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authorLei Yan2013-07-03 20:56:45 +0000
committerLei Yan2013-07-03 20:56:45 +0000
commit76ad4e6ae15f4d42ddd420cd14936c149aa0bb31 (patch)
tree7f82df4895e80788e5b9e9fb07b0d7adb97a0738 /wqflask/base/data_set.py
parentd95eff3f0410ec5cddd82398f6db0fffa5d9be0b (diff)
parent253df1a5adb060df3202de5b80a5065a3614e368 (diff)
downloadgenenetwork2-76ad4e6ae15f4d42ddd420cd14936c149aa0bb31.tar.gz
Merge /home/zas1024/gene
Diffstat (limited to 'wqflask/base/data_set.py')
-rwxr-xr-xwqflask/base/data_set.py105
1 files changed, 81 insertions, 24 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1668940c..03b24230 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -27,8 +27,12 @@ import string
import collections
import json
+import cPickle as pickle
import itertools
+from redis import Redis
+Redis = Redis()
+
from flask import Flask, g
import reaper
@@ -46,17 +50,18 @@ from pprint import pformat as pf
# Used by create_database to instantiate objects
DS_NAME_MAP = {}
-def create_dataset(dataset_name):
+def create_dataset(dataset_name, dataset_type = None):
#print("dataset_name:", dataset_name)
- query = """
- SELECT DBType.Name
- FROM DBList, DBType
- WHERE DBList.Name = '{}' and
- DBType.Id = DBList.DBTypeId
- """.format(escape(dataset_name))
- #print("query is: ", pf(query))
- dataset_type = g.db.execute(query).fetchone().Name
+ if not dataset_type:
+ query = """
+ SELECT DBType.Name
+ FROM DBList, DBType
+ WHERE DBList.Name = '{}' and
+ DBType.Id = DBList.DBTypeId
+ """.format(escape(dataset_name))
+ #print("query is: ", pf(query))
+ dataset_type = g.db.execute(query).fetchone().Name
#dataset_type = cursor.fetchone()[0]
#print("[blubber] dataset_type:", pf(dataset_type))
@@ -69,6 +74,36 @@ def create_dataset(dataset_name):
dataset_class = globals()[dataset_ob]
return dataset_class(dataset_name)
+def create_datasets_list():
+ key = "all_datasets"
+ result = Redis.get(key)
+
+ if result:
+ print("Cache hit!!!")
+ datasets = pickle.loads(result)
+
+ else:
+ datasets = list()
+ with Bench("Creating DataSets object"):
+ type_dict = {'Publish': 'PublishFreeze',
+ 'ProbeSet': 'ProbeSetFreeze',
+ 'Geno': 'GenoFreeze'}
+
+ for dataset_type in type_dict:
+ query = "SELECT Name FROM {}".format(type_dict[dataset_type])
+ for result in g.db.execute(query).fetchall():
+ #The query at the beginning of this function isn't necessary here, but still would
+ #rather just reuse it
+ print("type: {}\tname: {}".format(dataset_type, result.Name))
+ dataset = create_dataset(result.Name, dataset_type)
+ datasets.append(dataset)
+
+ Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
+ Redis.expire(key, 60*60)
+
+ return datasets
+
+
def create_in_clause(items):
"""Create an in clause for mysql"""
in_clause = ', '.join("'{}'".format(x) for x in mescape(*items))
@@ -167,8 +202,8 @@ class DatasetGroup(object):
self.incparentsf1 = False
self.allsamples = None
-
-
+
+
def get_markers(self):
#print("self.species is:", self.species)
if self.species == "human":
@@ -222,6 +257,27 @@ class DatasetGroup(object):
self.samplelist = list(genotype.prgy)
+#class DataSets(object):
+# """Builds a list of DataSets"""
+#
+# def __init__(self):
+# self.datasets = list()
+#
+
+
+ #query = """SELECT Name FROM ProbeSetFreeze
+ # UNION
+ # SELECT Name From PublishFreeze
+ # UNION
+ # SELECT Name From GenoFreeze"""
+ #
+ #for result in g.db.execute(query).fetchall():
+ # dataset = DataSet(result.Name)
+ # self.datasets.append(dataset)
+
+#ds = DataSets()
+#print("[orange] ds:", ds.datasets)
+
class DataSet(object):
"""
DataSet class defines a dataset in webqtl, can be either Microarray,
@@ -234,6 +290,8 @@ class DataSet(object):
assert name, "Need a name"
self.name = name
self.id = None
+ self.shortname = None
+ self.fullname = None
self.type = None
self.setup()
@@ -293,7 +351,7 @@ class DataSet(object):
self.name,
self.name,
self.name))
- #print("query_args are:", query_args)
+ print("query_args are:", query_args)
#print("""
# SELECT Id, Name, FullName, ShortName
@@ -301,17 +359,17 @@ class DataSet(object):
# WHERE public > %s AND
# (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
# """ % (query_args))
-
- self.id, self.name, self.fullname, self.shortname = g.db.execute("""
- SELECT Id, Name, FullName, ShortName
- FROM %s
- WHERE public > %s AND
- (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
- """ % (query_args)).fetchone()
-
- #self.cursor.execute(query)
- #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
+ try:
+ self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+ SELECT Id, Name, FullName, ShortName
+ FROM %s
+ WHERE public > %s AND
+ (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args)).fetchone()
+ except TypeError:
+ print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
+ pass
class PhenotypeDataSet(DataSet):
DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
@@ -940,6 +998,5 @@ def geno_mrna_confidentiality(ob):
authorized_users) = result.fetchall()[0]
if confidential:
- # Allow confidential data later
- NoConfindetialDataForYouTodaySorry
+ return True