From 15d15dc065752cdbc1b5959984a9aca3235545ca Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 22 Jun 2016 16:33:10 +0000
Subject: Search: taking search apart

---
 doc/Architecture.org              |  6 ++----
 wqflask/wqflask/do_search.py      |  1 +
 wqflask/wqflask/search_results.py | 23 ++++++++++++++++-------
 3 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/doc/Architecture.org b/doc/Architecture.org
index e8ffe69b..7736e2c1 100644
--- a/doc/Architecture.org
+++ b/doc/Architecture.org
@@ -29,8 +29,8 @@ When you hit a search with, for example,
 'http://localhost:5003/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29+&FormID=searchResult'
 it has the menu items as parameters. According to the routing table,
 the search is executed and Redis caching is used (we'll probably
-change that to gn_server). The logic is in search_result.py which
-invokes database functions in
+change that to the level of the gn_server). The logic is in
+search_result.py which invokes database functions in
 wqflask/dbFunction/webqtlDatabaseFunction.py, for example. The
 receiving template lives at [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/search_result_page.html][search_result_page.html]].
 
@@ -43,5 +43,3 @@ from the database. To get the menu data in YAML you can do something like
 : curl localhost:8880/int/menu/main.json|ruby extra/json2yaml.rb
 
 (json2yaml.rb is in the gn_server repo).
-
-
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 76bb15b2..7ee85929 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -39,6 +39,7 @@ class DoSearch(object):
         """Executes query and returns results"""
         query = self.normalize_spaces(query)
         logger.debug("in do_search query is:", pf(query))
+        @@
         results = g.db.execute(query, no_parameters=True).fetchall()
         return results
 
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 494e1047..1a034bdd 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -47,8 +47,11 @@ logger = getLogger(__name__ )
 class SearchResultPage(object):
     #maxReturn = 3000
 
-
     def __init__(self, kw):
+        """This class gets invoked after hitting submit on the main menu (in
+views.py).
+
+        """
 
         ###########################################
         #   Names and IDs of group / F2 set
@@ -67,9 +70,9 @@ class SearchResultPage(object):
         #else:
 
         self.uc_id = uuid.uuid4()
-        logger.debug("uc_id:", self.uc_id)
+        logger.debug("uc_id:", self.uc_id) # contains a unique id
 
-        logger.debug("kw is:", kw)
+        logger.debug("kw is:", kw)         # dict containing search terms
         if kw['search_terms_or']:
             self.and_or = "or"
             self.search_terms = kw['search_terms_or']
@@ -78,14 +81,14 @@ class SearchResultPage(object):
             self.search_terms = kw['search_terms_and']
         self.search_term_exists = True
         self.results = []
-        if kw['type'] == "Phenotypes":
+        if kw['type'] == "Phenotypes":     # split datatype on type field
             dataset_type = "Publish"
         elif kw['type'] == "Genotypes":
             dataset_type = "Geno"
         else:
-            dataset_type = "ProbeSet"
+            dataset_type = "ProbeSet"      # ProbeSet is default
         self.dataset = create_dataset(kw['dataset'], dataset_type)
-        logger.debug("KEYWORD:", self.search_terms)
+        logger.debug("search_terms:", self.search_terms)
         self.search()
         if self.search_term_exists:
             self.gen_search_result()
@@ -123,12 +126,16 @@ class SearchResultPage(object):
     #            self.species_groups[item['result_fields']['species']].append(
     #                                        item['result_fields']['group_name'])
 
-
     def search(self):
+        """This function sets up the actual search query in the form of a SQL
+statement and executes
+
+        """
         self.search_terms = parser.parse(self.search_terms)
         logger.debug("After parsing:", self.search_terms)
 
         if len(self.search_terms) > 1:
+            logger.debug("len(search_terms)>1")
             combined_from_clause = ""
             combined_where_clause = ""
             previous_from_clauses = [] #The same table can't be referenced twice in the from clause
@@ -155,9 +162,11 @@ class SearchResultPage(object):
             if self.search_term_exists:
                 combined_where_clause = "(" + combined_where_clause + ")"
                 final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause)
+                logger.debug(final_query)
                 results = the_search.execute(final_query)
                 self.results.extend(results)
         else:
+            logger.debug("len(search_terms)<=1")
             if self.search_terms == []:
                 self.search_term_exists = False
             else:
-- 
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