From 82bcb31455d658a462bfde711c862480fc9acd05 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 25 Oct 2012 18:09:11 -0500
Subject: Worked on search page code; got to the part that actually does the
search
Renamed RISet and cross to "group" throughout webqtlDataset.py and search_results.py
---
wqflask/base/webqtlDataset.py | 28 +-
wqflask/wqflask/search_results.py | 215 ++++-----
wqflask/wqflask/templates/index_page.html | 669 +++++++++++++++-----------
wqflask/wqflask/templates/new_index_page.html | 423 ----------------
wqflask/wqflask/templates/old_index_page.html | 320 ++++++++++++
wqflask/wqflask/views.py | 7 -
6 files changed, 821 insertions(+), 841 deletions(-)
delete mode 100644 wqflask/wqflask/templates/new_index_page.html
create mode 100644 wqflask/wqflask/templates/old_index_page.html
(limited to 'wqflask')
diff --git a/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py
index 4f98e90c..933077fd 100755
--- a/wqflask/base/webqtlDataset.py
+++ b/wqflask/base/webqtlDataset.py
@@ -34,6 +34,7 @@ class webqtlDataset:
"""
Dataset class defines a dataset in webqtl, can be either Microarray,
Published phenotype, genotype, or user input dataset(temp)
+
"""
def __init__(self, dbName, cursor=None):
@@ -42,7 +43,7 @@ class webqtlDataset:
self.id = 0
self.name = ''
self.type = ''
- self.riset = ''
+ self.group = ''
self.cursor = cursor
#temporary storage
@@ -81,14 +82,15 @@ class webqtlDataset:
self.name = dbName
if self.cursor and self.id == 0:
self.retrieveName()
-
- def __str__(self):
- return self.name
-
- __repr__ = __str__
+
+
+ # Delete this eventually
+ @property
+ def riset():
+ Weve_Renamed_This_As_Group
- def getRISet(self):
+ def get_group(self):
assert self.cursor
if self.type == 'Publish':
query = '''
@@ -124,12 +126,12 @@ class webqtlDataset:
else:
return ""
self.cursor.execute(query)
- RISet, RIID = self.cursor.fetchone()
- if RISet == 'BXD300':
- RISet = "BXD"
- self.riset = RISet
- self.risetid = RIID
- return RISet
+ group, RIID = self.cursor.fetchone()
+ if group == 'BXD300':
+ group = "BXD"
+ self.group = group
+ self.group_id = RIID
+ return group
def retrieveName(self):
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 1b846771..2269b9e7 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -36,17 +36,9 @@ from wqflask import parser
from utility import webqtlUtil
from dbFunction import webqtlDatabaseFunction
-#import logging
-#logging.basicConfig(filename=app.config['LOGFILE'], level=logging.INFO)
-#
-#_log = logging.getLogger("search")
-#_ch = logging.StreamHandler()
-#_log.addHandler(_ch)
-
from utility import formatting
import sys
-#_log.info("sys.path is: %s" % (sys.path))
#from base.JinjaPage import JinjaEnv, JinjaPage
@@ -64,116 +56,112 @@ class SearchResultPage(templatePage):
import logging_tree
logging_tree.printout()
self.fd = fd
- if not self.openMysql():
- print("ge0")
- #return
-
- print("Start...")
- print("Type of fd:", type(fd))
- print("Value of fd:", pf(fd))
- database = [fd['database']]
- print("End...")
-
- # change back to self.database
- if not self.database or self.database == 'spacer':
- #Error, No database selected
+ templatePage.__init__(self, fd)
+ assert self.openMysql(), "Couldn't open MySQL"
+
+ print("fd is:", pf(fd))
+ self.dataset = fd['dataset']
+
+ # change back to self.dataset
+ if not self.dataset or self.dataset == 'spacer':
+ #Error, No dataset selected
heading = "Search Result"
- detail = ['''No database was selected for this search, please
- go back and SELECT at least one database.''']
- print("ge0.6")
- self.error(heading=heading,detail=detail,error="No Database Selected")
- #return
+ detail = ['''No dataset was selected for this search, please
+ go back and SELECT at least one dataset.''']
+ self.error(heading=heading,detail=detail,error="No dataset Selected")
+ return
- print("ge1")
###########################################
# Names and IDs of RISet / F2 set
###########################################
- if self.database == ['_allPublish']:
+ if self.dataset == "All Phenotypes":
self.cursor.execute("""
select PublishFreeze.Name, InbredSet.Name, InbredSet.Id from PublishFreeze,
InbredSet where PublishFreeze.Name not like 'BXD300%' and InbredSet.Id =
PublishFreeze.InbredSetId""")
results = self.cursor.fetchall()
- self.database = map(lambda x: webqtlDataset(x[0], self.cursor), results)
- self.databaseCrosses = map(lambda x: x[1], results)
- self.databaseCrossIds = map(lambda x: x[2], results)
- self.singleCross = False
+ self.dataset = map(lambda x: webqtlDataset(x[0], self.cursor), results)
+ self.datasetGroups = map(lambda x: x[1], results)
+ self.datasetGroupIds = map(lambda x: x[2], results)
+ self.single_group = False
else:
- self.database = map(lambda x: webqtlDataset(x, self.cursor), self.database)
+ print("self.dataset is:", pf(self.dataset))
+ self.dataset = webqtlDataset(self.dataset, self.cursor)
+ print("self.dataset is now:", pf(self.dataset))
+ #self.dataset = map(lambda x: webqtlDataset(x, self.cursor), self.dataset)
#currently, webqtl won't allow multiple crosses
#for other than multiple publish db search
- #so we can use the first database as example
- if self.database[0].type=="Publish":
- pass
- elif self.database[0].type in ("Geno", "ProbeSet"):
+ #so we can use the first dataset as example
+ #if self.dataset.type=="Publish":
+ # pass
+ if self.dataset.type in ("Geno", "ProbeSet"):
#userExist = None
-
- for individualDB in self.database:
- # Can't use paramater substitution for table names apparently
- db_type = self.database[0].type + "Freeze"
- print("db_type [%s]: %s" % (type(db_type), db_type))
-
- query = '''SELECT Id, Name, FullName, confidentiality,
- AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type)
-
- self.cursor.execute(query, (individualDB,))
-
- (indId,
- indName,
- indFullName,
- confidential,
- AuthorisedUsers) = self.cursor.fetchall()[0]
-
- if confidential:
- access_to_confidential_dataset = 0
-
- #for the dataset that confidentiality is 1
- #1. 'admin' and 'root' can see all of the dataset
- #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
- if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
- access_to_confidential_dataset = 1
- else:
- AuthorisedUsersList=AuthorisedUsers.split(',')
- if AuthorisedUsersList.__contains__(self.userName):
- access_to_confidential_dataset = 1
-
- if not access_to_confidential_dataset:
- #Error, No database selected
- heading = "Search Result"
- detail = ["The %s database you selected is not open to the public at this time, please go back and SELECT other database." % indFullName]
- self.error(heading=heading,detail=detail,error="Confidential Database")
- return
- else:
- heading = "Search Result"
- detail = ['''The database has not been established yet, please
- go back and SELECT at least one database.''']
- self.error(heading=heading,detail=detail,error="No Database Selected")
- return
-
- print("ge2")
- self.database[0].getRISet()
- self.databaseCrosses = [self.database[0].riset]
- self.databaseCrossIds = [self.database[0].risetid]
- self.singleCross = True
- #XZ, August 24,2010: Since self.singleCross = True, it's safe to assign one species Id.
