def main():
parser = argparse.ArgumentParser()
parser.add_argument("csv_file", help=ARG_HELP_STRINGS["csv_file"])
parser.add_argument("-O", "--offsetting_mode", help=ARG_HELP_STRINGS["offsetting"])
parser.add_argument("-b", "--bypass-cert-verification", action="store_true",
help=ARG_HELP_STRINGS["bypass"])
parser.add_argument("-e", "--encoding", help=ARG_HELP_STRINGS["encoding"])
parser.add_argument("-f", "--force", action="store_true",
help=ARG_HELP_STRINGS["force"])
parser.add_argument("-i", "--ignore-header", action="store_true",
help=ARG_HELP_STRINGS["ignore_header"])
parser.add_argument("-j", "--force-header", action="store_true",
help=ARG_HELP_STRINGS["force_header"])
parser.add_argument("-l", "--locale", help=ARG_HELP_STRINGS["locale"])
parser.add_argument("-a", "--add-unknown-columns", action="store_true",
help=ARG_HELP_STRINGS["unknown_columns"])
parser.add_argument("-d", "--dialect", choices=["excel", "excel-tab", "unix"],
help=ARG_HELP_STRINGS["dialect"])
parser.add_argument("-v", "--verbose", action="store_true",
help=ARG_HELP_STRINGS["verbose"])
parser.add_argument("-o", "--overwrite", action="store_true",
help=ARG_HELP_STRINGS["overwrite"])
parser.add_argument("-u", "--update", action="store_true",
help=ARG_HELP_STRINGS["update"])
parser.add_argument("-r", "--round_monetary", action="store_true",
help=ARG_HELP_STRINGS["round_monetary"])
parser.add_argument("--no-crossref", action="store_true",
help=ARG_HELP_STRINGS["no_crossref"])
parser.add_argument("--no-pubmed", action="store_true",
help=ARG_HELP_STRINGS["no_pubmed"])
parser.add_argument("--no-doaj", action="store_true",
help=ARG_HELP_STRINGS["no_doaj"])
parser.add_argument("-institution", "--institution_column", type=int,
help=ARG_HELP_STRINGS["institution"])
parser.add_argument("-period", "--period_column", type=int,
help=ARG_HELP_STRINGS["period"])
parser.add_argument("-doi", "--doi_column", type=int,
help=ARG_HELP_STRINGS["doi"])
parser.add_argument("-euro", "--euro_column", type=int,
help=ARG_HELP_STRINGS["euro"])
parser.add_argument("-is_hybrid", "--is_hybrid_column", type=int,
help=ARG_HELP_STRINGS["is_hybrid"])
parser.add_argument("-publisher", "--publisher_column", type=int,
help=ARG_HELP_STRINGS["publisher"])
parser.add_argument("-journal_full_title", "--journal_full_title_column",
type=int, help=ARG_HELP_STRINGS["journal_full_title"])
parser.add_argument("-book_title", "--book_title_column",
type=int, help=ARG_HELP_STRINGS["book_title"])
parser.add_argument("-issn", "--issn_column",
type=int, help=ARG_HELP_STRINGS["issn"])
parser.add_argument("-isbn", "--isbn_column",
type=int, help=ARG_HELP_STRINGS["isbn"])
parser.add_argument("-backlist_oa", "--backlist_oa_column",
type=int, help=ARG_HELP_STRINGS["backlist_oa"])
parser.add_argument("-additional_isbns", "--additional_isbn_columns", type=int, nargs='+',
help=ARG_HELP_STRINGS["additional_isbns"])
parser.add_argument("-url", "--url_column",
type=int, help=ARG_HELP_STRINGS["url"])
parser.add_argument("-start", type=int, help=ARG_HELP_STRINGS["start"])
parser.add_argument("-end", type=int, help=ARG_HELP_STRINGS["end"])
args = parser.parse_args()
handler = logging.StreamHandler(sys.stderr)
handler.setFormatter(oat.ANSIColorFormatter())
bufferedHandler = oat.BufferedErrorHandler(handler)
bufferedHandler.setFormatter(oat.ANSIColorFormatter())
logging.root.addHandler(handler)
logging.root.addHandler(bufferedHandler)
logging.root.setLevel(logging.INFO)
if args.locale:
norm = locale.normalize(args.locale)
if norm != args.locale:
msg = "locale '{}' not found, normalised to '{}'".format(
args.locale, norm)
oat.print_y(msg)
try:
loc = locale.setlocale(locale.LC_ALL, norm)
oat.print_g("Using locale " + loc)
except locale.Error as loce:
msg = "Setting locale to {} failed: {}".format(norm, loce.message)
oat.print_r(msg)
sys.exit()
enc = None # CSV file encoding
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
msg = ("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
oat.print_g(msg)
enc = args.encoding
except LookupError:
msg = ("Error: '" + args.encoding + "' not found Python's " +
"codec collection. Either look for a valid name here " +
"(https://docs.python.org/2/library/codecs.html#standard-" +
"encodings) or omit this argument to enable automated " +
"guessing.")
