def test_unzip(self):
"""
Test uncompressing function.
"""
test_zipped_file = "./test/test.zip"
desired_dir = os.path.join(CFG_TMPSHAREDDIR, "apsharvest")
unzipped_folder = unzip(test_zipped_file, desired_dir)
self.assertTrue(
unzipped_folder.startswith(desired_dir),
"Unzipped folder is located in the wrong place %s!" % unzipped_folder,
)
unzipped_folder = unzip(test_zipped_file)
self.assertTrue(os.path.exists(unzipped_folder), "Unzipped folder does not exist!")
z = zipfile.ZipFile(test_zipped_file)
list_of_zipfiles = z.namelist()
found_list_of_files = get_files_and_folders(unzipped_folder)
self.assertTrue(len(list_of_zipfiles) == len(found_list_of_files), "Looks like all files were not extracted!")
except StandardError, e:
if 'urlopen' in str(e) or 'URL could not be opened' in str(e):
msg = "URL could not be opened: %s" % (url,)
write_message("Error: %s" % (msg,),
stream=sys.stderr)
write_message("No fulltext found for %s" %
(record.recid or record.doi,))
yield record, msg
continue
raise
finally:
request_end = time.time()
# Unzip the compressed file
unzipped_folder = unzip(result_file, base_directory=self.out_folder)
# Validate the checksum of the compressed fulltext file.
try:
checksum_validated_files = find_and_validate_md5_checksums(
in_folder=unzipped_folder,
md5key_filename=CFG_APSHARVEST_MD5_FILE)
except APSFileChecksumError, e:
info_msg = "Skipping %s in %s" % \
(record.recid or record.doi, unzipped_folder)
msg = "Error while validating checksum: %s\n%s\n%s" % \
(info_msg, str(e), traceback.format_exc()[:-1])
write_message(msg)
yield record, msg
continue
if not checksum_validated_files:
def apply_filter(rec):
""" Filters the record to be compatible within Inspire
Parameters:
* rec - dictionary: BibRecord structure
Returns: dictionary, BibRecord structure
"""
# Move recid from 001 to 035 if not hidden
cds_id = rec['001'][0][3]
if not 'hidden' in [x.lower() for x in record_get_field_values(rec, "980",
code="a")]:
record_add_field(rec, '035', subfields=[('9', 'CDS'), ('a', cds_id)])
# Clear control fields
record_strip_controlfields(rec)
# Clear other uninteresting fields
interesting_fields = ["024", "041", "035", "037", "088", "100",
"110", "111", "242", "245", "246", "260",
"269", "300", "502", "650", "653", "693",
"700", "710", "773", "856", "520", "500",
"980"]
for tag in rec.keys():
if tag not in interesting_fields:
record_delete_fields(rec, tag)
# 980 Determine Collections
collections = set([])
for value in record_get_field_values(rec, '980', code='a'):
if 'NOTE' in value.upper():
collections.add('NOTE')
if 'THESIS' in value.upper():
collections.add('THESIS')
if 'CONFERENCEPAPER' in value.upper():
collections.add('ConferencePaper')
if is_published(rec):
collections.add("PUBLISHED")
collections.add("CITEABLE")
if not 'NOTE' in collections:
# TODO: Move this to a KB
kb = ['ATLAS-CONF-', 'CMS-PAS-', 'ATL-', 'CMS-DP-',
'ALICE-INT-', 'LHCb-PUB-']
values = record_get_field_values(rec, "088", code='a')
for val, rep in product(values, kb):
if val.startswith(rep):
collections.add('NOTE')
break
# 980 Arxiv tag
if record_get_field_values(rec, '035', filter_subfield_code="a",
filter_subfield_value="arXiv"):
collections.add("arXiv")
# 980 HEP && CORE
collections.add('HEP')
collections.add('CORE')
# 980 Conference Note
if not 'ConferencePaper' in collections:
for value in record_get_field_values(rec, '962', code='n'):
if value[-2:].isdigit():
collections.add('ConferencePaper')
break
record_delete_fields(rec, "980")
intnote = record_get_field_values(rec, '690', filter_subfield_code="a",
filter_subfield_value='INTNOTE')
if intnote:
val_088 = record_get_field_values(rec, '088', filter_subfield_code="a")
for val in val_088:
if 'CMS' in val:
url = ('http://weblib.cern.ch/abstract?CERN-CMS' +
val.split('CMS', 1)[-1])
record_add_field(rec, '856', ind1='4', subfields=[('u', url)])
# 041 Language
languages = get_languages()
language_fields = record_get_field_instances(rec, '041')
record_delete_fields(rec, "041")
for field in language_fields:
subs = field_get_subfields(field)
if 'a' in subs:
if "eng" in subs['a']:
continue
new_value = translate_config(subs['a'][0], languages)
new_subs = [('a', new_value)]
record_add_field(rec, "041", subfields=new_subs)
# 035 Externals
scn_035_fields = record_get_field_instances(rec, '035')
forbidden_values = ["cercer",
"inspire",
"xx",
"cern annual report",
"cmscms",
"wai01"]
for field in scn_035_fields:
subs = field_get_subfields(field)
if '9' in subs:
if not 'a' in subs:
continue
for sub in subs['9']:
if sub.lower() in forbidden_values:
break
else:
# No forbidden values (We did not "break")
suffixes = [s.lower() for s in subs['9']]
if 'spires' in suffixes:
new_subs = [('a', 'SPIRES-%s' % subs['a'][0])]
record_add_field(rec, '970', subfields=new_subs)
continue
if 'a' in subs:
for sub in subs['a']:
if sub.lower() in forbidden_values:
record_delete_field(rec, tag="035",
field_position_global=field[4])
rep_088_fields = record_get_field_instances(rec, '088')
for field in rep_088_fields:
subs = field_get_subfields(field)
if '9' in subs:
for val in subs['9']:
if val.startswith('P0') or val.startswith('CM-P0'):
sf = [('9', 'CERN'), ('b', val)]
record_add_field(rec, '595', subfields=sf)
for key, val in field[0]:
if key in ['a', '9'] and not val.startswith('SIS-'):
record_add_field(rec, '037', subfields=[('a', val)])
record_delete_fields(rec, "088")
