From 8c8cec89a03b642b671f191ce8a6079883fe5500 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sat, 6 Mar 2021 16:47:26 -0600
Subject: move geno chr, mb to gsearch main query for phenotype search

---
 wqflask/wqflask/gsearch.py | 47 +++++++++++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 17 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 262ba3c2..44a8f7f7 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -169,16 +169,23 @@ class GSearch:
                 PublishXRef.`LRS`,
                 PublishXRef.`additive`,
                 InbredSet.`InbredSetCode`,
-                PublishXRef.`mean`
-                FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
-                WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
-                AND PublishFreeze.`InbredSetId`=InbredSet.`Id`
-                AND InbredSet.`SpeciesId`=Species.`Id`
+                PublishXRef.`mean`,
+                PublishFreeze.Id,
+                Geno.Chr as geno_chr,
+                Geno.Mb as geno_mb 
+                FROM Species 
+                INNER JOIN InbredSet ON InbredSet.`SpeciesId`=Species.`Id` 
+                INNER JOIN PublishFreeze ON PublishFreeze.`InbredSetId`=InbredSet.`Id` 
+                INNER JOIN PublishXRef ON PublishXRef.`InbredSetId`=InbredSet.`Id` 
+                INNER JOIN Phenotype ON PublishXRef.`PhenotypeId`=Phenotype.`Id` 
+                INNER JOIN Publication ON PublishXRef.`PublicationId`=Publication.`Id` 
+                LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id 
+                WHERE 
+                (
+                    (MATCH (Phenotype.Post_publication_description, Phenotype.Pre_publication_description, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code) AGAINST ('{1}' IN BOOLEAN MODE) )
+                    OR (MATCH (Publication.Abstract, Publication.Title, Publication.Authors) AGAINST ('{1}' IN BOOLEAN MODE) )
+                )
                 {0}
-                AND PublishXRef.`PhenotypeId`=Phenotype.`Id`
-                AND PublishXRef.`PublicationId`=Publication.`Id`
-                AND	(MATCH (Phenotype.Post_publication_description, Phenotype.Pre_publication_description, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code) AGAINST ('{1}' IN BOOLEAN MODE) )
-                AND	(MATCH (Publication.Abstract, Publication.Title, Publication.Authors) AGAINST ('{1}' IN BOOLEAN MODE) )
                 ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
                 LIMIT 6000
                 """.format(group_clause, search_term)
@@ -213,6 +220,9 @@ class GSearch:
                         this_trait['mean'] = f"{line[13]:.3f}"
                     else:
                         this_trait['mean'] = "N/A"
+                    this_trait['dataset_id'] = line[14]
+                    this_trait['locus_chr'] = line[15]
+                    this_trait['locus_mb'] = line[16]
                     this_trait['authors'] = line[7]
                     this_trait['year'] = line[8]
                     if this_trait['year'].isdigit():
@@ -233,17 +243,20 @@ class GSearch:
                     if line[11] != "" and line[11] != None:
                         this_trait['additive'] = '%.3f' % line[11]
 
+                    dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"])
+                    permissions = check_resource_availability(dataset_ob, this_trait['name'])
+                    if type(permissions['data']) is list:
+                        if "view" not in permissions['data']:
+                            continue
+                    else:
+                        if permissions['data'] == 'no-access':
+                            continue
+
                     this_trait['max_lrs_text'] = "N/A"
-                    trait_ob = create_trait(
-                        dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
-                    if not trait_ob:
-                        continue
                     if this_trait['dataset'] == this_trait['group'] + "Publish":
                         try:
-                            if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
-                                this_trait['max_lrs_text'] = "Chr" + \
-                                    str(trait_ob.locus_chr) + \
-                                    ": " + str(trait_ob.locus_mb)
+                            if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None:
+                                this_trait['max_lrs_text'] = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb'])
                         except:
                             this_trait['max_lrs_text'] = "N/A"
 
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