oat.print_r(msg)
sys.exit()
result = oat.analyze_csv_file(args.csv_file, enc=enc)
if result["success"]:
csv_analysis = result["data"]
print(csv_analysis)
else:
print(result["error_msg"])
sys.exit()
if args.dialect:
dialect = args.dialect
oat.print_g('Dialect sniffing results ignored, using built-in CSV dialect "' + dialect + '"')
else:
dialect = csv_analysis.dialect
if enc is None:
enc = csv_analysis.enc
has_header = csv_analysis.has_header or args.force_header
if enc is None:
print("Error: No encoding given for CSV file and automated " +
"detection failed. Please set the encoding manually via the " +
"--enc argument")
sys.exit()
csv_file = open(args.csv_file, "r", encoding=enc)
reader = csv.reader(csv_file, dialect=dialect)
first_row = next(reader)
num_columns = len(first_row)
print("\nCSV file has {} columns.".format(num_columns))
csv_file.seek(0)
reader = csv.reader(csv_file, dialect=dialect)
if args.update and args.overwrite:
oat.print_r("Error: Either use the -u or the -o option, not both.")
sys.exit()
if args.overwrite:
for column in OVERWRITE_STRATEGY.keys():
OVERWRITE_STRATEGY[column] = CSVColumn.OW_ALWAYS
elif not args.update:
for column in OVERWRITE_STRATEGY.keys():
OVERWRITE_STRATEGY[column] = CSVColumn.OW_ASK
additional_isbn_columns = []
if args.additional_isbn_columns:
for index in args.additional_isbn_columns:
if index > num_columns:
msg = "Error: Additional ISBN column index {} exceeds number of columns ({})."
oat.print_r(msg.format(index, num_columns))
sys.exit()
else:
additional_isbn_columns.append(index)
column_map = {
"institution": CSVColumn("institution", {"articles": CSVColumn.MANDATORY, "books": CSVColumn.MANDATORY}, args.institution_column, overwrite=OVERWRITE_STRATEGY["institution"]),
"period": CSVColumn("period",{"articles": CSVColumn.MANDATORY, "books": CSVColumn.MANDATORY}, args.period_column, overwrite=OVERWRITE_STRATEGY["period"]),
"euro": CSVColumn("euro", {"articles": CSVColumn.MANDATORY, "books": CSVColumn.MANDATORY}, args.euro_column, overwrite=OVERWRITE_STRATEGY["euro"]),
"doi": CSVColumn("doi", {"articles": CSVColumn.MANDATORY, "books": CSVColumn.MANDATORY}, args.doi_column, overwrite=OVERWRITE_STRATEGY["doi"]),
"is_hybrid": CSVColumn("is_hybrid", {"articles": CSVColumn.MANDATORY, "books": CSVColumn.NONE}, args.is_hybrid_column, overwrite=OVERWRITE_STRATEGY["is_hybrid"]),
"publisher": CSVColumn("publisher", {"articles": CSVColumn.BACKUP, "books": CSVColumn.NONE}, args.publisher_column, overwrite=OVERWRITE_STRATEGY["publisher"]),
"journal_full_title": CSVColumn("journal_full_title", {"articles": CSVColumn.BACKUP, "books": CSVColumn.NONE}, args.journal_full_title_column, overwrite=OVERWRITE_STRATEGY["journal_full_title"]),
"issn": CSVColumn("issn", {"articles": CSVColumn.BACKUP, "books": CSVColumn.NONE}, args.issn_column, overwrite=OVERWRITE_STRATEGY["issn"]),
"issn_print": CSVColumn("issn_print", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["issn_print"]),
"issn_electronic": CSVColumn("issn_electronic", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["issn_electronic"]),
"issn_l": CSVColumn("issn_l", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["issn_l"]),
"license_ref": CSVColumn("license_ref", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE} , None, overwrite=OVERWRITE_STRATEGY["license_ref"]),
"indexed_in_crossref": CSVColumn("indexed_in_crossref", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["indexed_in_crossref"]),
"pmid": CSVColumn("pmid", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["pmid"]),
"pmcid": CSVColumn("pmcid", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["pmcid"]),
"ut": CSVColumn("ut", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["ut"]),
"url": CSVColumn("url", {"articles": CSVColumn.BACKUP, "books": CSVColumn.NONE}, args.url_column, overwrite=OVERWRITE_STRATEGY["url"]),
"doaj": CSVColumn("doaj", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["doaj"]),
"agreement": CSVColumn("agreement", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["agreement"]),
"book_title": CSVColumn("book_title", {"articles": CSVColumn.NONE, "books": CSVColumn.RECOMMENDED}, args.book_title_column, overwrite=OVERWRITE_STRATEGY["book_title"]),
"backlist_oa": CSVColumn("backlist_oa", {"articles": CSVColumn.NONE, "books": CSVColumn.MANDATORY}, args.backlist_oa_column, overwrite=OVERWRITE_STRATEGY["backlist_oa"]),
"isbn": CSVColumn("isbn", {"articles": CSVColumn.NONE, "books": CSVColumn.BACKUP}, args.isbn_column, overwrite=OVERWRITE_STRATEGY["isbn"]),
"isbn_print": CSVColumn("isbn_print", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["isbn_print"]),
"isbn_electronic": CSVColumn("isbn_electronic", {"articles": CSVColumn.NONE, "books": CSVColumn.NONE}, None, overwrite=OVERWRITE_STRATEGY["isbn_electronic"])
}
header = None
if has_header:
for row in reader:
if not row: # Skip empty lines
continue
header = row # First non-empty row should be the header
if args.ignore_header:
print("Skipping header analysis due to command line argument.")
break
else:
print("\n *** Analyzing CSV header ***\n")
for (index, item) in enumerate(header):
if index in additional_isbn_columns:
msg = "Column named '{}' at index {} is designated as additional ISBN column"
print(msg.format(item, index))
continue
column_type = oat.get_column_type_from_whitelist(item)
if column_type is not None and column_map[column_type].index is None:
column_map[column_type].index = index
column_map[column_type].column_name = item
found_msg = ("Found column named '{}' at index {}, " +
"assuming this to be the '{}' column.")
