def get_approximate_matches(self, query):
"""
Approximate matching strategy using query_runs and multiple local
alignments (aka. diff) Return a list of matches.
"""
matches = []
# we exclude small and "weak" rules from the subset entirely: they are
# unlikely to be matchable with a seq match
rules_subset = (self.regular_rids | self.small_rids).difference(
self.weak_rids)
for query_run in query.query_runs:
if not query_run.is_matchable(include_low=True):
continue
# per query run hash matching just in case we are lucky
hash_matches = match_hash.hash_match(self, query_run)
if hash_matches:
matches.extend(hash_matches)
continue
# inverted index match and ranking, query run-level
# FIXME: we should consider aho matches to excludes them from candidates
# FIXME: also exclude from candidates any rule that is only aho-matchable
run_matches = []
MAX_CANDIDATES = 50
candidates = match_set.compute_candidates(
query_run, self, rules_subset=rules_subset, top=MAX_CANDIDATES)
# multiple sequence matching/alignment, query run-level
for candidate in candidates:
start_offset = 0
while True:
rule_matches = match_seq.match_sequence(
self, candidate, query_run, start_offset=start_offset)
if not rule_matches:
break
else:
matches_end = max(m.qend for m in rule_matches)
run_matches.extend(rule_matches)
if matches_end + 1 < query_run.end:
start_offset = matches_end + 1
continue
else:
break
matches.extend(match.merge_matches(run_matches, max_dist=MAX_DIST))
return matches
def get_approximate_matches(self, query, matched_qspans=None, **kwargs):
"""
Approximate matching strategy breaking a query in query_runs and using
exacat matching then multiple local alignments (aka. diff). Return a
list of matches.
"""
matches = []
rules_subset = self.approx_matchable_rules_subset
for query_run in query.query_runs:
if not query_run.is_matchable(include_low=False,
qspans=matched_qspans):
continue
# inverted index match and ranking, query run-level
# FIXME: we should consider aho matches to excludes them from candidates
# FIXME: also exclude from candidates any rule that is only aho-matchable
run_matches = []
MAX_CANDIDATES = 50
candidates = match_set.compute_candidates(
query_run, self, rules_subset=rules_subset, top=MAX_CANDIDATES)
# multiple sequence matching/alignment, query run-level
for candidate in candidates:
start_offset = 0
while True:
rule_matches = match_seq.match_sequence(
self, candidate, query_run, start_offset=start_offset)
if not rule_matches:
break
else:
matches_end = max(m.qend for m in rule_matches)
run_matches.extend(rule_matches)
if matches_end + 1 < query_run.end:
start_offset = matches_end + 1
continue
else:
break
matches.extend(match.merge_matches(run_matches, max_dist=MAX_DIST))
return matches
def get_approximate_matches(self, query, matched_qspans, existing_matches,
deadline=sys.maxsize, **kwargs):
"""
Approximate matching strategy breaking a query in query_runs and using
multiple local alignments (aka. diff). Return a list of matches.
"""
matches = []
matchable_rids = self.approx_matchable_rids
already_matched_qspans = matched_qspans[:]
MAX_NEAR_DUPE_CANDIDATES = 10
# first check if the whole file may be close, near-dupe match
whole_query_run = query.whole_query_run()
near_dupe_candidates = match_set.compute_candidates(
query_run=whole_query_run,
idx=self,
matchable_rids=matchable_rids,
top=MAX_NEAR_DUPE_CANDIDATES,
high_resemblance=True,
_use_bigrams=USE_BIGRAM_MULTISETS,
)
# if near duplicates, we only match the whole file at once against these
# candidates
if near_dupe_candidates:
if TRACE_APPROX_CANDIDATES:
logger_debug('get_query_run_approximate_matches: near dupe candidates:')
for rank, ((sv1, sv2), _rid, can, _inter) in enumerate(near_dupe_candidates, 1):
logger_debug(rank, sv1, sv2, can.identifier)
matched = self.get_query_run_approximate_matches(
whole_query_run, near_dupe_candidates, already_matched_qspans, deadline)
matches.extend(matched)
# subtract these
for match in matched:
qspan = match.qspan
query.subtract(qspan)
already_matched_qspans.append(qspan)
# break if deadline has passed
if time() > deadline:
return matches
# otherwise, and in all cases we break things in smaller query runs and
# match each separately
if USE_RULE_STARTS:
query.refine_runs()
if TRACE_APPROX:
logger_debug('get_approximate_matches: len(query.query_runs):', len(query.query_runs))
MAX_CANDIDATES = 70
for query_run in query.query_runs:
# inverted index match and ranking, query run-level
candidates = match_set.compute_candidates(
query_run=query_run,
idx=self,
matchable_rids=matchable_rids,
top=MAX_CANDIDATES,
high_resemblance=False,
_use_bigrams=USE_BIGRAM_MULTISETS,
)
if TRACE_APPROX_CANDIDATES:
logger_debug('get_query_run_approximate_matches: candidates:')
for rank, ((sv1, sv2), _rid, can, _inter) in enumerate(candidates, 1):
logger_debug(rank, sv1, sv2, can.identifier)
matched = self.get_query_run_approximate_matches(
query_run, candidates, matched_qspans, deadline)
matches.extend(matched)
# break if deadline has passed
if time() > deadline:
break
return matches
def match(self,
location=None,
query_string=None,
min_score=0,
detect_negative=True):
"""
Return a sequence of LicenseMatch by matching the file at `location` or
the `query_string` text against the index. Only include matches with
scores greater or equal to `min_score`.
`detect_negative` is for testing purpose only.
"""
assert 0 <= min_score <= 100
if TRACE:
print()
logger_debug('match start....')
if not location and not query_string:
return []
qry = query.build_query(location, query_string, self)
if not qry:
logger_debug('#match: No query returned for:', location)
return []
#######################################################################
# Whole file matching: hash, negative and exact matching
#######################################################################
whole_query_run = qry.whole_query_run()
if not whole_query_run or not whole_query_run.matchables:
logger_debug('#match: whole query not matchable')
return []
# hash
hash_matches = match_hash(self, whole_query_run)
if hash_matches:
self.debug_matches(hash_matches, '#match FINAL Hash matched',
location, query_string)
set_lines(hash_matches, qry.line_by_pos)
return hash_matches
# negative rules exact matching
negative = []
# note: detect_negative is false only to test negative rules detection proper
if detect_negative and self.negative_rids:
if TRACE: logger_debug('#match: NEGATIVE')
negative = self.negative_match(whole_query_run)
for neg in negative:
if TRACE_NEGATIVE:
self.debug_matches(negative,
' ##match: NEGATIVE subtracting #:',
location, query_string)
whole_query_run.subtract(neg.qspan)
if TRACE_NEGATIVE:
logger_debug(' #match: NEGATIVE found', negative)
# exact matches
if TRACE_EXACT: logger_debug('#match: EXACT')
exact_matches = exact_match(self, whole_query_run,
self.rules_automaton)
if TRACE_EXACT:
self.debug_matches(exact_matches, ' #match: EXACT matches#:',
location, query_string)
exact_matches, exact_discarded = refine_matches(exact_matches,
self,
query=qry)
if TRACE_EXACT:
self.debug_matches(exact_matches,
' #match: ===> exact matches refined')
if TRACE_EXACT:
self.debug_matches(exact_discarded,
' #match: ===> exact matches discarded')
matches = exact_matches
discarded = exact_discarded
#######################################################################
# Per query run matching.
#######################################################################
if TRACE: logger_debug('#match: #QUERY RUNS:', len(qry.query_runs))
# check if we have some matchable left
# collect qspans matched exactly e.g. with coverage 100%
# this coverage check is because we have provision to match fragments (unused for now)
matched_qspans = [
m.qspan for m in exact_matches if m.coverage() == 100
]
# do not match futher if we do not need to
if whole_query_run.is_matchable(include_low=True,
qspans=matched_qspans):
rules_subset = (self.regular_rids | self.small_rids)
for qrnum, query_run in enumerate(qry.query_runs, 1):
if TRACE_QUERY_RUN_SIMPLE:
logger_debug('#match: ===> processing query run #:', qrnum)
logger_debug(' #match:', query_run)
if not query_run.is_matchable(include_low=True):
if TRACE: logger_debug('#match: query_run NOT MATCHABLE')
continue
# hash match
#########################
hash_matches = match_hash(self, query_run)
if hash_matches:
if TRACE:
self.debug_matches(
hash_matches, ' #match Query run matches (hash)',
location, query_string)
matches.extend(hash_matches)
continue
# query run match proper using sequence matching
#########################################
if TRACE:
logger_debug(' #match: Query run MATCHING proper....')