- self.speciesId = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.database[0].riset)
+ # Can't use paramater substitution for table names apparently
+ db_type = self.dataset.type + "Freeze"
+ print("db_type [%s]: %s" % (type(db_type), db_type))
+
+ query = '''SELECT Id, Name, FullName, confidentiality,
+ AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type)
+
+ self.cursor.execute(query, self.dataset.name)
+
+ (indId,
+ indName,
+ indFullName,
+ confidential,
+ AuthorisedUsers) = self.cursor.fetchall()[0]
+
+ if confidential:
+ # Allow confidential data later
+ NoConfindetialDataForYouTodaySorry
+ #access_to_confidential_dataset = 0
+ #
+ ##for the dataset that confidentiality is 1
+ ##1. 'admin' and 'root' can see all of the dataset
+ ##2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
+ #if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
+ # access_to_confidential_dataset = 1
+ #else:
+ # AuthorisedUsersList=AuthorisedUsers.split(',')
+ # if AuthorisedUsersList.__contains__(self.userName):
+ # access_to_confidential_dataset = 1
+ #
+ #if not access_to_confidential_dataset:
+ # #Error, No dataset selected
+ # heading = "Search Result"
+ # detail = ["The %s dataset you selected is not open to the public at this time, please go back and SELECT other dataset." % indFullName]
+ # self.error(heading=heading,detail=detail,error="Confidential dataset")
+ # return
+ #else:
+ # heading = "Search Result"
+ # detail = ['''The dataset has not been established yet, please
+ # go back and SELECT at least one dataset.''']
+ # self.error(heading=heading,detail=detail,error="No dataset Selected")
+ # return
+
+ self.dataset.get_group()
+ self.single_group = True
+ #XZ, August 24,2010: Since self.single_group = True, it's safe to assign one species Id.
+ self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor,
+ self.dataset.group)
###########################################
- # make sure search from same type of databases
+ # make sure search from same type of datasets
###########################################
- #dbTypes = map(lambda X: X.type, self.database)
- dbTypes = [table.type for table in self.database]
- self.dbType = dbTypes[0]
- for item in dbTypes:
- if item != self.dbType:
- heading = "Search Result"
- detail = ["Search can only be performed among the same type of databases"]
- self.error(heading=heading,detail=detail,error="Error")
- return
-
- print("ge3")
- if self.dbType == "Publish":
+ #dbTypes = map(lambda X: X.type, self.dataset)
+ #db_types = [table.type for table in self.dataset]
+ #self.db_type = db_types[0]
+ #for item in dbTypes:
+ # if item != self.dbType:
+ # heading = "Search Result"
+ # detail = ["Search can only be performed among the same type of datasets"]
+ # self.error(heading=heading,detail=detail,error="Error")
+ # return
+
+
+ #self.db_type = self.dataset.type
+ if self.dataset.type == "Publish":
self.searchField = ['Phenotype.Post_publication_description',
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
@@ -185,7 +173,7 @@ class SearchResultPage(templatePage):
'Publication.Authors',
'PublishXRef.Id']
- elif self.dbType == "ProbeSet":
+ elif self.dataset.type == "ProbeSet":
self.searchField = ['Name',
'Description',
'Probe_Target_Description',
@@ -194,11 +182,12 @@ class SearchResultPage(templatePage):
'GenbankId',
'UniGeneId',
'RefSeq_TranscriptId']
- elif self.dbType == "Geno":
+ elif self.dataset.type == "Geno":
self.searchField = ['Name','Chr']
- print("ge4")
+
self.do_search()
+ self.gen_search_result()
###########################################
# Search Options
@@ -272,11 +261,11 @@ class SearchResultPage(templatePage):
# return
#self.nresults = self.executeQuery()
#
- #if len(self.database) > 1:
- # dbUrl = "Multiple phenotype databases"
+ #if len(self.dataset) > 1:
+ # dbUrl = "Multiple phenotype datasets"
# dbUrlLink = " were"
#else:
- # dbUrl = self.database[0].genHTML()
+ # dbUrl = self.dataset[0].genHTML()
# dbUrlLink = " was"
#SearchText = HT.Blockquote('GeneNetwork searched the ', dbUrl, ' for all records ')
@@ -355,17 +344,13 @@ class SearchResultPage(templatePage):
#TD_LR.append(HT.Paragraph('Search Results', Class="title"), SearchText)
- self.start_search()
- self.genSearchResultTable()
#self.dict['body'] = str(TD_LR)
#self.dict['js1'] = ''
#self.dict['js2'] = 'onLoad="pageOffset()"'
#self.dict['layer'] = self.generateWarningLayer()
- def start_search(self):
- pass
- def genSearchResultTable(self):
+ def gen_search_result(self):
#pageTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="100%",border=0)
@@ -399,8 +384,8 @@ class SearchResultPage(templatePage):
#tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0)
#seq = self.pageNumber*self.NPerPage+1 //Edited out because we show all results in one page now - Zach 2/22/11
seq = 1
- RISet = self.databaseCrosses[i]
- self.thisFormName = thisFormName = 'showDatabase'+RISet
+ group = self.databaseCrosses[i]
+ self.thisFormName = thisFormName = 'showDatabase'+group
#selectall = HT.Href(url="#", onClick="checkAll(document.getElementsByName('%s')[0]);" % thisFormName)
#selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
#selectall.append(selectall_img)
@@ -423,7 +408,7 @@ class SearchResultPage(templatePage):
tblobj = {}
mainfmName = thisFormName
- species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=RISet)
+ species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=group)
if thisTrait.db.type=="Geno":
tblobj['header'] = self.getTableHeaderForGeno(worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
@@ -480,7 +465,7 @@ class SearchResultPage(templatePage):
#traitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=thisFormName, submit=HT.Input(type='hidden'))
- hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':RISet}
+ hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','group':group}
hddn['incparentsf1']='ON'
# for key in hddn.keys():
# traitForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index db0b2d9e..695129a9 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -1,320 +1,423 @@
-{% extends "base.html" %}
-{% block title %}GeneNetwork{% endblock %}
-{% block content %}
- <!-- Start of body -->
- <tr>
- <td bgcolor="#EEEEEE" class="solidBorder">
- <table width="100%" cellspacing="0" cellpadding="5">
- <tr>
- <td valign="top" width="40%" align="left" height="10" bgcolor="#EEEEEE">
- <p style="font-size:18px;font-family:verdana;color:black"><b>Select and
- Search</b></p>
-
- <form method="get" action="/search" class="form-search" name="SEARCHFORM">
- <table width="100%">
- <!-- SPECIES SELECTION -->
-
- <tr>
- <td align="right" height="35" style=
- "font-size:14px;font-family:verdana;color:black" width="16%">
- <b>Species:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left">
- <div id="menu0">
- <select name="species" size="1" id="species" onchange=
- "fillOptions('species');">
- </select>
- </div>
- </td>
- </tr><!-- GROUP SELECTION -->
-
- <tr>
- <td align="right" height="35" style=
- "font-size:14px;font-family:verdana;color:black"><b>Group:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left">
- <div id="menu1">
- <select name="cross" size="1" id="cross" onchange="fillOptions('cross');">
- </select> <input type="button" class="btn" value="Info" onclick=
- "javascript:crossinfo();">
- </div>
- </td>
- </tr><!-- TYPE SELECTION -->
-
- <tr>
- <td align="right" height="35" style=
- "font-size:14px;font-family:verdana;color:black"><b>Type:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left">
- <div id="menu2">
- <select name="tissue" size="1" id="tissue" onchange=
- "fillOptions('tissue');">
- </select>
- </div>
- </td>
- </tr><!-- DATABASE SELECTION -->
-
- <tr>
- <td align="right" height="35" style=
- "font-size:14px;font-family:verdana;color:black"><b>Database:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left">
- <div id="menu3">
- <select name="database" size="1" id="database">