print(found_msg.format(item, index, column_type))
break
print("\n *** Starting heuristical analysis ***\n")
for row in reader:
if not row: # Skip empty lines
# We analyze the first non-empty line, a possible header should
# have been processed by now.
continue
column_candidates = {
"doi": [],
"period": [],
"euro": []
}
found_msg = "The entry in column {} looks like a potential {}: {}"
for (index, entry) in enumerate(row):
if index in [csvcolumn.index for csvcolumn in column_map.values()] + additional_isbn_columns:
# Skip columns already assigned
continue
entry = entry.strip()
# Search for a DOI
if column_map['doi'].index is None:
if oat.DOI_RE.match(entry):
column_id = str(index)
# identify column either numerically or by column header
if header:
column_id += " ('" + header[index] + "')"
print(found_msg.format(column_id, "DOI", entry))
column_candidates['doi'].append(index)
continue
# Search for a potential year string
if column_map['period'].index is None:
try:
maybe_period = int(entry)
now = datetime.date.today().year
# Should be a wide enough margin
if maybe_period >= 2000 and maybe_period <= now + 2:
column_id = str(index)
if header:
column_id += " ('" + header[index] + "')"
print(found_msg.format(column_id, "year", entry))
column_candidates['period'].append(index)
continue
except ValueError:
pass
# Search for a potential monetary amount
if column_map['euro'].index is None:
try:
maybe_euro = locale.atof(entry)
if maybe_euro >= 10 and maybe_euro <= 10000:
column_id = str(index)
if header:
column_id += " ('" + header[index] + "')"
print (found_msg.format(column_id, "euro amount", entry))
column_candidates['euro'].append(index)
continue
except ValueError:
pass
for column_type, candidates in column_candidates.items():
if column_map[column_type].index is not None:
continue
if len(candidates) > 1:
print("Could not reliably identify the '" + column_type +
"' column - more than one possible candiate!")
elif len(candidates) < 1:
print("No candidate found for column '" + column_type + "'!")
else:
index = candidates.pop()
column_map[column_type].index = index
if header:
column_id = header[index]
column_map[column_type].column_name = column_id
else:
column_id = index
msg = "Assuming column '{}' to be the '{}' column."
print(msg.format(column_id, column_type))
column_map[column_type].index = index
break
print("\n *** CSV file analysis summary ***\n")
index_dict = {csvc.index: csvc for csvc in column_map.values()}
for index in range(num_columns):
column_name = ""
if header:
column_name = header[index]
if index in index_dict:
column = index_dict[index]
msg = u"column number {} ({}) is the '{}' column ({})".format(
index, column_name, column.column_type, column.get_req_description())
print(msg)
elif index in additional_isbn_columns:
msg = u"column number {} ({}) is an additional ISBN column".format(index, column_name)
oat.print_c(msg)
else:
if args.add_unknown_columns:
msg = (u"column number {} ({}) is an unknown column, it will be " +
"appended to the generated CSV file")
print(msg.format(index, column_name))
if not column_name:
# Use a generic name
column_name = "unknown"
while column_name in column_map.keys():
# TODO: Replace by a numerical, increasing suffix
column_name += "_"
column_map[column_name] = CSVColumn(column_name, CSVColumn.NONE, index)
else:
msg = (u"column number {} ({}) is an unknown column, it will be " +
"ignored")
print(msg.format(index, column_name))
print()
for column in column_map.values():
if column.index is None:
msg = "The '{}' column could not be identified ({})"
print(msg.format(column.column_type, column.get_req_description()))
print()
article_mand_missing = [x.column_type for x in column_map.values() if x.requirement["articles"] == CSVColumn.MANDATORY and x.index is None]
article_back_missing = [x.column_type for x in column_map.values() if x.requirement["articles"] == CSVColumn.BACKUP and x.index is None]
book_mand_missing = [x.column_type for x in column_map.values() if x.requirement["books"] == CSVColumn.MANDATORY and x.index is None]
book_back_missing = [x.column_type for x in column_map.values() if x.requirement["books"] == CSVColumn.BACKUP and x.index is None]
if article_mand_missing:
msg = "Article enrichment is not possible - mandatory columns are missing ({})"
oat.print_y(msg.format(", ".join(article_mand_missing)))
elif article_back_missing:
msg = "Article enrichment is possible, but backup columns are missing ({}) - each record will need a valid DOI"
oat.print_b(msg.format(", ".join(article_back_missing)))
else:
oat.print_g("Article enrichment is possible with all backup columns in place")
if book_mand_missing:
msg = "Book enrichment is not possible - mandatory columns are missing ({})"
oat.print_y(msg.format(", ".join(book_mand_missing)))
elif book_back_missing:
msg = "Book enrichment is possible, but backup columns are missing ({}) - each record will need a valid DOI"
oat.print_b(msg.format(", ".join(book_back_missing)))
else:
oat.print_g("Book enrichment is possible with all backup columns in place")
print()
if article_mand_missing and book_mand_missing:
if not args.force:
oat.print_r("ERROR: Could not detect the minimum mandatory data set for any " +
"publication type. There are 2 ways to fix this:")
if not header:
print("1) Add a header row to your file and identify the " +
"column(s) by assigning them an appropiate column name.")
