def _get_csv_file_content(file_name, enc=None):
result = oat.analyze_csv_file(file_name, 500)
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
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()
dialect = csv_analysis.dialect
csv_file = open(file_name, "r")
content = []
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
header = []
if csv_analysis.has_header:
header.append(reader.next())
for row in reader:
content.append(row)
csv_file.close()
return (header, content)
def _get_csv_file_content(file_name, enc=None):
result = oat.analyze_csv_file(file_name, 500)
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
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()
dialect = csv_analysis.dialect
csv_file = open(file_name, "r")
content = []
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
header = []
if csv_analysis.has_header:
header.append(reader.next())
for row in reader:
content.append(row)
csv_file.close()
return (header, content)
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("-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("-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("-u",
"--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("-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"])
args = parser.parse_args()
enc = None # CSV file encoding
handler = logging.StreamHandler(sys.stderr)
handler.setFormatter(ANSIColorFormatter())
bufferedHandler = BufferedErrorHandler(handler)
bufferedHandler.setFormatter(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:
print "locale '{}' not found, normalized to '{}'".format(
args.locale, norm)
try:
loc = locale.setlocale(locale.LC_ALL, norm)
print "Using locale", loc
except locale.Error as loce:
print "Setting locale to " + norm + " failed: " + loce.message
sys.exit()
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
print("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
enc = args.encoding
except LookupError:
print("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.")
sys.exit()
result = oat.analyze_csv_file(args.csv_file)
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()
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!")
csv_file = open(args.csv_file, "r")
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
first_row = reader.next()
num_columns = len(first_row)
print "\nCSV file has {} columns.".format(num_columns)
csv_file.seek(0)
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
column_map = OrderedDict([
("institution",
CSVColumn("institution", CSVColumn.MANDATORY,
args.institution_column)),
("period", CSVColumn("period", CSVColumn.MANDATORY,
args.period_column)),
("euro", CSVColumn("euro", CSVColumn.MANDATORY, args.euro_column)),
("doi", CSVColumn("doi", CSVColumn.MANDATORY, args.doi_column)),
("is_hybrid",
CSVColumn("is_hybrid", CSVColumn.MANDATORY, args.is_hybrid_column)),
("publisher",
CSVColumn("publisher", CSVColumn.OPTIONAL, args.publisher_column)),
("journal_full_title",
CSVColumn("journal_full_title", CSVColumn.OPTIONAL,
args.journal_full_title_column)),
("issn", CSVColumn("issn", CSVColumn.OPTIONAL, args.issn_column)),
("issn_print", CSVColumn("issn_print", CSVColumn.NONE, None)),
("issn_electronic", CSVColumn("issn_electronic", CSVColumn.NONE,
None)),
("license_ref", CSVColumn("license_ref", CSVColumn.NONE, None)),
("indexed_in_crossref",
CSVColumn("indexed_in_crossref", CSVColumn.NONE, None)),
("pmid", CSVColumn("pmid", CSVColumn.NONE, None)),
("pmcid", CSVColumn("pmcid", CSVColumn.NONE, None)),
("ut", CSVColumn("ut", CSVColumn.NONE, None)),
("url", CSVColumn("url", CSVColumn.OPTIONAL, args.url_column)),
("doaj", CSVColumn("doaj", CSVColumn.NONE, None))
])
# Do not quote the values in the 'period' and 'euro' columns
quotemask = [
True,
False,
False,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
]
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
print("Found column named '{}' at index {}, " +
"assuming this to be the {} column.").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": []}
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 numerical or by column header
if header:
column_id += " ('" + header[index] + "')"
print("The entry in column {} looks like a " +
"DOI: {}").format(column_id, 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("The entry in column {} looks like a " +
"potential period: {}").format(column_id, 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)
# Are there APCs above 6000€ ??
if maybe_euro >= 10 and maybe_euro <= 6000:
column_id = str(index)
if header:
column_id += " ('" + header[index] + "')"
print("The entry in column {} looks like a " +
"potential euro amount: {}").format(
column_id, entry)
column_candidates['euro'].append(index)
continue
except ValueError:
pass
for column_type, candidates in column_candidates.iteritems():
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
print("Assuming column '{}' to be the '{}' " +
"column.").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 = filter(
lambda
(k, v): v.requirement == CSVColumn.MANDATORY and v.index is None,
column_map.iteritems())
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 = "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 = (
"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 = (
"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 = filter(
lambda (k, v): v.requirement == CSVColumn.OPTIONAL and v.index is None,
column_map.iteritems())
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 = raw_input("\nStart metadata aggregation? (y/n):")
while start not in ["y", "n"]:
start = raw_input("Please type 'y' or 'n':")
if start == "n":
sys.exit()
print "\n *** Starting metadata aggregation ***\n"
enriched_content = []
csv_file.seek(0)
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
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(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,
doaj_offline_analysis,
args.bypass_cert_verification)
enriched_content.append(enriched_row)
csv_file.close()
with open('out.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, quotemask, 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("-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("-u", "--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("-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.overwrite:
ow_strategy = CSVColumn.OW_ALWAYS
else:
ow_strategy = CSVColumn.OW_ASK
openapc_column_map = OrderedDict([
("institution", CSVColumn("institution", CSVColumn.MANDATORY, args.institution_column, overwrite=ow_strategy)),
("period", CSVColumn("period", CSVColumn.MANDATORY, args.period_column, overwrite=ow_strategy)),
("euro", CSVColumn("euro", CSVColumn.MANDATORY, args.euro_column, overwrite=ow_strategy)),
("doi", CSVColumn("doi", CSVColumn.MANDATORY, args.doi_column, overwrite=ow_strategy)),
("is_hybrid", CSVColumn("is_hybrid", CSVColumn.MANDATORY, args.is_hybrid_column, overwrite=ow_strategy)),
("publisher", CSVColumn("publisher", CSVColumn.OPTIONAL, args.publisher_column, overwrite=ow_strategy)),
("journal_full_title", CSVColumn("journal_full_title", CSVColumn.OPTIONAL,
args.journal_full_title_column, overwrite=ow_strategy)),
("issn", CSVColumn("issn", CSVColumn.OPTIONAL, args.issn_column, overwrite=ow_strategy)),
("issn_print", CSVColumn("issn_print", CSVColumn.NONE, None, overwrite=ow_strategy)),
("issn_electronic", CSVColumn("issn_electronic", CSVColumn.NONE, None, overwrite=ow_strategy)),
("issn_l", CSVColumn("issn_l", CSVColumn.NONE, None, overwrite=ow_strategy)),
("license_ref", CSVColumn("license_ref", CSVColumn.NONE, None, overwrite=ow_strategy)),
("indexed_in_crossref", CSVColumn("indexed_in_crossref", CSVColumn.NONE, None, overwrite=ow_strategy)),
