diff options
| -rw-r--r-- | wqflask/runserver.py | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/DataEditingPage.py | 461 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/trait_data_and_analysis.html | 7 | ||||
| -rw-r--r-- | 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 @@ <td valign="top" width="10"></td> - <td valign="top" width="740"><span class="fs13 fsI">Sall3</span></td> + <td valign="top" width="740"><span class="fs13 fsI">{{ thisTrait.symbol }}</span></td> </tr> <tr> @@ -52,7 +52,7 @@ <td valign="top" width="10"></td> - <td valign="top"><span class="fs13 fsI">B130022O04Rik, Msal, Msal-1, Sal, Salt, Spalt</span></td> + <td valign="top"><span class="fs13 fsI">{{ thisTrait.alias_fmt }}</span></td> </tr> <tr> @@ -60,7 +60,7 @@ <td valign="top" width="10"></td> - <td valign="top"><span class="fs13">sal-like 3 (Drosophila)</span></td> + <td valign="top"><span class="fs13">{{ thisTrait.description_fmt }}</span></td> </tr> <tr> @@ -5005,4 +5005,3 @@ </td> </tr><!-- End of body --> {% 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__) |