diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/webqtlDataset.py | 28 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 215 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/index_page.html | 669 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/new_index_page.html | 423 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/old_index_page.html | 320 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 7 |
6 files changed, 821 insertions, 841 deletions
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") |