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libgroups.py
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libgroups.py
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#
# Extension of specgen6 producing automatic groups of concepts of the ontology
#
# It uses the igraph library (http://igraph.sourceforge.net/) and so the python interface for igraph is needed.
#
# It uses the walktrap community algorithm
# Some weighting of the graph is implemented, that distinguish between the different types of edges, also a hierarchical weighting
# of the rdfs:subClassOf Edges is used. That means the weight of subClassOf Edges gets higher, the deeper its relative position is.
# Also some kind of scoring the count and size of group is implemented. "Good groupings" for human readers are one that have about 4 groups
# and not more than 9 concepts per group.
# For bigger ontologies some kind of filtering or other measures have to be implemented.
#
#
# Usage: just add --groups parameter behind the starting command to enable the grouping
# An Template with that uses groups and and css that created a nice laylout is required.
# A base template can be found in the "template" folder.
#
# Copyright 2012 Mario Rothe mario.rothe@gmail.com
# It is permited to do whatever you want with this code. So copy, edit, extend and use it as you like.
#
from collections import Counter
from igraph import *
from libvocab import Vocab;
import rdflib
from rdflib.namespace import Namespace
from rdflib.term import BNode
from igraph import Graph
RDF = Namespace("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
RDFS = Namespace('http://www.w3.org/2000/01/rdf-schema#')
OWL = Namespace('http://www.w3.org/2002/07/owl#')
NSBLACKLIST = ["http://www.w3.org/1999/02/22-rdf-syntax-ns#",
'http://www.w3.org/2000/01/rdf-schema#',
'http://www.w3.org/2002/07/owl#',
"http://www.w3.org/2001/XMLSchema#"]
borderGroups = 4
borderConcepts = 8.5
weightModularity = 1
weightGroups = 2
weightSize =2
edgeWeights = {
'default':1,
RDFS.subClassOf: 25.0,
RDFS.subPropertyOf:20.0,
RDFS.domain:10.0,
RDFS.range:5.0,
OWL.equivalentClass:50.0,
OWL.disjointWith:1.0
}
#subClass variables
baseline = 0.25
trange = 5
multi = 17
#util functions
def getStringForList(group,ns):
label = "{ ";
for uri in group:
label = label + uri.replace(ns,"")+", ";
label = label +"}";
return label;
def getLocalNameFromURI(uri):
return(getLocalNameFromString(str(uri)));
def getLocalNameFromString(suri):
if "#" in suri:
localname = suri[suri.rfind("#")+1:len(suri)];
return localname;
if "/" in suri:
localname = suri[suri.rfind("/")+1:len(suri)];
return localname;
return suri;
def verteil(x,expected,varianz):
#print("Varianz:",varianz)
#print("a = X-4/1.5",(x-expected)/varianz)
#print("b = a^2",math.pow(((x-expected)/varianz), 2))
expo = (-math.pow(((x-expected)/varianz),2)/2)
#print("c = -1/2*b: ",expo)
result = math.exp(expo)
#print("verteil: ",result)
return result
class Grouping(object):
def __init__(self, spec,ns):
self.spec = spec;
self.gen = UniqueIdGenerator();
self.ns = ns;
def createConceptGraph(self):
def getSubClassEdgeWeight(edge,elist):
def getPosToTop(elist,n,visited):
for e in elist:
if not e['type'] == RDFS.subClassOf:
continue;
if (e['source'] == n) & (not n in visited):
visited.append(n);
return getPosToTop(elist,e['target'],visited) +1;
return 0;
def getPosToBottom(elist,n,visited):
max = 0;
for e in elist:
if not e['type'] == RDFS.subClassOf:
continue;
if (e['target'] == n) & (not n in visited):
visited.append(n);
depth = getPosToBottom(elist, e['source'],visited)+1;
if (depth>max):
max = depth;
return max
posToTop = getPosToTop(elist,edge['target'],[])+1;