- </select> <input type="submit" class="btn" value="Info" name=
- "info_database">
- </div>
- </td>
- </tr><!-- USER HELP -->
-
- <tr>
- <td align="right" height="20" width="10%"></td>
-
- <td width="3%"></td>
-
- <td align="left" width="85%">
- <p class="fs12"> Databases marked with <b>**</b>
- suffix are not public yet.<br>
- Access requires <a href="/account.html" target=
- "_blank" class="fs14"><small>user login</small></a>.</p>
- </td>
- </tr><!-- GET ANY SEARCH -->
-
- <tr>
- <td align="right" height="35" nowrap="on" style=
- "font-size:14px;font-family:verdana;color:black" width="10%">
- <b>Search:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left"><input class="input-medium search-query"
- id="tfor" name="search_terms" style=
- "width:420px; background-color:white; font-family:verdana; font-size:14px"
- type="text" maxlength="500"></td>
- </tr><!-- GET ANY HELP -->
-
- <tr>
- <td align="right" height="20" width="10%"></td>
-
- <td width="3%"></td>
-
- <td width="85%" align="left">
- <p class="fs12"> Enter terms, genes, ID numbers in the
- <b>Search</b> field.<br>
- Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
- synap*).<br>
- Use <b>quotes</b> for terms such as <i>"tyrosine
- kinase"</i>.</p>
- </td>
- </tr><!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
-
- <tr align="center">
- <td width="3%"></td>
-
- <td width="3%"></td>
-
- <td align="left" height="40" colspan="3"><input id="btsearch" type="submit"
- class="btn btn-primary" value="Search"> <input type=
- "button" class="btn" value="Make Default" onclick=
- "setDefault(this.form);"> <input type="button" class=
- "btn" value="Advanced Search" onclick=
- "javascript:window.open('/index3.html', '_self');"></td>
- </tr>
- </table><input type="hidden" name="FormID" value="searchResult"> <input type=
- "hidden" name="RISet" value="BXD"> <script src="/javascript/selectDatasetMenu.js"
- type="text/javascript">
-</script>
- </form><!-- QUICK HELP -->
-
- <p> ______________________________________________________</p>
-
- <p style="font-size:13px;font-family:verdana;color:black"><b> Quick HELP
- Examples and</b> <a href="http://www.genenetwork.org/index4.html" target="_blank"
- class="fs14"><b>User's Guide</b></a></p> You can also use advanced
- commands. Copy these simple examples<br>
- into the <b>Get Any</b> or <b>Combined</b> search fields:
-
- <ul style="font-size:12px;font-family:verdana;color:black">
- <li><b><i>POSITION=(chr1 25 30)</i></b> finds genes, markers, or transcripts on
- chromosome 1 between 25 and 30 Mb.</li>
-
- <li><b><i>MEAN=(15 16) LRS=(23 46)</i></b> in the <b>Combined</b> field finds
- highly expressed genes (15 to 16 log2 units) AND with peak <a href=
- "http://www.genenetwork.org/glossary.html#L" target="_blank" class=
- "fs14"><small>LRS</small></a> linkage between 23 and 46.</li>
-
- <li><b><i>RIF=mitochondrial</i></b> searches RNA databases for <a href=
- "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank"
- class="fs14"><small>GeneRIF</small></a> links.</li>
-
- <li><b><i>WIKI=nicotine</i></b> searches <a href=
- "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank" class=
- "fs14"><small>GeneWiki</small></a> for genes that you or other users have annotated
- with the word <i>nicotine</i>.</li>
-
- <li><b><i>GO:0045202</i></b> searches for synapse-associated genes listed in the
- <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank" class=
- "fs14"><small>Gene Ontology</small></a>.</li>
-
- <li><b><i>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</i></b><br>
- in <b>Combined</b> finds synapse-associated genes with <a href=
- "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
- "fs14"><small>cis eQTL</small></a> on Chr 4 from 122 and 155 Mb with LRS scores
- between 9 and 999.</li>
-
- <li><b><i>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</i></b><br>
- in <b>Combined</b> finds diabetes-associated transcripts with peak <a href=
- "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
- "fs14"><small>trans eQTLs</small></a> on Chr 2 between 100 and 105 Mb with LRS
- scores between 9 and 999.</li>
+<!DOCTYPE html>
+<html lang="en">
+<head>
+ <meta charset="utf-8">
+ <title>GeneNetwork</title>
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <meta name="description" content="">
+ <meta name="author" content="">
+ <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.min.css" />
+ <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap-responsive.min.css" />
+ <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
+
+ <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
+ <!--[if lt IE 9]>
+ <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
+ <![endif]-->
+
+
+</head>
+
+<body data-spy="scroll" data-target=".bs-docs-sidebar">
+ <!-- Navbar
+ ================================================== -->
+ <div class="navbar navbar-inverse navbar-fixed-top">
+ <div class="navbar-inner">
+ <div class="container">
+ <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="brand" href="/">GeneNetwork</a>
+ <div class="nav-collapse collapse">
+ <ul class="nav">
+ <li class="active">
+ <a href="/">Home</a>
+ </li>
+ <li class="dropdown">
+ <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown">
+ Search <b class="caret"></b>
+ </a>
+ <ul class="dropdown-menu" role="menu" aria-labelledby="drop1">
+ <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li>
+ <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li>
+ <li class="divider"></li>
+ <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li>
+ </ul>
+ </li>
+ <li class="">
+ <a href="#">Help</a>
+ </li>
+ <li class="">
+ <a href="/whats_new">News</a>
+ </li>
+ <li class="">
+ <a href="./reference.html">References</a>
+ </li>
+ <li class="">
+ <a href="./policies">Policies</a>
+ </li>
+ <li class="">
+ <a href="./links">Links</a>
+ </li>
+ </ul>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <header class="jumbotron subhead" id="overview">
+ <div class="container">
+ <h1>GeneNetwork</h1>
+ <p class="lead">Open source bioinformatics for systems genetics<br />
+ Brought to you by the University of Tennessee</p>
+ </div>
+ </header>
+
+
+ <div class="container">
+ <div class="row">
+ <div class="span3 bs-docs-sidebar">
+ <ul class="nav nav-list bs-docs-sidenav">
+ <li><a href="#search"><i class="icon-chevron-right"></i> Search</a></li>
+ <li><a href="#getting-started"><i class="icon-chevron-right"></i> Getting started</a></li>
+ <li><a href="#advanced"><i class="icon-chevron-right"></i> Advanced commands</a></li>
+ <li><a href="#tour-info"><i class="icon-chevron-right"></i> Tour and more info</a></li>
+ <li><a href="#websites"><i class="icon-chevron-right"></i> Affiliates and mirrors</a></li>
</ul>
- </td><!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE) -->
- <!-- START OF TOP RIGHT PANEL -->
+ </div>
- <td valign="top" width="40%" bgcolor="#FFFFFF">
- <p style="font-size:15px;font-family:verdana;color:black"><b>Websites Affiliated with
- GeneNetwork</b></p>
+ <div class="span9">
+ <section id="search">
+ <div class="page-header">
+ <h1>Select and search</h1>
+ </div>
+ <form method="get" action="/search" name="SEARCHFORM">
+ <fieldset>
+ <!--<legend>Select and Search</legend>-->
+ <label for="species">Species:</label>
+ <select name="species" id="species" class="input-xlarge ds_selector">
+ </select>
- <p style="font-size:12px;font-family:verdana;color:black"></p>
+ <div class="input-append">
+ <label for="group">Group: </label>
+ <select name="group" id="group" class="input-xlarge ds_selector"></select>
+ <!--<i class="icon-question-sign"></i>-->
+ <input type="button" class="btn" value="Info" id="group_info" />
+ </div>
- <ul>
- <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
- Browser</a> at UTHSC</li>
- <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
- UTHSC</li>
+ <label for="tissue">Type:</label>
