gn_server: introduced one new query to fetch a dataset record and force fetch1 to return a tuple

4 files changed, 35 insertions, 23 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index c70738f7..ec3750dd 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -466,14 +466,20 @@ class DataSet(object):
         Weve_Renamed_This_As_Group
 
     def retrieve_other_names(self):
-        """
-        If the data set name parameter is not found in the 'Name' field of the data set table,
-        check if it is actually the FullName or ShortName instead.
+        """This method fetches the the dataset names in search_result.
+
+        If the data set name parameter is not found in the 'Name' field of
+        the data set table, check if it is actually the FullName or
+        ShortName instead.
 
-        This is not meant to retrieve the data set info if no name at all is passed.
+        This is not meant to retrieve the data set info if no name at
+        all is passed.
 
         """
 
+        def helper(r):
+            return r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"]
+
         try:
             if self.type == "ProbeSet":
                 query_args = tuple(escape(x) for x in (
@@ -482,14 +488,18 @@ class DataSet(object):
                     self.name,
                     self.name))
 
-                self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetchone("""
-                        SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
-                        FROM ProbeSetFreeze, ProbeFreeze, Tissue
-                        WHERE ProbeSetFreeze.public > %s AND
-                              ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
-                              ProbeFreeze.TissueId = Tissue.Id AND
-                             (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
-                  """ % (query_args))
+                # self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue =
+                result = fetch1("""
+SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
+FROM ProbeSetFreeze, ProbeFreeze, Tissue
+WHERE ProbeSetFreeze.public > %s
+AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+AND ProbeFreeze.TissueId = Tissue.Id
+AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
+                """ % (query_args),
+                                                                                                         "/dataset/"+self.name+".json",helper)
+                self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = result
+                logger.debug("retrieve_other_names result:",result)
             else:
                 query_args = tuple(escape(x) for x in (
                     (self.type + "Freeze"),
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 194a7650..6c195afa 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -14,17 +14,19 @@ logger = getLogger(__name__ )
 # from inspect import stack
 
 def fetch1(query, path=None, func=None):
-    """Fetch one result using either a SQL query or the URI path to
-GN_SERVER (when USE_GN_SERVER is True). Apply func to GN_SERVER result
-when set.
+    """Fetch one result as a Tuple using either a SQL query or the URI
+path to GN_SERVER (when USE_GN_SERVER is True). Apply func to
+GN_SERVER result when set (which should return a Tuple)
 
     """
     if USE_GN_SERVER and path:
         result = gn_server(path)
         if func != None:
-            return [func(result)]
+            res2 = func(result)
         else:
-            return [result]
+            res2 = result,
+        logger.debug(path,query,res2)
+        return res2
     else:
         return fetchone(query)
 
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 7fc096a9..ba998e91 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -21,6 +21,7 @@
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
 from db.call import fetch1
+from utility.tools import USE_GN_SERVER
 
 from utility.logger import getLogger
 logger = getLogger(__name__ )
@@ -42,13 +43,13 @@ def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
 
     """
-    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: r["species"])[0]
+    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: (r["species"],))[0]
     logger.debug("retrieve_species result:",result)
     return result
 
 
 def retrieve_species_id(group):
 
-    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: r["species_id"])[0]
+    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: (r["species_id"],))[0]
     logger.debug("retrieve_species_id result:",result)
     return result
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 86ee1c52..ddc0ea82 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -48,13 +48,12 @@ class GNLogger:
         """Set the undelying log level"""
         self.logger.setLevel(value)
 
-    def debug(self,level=0,*args):
+    def debug(self,*args):
         """Call logging.debug for multiple args. Use level=num to filter on
-LOG_LEVEL_DEBUG.
+LOG_LEVEL_DEBUG (NYI).
 
         """
-        if level <= LOG_LEVEL_DEBUG:
-            self.collect(self.logger.debug,*args)
+        self.collect(self.logger.debug,*args)
 
     def info(self,*args):
         """Call logging.info for multiple args"""