From f2ed5f043df623f68cf6936a8dbe9cbbeb89981d Mon Sep 17 00:00:00 2001
From: Sam Ockman
Date: Tue, 5 Jun 2012 02:29:16 -0400
Subject: Actually getting some results out of the trait and data analysis page
---
wqflask/runserver.py | 4 +-
wqflask/wqflask/show_trait/DataEditingPage.py | 461 +++++++++++----------
.../wqflask/templates/trait_data_and_analysis.html | 7 +-
wqflask/wqflask/views.py | 2 +-
4 files changed, 242 insertions(+), 232 deletions(-)
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 7bd82619..a61e4029 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -18,4 +18,6 @@ _log = logging.getLogger("search")
_ch = logging.StreamHandler()
_log.addHandler(_ch)
-app.run(host='0.0.0.0')
+app.run(host='0.0.0.0',
+ use_debugger=False,
+ use_reloader=True)
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index 6d709012..439797c5 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -22,8 +22,8 @@ class DataEditingPage(templatePage):
templatePage.__init__(self, fd)
- self.dict['title'] = 'Data Editing'
- TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa")
+ #self.dict['title'] = 'Data Editing'
+ #TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa")
if not self.openMysql():
return
@@ -156,43 +156,49 @@ class DataEditingPage(templatePage):
## Generate form and buttons
#############################
- mainForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
- name='dataInput', submit=HT.Input(type='hidden'))
+ #mainForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
+ # name='dataInput', submit=HT.Input(type='hidden'))
- next=HT.Input(type='submit', name='submit',value='Next',Class="button")
- reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button")
- correlationMenus = []
+ #next=HT.Input(type='submit', name='submit',value='Next',Class="button")
+ #reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button")
+ #correlationMenus = []
if thisTrait == None:
thisTrait = webqtlTrait(data=fd.allTraitData, db=None)
# Variance submit page only
if fd.enablevariance and not varianceDataPage:
- title2Body.append("Click the next button to go to the variance submission form.",
- HT.Center(next,reset))
+ pass
+ #title2Body.append("Click the next button to go to the variance submission form.",
+ # HT.Center(next,reset))
else:
- self.dispBasicStatistics(fd, title2Body, thisTrait)
- self.dispCorrelationTools(fd, title3Body, thisTrait)
- self.dispMappingTools(fd, title4Body, thisTrait)
+ pass
+ # We'll get this part working later
+ #self.dispBasicStatistics(fd, title2Body, thisTrait)
+ #self.dispCorrelationTools(fd, title3Body, thisTrait)
+ #self.dispMappingTools(fd, title4Body, thisTrait)
#############################
## Trait Value Table
#############################
+ #
+ #self.dispTraitValues(fd, title5Body, varianceDataPage, nCols, mainForm, thisTrait)
+ #
+ #if fd.allstrainlist:
+ # hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ')
+ #for key in hddn.keys():
+ # mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+ #
+ #if fd.enablevariance and not varianceDataPage:
+ # #pre dataediting page, need to submit variance
+ # mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body)
+ #else:
+ # mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body)
+ #TD_LR.append(HT.Paragraph(mainForm))
+ #self.dict['body'] = str(TD_LR)
- self.dispTraitValues(fd, title5Body, varianceDataPage, nCols, mainForm, thisTrait)
-
- if fd.allstrainlist:
- hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ')
- for key in hddn.keys():
- mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-
- if fd.enablevariance and not varianceDataPage:
- #pre dataediting page, need to submit variance
- mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body)
- else:
- mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body)
- TD_LR.append(HT.Paragraph(mainForm))
- self.dict['body'] = str(TD_LR)
+ # We'll need access to thisTrait in the Jinja2 Template, so we put it inside self
+ self.thisTrait = thisTrait
##########################################
## Function to display header
@@ -308,13 +314,13 @@ class DataEditingPage(templatePage):
if snpurl:
snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl)
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)
+ #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="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;")
- geneWikiButton.append(geneWikiButton_img)
+ #geneWikiButton.append(geneWikiButton_img)
geneWikiText = 'GeneWiki'
#XZ: display similar traits in other selected datasets
@@ -323,15 +329,15 @@ class DataEditingPage(templatePage):
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="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
- similarButton.append(similarButton_img)
+ #similarButton.append(similarButton_img)
similarText = "Find"
else:
pass
- tbl.append(HT.TR(
- HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span('%s' % thisTrait.symbol, valign="top", Class="fs13 fsI"), valign="top", width=740)
- ))
+ #tbl.append(HT.TR(
+ #HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on", width=90),
+ #HT.TD(width=10, valign="top"),
+ #HT.TD(HT.Span('%s' % thisTrait.symbol, valign="top", Class="fs13 fsI"), valign="top", width=740)
+ #))
else:
tbl.append(HT.TR(
HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on"),
@@ -343,24 +349,16 @@ class DataEditingPage(templatePage):
if thisTrait.alias:
alias = string.replace(thisTrait.alias, ";", " ")
alias = string.join(string.split(alias), ", ")
- tbl.append(HT.TR(
- HT.TD('Aliases: ', Class="fwb fs13", valign="top", nowrap="on"),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(alias, Class="fs13 fsI"), valign="top")
- ))
+ thisTrait.alias_fmt = alias
+
#XZ: Description
if thisTrait.description:
- tSpan = HT.Span(thisTrait.description, Class="fs13")
+ thisTrait.description_fmt = thisTrait.description
if thisTrait.probe_target_description:
- tSpan.append('; ', thisTrait.probe_target_description)
+ thisTrait.description_fmt += "; " + this.trait.probe_target_description
else:
- tSpan = HT.Span('Not available', Class="fs13")
- tbl.append(HT.TR(
- HT.TD('Description: ', Class="fwb fs13", valign="top", nowrap="on"),
- HT.TD(width=10, valign="top"),
- HT.TD(tSpan, valign="top")
- ))
+ thisTrait.description_fmt = "Not available"
#XZ: Location
@@ -372,19 +370,19 @@ class DataEditingPage(templatePage):
else:
tSpan = HT.Span('Not available', Class="fs13")
- #XZ: deal with direction
- if thisTrait.strand_probe == '+':
- tSpan.append(' on the plus strand ')
- elif thisTrait.strand_probe == '-':
- tSpan.append(' on the minus strand ')
- else:
- pass
-
- tbl.append(HT.TR(
- HT.TD('Location: ', Class="fwb fs13", valign="top", nowrap="on"),
- HT.TD(width=10, valign="top"),
- HT.TD(tSpan, valign="top")
- ))
+ ##XZ: deal with direction
+ #if thisTrait.strand_probe == '+':
+ # tSpan.append(' on the plus strand ')
+ #elif thisTrait.strand_probe == '-':
+ # tSpan.append(' on the minus strand ')
+ #else:
+ # pass
+ #
+ #tbl.append(HT.TR(
+ # HT.TD('Location: ', Class="fwb fs13", valign="top", nowrap="on"),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(tSpan, valign="top")
+ # ))
##display Verify Location button
try:
@@ -473,7 +471,7 @@ class DataEditingPage(templatePage):
% (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet)
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)
+ #probeButton.append(probeButton_img)
probeText = "Probes"
tSpan = HT.Span(Class="fs13")
@@ -481,26 +479,28 @@ class DataEditingPage(templatePage):
#XZ: deal with blat score and blat specificity.
