def convertOneChunk(gzDir, idFname, inIndexFile, outFile):
# for each row in index:
store = pubStore.PubWriterFile(outFile)
donePiis = pubGeneric.parseDoneIds(idFname)
# log to file
outBase = join(dirname(outFile), basename(outFile).split(".")[0])
logFname = outBase + ".log"
pubGeneric.setupLogging(__file__, None, logFileName=logFname)
idFname = outBase + "_ids.tab"
logging.debug("Writing ids to %s" % idFname)
idFh = open(idFname, "w")
idFh.write("#articleId\texternalId\n")
lastTsvFname = None
tsvFile = None
pmidFinder = pubCompare.PmidFinder()
for row in maxCommon.iterTsvRows(inIndexFile, encoding=None):
# open file and seek, if necessry
if tsvFile == None or lastTsvFname != row.tsvFile:
logging.debug("Seeking to %s in tsvfile %s" %
(row.offset, row.tsvFile))
tsvFile = gzip.open(join(gzDir, row.tsvFile))
tsvFile.seek(int(row.offset))
lastTsvFname = row.tsvFile
line = tsvFile.readline()
if row.url.startswith("!"):
logging.info("Ignoring %s, marked as duplicated" % row.url)
continue
#fields are: ["articleId", "tsvFile", "url", "offset"]
fields = line.split("\t")
url = fields[0]
logging.debug("Replacing weird bing chars")
content = fields[-1]
assert (url == row.url)
assert (len(content) != 0)
url = url.decode("utf8")
logging.debug("Converting to text")
content = convertMicrosoft(content)
artDict, fileDict = convertHtmlToDicts(url, content)
if artDict == None:
artDict, fileDict = minimalHtmlToDicts(url, content)
if artDict == None:
continue
artDict["pmid"] = pmidFinder.lookupPmid(artDict)
# write file
articleId = int(row.articleId)
fileId = articleId * 1000
store.writeFile(articleId, fileId, fileDict)
store.writeArticle(articleId, artDict)
store.close()
def convertOneChunk(gzDir, idFname, inIndexFile, outFile):
# for each row in index:
store = pubStore.PubWriterFile(outFile)
donePiis = pubGeneric.parseDoneIds(idFname)
# log to file
outBase = join(dirname(outFile), basename(outFile).split(".")[0])
logFname = outBase+".log"
pubGeneric.setupLogging(__file__, None, logFileName=logFname)
idFname = outBase+"_ids.tab"
logging.debug("Writing ids to %s" % idFname)
idFh = open(idFname, "w")
idFh.write("#articleId\texternalId\n")
lastTsvFname = None
tsvFile = None
pmidFinder = pubCompare.PmidFinder()
for row in maxCommon.iterTsvRows(inIndexFile, encoding=None):
# open file and seek, if necessry
if tsvFile==None or lastTsvFname!=row.tsvFile:
logging.debug("Seeking to %s in tsvfile %s" % (row.offset, row.tsvFile))
tsvFile = gzip.open(join(gzDir, row.tsvFile))
tsvFile.seek(int(row.offset))
lastTsvFname = row.tsvFile
line = tsvFile.readline()
if row.url.startswith("!"):
logging.info("Ignoring %s, marked as duplicated" % row.url)
continue
#fields are: ["articleId", "tsvFile", "url", "offset"]
fields = line.split("\t")
url = fields[0]
logging.debug("Replacing weird bing chars")
content = fields[-1]
assert(url==row.url)
assert(len(content)!=0)
url = url.decode("utf8")
logging.debug("Converting to text")
content = convertMicrosoft(content)
artDict, fileDict = convertHtmlToDicts(url, content)
if artDict==None:
artDict, fileDict = minimalHtmlToDicts(url, content)
if artDict==None:
continue
artDict["pmid"] = pmidFinder.lookupPmid(artDict)
# write file
articleId = int(row.articleId)
fileId = articleId*1000
store.writeFile(articleId, fileId, fileDict)
store.writeArticle(articleId, artDict)
store.close()
def convertOneChunk(zipDir, inIndexFile, inIdFile, outFile):
"""
get files from inIndexFile, parse Xml,
write everything to outfile in ascii format
"""
store = pubStore.PubWriterFile(outFile)
# read all already done IDs
donePiis = pubGeneric.parseDoneIds(inIdFile)
# open output id files
idFname = join(dirname(outFile), basename(outFile).split(".")[0]+".ids.tab")
logging.debug("Writing ids to %s" % idFname)
idFh = open(idFname, "w")
idFh.write("#articleId\tdoi\texternalId\tpmid\n")
i = 0
inRows = list(maxCommon.iterTsvRows(inIndexFile))
#doi2pmid = None
convCount = 0
skipCount = 0
pmidFinder = pubCompare.PmidFinder()
logging.info("Converting %d files" % len(inRows))
for row in inRows:
# read line
i+=1
articleId = row.articleId
zipFilename, filename = row.zipFilename, row.filename
articleId=int(articleId)
pii = splitext(basename(filename))[0]
if pii in donePiis:
logging.debug("PII %s has already been converted, skipping" % pii)
skipCount += 1
continue
donePiis.add(pii)
