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convertHumanView.py
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convertHumanView.py
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import argparse
import xml.etree.ElementTree as ET
from atomwrappers import *
import requests
def parse_args():
parser = argparse.ArgumentParser(description='convert human view db to atomese')
parser.add_argument('--dbowl', type=str, default='',
help='owl file with ontology')
parser.add_argument('--output', type=str, default='',
help='output schema file with atomspace (result.scm for example)')
return parser.parse_args()
def parseProperties(filename, property):
props = {}
with open(filename, 'rb') as file:
for line in file:
if line[:17].decode("utf-8") == property:
line = line.decode("utf-8")
splitted = line.split(":")[2].split("(")
props[splitted[0].split(" ")[0]] = splitted[1].split(")")[0]
return props
def transform_todots(id):
id = id.split("_")
id = id[0] + ":" + id[1]
return id
def checkIfInProps(id, props1, props2):
if id in props1:
id = props1[id]
elif id in props2:
id = props2[id]
else:
id = transform_todots(id)
return id
def makeSatisfLink(variable, restr, list_member):
tmp_eval_link = CEvaluationLink(CPredicateNode(restr), CListLink(CVariable(variable), list_member))
return CSatisfyingSetScopeLink(CVariable(variable), tmp_eval_link)
def makeRestrictionParentLink(id, parent, restriction_label, restriction_svf):
tmp_eval_link = CEvaluationLink(CPredicateNode(restriction_label), CConceptNode(restriction_svf))
tmp_simil_link = CSimilarityLink(CConceptNode(id), CConceptNode(parent))
return CContextLink(tmp_eval_link, tmp_simil_link)
def makeRestrictionParentLink2(id, parent, restriction_svf):
tmp_satisf_link = makeSatisfLink("$X", restriction_svf, CConceptNode(parent))
return CSubsetLink(CConceptNode(id), tmp_satisf_link)
def makeTwoRestrictionParentLink(id, parent, restriction_svf, restriction_svf2):
tmp_satisf_link = makeSatisfLink("$X", restriction_svf2, CConceptNode(parent))
tmp_satisf_link2 = makeSatisfLink("$Y", restriction_svf, tmp_satisf_link)
return CSubsetLink(CConceptNode(id), tmp_satisf_link2)
def makeDifficultCase(class_id_1, class_id_2, class_id_3, svf_prop_1, svf_prop_2):
tmp_satisf_link = makeSatisfLink("$X", svf_prop_1, CConceptNode(class_id_2))
part_1 = CAndLink(CConceptNode(class_id_1), tmp_satisf_link)
part_2 = makeSatisfLink("$Y", svf_prop_2, CConceptNode(class_id_3))
return CSubsetLink(part_1, part_2)
def makeRareCase(class_id_1, class_id_2, class_id_3, restriction_svf):
tmp_satisf_link = makeSatisfLink("$X", restriction_svf, CConceptNode(class_id_3))
tmp_and_link = CAndLink(CConceptNode(class_id_2), tmp_satisf_link)
return CSubsetLink(CConceptNode(class_id_1), tmp_and_link)
def makeRareCase2(classes, restrictions):
tmp_satisf_link = makeSatisfLink("$X", restrictions[-1], CConceptNode(classes[-1]))
tmp_and_link = CAndLink(CConceptNode(classes[-2]), tmp_satisf_link)
tmp_satisf_link_2 = makeSatisfLink("$Y", restrictions[-2], tmp_and_link)
tmp_and_link_2 = CAndLink(CConceptNode(classes[-3]), tmp_satisf_link_2)
tmp_satisf_link_3 = makeSatisfLink("$Z", restrictions[-3], tmp_and_link_2)
return CSubsetLink(CConceptNode(classes[-4]), tmp_satisf_link_3)
def makeDifficultCase2(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
part2 = makeSatisfLink("$Y", restrs[-2], tmp_satisf_link)
tmp_satisf_link_2 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-2]))
part1 = CAndLink(CConceptNode(classes[0]), tmp_satisf_link_2)
return CSubsetLink(part1, part2)
def makeDifficultCaseCore(classes, restrs):
part2 = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
part1 = CAndLink(CConceptNode(classes[0]), tmp_satisf_link)
return CSubsetLink(part1, part2)
def findAllInLine(line, toFind):
founded_ids = []
res = 0
prev_res = 0
while not (res == -1):
res = line[res:].find(toFind)
if (not (res == -1)):
res = res + len(toFind) + prev_res
prev_res = res
founded_ids.append(res)
return founded_ids
def parseSubclassLine(line, props1, props2):
obo_ids = findAllInLine(line, "obo:")
core_ids = findAllInLine(line, "core:")
svf_ids = findAllInLine(line, "ObjectSomeValuesFrom(")
intersection_ids = findAllInLine(line, "ObjectIntersectionOf(")
min_cardinality_id = findAllInLine(line, "ObjectMinCardinality(")
max_cardinality_id = findAllInLine(line, "ObjectMaxCardinality(")
classes = []
restrs = []
if(len(min_cardinality_id) > 0) or (len(max_cardinality_id) > 0):
return None #currently dont know how to deal with cardinalities
if ((len(obo_ids) == 2) & (len(core_ids) == 0) & (len(svf_ids) == 0)):
class_id = transform_todots(line[obo_ids[0]:obo_ids[1]].split(" ")[0])
parent_id = transform_todots(line[obo_ids[1]:].split(")")[0])
return CSubsetLink(CConceptNode(class_id), CConceptNode(parent_id))
elif ((len(obo_ids) == 3) & (len(core_ids) == 0) & (len(svf_ids) == 1)):
class_id = transform_todots(line[obo_ids[0]:obo_ids[1]].split(" ")[0])
svf_prop = checkIfInProps(line[obo_ids[1]:obo_ids[2]].split(" ")[0], props1, props2)
parent_id = transform_todots(line[obo_ids[2]:].split(")")[0])
return makeRestrictionParentLink2(class_id, parent_id, svf_prop)
elif ((len(obo_ids) == 2) & (len(core_ids) == 1) & (len(svf_ids) == 1)):
class_id = transform_todots(line[obo_ids[0]:core_ids[0]].split(" ")[0])
core = line[core_ids[0]:obo_ids[1]].split(" ")[0]
parent_id = transform_todots(line[obo_ids[1]:].split(")")[0])
return makeRestrictionParentLink2(class_id, parent_id, core)
elif ((len(obo_ids) == 4) & (len(core_ids) == 0) & (len(svf_ids) == 2) & (len(intersection_ids) == 0)):
if((svf_ids[0] > obo_ids[0]) & (svf_ids[0] < obo_ids[1]) & (svf_ids[1] > obo_ids[1]) & (svf_ids[1] < obo_ids[2]) & (svf_ids[1] < obo_ids[3])):
class_id = transform_todots(line[obo_ids[0]:obo_ids[1]].split(" ")[0])
svf_prop_1 = checkIfInProps(line[obo_ids[1]:obo_ids[2]].split(" ")[0], props1, props2)
svf_prop_2 = checkIfInProps(line[obo_ids[2]:obo_ids[3]].split(" ")[0], props1, props2)
parent_id = transform_todots(line[obo_ids[3]:].split(")")[0])
return makeTwoRestrictionParentLink(class_id, parent_id, svf_prop_1, svf_prop_2)
elif((len(obo_ids) == 5) & (len(svf_ids) == 2) & (len(intersection_ids) == 1)):
if ((obo_ids[0] > intersection_ids[0]) & (svf_ids[0] > obo_ids[0]) & (obo_ids[1] > svf_ids[0]) &
(obo_ids[2] < svf_ids[1])):
class_id_1 = transform_todots(line[obo_ids[0]:obo_ids[1]].split(" ")[0])
svf_prop_1 = checkIfInProps(line[obo_ids[1]:obo_ids[2]].split(" ")[0], props1, props2)
class_id_2 = transform_todots(line[obo_ids[2]:obo_ids[3]].split(")")[0])
svf_prop_2 = checkIfInProps(line[obo_ids[3]:obo_ids[4]].split(" ")[0], props1, props2)
class_id_3 = transform_todots(line[obo_ids[4]:].split(")")[0])
return makeDifficultCase(class_id_1, class_id_2, class_id_3, svf_prop_1, svf_prop_2)
elif((len(obo_ids) == 4) & (len(intersection_ids) == 1) & (len(svf_ids) == 1)):
if((obo_ids[0] < intersection_ids[0]) & (obo_ids[1] > intersection_ids[0]) & (obo_ids[2] > svf_ids[0])):
class_id_1 = transform_todots(line[obo_ids[0]:obo_ids[1]].split(" ")[0])
class_id_2 = transform_todots(line[obo_ids[1]:obo_ids[2]].split(" ")[0])
class_id_3 = transform_todots(line[obo_ids[3]:].split(")")[0])
restr_svf = checkIfInProps(line[obo_ids[2]:obo_ids[3]].split(" ")[0], props1, props2)
return makeRareCase(class_id_1, class_id_2, class_id_3, restr_svf)
elif((len(obo_ids) == 7) & (len(intersection_ids) == 2) & (len(svf_ids) == 3)):
classes.append(transform_todots(line[obo_ids[0]:obo_ids[1]].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[1]:obo_ids[2]].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[2]:obo_ids[3]].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[3]:obo_ids[4]].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[4]:obo_ids[5]].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[5]:obo_ids[6]].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[6]:].split(")")[0]))
return makeRareCase2(classes, restrs)
elif((len(intersection_ids) == 1) & (len(svf_ids) == 3) & (len(obo_ids) == 6)):
classes.append(transform_todots(line[obo_ids[0]:obo_ids[1]].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[1]:obo_ids[2]].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[2]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[3]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
return makeDifficultCase2(classes, restrs)
elif ((len(intersection_ids) == 1) & (len(svf_ids) == 2) & (len(obo_ids) == 4) & (len(core_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:obo_ids[1]].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[1]:obo_ids[2]].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[2]:].split(")")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(line[obo_ids[-1]:].split(")")[0])
return makeDifficultCaseCore(classes, restrs)
return None