# 037 Externals also...
rep_037_fields = record_get_field_instances(rec, '037')
for field in rep_037_fields:
subs = field_get_subfields(field)
if 'a' in subs:
for value in subs['a']:
if 'arXiv' in value:
new_subs = [('a', value), ('9', 'arXiv')]
for fld in record_get_field_instances(rec, '695'):
for key, val in field_get_subfield_instances(fld):
if key == 'a':
new_subs.append(('c', val))
break
nf = create_field(subfields=new_subs)
record_replace_field(rec, '037', nf, field[4])
for key, val in field[0]:
if key in ['a', '9'] and val.startswith('SIS-'):
record_delete_field(rec, '037', field_position_global=field[4])
for field in record_get_field_instances(rec, '242'):
record_add_field(rec, '246', subfields=field[0])
record_delete_fields(rec, '242')
# 269 Date normalization
for field in record_get_field_instances(rec, '269'):
for idx, (key, value) in enumerate(field[0]):
if key == "c":
field[0][idx] = ("c", convert_date_to_iso(value))
record_delete_fields(rec, "260")
if not 'THESIS' in collections:
for field in record_get_field_instances(rec, '260'):
record_add_field(rec, '269', subfields=field[0])
record_delete_fields(rec, '260')
# 300 page number
for field in record_get_field_instances(rec, '300'):
for idx, (key, value) in enumerate(field[0]):
if key == 'a':
if "mult." not in value and value != " p":
field[0][idx] = ('a', re.sub(r'[^\d-]+', '', value))
else:
record_delete_field(rec, '300',
field_position_global=field[4])
break
# 100 & 700 punctuate author names
author_names = record_get_field_instances(rec, '100')
author_names.extend(record_get_field_instances(rec, '700'))
for field in author_names:
subs = field_get_subfields(field)
if not 'i' in subs or 'XX' in subs['i']:
if not 'j' in subs or 'YY' in subs['j']:
for idx, (key, value) in enumerate(field[0]):
if key == 'a':
field[0][idx] = ('a', punctuate_authorname(value))
# 700 -> 701 Thesis supervisors
if 'THESIS' in collections:
for field in record_get_field_instances(rec, '700'):
record_add_field(rec, '701', subfields=field[0])
record_delete_fields(rec, '700')
# 501 move subfields
fields_501 = record_get_field_instances(rec, '502')
for idx, field in enumerate(fields_501):
new_subs = []
for key, value in field[0]:
if key == 'a':
new_subs.append(('b', value))
elif key == 'b':
new_subs.append(('c', value))
elif key == 'c':
new_subs.append(('d', value))
else:
new_subs.append((key, value))
fields_501[idx] = field_swap_subfields(field, new_subs)
# 650 Translate Categories
categories = get_categories()
category_fields = record_get_field_instances(rec, '650', ind1='1', ind2='7')
record_delete_fields(rec, "650")
for field in category_fields:
for idx, (key, value) in enumerate(field[0]):
if key == 'a':
new_value = translate_config(value, categories)
if new_value != value:
new_subs = [('2', 'INSPIRE'), ('a', new_value)]
else:
new_subs = [('2', 'SzGeCERN'), ('a', value)]
record_add_field(rec, "650", ind1="1", ind2="7",
subfields=new_subs)
break
# 653 Free Keywords
for field in record_get_field_instances(rec, '653', ind1='1'):
subs = field_get_subfields(field)
new_subs = []
if 'a' in subs:
for val in subs['a']:
new_subs.extend([('9', 'author'), ('a', val)])
new_field = create_field(subfields=new_subs, ind1='1')
record_replace_field(rec, '653', new_field, field_position_global=field[4])
experiments = get_experiments()
# 693 Remove if 'not applicable'
for field in record_get_field_instances(rec, '693'):
subs = field_get_subfields(field)
all_subs = subs.get('a', []) + subs.get('e', [])
if 'not applicable' in [x.lower() for x in all_subs]:
record_delete_field(rec, '693',
field_position_global=field[4])
new_subs = []
experiment_a = ""
experiment_e = ""
for (key, value) in subs.iteritems():
if key == 'a':
experiment_a = value[0]
new_subs.append((key, value[0]))
elif key == 'e':
experiment_e = value[0]
experiment = "%s---%s" % (experiment_a.replace(" ", "-"),
experiment_e)
translated_experiments = translate_config(experiment,
experiments)
new_subs.append(("e", translated_experiments))
record_delete_field(rec, tag="693",
field_position_global=field[4])
record_add_field(rec, "693", subfields=new_subs)
# 710 Collaboration
for field in record_get_field_instances(rec, '710'):
subs = field_get_subfield_instances(field)
for idx, (key, value) in enumerate(subs[:]):
if key == '5':
subs.pop(idx)
elif value.startswith('CERN. Geneva'):
subs.pop(idx)
if len(subs) == 0:
record_delete_field(rec, '710', field_position_global=field[4])
# 773 journal translations
journals = get_journals()
