예제 #1
0
파일: test1.py 프로젝트: afcarl/cxio_python
    def test_x(self):
        n1 = ElementMaker.create_nodes_aspect_element(1, 'node 1', 'N1')
        n2 = ElementMaker.create_nodes_aspect_element(2, 'node 2', 'N2')
        e = ElementMaker.create_edges_aspect_element(3, 1, 2, '1->2')
        nea = ElementMaker.create_network_attributes_aspect_element(
            1200, 'size', 12.3, CxConstants.DATA_TYPE_DOUBLE)
        noa = ElementMaker.create_node_attributes_aspect_element(
            1200, 1, 'weight', '12.0', CxConstants.DATA_TYPE_DOUBLE)
        eda = ElementMaker.create_edge_attributes_aspect_element(
            1200, 3, 'length', 303.409883, CxConstants.DATA_TYPE_DOUBLE)
        neal = ElementMaker.create_network_attributes_aspect_element(
            1200, 'used', ['true', 'false'],
            CxConstants.DATA_TYPE_LIST_OF_BOOLEAN)
        noal = ElementMaker.create_node_attributes_aspect_element(
            1200, 1, 'weights', ['1.1', '2.2'],
            CxConstants.DATA_TYPE_LIST_OF_DOUBLE)
        edal = ElementMaker.create_edge_attributes_aspect_element(
            1200, 3, 'lengths', ['23.3', '13.34'],
            CxConstants.DATA_TYPE_LIST_OF_DOUBLE)

        ha = ElementMaker.create_hidden_attributes_aspect_element(
            1200, 'size', 12.3, CxConstants.DATA_TYPE_DOUBLE)
        hal = ElementMaker.create_hidden_attributes_aspect_element(
            1200, 'used', ['true', 'false'],
            CxConstants.DATA_TYPE_LIST_OF_BOOLEAN)

        c1 = ElementMaker.create_cartesian_layout_element(
            1, 2000, 100.11, 200.22, 3.33)
        c2 = ElementMaker.create_cartesian_layout_element(
            2, 2000, -100.11, -200.22)
        sn = ElementMaker.create_sub_networks_aspect_element(1200, [1, 2], [3])
        v = ElementMaker.create_views_aspect_element(2000, 1200)
        g = ElementMaker.create_groups_aspect_element(555, 1200, 'group 1',
                                                      [1, 2], [3], [3])
        nr1 = ElementMaker.create_network_relations_aspect_element(
            1200, 3000, 'subnetwork', 'child 1200')
        nr2 = ElementMaker.create_network_relations_aspect_element(
            2000, 1200, 'view', 'view 2000')
        tc = ElementMaker.create_table_column_aspect_element(
            1200, 'node table', 'weight', CxConstants.DATA_TYPE_INTEGER)

        properties = {
            "NODE_BORDER_PAINT": "#CCCCCC",
            "NODE_BORDER_STROKE": "SOLID",
            "NODE_BORDER_TRANSPARENCY": "255"
        }
        dependencies = {
            "nodeCustomGraphicsSizeSync": "true",
            "nodeSizeLocked": "false"
        }
        mappings = {
            "NODE_LABEL": {
                "type": "PASSTHROUGH",
                "definition": "COL=name,T=string"
            }
        }

        vp = ElementMaker.create_visual_properties_aspect_element(
            "nodes:default", 1, 1200, properties, dependencies, mappings)

        prmd = ElementMaker.create_pre_metadata_element(
            'nodes', 1, 'v2.2', 1234567, [], 2)
        pomd1 = ElementMaker.create_post_metadata_element('nodes', 2)
        pomd2 = ElementMaker.create_post_metadata_element('edges', 1)

        fo = io.StringIO('')

        w = CxWriter(fo)

        w.add_pre_meta_data([prmd])

        w.start()

        w.start_aspect_fragment(CxConstants.NODES)
        w.write_aspect_element(n1)
        w.write_aspect_element(n2)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.EDGES)
        w.write_aspect_element(e)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.CARTESIAN_LAYOUT)
        w.write_aspect_element(c1)
        w.write_aspect_element(c2)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.NETWORK_ATTRIBUTES)
        w.write_aspect_element(nea)
        w.write_aspect_element(neal)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.NODE_ATTRIBUTES)
        w.write_aspect_element(noa)
        w.write_aspect_element(noal)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.EDGE_ATTRIBUTES)
        w.write_aspect_element(eda)
        w.write_aspect_element(edal)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.HIDDEN_ATTRIBUTES)
        w.write_aspect_element(ha)
        w.write_aspect_element(hal)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.SUB_NETWORKS)
        w.write_aspect_element(sn)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.VIEWS)
        w.write_aspect_element(v)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.GROUPS)
        w.write_aspect_element(g)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.NETWORK_RELATIONS)
        w.write_aspect_element(nr1)
        w.write_aspect_element(nr2)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.TABLE_COLUMN)
        w.write_aspect_element(tc)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.VISUAL_PROPERTIES)
        w.write_aspect_element(vp)
        w.end_aspect_fragment()

