def process_article(article):
processed = meta.assign_solution_concs(article)
if processed == 1:
meta.assign_species(article)
meta.assign_electrode_type(article)
meta.assign_strain(article)
meta.assign_prep_type(article)
meta.assign_rec_temp(article)
meta.assign_animal_age(article)
meta.assign_jxn_potential(article)
articlesProcessed += 1
if processed == -1:
if article.journal in jnNoFullText:
jnNoFullText[article.journal] += 1
else:
jnNoFullText[article.journal] = 1
articlesNoFullText += 1
if processed == -2:
if article.journal in jnNoMethodsTag:
jnNoMethodsTag[article.journal] += 1
else:
jnNoMethodsTag[article.journal] = 1
articlesNoMethodsTag += 1
if processed == -3:
if article.journal in jnMethodsTooSmall:
jnMethodsTooSmall[article.journal] += 1
else:
jnMethodsTooSmall[article.journal] = 1
articlesMethodsTooSmall += 1
def apply_article_metadata(article = None):
if article:
artObs = [article]
num_arts = 1
else:
# artObs = m.Article.objects.filter(metadata__isnull = True, articlefulltext__isnull = False).distinct()
artObs = m.Article.objects.filter(articlefulltext__isnull = False).distinct()
# artObs = artObs.exclude(articlefulltext__articlefulltextstat__metadata_processed = True)
# artObs = m.Article.objects.filter(articlefulltext__isnull = False, articlefulltext__articlefulltextstat__methods_tag_found = True).distinct()
# artObs = artObs.exclude(articlefulltext__articlefulltextstat__metadata_processed = True)
# artObs = artObs.exclude(articlefulltext__articlefulltextstat__metadata_human_assigned = True)
num_arts = artObs.count()
print 'annotating %s articles for metadata...' % num_arts
for i,art in enumerate(artObs):
if not article:
prog(i,num_arts)
assign_metadata.assign_species(art)
assign_metadata.assign_electrode_type(art)
assign_metadata.assign_strain(art)
assign_metadata.assign_rec_temp(art)
assign_metadata.assign_prep_type(art)
assign_metadata.assign_animal_age(art)
assign_metadata.assign_jxn_potential(art)
assign_metadata.assign_solution_concs(art)
aft_ob = art.get_full_text()
aftStatOb = m.ArticleFullTextStat.objects.get_or_create(article_full_text = aft_ob)[0]
aftStatOb.metadata_processed = True
aftStatOb.save()
def process_article(article_id):
article = m.Article.objects.get(id = int(article_id))
processed = meta.assign_solution_concs(article)
if processed == 1:
meta.assign_species(article)
meta.assign_electrode_type(article)
meta.assign_strain(article)
meta.assign_prep_type(article)
meta.assign_rec_temp(article)
meta.assign_animal_age(article)
meta.assign_jxn_potential(article)
print processed
if processed == -3:
global articlesMethodsTooSmall
articlesMethodsTooSmall += 1
'''
path = os.getcwd()
os.chdir("/Users/dtebaykin/Desktop/raw_full_texts")
articles = m.Article.objects.all()
for a in articles:
try:
meta.assign_solution_concs(a)
meta.assign_species(a)
meta.assign_electrode_type(a)
meta.assign_strain(a)
meta.assign_prep_type(a)
meta.assign_rec_temp(a)
meta.assign_animal_age(a)
meta.assign_jxn_potential(a)
except:
print "Exception occurred for article %s" % a.pk
os.chdir(path)
#print "Out of %s articles: %s processed, %s no full text, %s no methods tag, %s methods section #too small\n" % (articlesTotal, articlesProcessed, articlesNoFullText, articlesNoMethodsTag, articlesMethodsTooSmall)
# print "Journals with no full text attached: %s\n" % jnNoFullText
# print "Journals with no methods tag: %s\n" % jnNoMethodsTag
# print "Journals with methods section too short: %s\n" % jnMethodsTooSmall
print "done"