# open file from zipfile
fullZipPath = join(zipDir, zipFilename)
zipFile = zipfile.ZipFile(fullZipPath)
logging.debug("Parsing %s, file %s, %d files left" % (fullZipPath, filename, len(inRows)-i))
#if doi2pmid==None:
#doi2pmid = parseDoi2Pmid(baseDir)
xmlString = zipFile.open(filename).read()
try:
xmlTree = pubXml.etreeFromXml(xmlString)
except lxml.etree.XMLSyntaxError:
logging.error("XML parse error, skipping file %s, %s" % (zipFilename, filename))
continue
# parse xml
articleData = pubStore.createEmptyArticleDict(publisher="elsevier")
articleData = parseElsevier(xmlTree, articleData)
if articleData==None:
logging.warn("Parser got no data for %s" % filename)
continue
articleData["origFile"]=zipFilename+":"+filename
#if articleData["doi"] in doi2pmid:
#articleData["pmid"] = doi2pmid[articleData["doi"]]
articleData["externalId"]=pii
articleData["fulltextUrl"]="http://www.sciencedirect.com/science/svapps/pii/"+pii
#articleData["pmid"] = pmidFinder.lookupPmid(articleData)
# convert to ascii
asciiString, mimeType = treeToAscii_Elsevier(xmlTree)
if asciiString==None:
logging.warn("No ASCII for %s / %s" % (zipFilename, filename))
continue
store.writeArticle(articleId, articleData)
# write IDs to separate file
idRow = [str(articleData["articleId"]), articleData["doi"], articleData["externalId"], str(articleData["pmid"])]
idFh.write("\t".join(idRow))
idFh.write("\n")
# write to output
fileData = createFileData(articleData, mimeType, asciiString)
store.writeFile(articleId, (1000*(articleId))+1, fileData, externalId=articleData["externalId"])
convCount += 1
logging.info("Converted %d files, skipped %d" % (convCount, skipCount))
store.close()
idFh.close()
def convertOneChunk(zipDir, inIndexFile, inIdFile, outFile):
"""
get files from inIndexFile, parse Xml,
write everything to outfile in ascii format
"""
store = pubStore.PubWriterFile(outFile)
# read all already done IDs
donePiis = pubGeneric.parseDoneIds(inIdFile)
# open output id files
idFname = join(dirname(outFile),
basename(outFile).split(".")[0] + ".ids.tab")
logging.debug("Writing ids to %s" % idFname)
idFh = open(idFname, "w")
idFh.write("#articleId\tdoi\texternalId\tpmid\n")
i = 0
inRows = list(maxCommon.iterTsvRows(inIndexFile))
#doi2pmid = None
convCount = 0
skipCount = 0
pmidFinder = pubCompare.PmidFinder()
logging.info("Converting %d files" % len(inRows))
for row in inRows:
# read line
i += 1
articleId = row.articleId
zipFilename, filename = row.zipFilename, row.filename
articleId = int(articleId)
pii = splitext(basename(filename))[0]
if pii in donePiis:
logging.debug("PII %s has already been converted, skipping" % pii)
skipCount += 1
continue
donePiis.add(pii)
# open file from zipfile
fullZipPath = join(zipDir, zipFilename)
zipFile = zipfile.ZipFile(fullZipPath)
logging.debug("Parsing %s, file %s, %d files left" %
(fullZipPath, filename, len(inRows) - i))
#if doi2pmid==None:
#doi2pmid = parseDoi2Pmid(baseDir)
xmlString = zipFile.open(filename).read()
try:
xmlTree = pubXml.etreeFromXml(xmlString)
except lxml.etree.XMLSyntaxError:
logging.error("XML parse error, skipping file %s, %s" %
(zipFilename, filename))
continue
# parse xml
articleData = pubStore.createEmptyArticleDict(publisher="elsevier")
articleData = parseElsevier(xmlTree, articleData)
if articleData == None:
logging.warn("Parser got no data for %s" % filename)
continue
articleData["origFile"] = zipFilename + ":" + filename
#if articleData["doi"] in doi2pmid:
#articleData["pmid"] = doi2pmid[articleData["doi"]]
articleData["externalId"] = pii
articleData[
"fulltextUrl"] = "http://www.sciencedirect.com/science/svapps/pii/" + pii
#articleData["pmid"] = pmidFinder.lookupPmid(articleData)
# convert to ascii
asciiString, mimeType = treeToAscii_Elsevier(xmlTree)
if asciiString == None:
logging.warn("No ASCII for %s / %s" % (zipFilename, filename))
continue
store.writeArticle(articleId, articleData)
# write IDs to separate file
idRow = [
str(articleData["articleId"]), articleData["doi"],
articleData["externalId"],
str(articleData["pmid"])
]
idFh.write("\t".join(idRow))
idFh.write("\n")
# write to output
fileData = createFileData(articleData, mimeType, asciiString)
store.writeFile(articleId, (1000 * (articleId)) + 1,
fileData,
externalId=articleData["externalId"])
convCount += 1
logging.info("Converted %d files, skipped %d" % (convCount, skipCount))
store.close()
idFh.close()