        w.add_post_meta_data([pomd1, pomd2])

        w.end(True, "no error")

        json_str = fo.getvalue()
        print(json_str)

        # READING

        fi = io.StringIO(json_str)

        cx_reader = CxReader(fi)

        self.assertEquals(len(cx_reader.get_pre_meta_data()), 1)

        cx = cx_reader.parse_as_dictionary()

        self.assertEquals(cx_reader.get_error_msg(), "no error")
        self.assertEquals(cx_reader.get_is_success(), True)

        self.assertEquals(len(cx_reader.get_post_meta_data()), 2)

        self.assertEquals(len(cx[CxConstants.NODES]), 2)
        self.assertEquals(len(cx[CxConstants.EDGES]), 1)
        self.assertEquals(len(cx[CxConstants.CARTESIAN_LAYOUT]), 2)
        self.assertEquals(len(cx[CxConstants.NODE_ATTRIBUTES]), 2)
        self.assertEquals(len(cx[CxConstants.EDGE_ATTRIBUTES]), 2)
        self.assertEquals(len(cx[CxConstants.NETWORK_ATTRIBUTES]), 2)
        self.assertEquals(len(cx[CxConstants.HIDDEN_ATTRIBUTES]), 2)
        self.assertEquals(len(cx[CxConstants.SUB_NETWORKS]), 1)
        self.assertEquals(len(cx[CxConstants.VIEWS]), 1)
        self.assertEquals(len(cx[CxConstants.GROUPS]), 1)
        self.assertEquals(len(cx[CxConstants.NETWORK_RELATIONS]), 2)
        self.assertEquals(len(cx[CxConstants.TABLE_COLUMN]), 1)
        self.assertEquals(len(cx[CxConstants.VISUAL_PROPERTIES]), 1)

        sn2 = cx[CxConstants.SUB_NETWORKS][0]
        self.assertEquals(sn2.get_name(), CxConstants.SUB_NETWORKS)
        d = sn2.get_data()
        self.assertEquals(d['@id'], 1200)
        self.assertEquals(d['nodes'][0], 1)
        self.assertEquals(d['nodes'][1], 2)
        self.assertEquals(d['edges'][0], 3)

        v2 = cx[CxConstants.VIEWS][0]
        self.assertEquals(v2.get_name(), CxConstants.VIEWS)
        d = v2.get_data()
        self.assertEquals(d['@id'], 2000)
        self.assertEquals(d['s'], 1200)

        g2 = cx[CxConstants.GROUPS][0]
        self.assertEquals(g2.get_name(), CxConstants.GROUPS)
        d = g2.get_data()
        self.assertEquals(d['@id'], 555)
        self.assertEquals(d['name'], 'group 1')
        self.assertEquals(d['view'], 1200)
        self.assertEquals(len(d['internal_edges']), 1)
        self.assertEquals(len(d['external_edges']), 1)
        self.assertEquals(len(d['nodes']), 2)
        self.assertEquals(d['internal_edges'][0], 3)
        self.assertEquals(d['nodes'][0], 1)
        self.assertEquals(d['nodes'][1], 2)

        nr2 = cx[CxConstants.NETWORK_RELATIONS][0]
        self.assertEquals(nr2.get_name(), CxConstants.NETWORK_RELATIONS)
        d = nr2.get_data()
        self.assertEquals(d['c'], 1200)
        self.assertEquals(d['p'], 3000)
        self.assertEquals(d['r'], 'subnetwork')
        self.assertEquals(d['name'], 'child 1200')
예제 #2
0
    print(e)

print()
print()

# WRITING
# -------

# Writing to a string pretending to be a file/stream
fo = io.StringIO("")

# Creating a CX writer
w = CxWriter(fo)

# Adding pre meta data
w.add_pre_meta_data(cx_reader.get_pre_meta_data())

# Starting the json list
w.start()

# Writing various aspects

CxUtil.write_aspect_fragment(w, cx[CxConstants.NODES])