posToBottom = getPosToBottom(elist,edge['source'],[]);
height = posToTop+posToBottom;
if (height == 1):
relPosInHierachie = 0;
else:
relPosInHierachie = float(posToTop) / float(height);
abw = relPosInHierachie - baseline;
abwNorm = abw*trange;
res = multi*(math.atan(abwNorm) + math.pi/2);
return res;
def filter(subject,classlist):
if isinstance(subject,BNode): return True;
if (str(subject) in classlist): return True;
for ns in NSBLACKLIST:
if str(subject).startswith(ns):
return True;
return False;
graph = self.spec.graph
classtypes = [RDFS.Class, OWL.Class]
classlist = []
classObj = []
nlist=[];
elist=[];
#create nodes
for onetype in classtypes:
for classSub in graph.subjects(predicate=RDF.type, object=onetype):
#print("checking: " +str(classSub));
if not filter(classSub, classlist):
uri = str(classSub);
classlist.append(uri);
classObj.append(classSub);
#print("adding node: "+ uri);
nlist.append({'node':classSub,'uri':uri,'name':self.gen[uri],'label':str(uri).replace(self.ns, ""),"type":"Class"});
#else: print("filtered")
#print classObj
#if class != null create owl:Thing node
thing = OWL.Thing
uri = str(thing);
classlist.append(uri);
classObj.append(thing);
nlist.append({'node':thing,'uri':uri,'name':self.gen[uri],'label':str(uri).replace("http://www.w3.org/2002/07/owl#", ""),"type":"ExternalClass"});
#create edges
for c in classObj:
if (c == OWL.Thing):
continue;
found = False;
#build concept hierachy
for obj in graph.objects(c,RDFS.subClassOf):
if ( obj in classObj):
found = True;
#get source and target id
source = self.gen[str(c)];
target = self.gen[str(obj)];
elist.append({"type":RDFS.subClassOf,'source':source,'target':target,"proptype":"language"});
#add link to owl:thing if top node
if not found:
#print("add subclass link for level1 class " + str(c.uri));
source = self.gen[str(c)];
target = self.gen[str(OWL.Thing)];
elist.append({"type":RDFS.subClassOf,'source':source,'target':target,"proptype":"language"});
#add domain level edges
for sub,obj in graph.subject_objects(RDFS.domain):
#test if obj in classlist
if (obj in classObj):
prop = sub;
for rObj in graph.objects(prop,RDFS.range):
if (rObj in classObj):
#add a edge
dom = obj;
range = rObj;
source = self.gen[str(dom)];
target = self.gen[str(range)];
#print("Adding edge from "+ str(dom.uri) + " to " + str(range.uri) + " with Prop: "+str(prop.uri));
elist.append({"type":prop,'source':source,'target':target,"proptype":"domain"});
#add some other language level edges
for sub,obj in graph.subject_objects(OWL.equivalentClass):
if (sub in classObj) and (obj in classObj):
source = self.gen[str(sub)];
target = self.gen[str(obj)];
elist.append({"type":OWL.equivalentClass,'source':source,'target':target,"proptype":"language"});
for sub,obj in graph.subject_objects(OWL.disjointWith):
if (sub in classObj) and (obj in classObj):
source = self.gen[str(sub)];
target = self.gen[str(obj)];
elist.append({"type":OWL.disjointWith,'source':source,'target':target,"proptype":"language"});
#nodes and edges created
#weighting them
for edge in elist:
if (edge['type'] == RDFS.subClassOf):
weight = getSubClassEdgeWeight(edge,elist);
edge['weight'] = weight;
elif edge['proptype'] == 'domain':
weight = (edgeWeights[RDFS.domain]+edgeWeights[RDFS.range])/2;
edge['weight'] = weight;
else:
weight = edgeWeights[edge['type']]
if weight == None: weight =1;
edge['weight'] = weight;
#print nlist;
#print elist;
g = Graph.DictList(vertices= nlist , edges=elist, directed=True);
return g,classObj
## Group Size Part
def groupsCountScore(self,g,membership,border):
localmembers = [];
for i in range(0,len(membership)):
if g.vs[i]["type"] =="Class":
