def make_binaries (article, L, R, threshold=8000):
logger = LoggingUtil.init_logging (__file__)
result = []
for l in L:
for r in R:
distance = abs(l.docPos - r.docPos)
logger.debug ("Distance - {0}".format (distance))
if distance < threshold:
if article.date.find ("--") > -1:
article.date = "0-0-9000"
binary = KinaseBinary (id = 0,
L = l.word,
R = r.word,
docDist = abs(l.docPos - r.docPos),
paraDist = abs(l.paraPos - r.paraPos),
sentDist = abs(l.sentPos - r.sentPos),
code = 0,
fact = False,
refs = [],
pmid = article.id,
date = SerUtil.parse_date (article.date),
file_name = article.fileName)
logger.info ("Binary: {0}".format (binary))
result.append (binary)
return result
def find_before (pmid_date, facts):
logger.info ("Join facts with the pmid->date map to find interactions noticed before published discovery.")
ref_pmid_to_binary = facts.map (lambda r : ( r[1][1].pmid, r[1][0] ) ) # ( intact.REF[pmid] -> KinaseBinary )
# TEST. Add reference pmids with late dates.
pmid_date = pmid_date.union (ref_pmid_to_binary.map (lambda r : ( r[0], SerUtil.parse_date ("1-1-2300") )))
before = ref_pmid_to_binary. \
join (pmid_date). \
map (lambda r : r[1][0].copy (ref_date = r[1][1]) ). \
filter (lambda k : k.date and k.ref_date and k.date < k.ref_date). \
distinct ()
return before
def get_article_guesses (article):
guesses = article.AB + article.BC + article.AC + article.BB
skiplist = [ 'for', 'was', 'she', 'long' ]
result = []
for g in guesses:
if not g.L in skiplist and not g.R in skiplist:
g.pmid = article.id
try:
date = SUtil.parse_date (article.date)
if date:
g.date = calendar.timegm (date.timetuple())
# print ("Parsed guess date -> {0}".format (g.date))
except:
print ("No date parsed in {0} {1}".format (article.fileName, article.date))
traceback.print_exc ()
result.append ( ( make_key (g.L, g.R, g.pmid), Guesses.distance (g) ) )
return result