else:
print("1) Identify the missing column(s) by assigning them " +
"a different column name in the CSV header (You can " +
"use the column name(s) mentioned in the message above)")
print("2) Use command line parameters when calling this script " +
"to identify the missing columns (use -h for help) ")
sys.exit()
else:
oat.print_y("WARNING: Could not detect the minimum mandatory data set for any " +
"publication type - forced to continue.")
start = input("\nStart metadata aggregation? (y/n):")
while start not in ["y", "n"]:
start = input("Please type 'y' or 'n':")
if start == "n":
sys.exit()
print("\n *** Starting metadata aggregation ***\n")
enriched_content = {}
for record_type, fields in oat.COLUMN_SCHEMAS.items():
# add headers
enriched_content[record_type] = {
"count": 0,
"content": [list(fields)]
}
if not os.path.isdir("tempfiles"):
os.mkdir("tempfiles")
isbn_handling = oat.ISBNHandling("tempfiles/ISBNRangeFile.xml")
doab_analysis = oat.DOABAnalysis(isbn_handling, "tempfiles/DOAB.csv", verbose=False)
doaj_analysis = oat.DOAJAnalysis("tempfiles/DOAJ.csv")
csv_file.seek(0)
reader = csv.reader(csv_file, dialect=dialect)
header_processed = False
row_num = 0
for row in reader:
row_num += 1
if not row:
continue # skip empty lines
if not header_processed:
header_processed = True
if has_header:
# If the CSV file has a header, we are currently there - skip it
# to get to the first data row
continue
if args.start and args.start > row_num:
continue
if args.end and args.end < row_num:
continue
print("---Processing line number " + str(row_num) + "---")
result_type, enriched_row = oat.process_row(row, row_num, column_map, num_columns, additional_isbn_columns, doab_analysis, doaj_analysis,
args.no_crossref, args.no_pubmed,
args.no_doaj, args.round_monetary,
args.offsetting_mode)
for record_type, value in enriched_content.items():
if record_type == result_type:
value["content"].append(enriched_row)
value["count"] += 1
else:
empty_line = ["" for x in value["content"][0]]
value["content"].append(empty_line)
csv_file.close()
for record_type, value in enriched_content.items():
if value["count"] > 0:
with open('out_' + record_type + '.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, oat.OPENAPC_STANDARD_QUOTEMASK,
True, True, True)
writer.write_rows(value["content"])
if not bufferedHandler.buffer:
oat.print_g("Metadata enrichment successful, no errors occured")
else:
oat.print_r("There were errors during the enrichment process:\n")
# closing will implicitly flush the handler and print any buffered
# messages to stderr
bufferedHandler.close()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("csv_file", help=ARG_HELP_STRINGS["csv_file"])
parser.add_argument("-e", "--encoding", help=ARG_HELP_STRINGS["encoding"])
parser.add_argument("-start", type=int, default=1, help=ARG_HELP_STRINGS["start"])
parser.add_argument("-end", type=int, help=ARG_HELP_STRINGS["start"])
args = parser.parse_args()
handler = logging.StreamHandler(sys.stderr)
handler.setFormatter(oat.ANSIColorFormatter())
bufferedHandler = oat.BufferedErrorHandler(handler)
bufferedHandler.setFormatter(oat.ANSIColorFormatter())
logging.root.addHandler(handler)
logging.root.addHandler(bufferedHandler)
logging.root.setLevel(logging.INFO)
enc = None
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
msg = ("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
oat.print_g(msg)
enc = args.encoding
except LookupError:
msg = ("Error: '" + args.encoding + "' not found Python's " +
"codec collection. Either look for a valid name here " +
"(https://docs.python.org/2/library/codecs.html#standard-" +
"encodings) or omit this argument to enable automated " +
"guessing.")
oat.print_r(msg)
sys.exit()
head, content = oat.get_csv_file_content(args.csv_file, enc)
content = head + content
header = {"User-Agent": "Mozilla/5.0 Firefox/45.0"}
line_num = 0
for line in content:
line_num += 1
if args.start and args.start > line_num:
continue
if args.end and args.end < line_num:
continue
institution = line[0]
period = line[1]
doi = line[3]
is_hybrid = line[4]
publisher = line[5]
journal = line[6]
if publisher != "Elsevier" or is_hybrid != "TRUE":
continue
init_msg = (u"Line {}: Checking {} article from {}, published in " +
"{}...").format(line_num, institution, period, journal)
oat.print_b(init_msg)
url = 'http://doi.org/' + doi
req = urllib2.Request(url, None, header)
ret_value = {'success': True}
try:
response = urllib2.urlopen(req)
target = response.geturl()
resolve_msg = u"DOI {} resolved, led us to {}".format(doi, target)
if "sciencedirect.com" not in target:
oat.print_y(resolve_msg)
oat.print_y("Journal not located at sciencedirect, skipping...")
