def main():
conf = Config()
logging.basicConfig(format = "%(asctime)s %(name)s %(levelname) -5s : %(message)s")
log = logging.getLogger("reload_pubmed")
log.setLevel(logging.DEBUG)
pubmed = Pubmed()
log.info("Connecting ...")
conn = biomart_db_connect(conf["biomart.db"], log)
cursor = conn.cursor()
update_cursor = conn.cursor()
log.info("Querying experiments ...")
cursor.execute("""
select id, pub_pubmed, study_id, platf_id
from ent_experiment where pub_pubmed is not NULL""")
SPACES = re.compile("\s+")
row = cursor.fetchone()
while row is not None:
id, pmid, study_id, platf_id = row
log.info(">>> PMID: {}, STUDY: {}, PLATFORM: {}".format(pmid, study_id, platf_id))
pub = pubmed.find(pmid)
if pub is None:
log.error("PMID not found: {}".format(pmid))
continue
pub = pub[0]
for k, v in pub.items():
if v is not None and isinstance(v, basestring):
pub[k] = v.replace("'", r"\'")
sql = u"""
update ent_experiment
set pub_title='{}', pub_authors='{}', pub_year='{}', pub_journal='{}'
where id={}""".format(
pub["title"], pub["short_authors"],
pub["date"], pub["journal"], id)
log.debug(SPACES.sub(" ", sql.strip()))
update_cursor.execute(sql)
row = cursor.fetchone()
cursor.close()
update_cursor.close()
conn.close()
def process(self):
params=urlparse.parse_qs(urlparse.urlparse(self.path).query)
pm=Pubmed("*****@*****.**")
pm.query(params["query"])
pm.fetch()
pm.parse()
return json.dumps(convert_articles(pm.articles))
def get_pubmed_words(self, pubmed_id):
'''
return a dict in the same format as get_field_words: k=field, v=sanitized list of words
'''
words = dict()
pubmed = Pubmed(pubmed_id).populate()
for tag in Pubmed.text_tags:
try:
words[tag] = getattr(pubmed, tag)
except AttributeError as ae:
pass
return words
def insert(self, pmid, user):
medline = FetchMedline([pmid])
records = medline.get_records()
## it is weird you can't do record = records[0]??
for rec in records:
record = rec
# get pubmed instance
pubmed = Pubmed(record)
# insert journal
journal_no = Journal.insert(pubmed.journal_abbrev, user)
# insert reference
ref_no = 0
ref_query = self.query.filter_by(pubmed=pmid)
if ref_query.first():
ref_no = ref_query.first().reference_no
else:
ref_entry = self(user, pubmed.publish_status, pubmed.citation,
pubmed.year, pmid, 'PubMed script',
pubmed.pdf_status, pubmed.pages, pubmed.volume,
pubmed.title, pubmed.issue, journal_no)
db.session.add(ref_entry)
db.session.commit()
ref_no = ref_entry.reference_no
# insert abstract
Abstract.insert(ref_no, pubmed.abstract_txt)
# insert author
order = 0
for name in pubmed.authors:
order += 1
author_no = Author.insert(name, user)
AuthorEditor.insert(author_no, ref_no, order)
# insert ref_type
RefType.insert(pubmed.pub_type, ref_no, 'NCBI', user)
return ref_no
# First download nltk stuffs
home=os.environ["HOME"]
if not os.path.exists("%s/nltk_data" %home):
import nltk
nltk.download('all')
# Download neurosynth data
df = pandas.read_csv("database.txt",sep="\t")
pmids = df.id.unique().tolist()
print "NeuroSynth database has %s unique PMIDs" %(len(pmids))
# download abstract text
email = "*****@*****.**"
pm = Pubmed(email,pmc=False)
articles1 = pm.get_many_articles(pmids[:10000])
articles2 = pm.get_many_articles(pmids[10000:])
articles = articles1.copy()
articles.update(articles2)
if not os.path.exists("articles.pkl"):
pickle.dump(articles,open("articles.pkl","wb"))
# Write articles to file
#88390|"<text><p>sentence1</p><p>sentence2</p><p></text>"
#88390|"<text><p>sentence1</p><p>sentence2</p><p></text>"
# We should use utf-8 http://www.postgresql.org/docs/9.0/static/multibyte.html
filey = open(output_file,"wb")
count = 0
def main():
task.check_conf(["entities", "repositories", "biomart.db"])
conf = task.conf
insert_size = conf.get("biomart.insert_size", DEFAULT_INSERT_SIZE, dtype=int)
if "biomart.study_source" in conf:
study_source_map = conf["biomart.study_source"]
else:
study_source_map = conf.create_element()
log = task.logger()
exp_port = task.ports("experiment")
es = EntityServer(conf["entities"])
em = es.manager()
conn = biomart_db_connect(conf["biomart.db"], log)
