Python assign_animal_age Examples

Example #1

File: test_meta.py Project: gitter-badger/neuroelectro_org

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

Example #2

File: article_html_db_utils.py Project: neuroelectro/neuroelectro_org

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()

Example #3

File: process_article.py Project: BrennaL/neuroelectro_org

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

Example #4

File: extract_article_metadata.py Project: gsarma/neuroelectro_org

    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"