continue
oat.print_b(resolve_msg)
content_string = response.read()
single_match = pdflink_re.search(content_string)
if single_match:
link_url = single_match.groups()[0]
oat.print_g(u"PDF link found: " + link_url)
else:
multi_match = pdflink_multi_re.search(content_string)
if multi_match:
link_url = multi_match.groups()[0]
link_url = link_url.replace("&", "&")
oat.print_g(u"PDF link found (more than one document): " + link_url)
else:
error_msg = (u"No PDF link found! (line {}, DOI: {}, " +
"landing page: {})").format(line_num, doi, target)
logging.error(error_msg)
time.sleep(1)
except urllib2.HTTPError as httpe:
code = str(httpe.getcode())
oat.print_r("HTTPError: {} - {}".format(code, httpe.reason))
except urllib2.URLError as urle:
oat.print_r("URLError: {}".format(urle.reason))
if not bufferedHandler.buffer:
oat.print_g("\nLookup finished, all articles were accessible on sciencedirect")
else:
oat.print_r("\nLookup finished, not all articles could be accessed on sciencedirect:\n")
# closing will implicitly flush the handler and print any buffered
# messages to stderr
bufferedHandler.close()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("csv_file", help=ARG_HELP_STRINGS["csv_file"])
parser.add_argument("-O",
"--offsetting_mode",
help=ARG_HELP_STRINGS["offsetting"])
parser.add_argument("-b",
"--bypass-cert-verification",
action="store_true",
help=ARG_HELP_STRINGS["bypass"])
parser.add_argument("-d",
"--offline_doaj",
help=ARG_HELP_STRINGS["offline_doaj"])
parser.add_argument("-D",
"--offline_doaj_download",
help=ARG_HELP_STRINGS["offline_doaj_download"])
parser.add_argument("-e", "--encoding", help=ARG_HELP_STRINGS["encoding"])
parser.add_argument("-f",
"--force",
action="store_true",
help=ARG_HELP_STRINGS["force"])
parser.add_argument("-i",
"--ignore-header",
action="store_true",
help=ARG_HELP_STRINGS["ignore_header"])
parser.add_argument("-j",
"--force-header",
action="store_true",
help=ARG_HELP_STRINGS["force_header"])
parser.add_argument("-l", "--locale", help=ARG_HELP_STRINGS["locale"])
parser.add_argument("-a",
"--add-unknown-columns",
action="store_true",
help=ARG_HELP_STRINGS["unknown_columns"])
parser.add_argument("-v",
"--verbose",
action="store_true",
help=ARG_HELP_STRINGS["verbose"])
parser.add_argument("-o",
"--overwrite",
action="store_true",
help=ARG_HELP_STRINGS["overwrite"])
parser.add_argument("-u",
"--update",
action="store_true",
help=ARG_HELP_STRINGS["update"])
parser.add_argument("-r",
"--round_monetary",
action="store_true",
help=ARG_HELP_STRINGS["round_monetary"])
parser.add_argument("--no-crossref",
action="store_true",
help=ARG_HELP_STRINGS["no_crossref"])
parser.add_argument("--no-pubmed",
action="store_true",
help=ARG_HELP_STRINGS["no_pubmed"])
parser.add_argument("--no-doaj",
action="store_true",
help=ARG_HELP_STRINGS["no_doaj"])
parser.add_argument("-institution",
"--institution_column",
type=int,
help=ARG_HELP_STRINGS["institution"])
parser.add_argument("-period",
"--period_column",
type=int,
help=ARG_HELP_STRINGS["period"])
parser.add_argument("-doi",
"--doi_column",
type=int,
help=ARG_HELP_STRINGS["doi"])
parser.add_argument("-euro",
"--euro_column",
type=int,
help=ARG_HELP_STRINGS["euro"])
parser.add_argument("-is_hybrid",
"--is_hybrid_column",
type=int,
help=ARG_HELP_STRINGS["is_hybrid"])
parser.add_argument("-publisher",
"--publisher_column",
type=int,
help=ARG_HELP_STRINGS["publisher"])
parser.add_argument("-journal_full_title",
"--journal_full_title_column",
type=int,
help=ARG_HELP_STRINGS["journal_full_title"])
parser.add_argument("-issn",
"--issn_column",
type=int,
help=ARG_HELP_STRINGS["issn"])
parser.add_argument("-url",
"--url_column",
type=int,
help=ARG_HELP_STRINGS["url"])
parser.add_argument("-start", type=int, help=ARG_HELP_STRINGS["start"])
parser.add_argument("-end", type=int, help=ARG_HELP_STRINGS["end"])
parser.add_argument("-q",
"--quotemask",
default="tfftttttttttttttttt",
help=ARG_HELP_STRINGS["quotemask"])
parser.add_argument("-n",
"--no-openapc-quote-rules",
help=ARG_HELP_STRINGS["no_openapc_quote_rules"],
action="store_true",
default=False)
args = parser.parse_args()
handler = logging.StreamHandler(sys.stderr)
handler.setFormatter(oat.ANSIColorFormatter())
bufferedHandler = oat.BufferedErrorHandler(handler)
bufferedHandler.setFormatter(oat.ANSIColorFormatter())
logging.root.addHandler(handler)
logging.root.addHandler(bufferedHandler)
logging.root.setLevel(logging.INFO)
if args.offline_doaj and args.offline_doaj_download:
oat.print_r("Error: Either use the -d or the -D option, not both.")
sys.exit()
if args.locale:
norm = locale.normalize(args.locale)
if norm != args.locale:
msg = "locale '{}' not found, normalised to '{}'".format(
args.locale, norm)
oat.print_y(msg)
try:
loc = locale.setlocale(locale.LC_ALL, norm)
oat.print_g("Using locale " + loc)
except locale.Error as loce:
msg = "Setting locale to {} failed: {}".format(norm, loce.message)
oat.print_r(msg)
sys.exit()
enc = None # CSV file encoding
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
msg = ("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
oat.print_g(msg)
enc = args.encoding
except LookupError:
msg = ("Error: '" + args.encoding + "' not found Python's " +
"codec collection. Either look for a valid name here " +
"(https://docs.python.org/2/library/codecs.html#standard-" +
"encodings) or omit this argument to enable automated " +
"guessing.")