CxUtil.write_aspect_fragment(w, cx[CxConstants.EDGES])

CxUtil.write_aspect_fragment(w, cx[CxConstants.CARTESIAN_LAYOUT])

CxUtil.write_aspect_fragment(w, cx[CxConstants.EDGE_ATTRIBUTES])

# Adding post meta data
예제 #3
0
class NdexCXHelper:
    def __init__(self, output_stream):
        self.__contexts = {}
        self.__citation_id_counter = 0
        self.__support_id_counter = 0
        self.__edge_id_counter = 0
        self.__node_id_counter = 0
        self.__update_time = -1
        self.__current_name = None
        self.__cx_writer = CxWriter(output_stream)
        self.__aspect_names = ["@context", CxConstants.NODES, CxConstants.EDGES, CxConstants.NETWORK_ATTRIBUTES,
                               CxConstants.NODE_ATTRIBUTES, CxConstants.EDGE_ATTRIBUTES, CxConstants.CARTESIAN_LAYOUT,
                               "citations", "nodeCitations", "edgeCitations",
                               "nodeSupports", "edgeSupports", "provenanceHistory", "supports"]

    def get_cx_writer(self):
        return self.__cx_writer

    def start(self):
        self.__current_name = None
        self.__update_time = int(round(time.time() * 1000))
        self.__add_pre_metadata()
        self.__cx_writer.start()

    def end(self, success=True, error_msg=''):
        if self.__current_name is not None:
            self.__cx_writer.end_aspect_fragment()
        self.__current_name = None
        self.__add_post_metadata()
        self.__cx_writer.end(success, error_msg)

    def add_cx_context(self, prefix, uri):
        self.__contexts[prefix] = uri

    def emit_cx_context(self):
        self.__cx_writer.write_single_aspect_fragment(
            ElementMaker.create_ndex_context_element(self.__contexts))
        self.__current_name = None

    def emit_cx_node(self, node_name):
        self.__node_id_counter += 1
        self.__process_element(ElementMaker.create_nodes_aspect_element(
            self.__node_id_counter, node_name))
        return self.__node_id_counter

    def emit_cx_edge(self, source_id, target_id, interaction):
        self.__edge_id_counter += 1
        self.__process_element(
            ElementMaker.create_edges_aspect_element(self.__edge_id_counter, source_id,
                                                     target_id, interaction))
        return self.__edge_id_counter

    def emit_cx_node_attribute(self, node_id, name, value, data_type=None):
        self.__process_element(
            ElementMaker.create_node_attributes_aspect_element(None, node_id, name, value, data_type))

    def emit_cx_edge_attribute(self, edge_id, name, value, data_type=None):
        self.__process_element(
            ElementMaker.create_edge_attributes_aspect_element(None, edge_id, name, value, data_type))

    def emit_cx_network_attribute(self, sub_network_id, name, value, data_type=None):
        self.__process_element(
            ElementMaker.create_network_attributes_aspect_element(sub_network_id, name, value, data_type))

    def emit_cx_hidden_attribute(self, sub_network_id, name, value, data_type=None):
        self.__process_element(
            ElementMaker.create_hidden_attributes_aspect_element(sub_network_id, name, value, data_type))

    def emit_cx_cartesian_layout_element(self, node_id, view_id, x, y, z=None):
        self.__process_element(
            ElementMaker.create_cartesian_layout_element(node_id, view_id, x, y, z))

    def emit_cx_sub_networks(self, sub_network_id, node_ids, edge_ids):
        self.__process_element(
            ElementMaker.create_sub_networks_aspect_element(sub_network_id, node_ids, edge_ids))

    def emit_cx_views(self, view_id, sub_network_id):
        self.__process_element(
            ElementMaker.create_views_aspect_element(view_id, sub_network_id))

    def emit_cx_visual_properties(self, properties_of, applies_to, view, properties, dependencies=None,
                                  mappings=None):
        self.__process_element(
            ElementMaker.create_visual_properties_aspect_element(properties_of, applies_to, view, properties,
                                                                 dependencies,
                                                                 mappings))

    def emit_cx_table_column(self, sub_network, applies_to, name, data_type):
        self.__process_element(
            ElementMaker.create_table_column_aspect_element(sub_network, applies_to, name, data_type))

