def upload(self,
network_name=None,
network_file=None,
annotations_file=None,
type="public",
email="*****@*****.**"):
#cherrypy.log("Privacy: "+ type)
#cherrypy.log("annotations: "+ repr(network_file))
#cherrypy.log("network: "+ repr(annotations_file))
if cherrypy.request.method == "GET":
tmpl = lookup.get_template("upload_form.mako")
return tmpl.render()
else:
network_name = pinv.clean(network_name)
solr_url = '%s/solr/%s' % (settings.SOLR_SERVER, network_name)
time.sleep(2)
inv = InteractionNetwork(network_name, "description text",
network_file.file, annotations_file.file)
time.sleep(2)
message, result = pinv.create_new_solr(network_name)
time.sleep(2)
cherrypy.log("*** UPLOAD. Connecting to: " + solr_url)
si = sunburnt.SolrInterface(solr_url)
time.sleep(2)
inv.upload(si)
inv.createClusters(si, 3, 7)
cherrypy.log(str(inv.errors))
view_key, delete_key = auth.save_key(network_name, email, type)
if type == "private":
view_url = "http://biosual.cbio.uct.ac.za/pinViewer.html?core=%(core)s&key=%(key)s" % {
'core': network_name,
'key': view_key
}
delete_url = "http://biosual.cbio.uct.ac.za/solr/admin/cores?action=UNLOAD&deleteIndex=true&core=%(core)s&key=%(key)s" % {
'core': network_name,
'key': delete_key
}
else:
view_url = "http://biosual.cbio.uct.ac.za/pinViewer.html?core=%(core)s" % {
'core': network_name
}
delete_url = "http://biosual.cbio.uct.ac.za/solr/admin/cores?action=UNLOAD&deleteIndex=true&core=%(core)s&key=%(key)s" % {
'core': network_name,
'key': delete_key
}
msg = auth.sendmail(email, view_url, delete_url, network_name)
#cherrypy.log(msg);
errormessage = "<br/>".join(inv.errors)
tmpl = lookup.get_template("upload_result.mako")
return tmpl.render(network_name=network_name,
annotation_head="|".join(inv.ahead),
annotation_count=len(inv.annotations),
annotation_file=annotations_file.filename,
network_head="|".join(inv.nhead),
network_count=len(inv.network),
network_file=network_file.filename,
message="",
errors="<br/>".join(inv.errors))
def upload(self, network_name=None, network_file=None, annotations_file=None, type="public", email="*****@*****.**"):
#cherrypy.log("Privacy: "+ type)
#cherrypy.log("annotations: "+ repr(network_file))
#cherrypy.log("network: "+ repr(annotations_file))
if cherrypy.request.method == "GET":
tmpl = lookup.get_template("upload_form.mako")
return tmpl.render()
else:
network_name = pinv.clean(network_name)
solr_url = '%s/solr/%s'%(settings.SOLR_SERVER,network_name)
time.sleep(2)
inv = InteractionNetwork(network_name, "description text", network_file.file, annotations_file.file)
time.sleep(2)
message, result = pinv.create_new_solr(network_name)
time.sleep(2)
cherrypy.log("*** UPLOAD. Connecting to: "+ solr_url)
si = sunburnt.SolrInterface(solr_url)
time.sleep(2)
inv.upload(si)
inv.createClusters(si,3,7)
cherrypy.log(str(inv.errors));
view_key, delete_key = auth.save_key(network_name, email,type)
if type == "private":
view_url = "http://biosual.cbio.uct.ac.za/pinViewer.html?core=%(core)s&key=%(key)s" % {'core':network_name,'key':view_key}
delete_url = "http://biosual.cbio.uct.ac.za/solr/admin/cores?action=UNLOAD&deleteIndex=true&core=%(core)s&key=%(key)s" % {'core':network_name,'key':delete_key}
else:
view_url = "http://biosual.cbio.uct.ac.za/pinViewer.html?core=%(core)s" % {'core':network_name}
delete_url = "http://biosual.cbio.uct.ac.za/solr/admin/cores?action=UNLOAD&deleteIndex=true&core=%(core)s&key=%(key)s" % {'core':network_name,'key':delete_key}
msg =auth.sendmail(email,view_url, delete_url,network_name)
#cherrypy.log(msg);
errormessage = "<br/>".join(inv.errors)
tmpl = lookup.get_template("upload_result.mako")
return tmpl.render(network_name=network_name,
annotation_head="|".join(inv.ahead),
annotation_count=len(inv.annotations),
annotation_file=annotations_file.filename,
network_head="|".join(inv.nhead),
network_count=len(inv.network),
network_file=network_file.filename,
message="",
errors="<br/>".join(inv.errors))
def upload(self, network_name, network_file, annotations_file):
out = """<html>
<body>
Network name: %s<br/><br/>
Annotations columns: %s<br/>
Annotations count: %i<br />
Annotations filename: %s<br />
Network head: %s<br />
Network length: %i<br />
Network filename: %s<br />
%s
<br/>
Errors:<br/>
%s
</body>
</html>"""
network_name = pinv.clean(network_name)
if settings.TEST and not (network_file.file and annotations_file.file):
network_file.file = open("../data/test.txt")
annotations_file.file = open("../data/test_annot.txt")
solr_url = settings.SOLR_URL
solr_url = '%s/solr/%s' % (settings.SOLR_SERVER, network_name)
time.sleep(2)
inv = InteractionNetwork(network_name, "description text",
network_file.file, annotations_file.file)
time.sleep(2)
message, result = pinv.create_new_solr(network_name)
time.sleep(2)
print "--- UPLOAD. Connecting to:", solr_url
si = sunburnt.SolrInterface(solr_url)
time.sleep(2)
inv.upload(si)
errormessage = "<br/>".join(inv.errors)
return out % (network_name, "|".join(inv.ahead), len(
inv.annotations), repr(annotations_file.filename), "|".join(
inv.nhead), len(inv.network), repr(
network_file.filename), message, errormessage)
def upload(self, network_name, network_file, annotations_file):
out = """<html>
<body>
Network name: %s<br/><br/>
Annotations columns: %s<br/>
Annotations count: %i<br />
Annotations filename: %s<br />
Network head: %s<br />
Network length: %i<br />
Network filename: %s<br />
%s
<br/>
Errors:<br/>
%s
</body>
</html>"""
network_name = pinv.clean(network_name)
if settings.TEST and not (network_file.file and annotations_file.file):
network_file.file = open("../data/test.txt")
annotations_file.file = open("../data/test_annot.txt")
solr_url = settings.SOLR_URL
solr_url = '%s/solr/%s'%(settings.SOLR_SERVER,network_name)
time.sleep(2)
inv = InteractionNetwork(network_name, "description text", network_file.file, annotations_file.file)
time.sleep(2)
message, result = pinv.create_new_solr(network_name)
time.sleep(2)
print "--- UPLOAD. Connecting to:", solr_url
si = sunburnt.SolrInterface(solr_url)
time.sleep(2)
inv.upload(si)
errormessage = "<br/>".join(inv.errors)
return out % (network_name,"|".join(inv.ahead), len(inv.annotations), repr(annotations_file.filename),
"|".join(inv.nhead), len(inv.network), repr(network_file.filename),message,errormessage)