def makeEquivClasses(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_and_link = CAndLink(CConceptNode(classes[-2]), tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivClassesUnion(classes):
return CSimilarityLink(CConceptNode(classes[0]), COrLink(CConceptNode(classes[1]), CConceptNode(classes[2])))
def makeEquivClasses2svfs1inter(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
part2 = CAndLink(CConceptNode(classes[-3]), tmp_satisf_link, tmp_satisf_link_2)
return CSimilarityLink(CConceptNode(classes[0]), part2)
def makeEquivRareCase(classes):
return CSimilarityLink(CConceptNode(classes[0]), CAndLink(CConceptNode(classes[1]), CConceptNode(classes[2])))
def makeEquivRareCase2(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_and_link = CAndLink(CConceptNode(classes[-2]), tmp_satisf_link)
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], tmp_and_link)
tmp_and_link_2 = CAndLink(CConceptNode(classes[-3]), tmp_satisf_link_2)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link_2)
def makeEquivSVFCore(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[0], CConceptNode(classes[-1]))
tmp_and_link = CAndLink(CConceptNode(classes[-2]), tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase3(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[0], CConceptNode(classes[-1]))
tmp_and_link = CAndLink(CConceptNode(classes[-2]), CConceptNode(classes[-3]), tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquiv2Core2Svf1Inters(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_and_link = CAndLink(CConceptNode(classes[-3]), tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquiv3Svf1Intersect(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_and_link = CAndLink(CConceptNode(classes[-4]), tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquiv1Intersect2Svf1Core(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_and_link = CAndLink(CConceptNode(classes[-3]), tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquiv3Union(classes):
tmp_or_link = COrLink(CConceptNode(classes[-1]), CConceptNode(classes[-2]), CConceptNode(classes[-3]))
return CSimilarityLink(CConceptNode(classes[0]), tmp_or_link)
def makeEquiv4Svf1Inters(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_satisf_link_4 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-4]))
tmp_and_link = CAndLink(CConceptNode(classes[-5]), tmp_satisf_link_4, tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[-6]), tmp_and_link)
def makeEquiv4Svf1Inters2(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
and_part_3 = makeSatisfLink("$Y", restrs[-2], tmp_satisf_link)
tmp_satisf_link_2 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-2]))
and_part_2 = makeSatisfLink("$U", restrs[-4], tmp_satisf_link_2)
tmp_and_link = CAndLink(CConceptNode(classes[-3]), and_part_2, and_part_3)
return CSimilarityLink(CConceptNode(classes[-4]), tmp_and_link)
def makeEquiv2Svf1Intersect(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], tmp_satisf_link)
tmp_and_link = CAndLink(CConceptNode(classes[-2]), tmp_satisf_link_2)
return CSimilarityLink(CConceptNode(classes[-3]), tmp_and_link)
def makeEquiv3Svf1Union(classes, restrs):
part_2 = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_2 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
part_1 = CAndLink(tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(part_1, part_2)
def makeEquivRareCase4(classes, restrs):
part_2 = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_2 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_satisf_link_3 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-4]))
part_1 = COrLink(tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(part_1, part_2)
def makeEquiv4Svf1Inter1Core(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_satisf_link_4 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-4]))
tmp_and_link = CAndLink(CConceptNode(classes[-5]), tmp_satisf_link_4, tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase5(classes):
tmp_or_link = COrLink(CConceptNode(classes[-1]), CConceptNode(classes[-2]), CConceptNode(classes[-3]), CConceptNode(classes[-4]))
return CSimilarityLink(CConceptNode(classes[0]), tmp_or_link)
def makeEquiv3Svf1Intersect1Core(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_and_link = CAndLink(CConceptNode(classes[-4]), tmp_satisf_link, tmp_satisf_link_2, tmp_satisf_link_3)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquiv3svf1Intersect2(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], tmp_satisf_link)
