Got code that creates DataSets object running

Fixed one genofile that had extra quotation marks
in the comments that caused an error

Defaults mb_graph_interval to 1 for species without chromosome
lengths in megabases

4 files changed, 39 insertions, 31 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index f301cc05..e4bdb5c3 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -46,17 +46,18 @@ 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))
@@ -228,16 +229,17 @@ class DataSets(object):
     def __init__(self):
         self.datasets = list()
         
-        type_dict = {'phenotype': 'PublishFreeze',
-                   'mrna_assay': 'ProbeSetFreeze',
-                   'genotype': 'GenoFreeze'}
+        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
-                create_dataset(result.Name)
+                print("type: {}\tname: {}".format(dataset_type, result.Name))
+                create_dataset(result.Name, dataset_type)
         
         
         #query = """SELECT Name FROM ProbeSetFreeze
@@ -265,6 +267,8 @@ 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()
@@ -324,7 +328,7 @@ 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
@@ -332,17 +336,17 @@ 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'
@@ -971,6 +975,5 @@ 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/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 fcb34d31..e48506ab 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -54,7 +54,8 @@ def connect_db():
 @app.route("/")
 def index_page():
     print("Sending index_page")
-    ds = DataSets()
+    with Bench("Creating DataSets object"):
+        ds = DataSets()
     print("[orange] ds:", ds.datasets)
     return render_template("index_page.html")