("pmid", CSVColumn("pmid", CSVColumn.NONE, None, overwrite=ow_strategy)),
("pmcid", CSVColumn("pmcid", CSVColumn.NONE, None, overwrite=ow_strategy)),
("ut", CSVColumn("ut", CSVColumn.NONE, None, overwrite=ow_strategy)),
("url", CSVColumn("url", CSVColumn.OPTIONAL, args.url_column, overwrite=ow_strategy)),
("doaj", CSVColumn("doaj", CSVColumn.NONE, None, overwrite=ow_strategy))
])
offsetting_column_map = OrderedDict([
("institution", CSVColumn("institution", CSVColumn.MANDATORY, args.institution_column, overwrite=ow_strategy)),
("period", CSVColumn("period", CSVColumn.MANDATORY, args.period_column, overwrite=ow_strategy)),
("euro", CSVColumn("euro", CSVColumn.NONE, args.euro_column, overwrite=ow_strategy)),
("doi", CSVColumn("doi", CSVColumn.MANDATORY, args.doi_column, overwrite=ow_strategy)),
("is_hybrid", CSVColumn("is_hybrid", CSVColumn.MANDATORY, args.is_hybrid_column, overwrite=ow_strategy)),
("publisher", CSVColumn("publisher", CSVColumn.OPTIONAL, args.publisher_column, overwrite=ow_strategy)),
("journal_full_title", CSVColumn("journal_full_title", CSVColumn.OPTIONAL,
args.journal_full_title_column, overwrite=ow_strategy)),
("issn", CSVColumn("issn", CSVColumn.OPTIONAL, args.issn_column, overwrite=ow_strategy)),
("issn_print", CSVColumn("issn_print", CSVColumn.NONE, None, overwrite=ow_strategy)),
("issn_electronic", CSVColumn("issn_electronic", CSVColumn.NONE, None, overwrite=ow_strategy)),
("issn_l", CSVColumn("issn_l", CSVColumn.NONE, None, overwrite=ow_strategy)),
("license_ref", CSVColumn("license_ref", CSVColumn.NONE, None, overwrite=ow_strategy)),
("indexed_in_crossref", CSVColumn("indexed_in_crossref", CSVColumn.NONE, None, overwrite=ow_strategy)),
("pmid", CSVColumn("pmid", CSVColumn.NONE, None, overwrite=ow_strategy)),
("pmcid", CSVColumn("pmcid", CSVColumn.NONE, None, overwrite=ow_strategy)),
("ut", CSVColumn("ut", CSVColumn.NONE, None, overwrite=ow_strategy)),
("url", CSVColumn("url", CSVColumn.OPTIONAL, args.url_column, overwrite=ow_strategy)),
("doaj", CSVColumn("doaj", CSVColumn.NONE, None, overwrite=ow_strategy)),
("agreement", CSVColumn("agreement", CSVColumn.NONE, None, overwrite=ow_strategy)),
])
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 = filter(lambda k, v: v.requirement == CSVColumn.OPTIONAL and v.index is None,
column_map.items())
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("-v", "--verbose", action="store_true",
help=ARG_HELP_STRINGS["verbose"])
parser.add_argument("-l", "--locale", help=ARG_HELP_STRINGS["locale"])
parser.add_argument("-i", "--ignore-header", action="store_true",
help=ARG_HELP_STRINGS["headers"])
parser.add_argument("-f", "--force", action="store_true",
help=ARG_HELP_STRINGS["force"])
parser.add_argument("-b", "--bypass-cert-verification", action="store_true",
help=ARG_HELP_STRINGS["bypass"])
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"])
args = parser.parse_args()
enc = None # CSV file encoding
if args.locale:
norm = locale.normalize(args.locale)
if norm != args.locale:
print "locale '{}' not found, normalized to '{}'".format(
args.locale, norm)
try:
loc = locale.setlocale(locale.LC_ALL, norm)
print "Using locale", loc
except locale.Error as loce:
print "Setting locale to " + norm + " failed: " + loce.message
sys.exit()
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
print ("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
enc = args.encoding
except LookupError:
print ("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.")
sys.exit()
result = oat.analyze_csv_file(args.csv_file)
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
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")
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
first_row = reader.next()
num_columns = len(first_row)
print "\nCSV file has {} columns.".format(num_columns)
csv_file.seek(0)
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
column_map = OrderedDict([
("institution", CSVColumn("institution", CSVColumn.MANDATORY, args.institution_column)),
("period", CSVColumn("period", CSVColumn.MANDATORY, args.period_column)),
("euro", CSVColumn("euro", CSVColumn.MANDATORY, args.euro_column)),
("doi", CSVColumn("doi", CSVColumn.MANDATORY, args.doi_column)),
("is_hybrid", CSVColumn("is_hybrid", CSVColumn.MANDATORY, args.is_hybrid_column)),
("publisher", CSVColumn("publisher", CSVColumn.OPTIONAL, args.publisher_column)),
("journal_full_title", CSVColumn("journal_full_title", CSVColumn.OPTIONAL,
args.journal_full_title_column)),
("issn", CSVColumn("issn", CSVColumn.OPTIONAL, args.issn_column)),
("issn_print", CSVColumn("issn_print", CSVColumn.NONE, None)),
("issn_electronic", CSVColumn("issn_electronic", CSVColumn.NONE, None)),
("license_ref", CSVColumn("license_ref", CSVColumn.NONE, None)),
("indexed_in_crossref", CSVColumn("indexed_in_crossref", CSVColumn.NONE, None)),
("pmid", CSVColumn("pmid", CSVColumn.NONE, None)),
("pmcid", CSVColumn("pmcid", CSVColumn.NONE, None)),
("ut", CSVColumn("ut", CSVColumn.NONE, None)),
("url", CSVColumn("url", CSVColumn.OPTIONAL, args.url_column)),
("doaj", CSVColumn("doaj", CSVColumn.NONE, None))
])
# Do not quote the values in the 'period' and 'euro' columns
quotemask = [
True,
False,
False,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
]
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
print ("Found column named '{}' at index {}, " +
"assuming this to be the {} column.").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": []
}
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 numerical or by column header
if header:
column_id += " ('" + header[index] + "')"
print ("The entry in column {} looks like a " +
"DOI: {}").format(column_id, 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 ("The entry in column {} looks like a " +
"potential period: {}").format(column_id, 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)
# Are there APCs above 6000€ ??
if maybe_euro >= 10 and maybe_euro <= 6000:
column_id = str(index)
if header:
column_id += " ('" + header[index] + "')"
print ("The entry in column {} looks like a " +
"potential euro amount: {}").format(column_id,
entry)
column_candidates['euro'].append(index)
continue
except ValueError:
pass
for column_type, candidates in column_candidates.iteritems():
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
print ("Assuming column '{}' to be the '{}' " +
"column.").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 = filter(lambda (k, v): v.requirement == CSVColumn.MANDATORY and v.index is None,
column_map.iteritems())
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 = "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:
msg = ("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)
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 = filter(lambda (k, v): v.requirement == CSVColumn.OPTIONAL and v.index is None,
column_map.iteritems())
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 = raw_input("\nStart metadata aggregation? (y/n):")
while start not in ["y", "n"]:
start = raw_input("Please type 'y' or 'n':")
if start == "n":
sys.exit()
print "\n *** Starting metadata aggregation ***\n"
enriched_content = []
error_messages = []
csv_file.seek(0)
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
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(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
print "---Processing line number " + str(row_num) + "---"
if len(row) != num_columns:
error_msg = ("Syntax: the number of values in line {} ({}) " +
"differs from the number of columns ({}). Line left " +
"unchanged, please correct the error in the result " +
"file and re-run.")
