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-rwxr-xr-xwqflask/base/data_set.py52
-rwxr-xr-xwqflask/wqflask/database.py7
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py35
3 files changed, 59 insertions, 35 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1cd57b4b..706b193d 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -29,6 +29,7 @@ import json
import gzip
import cPickle as pickle
import itertools
+from operator import itemgetter
from redis import Redis
Redis = Redis()
@@ -292,6 +293,7 @@ class DatasetGroup(object):
self.incparentsf1 = False
self.allsamples = None
+ self._datasets = None
def get_specified_markers(self, markers = []):
self.markers = HumanMarkers(self.name, markers)
@@ -305,6 +307,56 @@ class DatasetGroup(object):
self.markers = marker_class(self.name)
+ def datasets(self):
+ key = "group_dataset_menu:v1:" + self.name
+ print("key is:", key)
+ with Bench("Loading cache"):
+ result = Redis.get(key)
+ if result:
+ self._datasets = pickle.loads(result)
+ return self._datasets
+
+ dataset_menu = []
+ print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
+ print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
+ results = g.db.execute('''
+ (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
+ FROM PublishFreeze,InbredSet
+ WHERE PublishFreeze.InbredSetId = InbredSet.Id
+ and InbredSet.Name = %s
+ and PublishFreeze.public > %s)
+ UNION
+ (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
+ FROM GenoFreeze, InbredSet
+ WHERE GenoFreeze.InbredSetId = InbredSet.Id
+ and InbredSet.Name = %s
+ and GenoFreeze.public > %s)
+ UNION
+ (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
+ FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
+ WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+ and ProbeFreeze.TissueId = Tissue.Id
+ and ProbeFreeze.InbredSetId = InbredSet.Id
+ and InbredSet.Name like %s
+ and ProbeSetFreeze.public > %s
+ ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
+ ''', (self.name, webqtlConfig.PUBLICTHRESH,
+ self.name, webqtlConfig.PUBLICTHRESH,
+ "%" + self.name + "%", webqtlConfig.PUBLICTHRESH))
+
+ for tissue_name, dataset in itertools.groupby(results.fetchall(), itemgetter(0)):
+ if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
+ for item in dataset:
+ dataset_menu.append(dict(tissue=None, datasets=[item[1:]]))
+ else:
+ dataset_sub_menu = [item[1:] for item in dataset]
+ dataset_menu.append(dict(tissue=tissue_name,
+ datasets=dataset_sub_menu))
+
+ Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
+ Redis.expire(key, 60*5)
+ self._datasets = dataset_menu
+ return self._datasets
def get_f1_parent_strains(self):
try:
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index e55f06a7..159c5d6c 100755
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -13,6 +13,11 @@ db_session = scoped_session(sessionmaker(autocommit=False,
Base = declarative_base()
Base.query = db_session.query_property()
+#import logging
+#
+#logging.basicConfig()
+#logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO)
+
def init_db():
# import all modules here that might define models so that
# they will be registered properly on the metadata. Otherwise
@@ -23,4 +28,4 @@ def init_db():
Base.metadata.create_all(bind=engine)
print("Done creating all...")
-init_db() \ No newline at end of file
+init_db()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index b28c9b76..9bce69d9 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -888,40 +888,7 @@ class ShowTrait(object):
this_group = 'BXD'
if this_group:
-
- dataset_menu = []
- print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
- print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
- results = g.db.execute("""SELECT PublishFreeze.FullName,PublishFreeze.Name FROM
- PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name = %s and PublishFreeze.public > %s""",
- (this_group, webqtlConfig.PUBLICTHRESH))
- for item in results.fetchall():
- dataset_menu.append(dict(tissue=None,
- datasets=[item]))
-
- results = g.db.execute("""SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,
- InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name =
- %s and GenoFreeze.public > %s""",
- (this_group, webqtlConfig.PUBLICTHRESH))
- for item in results.fetchall():
- dataset_menu.append(dict(tissue=None,
- datasets=[item]))
-
- #03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob.
- tissues = g.db.execute("SELECT Id, Name FROM Tissue order by Name")
- for item in tissues.fetchall():
- tissue_id, tissue_name = item
- data_sets = g.db.execute('''SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze,
- InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %s and
- ProbeSetFreeze.public > %s and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s
- order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ''',
- (tissue_id, webqtlConfig.PUBLICTHRESH, "%" + this_group + "%"))
- dataset_sub_menu = [item for item in data_sets.fetchall() if item]
- if dataset_sub_menu:
- dataset_menu.append(dict(tissue=tissue_name,
- datasets=dataset_sub_menu))
-
+ dataset_menu = self.dataset.group.datasets()
dataset_menu_selected = None
if len(dataset_menu):
if this_trait and this_trait.dataset: