Merge branch 'master' of https://github.com/genenetwork/genenetwork2

2 files changed, 18 insertions, 23 deletions

diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 3d693a4c..a6efb47f 100755
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -5,6 +5,8 @@ from base.data_set import create_dataset
 from base.trait import GeneralTrait
 from dbFunction import webqtlDatabaseFunction
 
+from utility.benchmark import Bench
+
 class GSearch(object):
 
 	def __init__(self, kw):
@@ -37,17 +39,21 @@ class GSearch(object):
 				AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
 				AND ProbeSetFreeze.public > 0
 				ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
-				LIMIT 1000
+				LIMIT 6000
 				""" % (self.terms)
-			re = g.db.execute(sql).fetchall()
+			with Bench("Running query"):
+			    re = g.db.execute(sql).fetchall()
 			self.trait_list = []
-			for line in re:
-				dataset = create_dataset(line[3], "ProbeSet")
-				trait_id = line[4]
-				this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True)
-				self.trait_list.append(this_trait)
-				species = webqtlDatabaseFunction.retrieve_species(dataset.group.name)
-				dataset.get_trait_info([this_trait], species)
+			with Bench("Creating trait objects"):
+				for line in re:
+					dataset = create_dataset(line[3], "ProbeSet")
+					trait_id = line[4]
+					#with Bench("Building trait object"):
+					this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+					self.trait_list.append(this_trait)
+					species = webqtlDatabaseFunction.retrieve_species(dataset.group.name)
+					#with Bench("Getting trait info"):
+					dataset.get_trait_info([this_trait], species)
 
 		elif self.type == "phenotype":
 			sql = """
@@ -79,7 +85,7 @@ class GSearch(object):
 					OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" 
 					OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]")
 				ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
-				LIMIT 1000
+				LIMIT 6000
 				""" % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
 			re = g.db.execute(sql).fetchall()
 			self.trait_list = []
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 29239adb..0d463d5b 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -9,7 +9,6 @@
     <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.min.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
@@ -134,10 +133,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
-    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
-    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
-    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
@@ -200,10 +195,7 @@
                         { "bSortable": false },
                         { "type": "cust-txt" }
                         ],
-                    "buttons": [
-                        'csv'
-                    ],
-                    "sDom": "RZBtr",
+                    "sDom": "RZtr",
                     "iDisplayLength": -1,
                     "autoWidth": false,
                     "bLengthChange": true,
@@ -226,10 +218,7 @@
                         null,
                         { "type": "cust-txt" }
                     ],
-                    "buttons": [
-                        'csv'
-                    ],
-                    "sDom": "RZBtr",
+                    "sDom": "RZtr",
                     "iDisplayLength": -1,
                     "autoWidth": false,
                     "bLengthChange": true,