Latest version of GN source codes

16 files changed, 23 insertions, 12 deletions

diff --git a/web/faq.html b/web/faq.html
index e7d26e37..e7d26e37 100644..100755
--- a/web/faq.html
+++ b/web/faq.html
diff --git a/web/footer.html b/web/footer.html
index 334de26f..334de26f 100644..100755
--- a/web/footer.html
+++ b/web/footer.html
diff --git a/web/header.html b/web/header.html
index 71d27162..71d27162 100644..100755
--- a/web/header.html
+++ b/web/header.html
diff --git a/web/javascript/footer.js b/web/javascript/footer.js
index 18585334..18585334 100644..100755
--- a/web/javascript/footer.js
+++ b/web/javascript/footer.js
diff --git a/web/javascript/header.js b/web/javascript/header.js
index 59fcacd8..59fcacd8 100644..100755
--- a/web/javascript/header.js
+++ b/web/javascript/header.js
diff --git a/web/javascript/selectDatasetMenu.js b/web/javascript/selectDatasetMenu.js
index 65fff775..3bfdc294 100755
--- a/web/javascript/selectDatasetMenu.js
+++ b/web/javascript/selectDatasetMenu.js
@@ -129,7 +129,7 @@ var dArr = [
 {txt:'UCLA CTB6B6CTF2 Muscle Female mlratio **',val:'UCLA_CTB6B6CTF2_MUSCLE_FEMALE'},
 {txt:'UCLA CTB6B6CTF2 Liver Female mlratio **',val:'UCLA_CTB6B6CTF2_LIVER_FEMALE'},
 {txt:'INIA Macaca fasicularis Amygdala (Jan10) RMA **',val:'INIA_MacFas_AMG_RMA_0110'},
-{txt:'VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile',val:'VUBXDMouseMidBrainQ0512'},
+{txt:'VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile **',val:'VUBXDMouseMidBrainQ0512'},
 {txt:'GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA',val:'GSE16780_UCLA_ML0911'},
 {txt:'EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **',val:'EPFLMouseMuscleCDRMA1211'},
 {txt:'EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **',val:'EPFLMouseMuscleRMA1211'},
diff --git a/web/javascript/webqtl.js b/web/javascript/webqtl.js
index f8dd1a4e..19ecf3b7 100644..100755
--- a/web/javascript/webqtl.js
+++ b/web/javascript/webqtl.js
@@ -945,7 +945,7 @@ function mixedChipError(methodName){
 Used by GoTreePage.py, add the parameter 'chipName'
 */
 function unknownChipError(chipName){
-	alert("Sorry, the analysis was interrupted because your selections from GeneNetwork apparently include data from platform"+ chipName +"which is unknown by WebGestalt. Please reselect traits and submit again.");
+	alert("Sorry, the analysis was interrupted because your selections from GeneNetwork apparently include data from platform "+ chipName +" which is unknown by WebGestalt. Please reselect traits and submit again.");
 	window.close();
 }
 
diff --git a/web/reference.html b/web/reference.html
index e0bf404c..e0bf404c 100644..100755
--- a/web/reference.html
+++ b/web/reference.html
diff --git a/web/webqtl/.htaccess b/web/webqtl/.htaccess
index d5e1aa95..ac3a9699 100755
--- a/web/webqtl/.htaccess
+++ b/web/webqtl/.htaccess
@@ -1,5 +1,5 @@
 AddHandler python-program .py
 PythonHandler main
-PythonInterpreter GeneNetwork
+PythonInterpreter leiyan
 PythonOption session FileSession
 PythonDebug On
diff --git a/web/webqtl/base/indexBody.py b/web/webqtl/base/indexBody.py
index aa67dffa..e73409a5 100755
--- a/web/webqtl/base/indexBody.py
+++ b/web/webqtl/base/indexBody.py
@@ -67,7 +67,7 @@ index_body_string = """
 					<!--  DATABASE  SELECTION -->		
 									<TR>
 										<TD align=right height=35 style="font-size:14px;font-family:verdana;color:black">
-											<B>Database:</B>
+											<B>Data Set:</B>
 										</TD>
 
 										<TD width="3%">
@@ -221,6 +221,7 @@ Quick HELP Examples and </B>
 				<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>____________________________
@@ -271,7 +272,7 @@ Quick HELP Examples and </B>
 								<LI><A HREF="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</A>
 								<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><A HREF="https://genenetwork.hubrecht.eu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</A> (Development)
-								<LI><A HREF="http://xzhou3.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</A>
+								<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><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><A HREF="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</A>
 							</UL>
diff --git a/web/webqtl/base/template.py b/web/webqtl/base/template.py
index 85bd86df..85bd86df 100644..100755
--- a/web/webqtl/base/template.py
+++ b/web/webqtl/base/template.py
diff --git a/web/webqtl/base/templatePage.py b/web/webqtl/base/templatePage.py
index 4dece24a..4dece24a 100644..100755
--- a/web/webqtl/base/templatePage.py
+++ b/web/webqtl/base/templatePage.py
diff --git a/web/webqtl/base/webqtlConfigLocal.py b/web/webqtl/base/webqtlConfigLocal.py
index 0c95fe7b..499dfba8 100755
--- a/web/webqtl/base/webqtlConfigLocal.py
+++ b/web/webqtl/base/webqtlConfigLocal.py
@@ -3,17 +3,15 @@
 #########################################
 