oat.print_r(msg)
sys.exit()
result = oat.analyze_csv_file(args.csv_file, enc=enc)
if result["success"]:
csv_analysis = result["data"]
print(csv_analysis)
else:
print(result["error_msg"])
sys.exit()
if enc is None:
enc = csv_analysis.enc
dialect = csv_analysis.dialect
has_header = csv_analysis.has_header or args.force_header
if enc is None:
print("Error: No encoding given for CSV file and automated " +
"detection failed. Please set the encoding manually via the " +
"--enc argument")
sys.exit()
reduced = args.quotemask.replace("f", "").replace("t", "")
if len(reduced) > 0:
print("Error: A quotemask may only contain the letters 't' and " +
"'f'!")
sys.exit()
mask = [True if x == "t" else False for x in args.quotemask]
doaj_offline_analysis = None
if args.offline_doaj:
if os.path.isfile(args.offline_doaj):
doaj_offline_analysis = oat.DOAJOfflineAnalysis(args.offline_doaj)
else:
oat.print_r("Error: " + args.offline_doaj + " does not seem "
"to be a file!")
sys.exit()
elif args.offline_doaj_download:
if os.path.isfile(args.offline_doaj_download):
oat.print_r("Error: Target file '" + args.offline_doaj_download +
"' already exists!")
sys.exit()
doaj_offline_analysis = oat.DOAJOfflineAnalysis(
args.offline_doaj_download, download=True)
csv_file = open(args.csv_file, "r", encoding=enc)
reader = csv.reader(csv_file, dialect=dialect)
first_row = next(reader)
num_columns = len(first_row)
print("\nCSV file has {} columns.".format(num_columns))
csv_file.seek(0)
reader = csv.reader(csv_file, dialect=dialect)
if args.update and args.overwrite:
oat.print_r("Error: Either use the -u or the -o option, not both.")
sys.exit()
if args.overwrite:
for column in OVERWRITE_STRATEGY.keys():
OVERWRITE_STRATEGY[column] = CSVColumn.OW_ALWAYS
elif not args.update:
for column in OVERWRITE_STRATEGY.keys():
OVERWRITE_STRATEGY[column] = CSVColumn.OW_ASK
openapc_column_map = OrderedDict([
("institution",
CSVColumn("institution",
CSVColumn.MANDATORY,
args.institution_column,
overwrite=OVERWRITE_STRATEGY["institution"])),
("period",
CSVColumn("period",
CSVColumn.MANDATORY,
args.period_column,
overwrite=OVERWRITE_STRATEGY["period"])),
("euro",
CSVColumn("euro",
CSVColumn.MANDATORY,
args.euro_column,
overwrite=OVERWRITE_STRATEGY["euro"])),
("doi",
CSVColumn("doi",
CSVColumn.MANDATORY,
args.doi_column,
overwrite=OVERWRITE_STRATEGY["doi"])),
("is_hybrid",
CSVColumn("is_hybrid",
CSVColumn.MANDATORY,
args.is_hybrid_column,
overwrite=OVERWRITE_STRATEGY["is_hybrid"])),
("publisher",
CSVColumn("publisher",
CSVColumn.OPTIONAL,
args.publisher_column,
overwrite=OVERWRITE_STRATEGY["publisher"])),
("journal_full_title",
CSVColumn("journal_full_title",
CSVColumn.OPTIONAL,
args.journal_full_title_column,
overwrite=OVERWRITE_STRATEGY["journal_full_title"])),
("issn",
CSVColumn("issn",
CSVColumn.OPTIONAL,
args.issn_column,
overwrite=OVERWRITE_STRATEGY["issn"])),
("issn_print",
CSVColumn("issn_print",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["issn_print"])),
("issn_electronic",
CSVColumn("issn_electronic",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["issn_electronic"])),
("issn_l",
CSVColumn("issn_l",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["issn_l"])),
("license_ref",
CSVColumn("license_ref",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["license_ref"])),
("indexed_in_crossref",
CSVColumn("indexed_in_crossref",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["indexed_in_crossref"])),
("pmid",
CSVColumn("pmid",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["pmid"])),
("pmcid",
CSVColumn("pmcid",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["pmcid"])),
("ut",
CSVColumn("ut",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["ut"])),
("url",
CSVColumn("url",
CSVColumn.OPTIONAL,
args.url_column,
overwrite=OVERWRITE_STRATEGY["url"])),
("doaj",
CSVColumn("doaj",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["doaj"]))
])
offsetting_column_map = OrderedDict([
("institution",
CSVColumn("institution",
CSVColumn.MANDATORY,
args.institution_column,
overwrite=OVERWRITE_STRATEGY["institution"])),
("period",
CSVColumn("period",
CSVColumn.MANDATORY,
args.period_column,
overwrite=OVERWRITE_STRATEGY["period"])),
("euro",
CSVColumn("euro",
CSVColumn.NONE,
args.euro_column,
overwrite=OVERWRITE_STRATEGY["euro"])),
("doi",
CSVColumn("doi",
CSVColumn.MANDATORY,
args.doi_column,
overwrite=OVERWRITE_STRATEGY["doi"])),
("is_hybrid",
CSVColumn("is_hybrid",
CSVColumn.MANDATORY,
args.is_hybrid_column,
overwrite=OVERWRITE_STRATEGY["is_hybrid"])),
("publisher",
CSVColumn("publisher",
CSVColumn.OPTIONAL,
args.publisher_column,
overwrite=OVERWRITE_STRATEGY["publisher"])),
("journal_full_title",
CSVColumn("journal_full_title",
CSVColumn.OPTIONAL,
args.journal_full_title_column,
overwrite=OVERWRITE_STRATEGY["journal_full_title"])),
("issn",
CSVColumn("issn",
CSVColumn.OPTIONAL,
args.issn_column,
overwrite=OVERWRITE_STRATEGY["issn"])),
("issn_print",
CSVColumn("issn_print",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["issn_print"])),
("issn_electronic",
CSVColumn("issn_electronic",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["issn_electronic"])),
("issn_l",
CSVColumn("issn_l",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["issn_l"])),
("license_ref",
CSVColumn("license_ref",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["license_ref"])),
("indexed_in_crossref",
CSVColumn("indexed_in_crossref",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["indexed_in_crossref"])),
("pmid",
CSVColumn("pmid",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["pmid"])),
("pmcid",
CSVColumn("pmcid",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["pmcid"])),
("ut",
CSVColumn("ut",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["ut"])),
("url",
CSVColumn("url",
CSVColumn.OPTIONAL,
args.url_column,
overwrite=OVERWRITE_STRATEGY["url"])),
("doaj",
CSVColumn("doaj",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["doaj"])),
("agreement",
CSVColumn("agreement",
CSVColumn.NONE,
None,
overwrite=OVERWRITE_STRATEGY["agreement"])),
])
if args.offsetting_mode:
column_map = offsetting_column_map
else:
column_map = openapc_column_map
header = None
if has_header:
for row in reader:
if not row: # Skip empty lines
continue
header = row # First non-empty row should be the header
if args.ignore_header:
print("Skipping header analysis due to command line argument.")
