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plotextractor_getter.py
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plotextractor_getter.py
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# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
## Invenio is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with Invenio; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
import urllib2, time, os, sys, re
from invenio.config import CFG_TMPDIR, \
CFG_PLOTEXTRACTOR_SOURCE_BASE_URL, \
CFG_PLOTEXTRACTOR_SOURCE_TARBALL_FOLDER, \
CFG_PLOTEXTRACTOR_SOURCE_PDF_FOLDER, \
CFG_PLOTEXTRACTOR_DOWNLOAD_TIMEOUT
from invenio.plotextractor_config import CFG_PLOTEXTRACTOR_DESY_BASE, \
CFG_PLOTEXTRACTOR_DESY_PIECE
from invenio.search_engine import get_record
from invenio.bibrecord import record_get_field_instances, \
field_get_subfield_values
from invenio.shellutils import run_shell_command
from invenio.plotextractor_output_utils import write_message
from invenio.urlutils import make_invenio_opener
PLOTEXTRACTOR_OPENER = make_invenio_opener('plotextractor')
PDF_EXTENSION = '.pdf'
ARXIV_HEADER = 'arXiv:'
HEP_EX = ['hep-ex/', 9405, ARXIV_HEADER + 'hep-ex_'] # experimental
# a note about hep-ex: the hep-ex papers from 9403 nad 9404 are stored
# in arXiv's servers as hep-ph
HEP_LAT = ['hep-lat/', 9107, ARXIV_HEADER + 'hep-lat_'] # lattice
HEP_PH = ['hep-ph/', 9203, ARXIV_HEADER + 'hep-ph_'] # phenomenology
HEP_TH = ['hep-th/', 9108, ARXIV_HEADER + 'hep-th_'] # theory
HEP_AREAS = [HEP_EX, HEP_LAT, HEP_PH, HEP_TH]
URL = 0
BEGIN_YEAR_MONTH_INDEX = 1
AREA_STRING_INDEX = 2
URL_MOVE = int('0704')
CENTURY_END = int('9912')
CENTURY_BEGIN = int('0001')
ARBITRARY_FROM_DATE = int('9101')
FIX_FOR_YEAR_END = 88
current_yearmonth = int(('%02d%02d' % (time.localtime().tm_year, \
time.localtime().tm_mon))[2:])
"""
each of the areas of hep began in a different year and month.
beginning in 0704, i.e. April 2007, arXiv moved its URLS from
ARXIV_BASE + E_PRINT + HEP_AREA + <<numbernodot>>
to
ARXIV_BASE + E_PRINT + <<number.with.dot>>
the papers for a given month are numbered between yymm.0001 and yymm.9999
after the URL move, and before that they are between yymm001 and yymm999
"""
help_param = 'help'
dir_param = 'dir'
from_param = 'from'
from_index_param = 'fromindex'
ref_file_param = 'reffile'
single_param = 'single'
param_abbrs = 'hd:f:i:r:s:'
params = [help_param, dir_param + '=', from_param + '=', from_index_param + '=',
ref_file_param + '=', single_param + '=']
def harvest(to_dir, from_date, from_index):
"""
Calls upon arXiv using URLS as described above in order to grab
all the tarballs from HEP areas.
@param: dir (string): the directory where everything that gets
downloaded will sit
@param: from_date (int): the date from which we would like to harvest,
in YYMM format
@param: from_index (int): the index where we want to begin our harvest
in YYMM. i.e. we want to start with the 345th record in 1002.
@output: TONS OF .tar.gz FILES FROM ARXIV
@return: (none)
"""
global current_yearmonth
if from_date > current_yearmonth and from_date < ARBITRARY_FROM_DATE:
write_message('Please choose a from date that is not in the future!')
sys.exit(1)
if from_date % 100 > 12:
write_message('Please choose a from date in the form YYMM')
sys.exit(1)
if from_date >= ARBITRARY_FROM_DATE or from_date < URL_MOVE:
for area in HEP_AREAS:
yearmonthindex = area[BEGIN_YEAR_MONTH_INDEX]