error_msg_fmt = error_msg.format(row_num, len(row), num_columns)
error_messages.append("Line {}: {}".format(row_num, error_msg_fmt))
oat.print_r(error_msg_fmt)
enriched_content.append(row)
continue
doi = row[column_map["doi"].index]
current_row = OrderedDict()
# Copy content of identified columns
for csv_column in column_map.values():
if csv_column.index is not None and len(row[csv_column.index]) > 0:
if csv_column.column_type == "euro":
# special case for monetary values: Cast to float to ensure
# the decimal point is a dot (instead of a comma)
euro_value = row[csv_column.index]
try:
euro = locale.atof(euro_value)
if euro.is_integer():
euro = int(euro)
current_row[csv_column.column_type] = str(euro)
except ValueError:
msg = ERROR_MSGS["locale"].format(euro_value,
csv_column.index)
oat.print_r(msg)
sys.exit()
else:
current_row[csv_column.column_type] = row[csv_column.index]
else:
current_row[csv_column.column_type] = "NA"
# include crossref metadata
crossref_result = oat.get_metadata_from_crossref(doi)
if crossref_result["success"]:
print "Crossref: DOI resolved: " + doi
current_row["indexed_in_crossref"] = "TRUE"
data = crossref_result["data"]
for key, value in data.iteritems():
if value is not None:
if key == "journal_full_title":
unified_value = oat.get_unified_journal_title(value)
if unified_value != value:
msg = INFO_MSGS["unify"].format("journal title",
value,
unified_value)
oat.print_b(msg)
new_value = unified_value
elif key == "publisher":
unified_value = oat.get_unified_publisher_name(value)
if unified_value != value:
msg = INFO_MSGS["unify"].format("publisher name",
value,
unified_value)
oat.print_b(msg)
new_value = unified_value
else:
new_value = value
else:
new_value = "NA"
if args.verbose:
print (u"WARNING: Element '{}' not found in in " +
"response for doi {}.").format(key, doi)
old_value = current_row[key]
current_row[key] = column_map[key].check_overwrite(old_value, new_value)
else:
error_msg = ("Crossref: Error while trying to resolve DOI " + doi +
": " + crossref_result["error_msg"])
oat.print_r(error_msg)
error_messages.append("Line {}: {}".format(row_num, error_msg))
current_row["indexed_in_crossref"] = "FALSE"
# include pubmed metadata
pubmed_result = oat.get_metadata_from_pubmed(doi)
if pubmed_result["success"]:
print "Pubmed: DOI resolved: " + doi
data = pubmed_result["data"]
for key, value in data.iteritems():
if value is not None:
new_value = value
else:
new_value = "NA"
if args.verbose:
print (u"WARNING: Element '{}' not found in in " +
"response for doi {}.").format(key, doi)
old_value = current_row[key]
current_row[key] = column_map[key].check_overwrite(old_value, new_value)
else:
error_msg = ("Pubmed: Error while trying to resolve DOI " + doi +
": " + pubmed_result["error_msg"])
oat.print_r(error_msg)
error_messages.append("Line {}: {}".format(row_num, error_msg))
# lookup in DOAJ. try the EISSN first, then ISSN and finally print ISSN
if current_row["doaj"] != "TRUE":
issns = []
if current_row["issn_electronic"] != "NA":
issns.append(current_row["issn_electronic"])
if current_row["issn"] != "NA":
issns.append(current_row["issn"])
if current_row["issn_print"] != "NA":
issns.append(current_row["issn_print"])
for issn in issns:
doaj_res = oat.lookup_journal_in_doaj(issn, args.bypass_cert_verification)
if doaj_res["data_received"]:
if doaj_res["data"]["in_doaj"]:
msg = "DOAJ: Journal ISSN ({}) found in DOAJ ('{}')."
print msg.format(issn, doaj_res["data"]["title"])
current_row["doaj"] = "TRUE"
break
else:
msg = "DOAJ: Journal ISSN ({}) not found in DOAJ."
current_row["doaj"] = "FALSE"
print msg.format(issn)
else:
msg = "DOAJ: Error while trying to look up ISSN {}: {}"
msg_fmt = msg.format(issn, doaj_res["error_msg"])
oat.print_r(msg_fmt)
error_messages.append("Line {}: {}".format(row_num, msg_fmt))
enriched_content.append(current_row.values())
csv_file.close()
with open('out.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, quotemask, True, True)
writer.write_rows(enriched_content)
if not error_messages:
oat.print_g("Metadata enrichment successful, no errors occured")
else:
oat.print_r("There were errors during the enrichment process:\n")
for msg in error_messages:
print msg + "\n"
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("-q", "--quotemask", help=ARG_HELP_STRINGS["quotemask"])
parser.add_argument("-o", "--openapc_quote_rules",
help=ARG_HELP_STRINGS["openapc_quote_rules"],
action="store_true", default=False)
subparsers = parser.add_subparsers(help='The column operation to perform')
delete_parser = subparsers.add_parser("delete", help="delete help")
delete_parser.add_argument("column_index", type=int, help='bar help')
delete_parser.set_defaults(func=delete_column)
insert_parser = subparsers.add_parser("insert", help="insert help")
insert_parser.add_argument("target_index", type=int, help='bar help')
insert_parser.add_argument("column_name", help='bar help')
insert_parser.add_argument("default_value", help='bar help')
insert_parser.set_defaults(func=insert_column)
move_parser = subparsers.add_parser("move", help="move help")
move_parser.add_argument("column_index", type=int, help='bar help')
move_parser.add_argument("target_index", type=int, help='bar help')
move_parser.set_defaults(func=move_column)
copy_parser = subparsers.add_parser("copy", help="copy help")
copy_parser.set_defaults(func=copy)
args = parser.parse_args()
quote_rules = args.openapc_quote_rules
enc = None #CSV file encoding
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
print ("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
enc = args.encoding
except LookupError:
print ("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.")
