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pubConvGoogle
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pubConvGoogle
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#!/usr/bin/env python
# required option, supplied by google when you register a search project
# Google also checks IP address
PROJECTID = "annotatepublicgenomedata-soe.ucsc.edu"
# maximum filesize to convert (binary)
MAXFILESIZE = 50000000
# maximum filesize to store (ASCII)
MAXASCIISIZE = 30000000
# how many chunks to split the index file in
CHUNKCOUNT=1000
# do not download any files from domains with a keyword in here
BLACKLIST = ["sciencedirect", "ncbi.nlm.nih.gov", "springerlink",\
"pnas", "nature.com", "genome.cshlp.org", "jstor.org", "sciencemag", \
"oxfordjournals", "blackwell", "wiley.com", "genecards", \
"biomedcentral", "jbc.org", "ukpmc", "plosone.org", "www.plos"]
WGETOPTIONS = " --tries=3 --dns-timeout=10 --read-timeout=10 --ignore-length --user-agent='Googlebot/2.1 (compatible; GenomeBot0.1-crawling-for-DNA; +http://hgwdev.soe.ucsc.edu/~max)'"
import optparse, os, sys, urllib, urllib2, xml.dom.minidom, logging, urlparse, time, codecs, glob, tempfile, traceback
from os.path import *
# add <scriptDir>/lib/ to package search path
progFile = os.path.abspath(sys.argv[0])
progDir = os.path.dirname(progFile)
pubToolsLibDir = os.path.join(progDir, "lib")
sys.path.insert(0, pubToolsLibDir)
import pubGeneric, pubStore, util, maxCommon, maxRun, pubConf
import robotexclusionrulesparser as rp
# === COMMAND LINE INTERFACE, OPTIONS AND HELP ===
parser = optparse.OptionParser("""usage: %prog [options] index|download targetDir ["search terms"] - search for hits with google and write to output file
command "index":
need to specify search terms
generates index.tab by querying Google for random nucleotides
command "download":
submits cluster jobs to download, no need to specify search terms again
""")
parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
parser.add_option("-v", "--verbose", dest="verbose", action="store_true", help="show more debug messages")
parser.add_option("-s", "--startSeqLen", dest="startSeqLen", action="store", type="int", help="minimum sequence length to try, default %default", default=5)
parser.add_option("-e", "--endSeqLen", dest="endSeqLen", action="store", type="int", help="maximum sequence length to try, default %default", default=5)
parser.add_option("-f", "--seqFile", dest="seqFile", action="store", help="file with sequences to try, instead of generating DNA sequences exhaustively", default=None)
parser.add_option("-l", "--maxDownload", dest="maxDownload", action="store", type="int", \
help="stop downloading after x files", default=1000)
(options, args) = parser.parse_args()
# --- PART COPIED FROM GOOGLE EXAMPLE ---
# Copyright 2007 Google Inc.
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
class Response(object):
'''A wrapper around the XML of a search response'''
def __init__(self, node):
'''Construct a wrapper around an XML search response.
Exposes the following properties:
terms : the requested search terms
size: the requested number of search results
start: the requested start index (offset 0)
first: the index (offset 1) of the first result in the response
last: the index (offset 1) of the last result in the response
total: the total number of search results
results: a sequence of Result instances
Args:
node: An xml.dom.Node instance containing the search response
'''
# Parse the response for information about the request
self.terms = GetText(node.getElementsByTagName('Q')[0])
params = node.getElementsByTagName('PARAM')
for param in params:
name = param.getAttribute('name')
if name == 'num':
self.size = param.getAttribute('value')
elif name == 'start':
self.start = param.getAttribute('value')
# Parse the response for metadata about the results
elemList = node.getElementsByTagName('RES')
if len(elemList)==0:
logging.info("No result found")
self.total=0
else:
res = elemList[0]
self.total = GetText(res.getElementsByTagName('M')[0])
self.first = res.getAttribute('SN')
self.last = res.getAttribute('EN')
self.results = []
# Parse the individual results
[self.results.append(Result(r)) for r in res.getElementsByTagName('R')]
def __str__(self):
'''Return a representation of this instance as a unicode string'''
s = 'terms: %s\n' % self.terms
s += 'size: %s\n' % self.size
s += 'start: %s\n' % self.start
s += 'first: %s\n' % self.first
s += 'last: %s\n' % self.last
s += 'total: %s\n' % self.total
s += 'results: \n'
for result in self.results:
s += unicode(result)
return s
class Result(object):
'''A wrapper around the XML of an individual result'''
def __init__(self, node):
'''Construct a wrapper around an XML search result.