+ <select name="type" id="type" class="input-xlarge ds_selector"></select>
- <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
- Cloud (EC2)</a></li>
+ <div class="input-append">
+ <label for="dataset">Dataset:</label>
+ <select name="dataset" id="dataset" class="input-xlarge"></select>
+ <input type="button" class="btn" value="Info" id="dataset_info" />
+ </div>
+ <!-- USER HELP -->
- <li>GeneNetwork Source Codes at <a href=
- "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
- <li>GeneNetwork Source Codes at <a href=
- "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
- </ul>
+ <!--<p >Databases marked with <b>**</b>-->
+ <!-- suffix are not public yet.<br>-->
+ <!-- Access requires <a href="/account.html" target=-->
+ <!-- "_blank" class="fs14">user login</a>.</p>-->
- <p>____________________________</p>
+ <!-- GET ANY SEARCH -->
- <p style="font-size:15px;font-family:verdana;color:black"><b>Getting Started</b>
- </p>
+ <label for="tfor">Search:</label>
- <ol style="font-size:12px;font-family:verdana;color:black">
- <li>Select <b>Species</b> (or select All)</li>
+ <input class="search-query input-xlarge"
+ id="tfor" name="search_terms"
+ type="text" maxlength="500">
- <li>Select <b>Group</b> (a specific sample)</li>
+ <!-- GET ANY HELP -->
- <li>Select <b>Type</b> of data:
+ <p>Enter terms, genes, ID numbers in the
+ <b>Search</b> field<br>
+ Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
+ synap*)<br>
+ Use <b>quotes</b> for terms such as <i>"tyrosine
+ kinase"</i></p>
- <ul>
- <li>Phenotype (traits)</li>
+ <!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
- <li>Genotype (markers)</li>
- <li>Expression (mRNAs)</li>
- </ul>
- </li>
+ <input id="btsearch" type="submit"
+ class="btn btn-primary" value="Search">
- <li>Select a <b>Database</b></li>
+ <input type="button" class="btn" value="Make Default"
+ id="make_default">
- <li>Enter search terms in the <b>Get Any</b> or <b>Combined</b> field: words,
- genes, ID numbers, probes, advanced search commands</li>
+ <input type="button" class=
+ "btn" value="Advanced Search" onclick=
+ "javascript:window.open('/index3.html', '_self');">
- <li>Click on the <b>Search</b> button</li>
+ <input type="hidden" name="FormID" value="searchResult"> <input type=
+ "hidden" name="RISet" value="BXD">
+ </fieldset>
+ </form>
+ </section>
- <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
- </ol>
+ <section id="getting-started">
+ <div class="page-header">
+ <h1>Getting started</h1>
+ </div>
- <p>____________________________</p>
+ <ol style="font-size:12px;font-family:verdana;color:black">
+ <li>Select <b>Species</b> (or All)</li>
- <p style="font-size:14px;font-family:verdana;color:black"><b>How to Use
- GeneNetwork</b></p>
+ <li>Select <b>Group</b> (a specific sample)</li>
- <blockquote>
- <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute
- GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
- "_blank" class="fs14"><small>Tour</small></a> that includes screen shots and
- typical steps in the analysis.</p>
- </blockquote>
+ <li>Select <b>Type</b> of data:
- <blockquote>
- <p style="font-size:12px;font-family:verdana;color:black">For information about
- resources and methods, select the <img src=
- "http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border="0" valign=
- "middle"> buttons.</p>
+ <ul>
+ <li>Phenotype (traits)</li>
- <p style="font-size:12px;font-family:verdana;color:black">Try the <a href=
- "http://alexandria.uthsc.edu/" target="_blank" class=
- "fs14"><small>Workstation</small></a> site to explore data and features that are
- being implemented.</p>
+ <li>Genotype (markers)</li>
- <p style="font-size:12px;font-family:verdana;color:black">Review the <a href=
- "/conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></a>
- and <a href="/statusandContact.html" target="_blank" class=
- "fs14"><small>Contacts</small></a> pages for information on the status of data sets
- and advice on their use and citation.</p>
- </blockquote>
+ <li>Expression (mRNAs)</li>
+ </ul>
+ </li>
- <p style="font-size:14px;font-family:verdana;color:black"><b>Mirror and Development
- Sites</b></p>
+ <li>Select a <b>Database</b></li>
- <ul>
- <li><a href="http://www.genenetwork.org/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</a> (main
- site)</li>
+ <li>Enter terms in the search field: words,
+ genes, ID numbers, probes, advanced search commands</li>
- <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
+ <li>Click the <b>Search</b> button</li>
- <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
+ <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
+ </ol>
- <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
+ <h3>User Guide</h3>
+ <h5>Read the
+ <a href="http://www.genenetwork.org/index4.html" target="_blank">
+ user guide</a>.</h5>
- <li><a href="https://genenetwork.hubrecht.eu/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</a>
- (Development)</li>
+ </section>
- <li><a href="http://genenetwork.memphis.edu/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
- <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li>
+ <section id="advanced">
+ <div class="page-header">
+ <h1>Advanced commands</h1>
+ </div>
- <li><a href="http://genenetwork.epfl.ch/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
- </ul>
+ <p>GeneNetwork supports a variety of advanced searches.</p>
- <p style="font-size:14px;font-family:verdana;color:black"><b>History and
- Archive</b></p>
-
- <blockquote>
- <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <a href=
- "http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time
- Machine</small></a> links to earlier versions that correspond to specific
- publication dates.</p>
- </blockquote>
- </td>
- </tr>
- </table>
- </td>
- </tr>
- <!-- End of body -->
- <script src="/javascript/searchtip.js" type="text/javascript">
- </script>
- <script type="text/javascript">
- $(document).ready(function () {
- initialDatasetSelection();
- });
- </script>
-{% endblock %}
+ <p>To try them out copy these examples into the search field:</p>
+
+ <ul>
+ <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
+ chromosome 1 between 25 and 30 Mb.</li>
+ <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
+ highly expressed genes (15 to 16 log2 units) AND with peak <a href=
+ "http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
+ linkage between 23 and 46.</li>
+
+ <li><b>RIF=mitochondrial</b> searches RNA databases for <a href=
+ "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank">
+ GeneRIF</a> links.</li>
+
+ <li><b>WIKI=nicotine</b> searches <a href=
+ "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank">
+ GeneWiki</a> for genes that you or other users have annotated
+ with the word <i>nicotine</i>.</li>
+
+ <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
+ <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
+ Gene Ontology</a>.</li>
+
+ <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
+ finds synapse-associated genes with <a href=
+ "http://www.genenetwork.org/glossary.html#E" target="_blank">
+ cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
+ between 9 and 999.</li>
+
+ <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
+ finds diabetes-associated transcripts with peak <a href=
+ "http://www.genenetwork.org/glossary.html#E" target="_blank">
+ trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
+ scores between 9 and 999.</li>
+ </ul>
+ </section>
+
+ <section id="tour-info">
+ <div class="page-header">
+ <h1>Tour and more info</h1>
+ </div>
+
+ <h3>Thirty minute tour</h3>
+ <p>
+ Take the 30 minute
+ GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
+ "_blank" class="fs14">tour</a> that includes screen shots and
+ typical steps in the analysis.
+ </p>
+
+ <h3>Even more info</h3>
+ <p>
+ For information about
+ resources and methods, select the Info buttons next to the Group
+ and Database fields above.