run_matches = []
candidates = compute_candidates(query_run,
self,
rules_subset=rules_subset,
top=40)
if TRACE_QUERY_RUN:
logger_debug(
' #match: query_run: number of candidates for seq match #',
len(candidates))
for candidate_num, candidate in enumerate(candidates):
if TRACE_QUERY_RUN:
logger_debug(
' #match: query_run: seq matching candidate#:',
candidate_num, 'candidate:', candidate)
start_offset = 0
while True:
rule_matches = match_sequence(
self,
candidate,
query_run,
start_offset=start_offset)
if TRACE_QUERY_RUN and rule_matches:
self.debug_matches(
rule_matches,
' #match: query_run: seq matches for candidate'
)
if not rule_matches:
break
else:
matches_end = max(m.qend for m in rule_matches)
run_matches.extend(rule_matches)
if matches_end + 1 < query_run.end:
start_offset = matches_end + 1
continue
else:
break
############################################################################
if TRACE_QUERY_RUN:
self.debug_matches(run_matches,
' #match: ===> Query run matches',
location,
query_string,
with_text=True)
run_matches = merge_matches(run_matches, max_dist=MAX_DIST)
matches.extend(run_matches)
if TRACE:
self.debug_matches(
run_matches, ' #match: Query run matches merged',
location, query_string)
# final matching merge, refinement and filtering
################################################
if matches:
logger_debug()
logger_debug(
'!!!!!!!!!!!!!!!!!!!!REFINING!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
self.debug_matches(matches,
'#match: ALL matches from all query runs',
location, query_string)
matches, whole_discarded = refine_matches(matches,
idx=self,
query=qry,
min_score=min_score,
max_dist=MAX_DIST // 2)
if TRACE_MATCHES_DISCARD:
discarded.extend(whole_discarded)
matches.sort()
set_lines(matches, qry.line_by_pos)
self.debug_matches(matches, '#match: FINAL MERGED', location,
query_string)
if TRACE_MATCHES_DISCARD:
self.debug_matches(discarded, '#match: FINAL DISCARDED',
location, query_string)
self.debug_matches(matches,
'#match: FINAL MATCHES',
location,
query_string,
with_text=True)
return matches
def match(self, location=None, query_string=None, min_score=0, detect_negative=True):
"""
Return a sequence of LicenseMatch by matching the file at `location` or
the `query_string` text against the index. Only include matches with
scores greater or equal to `min_score`.
`detect_negative` is for testing purpose only.
"""
assert 0 <= min_score <= 100
if TRACE:
print()
logger_debug('match start....')
if not location and not query_string:
return []
qry = query.build_query(location, query_string, self)
if not qry:
logger_debug('#match: No query returned for:', location)
return []
#######################################################################
# Whole file matching: hash and exact matching
#######################################################################
whole_query_run = qry.whole_query_run()
if not whole_query_run or not whole_query_run.matchables:
logger_debug('#match: whole query not matchable')
return []
# hash
hash_matches = match_hash.hash_match(self, whole_query_run)
if hash_matches:
if TRACE: self.debug_matches(hash_matches, '#match FINAL Hash matched', location, query_string)
match.set_lines(hash_matches, qry.line_by_pos)
return hash_matches
# negative rules exact matching
negative_matches = []
# note: detect_negative is false only to test negative rules detection proper
if detect_negative and self.negative_rids:
if TRACE: logger_debug('#match: NEGATIVE')
negative_matches = self.negative_match(whole_query_run)
for neg in negative_matches:
whole_query_run.subtract(neg.qspan)
# exact matches
if TRACE_EXACT: logger_debug('#match: EXACT')
exact_matches = match_aho.exact_match(self, whole_query_run, self.rules_automaton)
if TRACE_EXACT: self.debug_matches(exact_matches, ' #match: EXACT matches#:', location, query_string)
exact_matches, exact_discarded = match.refine_matches(exact_matches, self, query=qry, filter_false_positive=False, merge=False)
if TRACE_EXACT: self.debug_matches(exact_matches, ' #match: ===> exact matches refined')
if TRACE_EXACT: self.debug_matches(exact_discarded, ' #match: ===> exact matches discarded')
