def luup(x, y):
if x == cl.forest_tnu or y == cl.forest_tnu: return
assert cl.get_checklist(x) != cl.get_checklist(y)
if in_chain(x, y0) and in_chain(y, x0):
bar = best.get(x)
if bar and find_in_chain(bar.cod, y, x0):
if bar.cod == y:
art.proclaim(proposal, art.change_relation(bar, rel.eq, "extensional"))
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(proposal, art.extensional(y, x, rel.lt, "refines", "refined by"))
luup(x, cl.get_parent(y))
else:
bar = best.get(y)
if bar and find_in_chain(bar.cod, x, y0):
if bar.cod == y:
art.proclaim(proposal, bar)
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(proposal, art.extensional(x, y, rel.lt, "refines*", "refined by*"))
luup(cl.get_parent(x), y)
else:
# neither x nor y matches by name
art.proclaim(proposal, art.extensional(x, y, rel.eq, "similar="))
luup(cl.get_parent(x), cl.get_parent(y))
def luup(x, y):
if x == cl.forest_tnu or y == cl.forest_tnu: return
assert cl.get_checklist(x) != cl.get_checklist(y)
if in_chain(x, y0) and in_chain(y, x0):
bar = best.get(x)
if bar and find_in_chain(bar.cod, y, x0):
if bar.cod == y:
art.proclaim(draft, art.change_relation(bar, rel.eq, "extensional"))
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(draft, art.extensional(y, x, rel.lt, "presumed 0"))
luup(x, cl.get_parent(y))
else:
bar = best.get(y)
if bar and find_in_chain(bar.cod, x, y0):
if bar.cod == y:
art.proclaim(draft, bar)
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(draft, art.extensional(x, y, rel.lt, "presumed 1"))
luup(cl.get_parent(x), y)
else:
# neither x nor y matches by name
art.proclaim(draft, art.extensional(x, y, rel.eq, "presumed mutual"))
luup(cl.get_parent(x), cl.get_parent(y))
def is_match(ar):
c1 = cl.get_checklist(ar.dom)
c2 = cl.get_checklist(ar.cod)
if c1 == c2:
print("%s and %s both in %s" %
(cl.get_name(c1), c2.get_name(c2), c1.prefix))
return False
return True
def is_informative(syn):
name = cl.get_value(syn, canonical_name)
nodes = cl.get_nodes_with_value(cl.get_checklist(syn), canonical_name,
name)
if len(nodes) > 1:
# deal with tangle around Saimiri boliviensis and subspecies
return False
#if cl.is_accepted(nodes[0]):
# return False
return True
def subinfer_partners(x, other):
y = None
for child in cl.get_children(x):
child_ar = subinfer_partners(child, other) # an articulation
if child_ar != None:
child_y = child_ar.cod
if y == None:
y = child_y
else:
y = cl.mrca(y, child_y)
if y != None:
ar = art.extensional(x, y, rel.matches, "cross-mrca")
else:
ar = get_mutual(best, x)
if ar:
assert cl.get_checklist(ar.cod) != cl.get_checklist(x)
if dribble.watch(x):
dribble.log("# Cross-mrca: %s" % (art.express(ar)))
xmrcas[x] = ar
return ar # in B
def analyze_cross_mrcas(A, B, tipwards):
cross_mrcas = {}
def half_analyze_cross_mrcas(checklist, other):
def subanalyze_cross_mrcas(node, other):
result = None
probe = tipwards.get(node)
if probe:
# Could be: = < or >
result = probe.cod
else:
children = cl.get_children(node)
if children:
m = None # None is the identity for mrca
for child in children:
m2 = subanalyze_cross_mrcas(child, other)
if m2 != None:
m = cl.mrca(m, m2) if m != None else m2
if m != None:
result = m
if result:
assert cl.get_checklist(result) != cl.get_checklist(node)
if dribble.watch(node):
dribble.log("# Cross-mrca(%s) = %s" %
(cl.get_unique(node), cl.get_unique(result)))
cross_mrcas[node] = result
return result # in B
for root in cl.get_roots(checklist):
subanalyze_cross_mrcas(root, other)
half_analyze_cross_mrcas(A, B)
half_analyze_cross_mrcas(B, A)
# Sanity check
for node in cross_mrcas:
cross = cross_mrcas[node]
probe = cross_mrcas.get(cross)
if probe:
assert cl.get_checklist(probe) == cl.get_checklist(node)
else:
dribble.log("# No return cross-MRCA for %s -> %s -> ..." %\
(cl.get_unique(node), cl.get_unique(cross)))
return cross_mrcas
def subanalyze_cross_mrcas(node, other):
result = None
probe = tipwards.get(node)
if probe:
# Could be: = < or >
result = probe.cod
else:
children = cl.get_children(node)
if children:
m = None # None is the identity for mrca
for child in children:
m2 = subanalyze_cross_mrcas(child, other)
if m2 != None:
m = cl.mrca(m, m2) if m != None else m2
if m != None:
result = m
if result:
assert cl.get_checklist(result) != cl.get_checklist(node)
if dribble.watch(node):
dribble.log("# Cross-mrca(%s) = %s" %
(cl.get_unique(node), cl.get_unique(result)))
cross_mrcas[node] = result
return result # in B
def direct_matches(node, other):
assert node > 0
assert cl.get_checklist(node) != other
seen = []
arts = []
for prop in [
cl.ncbi_id, cl.eol_page_id, cl.scientific_name, cl.canonical_name,
cl.gbif_id
]:
val = cl.get_value(node, prop)
if val != None:
more = cl.get_nodes_with_value(other, prop, val)
for hit in more:
if hit and not hit in seen:
seen.append(hit)
arts.append(intensional(node, hit, prop.pet_name))
return arts
def bridge(dom, cod, re, reason, revreason=None):
assert cl.get_checklist(dom) != cl.get_checklist(cod)
assert reason
return _articulation(dom, cod, re, reason=reason, revreason=revreason)