endif %}structure_graph(ontology),graphic_group_labels',
'include': '[structure_graph(ontology),graphic_group_labels',
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_ids']
},
{'name': 'atlases_table_brief',
'description': 'see name',
'model': 'Atlas',
'criteria': 'structure_graph(ontology),graphic_group_labels',
'include': 'structure_graph(ontology),graphic_group_labels',
'only': ['atlases.id',
'atlases.name',
'atlases.image_type',
'ontologies.id',
'ontologies.name',
'structure_graphs.id',
'structure_graphs.name',
'graphic_group_labels.id',
'graphic_group_labels.name'],
'num_rows': 'all',
'count': False
}
]}
self.rma = RmaTemplate(query_manifest=self.templates)
def tearDown(self):
self.rma= None
self.templates = None
def test_atlases_list(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'atlases_list')
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::options%5Bnum_rows$eq%27all%27%5D%5Bcount$eqfalse%5D')
def test_structure_graphs_list(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'structure_graphs_list')
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::StructureGraph,rma::options%5Bnum_rows$eq%27all%27%5D%5Bcount$eqfalse%5D')
def test_structure_sets_list(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'structure_sets_list')
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::StructureSet,rma::options%5Bnum_rows$eq%27all%27%5D%5Bcount$eqfalse%5D')
def test_structures_by_graph_ids(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'structures_by_graph_ids',
graph_ids='1')
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,%5Bgraph_id$in1%5D,rma::options%5Bnum_rows$eq%27all%27%5D%5Border$eqstructures.graph_order%5D%5Bcount$eqfalse%5D')
def test_structures_by_two_graph_ids(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'structures_by_graph_ids',
graph_ids=[1, 2])
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,%5Bgraph_id$in1,2%5D,rma::options%5Bnum_rows$eq%27all%27%5D%5Border$eqstructures.graph_order%5D%5Bcount$eqfalse%5D')
def test_structures_by_graph_names(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'structures_by_graph_names',
graph_names=self.rma.quote_string('Human+Brain+Atlas'))
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,graph%5Bstructure_graphs.name$in%27Human+Brain+Atlas%27%5D,rma::options%5Bnum_rows$eq%27all%27%5D%5Border$eqstructures.graph_order%5D%5Bcount$eqfalse%5D')
def test_structures_by_set_ids(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'structures_by_graph_ids',
graph_ids='1')
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,%5Bgraph_id$in1%5D,rma::options%5Bnum_rows$eq%27all%27%5D%5Border$eqstructures.graph_order%5D%5Bcount$eqfalse%5D')
def test_atlases_table(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'atlases_table')
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::criteria,structure_graph%28ontology%29,graphic_group_labels,rma::include,%5Bstructure_graph%28ontology%29,graphic_group_labels,rma::options%5Bnum_rows$eq%27all%27%5D%5Bcount$eqfalse%5D')
def test_atlases_table_one_graph(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'atlases_table',
graph_ids=1)
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::criteria,%5Bgraph_id$in1%5D,structure_graph%28ontology%29,graphic_group_labels,rma::include,%5Bstructure_graph%28ontology%29,graphic_group_labels,rma::options%5Bnum_rows$eq%27all%27%5D%5Bcount$eqfalse%5D')
def test_atlases_table_brief(self):
ju.read_url_get = \
MagicMock(name='read_url_get',
return_value={ 'msg': [{ 'whatever': True }] })
self.rma.template_query('ontology_queries',
'atlases_table_brief')
ju.read_url_get.assert_called_once_with('http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::criteria,structure_graph%28ontology%29,graphic_group_labels,rma::include,structure_graph%28ontology%29,graphic_group_labels,rma::options%5Bonly$eq%27atlases.id,atlases.name,atlases.image_type,ontologies.id,ontologies.name,structure_graphs.id,structure_graphs.name,graphic_group_labels.id,graphic_group_labels.name%27%5D%5Bnum_rows$eq%27all%27%5D%5Bcount$eqfalse%5D')
def rma():