Exposes the following properties:
index: the index of the result (offset 1)
url: the address of the page matching the request
encoded_url: the url-encoded address of the page matching the request
title: the title of the page matching the request, includes <b> tags
title_no_bold: the title of the page matching the request, no <b> tags
Args:
node: An xml.dom.Node instance containing a search result
'''
self.index = node.getAttribute('N')
self.url = GetText(node.getElementsByTagName('U')[0])
self.encoded_url = GetText(node.getElementsByTagName('UE')[0])
titles = node.getElementsByTagName('T')
if len(titles)>0:
self.title = GetText(titles[0])
self.title_no_bold = GetText(node.getElementsByTagName('TNB')[0])
else:
self.title=""
self.title_no_bold = ""
#print self.url, self.title
def __str__(self):
'''Return a representation of this instance as a unicode string'''
s = ' index: %s\n' % self.index
s += ' url: %s\n' % self.url
s += ' encoded_url: %s\n' % self.encoded_url
s += ' title: %s\n' % self.title
s += ' title_no_bold: %s\n' % self.title_no_bold
return s
def parseWgetLog(logFile):
" parse a wget logfile and return mimetype "
# Content-Type: text/html; charset=utf-8
lines = logFile.readlines()
logging.log(5, "Wget logfile: %s" % " / ".join(lines))
for l in lines:
if l.strip().lower().startswith("content-type:"):
logging.debug("wget mime type line: %s" % l.strip("\n"))
mimeParts = l.strip("\n").split()
if len(mimeParts)>1:
mimeType = mimeParts[1]
mimeType = mimeType.split(";")[0]
return mimeType
logging.warn("No mimetype found, returning text/html")
return "text/html"
def wget(url, getMime=True):
" download url with wget and return (content, mimeType) tuple "
url = url.replace("'", "")
tmpFile = tempfile.NamedTemporaryFile(dir = pubConf.getTempDir(), prefix="WgetGoogleCrawler", suffix=".data")
cmd = "wget '%s' -O %s --server-response" % (url, tmpFile.name)
cmd += WGETOPTIONS
if getMime:
logFile = tempfile.NamedTemporaryFile(dir = pubConf.getTempDir(), \
prefix="WgetGoogleCrawler", suffix=".log")
cmd += " -o %s " % logFile.name
pubGeneric.runCommandTimeout(cmd, timeout=10)
if getMime:
mimeType = parseWgetLog(logFile)
else:
mimeType = None
data = tmpFile.read()
logging.debug("Downloaded raw data size: %d" % len(data))
if len(data)==0:
data = None
return data, mimeType
def GetText(node):
'''Extract the contents of a xml.dom.Nodelist as a string.
Args:
nodelist: An xml.dom.Node instance
Returns:
a string containing the contents of all node.TEXT_NODE instances
'''
text = []
for child in node.childNodes:
if child.nodeType == xml.dom.Node.TEXT_NODE:
text.append(child.data)
return ''.join(text)
def Search(id, size, start, terms):
'''Perform a search and print the results to standard out.
Args:
id: the assigned service id
size: the desired size of the search response ('small' or 'large')
start: the index of the first search result
terms: the terms to search for
Returns:
A Response instance representing the search results
'''
logging.debug("Running search for %s with start %d" % (terms, start))
BASE_URL = 'http://research.google.com/university/search/service'
values = {'clid': id, 'rsz': size, 'start': start, 'q': terms}
url = '?'.join([BASE_URL, urllib.urlencode(values)])
logging.debug("Getting %s" % url)
request = urllib2.Request(url)
response = urllib2.urlopen(request)
#print response.read()
document = xml.dom.minidom.parse(response)
return Response(document)
# END PART COPIED FROM GOOGLE
class WgetDownloader:
def __init__(self):
self.robotParsers = {} # cache for parsers: url -> robotParser
pass
def _blacklisted(self, url):
" True if URL is not blacklisted"
for blackListWord in BLACKLIST:
if blackListWord in url:
logging.debug("Ignoring URL, contains blacklist word %s" % blackListWord)
return True
logging.debug("URL is not blacklisted")
return False
def _robotOk(self, url):
" True if url is OK according to its robots.txt"
urlParts = urlparse.urlparse(url)
if urlParts.scheme!="http":
logging.debug("url is not http, skipping robots parsing")
return True
baseUrl = "http://"+urlParts.netloc
if not baseUrl in self.robotParsers:
rerp = rp.RobotExclusionRulesParser()
robUrl = urlparse.urljoin(baseUrl, "robots.txt")
logging.debug("Loading robots.txt from %s" % robUrl)
robContent, dummy = wget(robUrl, getMime=False)
if robContent!=None:
rerp.parse(robContent)
self.robotParsers[baseUrl] = rerp
else:
logging.debug("Could not load robots.txt, allowing download")
self.robotParsers[baseUrl] = None
return True
else:
rerp = self.robotParsers[baseUrl]
if rerp!=None:
isOk = rerp.is_allowed("*", url)
logging.debug("robots.txt allowed: %s" % str(isOk))
return isOk
else:
logging.debug("Cached robots.txt is None, allowing download")
return True
def get(self, url):
if not self._blacklisted(url) and self._robotOk(url):
return wget(url)
else:
return None, None
class PythonDownloader:
" NOT USED TOO MANY CRASHES / TIMEOUTS "
def __init__(self):
self.robotParsers = {} # cache for parsers: url -> robotParser
def _robotOk(self, url):
" True if url is OK according to its robots.txt"
urlParts = urlparse.urlparse(url)
if urlParts.scheme!="http":
logging.debug("url is not http, skipping")
return True
baseUrl = "http://"+urlParts.netloc
if not baseUrl in self.robotParsers:
rerp = rp.RobotExclusionRulesParser()
robUrl = urlparse.urljoin(baseUrl, "robots.txt")
logging.debug("Loading robots.txt from %s" % robUrl)
try:
rerp.fetch(robUrl)
except urllib2.URLError:
logging.info("Unusual error while opening robots.txt, skipping")
return False # better stay away from hosts that trigger strange errors
self.robotParsers[baseUrl] = rerp
else:
rerp = self.robotParsers[baseUrl]
if rerp!=None:
isOk = rerp.is_allowed("*", url)
logging.debug("robots.txt allowed: %s" % str(isOk))
return isOk
else:
logging.debug("robots.txt could not be opened, assuming that it's ok to download")
return True
def _blackListed(self, url):
" True if url is not blacklisted"
for blackListWord in BLACKLIST:
if blackListWord in url:
logging.debug("Ignoring URL, contains blacklist word %s" % blackListWord)
return True
return False
def get(self, url):
if self._blackListed(url):
return None, None
if not self._robotOk(url):
return None, None
try:
logging.debug("Starting download of %s" % url)
contentFile = util.httpGet(url)
except urllib2.HTTPError, ex:
logging.debug("Download error (HttpError): %s" % str(ex))
return None, None
except urllib2.URLError, ex:
logging.debug("Download error (UrlError): %s" % str(ex))
return None, None
contentData = contentFile.read()
mimeType = contentFile.info().gettype()
return contentData, mimeType
def downloadFileData(downloader, url, title):
""" given a list of (url, title)-objects, download them via http and convert
to ASCII and return as a fileData-dictioary (defined in pubStore.py)
"""
logging.debug("-- Starting download of url %s" % url)
contentData, mimeType = downloader.get(url)
if contentData==None:
logging.debug("Could not download")
return None
logging.debug("mimeType is %s" % mimeType)
# construct dict
fileData = {}
fileData["url"] = url
fileData["desc"] = title
fileData["content"] = contentData
fileData["mimeType"] = mimeType
fileData["articleId"] = "0"
fileData["fileId"] = "0"
fileData["fileType"] = ""
fileData["time"] = ""
fileData["url"] = url
fileData = pubGeneric.toAsciiEscape(fileData, mimeType=mimeType, \
maxTxtFileSize=MAXASCIISIZE, maxBinFileSize=MAXFILESIZE)
if fileData==None:
return None
logging.debug("Downloaded data ASCII-format size: %d" % len(fileData["content"]))
logging.log(5, "Data is"+fileData["content"])
return fileData
def responseToList(response):
" given a response object, return a list of (url, title) "
urlTitleList = []
for res in response.results:
urlTitleList.append((res.url, res.title_no_bold))
return urlTitleList
def googleIter(termString, maxResults=1000, logFh=None):
" search google for termString and return result as a (url, title)-tuple"
id = PROJECTID
size = "large"
start = 0
total = 1000
logWritten = False
while start + 20 <= maxResults and start + 20 < total:
logging.debug("start=%d, total=%d, maxResults=%d" % (start, total, maxResults))
while True:
try:
response = Search(id, size, start, termString)
