From 89dd9b4fe8e2e1011f28d8ff688bc9e14c344ef7 Mon Sep 17 00:00:00 2001 From: root Date: Tue, 22 May 2012 12:47:55 -0500 Subject: Latest version of GN source codes --- web/faq.html | 0 web/footer.html | 0 web/header.html | 0 web/javascript/footer.js | 0 web/javascript/header.js | 0 web/javascript/selectDatasetMenu.js | 2 +- web/javascript/webqtl.js | 2 +- web/reference.html | 0 web/webqtl/.htaccess | 2 +- web/webqtl/base/indexBody.py | 5 +++-- web/webqtl/base/template.py | 0 web/webqtl/base/templatePage.py | 0 web/webqtl/base/webqtlConfigLocal.py | 8 +++----- web/webqtl/intervalMapping/IntervalMappingPage.py | 0 web/webqtl/search/SearchResultPage.py | 16 ++++++++++++++-- web/webqtl/showTrait/ShowTraitPage.py | 0 16 files changed, 23 insertions(+), 12 deletions(-) mode change 100644 => 100755 web/faq.html mode change 100644 => 100755 web/footer.html mode change 100644 => 100755 web/header.html mode change 100644 => 100755 web/javascript/footer.js mode change 100644 => 100755 web/javascript/header.js mode change 100644 => 100755 web/javascript/webqtl.js mode change 100644 => 100755 web/reference.html mode change 100644 => 100755 web/webqtl/base/template.py mode change 100644 => 100755 web/webqtl/base/templatePage.py mode change 100644 => 100755 web/webqtl/intervalMapping/IntervalMappingPage.py mode change 100644 => 100755 web/webqtl/search/SearchResultPage.py mode change 100755 => 100644 web/webqtl/showTrait/ShowTraitPage.py diff --git a/web/faq.html b/web/faq.html old mode 100644 new mode 100755 diff --git a/web/footer.html b/web/footer.html old mode 100644 new mode 100755 diff --git a/web/header.html b/web/header.html old mode 100644 new mode 100755 diff --git a/web/javascript/footer.js b/web/javascript/footer.js old mode 100644 new mode 100755 diff --git a/web/javascript/header.js b/web/javascript/header.js old mode 100644 new mode 100755 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 old mode 100644 new mode 100755 index f8dd1a4e..19ecf3b7 --- 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 old mode 100644 new mode 100755 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: + Data Set: @@ -221,6 +221,7 @@ Quick HELP Examples and
  • Galaxy at UTHSC
  • GeneNetwork at Amazon Cloud (EC2)
  • GeneNetwork Source Codes at SourceForge
    • +
  • GeneNetwork Source Codes at GitHub

    • ____________________________ @@ -271,7 +272,7 @@ Quick HELP Examples and

  • California at UCLA
  • Germany at the HZI
  • Netherlands at the Hubrecht (Development) -
  • Memphis at the U of M +
  • Memphis at the U of M
  • Singapore at the NUS
  • Switzerland at the EPFL diff --git a/web/webqtl/base/template.py b/web/webqtl/base/template.py old mode 100644 new mode 100755 diff --git a/web/webqtl/base/templatePage.py b/web/webqtl/base/templatePage.py old mode 100644 new mode 100755 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 old mode 100644 new mode 100755 diff --git a/web/webqtl/search/SearchResultPage.py b/web/webqtl/search/SearchResultPage.py old mode 100644 new mode 100755 index 14d10731..029a54c4 --- 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 old mode 100755 new mode 100644 -- cgit v1.2.3