odML to graphML converter.

[msuzen]

graphML link is used in graphics community a lot. Here is a simple conversion code that can be used in odML. This would be helpful for importing odML to graph databases natively. Here is an example conversion that can be used as a basic starting point.

"""

 odml2graphml

 Basic odML to graphML converter

 (c) 2017 German Neuroinformatics Node (G-Node)

"""

import xml.etree.ElementTree as ET
from pygraphml import Graph
from pygraphml import GraphMLParser
import uuid

# Files
base_name     = 'rg_dummy'
odml_fname    = base_name + '.odml'
graphml_fname = base_name + '.graphml'

# Read odml
tree = ET.parse(odml_fname)
root = tree.getroot()

odml_graph            = Graph()
child_id              = 0
is_terminal_node_prev = False
prev_uuid_value       = 0
prev_node             = 0
is_odml_rel_node      = 0
prev_tag              = 'odML
for elem in tree.iter(): # iter over elements
    is_terminal_node = elem.getchildren() == []
    is_odml_tag      = elem.tag in ['section', 'odML', 'property']
    if(is_odml_tag):
        uuid_value          = str(uuid.uuid4()) # generate UUID for an element
        node                = odml_graph.add_node(uuid_value)
        node["odml_entity"] = elem.tag
        node["uuid"]        = uuid_value
        child_id            = 1
        is_odml_rel_node    = 0
        if(elem.tag == "odML"):
           odml_node = node
    else:
        node[elem.tag]        = elem.text
        node["labels"]        = ":reach2Grasp"
        is_terminal_node_prev = is_terminal_node
    if(is_odml_rel_node < 1 and child_id > 0 and is_odml_tag == True and prev_tag in ['section', 'property']):
       edge = odml_graph.add_edge(prev_node, node, directed=True)
       edge = odml_graph.add_edge(odml_node, node, directed=True)
       edge['relation'] = 'child'
    if(elem.tag in ['section', 'odML']):
       is_odml_rel_node   = 1
       prev_node          = node
       prev_uuid_value    = uuid_value
       prev_tag           = elem.tag
parser = GraphMLParser()
parser.write(odml_graph, graphml_fname)