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-2]))
tmp_and_link = CAndLink(CConceptNode(classes[-3]), tmp_satisf_link_3, tmp_satisf_link_2)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase6(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_and_link = CAndLink(CConceptNode(classes[-4]), tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquiv5Svf1Intersect(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_satisf_link_4 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-4]))
tmp_satisf_link_5 = makeSatisfLink("$V", restrs[-5], CConceptNode(classes[-5]))
tmp_and_link = CAndLink(CConceptNode(classes[-6]), tmp_satisf_link_5, tmp_satisf_link_4, tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase7(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], tmp_satisf_link)
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-2]))
tmp_satisf_link_4 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-3]))
tmp_and_link = CAndLink(CConceptNode(classes[-4]), tmp_satisf_link_4, tmp_satisf_link_3, tmp_satisf_link_2)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase8(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_satisf_link_4 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-4]))
tmp_satisf_link_5 = makeSatisfLink("$U", restrs[-5], CConceptNode(classes[-5]))
tmp_and_link = CAndLink(CConceptNode(classes[-6]), tmp_satisf_link_5, tmp_satisf_link_4, tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase9(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_satisf_link_4 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-4]))
tmp_and_link = CAndLink(CConceptNode(classes[-5]), tmp_satisf_link_4, tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase10(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_and_link = CAndLink(CConceptNode(classes[-4]), tmp_satisf_link_3, tmp_satisf_link_2, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase11(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], tmp_satisf_link_2)
tmp_satisf_link_4 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-3]))
tmp_satisf_link_5 = makeSatisfLink("$V", restrs[-5], tmp_satisf_link_4)
tmp_satisf_link_6 = makeSatisfLink("$W", restrs[-6], CConceptNode(classes[-4]))
tmp_and_link = CAndLink(CConceptNode(classes[-5]), tmp_satisf_link_6, tmp_satisf_link_5, tmp_satisf_link_3, tmp_satisf_link)
return CSimilarityLink(CConceptNode(classes[0]), tmp_and_link)
def makeEquivRareCase12(classes, restrs):
tmp_satisf_link = makeSatisfLink("$X", restrs[-1], CConceptNode(classes[-1]))
tmp_satisf_link_2 = makeSatisfLink("$Y", restrs[-2], CConceptNode(classes[-2]))
tmp_satisf_link_3 = makeSatisfLink("$Z", restrs[-3], CConceptNode(classes[-3]))
tmp_satisf_link_4 = makeSatisfLink("$U", restrs[-4], CConceptNode(classes[-4]))
tmp_satisf_link_5 = makeSatisfLink("$V", restrs[-5], CConceptNode(classes[-5]))
tmp_or_link = COrLink(tmp_satisf_link_5, tmp_satisf_link_4, tmp_satisf_link_3, tmp_satisf_link_2)
return CSimilarityLink(tmp_or_link, tmp_satisf_link)
def parseEquvalentLine(line, props1, props2):
obo_ids = findAllInLine(line, "obo:")
core_ids = findAllInLine(line, "core:")
svf_ids = findAllInLine(line, "ObjectSomeValuesFrom(")
intersection_ids = findAllInLine(line, "ObjectIntersectionOf(")
union_ids = findAllInLine(line, "ObjectUnionOf(")
min_cardinality_id = findAllInLine(line, "ObjectMinCardinality(")
max_cardinality_id = findAllInLine(line, "ObjectMaxCardinality(")
classes = []
restrs = []
if ((len(min_cardinality_id) > 0) or (len(max_cardinality_id) > 0)):
return None # currently dont know how to deal with cardinalities
elif((len(obo_ids) == 4) & (len(svf_ids) == 1) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
return makeEquivClasses(classes, restrs)
elif ((len(obo_ids) == 3) & (len(union_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[2]:].split(")")[0]))
return makeEquivClassesUnion(classes)
elif ((len(obo_ids) == 6) & (len(intersection_ids) == 1) & (len(svf_ids) == 2)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
return makeEquivClasses2svfs1inter(classes, restrs)
elif((len(obo_ids) == 3) & (len(intersection_ids) == 1) & (len(svf_ids) == 0)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[2]:].split(")")[0]))
return makeEquivRareCase(classes)