    def emit_cx_network_relations(self, child, parent, relationship=None, name=None):
        self.__process_element(ElementMaker.create_network_relations_aspect_element(child, parent, relationship, name))

    def emit_cx_groups(self, group_id, view_id, name, nodes, external_edges, internal_edges):
        self.__process_element(ElementMaker.create_groups_aspect_element(group_id,
                                                                         view_id, name, nodes,
                                                                         external_edges, internal_edges))

    def emit_cx_citation(self, citation_type, title, contributors, identifier, description):
        self.__citation_id_counter += 1
        self.__process_element(
            ElementMaker.create_ndex_citation_aspect_element(self.__citation_id_counter, citation_type, title,
                                                             contributors, identifier, description))
        return self.__citation_id_counter

    def emit_cx_support(self, cx_citation_id, text):
        self.__support_id_counter += 1
        self.__process_element(
            ElementMaker.create_ndex_support_aspect_element(self.__support_id_counter, cx_citation_id, text))
        return self.__support_id_counter

    def emit_cx_function_term(self, function_term):
        self.__process_element(ElementMaker.create_ndex_function_term_aspect_element(function_term))

    def emit_cx_node_citation(self, node_id, citation_id):
        self.__process_element(ElementMaker.create_ndex_node_citation_aspect_element(node_id, citation_id))

    def emit_cx_edge_citation(self, edge_id, citation_id):
        self.__process_element(ElementMaker.create_ndex_edge_citation_aspect_element(edge_id, citation_id))

    def emit_cx_node_support(self, node_id, support_id):
        self.__process_element(ElementMaker.create_ndex_node_support_aspect_element(node_id, support_id))

    def emit_cx_edge_support(self, edge_id, support_id):
        self.__process_element(ElementMaker.create_ndex_edge_support_aspect_element(edge_id, support_id))

    def __add_pre_metadata(self):
        pre_meta_data = []
        for aspect_name in self.__aspect_names:
            pre_meta_data.append(ElementMaker.create_pre_metadata_element(aspect_name, 1, '1.0', self.__update_time,
                                                                          [], 1))
        self.__cx_writer.add_pre_meta_data(pre_meta_data)

    def __add_post_metadata(self):
        post_meta_data = [
            ElementMaker.create_post_metadata_element('nodes', self.__node_id_counter),
            ElementMaker.create_post_metadata_element('edges', self.__edge_id_counter),
            ElementMaker.create_post_metadata_element('supports', self.__support_id_counter),
            ElementMaker.create_post_metadata_element('citations', self.__citation_id_counter)
        ]
        self.__cx_writer.add_post_meta_data(post_meta_data)

    def __process_element(self, element):
        aspect_name = element.get_name()
        if self.__current_name is None:
            self.__cx_writer.start_aspect_fragment(aspect_name)
        elif self.__current_name != aspect_name:
            self.__cx_writer.end_aspect_fragment()
            self.__cx_writer.start_aspect_fragment(aspect_name)
        self.__current_name = aspect_name
        self.__cx_writer.write_aspect_element(element)
예제 #4
0
            if n2 not in nn_id:
                nn_id[n2] = node_count
                id_nn[node_count] = n2
                node_count += 1
            edges.append(ElementMaker.create_edges_aspect_element(edge_count, nn_id[n1], nn_id[n2], interaction))
            edge_count += 1

# Writing CX:
w = CxWriter(fo)

w.set_pretty_formatting(True)

id_count = node_count + edge_count + 1

w.add_pre_meta_data(ElementMaker.create_pre_metadata_element(CxConstants.NODES, ASPECT_CONSISTENCY_GROUP,
                                                             ASPECT_VERSION, UPDATE_TIME, [], id_count,
                                                             len(id_nn)))
w.add_pre_meta_data(ElementMaker.create_pre_metadata_element(CxConstants.EDGES, ASPECT_CONSISTENCY_GROUP,
                                                             ASPECT_VERSION, UPDATE_TIME, [], id_count,
                                                             len(edges)))

w.start()
w.start_aspect_fragment(CxConstants.NODES)
for node_id, nn in id_nn.items():
    w.write_aspect_element(ElementMaker.create_nodes_aspect_element(node_id, nn))
w.end_aspect_fragment()
w.write_aspect_fragment(edges)
w.end()

