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-rwxr-xr-xwqflask/base/data_set.py99
-rw-r--r--wqflask/base/species.py10
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py7
-rw-r--r--wqflask/wqflask/search_results.py2
-rw-r--r--wqflask/wqflask/views.py13
5 files changed, 103 insertions, 28 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1668940c..803cbc4f 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 +74,19 @@ 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!!!")
+ result = pickle.loads(result)
+ else:
+ with Bench("Creating DataSets object"):
+ ds = DataSets()
+ Redis.set(key, pickle.dumps(result))
+ Redis.expire(key, 2*60)
+
+
def create_in_clause(items):
"""Create an in clause for mysql"""
in_clause = ', '.join("'{}'".format(x) for x in mescape(*items))
@@ -167,8 +185,8 @@ 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 +240,38 @@ class DatasetGroup(object):
self.samplelist = list(genotype.prgy)
+class DataSets(object):
+ """Builds a list of DataSets"""
+
+ def __init__(self):
+ self.datasets = list()
+
+ 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))
+ create_dataset(result.Name, dataset_type)
+
+
+ #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 +284,8 @@ 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 +345,7 @@ 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 +353,17 @@ 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 +992,5 @@ def geno_mrna_confidentiality(ob):
authorized_users) = result.fetchall()[0]
if confidential:
- # Allow confidential data later
- NoConfindetialDataForYouTodaySorry
+ return True
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 191f4535..ebc2bfed 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -56,6 +56,7 @@ class Chromosomes(object):
InbredSet.Name = %s
Order by OrderId
""", self.dataset.group.name).fetchall()
+ print("group: ", self.dataset.group.name)
print("bike:", results)
for item in results:
@@ -68,9 +69,14 @@ class Chromosomes(object):
def set_mb_graph_interval(self):
"""Empirical megabase interval"""
+ if self.chromosomes:
+ self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+ else:
+ self.mb_graph_interval = 1
+
#if self.chromosomes:
- assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
- self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+ #assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
+ #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
#else:
#self.mb_graph_interval = 1
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 1410ae0c..3b47e970 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -203,6 +203,13 @@ class CorrelationResults(object):
# mb = trait_object.mb
# )
+
+
+ trait_list = self.getTissueCorrelationByList( primary_trait_symbol = self.this_trait.symbol,
+ corr_results = self.correlation_results,
+ TissueProbeSetFreezeId = 1,
+ method=1)
+
#XZ, 09/18/2008: get all information about the user selected database.
#target_db_name = fd.corr_dataset
#self.target_db_name = start_vars['corr_dataset']
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index f76af374..504a67ce 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -162,8 +162,6 @@ class SearchResultPage(object):
import redis
Redis = redis.Redis()
-
-
#def get_group_species_tree(self):
# self.species_groups = collections.default_dict(list)
# for key in self.results:
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 90be7a71..bd56f7a9 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -27,6 +27,7 @@ from flask import render_template, request, make_response, Response, Flask, g, c
from wqflask import search_results
from base.data_set import DataSet # Used by YAML in marker_regression
+from base.data_set import create_datasets_list
from wqflask.show_trait import show_trait
from wqflask.show_trait import export_trait_data
from wqflask.marker_regression import marker_regression
@@ -53,6 +54,18 @@ def connect_db():
@app.route("/")
def index_page():
print("Sending index_page")
+ create_datasets_list()
+ #key = "all_datasets"
+ #result = Redis.get(key)
+ #if result:
+ # print("Cache hit!!!")
+ # result = pickle.loads(result)
+ #else:
+ # with Bench("Creating DataSets object"):
+ # ds = DataSets()
+ # Redis.set(key, pickle.dumps(result))
+ # Redis.expire(key, 2*60)
+ #print("[orange] ds:", ds.datasets)
return render_template("index_page.html")
@app.route("/data_sharing")
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-20 18:57:33 +0000