def test_format_import(self):
"""
Test import of format
"""
graph = read_web(self.web_file, auto_parse_format=False)
# Default graph attributes set
self.assertEqual(len(graph), 694)
self.assertEqual(len(graph.edges), 1386)
self.assertEqual(graph.directed, False)
self.assertEqual(graph_directionality(graph), 'undirectional')
self.assertEqual(graph.root, 1)
self.assertTrue(isinstance(graph, GraphAxis))
# No ORM or format auto detect set, all values should be strings
self.assertTrue(
isinstance(graph.query_nodes({
'key': 'ntrials'
}).value, PY_STRING))
self.assertTrue(
isinstance(
graph.query_nodes({
'key': 'rotate180_0'
}).value, PY_STRING))
for node in graph.query_nodes({'key': 'activereslist'}):
self.assertTrue(isinstance(node.value, list))
for node in graph.query_nodes({'type': 'FloatArray'}):
self.assertTrue(all([isinstance(n, str) for n in node.get()]))
def setUp(self):
"""
Haddock test class setup
Load a .web file for each test
"""
self.web = GraphAxis()
self.web.node_tools = NodeAxisTools
self.web = read_web(self.webfile, graph=self.web)
self.web.orm = haddock_orm
def test_format_export(self):
"""
Test export of format
"""
graph = read_web(self.web_file)
# Export graph as .web to file
web = write_web(graph)
outfile = os.path.join(FILEPATH, 'test_export.web')
with open(outfile, 'w') as otf:
otf.write(web)
self.tempfiles.append(outfile)
self.assertTrue(os.path.isfile(outfile))
# Import again and compare source graph
graph1 = read_web(outfile)
self.assertEqual(len(graph), len(graph1))
self.assertEqual(len(graph.edges), len(graph1.edges))
def test_format_import_orm(self):
"""
Test import of format with custom ORM classes
"""
web = GraphAxis()
web.orm.node_mapping.add(FloatArray,
lambda x: x.get('type') == 'FloatArray')
web = read_web(self.web_file, graph=web)
for node in web.query_nodes({'type': 'FloatArray'}):
self.assertTrue(all([isinstance(n, str) for n in node.get()]))
def test_xmlrpc_get_params(self):
"""
Test 'getProjectParams' endpoint method.
Try loading into Graph for the first two projects only
"""
for project in self.xmlrpc.list_projects()[:2]:
web = self.xmlrpc.get_params(project)
webfile = os.path.join(self.filedir, '{0}.web'.format(project))
with open(webfile, 'w') as wb:
wb.write(web)
self.tempfiles.append(webfile)
model = read_web(web)
model.node_tools = NodeAxisTools
self.assertTrue(os.path.isfile(webfile))
self.assertFalse(model.empty())
def test_format_import_autoformatparse(self):
"""
Test import of format with automatic parsing of data types (default)
"""
graph = read_web(self.web_file)
self.assertTrue(
isinstance(graph.query_nodes({
'key': 'ntrials'
}).value, int))
self.assertTrue(
isinstance(graph.query_nodes({
'key': 'rotate180_0'
}).value, bool))
for node in graph.query_nodes({'key': 'activereslist'}):
self.assertTrue(isinstance(node.value, list))
for node in graph.query_nodes({'type': 'FloatArray'}):
self.assertTrue(all([isinstance(n, float) for n in node.get()]))
import logging
import pkg_resources
from graphit.graph_io.io_web_format import read_web, write_web
from graphit.graph_axis.graph_axis_mixin import NodeAxisTools
from mdstudio_haddock.haddock_model import (edit_parameter_block,
new_parameter_block, new_project)
from mdstudio_haddock.haddock_model_classes import haddock_orm
logging.basicConfig(level=logging.INFO)
currpath = os.path.dirname(__file__)
schemadir = pkg_resources.resource_filename('mdstudio_haddock',
'/schemas/endpoints')
project = read_web('test_project.web')
project.orm = haddock_orm
project.node_tools = NodeAxisTools
project = new_project('mdstudio')
# Add first partner
partner1 = {
'pdb': {
'mode': 'submit',
'chain': 'A',
'code': None,
'pdbdata': open('1ckaA.pdb').read()
},
'r': {
'auto_passive':
