diff options
Diffstat (limited to 'web/webqtl/collection/AddToSelectionPage.py')
| -rw-r--r-- | web/webqtl/collection/AddToSelectionPage.py | 695 |
1 files changed, 695 insertions, 0 deletions
diff --git a/web/webqtl/collection/AddToSelectionPage.py b/web/webqtl/collection/AddToSelectionPage.py new file mode 100644 index 00000000..2a99e8c1 --- /dev/null +++ b/web/webqtl/collection/AddToSelectionPage.py @@ -0,0 +1,695 @@ +#AddToSelectionPage.py + +import string +from htmlgen import HTMLgen2 as HT +import os +import cPickle +import reaper + +from base import webqtlConfig +from base.templatePage import templatePage +from utility.THCell import THCell +from utility.TDCell import TDCell +from utility import webqtlUtil +from showTrait import ShowProbeInfoPage +# NL, 07/27/2010: add 'import webqtlDatabaseFunction' for retrieveSpecies function +from dbFunction import webqtlDatabaseFunction +from base.webqtlTrait import webqtlTrait + + +######################################### +# Add to Selection Page +######################################### +class AddToSelectionPage(templatePage): + + def __init__(self,fd): + + templatePage.__init__(self, fd) + + if not self.openMysql(): + return + + if not fd.genotype: + fd.readGenotype() + + self.searchResult = fd.formdata.getvalue('searchResult', []) + if type("1") == type(self.searchResult): + self.searchResult = [self.searchResult] + if fd.formdata.getvalue('fromDataEditingPage'): + searchResult2 = fd.formdata.getvalue('fullname') + if searchResult2: + self.searchResult.append(searchResult2) + + if self.searchResult: + pass + else: + templatePage.__init__(self, fd) + heading = 'Add Collections' + detail = ['You need to select at least one trait to add to your selection.'] + self.error(heading=heading,detail=detail) + return + + if self.genSelection(fd=fd): + self.writeHTML(fd) + + + + def genSelection(self, fd=None, checkPreSelection = 1): + collectionName = '%s_Select' % fd.RISet + + if checkPreSelection: + try: + preSelection = fd.input_session_data[collectionName] + preSelection = list(string.split(preSelection,',')) + except: + preSelection = [] + else: + preSelection = [] + + if preSelection: + for item in preSelection: + if item not in self.searchResult: + self.searchResult.append(item) + + self.searchResult = map(self.transfer2NewName, self.searchResult) + + for item in self.searchResult: + if not item: + self.searchResult.remove(item) + + if len(self.searchResult) > 3000: + heading = 'Add Collections' + detail = ['You are adding over 3000 traits to selections, please reduce your number of traits.'] + self.error(heading=heading,detail=detail) + return 0 + + searchResult2 = [] + self.theseTraits = [] + for item in self.searchResult: + try: + thisTrait = webqtlTrait(fullname=item, cursor=self.cursor) + thisTrait.retrieveInfo(QTL=1) + self.theseTraits.append(thisTrait) + searchResult2.append(item) + except: + pass + + allTraitStr = string.join(searchResult2,',') + + self.session_data_changed[collectionName] = allTraitStr + + return 1 + + + + def writeHTML(self,fd): + TD_LR = HT.TD(height=100,width="100%",bgColor='#eeeeee',valign="top") + pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") + tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0, align="Left") + seq = 1 + SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title") + + mintmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'showIntMap');}") + mintmap_img = HT.Image("/images/multiple_interval_mapping1_final.jpg", name='mintmap', alt="Multiple Interval Mapping", title="Multiple Interval Mapping", style="border:none;") + mintmap.append(mintmap_img) + mcorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'compCorr');}") + mcorr_img = HT.Image("/images/compare_correlates2_final.jpg", name='comparecorr', alt="Compare Correlates", title="Compare Correlates", style="border:none;") + mcorr.append(mcorr_img) + cormatrix = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');}") + cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", name='corrmatrix', alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;") + cormatrix.append(cormatrix_img) + networkGraph = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'networkGraph');}") + networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='networkgraph', alt="Network Graphs", title="Network Graphs", style="border:none;") + networkGraph.append(networkGraph_img) + heatmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');}") + heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='heatmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;") + heatmap.append(heatmap_img) + partialCorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'partialCorrInput');}") + partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;") + partialCorr.append(partialCorr_img) + + BN = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'BNInput');}") + networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='BayesianNetwork', alt="Bayesian Network", title="Bayesian