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path: root/web/webqtl/showTrait/DataEditingPage.py
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-rwxr-xr-x[-rw-r--r--]web/webqtl/showTrait/DataEditingPage.py49
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"
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 22:34:04 +0000