print('Aspect elements written: ')
for name, count in w.get_aspect_element_counts().items():
예제 #5
0
    def test_x(self):
        n1 = ElementMaker.create_nodes_aspect_element(1, 'node 1', 'N1')
        n2 = ElementMaker.create_nodes_aspect_element(2, 'node 2', 'N2')
        e = ElementMaker.create_edges_aspect_element(3, 1, 2, '1->2')
        nea = ElementMaker.create_network_attributes_aspect_element(1200, 'size', 12.3, CxConstants.DATA_TYPE_DOUBLE)
        noa = ElementMaker.create_node_attributes_aspect_element(1200, 1, 'weight', '12.0',
                                                                 CxConstants.DATA_TYPE_DOUBLE)
        eda = ElementMaker.create_edge_attributes_aspect_element(1200, 3, 'length', 303.409883,
                                                                 CxConstants.DATA_TYPE_DOUBLE)
        neal = ElementMaker.create_network_attributes_aspect_element(1200, 'used', ['true', 'false'],
                                                                     CxConstants.DATA_TYPE_LIST_OF_BOOLEAN)
        noal = ElementMaker.create_node_attributes_aspect_element(1200, 1, 'weights', ['1.1', '2.2'],
                                                                  CxConstants.DATA_TYPE_LIST_OF_DOUBLE)
        edal = ElementMaker.create_edge_attributes_aspect_element(1200, 3, 'lengths', ['23.3', '13.34'],
                                                                  CxConstants.DATA_TYPE_LIST_OF_DOUBLE)

        ha = ElementMaker.create_hidden_attributes_aspect_element(1200, 'size', 12.3, CxConstants.DATA_TYPE_DOUBLE)
        hal = ElementMaker.create_hidden_attributes_aspect_element(1200, 'used', ['true', 'false'],
                                                                   CxConstants.DATA_TYPE_LIST_OF_BOOLEAN)

        c1 = ElementMaker.create_cartesian_layout_element(1, 2000, 100.11, 200.22, 3.33)
        c2 = ElementMaker.create_cartesian_layout_element(2, 2000, -100.11, -200.22)
        sn = ElementMaker.create_sub_networks_aspect_element(1200, [1, 2], [3])
        v = ElementMaker.create_views_aspect_element(2000, 1200)
        g = ElementMaker.create_groups_aspect_element(555, 1200, 'group 1', [1, 2], [3], [3])
        nr1 = ElementMaker.create_network_relations_aspect_element(1200, 3000, 'subnetwork', 'child 1200')
        nr2 = ElementMaker.create_network_relations_aspect_element(2000, 1200, 'view', 'view 2000')
        tc = ElementMaker.create_table_column_aspect_element(1200, 'node table', 'weight',
                                                             CxConstants.DATA_TYPE_INTEGER)

        properties = {"NODE_BORDER_PAINT": "#CCCCCC",
                      "NODE_BORDER_STROKE": "SOLID",
                      "NODE_BORDER_TRANSPARENCY": "255"}
        dependencies = {"nodeCustomGraphicsSizeSync": "true",
                        "nodeSizeLocked": "false"}
        mappings = {"NODE_LABEL": {
            "type": "PASSTHROUGH",
            "definition": "COL=name,T=string"}}

        vp = ElementMaker.create_visual_properties_aspect_element("nodes:default", 1, 1200, properties, dependencies,
                                                                  mappings)

        prmd = ElementMaker.create_pre_metadata_element('nodes', 1, 'v2.2', 1234567, [], 2)
        pomd1 = ElementMaker.create_post_metadata_element('nodes', 2)
        pomd2 = ElementMaker.create_post_metadata_element('edges', 1)

        fo = io.StringIO('')

        w = CxWriter(fo)

        w.add_pre_meta_data([prmd])

        w.start()

        w.start_aspect_fragment(CxConstants.NODES)
        w.write_aspect_element(n1)
        w.write_aspect_element(n2)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.EDGES)
        w.write_aspect_element(e)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.CARTESIAN_LAYOUT)
        w.write_aspect_element(c1)
        w.write_aspect_element(c2)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.NETWORK_ATTRIBUTES)
        w.write_aspect_element(nea)
        w.write_aspect_element(neal)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.NODE_ATTRIBUTES)
        w.write_aspect_element(noa)
        w.write_aspect_element(noal)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.EDGE_ATTRIBUTES)
        w.write_aspect_element(eda)
        w.write_aspect_element(edal)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.HIDDEN_ATTRIBUTES)
        w.write_aspect_element(ha)
        w.write_aspect_element(hal)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.SUB_NETWORKS)
        w.write_aspect_element(sn)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.VIEWS)
        w.write_aspect_element(v)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.GROUPS)
        w.write_aspect_element(g)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.NETWORK_RELATIONS)
        w.write_aspect_element(nr1)
        w.write_aspect_element(nr2)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.TABLE_COLUMN)
        w.write_aspect_element(tc)
        w.end_aspect_fragment()

