Merge https://github.com/zsloan/genenetwork

Resolved conflicts:
	wqflask/base/trait.py
	wqflask/wqflask/correlation/correlationFunction.py
	wqflask/wqflask/correlation/correlation_function.py
	wqflask/wqflask/correlation/correlation_functions.py
	wqflask/wqflask/correlation/show_corr_results.py

1 files changed, 74 insertions, 20 deletions

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 4c544192..ad560659 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -29,25 +29,47 @@ It needs to be run manually when database has been changed.
 
 from __future__ import print_function, division
 
-import sys
+#from flask import config
+#
+#cdict = {}
+#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS')
+#print("cdict is:", cdict)
 
-sys.path.insert(0, "..")
+import our_settings
 
 import MySQLdb
 
 import simplejson as json
+import urlparse
 
-from pprint import pformat as pf
 
-from base import webqtlConfig
+#import sqlalchemy as sa
+
+from pprint import pformat as pf
 
+#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI)
 
 # build MySql database connection
-Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,
-                      host=webqtlConfig.MYSQL_SERVER,
-                      user=webqtlConfig.DB_USER,
-                      passwd=webqtlConfig.DB_PASSWD)
-Cursor = Con.cursor()
+
+#conn = Engine.connect()
+
+
+
+
+
+def parse_db_uri(db_uri):
+    """Converts a database URI to the db name, host name, user name, and password"""
+    
+    parsed_uri = urlparse.urlparse(our_settings.DB_URI)
+    
+    db_conn_info = dict(
+                        db = parsed_uri.path[1:],
+                        host = parsed_uri.hostname,
+                        user = parsed_uri.username,
+                        passwd = parsed_uri.password)
+    
+    return db_conn_info
+
 
 
 def get_species():
@@ -77,12 +99,14 @@ def get_groups(species):
 def get_types(groups):
     """Build types list"""
     types = {}
+    print("Groups: ", pf(groups))
     for species, group_dict in groups.iteritems():
         types[species] = {}
         for group_name, _group_full_name in group_dict:
             # make group an alias to shorten the code
             types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")]
             types[species][group_name] += build_types(species, group_name)
+
     return types
 
 
@@ -93,17 +117,32 @@ def build_types(species, group):
     (all types except phenotype/genotype are tissues)
      
     """
-    Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
+    
+    print("""select distinct Tissue.Name
+                       from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
+                       where Species.Name = '{}' and Species.Id = InbredSet.SpeciesId and
+                       InbredSet.Name = '{}' and
+                       ProbeFreeze.TissueId = Tissue.Id and
+                       ProbeFreeze.InbredSetId = InbredSet.Id and
+                       ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
+                       ProbeSetFreeze.public > 0
+                       order by Tissue.Name""".format(species, group))
+    Cursor.execute("""select distinct Tissue.Name
                        from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
                        where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
                        InbredSet.Name = %s and
                        ProbeFreeze.TissueId = Tissue.Id and
                        ProbeFreeze.InbredSetId = InbredSet.Id and
                        ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-                       ProbeSetFreeze.public > %s
-                       order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH))
-    return Cursor.fetchall()
-
+                       ProbeSetFreeze.public > 0
+                       order by Tissue.Name""", (species, group))
+    
+    results = []
+    for result in Cursor.fetchall():
+        if len(result):
+            results.append((result[0], result[0]))
+    
+    return results
 
 def get_datasets(types):
     """Build datasets list"""
@@ -111,9 +150,10 @@ def get_datasets(types):
     for species, group_dict in types.iteritems():
         datasets[species] = {}
         for group, type_list in group_dict.iteritems():
+            print("type_list: ", type_list)
             datasets[species][group] = {}
-            for type_name, _type_full_name in type_list:
-                datasets[species][group][type_name] = build_datasets(species, group, type_name)
+            for type_name in type_list:
+                datasets[species][group][type_name[0]] = build_datasets(species, group, type_name[0])
     return datasets
 
 
@@ -134,20 +174,30 @@ def build_datasets(species, group, type_name):
     if dataset_value:
         return [(dataset_value, dataset_text)]
     else:
+        print("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
+                    ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
+                    Species.Name = '{}' and Species.Id = InbredSet.SpeciesId and
+                    InbredSet.Name = '{}' and
+                    ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '{}'
+                    and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId =
+                    InbredSet.Id and ProbeSetFreeze.public > 0 order by
+                    ProbeSetFreeze.CreateTime desc""".format(species, group, type_name))
         Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
                     ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
                     Species.Name = %s and Species.Id = InbredSet.SpeciesId and
                     InbredSet.Name = %s and
                     ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s
                     and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId =
-                    InbredSet.Id and ProbeSetFreeze.public > %s order by
-                    ProbeSetFreeze.CreateTime desc""", (
-                        species, group, type_name, webqtlConfig.PUBLICTHRESH))
+                    InbredSet.Id and ProbeSetFreeze.public > 0 order by
+                    ProbeSetFreeze.CreateTime desc""", (species, group, type_name))
         return Cursor.fetchall()
 
 
 def main():
     """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
+
+    parse_db_uri(our_settings.DB_URI)
+
     species = get_species()
     groups = get_groups(species)
     types = get_types(groups)
@@ -167,6 +217,8 @@ def main():
                 datasets=datasets,
                 )
 
+    print("data:", data)
+
     output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json"""
 
     with open(output_file, 'w') as fh:
@@ -182,5 +234,7 @@ def _test_it():
     datasets = build_datasets("Mouse", "BXD", "Hippocampus")
     print("build_datasets:", pf(datasets))
 
-if __name__ == '__main__':
+if __name__ == '__main__':   
+    Conn = MySQLdb.Connect(**parse_db_uri(our_settings.DB_URI))
+    Cursor = Conn.cursor()
     main()