localmembers.append(membership[i])
count = len(list(set(localmembers)))
#print("Groups:",count);
if count <= 1:
return 0;
elif (count <= border):
return 1;
else:
return verteil(count,border,1.5);
def groupConceptCountScore(self,g,membership,border):
localmembers = [];
groupscores = {}
for i in range(0,len(membership)):
if g.vs[i]["type"] =="Class":
localmembers.append(membership[i])
countvec = Counter(localmembers)
for group,count in countvec.items():
if (count == 1):
groupscores[group] = 0;
elif (count <= border):
groupscores[group] = 1;
else:
groupscores[group] = verteil(count,border,4);
erg = 0.0
for (group,score) in groupscores.items():
add = countvec[group]*score/float(len(localmembers))
erg = erg+ add
return erg;
def processWalktrap(self,g):
sumweight = weightModularity+weightGroups+weightSize;
dendro = g.community_walktrap(weights='weight');
#plot(dendro);
scores = [];
for i in range(0,len(dendro.merges)):
membership = community_to_membership(dendro.merges,g.vcount(),i);
modScore = g.modularity(membership,weights='weight');
groupCountScore = self.groupsCountScore(g,membership,borderGroups);
groupConceptCountScore = self.groupConceptCountScore(g,membership,borderConcepts);
score = (weightModularity*modScore+weightGroups*groupCountScore+weightSize*groupConceptCountScore)/sumweight;
#print("modScore: ",modScore)
#print("groupCountScore: ",groupCountScore)
#print("groupConceptCountScore:",groupConceptCountScore)
#print("score: ",score);
scores.append(score);
maxIndex = scores.index(max(scores));
membership = community_to_membership(dendro.merges,g.vcount(),maxIndex);
return membership;
def getGroupsFromMembership(self,membership):
groups = {};
for i in range(0,len(membership)):
mod = str(membership[i]);
cl = self.gen.reverse_dict()[i];
# filter owl:Thing node
if cl == "http://www.w3.org/2002/07/owl#Thing":
continue;
# filter non-local nodes
if not str(cl).startswith(self.ns):
continue
if mod in groups:
groups[mod].append(cl);
else:
group = [cl];
groups[mod] = group;
return groups;
def extendGroupsWithProperties(self,groups,unusedPropertyGroup):
# Create a list of properties in the schema.
graph = self.spec.graph
proptypes = [RDF.Property, OWL.ObjectProperty, OWL.DatatypeProperty, OWL.AnnotationProperty]
proplist = []
for onetype in proptypes:
for sub in graph.subjects(RDF.type, onetype):
uri = str(sub)
if uri.startswith(self.ns) and not sub in proplist:
proplist.append(sub)
#print("found: "+str(len(proplist)) + " properties");
#now we have our local properties
for p in proplist:
puri = str(p);
#localProp = str(p.uri).replace(ns,"");
added = False;
for dStmt in graph.objects(p, RDFS.domain):
domClass = str(dStmt);
#check if local ns;
if not domClass.startswith(self.ns):
continue;
#localName = domClass.replace(ns, "");
#find correct group
for gid in groups.keys():
group = groups[gid];
if domClass in group:
added = True;
if not puri in group:
#print("Adding "+str(p.uri) +" to group "+str(id));
group.append(puri);
# if not added to domain site, look at range site for possible group
if not added:
for rStmt in graph.objects(p, RDFS.range):
rangeClass = str(rStmt);
#check if local ns;
if not rangeClass.startswith(self.ns):
continue;
#localName = rangeClass.replace(ns, "");
#find correct group
for gid in groups.keys():
group = groups[gid];
if rangeClass in group:
added = True;
if not puri in group:
#print("Adding "+str(p.uri) +" to group "+str(id));
group.append(puri);
# if not added to a group -- create 'special' unused group
if (unusedPropertyGroup):
unusedG = 'otherProperties';
if not added:
if unusedG in groups:
group = groups[unusedG];
if not puri in group:
group.append(puri);
else:
group = [puri];
groups[unusedG] = group;
#print("Added to unused : "+localProp);
return groups;
def createHTML(self,groups,labels):
html ='<div id="terms_grouped"> ';
for gid in groups:
group = groups[gid];
if gid in labels:
label = labels[gid];
else:
label = gid;
html +='<div class="group_table">\n<h3>'+label+'</h3><ul>\n';
for con in group:
html += '<li><a href="#'+getLocalNameFromString(con)+'">'+getLocalNameFromString(con)+'</a></li>\n';
html += '</ul></div>\n';
html += '</div>\n';
return html
def getHTMLGroups(self):
print("creating groups")
g,clObj = self.createConceptGraph();
membership = self.processWalktrap(g);
groups = self.getGroupsFromMembership(membership);
#print(groups);
groups = self.extendGroupsWithProperties(groups,False);
#print(groups);
print('creating labels for groups')
l = Labeling(self.spec,groups,clObj,self.ns)
labels = l.createLCALabels();
print("create html for groups")
html = self.createHTML(groups,labels);
print("processing of groups finished")
return html;
class Labeling(object):
def __init__(self, spec,groups,groupObjects,ns):
self.spec = spec;
self.groups = groups;
self.groupObj = groupObjects;
self.ns = ns;
def createLCALabels(self):
labelMap = {};
for gID in self.groups:
group = self.groups[gID];
label = self.getLCALabelForGroup(group);
labelMap[gID]= label;
return labelMap;
def getLCALabelForGroup(self,group):
#print("Get Label for Group:");
#print(getStringForList(group,self.ns));
if len(group)== 1:
return group[0].replace(self.ns, "")
label='';
lcalist = [];
for uri in group:
for cl in self.groupObj:
if str(cl) == uri:
lcalist.append(cl);
if len(lcalist)== 0:
print("no lca found for this group return: Properties")
return "Properties";
else:
if len(lcalist)==1:
#print("lca: "+str(lcalist[0]).replace(self.ns, ""));
label = str(lcalist[0]).replace(self.ns, "");
return label;
lcalist = self.getLowestCommonAnchestor(lcalist,[]);
label = self.getStringLabel(lcalist);
#print("lca: "+ label);
return label;
def getLCA(self,u,v):
def getPaths(r,paths):
found = False;
for upper in self.spec.graph.objects(r,RDFS.subClassOf):
#add object to path
paths.append(upper);
found = True;
paths = getPaths(upper, paths);
break;
if not found:
thingnode = OWL.Thing
paths.append(thingnode);
return paths;
pathU = [u];
pathV = [v];
#get path to root from u;
pathU = getPaths(u, pathU);
#get path to root from v;
pathV = getPaths(v, pathV);
#find first common resource in both paths
common = [x for x in pathU if x in pathV]
if len(common)== 0:
return None;
else:
return common[0];
def getLowestCommonAnchestor(self,LCAList,compared):
if len(LCAList)==1:
return LCAList;
for i in range(0,len(LCAList)-1):
for j in range(i+1,len(LCAList)):
u = LCAList[i];
v = LCAList[j];
# print("u: "+str(u).replace(self.ns, "")+" v: "+str(v).replace(self.ns, ""));
if ((u,v) in compared) or ((v,u) in compared):
#print("has been compared before - skip")
continue
else:
compared.append((u,v))
lca = self.getLCA(u,v);
if (lca == None or str(lca) =="http://www.w3.org/2002/07/owl#Thing"):
continue;
else:
LCAList.remove(u);
LCAList.remove(v);
if (lca not in LCAList):
LCAList.append(lca);
return self.getLowestCommonAnchestor(LCAList,compared);
return LCAList;
def getStringLabel(self,lcalist):
if len(lcalist)== 0:
return "";
if len(lcalist)==1:
return getLocalNameFromURI(lcalist[0]);
label ="";
for i in range(0,len(lcalist)-1):
label = label + getLocalNameFromURI(lcalist[i])+", ";
#print("LABEL:"+label);
label = label[0:len(label)-2]+ " and "+getLocalNameFromURI(lcalist[len(lcalist)-1]);
return label;
if __name__ == "__main__":
xlist = [1,2,3,4,5,6,7,8,9,10]
for x in xlist:
print("Groups",x)
print(verteil(x,4,1.5))