        w.start_aspect_fragment(CxConstants.VISUAL_PROPERTIES)
        w.write_aspect_element(vp)
        w.end_aspect_fragment()

        w.add_post_meta_data([pomd1, pomd2])

        w.end(True, "no error")

        json_str = fo.getvalue()
        print(json_str)

        # READING

        fi = io.StringIO(json_str)

        cx_reader = CxReader(fi)

        self.assertEquals(len(cx_reader.get_pre_meta_data()), 1)

        cx = cx_reader.parse_as_dictionary()

        self.assertEquals(cx_reader.get_error_msg(), "no error")
        self.assertEquals(cx_reader.get_is_success(), True)

        self.assertEquals(len(cx_reader.get_post_meta_data()), 2)

        self.assertEquals(len(cx[CxConstants.NODES]), 2)
        self.assertEquals(len(cx[CxConstants.EDGES]), 1)
        self.assertEquals(len(cx[CxConstants.CARTESIAN_LAYOUT]), 2)
        self.assertEquals(len(cx[CxConstants.NODE_ATTRIBUTES]), 2)
        self.assertEquals(len(cx[CxConstants.EDGE_ATTRIBUTES]), 2)
        self.assertEquals(len(cx[CxConstants.NETWORK_ATTRIBUTES]), 2)
        self.assertEquals(len(cx[CxConstants.HIDDEN_ATTRIBUTES]), 2)
        self.assertEquals(len(cx[CxConstants.SUB_NETWORKS]), 1)
        self.assertEquals(len(cx[CxConstants.VIEWS]), 1)
        self.assertEquals(len(cx[CxConstants.GROUPS]), 1)
        self.assertEquals(len(cx[CxConstants.NETWORK_RELATIONS]), 2)
        self.assertEquals(len(cx[CxConstants.TABLE_COLUMN]), 1)
        self.assertEquals(len(cx[CxConstants.VISUAL_PROPERTIES]), 1)

        sn2 = cx[CxConstants.SUB_NETWORKS][0]
        self.assertEquals(sn2.get_name(), CxConstants.SUB_NETWORKS)
        d = sn2.get_data()
        self.assertEquals(d['@id'], 1200)
        self.assertEquals(d['nodes'][0], 1)
        self.assertEquals(d['nodes'][1], 2)
        self.assertEquals(d['edges'][0], 3)

        v2 = cx[CxConstants.VIEWS][0]
        self.assertEquals(v2.get_name(), CxConstants.VIEWS)
        d = v2.get_data()
        self.assertEquals(d['@id'], 2000)
        self.assertEquals(d['s'], 1200)

        g2 = cx[CxConstants.GROUPS][0]
        self.assertEquals(g2.get_name(), CxConstants.GROUPS)
        d = g2.get_data()
        self.assertEquals(d['@id'], 555)
        self.assertEquals(d['name'], 'group 1')
        self.assertEquals(d['view'], 1200)
        self.assertEquals(len(d['internal_edges']), 1)
        self.assertEquals(len(d['external_edges']), 1)
        self.assertEquals(len(d['nodes']), 2)
        self.assertEquals(d['internal_edges'][0], 3)
        self.assertEquals(d['nodes'][0], 1)
        self.assertEquals(d['nodes'][1], 2)

        nr2 = cx[CxConstants.NETWORK_RELATIONS][0]
        self.assertEquals(nr2.get_name(), CxConstants.NETWORK_RELATIONS)
        d = nr2.get_data()
        self.assertEquals(d['c'], 1200)
        self.assertEquals(d['p'], 3000)
        self.assertEquals(d['r'], 'subnetwork')
        self.assertEquals(d['name'], 'child 1200')
예제 #6
0
파일: cx2cx.py 프로젝트: afcarl/cxio_python
fi = open(fi_name, 'r')
fo = open(fo_name, 'w')

print('Infile : ' + str(fi.name))
print('Outfile: ' + str(fo.name))
print()

r = CxReader(fi)

cx = r.parse_as_dictionary()

w = CxWriter(fo)

w.set_pretty_formatting(True)

w.add_pre_meta_data(r.get_pre_meta_data())
w.add_post_meta_data(r.get_post_meta_data())

w.start()
for name, fragment in cx.items():
    w.write_aspect_fragment(fragment)
w.end()

print('Aspect elements written: ')
for name, count in w.get_aspect_element_counts().items():
    print(name + ': ' + str(count))

print()
print('OK')