total = int(response.total)
break
except Exception, err:
logging.info("Exception during Search(): %s" % err)
open("errorlog.txt","a").write(str(err)+"\n")
traceback.print_exc()
time.sleep(10)
if logFh and not logWritten:
logFh.write("\t".join([termString, str(total)])+"\n")
logWritten = True
if total==0:
yield None, None
time.sleep(1)
break
for url, title in responseToList(response):
yield url, title
time.sleep(1)
start += 20
def dnaMotifGenerator(minLen, maxLen, symbols="ACTG"):
" generate random ACTG strings of length from minLen to maxLen "
for mLen in range(minLen, maxLen+1):
noToNucl = {}
for i in range(0, len(symbols)):
noToNucl[i]=symbols[i]
motifList = []
for x in xrange(0, len(symbols)**mLen):
motif = []
remainder = x
for i in reversed(range(0, mLen)):
digit = remainder / len(symbols)**i
remainder = remainder % len(symbols)**i
nucl = noToNucl[digit]
motif.append(nucl)
motif = "".join(motif)
yield motif
def seqFileIterator(fname):
" yield seqs from file, one per line "
for line in open(fname):
line = line.strip()
if len(line)==0:
continue
else:
yield line
def writeIndex(baseTerms, indexFname, seqIterator, maxDownload=1000):
""" search google for base terms (string) + sequences from seqIterator
and write resulting urls to indexFname
"""
logFname = join(dirname(indexFname), "log.tab")
if isfile(indexFname):
mode = "a"
logging.info("Reading old sequences, already crawled")
oldSeqs = set([row.searchTerm.split()[-1] for row in maxCommon.iterTsvRows(logFname)])
logFh = open(logFname, mode)
else:
mode = "w"
oldSeqs = set()
logFh = open(logFname, mode)
logFh.write("searchTerm\tcount\n")
logging.info("Writing index, base terms %s, file %s" % (baseTerms, indexFname))
outFh = codecs.open(indexFname, mode, encoding="utf8")
headers = ["urlId", "chunkId", "seq", "url", "title"]
outFh.write("\t".join(headers)+"\n")
urlCount = 0
#for seqLen in range(startLen, endLen+1):
for seq in seqIterator:
if seq in oldSeqs:
logging.info("Skipping %s, already done" % seq)
continue
logging.info("Sequence is %s" % seq)
if baseTerms!="":
terms = baseTerms+" "+seq
else:
terms = seq
for url, title in googleIter(terms, logFh=logFh, maxResults=maxDownload):
if url!=None:
chunkId = urlCount % CHUNKCOUNT
data = [str(urlCount), str(chunkId), seq, url, title]
outFh.write("\t".join(data)+"\n")
urlCount += 1
def downloadFiles(inFile, outFile):
" download all urls from inFile, convert to ASCII and write to outFile """
pw = pubStore.PubWriterFile(outFile)
#downloader = PythonDownloader()
downloader = WgetDownloader()
for row in maxCommon.iterTsvRows(inFile):
url, title = row.url, row.title
urlId = row.urlId
fileData = downloadFileData(downloader, url, title)
if fileData!=None:
pw.writeFile(0, urlId, fileData)
pw.close()
if __name__ == "__main__":
if args==[]:
parser.print_help()
exit(1)
command = args[0]
targetDir = args[1]
indexFname = join(targetDir, "index.tab")
splitIndexDir = join(targetDir, "index.split")
pubGeneric.setupLogging(progFile, options)
if command == "index":
terms = args[2]
#terms = "pcr primer"
targetDir = args[0]
maxCommon.mustBeEmptyDir(targetDir, makeDir=True)
if options.seqFile==None:
seqIterator = dnaMotifGenerator(options.startSeqLen, options.endSeqLen)
else:
seqIterator = seqFileIterator(options.seqFile)
writeIndex(terms, indexFname, seqIterator, maxDownload=options.maxDownload)
elif command=="download":
#maxCommon.mustBeEmptyDir(splitIndexDir, makeDir=True)
logging.info("Splitting index file %s for jobs" % indexFname)
pubStore.splitTabFileOnChunkId(indexFname, splitIndexDir)
runner = maxRun.Runner()
chunkFiles = glob.glob(join(splitIndexDir, "*.tab"))
for chunkFname in chunkFiles:
chunkId = splitext(basename(chunkFname))[0]
outFname = join(targetDir, chunkId+".zip")
cmd = "job:download {check in line %s} {check out exists %s}" % (chunkFname, outFname)
pubGeneric.recursiveSubmit(runner, cmd)
runner.finish()
elif command=="job:download":
inFile, outFile = args[1:]
pubGeneric.setupLogging(progFile, options, logFileName=splitext(outFile)[0]+".log")
downloadFiles(inFile, outFile)
else:
logging.info("Illegal command %s" % command)