sys.exit()
result = oat.analyze_csv_file(args.csv_file, 500)
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
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()
dialect = csv_analysis.dialect
csv_file = open(args.csv_file, "r")
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
new_rows = args.func(reader, args)
csv_file.close()
mask = None
if args.quotemask:
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]
with open('out.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, mask, quote_rules, False)
writer.write_rows(new_rows)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("original_file",
help=ARG_HELP_STRINGS["original_file"])
parser.add_argument("update_file", help=ARG_HELP_STRINGS["update_file"])
parser.add_argument("-e", "--encoding", help=ARG_HELP_STRINGS["encoding"])
parser.add_argument("-eu",
"--update_encoding",
help=ARG_HELP_STRINGS["update_encoding"])
parser.add_argument("-l", "--locale", help=ARG_HELP_STRINGS["locale"])
parser.add_argument("-lu",
"--update_locale",
help=ARG_HELP_STRINGS["update_locale"])
parser.add_argument("-a",
"--autocreate_mappings",
action="store_true",
help=ARG_HELP_STRINGS["autocreate_mappings"])
parser.add_argument("-g",
"--grouping",
action="store_true",
help=ARG_HELP_STRINGS["grouping"])
args = parser.parse_args()
params = {
"original": {
"file": args.original_file,
"encoding": args.encoding,
"locale": args.locale,
"csv_analysis": None,
"fieldnames": None,
"doi_field": None,
"euro_field": None,
"mappings": []
},
"update": {
"file": args.update_file,
"encoding": args.update_encoding,
"locale": args.update_locale,
"csv_analysis": None,
"fieldnames": None,
"doi_field": None,
"euro_field": None,
"mappings": []
}
}
def field_mapped(file_type, field_name):
if field_name == params[file_type]["euro_field"]:
return True
if field_name == params[file_type]["doi_field"]:
return True
if field_name in params[file_type]["mappings"]:
return True
return False
for file_type in params.keys():
msg = "*** Performing analysis for {} file ***"
oat.print_b(msg.format(file_type))
encoding = params[file_type]["encoding"]
if encoding is not None:
try:
codec = codecs.lookup(encoding)
msg = "Encoding '{}' found in Python's codec collection as '{}'"
print(msg.format(encoding, codec.name))
params[file_type]["encoding"] = encoding
except LookupError:
print(
"Error: '" + 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.")
sys.exit()
loc = params[file_type]["locale"]
if loc is not None:
norm = locale.normalize(loc)
if norm != loc:
msg = "locale '{}' not found, normalised to '{}'".format(
loc, norm)
oat.print_y(msg)
params[file_type]["locale"] = norm
csv_analysis = oat.analyze_csv_file(params[file_type]["file"],
enc=params[file_type]["encoding"])
if not csv_analysis["success"]:
oat.print_r(csv_analysis["error_msg"])
sys.exit()
params[file_type]["csv_analysis"] = csv_analysis["data"]
print(params[file_type]["csv_analysis"])
if params[file_type]["encoding"] is None:
guessed_enc = params[file_type]["csv_analysis"].enc
params[file_type]["encoding"] = guessed_enc
locale_name = "default locale"
if params[file_type]["locale"] is not None:
locale_name = "locale " + params[file_type]["locale"]
msg = "{} file will be opened with encoding {} and {}"
oat.print_g(
msg.format(file_type, params[file_type]["encoding"], locale_name))
with open(params[file_type]["file"],
"r",
encoding=params[file_type]["encoding"]) as f:
reader = csv.DictReader(
f, dialect=params[file_type]["csv_analysis"].dialect)
params[file_type]["fieldnames"] = list(reader.fieldnames)
for index, name in enumerate(params[file_type]["fieldnames"]):
field_type = oat.get_column_type_from_whitelist(name)
found = False
if field_type == "doi":
params[file_type]["doi_field"] = name
found = True
elif field_type == "euro":
params[file_type]["euro_field"] = name
found = True
if found:
msg = '{} file: Found {} column at index {} ("{}")'
msg = msg.format(file_type, field_type, index, name)
oat.print_b(msg)
for field_type in ["doi_field", "euro_field"]:
if params[file_type][field_type] is None:
msg = "Error: No {} found in {} file"
oat.print_r(msg.format(field_type, file_type))
sys.exit()
for orig_index, orig_field in enumerate(params["original"]["fieldnames"]):
if field_mapped("original", orig_field):
continue
norm_orig_field = orig_field.lower().strip()
for update_index, update_field in enumerate(
params["update"]["fieldnames"]):
if field_mapped("update", update_field):
continue
norm_update_field = update_field.lower().strip()
if norm_orig_field == norm_update_field:
if args.autocreate_mappings:
params["original"]["mappings"].append(orig_field)
params["update"]["mappings"].append(update_field)
msg = 'Auto-created mapping "{}" (update file, index {}) -> "{}" (original file, index {})'
oat.print_b(
msg.format(update_field, update_index, orig_field,
orig_index))
else:
msg = 'Possible mapping found: "{}" (update file, index {}) -> "{}" (original file, index {}). Create mapping (y/n)?'
msg = msg.format(update_field, update_index, orig_field,
orig_index)
create = input(msg)
while create not in ["y", "n"]:
create = input("Please type 'y' or 'n':")
if create == "y":
params["original"]["mappings"].append(orig_field)
params["update"]["mappings"].append(update_field)
update_mappings = {}
with open(params["update"]["file"],
"r",
encoding=params["update"]["encoding"]) as f:
doi_field = params["update"]["doi_field"]
euro_field = params["update"]["euro_field"]
reader = csv.DictReader(
f, dialect=params["update"]["csv_analysis"].dialect)
locale.setlocale(locale.LC_ALL, params["update"]["locale"])
for line in reader:
doi = oat.get_normalised_DOI(line[doi_field])
if doi is None:
msg = 'Warning: Empty or invalid DOI in update file (line {}): "{}"'
oat.print_y(msg.format(reader.line_num, line[doi_field]))
continue
if doi in update_mappings:
msg = "Error: Duplicate doi in update file ({})".format(
line[doi_field])
oat.print_r(msg)
sys.exit()
update_mappings[doi] = {}
euro_value = locale.atof(line[euro_field])
orig_euro_field = params["original"]["euro_field"]
update_mappings[doi][orig_euro_field] = euro_value
for index, update_field_name in enumerate(
params["update"]["mappings"]):
orig_field_name = params["original"]["mappings"][index]
update_mappings[doi][orig_field_name] = line[update_field_name]
#print(json.dumps(update_mappings, sort_keys=False, indent=4))
modified_content = []
fieldnames = None
with open(params["original"]["file"],
"r",
encoding=params["original"]["encoding"]) as f:
doi_field = params["original"]["doi_field"]
euro_field = params["original"]["euro_field"]
reader = csv.DictReader(
f, dialect=params["original"]["csv_analysis"].dialect)
fieldnames = list(reader.fieldnames)
locale.setlocale(locale.LC_ALL, params["original"]["locale"])
for line in reader:
doi = oat.get_normalised_DOI(line[doi_field])
if doi not in update_mappings:
msg = "line {}: DOI {} not found in update file!"
