def pmc_url(value):
'''Template tag filter go generate a direct link to this PubMed
Central article, based on a numeric PubMed Central ID.'''
try:
value = int(value)
except ValueError:
return u''
return pmc_access_url(value)
def pmc_url(value):
'''Template tag filter go generate a direct link to this PubMed
Central article, based on a numeric PubMed Central ID.'''
try:
value = int(value)
except ValueError:
return u''
return pmc_access_url(value)
def access_url(self):
'Direct link to this PubMed Central article, based on PubMed Central ID.'
return pmc_access_url(self.pmcid)
def handle(self, *args, **options):
self.verbosity = int(options['verbosity']) # 1 = normal, 0 = minimal, 2 = all
self.v_normal = 1
#counters
counts = defaultdict(int)
# check required options
if not options['username']:
raise CommandError('Username is required')
else:
if not options['password'] or options['password'] == '':
options['password'] = getpass()
#connection to repository
repo = Repository(username=options['username'], password=options['password'])
try:
#if pids specified, use that list
if len(args) != 0:
pids = list(args)
pid_set = [repo.get_object(pid=p, type=Publication) for p in pids]
else:
#search for Articles
pid_set = repo.get_objects_with_cmodel(Publication.ARTICLE_CONTENT_MODEL, Article)
except Exception as e:
raise CommandError('Error gettings pids (%s)' % e.message)
try:
articles = Paginator(pid_set, 20)
counts['total'] = articles.count
except Exception as e:
self.output(0, "Error paginating items: : %s " % (e.message))
#process all Articles
for p in articles.page_range:
try:
objs = articles.page(p).object_list
except Exception as e:
#print error and go to next iteration of loop
self.output(0,"Error getting page: %s : %s " % (p, e.message))
counts['errors'] +=1
continue
for article in objs:
try:
if not article.exists:
self.output(1, "Skipping %s because pid does not exist" % article.pid)
counts['skipped'] +=1
continue
else:
self.output(0,"Processing %s" % article.pid)
mods = article.descMetadata.content
nlm = article.contentMetadata.content if article.contentMetadata.exists else None
identifiers = []
#PMC info
if nlm:
pmc = nlm.docid
pmc_id = 'PMC%s' % pmc
access_url = pmc_access_url(pmc)
identifiers.extend([pmc_id, access_url])
if mods.ark_uri:
identifiers.append(mods.ark_uri)
identifiers.append(article.pid)
article.dc.content.identifier_list = identifiers
##########REMOVE dc.relation###########
# #
article.dc.content.relation_list = [] #
# #
#######################################
# save article
if not options['noact']:
article.save()
self.output(1, "SAVED")
except Exception as e:
self.output(0, "Error processing pid: %s : %s " % (article.pid, e.message))
counts['errors'] +=1
# summarize what was done
self.stdout.write("\n\n")
self.stdout.write("Total number selected: %s\n" % counts['total'])
self.stdout.write("Skipped: %s\n" % counts['skipped'])
self.stdout.write("Errors: %s\n" % counts['errors'])
def access_url(self):
'Direct link to this PubMed Central article, based on PubMed Central ID.'
return pmc_access_url(self.pmcid)
def handle(self, *args, **options):
self.verbosity = int(
options['verbosity']) # 1 = normal, 0 = minimal, 2 = all
self.v_normal = 1
#counters
counts = defaultdict(int)
# check required options
if not options['username']:
raise CommandError('Username is required')
else:
if not options['password'] or options['password'] == '':
options['password'] = getpass()
#connection to repository
repo = Repository(username=options['username'],
password=options['password'])
try:
#if pids specified, use that list
if len(args) != 0:
pids = list(args)
pid_set = [repo.get_object(pid=p, type=Article) for p in pids]
else:
#search for Articles
pid_set = repo.get_objects_with_cmodel(
Article.ARTICLE_CONTENT_MODEL, Article)
except Exception as e:
raise CommandError('Error gettings pids (%s)' % e.message)
try:
articles = Paginator(pid_set, 20)
counts['total'] = articles.count
except Exception as e:
self.output(0, "Error paginating items: : %s " % (e.message))
#process all Articles
for p in articles.page_range:
try:
objs = articles.page(p).object_list
except Exception as e:
#print error and go to next iteration of loop
self.output(0, "Error getting page: %s : %s " % (p, e.message))
counts['errors'] += 1
continue
for article in objs:
try:
if not article.exists:
self.output(
1, "Skipping %s because pid does not exist" %
article.pid)
counts['skipped'] += 1
continue
else:
self.output(0, "Processing %s" % article.pid)
mods = article.descMetadata.content
nlm = article.contentMetadata.content if article.contentMetadata.exists else None
identifiers = []
#PMC info
if nlm:
pmc = nlm.docid
pmc_id = 'PMC%s' % pmc
access_url = pmc_access_url(pmc)
identifiers.extend([pmc_id, access_url])
if mods.ark_uri:
identifiers.append(mods.ark_uri)
identifiers.append(article.pid)
article.dc.content.identifier_list = identifiers
##########REMOVE dc.relation###########
# #
article.dc.content.relation_list = [] #
# #
#######################################
# save article
if not options['noact']:
article.save()
self.output(1, "SAVED")
except Exception as e:
self.output(
0, "Error processing pid: %s : %s " %
(article.pid, e.message))
counts['errors'] += 1
# summarize what was done
self.stdout.write("\n\n")
self.stdout.write("Total number selected: %s\n" % counts['total'])
self.stdout.write("Skipped: %s\n" % counts['skipped'])
self.stdout.write("Errors: %s\n" % counts['errors'])