def findMethods(text):
" find mat & method section in text "
sections = pubGeneric.sectionRanges(text)
if sections==None:
return None
if "methods" not in sections:
return None
methodStart, methodEnd = sections["methods"]
text = text[methodStart:methodEnd]
return text
def findMethods(text):
" find mat & method section in text "
sections = pubGeneric.sectionRanges(text)
if sections == None:
return None
if "methods" not in sections:
return None
methodStart, methodEnd = sections["methods"]
text = text[methodStart:methodEnd]
return text
def writeAnnotations(alg, articleData, fileData, outFh, annotIdAdd, doSectioning, addFields):
""" use alg to annotate fileData, write to outFh, adding annotIdAdd to all annotations
return next free annotation id.
"""
annotDigits = int(pubConf.ANNOTDIGITS)
fileDigits = int(pubConf.FILEDIGITS)
annotIdStart = (int(fileData.fileId) * (10**annotDigits)) + annotIdAdd
logging.debug("fileId %s, annotIdStart %d, fileLen %d" % (fileData.fileId, annotIdStart, len(fileData.content)))
text = fileData.content.replace("\a", "\n")
if fileData.fileType=="supp":
sections = {"supplement": (0, len(text))}
else:
allTextSections = {"unknown": (0, len(text))}
if doSectioning:
sections = pubGeneric.sectionRanges(text)
if sections==None:
sections = allTextSections
else:
sections = allTextSections
annotCount = 0
for section, sectionRange in sections.iteritems():
secStart, secEnd = sectionRange
if section!="unknown":
logging.debug("Annotating section %s, from %d to %d" % (section, secStart, secEnd))
secText = text[secStart:secEnd]
fileData = fileData._replace(content=secText)
annots = alg.annotateFile(articleData, fileData)
if annots==None:
logging.debug("No annotations received")
continue
for row in annots:
# prefix with fileId, extId
logging.debug("received annotation row: %s" % str(row))
fields = ["%018d" % (int(annotIdStart)+annotCount)]
if articleData!=None:
extId = articleData.externalId
else:
extId = "0"
fields.append(extId)
# add addFields
artDict = articleData._asdict()
if addFields!=None:
for addField in addFields:
fields.append(artDict.get(addField, ""))
# add other fields
fields.extend(row)
# check if alg actually returns coordinates
if alg.headers[0]=="start" and alg.headers[1]=="end":
start, end = row[0:2]
if (start,end) == (0,0):
snippet = None
else:
snippet = getSnippet(secText, start, end)
# lift start and end if sectioning
start = secStart+int(start)
end = secStart+int(end)
# postfix with snippet
logging.debug("Got row: %s" % str(row))
if doSectioning:
fields.append(section)
if snippet!=None:
fields.append(snippet)
#fields = [unicode(x).encode("utf8") for x in fields]
fields = [pubStore.removeTabNl(unicode(x)) for x in fields]
line = "\t".join(fields)
outFh.write(line+"\n")
annotCount+=1
assert(annotCount<10**annotDigits) # we can only store 100.000 annotations per file
return annotCount