# nasty casing!
# I find this particularly horrid because we have to wrap dates..
# i.e. although 9901 is more than 0001, we might want things in
# 0001 and not from 9901
if from_date < current_yearmonth:
# we want to start in the new century; skip the while below
yearmonthindex = CENTURY_END
elif from_date < CENTURY_END:
yearmonthindex = from_date
# grab stuff from between 92 and 99
old_URL_harvest(yearmonthindex, CENTURY_END, to_dir, area)
yearmonthindex = CENTURY_BEGIN
# more nasty casing
if from_date < URL_MOVE:
# that means we want to start sometime before the weird
# url change
yearmonthindex = from_date
elif from_date > URL_MOVE and from_date < ARBITRARY_FROM_DATE:
# we don't want to start yet
yearmonthindex = URL_MOVE
# grab stuff from between 00 and 07
old_URL_harvest(yearmonthindex, URL_MOVE, to_dir, area)
# also after the URL move, there was no distinction between
# papers from different areas. hence, outside the for loop
# even more nasty casing!
if from_date < current_yearmonth and from_date > URL_MOVE:
# we want to start someplace after the URL move and before now
yearmonthindex = from_date
else:
yearmonthindex = URL_MOVE
# grab stuff from between 07 and today
new_URL_harvest(yearmonthindex, from_index, to_dir)
def make_single_directory(to_dir, dirname):
"""
Makes a subdirectory for the arXiv record we are working with and
returns its exact location.
@param: to_dir (string): the name of the directory we want to make it
in
@param: dirname (string): the name of the directory we want to create
@output: a new directory called dirname located in to_dir
@return: the absolute path to the new directory
"""
new_dir = os.path.join(to_dir, dirname)
if not os.path.isdir(new_dir):
try:
os.mkdir(new_dir)
except OSError:
write_message('Failed to make new dir...')
return to_dir
return new_dir
def make_useful_directories(yearmonthindex, to_dir):
"""
Builds up the hierarchical filestructure for saving these things
in a useful way.
@param: yearmonthindex (int): YYMM
@param: to_dir (string): where we want to build the directories from
@return month_dir (string): the new directory we are going to put
stuff in
"""
year = yearmonthindex / 100
if year >= (ARBITRARY_FROM_DATE / 100):
year = '19%02d' % year
else:
year = '20%02d' % year
month = '%02d' % (yearmonthindex % 100)
year_dir = os.path.join(to_dir, year)
if not os.path.isdir(year_dir):
os.mkdir(year_dir)
month_dir = os.path.join(year_dir, month)
if not os.path.isdir(month_dir):
os.mkdir(month_dir)
return month_dir
def get_list_of_all_matching_files(basedir, filetypes):
"""
This function uses the os module in order tocrawl
through the directory tree rooted at basedir and find all the files
therein that include filetype in their 'file' output. Returns a list
of absolute paths to all files.
@param: basedir (string): the directory where we want to start crawling
@param: filetypes ([string, string]): something that will be contained in
the output of running 'file' on the types of files we're looking for
@return: file_paths ([string, string, ...]): a list of full paths to
the files that we discovered
"""
file_paths = []
for dirpath, dummy0, filenames in os.walk(basedir):
for filename in filenames:
full_path = os.path.join(dirpath, filename)
dummy1, cmd_out, dummy2 = run_shell_command('file %s', (full_path,))
for filetype in filetypes:
if cmd_out.find(filetype) > -1:
file_paths.append(full_path)
return file_paths
def tarballs_by_recids(recids, sdir):
"""
Take a string representing one recid or several and get the associated
tarballs for those ids.
@param: recids (string): the record id or ids
@param: sdir (string): where the tarballs should live
@return: tarballs ([string, string, ...]): locations of tarballs
"""
list_of_ids = []
if ',' in recids:
recids = recids.split(',')
for recid in recids:
if '-' in recid:
low, high = recid.split('-')
recid = range(int(low), int(high))
list_of_ids.extend(recid)
else:
recid = int(recid)
list_of_ids.append(recid)
else:
if '-' in recids:
low, high = recid.split('-')
list_of_ids = range(int(low), int(high))
else:
list_of_ids = int(recid)
arXiv_ids = []
for recid in list_of_ids:
rec = get_record(recid)
for afieldinstance in record_get_field_instances(rec, tag='037'):
if 'arXiv' == field_get_subfield_values(afieldinstance, '9')[0]:
arXiv_id = field_get_subfield_values(afieldinstance, 'a')[0]
arXiv_ids.append(arXiv_id)
return tarballs_by_arXiv_id(arXiv_ids, sdir)
def tarballs_by_arXiv_id(arXiv_ids, sdir):
"""
Takes an list of arXiv ids and downloads their tarballs
and returns a list of the tarballs' locations.