oat.print_r(msg.format(reader.line_num, doi))
continue
changes = []
old_euro_value = locale.atof(line[euro_field])
new_euro_value = update_mappings[doi][euro_field]
if old_euro_value != new_euro_value:
changes.append(
Change(euro_field,
old_euro_value,
new_euro_value,
monetary=True))
for field in update_mappings[doi].keys():
if field == euro_field:
continue
if line[field] != update_mappings[doi][field]:
changes.append(
Change(field, line[field],
update_mappings[doi][field]))
if not changes:
msg = "line {}: DOI {} found in update file, but nothing changed."
oat.print_g(msg.format(reader.line_num, doi))
else:
msg = "line {}: DOI {} found in update file with the following updates:"
oat.print_y(msg.format(reader.line_num, doi))
for change in changes:
oat.print_y(str(change))
if change.monetary:
line[change.field_name] = locale.currency(
change.new_value,
symbol=False,
grouping=args.grouping)
else:
line[change.field_name] = change.new_value
del (update_mappings[doi])
modified_content.append(line)
if update_mappings:
oat.print_y(
"{} entries in update file not contained in original file:".
format(len(update_mappings)))
for doi, changes in update_mappings.items():
oat.print_y(doi)
new_line = changes
new_line[params["original"]["doi_field"]] = doi
formatted_euro = locale.currency(
new_line[params["original"]["euro_field"]],
symbol=False,
grouping=args.grouping)
new_line[params["original"]["euro_field"]] = formatted_euro
modified_content.append(new_line)
with open("out.csv", "w", encoding=params["original"]["encoding"]) as out:
writer = csv.DictWriter(
out,
fieldnames,
dialect=params["original"]["csv_analysis"].dialect)
writer.writeheader()
for line in modified_content:
writer.writerow(line)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("apc_file", help=ARG_HELP_STRINGS["apc_file"])
parser.add_argument("issn_l_file", help=ARG_HELP_STRINGS["issn_l_file"])
parser.add_argument("-e", "--encoding", help=ARG_HELP_STRINGS["encoding"])
parser.add_argument("-q",
"--quotemask",
help=ARG_HELP_STRINGS["quotemask"])
parser.add_argument("-o",
"--openapc_quote_rules",
help=ARG_HELP_STRINGS["openapc_quote_rules"],
action="store_true",
default=False)
args = parser.parse_args()
quote_rules = args.openapc_quote_rules
mask = None
if args.quotemask:
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]
enc = None
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
print("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
enc = args.encoding
except LookupError:
print("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.")
sys.exit()
result = oat.analyze_csv_file(args.apc_file, 500)
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
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()
dialect = csv_analysis.dialect
csv_file = open(args.apc_file, "r")
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
oat.print_g("Preparing mapping table...")
itself = other = 0
issn_l_re = re.compile(
"^(?P<issn>\d{4}-\d{3}[\dxX])\t(?P<issn_l>\d{4}-\d{3}[\dxX])$")
issn_l_file = open(args.issn_l_file, "r")
issn_l_dict = {}
for i, line in enumerate(issn_l_file):
if i % 100000 == 0:
print str(i) + " lines processed."
match = issn_l_re.match(line)
if match:
match_dict = match.groupdict()
issn_l_dict[match_dict['issn']] = match_dict['issn_l']
if match_dict['issn'] == match_dict['issn_l']:
itself += 1
else:
other += 1
print str(itself) + " ISSNs pointing to itself as ISSN-L, " + str(
other) + " to another value."
oat.print_g("Starting enrichment...")
issn_matches = issn_p_matches = issn_e_matches = unmatched = different = 0
enriched_lines = []
for line in reader:
if len(line) == 0:
enriched_lines.append(line)
continue
issn = reformat_issn(line[7])
issn_p = reformat_issn(line[8])
issn_e = reformat_issn(line[9])
target = None
if issn in issn_l_dict:
target = issn_l_dict[issn]
line[10] = target
issn_matches += 1
elif issn_p in issn_l_dict:
target = issn_l_dict[issn_p]
line[10] = target
issn_p_matches += 1
elif issn_e in issn_l_dict:
target = issn_l_dict[issn_e]
line[10] = target
issn_e_matches += 1
else:
unmatched += 1
if target is not None and target not in [issn, issn_p, issn_e]:
different += 1
enriched_lines.append(line)
print "{} issn_l values mapped by issn, {} by issn_p, {} by issn_e. {} could not be assigned.\n In {} cases the ISSN-L was different from all existing ISSN values".format(
issn_matches, issn_p_matches, issn_e_matches, unmatched, different)
with open('out.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, mask, quote_rules, False)
writer.write_rows(enriched_lines)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("apc_file", help=ARG_HELP_STRINGS["apc_file"])
parser.add_argument("issn_l_file", help=ARG_HELP_STRINGS["issn_l_file"])
parser.add_argument("-e", "--encoding", help=ARG_HELP_STRINGS["encoding"])
parser.add_argument("-q", "--quotemask", help=ARG_HELP_STRINGS["quotemask"])
parser.add_argument("-o", "--openapc_quote_rules",
help=ARG_HELP_STRINGS["openapc_quote_rules"],
action="store_true", default=False)
args = parser.parse_args()
quote_rules = args.openapc_quote_rules
mask = None
if args.quotemask:
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]
enc = None
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
print ("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
enc = args.encoding
except LookupError:
print ("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.")
sys.exit()
result = oat.analyze_csv_file(args.apc_file, 500)
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
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()
dialect = csv_analysis.dialect
has_header = csv_analysis.has_header
csv_file = open(args.apc_file, "r")
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
oat.print_g("Preparing mapping table...")
itself = other = 0
issn_l_re = re.compile("^(?P<issn>\d{4}-\d{3}[\dxX])\t(?P<issn_l>\d{4}-\d{3}[\dxX])$")
issn_l_file = open(args.issn_l_file, "r")
issn_l_dict = {}
for i, line in enumerate(issn_l_file):
if i % 100000 == 0:
print str(i) + " lines processed."
match = issn_l_re.match(line)
if match:
match_dict = match.groupdict()
issn_l_dict[match_dict['issn']] = match_dict['issn_l']
if match_dict['issn'] == match_dict['issn_l']:
itself += 1
else:
other += 1
print str(itself) + " ISSNs pointing to itself as ISSN-L, " + str(other) + " to another value."
oat.print_g("Starting enrichment...")