elif((len(obo_ids) == 6) & (len(svf_ids) == 2) & (len(intersection_ids) == 2)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
return makeEquivRareCase2(classes, restrs)
elif((len(obo_ids) == 3) & (len(core_ids) == 1) & (len(intersection_ids) == 1) & (len(svf_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[2]:].split(")")[0]))
return makeEquivSVFCore(classes, restrs)
elif((len(obo_ids) == 5) & (len(svf_ids) == 1) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[2]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[3]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[4]:].split(")")[0]))
return makeEquivRareCase3(classes, restrs)
elif((len(obo_ids) == 4) & (len(core_ids) == 2) & (len(svf_ids) == 2) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[2]:].split(")")[0]))
restrs.append(line[core_ids[1]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
return makeEquiv2Core2Svf1Inters(classes, restrs)
elif ((len(obo_ids) == 8) & (len(intersection_ids) == 1) & (len(svf_ids) == 3)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
return makeEquiv3Svf1Intersect(classes, restrs)
elif((len(obo_ids) == 5) & (len(svf_ids) == 2) & (len(intersection_ids) == 1) & (len(core_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[4]:].split(")")[0]))
return makeEquiv1Intersect2Svf1Core(classes, restrs)
elif((len(obo_ids) == 4) & (len(union_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[2]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
return makeEquiv3Union(classes)
elif((len(svf_ids) == 4) & (len(obo_ids) == 10) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[8]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[9]:].split(")")[0]))
return makeEquiv4Svf1Inters(classes, restrs)
elif((len(obo_ids) == 8) & (len(svf_ids) == 4) & (len(intersection_ids) == 1) & (len(core_ids) == 0)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
restrs.append(checkIfInProps(line[obo_ids[3]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[4]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[5]:].split(" ")[0], props1, props2))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
return makeEquiv4Svf1Inters2(classes, restrs)
elif((len(obo_ids) == 5) & (len(svf_ids) == 2) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
restrs.append(checkIfInProps(line[obo_ids[3]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[4]:].split(")")[0]))
return makeEquiv2Svf1Intersect(classes, restrs)
elif((len(svf_ids) == 3) & (len(obo_ids) == 6) & (len(union_ids) == 1)):
restrs.append(checkIfInProps(line[obo_ids[0]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[1]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
return makeEquiv3Svf1Union(classes, restrs)
elif((len(svf_ids) == 4) & (len(union_ids) == 1) & (len(obo_ids) == 8)):
restrs.append(checkIfInProps(line[obo_ids[0]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[1]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
return makeEquivRareCase4(classes, restrs)
elif((len(obo_ids) == 9) & (len(core_ids) == 1) & (len(svf_ids) == 4) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[8]:].split(")")[0]))
return makeEquiv4Svf1Inter1Core(classes, restrs)
elif((len(obo_ids) == 5) & (len(union_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[2]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[3]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[4]:].split(")")[0]))
return makeEquivRareCase5(classes)
elif((len(obo_ids) == 7) & (len(core_ids) == 1) & (len(svf_ids) == 3) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[6]:].split(")")[0]))
return makeEquiv3Svf1Intersect1Core(classes, restrs)
elif((len(obo_ids) == 7) & (len(svf_ids) == 3) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
restrs.append(checkIfInProps(line[obo_ids[5]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[6]:].split(")")[0]))
return makeEquiv3svf1Intersect2(classes, restrs)
elif((len(obo_ids) == 6) & (len(core_ids) == 2) & (len(svf_ids) == 3) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[4]:].split(")")[0]))
restrs.append(line[core_ids[1]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
return makeEquivRareCase6(classes, restrs)
elif((len(obo_ids) == 12) & (len(svf_ids) == 5) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[8]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[9]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[10]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[11]:].split(")")[0]))
