Created quick_search_table.py to create table with all of the

information needed for the the quick search features (which searches
across all datasets)

2 files changed, 81 insertions, 10 deletions

diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py
new file mode 100644
index 00000000..a337a543
--- /dev/null
+++ b/wqflask/maintenance/quick_search_table.py
@@ -0,0 +1,50 @@
+from __future__ import print_function, division, absolute_import
+
+import sys
+sys.path.append("../../..")
+
+import sqlalchemy as sa
+from sqlalchemy.dialects import mysql
+from sqlalchemy.orm import scoped_session, sessionmaker, relationship, backref
+from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.ext.declarative import declarative_base
+
+import zach_settings as zs
+
+Engine = sa.create_engine(zs.SQLALCHEMY_DATABASE_URI,
+                       #encoding='utf-8',
+                       #client_encoding='utf-8',
+                       echo="debug",
+                       )
+
+Session = scoped_session(sessionmaker(bind=Engine)) #, extension=VersionedListener()))
+#Xsession = Session()
+
+Base = declarative_base(bind=Engine)
+Metadata = sa.MetaData()
+Metadata.bind = Engine
+
+
+class ProbeSet(Base):
+    __tablename__ = 'ProbeSet'
+    __table_args__ = {'autoload': True}
+
+def main():
+    for ps in page_query(Session.query(ProbeSet)):   #all()
+    #for ps in probe_sets:
+        print("--->", ps)
+        
+def page_query(q):
+    """http://stackoverflow.com/a/1217947/1175849"""
+    offset = 0
+    while True:
+        r = False
+        for elem in q.limit(1000).offset(offset):
+           r = True
+           yield elem
+        offset += 1000
+        if not r:
+            break
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1b1b56fb..bbb16054 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -13,6 +13,7 @@ sys.path.append("..")
 
 from dbFunction import webqtlDatabaseFunction
 
+from utility.benchmark import Bench
 
 class DoSearch(object):
     """Parent class containing parameters/functions used for all searches"""
@@ -63,9 +64,9 @@ class DoSearch(object):
 
 class QuickMrnaAssaySearch(DoSearch):
     """A general search for mRNA assays"""
-    
+
     DoSearch.search_types['quick_mrna_assay'] = "QuickMrnaAssaySearch"
-    
+
     base_query = """SELECT ProbeSet.Name as ProbeSet_Name,
                 ProbeSet.Symbol as ProbeSet_Symbol,
                 ProbeSet.description as ProbeSet_Description,
@@ -73,7 +74,7 @@ class QuickMrnaAssaySearch(DoSearch):
                 ProbeSet.Mb as ProbeSet_Mb,
                 ProbeSet.name_num as ProbeSet_name_num
                 FROM ProbeSet """
-                
+
     header_fields = ['',
                      'Record ID',
                      'Symbol',
@@ -190,6 +191,23 @@ class PhenotypeSearch(DoSearch):
                      'Max LRS',
                      'Max LRS Location']
 
+    #def get_fields_clause(self):
+    #    """Generate clause for WHERE portion of query"""
+    #
+    #    #Todo: Zach will figure out exactly what both these lines mean
+    #    #and comment here
+    #    if "'" not in self.search_term[0]:
+    #        search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]"
+    #
+    #    # This adds a clause to the query that matches the search term
+    #    # against each field in the search_fields tuple
+    #    fields_clause = []
+    #    for field in self.search_fields:
+    #        fields_clause.append('''%s REGEXP "%s"''' % (field, search_term))
+    #    fields_clause = "(%s) and " % ' OR '.join(fields_clause)
+    #
+    #    return fields_clause
+
     def get_fields_clause(self):
         """Generate clause for WHERE portion of query"""
 
@@ -200,13 +218,13 @@ class PhenotypeSearch(DoSearch):
 
         # This adds a clause to the query that matches the search term
         # against each field in the search_fields tuple
-        fields_clause = []
-        for field in self.search_fields:
-            fields_clause.append('''%s REGEXP "%s"''' % (field, search_term))
-        fields_clause = "(%s) and " % ' OR '.join(fields_clause)
+        fields_clause = "MATCH("
+        fields_clause += ",".join(self.search_fields) + ") "
+        fields_clause += "AGAINST('{}' IN BOOLEAN MODE)".format(self.search_term[0])
 
         return fields_clause
 
+
     def compile_final_query(self, from_clause = '', where_clause = ''):
         """Generates the final query string"""
 
@@ -262,13 +280,13 @@ class QuickPhenotypeSearch(PhenotypeSearch):
                     'Publication.PubMed_ID',
                     'Publication.Abstract',
                     'Publication.Title',
-                    'Publication.Authors')    
+                    'Publication.Authors')
     
     def compile_final_query(self, where_clause = ''):
         """Generates the final query string"""
 
         query = (self.base_query +
-                 """WHERE %s
+                 """WHERE (%s) and
                     PublishXRef.PhenotypeId = Phenotype.Id and
                     PublishXRef.PublicationId = Publication.Id and
                     PublishXRef.InbredSetId = InbredSet.Id and
@@ -283,7 +301,10 @@ class QuickPhenotypeSearch(PhenotypeSearch):
 
         query = self.compile_final_query(where_clause = self.get_fields_clause())
 
-        return self.execute(query)
+        with Bench("Doing quick phenotype search"):
+            results = self.execute(query)
+
+        return results
 
 class GenotypeSearch(DoSearch):
     """A search within a genotype dataset"""