def get_journal_from_file_path(file_path, pmid):
"""returns a neuroelectro Journal object given a standardized file path and pmid as input
adds journal to database """
journal_short_name = file_path.split('/')[-2]
try:
journal_ob = m.Journal.objects.get(short_title = journal_short_name)
except ObjectDoesNotExist:
# journal short_title not found from path, try getting from pubmed directly
journal_title = get_journal(pmid)
try:
journal_ob = m.Journal.objects.get(short_title = journal_short_name)
except ObjectDoesNotExist:
article = add_single_article_full(pmid, overwrite_existing = False)
# check if returned article is None
if article is None:
return None
journal_ob = article.journal
return journal_ob
from db_functions.pubmed_functions import add_single_article_full, get_journal
from article_text_mining.mine_ephys_prop_in_table import assocDataTableEphysVal
from article_text_processing import remove_spurious_table_headers
from article_text_mining.auto_assign_neurons_table import assocNeuronstoArticleMult2
from article_text_mining.deprecated.db_add_full_text_wiley import make_html_filename
import assign_metadata
def add_article_full_text_from_file(file_name, path):
os.chdir(path)
try:
pmid_str = re.match('\d+', file_name).group()
except Exception, e:
print "No pubmed id found in file name %s, skipping..." % file_name
return None
journal_name = get_journal(pmid_str)
# is journal one among list of full text journals?
if not isFullTextJournal(journal_name):
# with open("analyzed_files.txt", "a") as af:
# write_str = '%s\n' % file_name
# af.write(write_str)
print "Journal %s is not a full text journal, skipping..." % journal_name
return None
# does journal already have full text assoc with it?
if m.ArticleFullText.objects.filter(article__pmid = pmid_str).count() > 0:
print "Article %s already in db, skipping..." % pmid_str
return None
print 'adding article with pmid: %s' % pmid_str
a = add_single_article_full(int(pmid_str))
if a is None:
