def import_article(journal, article_data, create=True, update=False):
if not article_data or not isinstance(article_data, dict):
raise ValueError("given data to import is empty/invalid")
expected_keys = ['doi', 'volume', 'path', 'article-type', 'manuscript_id']
# data wrangling
try:
kwargs = subdict(article_data, expected_keys)
# JATS XML doesn't contain the manuscript ID. derive it from doi
if 'manuscript_id' not in kwargs and 'doi' in kwargs:
kwargs['manuscript_id'] = doi2msid(kwargs['doi'])
elif 'doi' not in kwargs and 'manuscript_id' in kwargs:
kwargs['doi'] = msid2doi(kwargs['manuscript_id'])
context = {'article': kwargs['doi']}
LOG.info("importing Article", extra=context)
# post process data
kwargs.update({
'journal': journal,
'volume': int(kwargs['volume']),
'type': kwargs['article-type'],
})
delall(kwargs, ['path', 'article-type'])
except KeyError:
raise ValueError("expected keys invalid/not present: %s" % ", ".join(expected_keys))
# attempt to insert
article_key = subdict(kwargs, ['doi', 'version'])
try:
article_obj = models.Article.objects.get(**article_key)
avobj = import_article_version(article_obj, article_data, create, update)
LOG.info("Article exists, updating", extra=context)
for key, val in kwargs.items():
setattr(article_obj, key, val)
article_obj.save()
return article_obj, avobj
except models.Article.DoesNotExist:
# we've been told not to create new articles.
# this is now a legitimate exception
if not create:
raise
article_obj = models.Article(**kwargs)
article_obj.save()
avobj = import_article_version(article_obj, article_data, create, update)
LOG.info("created new Article %s" % article_obj)
return article_obj, avobj
def import_article_version(article, article_data, create=True, update=False):
expected_keys = ['title', 'version', 'update', 'pub-date', 'status']
kwargs = subdict(article_data, expected_keys)
try:
doi = article_data['doi']
version = int(kwargs['version'])
version_date = kwargs.get('update')
datetime_published = kwargs['pub-date']
context = {'article': doi, 'version': version}
LOG.info("importing ArticleVersion", extra=context)
if version_date and version == 1:
# this is so common it's not even worth a debug
#LOG.warn("inconsistency: a v1 has an 'update' date", extra=context)
d1, d2 = striptz(version_date), striptz(datetime_published)
if d1 != d2:
c = {}
c.update(context)
c.update({'pub-date': datetime_published, 'update': version_date})
LOG.warn("double inconsistency: not only do we have an 'update' date for a v1, it doesn't match the date published", extra=c)
# 'update' date occurred before publish date ...
if d1 < d2:
LOG.warn("triple inconsistency: not only do we have an 'update' date for a v1 that doesn't match the date published, it was actually updated *before* it was published", extra=c)
if version == 1:
version_date = datetime_published
if not version_date and version > 1:
LOG.warn("inconsistency: a version > 1 does not have an 'update' date", extra=context)
if settings.FAIL_ON_NO_UPDATE_DATE:
msg = "no 'update' date found for ArticleVersion"
raise ValueError(msg)
msg = "no 'update' date found for ArticleVersion, using None instead"
LOG.warn(msg, extra=context)
version_date = None
# post process data
kwargs.update({
'article': article,
'version': version,
'datetime_published': todt(version_date),
'status': kwargs['status'].lower(),
})
delall(kwargs, ['pub-date', 'update'])
except KeyError:
LOG.error("expected keys invalid/not present",
extra={'expected_keys': expected_keys})
raise
try:
avobj = models.ArticleVersion.objects.get(article=article, version=kwargs['version'])
if not update:
msg = "Article with version does exists but update == False"
LOG.warn(msg, extra=context)
raise AssertionError(msg)
LOG.debug("ArticleVersion found, updating")
for key, val in kwargs.items():
setattr(avobj, key, val)
avobj.save()
LOG.info("updated existing ArticleVersion", extra=context)
return avobj
except models.ArticleVersion.DoesNotExist:
if not create:
msg = "ArticleVersion with version does not exist and create == False"
LOG.warn(msg, extra=context)
raise
LOG.debug("ArticleVersion NOT found, creating", extra=context)
avobj = models.ArticleVersion(**kwargs)
avobj.save()
LOG.info("created new ArticleVersion", extra=context)
return avobj
