def test_export_lig(self):
ids = '19465464,18945920'.split(",")
#ret = pubmed.exportReference(ids)
sample_ris = fileutil.contentsOfFile("test/sample-medline.ris", False)
#print "Sample %s" %sample_ris
ret = pubmed.medline2ris(sample_ris)
self.assertTrue(ret)
fileutil.writeFile("tmp/output.ris", ret)
print "##%s##" % ret
self.assertIn('TY - JOUR', ret)
def test_export_lig(self):
ids='19465464,18945920'.split(",")
#ret = pubmed.exportReference(ids)
sample_ris = fileutil.contentsOfFile("test/sample-medline.ris", False)
#print "Sample %s" %sample_ris
ret = pubmed.medline2ris(sample_ris)
self.assertTrue(ret)
fileutil.writeFile("tmp/output.ris", ret)
print "##%s##" %ret
self.assertIn('TY - JOUR', ret)
def persist(req):
jsondata = req.REQUEST.get("data")
initdata = json.loads(jsondata)
logger.debug("Persisting")
logger.debug( "%s" % (initdata) )
fileutil.writeFile("test1", jsondata)
try:
if(initdata['_id'][:4] == 'conn'):
con = Connection(initdata)
con.save()
return SmartResponse(con._id, req)
else:
network = Network(initdata)
network.save()
index(network.name, network)
return SmartResponse(network._id, req)
except Error as e:
logger.error("Error saving data: %s" %traceback.format_exc())
return SmartResponse(e, req)
def persist(req):
jsondata = req.REQUEST.get("data")
initdata = json.loads(jsondata)
logger.debug("Persisting")
logger.debug("%s" % (initdata))
fileutil.writeFile("test1", jsondata)
try:
if (initdata['_id'][:4] == 'conn'):
con = Connection(initdata)
con.save()
return SmartResponse(con._id, req)
else:
network = Network(initdata)
network.save()
index(network.name, network)
return SmartResponse(network._id, req)
except Error as e:
logger.error("Error saving data: %s" % traceback.format_exc())
return SmartResponse(e, req)
def exportReference(pubmed_ids):
#url = "http://togows.dbcls.jp/entry/pubmed/"
#url = 'http://www.ncbi.nlm.nih.gov/pubmed'
#pubmed_ids = '19465464,18945920'.split(",")
url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&rettype=medline&retmode=text&id="
ids = ",".join(pubmed_ids)
url += ids
logger.debug( "Loading %s" %url)
r = requests.get(url)
if r.status_code == 200:
from django.utils.encoding import smart_str
content = smart_str(r.text)
else:
raise Exception("Failed to open %s" %url)
logger.debug( "Writing raw data to tmp/raw-medline.ris")
fileutil.writeFile("tmp/raw-medline.ris", content)
#print content
#from myutil import fileutil
#fileutil.writeFile("out.html", content)
return medline2ris(content)
def exportReference(pubmed_ids):
#url = "http://togows.dbcls.jp/entry/pubmed/"
#url = 'http://www.ncbi.nlm.nih.gov/pubmed'
#pubmed_ids = '19465464,18945920'.split(",")
url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&rettype=medline&retmode=text&id="
ids = ",".join(pubmed_ids)
url += ids
logger.debug("Loading %s" % url)
r = requests.get(url)
if r.status_code == 200:
from django.utils.encoding import smart_str
content = smart_str(r.text)
else:
raise Exception("Failed to open %s" % url)
logger.debug("Writing raw data to tmp/raw-medline.ris")
fileutil.writeFile("tmp/raw-medline.ris", content)
#print content
#from myutil import fileutil
#fileutil.writeFile("out.html", content)
return medline2ris(content)
