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Add documents_doi.csv to tabs_collection export #87

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Initial plan
Copilot Feb 4, 2026
bc61cc4
Add documents_doi.csv dumper with DOI and language pairs
Copilot Feb 4, 2026
7c31abd
Fix typo in help text: 'Logggin' -> 'Logging'
Copilot Feb 4, 2026
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205 changes: 205 additions & 0 deletions publication/documents_doi.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,205 @@
# coding: utf-8
"""
Este processamento gera uma tabulação de DOIs e suas línguas correspondentes
para cada artigo da coleção SciELO.
"""
import argparse
import logging
import codecs
import datetime
import re

import utils

logger = logging.getLogger(__name__)

# DOI regex pattern to validate DOI format
DOI_REGEX = re.compile(r'10\.\d{4,}(?:\.\d+)?\/\S+')


def _config_logging(logging_level='INFO', logging_file=None):

allowed_levels = {
'DEBUG': logging.DEBUG,
'INFO': logging.INFO,
'WARNING': logging.WARNING,
'ERROR': logging.ERROR,
'CRITICAL': logging.CRITICAL
}

formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')

logger.setLevel(allowed_levels.get(logging_level, 'INFO'))

if logging_file:
hl = logging.FileHandler(logging_file, mode='a')
else:
hl = logging.StreamHandler()

hl.setFormatter(formatter)
hl.setLevel(allowed_levels.get(logging_level, 'INFO'))

logger.addHandler(hl)

return logger


def get_doi_and_lang(document):
"""
This method retrieves the lang and DOI pairs from a document.
Based on xylose's doi_and_lang property.
"""
items = []

# Try to get v337 field from document data
try:
raw_doi = document.data.get('article', {}).get('v337')
for item in raw_doi or []:
lang = item.get("l")
doi = item.get("d")
if lang and doi:
# Check if lang and doi are swapped
if len(DOI_REGEX.findall(lang)) == 1 and len(doi) == 2:
lang, doi = doi, lang
if len(DOI_REGEX.findall(doi)) == 1 and len(lang) == 2:
items.append((lang, doi))
except (AttributeError, KeyError):
pass

# Add the main DOI with original language if available
if document.doi:
try:
original_lang = document.original_language()
except (AttributeError, KeyError):
# Try to get the first language from languages() method
try:
languages = document.languages()
original_lang = languages[0] if languages else None
except (AttributeError, KeyError, IndexError):
original_lang = None

item = (original_lang, document.doi)
if all(item) and item not in items:
items.insert(0, item)

return items


class Dumper(object):

def __init__(self, collection, issns=None, output_file=None):

self._ratchet = utils.ratchet_server()
self._articlemeta = utils.articlemeta_server()
self.collection = collection
self.issns = issns
self.output_file = codecs.open(output_file, 'w', encoding='utf-8') if output_file else output_file
header = []
header.append(u"extraction date")
header.append(u"study unit")
header.append(u"collection")
header.append(u"document publishing ID (PID SciELO)")
header.append(u"document language")
header.append(u"doi corresponding language")

self.write(u','.join([u'"%s"' % i.replace(u'"', u'""') for i in header]))

def write(self, line):
if not self.output_file:
print(line.encode('utf-8'))
else:
self.output_file.write('%s\r\n' % line)

def run(self):
for item in self.items():
self.write(item)
logger.info('Export finished')

def items(self):

if not self.issns:
self.issns = [None]

for issn in self.issns:
for data in self._articlemeta.documents(collection=self.collection, issn=issn):
logger.debug('Reading document: %s' % data.publisher_id)
for line in self.fmt_csv(data):
yield line

def fmt_csv(self, data):
"""
Returns a list of CSV lines, one for each DOI/language pair.
"""
lines = []
doi_lang_pairs = get_doi_and_lang(data)

# If no DOI information is available, skip this document
if not doi_lang_pairs:
return lines

extraction_date = datetime.datetime.now().isoformat()[0:10]

for lang, doi in doi_lang_pairs:
line = []
line.append(extraction_date)
line.append(u'document')
line.append(data.collection_acronym)
line.append(data.publisher_id)
line.append(lang or u'')
line.append(doi or u'')

joined_line = ','.join(['"%s"' % i.replace('"', '""') for i in line])
lines.append(joined_line)

return lines


def main():

parser = argparse.ArgumentParser(
description='Dump DOI and language pairs by article'
)

parser.add_argument(
'issns',
nargs='*',
help='ISSN\'s separated by spaces'
)

parser.add_argument(
'--collection',
'-c',
help='Collection Acronym'
)

parser.add_argument(
'--output_file',
'-r',
help='File to receive the dumped data'
)

parser.add_argument(
'--logging_file',
'-o',
help='Full path to the log file'
)

parser.add_argument(
'--logging_level',
'-l',
default='DEBUG',
choices=['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'],
help='Logging level'
)

args = parser.parse_args()
_config_logging(args.logging_level, args.logging_file)
logger.info('Dumping data for: %s' % args.collection)

issns = None
if len(args.issns) > 0:
issns = utils.ckeck_given_issns(args.issns)

dumper = Dumper(args.collection, issns, args.output_file)

dumper.run()
6 changes: 5 additions & 1 deletion publication/dumper.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,8 @@
documents_languages,
documents_licenses,
documents_authors,
documents_dates
documents_dates,
documents_doi
)


Expand Down Expand Up @@ -62,6 +63,7 @@ def __init__(self, collection, home_nationality=None, issns=None):
self.documents_licenses = documents_licenses.Dumper(collection, output_file='documents_licenses.csv')
self.documents_authors = documents_authors.Dumper(collection, output_file='documents_authors.csv')
self.documents_dates = documents_dates.Dumper(collection, output_file='documents_dates.csv')
self.documents_doi = documents_doi.Dumper(collection, output_file='documents_doi.csv')
if self.home_nationality:
self.documents_affiliations_nationality = documents_affiliations_nationality.Dumper(home_nationality, collection, output_file='documents_affiliation_nationality.csv')

Expand All @@ -79,6 +81,8 @@ def run(self):
self.documents_licenses.write(self.documents_licenses.fmt_csv(data))
self.documents_authors.write(self.documents_authors.fmt_csv(data))
self.documents_dates.write(self.documents_dates.fmt_csv(data))
for line in self.documents_doi.fmt_csv(data):
self.documents_doi.write(line)
if self.home_nationality:
self.documents_affiliations_nationality.write(self.documents_affiliations_nationality.fmt_csv(data))

Expand Down