@param: arXiv_ids ([string, string, ...]): the arXiv ids you
would like to have tarballs for
@param: sdir (string): the place to download these tarballs to
@return: tarballs ([string, ...]): a list of the tarballs downloaded
"""
tarballs = []
for arXiv_id in arXiv_ids:
if 'arXiv' not in arXiv_id:
arXiv_id = 'arXiv:' + arXiv_id
tarball, dummy_pdf = harvest_single(arXiv_id, sdir, ("tarball",))
if tarball != None:
tarballs.append(tarball)
time.sleep(CFG_PLOTEXTRACTOR_DOWNLOAD_TIMEOUT)
return tarballs
def parse_and_download(infile, sdir):
"""
Read the write_messageation in the input file and download the corresponding
tarballs from arxiv.
@param: infile (string): the name of the file to parse
@param: sdir (string): where to put the downloaded tarballs
"""
tarfiles = []
tardir = os.path.join(sdir, 'tarballs')
if not os.path.isdir(tardir):
try:
os.makedirs(tardir)
except:
write_message(sys.exc_info()[0])
write_message('files will be loose, not in ' + tardir)
tardir = sdir
infile = open(infile)
for line in infile.readlines():
line = line.strip()
if line.startswith('http://'):
# hurray!
url = line
filename = url.split('/')[-1]
if not download(url, tardir, filename):
write_message(filename + ' may already exist')
write_message(sys.exc_info()[0])
filename = os.path.join(tardir, filename)
tarfiles.append(filename)
time.sleep(CFG_PLOTEXTRACTOR_DOWNLOAD_TIMEOUT) # be nice!
elif line.startswith('arXiv'):
tarfiles.extend(tarballs_by_arXiv_id([line.strip()], sdir))
return tarfiles
def harvest_single(single, to_dir, selection=("tarball", "pdf")):
"""
if we only want to harvest one id (arXiv or DESY), we can use this.
@param: single (string): an id from arXiv or DESY
@param: to_dir (string): where the output should be saved
@output: the PDF and source tarball (if applicable) of this single record
@return: (tarball, pdf): the location of the source tarball and PDF, None
if not found
"""
if single.find('arXiv') > -1 and 'arxiv.org' in CFG_PLOTEXTRACTOR_SOURCE_BASE_URL.lower():
id_str = re.findall('[a-zA-Z\\-]+/\\d+|\\d+\\.\\d+', single)[0]
idno = id_str.split('/')
if len(idno) > 0:
idno = idno[-1]
yymm = int(idno[:4])
yymm_dir = make_useful_directories(yymm, to_dir)
url_for_file = CFG_PLOTEXTRACTOR_SOURCE_BASE_URL + \
CFG_PLOTEXTRACTOR_SOURCE_TARBALL_FOLDER + \
id_str
url_for_pdf = CFG_PLOTEXTRACTOR_SOURCE_BASE_URL + \
CFG_PLOTEXTRACTOR_SOURCE_PDF_FOLDER + \
id_str + '.pdf' # adds '.pdf' to avoid arXiv internal redirect from arXivID to arXivID.pdf
individual_file = 'arXiv:' + id_str.replace('/', '_')
individual_dir = make_single_directory(yymm_dir, individual_file)
abs_path = os.path.join(individual_dir, individual_file)
tarball = abs_path
pdf = abs_path + '.pdf'
write_message('download ' + url_for_file + ' to ' + abs_path)
if "tarball" in selection and not download(url_for_file, individual_file, individual_dir):
write_message('download of tarball failed/skipped')
tarball = None
if "pdf" in selection and not download(url_for_pdf, individual_file + '.pdf', individual_dir):
write_message('download of pdf failed/skipped')
pdf = None
return (tarball, pdf)
elif single.find('arXiv') > -1 and CFG_PLOTEXTRACTOR_SOURCE_BASE_URL != '':
# hmm... is it a filesystem?
if CFG_PLOTEXTRACTOR_SOURCE_BASE_URL.startswith('/'):
if not os.path.exists(CFG_PLOTEXTRACTOR_SOURCE_BASE_URL):
write_message('PROBLEM WITH CFG_PLOTEXTRACTOR_SOURCE_BASE_URL: we cannot ' + \
'find this folder!')