issn_matches = issn_p_matches = issn_e_matches = unmatched = different = corrections = 0
enriched_lines = []
for line in reader:
if len(line) == 0:
enriched_lines.append(line)
continue
issn = reformat_issn(line[7])
issn_p = reformat_issn(line[8])
issn_e = reformat_issn(line[9])
target = None
if issn in issn_l_dict:
target = issn_l_dict[issn]
corrected_target = oat.get_corrected_issn_l(target)
if corrected_target != target:
corrections += 1
line[10] = corrected_target
issn_matches += 1
elif issn_p in issn_l_dict:
target = issn_l_dict[issn_p]
corrected_target = oat.get_corrected_issn_l(target)
if corrected_target != target:
corrections += 1
line[10] = corrected_target
issn_p_matches += 1
elif issn_e in issn_l_dict:
target = issn_l_dict[issn_e]
corrected_target = oat.get_corrected_issn_l(target)
if corrected_target != target:
corrections += 1
line[10] = corrected_target
issn_e_matches += 1
else:
unmatched += 1
if target is not None and target not in [issn, issn_p, issn_e]:
different += 1
enriched_lines.append(line)
print "{} issn_l values mapped by issn, {} by issn_p, {} by issn_e. {} could not be assigned.\n{} issn_l values were corrected during the process.\n In {} cases the ISSN-L was different from all existing ISSN values".format(issn_matches, issn_p_matches, issn_e_matches, unmatched, corrections, different)
with open('out.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, mask, quote_rules, has_header)
writer.write_rows(enriched_lines)
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("-q",
"--quotemask",
help=ARG_HELP_STRINGS["quotemask"])
parser.add_argument("-o",
"--openapc_quote_rules",
help=ARG_HELP_STRINGS["openapc_quote_rules"],
action="store_true",
default=False)
subparsers = parser.add_subparsers(help='The column operation to perform')
delete_parser = subparsers.add_parser("delete", help="delete help")
delete_parser.add_argument("column_index", type=int, help='bar help')
delete_parser.set_defaults(func=delete_column)
insert_parser = subparsers.add_parser("insert", help="insert help")
insert_parser.add_argument("target_index", type=int, help='bar help')
insert_parser.add_argument("column_name", help='bar help')
insert_parser.add_argument("default_value", help='bar help')
insert_parser.set_defaults(func=insert_column)
move_parser = subparsers.add_parser("move", help="move help")
move_parser.add_argument("column_index", type=int, help='bar help')
move_parser.add_argument("target_index", type=int, help='bar help')
move_parser.set_defaults(func=move_column)
copy_parser = subparsers.add_parser("copy", help="copy help")
copy_parser.set_defaults(func=copy)
args = parser.parse_args()
quote_rules = args.openapc_quote_rules
enc = None #CSV file encoding
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
print("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
enc = args.encoding
except LookupError:
print("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.")
sys.exit()
result = oat.analyze_csv_file(args.csv_file, 500)
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
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()
dialect = csv_analysis.dialect
csv_file = open(args.csv_file, "r")
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
new_rows = args.func(reader, args)
csv_file.close()
mask = None
if args.quotemask:
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]
with open('out.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, mask, quote_rules, True)
writer.write_rows(new_rows)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("original_file", help=ARG_HELP_STRINGS["original_file"])
parser.add_argument("update_file", help=ARG_HELP_STRINGS["update_file"])
parser.add_argument("-e", "--encoding", help=ARG_HELP_STRINGS["encoding"])
parser.add_argument("-eu", "--update_encoding", help=ARG_HELP_STRINGS["update_encoding"])
parser.add_argument("-l", "--locale", help=ARG_HELP_STRINGS["locale"])
parser.add_argument("-lu", "--update_locale", help=ARG_HELP_STRINGS["update_locale"])
parser.add_argument("-a", "--autocreate_mappings", action="store_true", help=ARG_HELP_STRINGS["autocreate_mappings"])
parser.add_argument("-g", "--grouping", action="store_true", help=ARG_HELP_STRINGS["grouping"])
args = parser.parse_args()
params = {
"original": {
"file": args.original_file,
"encoding": args.encoding,
"locale": args.locale,
"csv_analysis": None,
"fieldnames": None,
"doi_field": None,
"euro_field": None,
"mappings": []
},
"update": {
"file": args.update_file,
"encoding": args.update_encoding,
"locale": args.update_locale,
"csv_analysis": None,
"fieldnames": None,
"doi_field": None,
"euro_field": None,
"mappings": []
}
}
def field_mapped(file_type, field_name):
if field_name == params[file_type]["euro_field"]:
return True
if field_name == params[file_type]["doi_field"]:
return True
if field_name in params[file_type]["mappings"]:
return True
return False
for file_type in params.keys():
msg = "*** Performing analysis for {} file ***"
oat.print_b(msg.format(file_type))
encoding = params[file_type]["encoding"]
if encoding is not None:
try:
codec = codecs.lookup(encoding)
msg = "Encoding '{}' found in Python's codec collection as '{}'"
print(msg.format(encoding, codec.name))
params[file_type]["encoding"] = encoding
except LookupError:
print ("Error: '" + 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.")
sys.exit()
loc = params[file_type]["locale"]
if loc is not None:
norm = locale.normalize(loc)
if norm != loc:
msg = "locale '{}' not found, normalised to '{}'".format(loc, norm)
oat.print_y(msg)
params[file_type]["locale"] = norm
csv_analysis = oat.analyze_csv_file(params[file_type]["file"], enc=params[file_type]["encoding"])
if not csv_analysis["success"]:
oat.print_r(csv_analysis["error_msg"])
sys.exit()
params[file_type]["csv_analysis"] = csv_analysis["data"]
print(params[file_type]["csv_analysis"])
if params[file_type]["encoding"] is None:
guessed_enc = params[file_type]["csv_analysis"].enc
params[file_type]["encoding"] = guessed_enc
locale_name = "default locale"
if params[file_type]["locale"] is not None:
locale_name = "locale " + params[file_type]["locale"]
msg = "{} file will be opened with encoding {} and {}"
oat.print_g(msg.format(file_type, params[file_type]["encoding"], locale_name))
with open(params[file_type]["file"], "r", encoding=params[file_type]["encoding"]) as f:
reader = csv.DictReader(f, dialect=params[file_type]["csv_analysis"].dialect)
params[file_type]["fieldnames"] = list(reader.fieldnames)
for index, name in enumerate(params[file_type]["fieldnames"]):
field_type = oat.get_column_type_from_whitelist(name)
found = False
if field_type == "doi":
params[file_type]["doi_field"] = name
found = True
elif field_type == "euro":
params[file_type]["euro_field"] = name
found = True
if found:
msg = '{} file: Found {} column at index {} ("{}")'
msg = msg.format(file_type, field_type, index, name)
oat.print_b(msg)
for field_type in ["doi_field", "euro_field"]:
if params[file_type][field_type] is None:
msg = "Error: No {} found in {} file"
oat.print_r(msg.format(field_type, file_type))
sys.exit()
for orig_index, orig_field in enumerate(params["original"]["fieldnames"]):
if field_mapped("original", orig_field):
continue
norm_orig_field = orig_field.lower().strip()
for update_index, update_field in enumerate(params["update"]["fieldnames"]):
if field_mapped("update", update_field):
continue
norm_update_field = update_field.lower().strip()
if norm_orig_field == norm_update_field:
if args.autocreate_mappings:
params["original"]["mappings"].append(orig_field)
params["update"]["mappings"].append(update_field)
msg = 'Auto-created mapping "{}" (update file, index {}) -> "{}" (original file, index {})'
oat.print_b(msg.format(update_field, update_index, orig_field, orig_index))
else:
msg = 'Possible mapping found: "{}" (update file, index {}) -> "{}" (original file, index {}). Create mapping (y/n)?'