for field in record_get_field_instances(rec, '773'):
subs = field_get_subfield_instances(field)
new_subs = []
for idx, (key, value) in enumerate(subs):
if key == 'p':
new_subs.append((key, translate_config(value, journals)))
else:
new_subs.append((key, value))
record_delete_field(rec, tag="773",
field_position_global=field[4])
record_add_field(rec, "773", subfields=new_subs)
# FFT (856) Dealing with graphs
figure_counter = 0
for field in record_get_field_instances(rec, '856', ind1='4'):
subs = field_get_subfields(field)
newsubs = []
remove = False
if 'z' in subs:
is_figure = [s for s in subs['z'] if "figure" in s.lower()]
if is_figure and 'u' in subs:
is_subformat = [s for s in subs['u'] if "subformat" in s.lower()]
if not is_subformat:
url = subs['u'][0]
if url.endswith(".pdf"):
# We try to convert
fd, local_url = mkstemp(suffix=os.path.basename(url), dir=CFG_TMPSHAREDDIR)
os.close(fd)
_print("Downloading %s into %s" % (url, local_url), verbose=5)
plotfile = ""
try:
plotfile = download_url(url=url,
download_to_file=local_url,
timeout=30.0)
except InvenioFileDownloadError:
_print("Download failed while attempting to reach %s. Skipping.." % (url,))
remove = True
if plotfile:
converted = convert_images([plotfile])
if converted:
url = converted.pop()
_print("Successfully converted %s to %s" % (local_url, url), verbose=5)
else:
_print("Conversion failed on %s" % (local_url,))
url = None
remove = True
if url:
newsubs.append(('a', url))
newsubs.append(('t', 'Plot'))
figure_counter += 1
if 'y' in subs:
newsubs.append(('d', "%05d %s" % (figure_counter, subs['y'][0])))
newsubs.append(('n', subs['y'][0]))
else:
# Get basename without extension.
name = os.path.basename(os.path.splitext(subs['u'][0])[0])
newsubs.append(('d', "%05d %s" % (figure_counter, name)))
newsubs.append(('n', name))
if not newsubs and 'u' in subs:
is_fulltext = [s for s in subs['u'] if ".pdf" in s and not "subformat=pdfa" in s]
if is_fulltext:
newsubs = [('t', 'INSPIRE-PUBLIC'), ('a', subs['u'][0])]
if not newsubs and 'u' in subs:
remove = True
is_zipfile = [s for s in subs['u'] if ".zip" in s]
if is_zipfile:
url = is_zipfile[0]
local_url = os.path.join(CFG_TMPSHAREDDIR, os.path.basename(url))
_print("Downloading %s into %s" % (url, local_url), verbose=5)
zipped_archive = ""
try:
zipped_archive = download_url(url=is_zipfile[0],
download_to_file=local_url,
timeout=30.0)
except InvenioFileDownloadError:
_print("Download failed while attempting to reach %s. Skipping.."
% (is_zipfile[0],))
remove = True
if zipped_archive:
unzipped_archive = unzip(zipped_archive)
list_of_pngs = locate("*.png", unzipped_archive)
for png in list_of_pngs:
if "_vti_" in png or "__MACOSX" in png:
continue
figure_counter += 1
plotsubs = []
plotsubs.append(('a', png))
caption = '%05d %s' % (figure_counter, os.path.basename(png))
plotsubs.append(('d', caption))
plotsubs.append(('t', 'Plot'))
record_add_field(rec, 'FFT', subfields=plotsubs)
if not remove and not newsubs and 'u' in subs:
urls = ('http://cdsweb.cern.ch', 'http://cms.cern.ch',
'http://cmsdoc.cern.ch', 'http://documents.cern.ch',
'http://preprints.cern.ch', 'http://cds.cern.ch')
for val in subs['u']:
if any(url in val for url in urls):
remove = True
break
if val.endswith('ps.gz'):
remove = True
if newsubs:
record_add_field(rec, 'FFT', subfields=newsubs)
remove = True
if remove:
record_delete_field(rec, '856', ind1='4',
field_position_global=field[4])
# 500 - Preliminary results
if "THESIS" not in collections:
subs = [('a', "Preliminary results")]
record_add_field(rec, "500", subfields=subs)
for collection in collections:
record_add_field(rec, '980', subfields=[('a', collection)])
return rec
def apply_filter(rec):
""" Filters the record to be compatible within Inspire
Parameters:
* rec - dictionary: BibRecord structure
Returns: dictionary, BibRecord structure
"""
# Move recid from 001 to 035 if not hidden
cds_id = rec["001"][0][3]
if not "hidden" in [x.lower() for x in record_get_field_values(rec, "980", code="a")]:
record_add_field(rec, "035", subfields=[("9", "CDS"), ("a", cds_id)])
# Clear control fields
record_strip_controlfields(rec)
# Clear other uninteresting fields
interesting_fields = [
"024",
"041",
"035",
"037",
"088",
"100",
"110",
"111",
"242",
"245",
"246",
"260",
"269",
"300",
"502",
"650",
"653",
"693",
"700",
"710",
"773",
"856",
"520",
"500",
"980",
]
for tag in rec.keys():
if tag not in interesting_fields:
record_delete_fields(rec, tag)
# 980 Determine Collections
collections = set([])
for value in record_get_field_values(rec, "980", code="a"):
