From 4417a7749b70ffd59020a30dee6cfab6d50efea0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 25 Feb 2020 13:27:37 -0600
Subject: Regular and global search should now support searches using the
 phenotype 3 letter codes and display them correctly in results

---
 wqflask/wqflask/do_search.py | 11 +++++------
 wqflask/wqflask/gsearch.py   | 34 ++++++++++++++++++++++------------
 2 files changed, 27 insertions(+), 18 deletions(-)

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 5cb06305..b56a858a 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -37,10 +37,6 @@ class DoSearch(object):
             logger.debug("self.dataset.group is: ", pf(self.dataset.group))
             #Get group information for dataset and the species id
 
-            if self.dataset.type == "Publish":
-                if len(self.search_term[0].split("_")) > 1:
-                    self.search_term[0] = self.search_term[0].split("_")[1]
-
             self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
 
     def execute(self, query):
@@ -234,8 +230,11 @@ class PhenotypeSearch(DoSearch):
         #Todo: Zach will figure out exactly what both these lines mean
         #and comment here
 
-        if "'" not in self.search_term[0]:
-            search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]"
+        #if "'" not in self.search_term[0]:
+        search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]"
+        if "_" in self.search_term[0]:
+            if len(self.search_term[0].split("_")[0]) == 3:
+                search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0].split("_")[1]) + "[[:>:]]"
 
         # This adds a clause to the query that matches the search term
         # against each field in the search_fields tuple
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 9e06abfe..b3a45f45 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -119,6 +119,12 @@ class GSearch(object):
                                 'Additive Effect']
 
         elif self.type == "phenotype":
+            search_term = self.terms
+            group_clause = ""
+            if "_" in self.terms:
+                if len(self.terms.split("_")[0]) == 3:
+                    search_term = self.terms.split("_")[1]
+                    group_clause = "AND InbredSet.`InbredSetCode` = '{}'".format(self.terms.split("_")[0])
             sql = """
                 SELECT
                 Species.`Name`,
@@ -138,21 +144,22 @@ class GSearch(object):
                 WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
                 AND PublishFreeze.`InbredSetId`=InbredSet.`Id`
                 AND InbredSet.`SpeciesId`=Species.`Id`
+                {0}
                 AND PublishXRef.`PhenotypeId`=Phenotype.`Id`
                 AND PublishXRef.`PublicationId`=Publication.`Id`
-                AND	  (Phenotype.Post_publication_description REGEXP "[[:<:]]%s[[:>:]]"
-                    OR Phenotype.Pre_publication_description REGEXP "[[:<:]]%s[[:>:]]"
-                    OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]"
-                    OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]"
-                    OR Phenotype.Lab_code REGEXP "[[:<:]]%s[[:>:]]"
-                    OR Publication.PubMed_ID REGEXP "[[:<:]]%s[[:>:]]"
-                    OR Publication.Abstract REGEXP "[[:<:]]%s[[:>:]]"
-                    OR Publication.Title REGEXP "[[:<:]]%s[[:>:]]"
-                    OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]"
-                    OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]")
+                AND	  (Phenotype.Post_publication_description REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR Phenotype.Pre_publication_description REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR Phenotype.Lab_code REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR Publication.PubMed_ID REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR Publication.Abstract REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR Publication.Title REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR Publication.Authors REGEXP "[[:<:]]{1}[[:>:]]"
+                    OR PublishXRef.Id REGEXP "[[:<:]]{1}[[:>:]]")
                 ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
                 LIMIT 6000
-                """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
+                """.format(group_clause, search_term)
             logger.sql(sql)
             re = g.db.execute(sql).fetchall()
             trait_list = []
@@ -161,7 +168,10 @@ class GSearch(object):
                     this_trait = {}
                     this_trait['index'] = i + 1
                     this_trait['name'] = str(line[4])
-                    this_trait['display_name'] = this_trait['name']
+                    if len(str(line[12])) == 3:
+                        this_trait['display_name'] = str(line[12]) + "_" + this_trait['name']
+                    else:
+                        this_trait['display_name'] = this_trait['name']
                     this_trait['dataset'] = line[2]
                     this_trait['dataset_fullname'] = line[3]
                     this_trait['hmac'] = user_manager.data_hmac('{}:{}'.format(line[4], line[2]))
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