 MYSQL_SERVER = 'localhost'
-DB_NAME = 'db_webqtl'
+DB_NAME = 'db_webqtl_leiyan'
 DB_USER = 'webqtlupd'
 DB_PASSWD = 'webqtl'
 
 MYSQL_UPDSERVER = 'localhost'
-DB_UPDNAME = 'db_webqtl'
+DB_UPDNAME = 'db_webqtl_leiyan'
 DB_UPDUSER = 'webqtlupd'
 DB_UPDPASSWD = 'webqtl'
 
-GNROOT = '/gnshare/gn/'
+GNROOT = '/home/leiyan/gn/'
 PythonPath = '/usr/bin/python'
 PIDDLE_FONT_PATH = '/usr/lib/python2.4/site-packages/piddle/truetypefonts/'
-
-TEXTUI=0   # This is to protect GN production server. If set to 0, no text UI is allowed.
diff --git a/web/webqtl/intervalMapping/IntervalMappingPage.py b/web/webqtl/intervalMapping/IntervalMappingPage.py
index 4bdf45ab..4bdf45ab 100644..100755
--- a/web/webqtl/intervalMapping/IntervalMappingPage.py
+++ b/web/webqtl/intervalMapping/IntervalMappingPage.py
diff --git a/web/webqtl/search/SearchResultPage.py b/web/webqtl/search/SearchResultPage.py
index 14d10731..029a54c4 100644..100755
--- a/web/webqtl/search/SearchResultPage.py
+++ b/web/webqtl/search/SearchResultPage.py
@@ -20,8 +20,10 @@ from base.templatePage import templatePage
 from utility import webqtlUtil
 from dbFunction import webqtlDatabaseFunction
 
+import PubmedSearch
+
 import logging
-logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO)
+logging.basicConfig(filename="/tmp/gn_log_leiyan", level=logging.INFO)
 _log = logging.getLogger("search")
 
 class SearchResultPage(templatePage):
@@ -155,7 +157,16 @@ class SearchResultPage(templatePage):
 			geneIdListQuery = " geneId=%s" % string.join(string.split(geneIdListQuery), "-")
 
 		self.ANDkeyword = fd.formdata.getfirst('ANDkeyword', "")
+		_log.info("self.ANDkeyword[1]: " + self.ANDkeyword)
+		pubmedSearchObject = PubmedSearch.PubmedSearch(self.ANDkeyword, self.database[0].id)
+		self.ANDkeyword = pubmedSearchObject.getNewS()
+		_log.info("self.ANDkeyword[2]: " + self.ANDkeyword)
+
 		self.ORkeyword = fd.formdata.getfirst('ORkeyword', "")
+		_log.info("self.ORkeyword[1]: " + self.ORkeyword)
+		pubmedSearchObject = PubmedSearch.PubmedSearch(self.ORkeyword, self.database[0].id)
+		self.ORkeyword = pubmedSearchObject.getNewS()
+		_log.info("self.ORkeyword[2]: "+self.ORkeyword)
 
 		self.ORkeyword += geneIdListQuery
 
@@ -485,7 +496,7 @@ class SearchResultPage(templatePage):
 		self.results = []
 		for item in searchCountQuery:
 		    start_time = datetime.datetime.now()
-		    _log.info("Executing query: %s"%(item))
+		    _log.info("111 Executing query: %s"%(item))
 		    self.cursor.execute(item)
 		    allResults.append(self.cursor.fetchall())
 		    end_time = datetime.datetime.now()
@@ -497,6 +508,7 @@ class SearchResultPage(templatePage):
 		#searchCountQuery retrieve all the results, for counting use only
 		if searchCountQuery != searchQuery:
 			for item in searchQuery:
+				_log.info("222 Executing query: %s"%(item))
 				self.cursor.execute(item)
 				self.results.append(self.cursor.fetchall())
 		else:
diff --git a/web/webqtl/showTrait/ShowTraitPage.py b/web/webqtl/showTrait/ShowTraitPage.py
index 82511228..82511228 100755..100644
--- a/web/webqtl/showTrait/ShowTraitPage.py
+++ b/web/webqtl/showTrait/ShowTraitPage.py