templates = \
{"ontology_queries": [
{'name': 'structures_by_graph_ids',
'description': 'see name',
'model': 'Structure',
'criteria': '[graph_id$in{{ graph_ids }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_ids']
},
{'name': 'structures_by_graph_names',
'description': 'see name',
'model': 'Structure',
'criteria': 'graph[structure_graphs.name$in{{ graph_names }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_names']
},
{'name': 'structures_by_set_ids',
'description': 'see name',
'model': 'Structure',
'criteria': '[structure_set_id$in{{ set_ids }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['set_ids']
},
{'name': 'structures_by_set_names',
'description': 'see name',
'model': 'Structure',
'criteria': 'structure_sets[name$in{{ set_names }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['set_names']
},
{'name': 'structure_graphs_list',
'description': 'see name',
'model': 'StructureGraph',
'num_rows': 'all',
'count': False
},
{'name': 'structure_sets_list',
'description': 'see name',
'model': 'StructureSet',
'num_rows': 'all',
'count': False
},
{'name': 'atlases_list',
'description': 'see name',
'model': 'Atlas',
'num_rows': 'all',
'count': False
},
{'name': 'atlases_table',
'description': 'see name',
'model': 'Atlas',
'criteria': '{% if graph_ids is defined %}[graph_id$in{{ graph_ids }}],{% endif %}structure_graph(ontology),graphic_group_labels',
'include': '[structure_graph(ontology),graphic_group_labels',
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_ids']
},
{'name': 'atlases_table_brief',
'description': 'see name',
'model': 'Atlas',
'criteria': 'structure_graph(ontology),graphic_group_labels',
'include': 'structure_graph(ontology),graphic_group_labels',
'only': ['atlases.id',
'atlases.name',
'atlases.image_type',
'ontologies.id',
'ontologies.name',
'structure_graphs.id',
'structure_graphs.name',
'graphic_group_labels.id',
'graphic_group_labels.name'],
'num_rows': 'all',
'count': False
}
]}
rma = RmaTemplate(query_manifest=templates)
return rma
def setUp(self):
self.templates = \
{"ontology_queries": [
{'name': 'structures_by_graph_ids',
'description': 'see name',
'model': 'Structure',
'criteria': '[graph_id$in{{ graph_ids }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_ids']
},
{'name': 'structures_by_graph_names',
'description': 'see name',
'model': 'Structure',
'criteria': 'graph[structure_graphs.name$in{{ graph_names }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_names']
},
{'name': 'structures_by_set_ids',
'description': 'see name',
'model': 'Structure',
'criteria': '[structure_set_id$in{{ set_ids }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['set_ids']
},
{'name': 'structures_by_set_names',
'description': 'see name',
'model': 'Structure',
'criteria': 'structure_sets[name$in{{ set_names }}]',
'order': ['structures.graph_order'],
'num_rows': 'all',
'count': False,
'criteria_params': ['set_names']
},
{'name': 'structure_graphs_list',
'description': 'see name',
'model': 'StructureGraph',
'num_rows': 'all',
'count': False
},
{'name': 'structure_sets_list',
'description': 'see name',
'model': 'StructureSet',
'num_rows': 'all',
'count': False
},
{'name': 'atlases_list',
'description': 'see name',
'model': 'Atlas',
'num_rows': 'all',
'count': False
},
{'name': 'atlases_table',
'description': 'see name',
'model': 'Atlas',
'criteria': '{% if graph_ids is defined %}[graph_id$in{{ graph_ids }}],{% endif %}structure_graph(ontology),graphic_group_labels',
'include': '[structure_graph(ontology),graphic_group_labels',
'num_rows': 'all',
'count': False,
'criteria_params': ['graph_ids']
},
{'name': 'atlases_table_brief',
'description': 'see name',
'model': 'Atlas',
'criteria': 'structure_graph(ontology),graphic_group_labels',
'include': 'structure_graph(ontology),graphic_group_labels',
'only': ['atlases.id',
'atlases.name',
'atlases.image_type',
'ontologies.id',
'ontologies.name',
'structure_graphs.id',
'structure_graphs.name',
'graphic_group_labels.id',
'graphic_group_labels.name'],
'num_rows': 'all',
'count': False
}
]}
self.rma = RmaTemplate(query_manifest=self.templates)