msg = msg.format(update_field, update_index, orig_field, orig_index)
create = input(msg)
while create not in ["y", "n"]:
create = input("Please type 'y' or 'n':")
if create == "y":
params["original"]["mappings"].append(orig_field)
params["update"]["mappings"].append(update_field)
update_mappings = {}
with open(params["update"]["file"], "r", encoding=params["update"]["encoding"]) as f:
doi_field = params["update"]["doi_field"]
euro_field = params["update"]["euro_field"]
reader = csv.DictReader(f, dialect=params["update"]["csv_analysis"].dialect)
locale.setlocale(locale.LC_ALL, params["update"]["locale"])
for line in reader:
doi = oat.get_normalised_DOI(line[doi_field])
if doi is None:
msg = 'Warning: Empty or invalid DOI in update file (line {}): "{}"'
oat.print_y(msg.format(reader.line_num, line[doi_field]))
continue
if doi in update_mappings:
msg = "Error: Duplicate doi in update file ({})".format(line[doi_field])
oat.print_r(msg)
sys.exit()
update_mappings[doi] = {}
euro_value = locale.atof(line[euro_field])
orig_euro_field = params["original"]["euro_field"]
update_mappings[doi][orig_euro_field] = euro_value
for index, update_field_name in enumerate(params["update"]["mappings"]):
orig_field_name = params["original"]["mappings"][index]
update_mappings[doi][orig_field_name] = line[update_field_name]
#print(json.dumps(update_mappings, sort_keys=False, indent=4))
modified_content = []
fieldnames = None
with open(params["original"]["file"], "r", encoding=params["original"]["encoding"]) as f:
doi_field = params["original"]["doi_field"]
euro_field = params["original"]["euro_field"]
reader = csv.DictReader(f, dialect=params["original"]["csv_analysis"].dialect)
fieldnames = list(reader.fieldnames)
locale.setlocale(locale.LC_ALL, params["original"]["locale"])
for line in reader:
doi = oat.get_normalised_DOI(line[doi_field])
if doi not in update_mappings:
msg = "line {}: DOI {} not found in update file!"
oat.print_r(msg.format(reader.line_num, doi))
continue
changes = []
old_euro_value = locale.atof(line[euro_field])
new_euro_value = update_mappings[doi][euro_field]
if old_euro_value != new_euro_value:
changes.append(Change(euro_field, old_euro_value, new_euro_value, monetary=True))
for field in update_mappings[doi].keys():
if field == euro_field:
continue
if line[field] != update_mappings[doi][field]:
changes.append(Change(field, line[field], update_mappings[doi][field]))
if not changes:
msg = "line {}: DOI {} found in update file, but nothing changed."
oat.print_g(msg.format(reader.line_num, doi))
else:
msg = "line {}: DOI {} found in update file with the following updates:"
oat.print_y(msg.format(reader.line_num, doi))
for change in changes:
oat.print_y(str(change))
if change.monetary:
line[change.field_name] = locale.currency(change.new_value,symbol=False, grouping=args.grouping)
else:
line[change.field_name] = change.new_value
del(update_mappings[doi])
modified_content.append(line)
if update_mappings:
oat.print_y("{} entries in update file not contained in original file:".format(len(update_mappings)))
for doi, changes in update_mappings.items():
oat.print_y(doi)
new_line = changes
new_line[params["original"]["doi_field"]] = doi
formatted_euro = locale.currency(new_line[params["original"]["euro_field"]], symbol=False, grouping=args.grouping)
new_line[params["original"]["euro_field"]] = formatted_euro
modified_content.append(new_line)
with open("out.csv", "w", encoding=params["original"]["encoding"]) as out:
writer = csv.DictWriter(out, fieldnames, dialect=params["original"]["csv_analysis"].dialect)
writer.writeheader()
for line in modified_content:
writer.writerow(line)
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("-v",
"--verbose",
action="store_true",
help=ARG_HELP_STRINGS["verbose"])
parser.add_argument("-l", "--locale", help=ARG_HELP_STRINGS["locale"])
parser.add_argument("-i",
"--ignore-header",
action="store_true",
help=ARG_HELP_STRINGS["headers"])
parser.add_argument("-f",
"--force",
action="store_true",
help=ARG_HELP_STRINGS["force"])
parser.add_argument("-b",
"--bypass-cert-verification",
action="store_true",
help=ARG_HELP_STRINGS["bypass"])
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"])
args = parser.parse_args()
enc = None # CSV file encoding
if args.locale:
norm = locale.normalize(args.locale)
if norm != args.locale:
print "locale '{}' not found, normalized to '{}'".format(
args.locale, norm)
try:
loc = locale.setlocale(locale.LC_ALL, norm)
print "Using locale", loc
except locale.Error as loce:
print "Setting locale to " + norm + " failed: " + loce.message
sys.exit()
if args.encoding:
try:
codec = codecs.lookup(args.encoding)
print("Encoding '{}' found in Python's codec collection " +
"as '{}'").format(args.encoding, codec.name)
enc = args.encoding
except LookupError:
print("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.")
sys.exit()
result = oat.analyze_csv_file(args.csv_file)
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
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")
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
first_row = reader.next()
num_columns = len(first_row)
print "\nCSV file has {} columns.".format(num_columns)
csv_file.seek(0)
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
column_map = OrderedDict([
("institution",
CSVColumn("institution", CSVColumn.MANDATORY,
args.institution_column)),
("period", CSVColumn("period", CSVColumn.MANDATORY,
args.period_column)),
("euro", CSVColumn("euro", CSVColumn.MANDATORY, args.euro_column)),
("doi", CSVColumn("doi", CSVColumn.MANDATORY, args.doi_column)),
("is_hybrid",
CSVColumn("is_hybrid", CSVColumn.MANDATORY, args.is_hybrid_column)),
("publisher",
CSVColumn("publisher", CSVColumn.OPTIONAL, args.publisher_column)),
("journal_full_title",
CSVColumn("journal_full_title", CSVColumn.OPTIONAL,
args.journal_full_title_column)),
("issn", CSVColumn("issn", CSVColumn.OPTIONAL, args.issn_column)),
("issn_print", CSVColumn("issn_print", CSVColumn.NONE, None)),
("issn_electronic", CSVColumn("issn_electronic", CSVColumn.NONE,
None)),
("license_ref", CSVColumn("license_ref", CSVColumn.NONE, None)),
("indexed_in_crossref",
CSVColumn("indexed_in_crossref", CSVColumn.NONE, None)),
("pmid", CSVColumn("pmid", CSVColumn.NONE, None)),
("pmcid", CSVColumn("pmcid", CSVColumn.NONE, None)),
("ut", CSVColumn("ut", CSVColumn.NONE, None)),
("url", CSVColumn("url", CSVColumn.OPTIONAL, args.url_column)),
("doaj", CSVColumn("doaj", CSVColumn.NONE, None))
])
# Do not quote the values in the 'period' and 'euro' columns
quotemask = [
True,
False,
False,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
True,
]
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
print("Found column named '{}' at index {}, " +
"assuming this to be the {} column.").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": []}
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 numerical or by column header
if header:
column_id += " ('" + header[index] + "')"
print("The entry in column {} looks like a " +
"DOI: {}").format(column_id, 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("The entry in column {} looks like a " +
"potential period: {}").format(column_id, 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)