if thisTrait.probe_set_specificity or thisTrait.probe_set_blat_score:
if thisTrait.probe_set_specificity:
- tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), " "*3)
+ pass
+ #tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), " "*3)
if thisTrait.probe_set_blat_score:
- tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), " "*2)
+ pass
+ #tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), " "*2)
onClick="openNewWin('/blatInfo.html')"
- tbl.append(HT.TR(
- HT.TD('Target Score: ', Class="fwb fs13", valign="top", nowrap="on"),
- HT.TD(width=10, valign="top"),
- HT.TD(tSpan, valign="top")
- ))
-
- tSpan = HT.Span(Class="fs13")
- tSpan.append(str(_Species).capitalize(), ", ", fd.RISet)
-
- tbl.append(HT.TR(
- HT.TD('Species and Group: ', Class="fwb fs13", valign="top", nowrap="on"),
- HT.TD(width=10, valign="top"),
- HT.TD(tSpan, valign="top")
- ))
+ #tbl.append(HT.TR(
+ # HT.TD('Target Score: ', Class="fwb fs13", valign="top", nowrap="on"),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(tSpan, valign="top")
+ # ))
+
+ #tSpan = HT.Span(Class="fs13")
+ #tSpan.append(str(_Species).capitalize(), ", ", fd.RISet)
+ #
+ #tbl.append(HT.TR(
+ # HT.TD('Species and Group: ', Class="fwb fs13", valign="top", nowrap="on"),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(tSpan, valign="top")
+ # ))
if thisTrait.cellid:
self.cursor.execute("""
@@ -515,12 +515,13 @@ class DataEditingPage(templatePage):
HT.TD(HT.Span('%s' % probeDBName, Class="non_bold"), valign="top")
))
else:
- tbl.append(HT.TR(
- HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name,
- target='_blank', Class="fs13 fwn non_bold"), valign="top")
- ))
+ #tbl.append(HT.TR(
+ # HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name,
+ # target='_blank', Class="fs13 fwn non_bold"), valign="top")
+ # ))
+ pass
#XZ: ID links
if thisTrait.genbankid or thisTrait.geneid or thisTrait.unigeneid or thisTrait.omim or thisTrait.homologeneid:
@@ -529,7 +530,7 @@ class DataEditingPage(templatePage):
if thisTrait.geneid:
gurl = HT.Href(text= 'Gene', target='_blank',\
url=webqtlConfig.NCBI_LOCUSID % thisTrait.geneid, Class="fs14 fwn", title="Info from NCBI Entrez Gene")
- tSpan.append(HT.Span(gurl, style=idStyle), " "*2)
+ #tSpan.append(HT.Span(gurl, style=idStyle), " "*2)
if thisTrait.omim:
gurl = HT.Href(text= 'OMIM', target='_blank', \
url= webqtlConfig.OMIM_ID % thisTrait.omim,Class="fs14 fwn", title="Summary from On Mendelian Inheritance in Man")
@@ -538,7 +539,7 @@ class DataEditingPage(templatePage):
try:
gurl = HT.Href(text= 'UniGene',target='_blank',\
url= webqtlConfig.UNIGEN_ID % tuple(string.split(thisTrait.unigeneid,'.')[:2]),Class="fs14 fwn", title="UniGene ID")
- tSpan.append(HT.Span(gurl, style=idStyle), " "*2)
+ #tSpan.append(HT.Span(gurl, style=idStyle), " "*2)
except:
pass
if thisTrait.genbankid:
@@ -547,19 +548,19 @@ class DataEditingPage(templatePage):
thisTrait.genbankid=thisTrait.genbankid[0:-1]
gurl = HT.Href(text= 'GenBank', target='_blank', \
url= webqtlConfig.GENBANK_ID % thisTrait.genbankid,Class="fs14 fwn", title="Find the original GenBank sequence used to design the probes")
- tSpan.append(HT.Span(gurl, style=idStyle), " "*2)
+ #tSpan.append(HT.Span(gurl, style=idStyle), " "*2)
if thisTrait.homologeneid:
hurl = HT.Href(text= 'HomoloGene', target='_blank',\
url=webqtlConfig.HOMOLOGENE_ID % thisTrait.homologeneid, Class="fs14 fwn", title="Find similar genes in other species")
- tSpan.append(HT.Span(hurl, style=idStyle), " "*2)
+ #tSpan.append(HT.Span(hurl, style=idStyle), " "*2)
- tbl.append(
- HT.TR(HT.TD(colspan=3,height=6)),
- HT.TR(
- HT.TD('Resource Links: ', Class="fwb fs13", valign="top", nowrap="on"),
- HT.TD(width=10, valign="top"),
- HT.TD(tSpan, valign="top")
- ))
+ #tbl.append(
+ # HT.TR(HT.TD(colspan=3,height=6)),
+ # HT.TR(
+ # HT.TD('Resource Links: ', Class="fwb fs13", valign="top", nowrap="on"),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(tSpan, valign="top")
+ # ))
#XZ: Resource Links:
if thisTrait.symbol:
@@ -581,9 +582,9 @@ class DataEditingPage(templatePage):
if chr and txst and txen and kgId:
txst = int(txst*1000000)
txen = int(txen*1000000)
- tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
- title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle)
- , " "*2)
+ #tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
+ # title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle)
+ # , " "*2)
except:
pass
if _Species == "mouse":
@@ -611,14 +612,15 @@ class DataEditingPage(templatePage):