+ </p>
+
+ <p>The <a href=
+ "/conditionsofUse.html" target="_blank">conditions</a>
+ and <a href="/statusandContact.html" target="_blank">contact
+ </a> pages have information on the status of data sets
+ and advice on their use and citation.</p>
+
+ </section>
+
+ <section id="websites">
+ <div class="page-header">
+ <h1>Affiliates and mirrors</h1>
+ </div>
+ <h3>Websites affiliated with GeneNetwork</h3>
+ <ul>
+ <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
+ browser</a> at UTHSC</li>
+
+ <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
+ UTHSC</li>
+
+ <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+ Cloud (EC2)</a></li>
+
+ <li>GeneNetwork Source Code at <a href=
+ "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+
+ <li>GeneNetwork Source Code at <a href=
+ "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
+ </ul>
+ <h3>Mirror and development sites</h3>
+ <ul>
+ <li><a href="http://www.genenetwork.org/" target="_blank">
+ Main GN site</a> at UTHSC</li>
+
+ <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">
+ Australia</a> at the UWA</li>
+
+ <li><a href="http://gn.genetics.ucla.edu/" target="_blank">
+ California</a> at UCLA</li>
+
+ <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">
+ Germany</a> at the HZI</li>
+
+ <li><a href="https://genenetwork.hubrecht.eu/" target="_blank">
+ Netherlands</a> at the Hubrecht
+ (development)</li>
+
+ <li><a href="http://genenetwork.memphis.edu/" target="_blank">
+ Memphis</a> at the U of M</li>
+
+ <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank">
+ Singapore</a> at the NUS</li>
+
+ <li><a href="http://genenetwork.epfl.ch/" target="_blank">
+ Switzerland</a> at the EPFL</li>
+ </ul>
+ <h3>History and archive</h3>
+
+ <p>The
+ <a href="http://artemis.uthsc.edu" target="_blank">
+ time machine</a>
+ has earlier versions that correspond to specific publication dates.
+ </p>
+
+ <h3>The next generation</h3>
+ <p>Try the <a href=
+ "http://alexandria.uthsc.edu/" target="_blank">
+ development</a> site to explore experimental data and features.</p>
+ </section>
+ </div>
+ </div>
+ </div>
+
+ <!-- Footer
+ ================================================== -->
+ <footer class="footer">
+ <div class="container">
+ <p class="pull-right"><a href="#">Back to top</a></p>
+
+ <p>Launched in 1994 as
+ <A HREF="http://www.ncbi.nlm.nih.gov/pubmed?term=8043953">
+ The Portable Dictionary of the Mouse Genome</A> and in 2001 as WebQTL.
+ </p>
+ <p>Operated by
+ <A HREF="mailto:rwilliams@uthsc.edu">Rob Williams</A>,
+ <A HREF="mailto:lyan6@uthsc.edu">Lei Yan</A>,
+ <A HREF="mailto:zachary.a.sloan@gmail.com">Zachary Sloan</A>, and
+ <A HREF="mailto:acenteno@uthsc.edu" target="_blank">Arthur Centeno</A>.
+ </p>
+ <p>
+ Designed and coded by <a href="http://penguinpython.com">Sam Ockman</a>, Xiaodong Zhou,
+ Christian Fernandez,
+ Ning Liu, Rudi Alberts, Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams,
+ and <A HREF="/credit.html">colleagues</A>.
+ </p>
+
+ <p>Built with <a href="http://twitter.github.com/bootstrap/">bootstrap</a>,
+ <a href="http://coffeescript.org/">coffeescript</a>,
+ <a href="http://flask.pocoo.org/">flask</a>,
+ <a href="http://en.wikipedia.org/wiki/Linux">linux</a>,
+ <a href="http://www.python.org/">python</a> and good intentions.
+ </p>
+ <p>Special thanks to CYP1A2 and AHR.</p>
+ <br />
+ <p>GeneNetwork is supported by:</p>
+ <UL>
+ <LI>
+ <a target="_blank" href="http://citg.uthsc.edu">
+ The UT Center for Integrative and Translational Genomics
+ </A>
+ </li>
+ <LI><a target="_blank" href="http://www.iniastress.org">NIAAA</A>
+ Integrative Neuroscience Initiative on Alcoholism
+ (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425)
+ </li>
+ <LI>
+ <a target="_blank"
+ href="http://www.drugabuse.gov/about/organization/Genetics/geneexpression/index.html">NIDA</A>, <a class="smallsize" target="_blank" href="http://www.nimh.nih.gov/">NIMH</A>
+ , and <a class="smallsize" target="_blank" href="http://www.niaaa.nih.gov/">
+ NIAAA</A> (P20-DA 21131)
+ </li>
+ <LI>NCI <a target="_blank" href="http://emice.nci.nih.gov/">MMHCC</A> (U01CA105417) and
+ <a target="_blank" href="http://www.ncrr.nih.gov/">NCRR</A>
+ <a target="_blank" href="http://www.nbirn.net/TestBeds/Mouse/index.htm">BIRN</A>
+ (U24 RR021760)
+ </li>
+ </UL>
+ <!--</p>-->
+
+ <ul class="footer-links">
+ <li><a href="http://atlas.uthsc.edu/mailman/listinfo/genenetwork" target="_blank">Join the mailing list</a></li>
+ <!--<li><a href="#">Friend us on facebook</a></li>-->
+ <!--<li><a href="#">Follow us on twitter</a></li>-->
+ </ul>
+ </div>
+ </footer>
+
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
+ <script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
+ <script>
+ //http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working
+ var $window = $(window)
+ $('.bs-docs-sidenav').affix({
+ offset: {
+ top: function () { return $window.width() <= 980 ? 290 : 210 }
+ , bottom: 270
+ }
+ })
+ </script>
+ <!--<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>-->
+ <!--<script src="/static/new/javascript/dataset_menu_structure.json"></script>-->
+ <!--<script src="/static/new/javascript/dataset_select_items.js"></script>-->
+ <script src="/static/new/js_external/jquery.cookie.js"></script>
+ <script type="text/javascript" src="/static/new/js_external/json2.js"></script>
+ <script src="/static/new/javascript/dataset_select_menu.js"></script>
+</body>
+</html>
diff --git a/wqflask/wqflask/templates/new_index_page.html b/wqflask/wqflask/templates/new_index_page.html
deleted file mode 100644
index 695129a9..00000000
--- a/wqflask/wqflask/templates/new_index_page.html
+++ /dev/null
@@ -1,423 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
- <meta charset="utf-8">
- <title>GeneNetwork</title>
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
- <meta name="description" content="">
- <meta name="author" content="">
- <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.min.css" />
- <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap-responsive.min.css" />
- <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
-
- <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
- <!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
- <![endif]-->
-
-
-</head>
-
-<body data-spy="scroll" data-target=".bs-docs-sidebar">
- <!-- Navbar
- ================================================== -->
- <div class="navbar navbar-inverse navbar-fixed-top">
- <div class="navbar-inner">
- <div class="container">
- <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
- <span class="icon-bar"></span>
- <span class="icon-bar"></span>
- <span class="icon-bar"></span>
- </button>
- <a class="brand" href="/">GeneNetwork</a>
- <div class="nav-collapse collapse">
- <ul class="nav">
- <li class="active">
- <a href="/">Home</a>
- </li>
- <li class="dropdown">
- <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown">
- Search <b class="caret"></b>
- </a>
- <ul class="dropdown-menu" role="menu" aria-labelledby="drop1">
- <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li>
- <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li>
- <li class="divider"></li>
- <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li>
- </ul>
- </li>
- <li class="">
- <a href="#">Help</a>
- </li>
- <li class="">
- <a href="/whats_new">News</a>
- </li>
- <li class="">
- <a href="./reference.html">References</a>
- </li>
- <li class="">
- <a href="./policies">Policies</a>
- </li>
- <li class="">
- <a href="./links">Links</a>
- </li>
- </ul>
- </div>
- </div>
- </div>
- </div>
-
- <header class="jumbotron subhead" id="overview">
- <div class="container">