break
else:
print("\n *** Analyzing CSV header ***\n")
for (index, item) in enumerate(header):
column_type = oat.get_column_type_from_whitelist(item)
if column_type is not None and column_map[
column_type].index is None:
column_map[column_type].index = index
column_map[column_type].column_name = item
found_msg = ("Found column named '{}' at index {}, " +
"assuming this to be the {} column.")
print(found_msg.format(item, index, column_type))
break
print("\n *** Starting heuristical analysis ***\n")
for row in reader:
if not row: # Skip empty lines
# We analyze the first non-empty line, a possible header should
# have been processed by now.
continue
column_candidates = {"doi": [], "period": [], "euro": []}
found_msg = "The entry in column {} looks like a potential {}: {}"
for (index, entry) in enumerate(row):
if index in [csvcolumn.index for csvcolumn in column_map.values()]:
# Skip columns already assigned
continue
entry = entry.strip()
# Search for a DOI
if column_map['doi'].index is None:
if oat.DOI_RE.match(entry):
column_id = str(index)
# identify column either numerically or by column header
if header:
column_id += " ('" + header[index] + "')"
print(found_msg.format(column_id, "DOI", entry))
column_candidates['doi'].append(index)
continue
# Search for a potential year string
if column_map['period'].index is None:
try:
maybe_period = int(entry)
now = datetime.date.today().year
# Should be a wide enough margin
if maybe_period >= 2000 and maybe_period <= now + 2:
column_id = str(index)
if header:
column_id += " ('" + header[index] + "')"
print(found_msg.format(column_id, "year", entry))
column_candidates['period'].append(index)
continue
except ValueError:
pass
# Search for a potential monetary amount
if column_map['euro'].index is None:
try:
maybe_euro = locale.atof(entry)
if maybe_euro >= 10 and maybe_euro <= 10000:
column_id = str(index)
if header:
column_id += " ('" + header[index] + "')"
print(found_msg.format(column_id, "euro amount",
entry))
column_candidates['euro'].append(index)
continue
except ValueError:
pass
for column_type, candidates in column_candidates.items():
if column_map[column_type].index is not None:
continue
if len(candidates) > 1:
print("Could not reliably identify the '" + column_type +
"' column - more than one possible candiate!")
elif len(candidates) < 1:
print("No candidate found for column '" + column_type + "'!")
else:
index = candidates.pop()
column_map[column_type].index = index
if header:
column_id = header[index]
column_map[column_type].column_name = column_id
else:
column_id = index
msg = "Assuming column '{}' to be the '{}' column."
print(msg.format(column_id, column_type))
column_map[column_type].index = index
break
# Wrap up: Check if there any mandatory column types left which have not
# yet been identified - we cannot continue in that case (unless forced).
unassigned = [
x for x in iter(column_map.items())
if x[1].requirement == CSVColumn.MANDATORY and x[1].index is None
]
if unassigned:
for item in unassigned:
print("The {} column is still unidentified.".format(item[0]))
if header:
print("The CSV header is:\n" + dialect.delimiter.join(header))
if not args.force:
print("ERROR: We cannot continue because not all mandatory " +
"column types in the CSV file could be automatically " +
"identified. There are 2 ways to fix this:")
if not header:
print("1) Add a header row to your file and identify the " +
"column(s) by assigning them an appropiate column name.")
else:
print("1) Identify the missing column(s) by assigning them " +
"a different column name in the CSV header (You can " +
"use the column name(s) mentioned in the message above)")
print("2) Use command line parameters when calling this script " +
"to identify the missing columns (use -h for help) ")
sys.exit()
else:
print("WARNING: Not all mandatory column types in the CSV file " +
"could be automatically identified - forced to continue.")