예제 #7
0
                node_count += 1
            edges.append(
                ElementMaker.create_edges_aspect_element(
                    edge_count, nn_id[n1], nn_id[n2], interaction))
            edge_count += 1

# Writing CX:
w = CxWriter(fo)

w.set_pretty_formatting(True)

id_count = node_count + edge_count + 1

w.add_pre_meta_data(
    ElementMaker.create_pre_metadata_element(CxConstants.NODES,
                                             ASPECT_CONSISTENCY_GROUP,
                                             ASPECT_VERSION, UPDATE_TIME, [],
                                             id_count, len(id_nn)))
w.add_pre_meta_data(
    ElementMaker.create_pre_metadata_element(CxConstants.EDGES,
                                             ASPECT_CONSISTENCY_GROUP,
                                             ASPECT_VERSION, UPDATE_TIME, [],
                                             id_count, len(edges)))

w.start()
w.start_aspect_fragment(CxConstants.NODES)
for node_id, nn in id_nn.items():
    w.write_aspect_element(
        ElementMaker.create_nodes_aspect_element(node_id, nn))
w.end_aspect_fragment()
w.write_aspect_fragment(edges)
예제 #8
0
class NdexCXHelper:
    def __init__(self, output_stream):
        self.__contexts = {}
        self.__citation_id_counter = 0
        self.__support_id_counter = 0
        self.__edge_id_counter = 0
        self.__node_id_counter = 0
        self.__update_time = -1
        self.__current_name = None
        self.__cx_writer = CxWriter(output_stream)
        self.__aspect_names = [
            "@context", CxConstants.NODES, CxConstants.EDGES,
            CxConstants.NETWORK_ATTRIBUTES, CxConstants.NODE_ATTRIBUTES,
            CxConstants.EDGE_ATTRIBUTES, CxConstants.CARTESIAN_LAYOUT,
            "citations", "nodeCitations", "edgeCitations", "nodeSupports",
            "edgeSupports", "provenanceHistory", "supports"
        ]

    def get_cx_writer(self):
        return self.__cx_writer

    def start(self):
        self.__current_name = None
        self.__update_time = int(round(time.time() * 1000))
        self.__add_pre_metadata()
        self.__cx_writer.start()

    def end(self, success=True, error_msg=''):
        if self.__current_name is not None:
            self.__cx_writer.end_aspect_fragment()
        self.__current_name = None
        self.__add_post_metadata()
        self.__cx_writer.end(success, error_msg)

    def add_cx_context(self, prefix, uri):
        self.__contexts[prefix] = uri

    def emit_cx_context(self):
        self.__cx_writer.write_single_aspect_fragment(
            ElementMaker.create_ndex_context_element(self.__contexts))
        self.__current_name = None

    def emit_cx_node(self, node_name):
        self.__node_id_counter += 1
        self.__process_element(
            ElementMaker.create_nodes_aspect_element(self.__node_id_counter,
                                                     node_name))
        return self.__node_id_counter

    def emit_cx_edge(self, source_id, target_id, interaction):
        self.__edge_id_counter += 1
        self.__process_element(
            ElementMaker.create_edges_aspect_element(self.__edge_id_counter,
                                                     source_id, target_id,
                                                     interaction))
        return self.__edge_id_counter

    def emit_cx_node_attribute(self, node_id, name, value, data_type=None):
        self.__process_element(
            ElementMaker.create_node_attributes_aspect_element(
                None, node_id, name, value, data_type))

    def emit_cx_edge_attribute(self, edge_id, name, value, data_type=None):
        self.__process_element(
            ElementMaker.create_edge_attributes_aspect_element(
                None, edge_id, name, value, data_type))

    def emit_cx_network_attribute(self,
                                  sub_network_id,
                                  name,
                                  value,
                                  data_type=None):
        self.__process_element(
            ElementMaker.create_network_attributes_aspect_element(
                sub_network_id, name, value, data_type))

    def emit_cx_hidden_attribute(self,
                                 sub_network_id,
                                 name,
                                 value,
                                 data_type=None):
        self.__process_element(
            ElementMaker.create_hidden_attributes_aspect_element(
                sub_network_id, name, value, data_type))

