def print_trees(graph, bridge):
PPO = 'ro:proper_part_of'
HPP = 'ro:has_proper_part'
hpp = HPP.replace('ro:', graph.namespaces['ro'])
ppo = PPO.replace('ro:', graph.namespaces['ro'])
a, b = creatTree(*Query(tc.red('birnlex_796'), HPP, 'OUTGOING', 10), # FIXME seems to be a last one wins bug here with birnlex_796 vs NIFGA:birnlex_796 depending on the has seed...
json=graph.make_scigraph_json(HPP))
c, d = creatTree(*Query('NIFGA:birnlex_796', hpp, 'OUTGOING', 10), graph=sgg)
j = bridge.make_scigraph_json(HPP) # issue https://github.com/RDFLib/rdflib/pull/661
e, f = creatTree(*Query('UBERON:0000955', HPP, 'OUTGOING', 10), json=j)
k_, l_ = creatTree(*Query('NIFGA:nlx_anat_101177', ppo, 'INCOMING', 10), graph=sgg)
merge = dict(d[-1]) # full tree with ppo converted to hpp
merge['nodes'].extend(l_[-1]['nodes'])
merge['edges'].extend([{'sub':e['obj'], 'pred':hpp, 'obj':e['sub']} for e in l_[-1]['edges']])
m_, n_ = creatTree(*Query('NIFGA:birnlex_796', hpp, 'OUTGOING', 10), json=merge)
print('nifga dep')
print(a)
print('nifga live')
print(c)
print('new bridge')
print(e)
print('nifga total (both directions)')
print(m_)
print('nifga white matter')
print(k_)
return a, b, c, d, e, f, k_, l_, m_, n_
def print_trees(graph, bridge):
PPO = 'ro:proper_part_of'
HPP = 'ro:has_proper_part'
hpp = HPP.replace('ro:', graph.namespaces['ro'])
ppo = PPO.replace('ro:', graph.namespaces['ro'])
a, b = creatTree(
*Query(
tc.red('birnlex_796'), HPP, 'OUTGOING', 10
), # FIXME seems to be a last one wins bug here with birnlex_796 vs NIFGA:birnlex_796 depending on the has seed...
json=graph.make_scigraph_json(HPP))
c, d = creatTree(*Query('NIFGA:birnlex_796', hpp, 'OUTGOING', 10),
graph=sgg)
j = bridge.make_scigraph_json(
HPP) # issue https://github.com/RDFLib/rdflib/pull/661
e, f = creatTree(*Query('UBERON:0000955', HPP, 'OUTGOING', 10), json=j)
k_, l_ = creatTree(*Query('NIFGA:nlx_anat_101177', ppo, 'INCOMING', 10),
graph=sgg)
merge = dict(d[-1]) # full tree with ppo converted to hpp
merge['nodes'].extend(l_[-1]['nodes'])
merge['edges'].extend([{
'sub': e['obj'],
'pred': hpp,
'obj': e['sub']
} for e in l_[-1]['edges']])
m_, n_ = creatTree(*Query('NIFGA:birnlex_796', hpp, 'OUTGOING', 10),
json=merge)
print('nifga dep')
print(a)
print('nifga live')
print(c)
print('new bridge')
print(e)
print('nifga total (both directions)')
print(m_)
print('nifga white matter')
print(k_)
return a, b, c, d, e, f, k_, l_, m_, n_
def equiv(curie, label):
if curie in manual:
replaced_by[curie] = manual[curie]
return manual[curie]
ec = sgg.getNeighbors(curie, relationshipType='equivalentClass')
nodes = [n for n in ec['nodes'] if n['id'] != curie]
if len(nodes) > 1:
#print('wtf node', [n['id'] for n in nodes], curie)
for node in nodes:
id_ = node['id']
label_ = node['lbl']
if id_.startswith('UBERON'):
if curie in replaced_by:
one = replaced_by[curie]
replaced_by[curie] = one, id_
print('WE GOT DUPES', curie, label, one, id_) # TODO
else:
replaced_by[curie] = id_
else:
internal_equivs[curie] = id_
elif not nodes:
node = sgg.getNode(curie)['nodes'][0]
if OWL.deprecated.toPython() in node['meta']:
print('THIS CLASS IS DEPRECATED', curie)
lbl = node['lbl']
if lbl.startswith(
'Predominantly white regional') or lbl.startswith(
'Predominantly gray regional'):
print('\tHE\'S DEAD JIM!', lbl, node['id'])
replaced_by[curie] = 'NOREP'
if IRBC in node['meta']:
existing_replaced = node['meta'][IRBC][0]
ec2 = sgg.getNeighbors(existing_replaced,
relationshipType='equivalentClass')
print('\tFOUND ONE', existing_replaced)
#scigPrint.pprint_node(sgg.getNode(existing_replaced))
if ec2['edges']: # pass the buck if we can
print('\t', end='')
scigPrint.pprint_edge(ec2['edges'][0])
rb = ec2['edges'][0]['obj']
print('\tPASSING BUCK : (%s -> %s -> %s)' %
(curie, existing_replaced, rb))
irbcs[curie] = (existing_replaced, rb)
replaced_by[curie] = rb
return nodes
else:
er_node = sgv.findById(existing_replaced)
if not er_node['deprecated']:
if not er_node['curie'].startswith('NIFGA:'):
print('\tPASSING BUCK : (%s -> %s)' %
(curie, er_node['curie']))
return nodes
print(
'\tERROR: could not pass buck, we are at a dead end at',
er_node) # TODO
print()
moar = [
t for t in sgv.findByTerm(label)
if t['curie'].startswith('UBERON')
]
if moar:
#print(moar)
#replaced_by[curie] = moar[0]['curie']
if len(moar) > 1:
print('WARNING', curie, label,
[(m['curie'], m['labels'][0]) for m in moar])
for node in moar:
#if node['curie'] in uberon_obsolete: # node['deprecated']?