return (None, None)
for root, files, dummy in os.walk(CFG_PLOTEXTRACTOR_SOURCE_BASE_URL):
for file_name in files:
id_no = single.replace('arXiv', '')
if file_name.find(id_no) > -1 or\
file_name.find(id_no.replace('/', '_')) > -1 or\
file_name.find(id_no.replace('_', '/')) > -1 or\
file_name.find(id_no.replace(':', '')) > -1:
# that's our file! probably.
return (os.path.join(root, file_name), None)
# well, no luck there
return (None, None)
# okay... is it... a website?
elif CFG_PLOTEXTRACTOR_SOURCE_BASE_URL.startswith('http') and "tarball" in selection:
url_for_file = CFG_PLOTEXTRACTOR_SOURCE_BASE_URL + single
individual_file = os.path.join(to_dir, single)
download(url_for_file, individual_file, to_dir)
return (individual_file, None)
# well, I don't know what to do with it
else:
write_message('unsure how to handle CFG_PLOTEXTRACTOR_SOURCE_BASE_URL. ' + \
'please fix the harvest_single function in ' + \
'miscutil/lib/plotextractor_getter.py')
return (None, None)
elif single.find('DESY') > -1 and "pdf" in selection:
# also okay!
idno = re.findall('\\d{2,4}-\\d{3}', single)[0]
year, number = idno.split('-')
if len(year) < 4:
if int(year) > 92:
year = '19' + year
else:
year = '20' + year
year_dir = make_single_directory(to_dir, year)
desy_dir = make_single_directory(year_dir, 'DESY')
individual_dir = make_single_directory(desy_dir, number)
id_no = year[2:] + '-' + number + '.pdf'
url_for_file = CFG_PLOTEXTRACTOR_DESY_BASE + year + \
CFG_PLOTEXTRACTOR_DESY_PIECE + id_no
individual_file = id_no
write_message('download ' + url_for_file + ' to ' + \
os.path.join(individual_dir, individual_file))
download(url_for_file, individual_file, individual_dir)
return (None, individual_file)
write_message('END')
return (None, None)
def src_pdf_from_marc(marc_file):
"""
Given a marc file, this function attempts to determine where to find
a pdf for that record
@param: marc_file (string): the location of a marc file we can look at
@return: pdfloc (string): the location of the downloaded PDF source file,
None if no pdf was downloaded
"""
if not os.path.exists(marc_file):
return None
marc_file = open(marc_file)
marc_text = marc_file.read()
marc_file.close()
arXiv_match = '(([a-zA-Z\\-]+/\\d{7})|(\\d{4}\\.\\d{4}))'
DESY_match = 'DESY-\\d{2,4}-\\d{3}'
pdf_loc = None
to_dir = os.path.join(CFG_TMPDIR, 'plotdata')
possible_match = re.search(arXiv_match, marc_text)
if possible_match != None:
# it's listed on arXiv, hooray!
arXiv_id = possible_match.group(0)
dummy1, pdf_loc = harvest_single(arXiv_id, to_dir, ("pdf",))
possible_match = re.search(DESY_match, marc_text)
if possible_match != None:
# it's listed on DESY, hooray!
desy_id = possible_match.group(0)
dummy1, pdf_loc = harvest_single(desy_id, to_dir, ("pdf",))
return pdf_loc
def harvest_from_file(filename, to_dir):
"""
Harvest from the file Tibor made.
Format of a single entry:
oai:arXiv.org:area/YYMMIII
or
oai:arXiv.org:YYMM.IIII
"""
ok_format = '^oai:arXiv.org:(([a-zA-Z\\-]+/\\d+)|(\\d+\\.\\d+))$'
try:
names_file = open(filename)
for arXiv_name in names_file.readlines():
if re.match(ok_format, arXiv_name) == None:
write_message('error on ' + arXiv_name + '. continuing.')
continue
harvest_single(arXiv_name, to_dir)
time.sleep(CFG_PLOTEXTRACTOR_DOWNLOAD_TIMEOUT)
except IOError:
write_message('Something is wrong with the file!')
def old_URL_harvest(from_date, to_date, to_dir, area):
"""
Grab all the PDFs and tarballs off arXiv between from_date and to_date,
where from_date and to_date are in YYMM form, and put them in their own
separate folders inside of to_dir. Folder hierarchy will be
to_dir/YYYY/MM/arXiv_id/stuff_downloaded_from_arXiv
this obeys the old URL format
@param: from_date (int): YYMM form of the date where we want to start
harvesting
@param: to_date (int): YYMM form of the date where we want to stop
harvesting
@param: to_dir (string): the base directory to put all these subdirs in
@param: area (int): the index in the HEP_AREAS array of the area we are
currently working on downloading
@output: PDFs and tarballs from arXiv in a hierarchy rooted at to_dir
@return: None
"""
yearmonthindex = from_date
while yearmonthindex < to_date:
sub_dir = make_useful_directories(yearmonthindex, to_dir)
for paperindex in range(1, 1000):
