def post(self):
# logging.info("yeah!")
user = UserData.current()
name = self.request.get("name")
if name == "":
self.redirect("/collections/")
return
coll = SNPCollection.all().ancestor(user).filter("name =", name).get()
if coll is None:
coll = SNPCollection(parent=user, name=name)
coll.put()
self.redirect("/collection/?name=%s" % name)
return
def get(self):
# user = users.get_current_user()
user = UserData.current()
collections = SNPCollection.all().ancestor(user)
# check or update cache
# render from template
render = self.render("collectionlist.html",collections=collections)
self.out(rendered=render, )
def get(self, name):
user = UserData.current()
coll = SNPCollection.all().ancestor(user).filter("name =", name).get()
if coll is None:
logging.info("collection does not exist")
self.redirect("/collections/")
return
logging.info("deleting collection %s" % name)
coll.delete()
self.redirect("/collections/")
return
def testCreateCollection(self):
"""Test collection creation
- try to create a new collection called 'test'
- test that this collection has actually been added to the database afterwards
"""
test_coll = "test"
response = self.testapp.post('/collection/', {'name': test_coll})
user = UserData.current()
coll = SNPCollection.all().ancestor(user).filter("name =", test_coll).get()
self.assertIsNotNone(coll)
def get(self, collection_id):
# snp_disease_collection for diseases grouped by snp
# render = memcache.get(collection_id, namespace="snp_disease_collection")
# if render is None:
user = UserData.current()
# coll = db.get(db.Key.from_path("SNPCollection", collection_id, parent=user.key()))
coll = SNPCollection.all().ancestor(user).filter("name =", collection_id).get()
if coll is None:
self.redirect("/collections/")
return
snps = db.get(coll.snps)
render = self.render("snp_disease_collection.html", snps=snps, collection=coll)
# memcache.set(collection_id, render, namespace="snp_disease_collection")
self.out(rendered=render)
def get(self):
"""view or create specified collection"""
collection_name = self.request.get("name")
if collection_name == "":
self.redirect("/collections/")
return
# login is mandatory
# user = users.get_current_user()
user = UserData.current()
# query for particular collection, creating if it does not exist
coll = SNPCollection.all().ancestor(user).filter("name =", collection_name).get()
if coll is None:
# should have a 404-page
self.redirect("/collections/")
return
# check or update cache
# render from template
render = self.render("collectionview.html",collection=coll)
self.out(rendered=render)
def get(self, collection_name):
# user = users.get_current_user()
user = UserData.current()
coll = SNPCollection.all().ancestor(user).filter("name =", collection_name).get()
if coll is None:
# logging.info("redirecting")
# if collection doesn't exist - redirect to list of collections
self.redirect("/collections/")
return
# we support a number of actions
# addsnps = add a list of snps to a collection
# action = self.requst.get("action")
error = []
warning = []
# action = "addsnps"
# if action == "addsnps":
logging.info("adding snps to coll: %s" % collection_name)
snps = self.request.get("snps")
# for testing
# snps = '10260404,3825776,12284594,rs1805007,12345'
# comma seperated list of snps
snpids = [snp.strip() for snp in snps.split(',')]
# verify input:
# - if snpid is not a valid integer-value
# replace with None and add to list of 'invalid' ids
# (might be because its prefixed with RS/rs)
invalid_keys = []
for i in xrange(len(snpids)):
snp = snpids[i]
try:
# try to convert to int
int(snp)
except:
invalid_keys.append(snp)
snpids[i] = None
# collect errors
if len(invalid_keys) > 0:
error.append("invalid keys: %s" % invalid_keys)
# generate composite keys from the list of SNPs which are not None
snpids = [snpid for snpid in snpids if not snpid is None]
keys = [db.Key.from_path("Snp", snpid) for snpid in snpids]
# logging.debug("keys to add: ")
# retrieve all Snp-instances from these keys
# - note: invalid keys / non-existent keys return with 'None'
# aka: "the SNP-id might be valid, but it is not in the GWAS catalog"
snp_keys = db.get(keys)
# logging.info(snp_keys)
# logging.info("ids: %s" % [snp.key() for snp in snp_keys if snp])
# all 'None' keys are from ids unknown to GWAS, compile a list of these
unknown_keys = [snpids[i] for i in xrange(len(snp_keys)) if snp_keys[i] is None]
if unknown_keys:
warning.append("Keys unknown to the GWAS catalog: %s" % unknown_keys)
# add keys to collection
# list = [snp.key() for snp in snp_keys if snp]
# logging.info("WTF: %s" % list)
for key in [snp.key() for snp in snp_keys if snp is not None]:
if key not in coll.snps:
coll.snps.append(key)
coll.count = len(coll.snps)
coll.put()
# try:
# coll.addMultipleSNP(snp_keys)
# except Exception, e:
# logging.warning("issues inserting: %s" % e)
# error.append("Unknown issue adding snps to collection")
# render
logging.info("errors: %s" % error )
logging.info("warning: %s" % warning)
render = self.render("collectionview.html", collection=coll)
self.out(rendered=render, error=error, warning=warning)