#continue
ns = sgg.getNode(node['curie'])
assert len(
ns['nodes']) == 1, "WTF IS GOING ON %s" % node['curie']
ns = ns['nodes'][0]
if _doprint:
print(
'Found putative replacement in moar: (%s -> %s)' %
(curie, ns['id']))
if DBX in ns['meta']:
print(' ' * 8, node['curie'], ns['meta'][DBX],
node['labels'][0], node['synonyms'])
if AID in ns['meta']:
print(' ' * 8, node['curie'], ns['meta'][AID],
node['labels'][0], node['synonyms'])
if CON in ns['meta']:
print(' ' * 8, node['curie'], ns['meta'][CON],
node['labels'][0], node['synonyms'])
replaced_by[curie] = ns['id']
else:
replaced_by[curie] = None
if False: # review
print('NO FORWARD EQUIV', tc.red(curie), label) # TODO
for k, v in sorted(
sgg.getNode(curie)['nodes'][0]['meta'].items()):
if type(v) == iter:
print(' ' * 4, k)
for _ in v:
print(' ' * 8, _)
else:
print(' ' * 4, k, v)
else:
node = nodes[0]
replaced_by[curie] = node['id']
exact[curie] = node['id']
return nodes
def equiv(curie, label):
if curie in manual:
replaced_by[curie] = manual[curie]
return manual[curie]
ec = sgg.getNeighbors(curie, relationshipType='equivalentClass')
nodes = [n for n in ec['nodes'] if n['id'] != curie]
if len(nodes) > 1:
#print('wtf node', [n['id'] for n in nodes], curie)
for node in nodes:
id_ = node['id']
label_ = node['lbl']
if id_.startswith('UBERON'):
if curie in replaced_by:
one = replaced_by[curie]
replaced_by[curie] = one, id_
print('WE GOT DUPES', curie, label, one, id_) # TODO
else:
replaced_by[curie] = id_
else:
internal_equivs[curie] = id_
elif not nodes:
node = sgg.getNode(curie)['nodes'][0]
if OWL.deprecated.toPython() in node['meta']:
print('THIS CLASS IS DEPRECATED', curie)
lbl = node['lbl']
if lbl.startswith('Predominantly white regional') or lbl.startswith('Predominantly gray regional'):
print('\tHE\'S DEAD JIM!', lbl, node['id'])
replaced_by[curie] = 'NOREP'
if IRBC in node['meta']:
existing_replaced = node['meta'][IRBC][0]
ec2 = sgg.getNeighbors(existing_replaced, relationshipType='equivalentClass')
print('\tFOUND ONE', existing_replaced)
#scigPrint.pprint_node(sgg.getNode(existing_replaced))
if ec2['edges']: # pass the buck if we can
print('\t',end='')
scigPrint.pprint_edge(ec2['edges'][0])
rb = ec2['edges'][0]['obj']
print('\tPASSING BUCK : (%s -> %s -> %s)' % (curie, existing_replaced, rb))
irbcs[curie] = (existing_replaced, rb)
replaced_by[curie] = rb
return nodes
else:
er_node = sgv.findById(existing_replaced)
if not er_node['deprecated']:
if not er_node['curie'].startswith('NIFGA:'):
print('\tPASSING BUCK : (%s -> %s)' % (curie, er_node['curie']))
return nodes
print('\tERROR: could not pass buck, we are at a dead end at', er_node) # TODO
print()
moar = [t for t in sgv.findByTerm(label) if t['curie'].startswith('UBERON')]
if moar:
#print(moar)
#replaced_by[curie] = moar[0]['curie']
if len(moar) > 1:
print('WARNING', curie, label, [(m['curie'], m['labels'][0]) for m in moar])
for node in moar:
#if node['curie'] in uberon_obsolete: # node['deprecated']?
#continue
ns = sgg.getNode(node['curie'])
assert len(ns['nodes']) == 1, "WTF IS GOING ON %s" % node['curie']
ns = ns['nodes'][0]
if _doprint:
print('Found putative replacement in moar: (%s -> %s)' % (curie, ns['id']))
if DBX in ns['meta']:
print(' ' * 8, node['curie'], ns['meta'][DBX],
node['labels'][0], node['synonyms'])
if AID in ns['meta']:
print(' ' * 8, node['curie'], ns['meta'][AID],
node['labels'][0], node['synonyms'])
if CON in ns['meta']:
print(' ' * 8, node['curie'], ns['meta'][CON],
node['labels'][0], node['synonyms'])
replaced_by[curie] = ns['id']
else:
replaced_by[curie] = None
if False: # review
print('NO FORWARD EQUIV', tc.red(curie), label) # TODO
for k,v in sorted(sgg.getNode(curie)['nodes'][0]['meta'].items()):
if type(v) == iter:
print(' ' * 4, k)
for _ in v:
print(' ' * 8, _)
else:
print(' ' * 4, k, v)
else:
node = nodes[0]
replaced_by[curie] = node['id']
exact[curie] = node['id']
return nodes