def report_on_collisions(A, B, al):
index = cl.index_by_value(A, canonical_name)
for name in index:
A_nodes = index[name]
if len(A_nodes) == 1:
B_nodes = cl.get_nodes_with_value(B, canonical_name, name)
if B_nodes and len(B_nodes) == 1:
A_node = A_nodes[0]
B_node = B_nodes[0]
if cl.is_accepted(A_node) and cl.is_accepted(B_node):
ar1 = al.get(A_node)
ar2 = al.get(B_node)
ar1_bad = (ar1 and ar1.relation == rel.eq
and ar1.cod != B_node)
ar2_bad = (ar2 and ar2.relation == rel.eq
and ar2.cod != A_node)
if ar1_bad or ar2_bad:
dribble.log(
"# \"%s\" names different taxa in the two checklists"
% name)
dribble.log(" %s [%s]" %
(art.express(ar1),
art.reason(ar1) if ar1 else "-"))
dribble.log(" %s [%s]" %
(art.express(ar2),
art.reason(ar2) if ar2 else "-"))
def process(node, less):
if not draft.get(node):
e = extensional_match(node, xmrcas)
if e:
if e.relation == rel.lt:
if less and e.cod == less.cod:
print("# Suppressing %s because redundant with\n %s" %
(art.express(e), art.express(less)))
pass
else:
less = e
ext[node] = e
else:
less = None
ext[node] = e
else:
less = None
for child in cl.get_children(node):
process(child, less)
def process(here, there):
for node in here.get_all_nodes():
if cl.is_accepted(node) and not node in best:
ar = best_intensional_match(node, there)
if dribble.watch(node):
dribble.log("# Best: %s" % art.express(ar))
if ar:
assert ar.dom == node
assert cl.is_accepted(ar.cod)
art.half_proclaim(best, ar)
def filter(node):
debug = dribble.watch(node)
found_match = None
for child in cl.get_children(node):
ar = filter(child)
if ar:
found_match = ar
if found_match: # Some descendant is a particle
if debug: dribble.log("# %s: descendant matches, not keeping: %s" %
(cl.get_unique(node), art.express(found_match)))
return found_match
elif node in amap:
ar = amap[node]
tw[ar.dom] = ar
if debug: dribble.log("# %s is a tipward match, keeping: %s" %
(cl.get_unique(node), art.express(ar)))
return ar
else:
if debug: dribble.log("# %s is unmatched" % cl.get_unique(node))
return None
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 extensional_match(node, xmrcas):
partner = xmrcas.get(node) # node in other checklist; 'conode'
if not partner:
# Descendant of a particle
if dribble.watch(node):
dribble.log("# EM: %s is not tipward." % cl.get_unique(node))
return None
back = xmrcas.get(partner) # 'bounce'
if not back:
# Not sure how this can happen but it does (NCBI vs. GBIF)
dribble.log("%s <= %s <= nowhere" % (cl.get_unique(node),
cl.get_unique(partner)))
if dribble.watch(node):
dribble.log("# EM: %s killed because aborted round trip." % cl.get_unique(node))
return None
# node <= partner <= back
how = cl.how_related(node, back) # Alway rcc5
if how == rel.eq:
# Should end up being eq iff name match or unique match
# Can test for unique match by looking at xmrca of parent
# Could be part of a 'monotypic' chain; fix later
how = rel.matches
reason = "mutual-cross-mrca"
elif how == rel.gt:
how = rel.matches
reason = "monotypic-inversion"
elif how == rel.disjoint:
reason = "particle-set-exclusion"
else: # must be rel.lt
# Assume resolution (node < partner) until conflict is proven
reason = "refinement"
# Look for an intersection between any partner-child and node
# x is in A checklist, y is in B checklist
for pchild in cl.get_children(partner):
pchild_back = xmrcas.get(pchild)
if pchild_back == None:
# pchild ! node
pass
else:
(d, e) = cross_compare(node, pchild, xmrcas)
# d < node while e ! node
if d and e:
how = rel.conflict
reason = ("%s is in; its sibling %s is not" %
(cl.get_unique(d), cl.get_unique(e)))
dribble.log("** %s conflicts with %s because\n"
" %s ! %s\n (but sibling %s < %s)" %
(cl.get_unique(node),
cl.get_unique(partner),
cl.get_unique(e),
cl.get_unique(node),
cl.get_unique(d),
cl.get_unique(node)))
break
elif e:
reason = ("%s is not in it" % cl.get_unique(e))
ar = art.extensional(node, partner, how, reason)
if dribble.watch(node):
dribble.log("# Extensional articulation %s" % art.express(ar))
return ar