# Are there APCs above 6000€ ??
if maybe_euro >= 10 and maybe_euro <= 6000:
column_id = str(index)
if header:
column_id += " ('" + header[index] + "')"
print("The entry in column {} looks like a " +
"potential euro amount: {}").format(
column_id, entry)
column_candidates['euro'].append(index)
continue
except ValueError:
pass
for column_type, candidates in column_candidates.iteritems():
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
print("Assuming column '{}' to be the '{}' " +
"column.").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 = filter(
lambda
(k, v): v.requirement == CSVColumn.MANDATORY and v.index is None,
column_map.iteritems())
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 = "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:
msg = ("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)
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 = filter(
lambda (k, v): v.requirement == CSVColumn.OPTIONAL and v.index is None,
column_map.iteritems())
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 = raw_input("\nStart metadata aggregation? (y/n):")
while start not in ["y", "n"]:
start = raw_input("Please type 'y' or 'n':")
if start == "n":
sys.exit()
print "\n *** Starting metadata aggregation ***\n"
enriched_content = []
error_messages = []
csv_file.seek(0)
reader = oat.UnicodeReader(csv_file, dialect=dialect, encoding=enc)
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(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
print "---Processing line number " + str(row_num) + "---"
if len(row) != num_columns:
error_msg = (
"Syntax: the number of values in line {} ({}) " +
"differs from the number of columns ({}). Line left " +
"unchanged, please correct the error in the result " +
"file and re-run.")
error_msg_fmt = error_msg.format(row_num, len(row), num_columns)
error_messages.append("Line {}: {}".format(row_num, error_msg_fmt))
oat.print_r(error_msg_fmt)
enriched_content.append(row)
continue
doi = row[column_map["doi"].index]
current_row = OrderedDict()
# Copy content of identified columns
for csv_column in column_map.values():
if csv_column.index is not None and len(row[csv_column.index]) > 0:
if csv_column.column_type == "euro":
# special case for monetary values: Cast to float to ensure
# the decimal point is a dot (instead of a comma)
euro_value = row[csv_column.index]
try:
euro = locale.atof(euro_value)
if euro.is_integer():
euro = int(euro)
current_row[csv_column.column_type] = str(euro)
except ValueError:
msg = ERROR_MSGS["locale"].format(
euro_value, csv_column.index)
oat.print_r(msg)
sys.exit()
else:
current_row[csv_column.column_type] = row[csv_column.index]
else:
current_row[csv_column.column_type] = "NA"
# include crossref metadata
crossref_result = oat.get_metadata_from_crossref(doi)
if crossref_result["success"]:
print "Crossref: DOI resolved: " + doi
current_row["indexed_in_crossref"] = "TRUE"
data = crossref_result["data"]
for key, value in data.iteritems():
if value is not None:
if key == "journal_full_title":
unified_value = oat.get_unified_journal_title(value)
if unified_value != value:
msg = INFO_MSGS["unify"].format(
"journal title", value, unified_value)
oat.print_b(msg)
new_value = unified_value
elif key == "publisher":
unified_value = oat.get_unified_publisher_name(value)
if unified_value != value:
msg = INFO_MSGS["unify"].format(
"publisher name", value, unified_value)
oat.print_b(msg)
new_value = unified_value
else:
new_value = value
else:
new_value = "NA"
if args.verbose:
print(u"WARNING: Element '{}' not found in in " +
"response for doi {}.").format(key, doi)
old_value = current_row[key]
current_row[key] = column_map[key].check_overwrite(
old_value, new_value)
else:
error_msg = ("Crossref: Error while trying to resolve DOI " + doi +
": " + crossref_result["error_msg"])
oat.print_r(error_msg)
error_messages.append("Line {}: {}".format(row_num, error_msg))
current_row["indexed_in_crossref"] = "FALSE"
# include pubmed metadata
pubmed_result = oat.get_metadata_from_pubmed(doi)
if pubmed_result["success"]:
print "Pubmed: DOI resolved: " + doi
data = pubmed_result["data"]
for key, value in data.iteritems():
if value is not None:
new_value = value
else:
new_value = "NA"
if args.verbose:
print(u"WARNING: Element '{}' not found in in " +
"response for doi {}.").format(key, doi)
old_value = current_row[key]
current_row[key] = column_map[key].check_overwrite(
old_value, new_value)
else:
error_msg = ("Pubmed: Error while trying to resolve DOI " + doi +
": " + pubmed_result["error_msg"])
oat.print_r(error_msg)
error_messages.append("Line {}: {}".format(row_num, error_msg))
# lookup in DOAJ. try the EISSN first, then ISSN and finally print ISSN
if current_row["doaj"] != "TRUE":
issns = []
if current_row["issn_electronic"] != "NA":
issns.append(current_row["issn_electronic"])
if current_row["issn"] != "NA":
issns.append(current_row["issn"])
if current_row["issn_print"] != "NA":
issns.append(current_row["issn_print"])
for issn in issns:
doaj_res = oat.lookup_journal_in_doaj(
issn, args.bypass_cert_verification)
if doaj_res["data_received"]:
if doaj_res["data"]["in_doaj"]:
msg = "DOAJ: Journal ISSN ({}) found in DOAJ ('{}')."
print msg.format(issn, doaj_res["data"]["title"])
current_row["doaj"] = "TRUE"
break
else:
msg = "DOAJ: Journal ISSN ({}) not found in DOAJ."
current_row["doaj"] = "FALSE"
print msg.format(issn)
else:
msg = "DOAJ: Error while trying to look up ISSN {}: {}"
msg_fmt = msg.format(issn, doaj_res["error_msg"])
oat.print_r(msg_fmt)
error_messages.append("Line {}: {}".format(
row_num, msg_fmt))
enriched_content.append(current_row.values())
csv_file.close()
with open('out.csv', 'w') as out:
writer = oat.OpenAPCUnicodeWriter(out, quotemask, True, True)
writer.write_rows(enriched_content)
if not error_messages:
oat.print_g("Metadata enrichment successful, no errors occured")
else:
oat.print_r("There were errors during the enrichment process:\n")
for msg in error_messages:
print msg + "\n"