Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

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')+'/'