- <h1>GeneNetwork</h1>
- <p class="lead">Open source bioinformatics for systems genetics<br />
- Brought to you by the University of Tennessee</p>
- </div>
- </header>
-
-
- <div class="container">
- <div class="row">
- <div class="span3 bs-docs-sidebar">
- <ul class="nav nav-list bs-docs-sidenav">
- <li><a href="#search"><i class="icon-chevron-right"></i> Search</a></li>
- <li><a href="#getting-started"><i class="icon-chevron-right"></i> Getting started</a></li>
- <li><a href="#advanced"><i class="icon-chevron-right"></i> Advanced commands</a></li>
- <li><a href="#tour-info"><i class="icon-chevron-right"></i> Tour and more info</a></li>
- <li><a href="#websites"><i class="icon-chevron-right"></i> Affiliates and mirrors</a></li>
- </ul>
- </div>
-
- <div class="span9">
- <section id="search">
- <div class="page-header">
- <h1>Select and search</h1>
- </div>
- <form method="get" action="/search" name="SEARCHFORM">
- <fieldset>
- <!--<legend>Select and Search</legend>-->
- <label for="species">Species:</label>
- <select name="species" id="species" class="input-xlarge ds_selector">
- </select>
-
- <div class="input-append">
- <label for="group">Group: </label>
- <select name="group" id="group" class="input-xlarge ds_selector"></select>
- <!--<i class="icon-question-sign"></i>-->
- <input type="button" class="btn" value="Info" id="group_info" />
- </div>
-
-
- <label for="tissue">Type:</label>
- <select name="type" id="type" class="input-xlarge ds_selector"></select>
-
- <div class="input-append">
- <label for="dataset">Dataset:</label>
- <select name="dataset" id="dataset" class="input-xlarge"></select>
- <input type="button" class="btn" value="Info" id="dataset_info" />
- </div>
- <!-- USER HELP -->
-
-
- <!--<p >Databases marked with <b>**</b>-->
- <!-- suffix are not public yet.<br>-->
- <!-- Access requires <a href="/account.html" target=-->
- <!-- "_blank" class="fs14">user login</a>.</p>-->
-
- <!-- GET ANY SEARCH -->
-
- <label for="tfor">Search:</label>
-
- <input class="search-query input-xlarge"
- id="tfor" name="search_terms"
- type="text" maxlength="500">
-
- <!-- GET ANY HELP -->
-
- <p>Enter terms, genes, ID numbers in the
- <b>Search</b> field<br>
- Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
- synap*)<br>
- Use <b>quotes</b> for terms such as <i>"tyrosine
- kinase"</i></p>
-
- <!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
-
-
- <input id="btsearch" type="submit"
- class="btn btn-primary" value="Search">
-
- <input type="button" class="btn" value="Make Default"
- id="make_default">
-
- <input type="button" class=
- "btn" value="Advanced Search" onclick=
- "javascript:window.open('/index3.html', '_self');">
-
- <input type="hidden" name="FormID" value="searchResult"> <input type=
- "hidden" name="RISet" value="BXD">
- </fieldset>
- </form>
- </section>
-
- <section id="getting-started">
- <div class="page-header">
- <h1>Getting started</h1>
- </div>
-
- <ol style="font-size:12px;font-family:verdana;color:black">
- <li>Select <b>Species</b> (or All)</li>
-
- <li>Select <b>Group</b> (a specific sample)</li>
-
- <li>Select <b>Type</b> of data:
-
- <ul>
- <li>Phenotype (traits)</li>
-
- <li>Genotype (markers)</li>
-
- <li>Expression (mRNAs)</li>
- </ul>
- </li>
-
- <li>Select a <b>Database</b></li>
-
- <li>Enter terms in the search field: words,
- genes, ID numbers, probes, advanced search commands</li>
-
- <li>Click the <b>Search</b> button</li>
-
- <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
- </ol>
-
- <h3>User Guide</h3>
- <h5>Read the
- <a href="http://www.genenetwork.org/index4.html" target="_blank">
- user guide</a>.</h5>
-
- </section>
-
-
- <section id="advanced">
- <div class="page-header">
- <h1>Advanced commands</h1>
- </div>
-
- <p>GeneNetwork supports a variety of advanced searches.</p>
-
- <p>To try them out copy these examples into the search field:</p>
-
- <ul>
- <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
- chromosome 1 between 25 and 30 Mb.</li>
-
- <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
- highly expressed genes (15 to 16 log2 units) AND with peak <a href=
- "http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
- linkage between 23 and 46.</li>
-
- <li><b>RIF=mitochondrial</b> searches RNA databases for <a href=
- "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank">
- GeneRIF</a> links.</li>
-
- <li><b>WIKI=nicotine</b> searches <a href=
- "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank">
- GeneWiki</a> for genes that you or other users have annotated
- with the word <i>nicotine</i>.</li>
-
- <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
- <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
- Gene Ontology</a>.</li>
-
- <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
- finds synapse-associated genes with <a href=
- "http://www.genenetwork.org/glossary.html#E" target="_blank">
- cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
- between 9 and 999.</li>
-
- <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
- finds diabetes-associated transcripts with peak <a href=
- "http://www.genenetwork.org/glossary.html#E" target="_blank">
- trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
- scores between 9 and 999.</li>
- </ul>
- </section>
-
- <section id="tour-info">
- <div class="page-header">
- <h1>Tour and more info</h1>
- </div>
-
- <h3>Thirty minute tour</h3>
- <p>
- Take the 30 minute
- GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
- "_blank" class="fs14">tour</a> that includes screen shots and
- typical steps in the analysis.
- </p>
-
- <h3>Even more info</h3>
- <p>
- For information about
- resources and methods, select the Info buttons next to the Group
- and Database fields above.
- </p>
-
- <p>The <a href=
- "/conditionsofUse.html" target="_blank">conditions</a>
- and <a href="/statusandContact.html" target="_blank">contact
- </a> pages have information on the status of data sets
- and advice on their use and citation.</p>
-
- </section>
-
- <section id="websites">
- <div class="page-header">
- <h1>Affiliates and mirrors</h1>
- </div>
- <h3>Websites affiliated with GeneNetwork</h3>
- <ul>
- <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
- browser</a> at UTHSC</li>
-
- <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
- UTHSC</li>
-
- <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
- Cloud (EC2)</a></li>
-
- <li>GeneNetwork Source Code at <a href=
- "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
-
- <li>GeneNetwork Source Code at <a href=
- "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
- </ul>
- <h3>Mirror and development sites</h3>
- <ul>
- <li><a href="http://www.genenetwork.org/" target="_blank">
- Main GN site</a> at UTHSC</li>
-
- <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">
- Australia</a> at the UWA</li>
-
- <li><a href="http://gn.genetics.ucla.edu/" target="_blank">
- California</a> at UCLA</li>
-
- <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">
- Germany</a> at the HZI</li>
-
- <li><a href="https://genenetwork.hubrecht.eu/" target="_blank">
- Netherlands</a> at the Hubrecht
- (development)</li>
-
- <li><a href="http://genenetwork.memphis.edu/" target="_blank">
- Memphis</a> at the U of M</li>
-
- <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank">
- Singapore</a> at the NUS</li>
-
- <li><a href="http://genenetwork.epfl.ch/" target="_blank">
- Switzerland</a> at the EPFL</li>
- </ul>
- <h3>History and archive</h3>
-
- <p>The
- <a href="http://artemis.uthsc.edu" target="_blank">
- time machine</a>
- has earlier versions that correspond to specific publication dates.
