Merge branch 'flask' of http://github.com/zsloan/genenetwork

1 files changed, 33 insertions, 16 deletions

diff --git a/web/webqtl/showTrait/DataEditingPage.py b/web/webqtl/showTrait/DataEditingPage.py
index f38b9880..c240d8a0 100644..100755
--- a/web/webqtl/showTrait/DataEditingPage.py
+++ b/web/webqtl/showTrait/DataEditingPage.py
@@ -280,13 +280,13 @@ class DataEditingPage(templatePage):
 
 					if snpurl:
 						snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl)
-						snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="addselect", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;")
+						snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;")
 						snpBrowserButton.append(snpBrowserButton_img)	
 						snpBrowserText = "SNPs"				
 
 				#XZ: Show GeneWiki for all species
 				geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol))
-				geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="addselect", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;")
+				geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;")
 				geneWikiButton.append(geneWikiButton_img)
 				geneWikiText = 'GeneWiki'					
 
@@ -295,7 +295,7 @@ class DataEditingPage(templatePage):
 					 if _Species in ("mouse", "rat", "human"):
 						similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species)
 						similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl)
-						similarButton_img = HT.Image("/images/find_icon.jpg", name="addselect", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
+						similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
 						similarButton.append(similarButton_img)
 						similarText = "Find"		
 				else:
@@ -416,13 +416,15 @@ class DataEditingPage(templatePage):
 					UTHSC_BLAT_URL = ""
 				
 				if UCSC_BLAT_URL:
-					verifyButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
-					verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="addselect", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
+					verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL)
+					verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", 
+						title=" Check probe locations at UCSC ", style="border:none;")
 					verifyButton.append(verifyButtonImg)
 					verifyText = 'Verify'
 				if UTHSC_BLAT_URL:	
-					rnaseqButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
-					rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="addselect", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
+					rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL)
+					rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", 
+						title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
 					rnaseqButton.append(rnaseqButtonImg)
 					rnaseqText = 'RNA-seq'											
 				tSpan.append(HT.BR())
@@ -442,8 +444,8 @@ class DataEditingPage(templatePage):
 				if probeResult[0] > 0:
 					probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \
 						% (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet)
-					probeButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % probeurl)
-					probeButton_img = HT.Image("/images/probe_icon.jpg", name="addselect", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;")
+					probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl)
+					probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;")
 					probeButton.append(probeButton_img)
 					probeText = "Probes"	
 
@@ -590,10 +592,24 @@ class DataEditingPage(templatePage):
 					url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \
 					% thisTrait.symbol,Class="fs14 fwn", \
 					title="Protein interactions: known and inferred"), style=linkStyle), " "*2)
-				if thisTrait.geneid:
+				if thisTrait.symbol:
+					#ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input
+					#We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users
+					if _Species == "mouse":
+						species_scientific = "Mus%20musculus"
+					elif _Species == "rat":
+						species_scientific = "Rattus%20norvegicus"
+					elif _Species == "human":
+						species_scientific = "Homo%20sapiens"
+					elif _Species == "drosophila":
+						species_scientific = "Drosophila%20melanogaster"
+					else:
+						species_scientific = "all"
+
+					species_scientific
 					tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \
-						url="http://www.pantherdb.org/genes/gene.do?acc=%s"  \
-						% thisTrait.geneid,Class="fs14 fwn", \
+						url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s"  \
+						% (species_scientific, thisTrait.symbol),Class="fs14 fwn", \
 					title="Gene and protein data resources from Celera-ABI"), style=linkStyle), " "*2)
 				else:
 					pass
@@ -755,12 +771,13 @@ class DataEditingPage(templatePage):
 					UCSC_BLAT_URL = ""
 					UTHSC_BLAT_URL = ""
 				if UCSC_BLAT_URL:
-					verifyButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
-					verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="addselect", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
+					#verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
+					verifyButton = HT.Href(url="#")
+					verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
 					verifyButton.append(verifyButtonImg)	
 					verifyText = "Verify"
-					rnaseqButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
-					rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="addselect", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
+					rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
+					rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
 					rnaseqButton.append(rnaseqButtonImg)			
 					rnaseqText = "RNA-seq"