    def emit_cx_cartesian_layout_element(self, node_id, view_id, x, y, z=None):
        self.__process_element(
            ElementMaker.create_cartesian_layout_element(
                node_id, view_id, x, y, z))

    def emit_cx_sub_networks(self, sub_network_id, node_ids, edge_ids):
        self.__process_element(
            ElementMaker.create_sub_networks_aspect_element(
                sub_network_id, node_ids, edge_ids))

    def emit_cx_views(self, view_id, sub_network_id):
        self.__process_element(
            ElementMaker.create_views_aspect_element(view_id, sub_network_id))

    def emit_cx_visual_properties(self,
                                  properties_of,
                                  applies_to,
                                  view,
                                  properties,
                                  dependencies=None,
                                  mappings=None):
        self.__process_element(
            ElementMaker.create_visual_properties_aspect_element(
                properties_of, applies_to, view, properties, dependencies,
                mappings))

    def emit_cx_table_column(self, sub_network, applies_to, name, data_type):
        self.__process_element(
            ElementMaker.create_table_column_aspect_element(
                sub_network, applies_to, name, data_type))

    def emit_cx_network_relations(self,
                                  child,
                                  parent,
                                  relationship=None,
                                  name=None):
        self.__process_element(
            ElementMaker.create_network_relations_aspect_element(
                child, parent, relationship, name))

    def emit_cx_groups(self, group_id, view_id, name, nodes, external_edges,
                       internal_edges):
        self.__process_element(
            ElementMaker.create_groups_aspect_element(group_id, view_id, name,
                                                      nodes, external_edges,
                                                      internal_edges))

    def emit_cx_citation(self, citation_type, title, contributors, identifier,
                         description):
        self.__citation_id_counter += 1
        self.__process_element(
            ElementMaker.create_ndex_citation_aspect_element(
                self.__citation_id_counter, citation_type, title, contributors,
                identifier, description))
        return self.__citation_id_counter

    def emit_cx_support(self, cx_citation_id, text):
        self.__support_id_counter += 1
        self.__process_element(
            ElementMaker.create_ndex_support_aspect_element(
                self.__support_id_counter, cx_citation_id, text))
        return self.__support_id_counter

    def emit_cx_function_term(self, function_term):
        self.__process_element(
            ElementMaker.create_ndex_function_term_aspect_element(
                function_term))

    def emit_cx_node_citation(self, node_id, citation_id):
        self.__process_element(
            ElementMaker.create_ndex_node_citation_aspect_element(
                node_id, citation_id))

    def emit_cx_edge_citation(self, edge_id, citation_id):
        self.__process_element(
            ElementMaker.create_ndex_edge_citation_aspect_element(
                edge_id, citation_id))

    def emit_cx_node_support(self, node_id, support_id):
        self.__process_element(
            ElementMaker.create_ndex_node_support_aspect_element(
                node_id, support_id))

    def emit_cx_edge_support(self, edge_id, support_id):
        self.__process_element(
            ElementMaker.create_ndex_edge_support_aspect_element(
                edge_id, support_id))

    def __add_pre_metadata(self):
        pre_meta_data = []
        for aspect_name in self.__aspect_names:
            pre_meta_data.append(
                ElementMaker.create_pre_metadata_element(
                    aspect_name, 1, '1.0', self.__update_time, [], 1))
        self.__cx_writer.add_pre_meta_data(pre_meta_data)

    def __add_post_metadata(self):
        post_meta_data = [
            ElementMaker.create_post_metadata_element('nodes',
                                                      self.__node_id_counter),
            ElementMaker.create_post_metadata_element('edges',
                                                      self.__edge_id_counter),
            ElementMaker.create_post_metadata_element(
                'supports', self.__support_id_counter),
            ElementMaker.create_post_metadata_element(
                'citations', self.__citation_id_counter)
        ]
        self.__cx_writer.add_post_meta_data(post_meta_data)

    def __process_element(self, element):
        aspect_name = element.get_name()
        if self.__current_name is None:
            self.__cx_writer.start_aspect_fragment(aspect_name)
        elif self.__current_name != aspect_name:
            self.__cx_writer.end_aspect_fragment()
            self.__cx_writer.start_aspect_fragment(aspect_name)
        self.__current_name = aspect_name
        self.__cx_writer.write_aspect_element(element)