print("\n *** CSV file analysis summary ***\n")
index_dict = {csvc.index: csvc for csvc in column_map.values()}
for index in range(num_columns):
column_name = ""
if header:
column_name = header[index]
if index in index_dict:
column = index_dict[index]
msg = u"column number {} ({}) is the {} column '{}'".format(
index, column_name, column.requirement, column.column_type)
if column.requirement in [CSVColumn.MANDATORY, CSVColumn.OPTIONAL]:
oat.print_g(msg)
else:
oat.print_b(msg)
else:
if args.add_unknown_columns:
msg = (
u"column number {} ({}) is an unknown column, it will be "
+ "appended to the generated CSV file")
oat.print_y(msg.format(index, column_name))
if not column_name:
# Use a generic name
column_name = "unknown"
while column_name in column_map.keys():
# TODO: Replace by a numerical, increasing suffix
column_name += "_"
column_map[column_name] = CSVColumn(column_name,
CSVColumn.NONE, index)
else:
msg = (
u"column number {} ({}) is an unknown column, it will be "
+ "ignored")
oat.print_y(msg.format(index, column_name))
print()
for column in column_map.values():
if column.index is None:
msg = "The {} column '{}' could not be identified."
print(msg.format(column.requirement, column.column_type))
# Check for unassigned optional column types. We can continue but should
# issue a warning as all entries will need a valid DOI in this case.
unassigned = [
k for k, v in column_map.items()
if v.requirement == CSVColumn.OPTIONAL and v.index is None
]
if unassigned:
print("\nWARNING: Not all optional column types could be " +
"identified. Metadata aggregation is still possible, but " +
"every entry in the CSV file will need a valid DOI.")
start = input("\nStart metadata aggregation? (y/n):")
while start not in ["y", "n"]:
start = input("Please type 'y' or 'n':")
if start == "n":
sys.exit()
print("\n *** Starting metadata aggregation ***\n")
enriched_content = []
csv_file.seek(0)
reader = csv.reader(csv_file, dialect=dialect)
header_processed = False
row_num = 0
for row in reader:
row_num += 1
if not row:
continue # skip empty lines
if not header_processed:
header_processed = True
enriched_content.append(list(column_map.keys()))
if has_header:
# If the CSV file has a header, we are currently there - skip it
# to get to the first data row
continue
if args.start and args.start > row_num:
continue
if args.end and args.end < row_num:
continue
print("---Processing line number " + str(row_num) + "---")
enriched_row = oat.process_row(row, row_num, column_map, num_columns,
args.no_crossref, args.no_pubmed,
args.no_doaj, doaj_offline_analysis,
args.round_monetary,
args.offsetting_mode)
enriched_content.append(enriched_row)
csv_file.close()
with open('out.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, mask,
not args.no_openapc_quote_rules,
True, True)
writer.write_rows(enriched_content)
if not bufferedHandler.buffer:
oat.print_g("Metadata enrichment successful, no errors occured")
else:
oat.print_r("There were errors during the enrichment process:\n")
# closing will implicitly flush the handler and print any buffered
# messages to stderr
bufferedHandler.close()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("csv_file", help=ARG_HELP_STRINGS["csv_file"])
parser.add_argument("-e", "--encoding", help=ARG_HELP_STRINGS["encoding"])
parser.add_argument("-start", type=int, default=1, help=ARG_HELP_STRINGS["start"])
parser.add_argument("-end", type=int, help=ARG_HELP_STRINGS["start"])
args = parser.parse_args()
handler = logging.StreamHandler(sys.stderr)
handler.setFormatter(oat.ANSIColorFormatter())
bufferedHandler = oat.BufferedErrorHandler(handler)
bufferedHandler.setFormatter(oat.ANSIColorFormatter())
logging.root.addHandler(handler)
logging.root.addHandler(bufferedHandler)
logging.root.setLevel(logging.INFO)
enc = None
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
msg = "Encoding '{}' found in Python's codec collection as '{}'"
oat.print_g(msg.format(args.encoding, codec.name))
enc = args.encoding
except LookupError:
msg = ("Error: '" + args.encoding + "' not found Python's " +
"codec collection. Either look for a valid name here " +
"(https://docs.python.org/2/library/codecs.html#standard-" +
"encodings) or omit this argument to enable automated " +
"guessing.")
oat.print_r(msg)
sys.exit()
head, content = oat.get_csv_file_content(args.csv_file, enc)
content = head + content
line_num = 0
for line in content:
line_num += 1
if args.start and args.start > line_num:
continue
if args.end and args.end < line_num:
continue
# Check hybrid status
if line[4] != "TRUE":
continue
institution = line[0]
period = line[1]
doi = line[3]
publisher = line[5]
journal = line[6]
for lpl in lpl_list:
if lpl.publisher_matches(publisher):
init_msg = (u"Line {}: Checking {} article from {}, published in '" +
"{}'...").format(line_num, institution, period, journal)
oat.print_b(init_msg)
page_content = get_landingpage_content(doi, lpl)
if page_content is None:
continue
pdf_link = lpl.search_for_oa(page_content)
if pdf_link is None:
error_msg = (u"No PDF link found! (line {}, DOI: " +
"http://doi.org/{}").format(line_num, doi)
logging.error(error_msg)
elif pdf_link == "":
warning_msg = (u"A RegexGroup matched, but no PDF " +
"link was found! (line {}, DOI: " +
"http://doi.org/{}").format(line_num, doi)
logging.warning(warning_msg)
else:
oat.print_g(u"PDF link found: " + pdf_link)
time.sleep(1)
if not bufferedHandler.buffer:
oat.print_g("\nLookup finished, all articles were accessible")
else:
oat.print_r("\nLookup finished, not all articles could be accessed:\n")
# closing will implicitly flush the handler and print any buffered
# messages to stderr
bufferedHandler.close()