- </p>
-
- <h3>The next generation</h3>
- <p>Try the <a href=
- "http://alexandria.uthsc.edu/" target="_blank">
- development</a> site to explore experimental data and features.</p>
- </section>
- </div>
- </div>
- </div>
-
- <!-- Footer
- ================================================== -->
- <footer class="footer">
- <div class="container">
- <p class="pull-right"><a href="#">Back to top</a></p>
-
- <p>Launched in 1994 as
- <A HREF="http://www.ncbi.nlm.nih.gov/pubmed?term=8043953">
- The Portable Dictionary of the Mouse Genome</A> and in 2001 as WebQTL.
- </p>
- <p>Operated by
- <A HREF="mailto:rwilliams@uthsc.edu">Rob Williams</A>,
- <A HREF="mailto:lyan6@uthsc.edu">Lei Yan</A>,
- <A HREF="mailto:zachary.a.sloan@gmail.com">Zachary Sloan</A>, and
- <A HREF="mailto:acenteno@uthsc.edu" target="_blank">Arthur Centeno</A>.
- </p>
- <p>
- Designed and coded by <a href="http://penguinpython.com">Sam Ockman</a>, Xiaodong Zhou,
- Christian Fernandez,
- Ning Liu, Rudi Alberts, Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams,
- and <A HREF="/credit.html">colleagues</A>.
- </p>
-
- <p>Built with <a href="http://twitter.github.com/bootstrap/">bootstrap</a>,
- <a href="http://coffeescript.org/">coffeescript</a>,
- <a href="http://flask.pocoo.org/">flask</a>,
- <a href="http://en.wikipedia.org/wiki/Linux">linux</a>,
- <a href="http://www.python.org/">python</a> and good intentions.
- </p>
- <p>Special thanks to CYP1A2 and AHR.</p>
- <br />
- <p>GeneNetwork is supported by:</p>
- <UL>
- <LI>
- <a target="_blank" href="http://citg.uthsc.edu">
- The UT Center for Integrative and Translational Genomics
- </A>
- </li>
- <LI><a target="_blank" href="http://www.iniastress.org">NIAAA</A>
- Integrative Neuroscience Initiative on Alcoholism
- (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425)
- </li>
- <LI>
- <a target="_blank"
- href="http://www.drugabuse.gov/about/organization/Genetics/geneexpression/index.html">NIDA</A>, <a class="smallsize" target="_blank" href="http://www.nimh.nih.gov/">NIMH</A>
- , and <a class="smallsize" target="_blank" href="http://www.niaaa.nih.gov/">
- NIAAA</A> (P20-DA 21131)
- </li>
- <LI>NCI <a target="_blank" href="http://emice.nci.nih.gov/">MMHCC</A> (U01CA105417) and
- <a target="_blank" href="http://www.ncrr.nih.gov/">NCRR</A>
- <a target="_blank" href="http://www.nbirn.net/TestBeds/Mouse/index.htm">BIRN</A>
- (U24 RR021760)
- </li>
- </UL>
- <!--</p>-->
-
- <ul class="footer-links">
- <li><a href="http://atlas.uthsc.edu/mailman/listinfo/genenetwork" target="_blank">Join the mailing list</a></li>
- <!--<li><a href="#">Friend us on facebook</a></li>-->
- <!--<li><a href="#">Follow us on twitter</a></li>-->
- </ul>
- </div>
- </footer>
-
- <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
- <script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
- <script>
- //http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working
- var $window = $(window)
- $('.bs-docs-sidenav').affix({
- offset: {
- top: function () { return $window.width() <= 980 ? 290 : 210 }
- , bottom: 270
- }
- })
- </script>
- <!--<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>-->
- <!--<script src="/static/new/javascript/dataset_menu_structure.json"></script>-->
- <!--<script src="/static/new/javascript/dataset_select_items.js"></script>-->
- <script src="/static/new/js_external/jquery.cookie.js"></script>
- <script type="text/javascript" src="/static/new/js_external/json2.js"></script>
- <script src="/static/new/javascript/dataset_select_menu.js"></script>
-</body>
-</html>
diff --git a/wqflask/wqflask/templates/old_index_page.html b/wqflask/wqflask/templates/old_index_page.html
new file mode 100644
index 00000000..db0b2d9e
--- /dev/null
+++ b/wqflask/wqflask/templates/old_index_page.html
@@ -0,0 +1,320 @@
+{% extends "base.html" %}
+{% block title %}GeneNetwork{% endblock %}
+{% block content %}
+ <!-- Start of body -->
+ <tr>
+ <td bgcolor="#EEEEEE" class="solidBorder">
+ <table width="100%" cellspacing="0" cellpadding="5">
+ <tr>
+ <td valign="top" width="40%" align="left" height="10" bgcolor="#EEEEEE">
+ <p style="font-size:18px;font-family:verdana;color:black"><b>Select and
+ Search</b></p>
+
+ <form method="get" action="/search" class="form-search" name="SEARCHFORM">
+ <table width="100%">
+ <!-- SPECIES SELECTION -->
+
+ <tr>
+ <td align="right" height="35" style=
+ "font-size:14px;font-family:verdana;color:black" width="16%">
+ <b>Species:</b></td>
+
+ <td width="3%"></td>
+
+ <td nowrap width="85%" align="left">
+ <div id="menu0">
+ <select name="species" size="1" id="species" onchange=
+ "fillOptions('species');">
+ </select>
+ </div>
+ </td>
+ </tr><!-- GROUP SELECTION -->
+
+ <tr>
+ <td align="right" height="35" style=
+ "font-size:14px;font-family:verdana;color:black"><b>Group:</b></td>
+
+ <td width="3%"></td>
+
+ <td nowrap width="85%" align="left">
+ <div id="menu1">
+ <select name="cross" size="1" id="cross" onchange="fillOptions('cross');">
+ </select> <input type="button" class="btn" value="Info" onclick=
+ "javascript:crossinfo();">
+ </div>
+ </td>
+ </tr><!-- TYPE SELECTION -->
+
+ <tr>
+ <td align="right" height="35" style=
+ "font-size:14px;font-family:verdana;color:black"><b>Type:</b></td>
+
+ <td width="3%"></td>
+
+ <td nowrap width="85%" align="left">
+ <div id="menu2">
+ <select name="tissue" size="1" id="tissue" onchange=
+ "fillOptions('tissue');">
+ </select>
+ </div>
+ </td>
+ </tr><!-- DATABASE SELECTION -->
+
+ <tr>
+ <td align="right" height="35" style=
+ "font-size:14px;font-family:verdana;color:black"><b>Database:</b></td>
+
+ <td width="3%"></td>
+
+ <td nowrap width="85%" align="left">
+ <div id="menu3">
+ <select name="database" size="1" id="database">
+ </select> <input type="submit" class="btn" value="Info" name=
+ "info_database">
+ </div>
+ </td>
+ </tr><!-- USER HELP -->
+
+ <tr>
+ <td align="right" height="20" width="10%"></td>
+
+ <td width="3%"></td>
+
+ <td align="left" width="85%">
+ <p class="fs12"> Databases marked with <b>**</b>
+ suffix are not public yet.<br>
+ Access requires <a href="/account.html" target=
+ "_blank" class="fs14"><small>user login</small></a>.</p>
+ </td>
+ </tr><!-- GET ANY SEARCH -->
+
+ <tr>
+ <td align="right" height="35" nowrap="on" style=
+ "font-size:14px;font-family:verdana;color:black" width="10%">
+ <b>Search:</b></td>
+
+ <td width="3%"></td>
+
+ <td nowrap width="85%" align="left"><input class="input-medium search-query"
+ id="tfor" name="search_terms" style=
+ "width:420px; background-color:white; font-family:verdana; font-size:14px"
+ type="text" maxlength="500"></td>
+ </tr><!-- GET ANY HELP -->
+
+ <tr>
+ <td align="right" height="20" width="10%"></td>
+
+ <td width="3%"></td>
+
+ <td width="85%" align="left">
+ <p class="fs12"> Enter terms, genes, ID numbers in the
+ <b>Search</b> field.<br>
+ Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
+ synap*).<br>
+ Use <b>quotes</b> for terms such as <i>"tyrosine
+ kinase"</i>.</p>
+ </td>
+ </tr><!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
+
+ <tr align="center">
+ <td width="3%"></td>
+
+ <td width="3%"></td>
+
+ <td align="left" height="40" colspan="3"><input id="btsearch" type="submit"
+ class="btn btn-primary" value="Search"> <input type=
+ "button" class="btn" value="Make Default" onclick=
+ "setDefault(this.form);"> <input type="button" class=
+ "btn" value="Advanced Search" onclick=
+ "javascript:window.open('/index3.html', '_self');"></td>
+ </tr>