# % (thisTrait.symbol,symatlas_species),Class="fs14 fwn", \
# title="Expression across many tissues and cell types"), style=linkStyle), " "*2)
if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"):
- tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\
- url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \
- % (_Species, thisTrait.geneid),Class="fs14 fwn", \
- title="Expression across many tissues and cell types"), style=linkStyle), " "*2)
- tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\
- 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)
+ #tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\
+ # url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \
+ # % (_Species, thisTrait.geneid),Class="fs14 fwn", \
+ # title="Expression across many tissues and cell types"), style=linkStyle), " "*2)
+ pass
+ #tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\
+ # 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.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
@@ -634,30 +636,30 @@ class DataEditingPage(templatePage):
species_scientific = "all"
species_scientific
- tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \
- 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)
+ #tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \
+ # 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
#tSpan.append(HT.Span(HT.Href(text= 'BIND',target="mainFrame",\
# url="http://bind.ca/?textquery=%s" \
# % thisTrait.symbol,Class="fs14 fwn", \
# title="Protein interactions"), style=linkStyle), " "*2)
- if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"):
- tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\
- url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \
- % thisTrait.geneid, Class="fs14 fwn", \
- title="Meta-analysis of gene expression data"), style=linkStyle), " "*2)
- tSpan.append(HT.Span(HT.Href(text= 'SynDB',target="mainFrame",\
- url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \
- % thisTrait.symbol, Class="fs14 fwn", \
- title="Brain synapse database"), style=linkStyle), " "*2)
- if _Species == "mouse":
- tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
- url="http://mouse.brain-map.org/brain/%s.html" \
- % thisTrait.symbol, Class="fs14 fwn", \
- title="Allen Brain Atlas"), style=linkStyle), " "*2)
+ #if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"):
+ # tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\
+ # url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \
+ # % thisTrait.geneid, Class="fs14 fwn", \
+ # title="Meta-analysis of gene expression data"), style=linkStyle), " "*2)
+ #tSpan.append(HT.Span(HT.Href(text= 'SynDB',target="mainFrame",\
+ # url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \
+ # % thisTrait.symbol, Class="fs14 fwn", \
+ # title="Brain synapse database"), style=linkStyle), " "*2)
+ #if _Species == "mouse":
+ # tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
+ # url="http://mouse.brain-map.org/brain/%s.html" \
+ # % thisTrait.symbol, Class="fs14 fwn", \
+ # title="Allen Brain Atlas"), style=linkStyle), " "*2)
if thisTrait.geneid:
#if _Species == "mouse":
@@ -666,20 +668,22 @@ class DataEditingPage(templatePage):
# % thisTrait.geneid, Class="fs14 fwn", \
# title="Allen Brain Atlas"), style=linkStyle), " "*2)
if _Species == "human":
- tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
- url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \
- % thisTrait.geneid, Class="fs14 fwn", \
- title="Allen Brain Atlas"), style=linkStyle), " "*2)
- tbl.append(
- HT.TR(HT.TD(colspan=3,height=6)),
- HT.TR(
- HT.TD(' '),
- HT.TD(width=10, valign="top"),
- HT.TD(tSpan, valign="top")))
+ #tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
+ # url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \
+ # % thisTrait.geneid, Class="fs14 fwn", \
+ # title="Allen Brain Atlas"), style=linkStyle), " "*2)
+ pass
+
+ #tbl.append(
+ # HT.TR(HT.TD(colspan=3,height=6)),
+ # HT.TR(
+ # HT.TD(' '),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(tSpan, valign="top")))
- menuTable = HT.TableLite(cellpadding=2, Class="collap", width="620", id="target1")
- menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(similarButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(geneWikiButton, align="center"),HT.TD(snpBrowserButton, align="center"),HT.TD(rnaseqButton, align="center"),HT.TD(probeButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
- menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(similarText, align="center"),HT.TD(verifyText, align="center"),HT.TD(geneWikiText, align="center"),HT.TD(snpBrowserText, align="center"),HT.TD(rnaseqText, align="center"),HT.TD(probeText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
