aboutsummaryrefslogtreecommitdiff
path: root/web
diff options
context:
space:
mode:
Diffstat (limited to 'web')
-rwxr-xr-x[-rw-r--r--]web/faq.html0
-rwxr-xr-x[-rw-r--r--]web/footer.html0
-rwxr-xr-x[-rw-r--r--]web/header.html0
-rwxr-xr-x[-rw-r--r--]web/javascript/footer.js0
-rwxr-xr-x[-rw-r--r--]web/javascript/header.js0
-rwxr-xr-xweb/javascript/selectDatasetMenu.js2
-rwxr-xr-x[-rw-r--r--]web/javascript/webqtl.js2
-rwxr-xr-x[-rw-r--r--]web/reference.html0
-rwxr-xr-xweb/webqtl/.htaccess2
-rwxr-xr-xweb/webqtl/base/indexBody.py5
-rwxr-xr-x[-rw-r--r--]web/webqtl/base/template.py0
-rwxr-xr-x[-rw-r--r--]web/webqtl/base/templatePage.py0
-rwxr-xr-xweb/webqtl/base/webqtlConfigLocal.py8
-rwxr-xr-x[-rw-r--r--]web/webqtl/intervalMapping/IntervalMappingPage.py0
-rwxr-xr-x[-rw-r--r--]web/webqtl/search/SearchResultPage.py16
-rw-r--r--[-rwxr-xr-x]web/webqtl/showTrait/ShowTraitPage.py0
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 18:48:41 +0000