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-rw-r--r--wqflask/base/data_set.py113
-rw-r--r--wqflask/base/webqtlCaseData.py41
-rw-r--r--wqflask/base/webqtlConfig.py2
3 files changed, 68 insertions, 88 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5d562871..cfba9104 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -93,7 +93,7 @@ Publish or ProbeSet. E.g.
"""
self.redis_instance = redis_instance
self.datasets = {}
- data = redis_instance.get("dataset_structure")
+ data = self.redis_instance.get("dataset_structure")
if data:
self.datasets = json.loads(data)
else: # ZS: I don't think this should ever run unless Redis is emptied
@@ -115,73 +115,58 @@ Publish or ProbeSet. E.g.
except:
pass
- redis_instance.set("dataset_structure", json.dumps(self.datasets))
+ self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
- # Set LOG_LEVEL_DEBUG=5 to see the following:
- logger.debugf(5, "datasets", self.datasets)
+ def set_dataset_key(self, t, name):
+ """If name is not in the object's dataset dictionary, set it, and update
+ dataset_structure in Redis
+
+ args:
+ t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
+ 'other_pheno', 'geno'
+ name: The name of the key to inserted in the datasets dictionary
+
+ """
+ sql_query_mapping = {
+ 'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ +
+ """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """),
+ 'pheno': ("""SELECT InfoFiles.GN_AccesionId """ +
+ """FROM InfoFiles, PublishFreeze, InbredSet """ +
+ """WHERE InbredSet.Name = '{}' AND """ +
+ """PublishFreeze.InbredSetId = InbredSet.Id AND """ +
+ """InfoFiles.InfoPageName = PublishFreeze.Name"""),
+ 'other_pheno': ("""SELECT PublishFreeze.Name """ +
+ """FROM PublishFreeze, InbredSet """ +
+ """WHERE InbredSet.Name = '{}' AND """ +
+ """PublishFreeze.InbredSetId = InbredSet.Id"""),
+ 'geno': ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ +
+ """GenoFreeze.Name = "{}" """)
+ }
+
+ dataset_name_mapping = {
+ "mrna_expr": "ProbeSet",
+ "pheno": "Publish",
+ "other_pheno": "Publish",
+ "geno": "Geno",
+ }
+
+ if t in ['pheno', 'other_pheno']:
+ name = name.replace("Publish", "")
+ if bool(len(g.db.execute(sql_query_mapping[t].format(name)))):
+ self.datasets[name] = dataset_name_mapping[t]
+ self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+ return True
+
+ return None
def __call__(self, name):
+
if name not in self.datasets:
- mrna_expr_query = """
- SELECT
- ProbeSetFreeze.Id
- FROM
- ProbeSetFreeze
- WHERE
- ProbeSetFreeze.Name = "{0}"
- """.format(name)
-
- results = g.db.execute(mrna_expr_query).fetchall()
- if len(results):
- self.datasets[name] = "ProbeSet"
- redis_instance.set("dataset_structure", json.dumps(self.datasets))
- return self.datasets[name]
-
- group_name = name.replace("Publish", "")
-
- pheno_query = """SELECT InfoFiles.GN_AccesionId
- FROM InfoFiles, PublishFreeze, InbredSet
- WHERE InbredSet.Name = '{0}' AND
- PublishFreeze.InbredSetId = InbredSet.Id AND
- InfoFiles.InfoPageName = PublishFreeze.Name""".format(group_name)
-
- results = g.db.execute(pheno_query).fetchall()
- if len(results):
- self.datasets[name] = "Publish"
- redis_instance.set("dataset_structure", json.dumps(self.datasets))
- return self.datasets[name]
-
- # ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary
- other_pheno_query = """SELECT PublishFreeze.Name
- FROM PublishFreeze, InbredSet
- WHERE InbredSet.Name = '{}' AND
- PublishFreeze.InbredSetId = InbredSet.Id""".format(group_name)
-
- results = g.db.execute(other_pheno_query).fetchall()
- if len(results):
- self.datasets[name] = "Publish"
- redis_instance.set("dataset_structure", json.dumps(self.datasets))
- return self.datasets[name]
-
- geno_query = """
- SELECT
- GenoFreeze.Id
- FROM
- GenoFreeze
- WHERE
- GenoFreeze.Name = "{0}"
- """.format(name)
-
- results = g.db.execute(geno_query).fetchall()
- if len(results):
- self.datasets[name] = "Geno"
- self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
- return self.datasets[name]
-
- # ZS: It shouldn't ever reach this
- return None
- else:
- return self.datasets[name]
+ for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
+ # This has side-effects, with the end result being a truth-y value
+ if(self.set_dataset_key(t, name)):
+ break
+ return self.datasets.get(name, None) # Return None if name has not been set
# Do the intensive work at startup one time only
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index d8487f01..2844cedd 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -19,8 +19,7 @@
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
+
from utility.logger import getLogger
logger = getLogger(__name__)
@@ -29,7 +28,7 @@ import utility.tools
utility.tools.show_settings()
-class webqtlCaseData(object):
+class webqtlCaseData:
"""one case data in one trait"""
def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
@@ -43,44 +42,40 @@ class webqtlCaseData(object):
self.outlier = None # Not set to True/False until later
def __repr__(self):
- str = "<webqtlCaseData> "
- if self.value != None:
- str += "value=%2.3f" % self.value
- if self.variance != None:
- str += " variance=%2.3f" % self.variance
+ case_data_string = "<webqtlCaseData> "
+ if self.value is not None:
+ case_data_string += "value=%2.3f" % self.value
+ if self.variance is not None:
+ case_data_string += " variance=%2.3f" % self.variance
if self.num_cases:
- str += " ndata=%s" % self.num_cases
+ case_data_string += " ndata=%s" % self.num_cases
if self.name:
- str += " name=%s" % self.name
+ case_data_string += " name=%s" % self.name
if self.name2:
- str += " name2=%s" % self.name2
- return str
+ case_data_string += " name2=%s" % self.name2
+ return case_data_string
@property
def class_outlier(self):
"""Template helper"""
if self.outlier:
return "outlier"
- else:
- return ""
+ return ""
@property
def display_value(self):
- if self.value != None:
+ if self.value is not None:
return "%2.3f" % self.value
- else:
- return "x"
+ return "x"
@property
def display_variance(self):
- if self.variance != None:
+ if self.variance is not None:
return "%2.3f" % self.variance
- else:
- return "x"
+ return "x"
@property
def display_num_cases(self):
- if self.num_cases != None:
+ if self.num_cases is not None:
return "%s" % self.num_cases
- else:
- return "x"
+ return "x"
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 3d86bc22..862ac881 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -85,7 +85,7 @@ assert_writable_dir(GENERATED_TEXT_DIR)
# Flat file directories
GENODIR = flat_files('genotype')+'/'
assert_dir(GENODIR)
-assert_dir(GENODIR+'bimbam') # for gemma
+# assert_dir(GENODIR+'bimbam') # for gemma
# JSON genotypes are OBSOLETE
JSON_GENODIR = flat_files('genotype/json')+'/'
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-20 08:15:01 +0000