db_engine = conf.get("biomart.db.engine", DEFAULT_DB_ENGINE)
cursor = conn.cursor()
cursor.execute("""
CREATE TABLE ent_experiment (
id int(11) NOT NULL,
exp_name varchar(64) NOT NULL,
study_id varchar(32) NOT NULL,
study_source varchar(32) DEFAULT NULL,
study_source_url varchar(512) DEFAULT NULL,
study_link varchar(512) DEFAULT NULL,
pub_pubmed varchar(32) DEFAULT NULL,
pub_title varchar(300) DEFAULT NULL,
pub_authors varchar(300) DEFAULT NULL,
pub_year varchar(16) DEFAULT NULL,
pub_journal varchar(200) DEFAULT NULL,
platf_id varchar(32) NOT NULL,
platf_title varchar(250) DEFAULT NULL,
platf_technology varchar(96) DEFAULT NULL,
PRIMARY KEY (id),
KEY exp_name (exp_name),
KEY pub_pubmed (pub_pubmed),
KEY pub_title (pub_title),
KEY pub_authors (pub_authors),
KEY pub_year (pub_year),
KEY pub_journal (pub_journal),
KEY platf_title (platf_title),
KEY platf_technology (platf_technology)
) ENGINE={} CHARACTER SET utf8 COLLATE utf8_general_ci""".format(db_engine))
ib = BatchInsert(cursor, "ent_experiment",
["id", "exp_name", "study_id", "study_source", "study_source_url", "study_link",
"pub_title", "pub_authors", "pub_year", "pub_pubmed", "pub_journal",
"platf_id", "platf_title", "platf_technology"], insert_size)
pubmed = Pubmed()
for i, exp in enumerate(exp_port, 1):
study_id = exp[0]
platform_id = exp[1]
study = em.find(study_id, types.SOURCE_STUDY)
if study is None:
log.error("{} not found: {}".format(types.SOURCE_STUDY, study_id))
continue
platf = em.find(platform_id, types.SOURCE_PLATFORM)
if platf is None:
log.error("{} not found: {}".format(types.SOURCE_PLATFORM, platform_id))
continue
log.info("Experiment for study {} and platform {} ...".format(study_id, platform_id))
pub = {}
for k in ["title", "short_authors", "date", "journal"]:
pub[k] = None
if "pubmed" in study:
pmid = study["pubmed"]
if isinstance(pmid, (DataElementList, list)):
pmid = pmid[0]
log.warn("Study {} with many pubmed_id's, only the first {} will be considered".format(study_id, pmid))
log.debug("Retrieving information for pubmed_id '{}' ...".format(pmid))
try:
pub = pubmed.find(pmid)
if len(pub) == 0:
log.error("No publication information found for pubmed_id '{}' in experiment ({}, {})".format(pmid, study_id, platform_id))
else:
pub = pub[0]
except Exception as ex:
log.error("Error retrieving pubmed information for experiment ({}, {}) with pubmed_id '{}'".format(study_id, platform_id, pmid))
log.exception(ex)
else:
pmid = None
log.warn("Study {} has no 'pubmed_id' annotation".format(study_id))
if "title" not in study:
log.error("Study {} doesn't have annotation for 'pubmed_id' nor 'title'".format(study_id))
elif "SO/contact_details[0]/contact_name" not in study \
and "SO/contact_details/contact_name" not in study:
log.error("Study {} doesn't have annotation for 'pubmed_id' nor 'SO.contact_details[0].contact_name'".format(study_id))
else:
try:
pub["title"] = study["title"]
if "SO/contact_details[0]/contact_name" in study:
pub["short_authors"] = study["SO/contact_details[0]/contact_name"]
else:
pub["short_authors"] = study["SO/contact_details/contact_name"]
if "SO/submission/pub_date" in study:
pub["date"] = study["SO/submission/pub_date"]
else:
pub["date"] = ""
except Exception as ex:
log.debug(study)
log.execption(ex)
for k, v in pub.items():
if v is not None and isinstance(v, basestring):
pub[k] = v.replace("'", r"\'")
exp_name = "{}; {}".format(study_id, platform_id)
study_source = None
study_source_url = None
study_link = None
parts = study_id.split("-")
if len(parts) >= 2 and parts[0] in study_source_map:
ss = study_source_map[parts[0]]
study_source = ss.get("name")
study_source_url = ss.get("home_url")
try:
study_link = ss.get("link", "").format(parts[1])
except:
pass
ib.insert(i, exp_name, study_id, study_source, study_source_url, study_link,
pub["title"], pub["short_authors"], pub["date"], pmid, pub["journal"],
platform_id, platf["SO/platform_title"], "")
log.debug("{} experiments inserted".format(ib.count))
ib.close()
cursor.close()
conn.close()
em.close()
es.close()