if "NOTE" in value.upper():
collections.add("NOTE")
if "THESIS" in value.upper():
collections.add("THESIS")
if "CONFERENCEPAPER" in value.upper():
collections.add("ConferencePaper")
if is_published(rec):
collections.add("PUBLISHED")
collections.add("CITEABLE")
if not "NOTE" in collections:
# TODO: Move this to a KB
kb = ["ATLAS-CONF-", "CMS-PAS-", "ATL-", "CMS-DP-", "ALICE-INT-", "LHCb-PUB-"]
values = record_get_field_values(rec, "088", code="a")
for val, rep in product(values, kb):
if val.startswith(rep):
collections.add("NOTE")
break
# 980 Arxiv tag
if record_get_field_values(rec, "035", filter_subfield_code="a", filter_subfield_value="arXiv"):
collections.add("arXiv")
# 980 HEP && CORE
collections.add("HEP")
collections.add("CORE")
# 980 Conference Note
if not "ConferencePaper" in collections:
for value in record_get_field_values(rec, "962", code="n"):
if value[-2:].isdigit():
collections.add("ConferencePaper")
break
record_delete_fields(rec, "980")
intnote = record_get_field_values(rec, "690", filter_subfield_code="a", filter_subfield_value="INTNOTE")
if intnote:
val_088 = record_get_field_values(rec, "088", filter_subfield_code="a")
for val in val_088:
if "CMS" in val:
url = "http://weblib.cern.ch/abstract?CERN-CMS" + val.split("CMS", 1)[-1]
record_add_field(rec, "856", ind1="4", subfields=[("u", url)])
# 041 Language
languages = get_languages()
language_fields = record_get_field_instances(rec, "041")
record_delete_fields(rec, "041")
for field in language_fields:
subs = field_get_subfields(field)
if "a" in subs:
if "eng" in subs["a"]:
continue
new_value = translate_config(subs["a"][0], languages)
new_subs = [("a", new_value)]
record_add_field(rec, "041", subfields=new_subs)
# 035 Externals
scn_035_fields = record_get_field_instances(rec, "035")
forbidden_values = ["cercer", "inspire", "xx", "cern annual report", "cmscms", "wai01"]
for field in scn_035_fields:
subs = field_get_subfields(field)
if "9" in subs:
if not "a" in subs:
continue
for sub in subs["9"]:
if sub.lower() in forbidden_values:
break
else:
# No forbidden values (We did not "break")
suffixes = [s.lower() for s in subs["9"]]
if "spires" in suffixes:
new_subs = [("a", "SPIRES-%s" % subs["a"][0])]
record_add_field(rec, "970", subfields=new_subs)
continue
if "a" in subs:
for sub in subs["a"]:
if sub.lower() in forbidden_values:
record_delete_field(rec, tag="035", field_position_global=field[4])
rep_088_fields = record_get_field_instances(rec, "088")
for field in rep_088_fields:
subs = field_get_subfields(field)
if "9" in subs:
for val in subs["9"]:
if val.startswith("P0") or val.startswith("CM-P0"):
sf = [("9", "CERN"), ("b", val)]
record_add_field(rec, "595", subfields=sf)
for key, val in field[0]:
if key in ["a", "9"] and not val.startswith("SIS-"):
record_add_field(rec, "037", subfields=[("a", val)])
record_delete_fields(rec, "088")
# 037 Externals also...
rep_037_fields = record_get_field_instances(rec, "037")
for field in rep_037_fields:
subs = field_get_subfields(field)
if "a" in subs:
for value in subs["a"]:
if "arXiv" in value:
new_subs = [("a", value), ("9", "arXiv")]
for fld in record_get_field_instances(rec, "695"):
for key, val in field_get_subfield_instances(fld):
if key == "a":
new_subs.append(("c", val))
break
nf = create_field(subfields=new_subs)
record_replace_field(rec, "037", nf, field[4])
for key, val in field[0]:
if key in ["a", "9"] and val.startswith("SIS-"):
record_delete_field(rec, "037", field_position_global=field[4])
for field in record_get_field_instances(rec, "242"):
record_add_field(rec, "246", subfields=field[0])
record_delete_fields(rec, "242")
# 269 Date normalization
for field in record_get_field_instances(rec, "269"):
for idx, (key, value) in enumerate(field[0]):
if key == "c":
field[0][idx] = ("c", convert_date_to_iso(value))
record_delete_fields(rec, "260")
if not "THESIS" in collections:
for field in record_get_field_instances(rec, "260"):
record_add_field(rec, "269", subfields=field[0])
record_delete_fields(rec, "260")
# 300 page number
for field in record_get_field_instances(rec, "300"):
for idx, (key, value) in enumerate(field[0]):
if key == "a":
if "mult." not in value and value != " p":
field[0][idx] = ("a", re.sub(r"[^\d-]+", "", value))
else:
record_delete_field(rec, "300", field_position_global=field[4])
break
# 100 & 700 punctuate author names
author_names = record_get_field_instances(rec, "100")
author_names.extend(record_get_field_instances(rec, "700"))
for field in author_names:
subs = field_get_subfields(field)
if not "i" in subs or "XX" in subs["i"]:
if not "j" in subs or "YY" in subs["j"]:
for idx, (key, value) in enumerate(field[0]):
if key == "a":
field[0][idx] = ("a", punctuate_authorname(value))
# 700 -> 701 Thesis supervisors
if "THESIS" in collections:
for field in record_get_field_instances(rec, "700"):
record_add_field(rec, "701", subfields=field[0])
record_delete_fields(rec, "700")
# 501 move subfields
fields_501 = record_get_field_instances(rec, "502")
for idx, field in enumerate(fields_501):
new_subs = []
for key, value in field[0]:
if key == "a":
new_subs.append(("b", value))
elif key == "b":
new_subs.append(("c", value))
elif key == "c":
new_subs.append(("d", value))
else:
new_subs.append((key, value))
fields_501[idx] = field_swap_subfields(field, new_subs)
# 650 Translate Categories
categories = get_categories()
category_fields = record_get_field_instances(rec, "650", ind1="1", ind2="7")
record_delete_fields(rec, "650")
for field in category_fields:
for idx, (key, value) in enumerate(field[0]):
if key == "a":
new_value = translate_config(value, categories)
if new_value != value:
new_subs = [("2", "INSPIRE"), ("a", new_value)]
else:
new_subs = [("2", "SzGeCERN"), ("a", value)]
record_add_field(rec, "650", ind1="1", ind2="7", subfields=new_subs)
break
# 653 Free Keywords
for field in record_get_field_instances(rec, "653", ind1="1"):
subs = field_get_subfields(field)
new_subs = []
if "a" in subs:
for val in subs["a"]:
new_subs.extend([("9", "author"), ("a", val)])
new_field = create_field(subfields=new_subs, ind1="1")
record_replace_field(rec, "653", new_field, field_position_global=field[4])
experiments = get_experiments()
# 693 Remove if 'not applicable'
for field in record_get_field_instances(rec, "693"):
subs = field_get_subfields(field)
all_subs = subs.get("a", []) + subs.get("e", [])
if "not applicable" in [x.lower() for x in all_subs]:
record_delete_field(rec, "693", field_position_global=field[4])
new_subs = []
experiment_a = ""
experiment_e = ""
for (key, value) in subs.iteritems():
if key == "a":
experiment_a = value[0]
new_subs.append((key, value[0]))
elif key == "e":
experiment_e = value[0]
experiment = "%s---%s" % (experiment_a.replace(" ", "-"), experiment_e)
translated_experiments = translate_config(experiment, experiments)
new_subs.append(("e", translated_experiments))
record_delete_field(rec, tag="693", field_position_global=field[4])
record_add_field(rec, "693", subfields=new_subs)
# 710 Collaboration
for field in record_get_field_instances(rec, "710"):
subs = field_get_subfield_instances(field)
for idx, (key, value) in enumerate(subs[:]):
if key == "5":
subs.pop(idx)
elif value.startswith("CERN. Geneva"):
subs.pop(idx)
if len(subs) == 0:
record_delete_field(rec, "710", field_position_global=field[4])
# 773 journal translations
journals = get_journals()
for field in record_get_field_instances(rec, "773"):
subs = field_get_subfield_instances(field)
new_subs = []
for idx, (key, value) in enumerate(subs):
if key == "p":
new_subs.append((key, translate_config(value, journals)))
else:
new_subs.append((key, value))
record_delete_field(rec, tag="773", field_position_global=field[4])
record_add_field(rec, "773", subfields=new_subs)
# FFT (856) Dealing with graphs
figure_counter = 0
for field in record_get_field_instances(rec, "856", ind1="4"):
subs = field_get_subfields(field)
newsubs = []
remove = False
if "z" in subs:
is_figure = [s for s in subs["z"] if "figure" in s.lower()]
if is_figure and "u" in subs:
is_subformat = [s for s in subs["u"] if "subformat" in s.lower()]
if not is_subformat:
url = subs["u"][0]
if url.endswith(".pdf"):
# We try to convert
fd, local_url = mkstemp(suffix=os.path.basename(url), dir=CFG_TMPSHAREDDIR)
os.close(fd)
_print("Downloading %s into %s" % (url, local_url), verbose=5)
plotfile = ""
try:
plotfile = download_url(url=url, download_to_file=local_url, timeout=30.0)
except InvenioFileDownloadError:
_print("Download failed while attempting to reach %s. Skipping.." % (url,))
remove = True
if plotfile:
converted = convert_images([plotfile])
if converted:
url = converted.pop()
_print("Successfully converted %s to %s" % (local_url, url), verbose=5)
else:
_print("Conversion failed on %s" % (local_url,))
url = None
remove = True
if url:
newsubs.append(("a", url))
newsubs.append(("t", "Plot"))
figure_counter += 1
if "y" in subs:
newsubs.append(("d", "%05d %s" % (figure_counter, subs["y"][0])))
newsubs.append(("n", subs["y"][0]))
else:
# Get basename without extension.
name = os.path.basename(os.path.splitext(subs["u"][0])[0])
newsubs.append(("d", "%05d %s" % (figure_counter, name)))
newsubs.append(("n", name))
if not newsubs and "u" in subs:
is_fulltext = [s for s in subs["u"] if ".pdf" in s]
if is_fulltext:
newsubs = [("t", "INSPIRE-PUBLIC"), ("a", subs["u"][0])]
if not newsubs and "u" in subs:
remove = True
is_zipfile = [s for s in subs["u"] if ".zip" in s]
if is_zipfile:
url = is_zipfile[0]
local_url = os.path.join(CFG_TMPSHAREDDIR, os.path.basename(url))
_print("Downloading %s into %s" % (url, local_url), verbose=5)
zipped_archive = ""
try:
zipped_archive = download_url(url=is_zipfile[0], download_to_file=local_url, timeout=30.0)
except InvenioFileDownloadError:
_print("Download failed while attempting to reach %s. Skipping.." % (is_zipfile[0],))
remove = True
if zipped_archive:
unzipped_archive = unzip(zipped_archive)
list_of_pngs = locate("*.png", unzipped_archive)
for png in list_of_pngs:
if "_vti_" in png or "__MACOSX" in png:
continue
figure_counter += 1
plotsubs = []
plotsubs.append(("a", png))
caption = "%05d %s" % (figure_counter, os.path.basename(png))
plotsubs.append(("d", caption))
plotsubs.append(("t", "Plot"))
record_add_field(rec, "FFT", subfields=plotsubs)
if not remove and not newsubs and "u" in subs:
urls = (
"http://cdsweb.cern.ch",
"http://cms.cern.ch",
"http://cmsdoc.cern.ch",
"http://documents.cern.ch",
"http://preprints.cern.ch",
"http://cds.cern.ch",
)
for val in subs["u"]:
if any(url in val for url in urls):
remove = True
break
if val.endswith("ps.gz"):
remove = True
if newsubs:
record_add_field(rec, "FFT", subfields=newsubs)
remove = True
if remove:
record_delete_field(rec, "856", ind1="4", field_position_global=field[4])
# 500 - Preliminary results
if "THESIS" not in collections:
subs = [("a", "Preliminary results")]
record_add_field(rec, "500", subfields=subs)
for collection in collections:
record_add_field(rec, "980", subfields=[("a", collection)])
return rec
continue
except APSHarvesterFileExits:
write_message("File exists at %s" % (result_file,), verbose=2)
except StandardError, e:
if 'urlopen' in str(e) or 'URL could not be opened' in str(e):
write_message("Error: URL could not be opened: %s" % (url,),
stream=sys.stderr)
write_message("No fulltext found for %s" %
(record.recid or record.doi,))
yield record, "%s cannot be opened." % (url,)
raise
# Unzip the compressed file
unzipped_folder = unzip(result_file)
# Validate the checksum of the compressed fulltext file.
try:
checksum_validated_files = find_and_validate_md5_checksums(
in_folder=unzipped_folder,
md5key_filename=CFG_APSHARVEST_MD5_FILE)
except InvenioFileChecksumError, e:
write_message("Error while validating checksum: %s" % (str(e),))
write_message("Skipping %s in %s" %
(record.recid or record.doi, unzipped_folder))
continue
if not checksum_validated_files:
write_message("Warning: No files found to perform checksum"
" validation on inside %s" % (unzipped_folder,))
elif len(checksum_validated_files) != 1 or \
write_message("File exists at %s" % (result_file, ), verbose=2)
except StandardError, e:
if 'urlopen' in str(e) or 'URL could not be opened' in str(e):
msg = "URL could not be opened: %s" % (url, )
write_message("Error: %s" % (msg, ), stream=sys.stderr)
write_message("No fulltext found for %s" %
(record.recid or record.doi, ))
yield record, msg
continue
raise
finally:
request_end = time.time()
# Unzip the compressed file
unzipped_folder = unzip(result_file, base_directory=out_folder)
# Validate the checksum of the compressed fulltext file.
try:
checksum_validated_files = find_and_validate_md5_checksums(
in_folder=unzipped_folder,
md5key_filename=CFG_APSHARVEST_MD5_FILE)
except InvenioFileChecksumError, e:
info_msg = "Skipping %s in %s" % \
(record.recid or record.doi, unzipped_folder)
msg = "Error while validating checksum: %s\n%s\n%s" % \
(info_msg, str(e), traceback.format_exc()[:-1])
write_message(msg)
yield record, msg
continue
if not checksum_validated_files:
write_message("File exists at %s" % (result_file, ), verbose=2)
except StandardError, e:
if 'urlopen' in str(e) or 'URL could not be opened' in str(e):
msg = "URL could not be opened: %s" % (url, )
write_message("Error: %s" % (msg, ), stream=sys.stderr)
write_message("No fulltext found for %s" %
(record.recid or record.doi, ))
yield record, msg
continue
raise
finally:
request_end = time.time()
# Unzip the compressed file
unzipped_folder = unzip(result_file)
# Validate the checksum of the compressed fulltext file.
try:
checksum_validated_files = find_and_validate_md5_checksums(
in_folder=unzipped_folder,
md5key_filename=CFG_APSHARVEST_MD5_FILE)
except InvenioFileChecksumError, e:
info_msg = "Skipping %s in %s" % \
(record.recid or record.doi, unzipped_folder)
msg = "Error while validating checksum: %s\n%s\n%s" % \
(info_msg, str(e), traceback.format_exc()[:-1])
write_message(msg)
yield record, msg
continue
if not checksum_validated_files:
def apply_filter(rec):
""" Filters the record to be compatible within Inspire
Parameters:
* rec - dictionary: BibRecord structure
Returns: dictionary, BibRecord structure
"""
# Move recid from 001 to 035
cds_id = rec['001'][0][3]
record_add_field(rec, '035', subfields=[('9', 'CDS'), ('a', cds_id)])
# Clear control fields
record_strip_controlfields(rec)
# Clear other uninteresting fields
interesting_fields = [
"024", "041", "035", "037", "088", "100", "110", "111", "242", "245",
"246", "260", "269", "300", "502", "650", "653", "693", "700", "710",
"773", "856", "520", "500", "980"
]
for tag in rec.keys():
if tag not in interesting_fields:
record_delete_fields(rec, tag)
# 980 Determine Collections
collections = set([])
for value in record_get_field_values(rec, '980', code='a'):
if 'NOTE' in value.upper():
collections.add('NOTE')
if 'THESIS' in value.upper():
collections.add('THESIS')
if is_published(rec):
collections.add("PUBLISHED")
collections.add("CITEABLE")
# 980 Arxiv tag
if record_get_field_values(rec,
'035',
filter_subfield_code="a",
filter_subfield_value="arXiv"):
collections.add("arXiv")
# 980 HEP && CORE
collections.add('HEP')
collections.add('CORE')
record_delete_fields(rec, "980")
intnote = record_get_field_values(rec,
'690',
filter_subfield_code="a",
filter_subfield_value='INTNOTE')
if intnote:
val_088 = record_get_field_values(rec, '088', filter_subfield_code="a")
for val in val_088:
if 'CMS' in val:
url = ('http://weblib.cern.ch/abstract?CERN-CMS' +
val.split('CMS', 1)[-1])
record_add_field(rec, '856', ind1='4', subfields=[('u', url)])
# 041 Language
languages = get_languages()
language_fields = record_get_field_instances(rec, '041')
record_delete_fields(rec, "041")
for field in language_fields:
subs = field_get_subfields(field)
if 'a' in subs:
if "eng" in subs['a']:
continue
new_value = translate_config(subs['a'][0], languages)
new_subs = [('a', new_value)]
record_add_field(rec, "041", subfields=new_subs)
# 035 Externals
scn_035_fields = record_get_field_instances(rec, '035')
forbidden_values = [
"cercer", "inspire", "xx", "cern annual report", "cmscms", "wai01"
]
for field in scn_035_fields:
subs = field_get_subfields(field)
if '9' in subs:
if not 'a' in subs:
continue
for sub in subs['9']:
if sub.lower() in forbidden_values:
break
else:
# No forbidden values (We did not "break")
suffixes = [s.lower() for s in subs['9']]
if 'spires' in suffixes:
new_sub = ('a', 'SPIRES-%s' % subs['a'])
record_add_field(rec, '970', subfields=new_sub)
continue
if 'a' in subs:
for sub in subs['a']:
if sub.lower() in forbidden_values:
record_delete_field(rec,
tag="035",
field_position_global=field[4])
rep_088_fields = record_get_field_instances(rec, '088')
for field in rep_088_fields:
subs = field_get_subfields(field)
if '9' in subs:
for val in subs['9']:
if val.startswith('P0') or val.startswith('CM-P0'):
sf = [('9', 'CERN'), ('b', val)]
record_add_field(rec, '595', subfields=sf)
for key, val in field[0]:
if key in ['a', '9'] and not val.startswith('SIS-'):
record_add_field(rec, '037', subfields=[('a', val)])
record_delete_fields(rec, "088")
rep_037_fields = record_get_field_instances(rec, '037')
for field in rep_037_fields:
subs = field_get_subfields(field)
if 'a' in subs:
for value in subs['a']:
if 'arXiv' in value:
new_subs = [('a', value), ('9', 'arXiv')]
for fld in record_get_field_instances(rec, '695'):
for key, val in field_get_subfield_instances(fld):
if key == 'a':
new_subs.append(('c', val))
break
nf = create_field(subfields=new_subs)
record_replace_field(rec, '037', nf, field[4])
for key, val in field[0]:
if key in ['a', '9'] and val.startswith('SIS-'):
record_delete_field(rec, '037', field_position_global=field[4])
for field in record_get_field_instances(rec, '242'):
record_add_field(rec, '246', subfields=field[0])
record_delete_fields(rec, '242')
# 269 Date normalization
for field in record_get_field_instances(rec, '269'):
for idx, (key, value) in enumerate(field[0]):
if key == "c":
field[0][idx] = ("c", convert_date_to_iso(value))
record_delete_fields(rec, "260")
if not 'THESIS' in collections:
for field in record_get_field_instances(rec, '260'):
record_add_field(rec, '269', subfields=field[0])
record_delete_fields(rec, '260')
# 300 page number
for field in record_get_field_instances(rec, '300'):
for idx, (key, value) in enumerate(field[0]):
if key == 'a':
if "mult." not in value and value != " p":
field[0][idx] = ('a', re.sub(r'[^\d-]+', '', value))
else:
record_delete_field(rec,
'300',
field_position_global=field[4])
break
# 100 & 700 punctuate author names
author_names = record_get_field_instances(rec, '100')
author_names.extend(record_get_field_instances(rec, '700'))
for field in author_names:
subs = field_get_subfields(field)
if not 'i' in subs or 'XX' in subs['i']:
if not 'j' in subs or 'YY' in subs['j']:
for idx, (key, value) in enumerate(field[0]):
if key == 'a':
field[0][idx] = ('a', punctuate_authorname(value))
# 700 -> 701 Thesis supervisors
if 'THESIS' in collections:
for field in record_get_field_instances(rec, '700'):
record_add_field(rec, '701', subfields=field[0])
record_delete_fields(rec, '700')
# 501 move subfields
fields_501 = record_get_field_instances(rec, '502')
for idx, field in enumerate(fields_501):
new_subs = []
for key, value in field[0]:
if key == 'a':
new_subs.append(('b', value))
elif key == 'b':
new_subs.append(('c', value))
elif key == 'c':
new_subs.append(('d', value))
else:
new_subs.append((key, value))
fields_501[idx] = field_swap_subfields(field, new_subs)
# 650 Translate Categories
categories = get_categories()
category_fields = record_get_field_instances(rec,
'650',
ind1='1',
ind2='7')
record_delete_fields(rec, "650")
for field in category_fields:
for idx, (key, value) in enumerate(field[0]):
if key == 'a':
new_value = translate_config(value, categories)
if new_value != value:
new_subs = [('2', 'INSPIRE'), ('a', new_value)]
else:
new_subs = [('2', 'SzGeCERN'), ('a', value)]
record_add_field(rec,
"650",
ind1="1",
ind2="7",
subfields=new_subs)
break
# 653 Free Keywords
for field in record_get_field_instances(rec, '653', ind1='1'):
subs = field_get_subfields(field)
new_subs = []
if 'a' in subs:
for val in subs['a']:
new_subs.extend([('9', 'author'), ('a', val)])
new_field = create_field(subfields=new_subs)
record_replace_field(rec,
'653',
new_field,
field_position_global=field[4])
experiments = get_experiments()
# 693 Remove if 'not applicable'
for field in record_get_field_instances(rec, '693'):
subs = field_get_subfields(field)
if 'not applicable' in [x.lower() for x in subs['a']]:
if 'not applicable' in [x.lower() for x in subs['e']]:
record_delete_field(rec, '693', field_position_global=field[4])
new_subs = []
experiment_a = ""
experiment_e = ""
for (key, value) in subs.iteritems():
if key == 'a':
experiment_a = value[0]
new_subs.append((key, value[0]))
elif key == 'e':
experiment_e = value[0]
experiment = "%s---%s" % (experiment_a.replace(" ", "-"), experiment_e)
translated_experiments = translate_config(experiment, experiments)
new_subs.append(("e", translated_experiments))
record_delete_field(rec, tag="693", field_position_global=field[4])
record_add_field(rec, "693", subfields=new_subs)
# 710 Collaboration
for field in record_get_field_instances(rec, '710'):
subs = field_get_subfield_instances(field)
for idx, (key, value) in enumerate(subs[:]):
if key == '5':
subs.pop(idx)
elif value.startswith('CERN. Geneva'):
subs.pop(idx)
if len(subs) == 0:
record_delete_field(rec, '710', field_position_global=field[4])
# 773 journal translations
journals = get_journals()
for field in record_get_field_instances(rec, '773'):
subs = field_get_subfield_instances(field)
new_subs = []
for idx, (key, value) in enumerate(subs):
if key == 'p':
new_subs.append((key, translate_config(value, journals)))
else:
new_subs.append((key, value))
record_delete_field(rec, tag="773", field_position_global=field[4])
record_add_field(rec, "773", subfields=new_subs)
# FFT (856) Dealing with graphs
figure_counter = 0
for field in record_get_field_instances(rec, '856', ind1='4'):
subs = field_get_subfields(field)
newsubs = []
remove = False
if 'z' in subs:
is_figure = [s for s in subs['z'] if "figure" in s.lower()]
if is_figure and 'u' in subs:
is_subformat = [
s for s in subs['u'] if "subformat" in s.lower()
]
if not is_subformat:
url = subs['u'][0]
if url.endswith(".pdf"):
# We try to convert
fd, local_url = mkstemp(suffix=os.path.basename(url),
dir=CFG_TMPSHAREDDIR)
os.close(fd)
_print("Downloading %s into %s" % (url, local_url),
verbose=5)
plotfile = ""
try:
plotfile = download_file(url_for_file=url,
downloaded_file=local_url,
timeout=30.0)
except InvenioDownloadError:
_print(
"Download failed while attempting to reach %s. Skipping.."
% (url, ))
remove = True
if plotfile:
converted = convert_images([plotfile])
if converted:
url = converted.pop()
_print("Successfully converted %s to %s" %
(local_url, url),
verbose=5)
else:
_print("Conversion failed on %s" %
(local_url, ))
url = None
remove = True
if url:
newsubs.append(('a', url))
newsubs.append(('t', 'Plot'))
figure_counter += 1
if 'y' in subs:
newsubs.append(
('d',
"%05d %s" % (figure_counter, subs['y'][0])))
else:
newsubs.append(
('d', "%05d %s" %
(figure_counter, os.path.basename(url))))
if not newsubs and 'u' in subs:
is_fulltext = [s for s in subs['u'] if ".pdf" in s]
if is_fulltext:
newsubs = [('t', 'INSPIRE-PUBLIC'), ('a', subs['u'][0])]
if not newsubs and 'u' in subs:
remove = True
is_zipfile = [s for s in subs['u'] if ".zip" in s]
if is_zipfile:
url = is_zipfile[0]
local_url = os.path.join(CFG_TMPSHAREDDIR,
os.path.basename(url))
_print("Downloading %s into %s" % (url, local_url), verbose=5)
zipped_archive = ""
try:
zipped_archive = download_file(url_for_file=is_zipfile[0],
downloaded_file=local_url,
timeout=30.0)
except InvenioDownloadError:
_print(
"Download failed while attempting to reach %s. Skipping.."
% (is_zipfile[0], ))
remove = True
if zipped_archive:
unzipped_archive = unzip(zipped_archive)
list_of_pngs = locate("*.png", unzipped_archive)
for png in list_of_pngs:
if "_vti_" in png or "__MACOSX" in png:
continue
figure_counter += 1
plotsubs = []
plotsubs.append(('a', png))
caption = '%05d %s' % (figure_counter,
os.path.basename(png))
plotsubs.append(('d', caption))
plotsubs.append(('t', 'Plot'))
record_add_field(rec, 'FFT', subfields=plotsubs)
if not remove and not newsubs and 'u' in subs:
urls = ('http://cdsweb.cern.ch', 'http://cms.cern.ch',
'http://cmsdoc.cern.ch', 'http://documents.cern.ch',
'http://preprints.cern.ch', 'http://cds.cern.ch')
for val in subs['u']:
if any(url in val for url in urls):
remove = True
break
if val.endswith('ps.gz'):
remove = True
if newsubs:
record_add_field(rec, 'FFT', subfields=newsubs)
remove = True
if remove:
record_delete_field(rec,
'856',
ind1='4',
field_position_global=field[4])
# 500 - Preliminary results
subs = [('a', "Preliminary results")]
record_add_field(rec, "500", subfields=subs)
for collection in collections:
record_add_field(rec, '980', subfields=[('a', collection)])
return rec