# for whatever reason, we can't count on these things to
# start at 1 (in HEP_PH from 9403 to CENTURY_END only).
# they start at frickin 202.
#if area == HEP_PH and yearmonthindex < ARBITRARY_FROM_INDEX:
# paperindex = paperindex + 201
# of note: before the URL change happened in 0704, it was
# also the case that the paper numbers only had 3 digits
next_to_harvest = '%04d%03d' % (yearmonthindex, paperindex)
arXiv_id = area[AREA_STRING_INDEX] + next_to_harvest
individual_dir = make_single_directory(sub_dir, arXiv_id)
full_url = CFG_PLOTEXTRACTOR_SOURCE_BASE_URL + CFG_PLOTEXTRACTOR_SOURCE_TARBALL_FOLDER + \
area[URL] + next_to_harvest
if not download(full_url, \
area[AREA_STRING_INDEX] + next_to_harvest, individual_dir):
break
full_pdf_url = CFG_PLOTEXTRACTOR_SOURCE_BASE_URL + CFG_PLOTEXTRACTOR_SOURCE_PDF_FOLDER + \
area[URL] + next_to_harvest
download(full_pdf_url, \
area[AREA_STRING_INDEX] + next_to_harvest + PDF_EXTENSION, \
individual_dir)
time.sleep(CFG_PLOTEXTRACTOR_DOWNLOAD_TIMEOUT)
if yearmonthindex % 100 == 12:
# we reached the end of the year!
yearmonthindex = yearmonthindex + FIX_FOR_YEAR_END
yearmonthindex = yearmonthindex + 1
def new_URL_harvest(from_date, from_index, to_dir):
"""
Grab all the PDFs and tarballs off arXiv between from_date and to_date,
where from_date and to_date are in YYMM form, and put them in their own
separate folders inside of to_dir. Folder hierarchy will be
to_dir/YYYY/MM/arXiv_id/stuff_downloaded_from_arXiv
this obeys the new URL format
@param: from_date (int): YYMM form of the date where we want to start
harvesting
@param: to_date (int): YYMM form of the date where we want to stop
harvesting
@param: to_dir (string): the base directory to put all these subdirs in
@output: PDFs and tarballs from arXiv in a hierarchy rooted at to_dir
@return: None
"""
global current_yearmonth
yearmonthindex = from_date
while yearmonthindex < current_yearmonth:
if yearmonthindex == from_date:
fro = from_index
else:
fro = 1
sub_dir = make_useful_directories(yearmonthindex, to_dir)
for paperindex in range(fro, 10000):
# of note: after the URL change happened in 0704, it was
# the case that paper numbers had 4 digits
next_to_harvest = '%04d.%04d' % (yearmonthindex, paperindex)
arXiv_id = ARXIV_HEADER + next_to_harvest
individual_dir = make_single_directory(sub_dir, arXiv_id)
full_url = CFG_PLOTEXTRACTOR_SOURCE_BASE_URL + CFG_PLOTEXTRACTOR_SOURCE_TARBALL_FOLDER + \
next_to_harvest
if not download(full_url, ARXIV_HEADER + next_to_harvest, \
individual_dir):
break
full_pdf_url = CFG_PLOTEXTRACTOR_SOURCE_BASE_URL + CFG_PLOTEXTRACTOR_SOURCE_PDF_FOLDER + \
next_to_harvest
download(full_pdf_url, \
ARXIV_HEADER + next_to_harvest + PDF_EXTENSION, \
individual_dir)
time.sleep(CFG_PLOTEXTRACTOR_DOWNLOAD_TIMEOUT) # be nice to remote server
if yearmonthindex % 100 == 12:
# we reached the end of the year!
yearmonthindex = yearmonthindex + FIX_FOR_YEAR_END
yearmonthindex = yearmonthindex + 1
def download(url, filename, to_dir):
"""
Actually does the call and download given a URL and desired output
filename.
@param: url (string): where the file lives on the interwebs
@param: filename (string): where the file should live after download
@param: to_dir (string): the dir where our new files will live
@output: a file in to_dir
@return: True on success, False on failure
"""
new_file = os.path.join(to_dir, filename)
try:
conn = PLOTEXTRACTOR_OPENER.open(url)
response = conn.read()
conn.close()
new_file_fd = open(new_file, 'w')
new_file_fd.write(response)
new_file_fd.close()
write_message('Downloaded to ' + new_file)
return True
except (IOError, urllib2.URLError), e:
# this could be a permissions error, but it probably means that
# there's nothing left in that section YYMM
write_message('Error downloading from %s: \n%s\n' % (url, str(e)))
return False

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