return makeEquiv5Svf1Intersect(classes, restrs)
elif((len(obo_ids) == 9) & (len(svf_ids) == 4) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
restrs.append(checkIfInProps(line[obo_ids[7]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[8]:].split(")")[0]))
return makeEquivRareCase7(classes, restrs)
elif((len(obo_ids) == 10) & (len(core_ids) == 2) & (len(svf_ids) == 5) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[8]:].split(")")[0]))
restrs.append(line[core_ids[1]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[9]:].split(")")[0]))
return makeEquivRareCase8(classes, restrs)
elif((len(obo_ids) == 8) & (len(core_ids) == 2) & (len(svf_ids) == 4) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[6]:].split(")")[0]))
restrs.append(line[core_ids[1]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
return makeEquivRareCase9(classes, restrs)
elif ((len(core_ids) == 3) & (len(obo_ids) == 5) & (len(svf_ids) == 3) & (len(intersection_ids) == 1)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(line[core_ids[0]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[2]:].split(")")[0]))
restrs.append(line[core_ids[1]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(line[core_ids[2]:].split(" ")[0])
classes.append(transform_todots(line[obo_ids[4]:].split(")")[0]))
return makeEquivRareCase10(classes, restrs)
elif((len(obo_ids) == 12) & (len(intersection_ids) == 1) & (len(svf_ids) == 6)):
classes.append(transform_todots(line[obo_ids[0]:].split(" ")[0]))
classes.append(transform_todots(line[obo_ids[1]:].split(" ")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
restrs.append(checkIfInProps(line[obo_ids[5]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[6]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[7]:].split(" ")[0], props1, props2))
restrs.append(checkIfInProps(line[obo_ids[8]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[9]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[10]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[11]:].split(")")[0]))
return makeEquivRareCase11(classes, restrs)
elif((len(obo_ids) == 10) & (len(union_ids) == 1) & (len(svf_ids) == 5)):
restrs.append(checkIfInProps(line[obo_ids[0]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[1]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[2]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[3]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[4]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[5]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[6]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[7]:].split(")")[0]))
restrs.append(checkIfInProps(line[obo_ids[8]:].split(" ")[0], props1, props2))
classes.append(transform_todots(line[obo_ids[9]:].split(")")[0]))
return makeEquivRareCase12(classes, restrs)
return None
def ParseOntology(filename):
tmp = []
annotation_props = parseProperties(filename, "# Annotation Property")
object_props = parseProperties(filename, "# Object Property")
with open (filename, 'rb') as file:
for line in file:
line = line.decode("utf-8")
if line[:7] == "# Class":
splitted = line.split(":")[2].split("(")
try:
class_id = transform_todots(splitted[0]).split(" ")[0]
class_name = splitted[1].split(")")[0]
tmp.append(CEvaluationLink(CPredicateNode("has_name"),
CListLink(CConceptNode(class_id), CConceptNode(class_name))))
except Exception:
continue
elif line[:10] == "SubClassOf":
parsed_subclass_line = parseSubclassLine(line, annotation_props, object_props)
if(parsed_subclass_line):
tmp.append(parsed_subclass_line)
elif line[:17] == "EquivalentClasses":
parsed_equivalent_line = parseEquvalentLine(line, annotation_props, object_props)
if (parsed_equivalent_line):
tmp.append(parsed_equivalent_line)
return tmp
def main():
args = parse_args()
if (not (args.dbowl)):
resp = requests.get("http://ontologies.berkeleybop.org/uberon/subsets/human-view.owl")
human_view_file = "/home/daddywesker/human-view.owl"
open(human_view_file, 'wb').write(resp.content)
else:
human_view_file = args.dbowl
db_dict = ParseOntology(human_view_file)
if (not (args.output)):
output = open("result.scm", 'wt')
else:
output = open(args.output, 'wt')
classes_to_print = '\n'.join([x.recursive_print() for x in db_dict])
output.write(classes_to_print)
output.close()
if __name__ == '__main__':
main()