matches = exact_matches
discarded = exact_discarded
#######################################################################
# Per query run matching.
#######################################################################
if TRACE: logger_debug('#match: #QUERY RUNS:', len(qry.query_runs))
# check if we have some matchable left
# collect qspans matched exactly e.g. with coverage 100%
# this coverage check is because we have provision to match fragments (unused for now)
matched_qspans = [m.qspan for m in exact_matches if m.coverage() == 100]
# do not match futher if we do not need to
if whole_query_run.is_matchable(include_low=True, qspans=matched_qspans):
# FIXME: we should exclude small and "weak" rules from the subset entirely
# they are unlikely to be matchable with a seq match
rules_subset = (self.regular_rids | self.small_rids)
for qrnum, query_run in enumerate(qry.query_runs, 1):
if TRACE_QUERY_RUN_SIMPLE:
logger_debug('#match: ===> processing query run #:', qrnum)
logger_debug(' #match:query_run:', query_run)
if not query_run.is_matchable(include_low=True):
if TRACE: logger_debug('#match: query_run NOT MATCHABLE')
continue
# hash match
#########################
hash_matches = match_hash.hash_match(self, query_run)
if hash_matches:
if TRACE: self.debug_matches(hash_matches, ' #match Query run matches (hash)', location, query_string)
matches.extend(hash_matches)
continue
# FIXME: why do not we aho match again here? This would avoid
# going into the costly set and seq re-match that may not be needed at all
# alternatively we should consider aho matches to excludes them from candidates
# query run match proper using sequence matching
#########################################
if TRACE: logger_debug(' #match: Query run MATCHING proper....')
run_matches = []
candidates = match_set.compute_candidates(query_run, self, rules_subset=rules_subset, top=40)
if TRACE_CANDIDATES: logger_debug(' #match: query_run: number of candidates for seq match #', len(candidates))
for candidate_num, candidate in enumerate(candidates):
if TRACE_QUERY_RUN:
_, canrule, _ = candidate
logger_debug(' #match: query_run: seq matching candidate#:', candidate_num, 'candidate:', canrule)
start_offset = 0
while True:
rule_matches = match_seq.match_sequence(self, candidate, query_run, start_offset=start_offset)
if TRACE_QUERY_RUN and rule_matches:
self.debug_matches(rule_matches, ' #match: query_run: seq matches for candidate', with_text=True, query=qry)
if not rule_matches:
break
else:
matches_end = max(m.qend for m in rule_matches)
run_matches.extend(rule_matches)
if matches_end + 1 < query_run.end:
start_offset = matches_end + 1
continue
else:
break
############################################################################
if TRACE_QUERY_RUN: self.debug_matches(run_matches, ' #match: ===> Query run matches', location, query_string, with_text=True, query=qry)
run_matches = match.merge_matches(run_matches, max_dist=MAX_DIST)
matches.extend(run_matches)
if TRACE: self.debug_matches(run_matches, ' #match: Query run matches merged', location, query_string)
# final matching merge, refinement and filtering
################################################
if matches:
logger_debug()
logger_debug('!!!!!!!!!!!!!!!!!!!!REFINING!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
self.debug_matches(matches, '#match: ALL matches from all query runs', location, query_string)
matches, whole_discarded = match.refine_matches(matches, idx=self, query=qry, min_score=min_score, max_dist=MAX_DIST // 2, filter_false_positive=True)
if TRACE_MATCHES_DISCARD:
discarded.extend(whole_discarded)
matches.sort()
match.set_lines(matches, qry.line_by_pos)
self.debug_matches(matches, '#match: FINAL MERGED', location, query_string)
if TRACE_MATCHES_DISCARD: self.debug_matches(discarded, '#match: FINAL DISCARDED', location, query_string)
self.debug_matches(matches, '#match: FINAL MATCHES', location, query_string, with_text=True, query=qry)
return matches
