mRNA Assay searches without trait creation should work now

2 files changed, 36 insertions, 38 deletions

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1478d2b6..4448e81e 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -78,16 +78,31 @@ class MrnaAssaySearch(DoSearch):
 
     DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch"
 
-    base_query = """SELECT distinct ProbeSet.Name as TNAME,
-                0 as thistable,
-                ProbeSetXRef.Mean as TMEAN,
-                ProbeSetXRef.LRS as TLRS,
-                ProbeSetXRef.PVALUE as TPVALUE,
-                ProbeSet.Chr_num as TCHR_NUM,
-                ProbeSet.Mb as TMB,
-                ProbeSet.Symbol as TSYMBOL,
-                ProbeSet.name_num as TNAME_NUM
-                FROM ProbeSetXRef, ProbeSet """
+    base_query = """
+                SELECT
+                ProbeSetFreeze.`Name`,
+                ProbeSetFreeze.`FullName`,
+                ProbeSet.`Name`,
+                ProbeSet.`Symbol`,
+                CAST(ProbeSet.`description` AS BINARY),
+                CAST(ProbeSet.`Probe_Target_Description` AS BINARY),
+                ProbeSet.`Chr`,
+                ProbeSet.`Mb`,
+                ProbeSetXRef.`Mean`,
+                ProbeSetXRef.`LRS`,
+                ProbeSetXRef.`Locus`,
+                ProbeSetXRef.`pValue`,
+                ProbeSetXRef.`additive`,
+                Geno.`Chr` as geno_chr,
+                Geno.`Mb` as geno_mb
+                FROM Species
+                INNER JOIN InbredSet ON InbredSet.`SpeciesId`= Species.`Id`
+                INNER JOIN ProbeFreeze ON ProbeFreeze.`InbredSetId` = InbredSet.`Id`
+                INNER JOIN Tissue ON ProbeFreeze.`TissueId` = Tissue.`Id`
+                INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.`ProbeFreezeId` = ProbeFreeze.`Id`
+                INNER JOIN ProbeSetXRef ON ProbeSetXRef.`ProbeSetFreezeId` = ProbeSetFreeze.`Id`
+                INNER JOIN ProbeSet ON ProbeSet.`Id` = ProbeSetXRef.`ProbeSetId`
+                LEFT JOIN Geno ON ProbeSetXRef.`Locus` = Geno.`Name` AND Geno.`SpeciesId` = Species.`Id` """
 
     header_fields = ['Index',
                      'Record',
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index b8e9f5de..97cc6581 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -130,38 +130,21 @@ class SearchResultPage(object):
             trait_dict['dataset'] = self.dataset.name
             trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait_dict['name'], trait_dict['dataset']))
             if self.dataset.type == "ProbeSet":
-                trait_dict['symbol'] = "N/A"
-                if result[10]:
-                    trait_dict['symbol'] = result[10]
-                trait_dict['description'] = "N/A"
-                description_string = result[2]
-                if str(description_string) != "" and description_string != None:
-                    description_display = description_string
-                else:
-                    description_display = trait_dict['symbol']
+                trait_dict['symbol'] = "N/A" if result[3] is None else result[3].strip()
+                description_text = "N/A" if result[4] is None or str(result[4]) == "" else trait_dict['symbol']
 
-                target_string = result[3]
-                if str(target_string) != "" and target_string != None:
-                    description_display = description_display + "; " + target_string.strip()
+                target_string = result[5]
+                description_display = description_text if target_string is None or str(target_string) == "" else description_text + "; " + str(target_string).strip()
                 trait_dict['description'] = description_display
 
                 trait_dict['location'] = "N/A"
-                if (result[8] != "NULL" and result[8] != "") and (result[9] != 0):
-                    trait_dict['location'] = f"Chr{result[8]}: {float(result[9]):.6f}"
-                trait_dict['mean'] = "N/A"
-                trait_dict['additive'] = "N/A"
-                if result[4] != "" and result[4] != None:
-                    trait_dict['mean'] = f"{result[4]:.3f}"
-                try:
-                    trait_dict['lod_score'] = f"{float(result[5]) / 4.61:.1f}"
-                except:
-                    trait_dict['lod_score'] = "N/A"
-                try:
-                    trait_dict['lrs_location'] = f"Chr{result[12]}: {float(result[13]):.6f}"
-                except:
-                    trait_dict['lrs_location'] = "N/A"
-                if result[5] != "":
-                    trait_dict['additive'] = f"{result[7]:.3f}"
+                if (result[6] is not None) and (result[6] != "") and (result[7] is not None) and (result[7] != 0):
+                    trait_dict['location'] = f"Chr{result[6]}: {float(result[7]):.6f}"
+
+                trait_dict['mean'] = "N/A" if result[8] is None or result[8] == "" else f"{result[8]:.3f}"
+                trait_dict['additive'] = "N/A" if result[12] is None or result[12] == "" else f"{result[12]:.3f}"
+                trait_dict['lod_score'] = "N/A" if result[9] is None or result[9] == "" else f"{float(result[9]) / 4.61:.1f}"
+                trait_dict['lrs_location'] = "N/A" if result[13] is None or result[13] == "" or result[14] is None else f"Chr{result[13]}: {float(result[14]):.6f}"
             elif self.dataset.type == "Geno":
                 trait_dict['location'] = "N/A"
                 if (result[4] != "NULL" and result[4] != "") and (result[5] != 0):