+ </table><input type="hidden" name="FormID" value="searchResult"> <input type=
+ "hidden" name="RISet" value="BXD"> <script src="/javascript/selectDatasetMenu.js"
+ type="text/javascript">
+</script>
+ </form><!-- QUICK HELP -->
+
+ <p> ______________________________________________________</p>
+
+ <p style="font-size:13px;font-family:verdana;color:black"><b> Quick HELP
+ Examples and</b> <a href="http://www.genenetwork.org/index4.html" target="_blank"
+ class="fs14"><b>User's Guide</b></a></p> You can also use advanced
+ commands. Copy these simple examples<br>
+ into the <b>Get Any</b> or <b>Combined</b> search fields:
+
+ <ul style="font-size:12px;font-family:verdana;color:black">
+ <li><b><i>POSITION=(chr1 25 30)</i></b> finds genes, markers, or transcripts on
+ chromosome 1 between 25 and 30 Mb.</li>
+
+ <li><b><i>MEAN=(15 16) LRS=(23 46)</i></b> in the <b>Combined</b> field finds
+ highly expressed genes (15 to 16 log2 units) AND with peak <a href=
+ "http://www.genenetwork.org/glossary.html#L" target="_blank" class=
+ "fs14"><small>LRS</small></a> linkage between 23 and 46.</li>
+
+ <li><b><i>RIF=mitochondrial</i></b> searches RNA databases for <a href=
+ "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank"
+ class="fs14"><small>GeneRIF</small></a> links.</li>
+
+ <li><b><i>WIKI=nicotine</i></b> searches <a href=
+ "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank" class=
+ "fs14"><small>GeneWiki</small></a> for genes that you or other users have annotated
+ with the word <i>nicotine</i>.</li>
+
+ <li><b><i>GO:0045202</i></b> searches for synapse-associated genes listed in the
+ <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank" class=
+ "fs14"><small>Gene Ontology</small></a>.</li>
+
+ <li><b><i>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</i></b><br>
+ in <b>Combined</b> finds synapse-associated genes with <a href=
+ "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
+ "fs14"><small>cis eQTL</small></a> on Chr 4 from 122 and 155 Mb with LRS scores
+ between 9 and 999.</li>
+
+ <li><b><i>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</i></b><br>
+ in <b>Combined</b> finds diabetes-associated transcripts with peak <a href=
+ "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
+ "fs14"><small>trans eQTLs</small></a> on Chr 2 between 100 and 105 Mb with LRS
+ scores between 9 and 999.</li>
+ </ul>
+ </td><!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE) -->
+ <!-- START OF TOP RIGHT PANEL -->
+
+ <td valign="top" width="40%" bgcolor="#FFFFFF">
+ <p style="font-size:15px;font-family:verdana;color:black"><b>Websites Affiliated with
+ GeneNetwork</b></p>
+
+ <p style="font-size:12px;font-family:verdana;color:black"></p>
+
+ <ul>
+ <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
+ Browser</a> at UTHSC</li>
+
+ <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
+ UTHSC</li>
+
+ <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+ Cloud (EC2)</a></li>
+
+ <li>GeneNetwork Source Codes at <a href=
+ "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+
+ <li>GeneNetwork Source Codes at <a href=
+ "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
+ </ul>
+
+ <p>____________________________</p>
+
+ <p style="font-size:15px;font-family:verdana;color:black"><b>Getting Started</b>
+ </p>
+
+ <ol style="font-size:12px;font-family:verdana;color:black">
+ <li>Select <b>Species</b> (or select All)</li>
+
+ <li>Select <b>Group</b> (a specific sample)</li>
+
+ <li>Select <b>Type</b> of data:
+
+ <ul>
+ <li>Phenotype (traits)</li>
+
+ <li>Genotype (markers)</li>
+
+ <li>Expression (mRNAs)</li>
+ </ul>
+ </li>
+
+ <li>Select a <b>Database</b></li>
+
+ <li>Enter search terms in the <b>Get Any</b> or <b>Combined</b> field: words,
+ genes, ID numbers, probes, advanced search commands</li>
+
+ <li>Click on the <b>Search</b> button</li>
+
+ <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
+ </ol>
+
+ <p>____________________________</p>
+
+ <p style="font-size:14px;font-family:verdana;color:black"><b>How to Use
+ GeneNetwork</b></p>
+
+ <blockquote>
+ <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute
+ GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
+ "_blank" class="fs14"><small>Tour</small></a> that includes screen shots and
+ typical steps in the analysis.</p>
+ </blockquote>
+
+ <blockquote>
+ <p style="font-size:12px;font-family:verdana;color:black">For information about
+ resources and methods, select the <img src=
+ "http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border="0" valign=
+ "middle"> buttons.</p>
+
+ <p style="font-size:12px;font-family:verdana;color:black">Try the <a href=
+ "http://alexandria.uthsc.edu/" target="_blank" class=
+ "fs14"><small>Workstation</small></a> site to explore data and features that are
+ being implemented.</p>
+
+ <p style="font-size:12px;font-family:verdana;color:black">Review the <a href=
+ "/conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></a>
+ and <a href="/statusandContact.html" target="_blank" class=
+ "fs14"><small>Contacts</small></a> pages for information on the status of data sets
+ and advice on their use and citation.</p>
+ </blockquote>
+
+ <p style="font-size:14px;font-family:verdana;color:black"><b>Mirror and Development
+ Sites</b></p>
+
+ <ul>
+ <li><a href="http://www.genenetwork.org/" target="_blank" style=
+ "font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</a> (main
+ site)</li>
+
+ <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style=
+ "font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
+
+ <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style=
+ "font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
+
+ <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style=
+ "font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
+
+ <li><a href="https://genenetwork.hubrecht.eu/" target="_blank" style=
+ "font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</a>
+ (Development)</li>
+
+ <li><a href="http://genenetwork.memphis.edu/" target="_blank" style=
+ "font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
+
+ <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style=
+ "font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li>
+
+ <li><a href="http://genenetwork.epfl.ch/" target="_blank" style=
+ "font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
+ </ul>
+
+ <p style="font-size:14px;font-family:verdana;color:black"><b>History and
+ Archive</b></p>
+
+ <blockquote>
+ <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <a href=
+ "http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time
+ Machine</small></a> links to earlier versions that correspond to specific
+ publication dates.</p>
+ </blockquote>
+ </td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ <!-- End of body -->
+ <script src="/javascript/searchtip.js" type="text/javascript">
+ </script>
+ <script type="text/javascript">
+ $(document).ready(function () {
+ initialDatasetSelection();
+ });
+ </script>
+{% endblock %}
+
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index d639ed07..629a5b15 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -33,13 +33,6 @@ def index_page():
print("Sending index_page")
return render_template("index_page.html")
-
-@app.route("/new")
-def new_index_page():
- print("Sending index_page")
-
- return render_template("new_index_page.html")
-
@app.route("/data_sharing")
def data_sharing_page():
print("In data_sharing")
--
cgit v1.2.3