+ #menuTable = HT.TableLite(cellpadding=2, Class="collap", width="620", id="target1")
+ #menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(similarButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(geneWikiButton, align="center"),HT.TD(snpBrowserButton, align="center"),HT.TD(rnaseqButton, align="center"),HT.TD(probeButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
+ #menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(similarText, align="center"),HT.TD(verifyText, align="center"),HT.TD(geneWikiText, align="center"),HT.TD(snpBrowserText, align="center"),HT.TD(rnaseqText, align="center"),HT.TD(probeText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
#for zhou mi's cliques, need to be removed
@@ -690,91 +694,95 @@ class DataEditingPage(templatePage):
#linkTable.append(HT.TR(linkTD))
#Info2Disp.append(linkTable)
- title1Body.append(tbl, HT.BR(), menuTable)
+ #title1Body.append(tbl, HT.BR(), menuTable)
elif thisTrait and thisTrait.db and thisTrait.db.type =='Publish': #Check if trait is phenotype
if thisTrait.confidential:
- tbl.append(HT.TR(
- HT.TD('Pre-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.pre_publication_description, Class="fs13"), valign="top", width=740)
- ))
+ pass
+ #tbl.append(HT.TR(
+ # HT.TD('Pre-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.pre_publication_description, Class="fs13"), valign="top", width=740)
+ # ))
if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
- tbl.append(HT.TR(
- HT.TD('Post-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740)
- ))
- tbl.append(HT.TR(
- HT.TD('Pre-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.pre_publication_abbreviation, Class="fs13"), valign="top", width=740)
- ))
- tbl.append(HT.TR(
- HT.TD('Post-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.post_publication_abbreviation, Class="fs13"), valign="top", width=740)
- ))
- tbl.append(HT.TR(
- HT.TD('Lab code: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.lab_code, Class="fs13"), valign="top", width=740)
- ))
- tbl.append(HT.TR(
- HT.TD('Owner: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.owner, Class="fs13"), valign="top", width=740)
- ))
+ #tbl.append(HT.TR(
+ # HT.TD('Post-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740)
+ # ))
+ #tbl.append(HT.TR(
+ # HT.TD('Pre-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.pre_publication_abbreviation, Class="fs13"), valign="top", width=740)
+ # ))
+ #tbl.append(HT.TR(
+ # HT.TD('Post-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.post_publication_abbreviation, Class="fs13"), valign="top", width=740)
+ # ))
+ #tbl.append(HT.TR(
+ # HT.TD('Lab code: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.lab_code, Class="fs13"), valign="top", width=740)
+ # ))
+ pass
+ #tbl.append(HT.TR(
+ # HT.TD('Owner: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.owner, Class="fs13"), valign="top", width=740)
+ # ))
else:
- tbl.append(HT.TR(
- HT.TD('Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740)
- ))
- tbl.append(HT.TR(
- HT.TD('Authors: ', Class="fs13 fwb",
- valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.authors, Class="fs13"),
- valign="top", width=740)
- ))
- tbl.append(HT.TR(
- HT.TD('Title: ', Class="fs13 fwb",
- valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(thisTrait.title, Class="fs13"),
- valign="top", width=740)
- ))
+ pass
+ #tbl.append(HT.TR(
+ # HT.TD('Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740)
+ # ))
+ #tbl.append(HT.TR(
+ # HT.TD('Authors: ', Class="fs13 fwb",
+ # valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.authors, Class="fs13"),
+ # valign="top", width=740)
+ # ))
+ #tbl.append(HT.TR(
+ # HT.TD('Title: ', Class="fs13 fwb",
+ # valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(thisTrait.title, Class="fs13"),
+ # valign="top", width=740)
+ # ))
if thisTrait.journal:
journal = thisTrait.journal
if thisTrait.year:
journal = thisTrait.journal + " (%s)" % thisTrait.year
-
- tbl.append(HT.TR(
- HT.TD('Journal: ', Class="fs13 fwb",
- valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(journal, Class="fs13"),
- valign="top", width=740)
- ))
+ #
+ #tbl.append(HT.TR(
+ # HT.TD('Journal: ', Class="fs13 fwb",
+ # valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(journal, Class="fs13"),
+ # valign="top", width=740)
+ # ))
PubMedLink = ""
if thisTrait.pubmed_id:
PubMedLink = webqtlConfig.PUBMEDLINK_URL % thisTrait.pubmed_id
if PubMedLink:
- tbl.append(HT.TR(
- HT.TD('Link: ', Class="fs13 fwb",
- valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(HT.Href(url=PubMedLink, text="PubMed",target='_blank',Class="fs14 fwn"),
- style = "background:#cddcff;padding:2"), valign="top", width=740)
- ))
+ #tbl.append(HT.TR(
+ # HT.TD('Link: ', Class="fs13 fwb",
+ # valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(HT.Href(url=PubMedLink, text="PubMed",target='_blank',Class="fs14 fwn"),
+ # style = "background:#cddcff;padding:2"), valign="top", width=740)
+ # ))
+ pass
menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1")
- menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
- menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
+ #menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
+ #menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
- title1Body.append(tbl, HT.BR(), menuTable)
+ #title1Body.append(tbl, HT.BR(), menuTable)
elif thisTrait and thisTrait.db and thisTrait.db.type == 'Geno': #Check if trait is genotype
@@ -808,32 +816,33 @@ class DataEditingPage(templatePage):
rnaseqButton.append(rnaseqButtonImg)
rnaseqText = "RNA-seq"
- tbl.append(HT.TR(
- HT.TD('Location: ', Class="fs13 fwb",
- valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Span(location, Class="fs13"), valign="top", width=740)
- ),
- HT.TR(
- HT.TD('SNP Search: ', Class="fs13 fwb",
- valign="top", nowrap="on", width=90),
- HT.TD(width=10, valign="top"),
- HT.TD(HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp&cmd=search&term=%s" % thisTrait.name, 'NCBI',Class="fs13"),
- valign="top", width=740)
- ))
+ #tbl.append(HT.TR(
+ # HT.TD('Location: ', Class="fs13 fwb",
+ # valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Span(location, Class="fs13"), valign="top", width=740)
+ # ),
+ # HT.TR(
+ # HT.TD('SNP Search: ', Class="fs13 fwb",
+ # valign="top", nowrap="on", width=90),
+ # HT.TD(width=10, valign="top"),
+ # HT.TD(HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp&cmd=search&term=%s" % thisTrait.name, 'NCBI',Class="fs13"),
+ # valign="top", width=740)
+ # ))
menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1")
- menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
- menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
+ #menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
+ #menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
- title1Body.append(tbl, HT.BR(), menuTable)
+ #title1Body.append(tbl, HT.BR(), menuTable)
elif (thisTrait == None or thisTrait.db.type == 'Temp'): #if temporary trait (user-submitted trait or PCA trait)
- TempInfo = HT.Paragraph()
+ #TempInfo = HT.Paragraph()
if thisTrait != None:
if thisTrait.description:
- tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),' %s ' % thisTrait.description,HT.BR()), colspan=3, height=15))
+ pass
+ #tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),' %s ' % thisTrait.description,HT.BR()), colspan=3, height=15))
else:
tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),'not available',HT.BR(),HT.BR()), colspan=3, height=15))
@@ -842,10 +851,10 @@ class DataEditingPage(templatePage):
else:
menuTable = HT.TableLite(cellpadding=2, Class="collap", width="80", id="target1")
- menuTable.append(HT.TR(HT.TD(addSelectionButton, align="right"),HT.TD(updateButton, align="right"), colspan=3, height=50, style="vertical-align:bottom;") )
- menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
-
- title1Body.append(tbl, HT.BR(), menuTable)
+ #menuTable.append(HT.TR(HT.TD(addSelectionButton, align="right"),HT.TD(updateButton, align="right"), colspan=3, height=50, style="vertical-align:bottom;") )
+ #menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
+ #
+ #title1Body.append(tbl, HT.BR(), menuTable)
else:
pass
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index 1325e4b0..fb2e373c 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -44,7 +44,7 @@
|
- Sall3 |
+ {{ thisTrait.symbol }} |
@@ -52,7 +52,7 @@
|
- B130022O04Rik, Msal, Msal-1, Sal, Salt, Spalt |
+ {{ thisTrait.alias_fmt }} |
@@ -60,7 +60,7 @@
|
- sal-like 3 (Drosophila) |
+ {{ thisTrait.description_fmt }} |
@@ -5005,4 +5005,3 @@
{% endblock %}
-
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3457f0ff..58eeddd3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -26,4 +26,4 @@ def showDatabaseBXD():
# Here it's currently too complicated not to use an fd that is a webqtlFormData
fd = webqtlFormData.webqtlFormData(request.args)
template_vars = show_trait_page.ShowTraitPage(fd)
- return render_template("trait_data_and_analysis.html")
+ return render_template("trait_data_and_analysis.html", **template_vars.__dict__)
--
cgit v1.2.3