Network", style="border:none;") + BN.append(networkGraph_img) + + removeselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('showDatabase')[0], 'removeSelection');" % fd.RISet) + removeselect_img = HT.Image("/images/remove_selection1_final.jpg", name="removeselect", alt="Remove Selection", title="Remove Selection", style="border:none;") + removeselect.append(removeselect_img) + selectall = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', true);") + selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;") + selectall.append(selectall_img) + reset = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', false);") + reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;") + reset.append(reset_img) + exportSelect = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'exportSelectionDetailInfo');") + exportSelect_img = HT.Image("/images/export2_final.jpg", name="exportSelection", alt="Export Selection", title="Export Selection", style="border:none;") + exportSelect.append(exportSelect_img) + selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('showDatabase')[0]);") + selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;") + selectinvert.append(selectinvert_img) + + chrMenu = HT.Input(type='hidden',name='chromosomes',value='all') + + importFile = HT.Input(type='file', name='importfile', size=15) + importButton = HT.Input(type='button',name='importSelection',value='Load Collection', onClick="addRmvSelection('%s', this.form, 'importSelect');" % fd.RISet,Class="button") + exportButton = HT.Input(type='button' ,name='exportSelection',value='Save Collection', onClick="databaseFunc(this.form,'exportSelect');", Class="button") + importMenu = HT.Select(name='importmethod') + importMenu.append(('append','append')) + importMenu.append(('replace','replace')) + + ODE = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'ODE');") + ODE_img = HT.Image("/images/ODE_logo_final.jpg", name="ode", alt="ODE", title="ODE", style="border:none") + ODE.append(ODE_img) + + GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'GCAT');") + GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none") + GCATButton.append(GCATButton_img) + + GeneSet = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0],'GOTree');") + GeneSet_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none") + GeneSet.append(GeneSet_img) + + #need to be refined + if fd.genotype.Mbmap: + scale = HT.Input(name="scale", value="physic", type="hidden") + else: + scale = "" + + formMain = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden')) + + #XZ, July 22, 2011: I add parameters for interval mapping + hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet,'incparentsf1':'ON','showHideOptions':'more','scale':'physic','additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'intervalAnalystCheck':'ON','bootCheck':None, 'permCheck':None, 'applyVarianceSE':None} + for key in hddn.keys(): + formMain.append(HT.Input(name=key, value=hddn[key], type='hidden')) + + if not self.searchResult: + SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title") + formMain.append(HT.HR(width="70%", color = "blue"),importFile, ' ', importMenu, ' ', importButton) + TD_LR.append(SelectionHeading,HT.Blockquote('No trait has been added to this selection.'), HT.Center(HT.BR(), HT.BR(), HT.BR(), HT.BR(), formMain)) + self.dict['body'] = str(TD_LR) + self.dict['title'] = "%s Trait Collection" % fd.RISet + return + + ######################################### + # Creating table object for AJAX table # + ######################################### + tblobj = {} + mainfmName = 'showDatabase' + # NL, 07/27/2010. retrieveSpecies function has been moved from webqtlTrait.py to webqtlDatabaseFunction.py; + species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + if species == 'human': + chrMenu = scale = mintmap = heatmap = "" + + tblobj['header'] = self.getCollectionTableHeader() + + sortby = self.getSortByValue() + + thisRISet = fd.RISet + tblobj['body'] = self.getCollectionTableBody(RISet=thisRISet, traitList=self.theseTraits, formName=mainfmName, species=species) + + filename= webqtlUtil.genRandStr("Search_") + + objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') + cPickle.dump(tblobj, objfile) + objfile.close() + + + div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), Id="sortable") + + + containerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left") + postContainerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left") + + optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="400", border=0, align="Left") + optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(removeselect), HT.TD(exportSelect))) + optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*1,"Remove"), HT.TD(" "*1,"Export"))) + postContainerTable.append(HT.TR(HT.TD(optionsTable))) + containerTable.append(HT.TR(HT.TD(optionsTable))) + + functionTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="480",border=0, align="Left") + functionRow = HT.TR(HT.TD(networkGraph, width="16.7%"), HT.TD(cormatrix, width="16.7%"), HT.TD(partialCorr, width="16.7%"), HT.TD(mcorr, width="16.7%"), HT.TD(mintmap, width="16.7%"), HT.TD(heatmap)) + if species == "human": + labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare"))) + else: + labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")), HT.TD(HT.Text("QTL Map")), HT.TD(HT.Text(text="Heat Map"))) + functionTable.append(functionRow, labelRow) + postContainerTable.append(HT.TR(HT.TD(functionTable))) + containerTable.append(HT.TR(HT.TD(functionTable))) + + moreOptions = HT.Input(type='button',name='options',value='More Options', onClick="",Class="toggle") + fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle") + + + + if (fd.formdata.getvalue('showHideOptions') == 'less'): + postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide")))) + containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide")))) + else: + postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide")))) + containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide")))) + + + LinkOutTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="320",border=0, align="Left") + LinkOutRow = HT.TR(HT.TD(GeneSet, width="33%"), HT.TD(GCATButton, width="33%"), HT.TD(ODE, width="33%"), style="display:none;", Class="extra_options") + LinkOutLabels = HT.TR(HT.TD(HT.Text("Gene Set")), HT.TD(" "*2, HT.Text("GCAT")), HT.TD(" "*3, HT.Text("ODE")), style="display:none;", Class="extra_options") + LinkOutTable.append(LinkOutRow,LinkOutLabels) + postContainerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable))) + containerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable))) + + pageTable.append(HT.TR(HT.TD(containerTable))) + chrMenu = scale = "" + + pageTable.append(HT.TR(HT.TD(div))) + pageTable.append(HT.TR(HT.TD(" "))) + if len(self.theseTraits) > 20: + pageTable.append(HT.TR(HT.TD(postContainerTable))) + pageTable.append(HT.TR(HT.TD(importFile, ' ', importMenu, ' ', importButton, ' '*10, exportButton))) + #Took out scaleMenu since it will be replaced with a jquery popup in the future - Zach 5/10/2010 + formMain.append(chrMenu,scale,pageTable) + + #Updated by NL, deleted showHideJS, moved jquery to jqueryFunction.js + self.dict['js1'] = '' + TD_LR.append(SelectionHeading,formMain) + + self.dict['body'] = str(TD_LR) + self.dict['js2'] = 'onLoad="pageOffset()"' + self.dict['layer'] = self.generateWarningLayer() + self.dict['title'] = "%s Trait Collection" % thisRISet + + def transfer2NewName(self, str): + "this is temporary" + if str.find("::") < 0: + return str.replace(":", "::") + else: + return str + + def generateWarningLayer(self): + + layerString = """ + <!-- BEGIN FLOATING LAYER CODE //--> + <div id="warningLayer" style="padding:3px; border: 1px solid #222; + background-color: #fff; position:absolute;width:250px;left:100;top:100;visibility:hidden"> + <table border="0" width="250" class="cbrb" cellspacing="0" cellpadding="5"> + <tr> + <td width="100%"> + <table border="0" width="100%" cellspacing="0" cellpadding="0" height="36"> + <tr> + <td class="cbrb cw ff15 fwb" align="Center" width="100%" style="padding:4px"> + Sort Table + </td> + </tr> + <tr> + <td width="100%" bgcolor="#eeeeee" align="Center" style="padding:4px"> + <!-- PLACE YOUR CONTENT HERE //--> + Resorting this table <br> + <!-- END OF CONTENT AREA //--> + </td> + </tr> + </table> + </td> + </tr> + </table> + </div> + <!-- END FLOATING LAYER CODE //--> + + """ + + return layerString + + def getCollectionTableHeader(self): + + tblobj_header = [] + + className = "fs13 fwb ffl b1 cw cbrb" + + tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0), + THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=1), + THCell(HT.TD('Trait', HT.BR(), 'ID', HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=2), + THCell(HT.TD('Symbol', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="symbol", idx=3), + THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=4), + THCell(HT.TD('Location', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=5), + THCell(HT.TD('Mean', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=6), + THCell(HT.TD('N', HT.BR(), 'Cases', HT.BR(), valign="top", Class=className, nowrap="on"), text="samples", idx=7), + THCell(HT.TD('Max LRS', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs", idx=8), + THCell(HT.TD('Max LRS Location',HT.BR(),'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs_location", idx=9)]] + + return tblobj_header + + def getCollectionTableBody(self, RISet=None, traitList=None, formName=None, species=''): + + tblobj_body = [] + + className = "fs12 fwn b1 c222" + + for thisTrait in traitList: + tr = [] + + if not thisTrait.haveinfo: + thisTrait.retrieveInfo(QTL=1) + + if thisTrait.riset != RISet: + continue + + trId = str(thisTrait) + + #XZ: check box column + tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className))) + + #XZ: Dataset column + tr.append(TDCell(HT.TD(thisTrait.db.name, Class="fs12 fwn b1 c222"), thisTrait.db.name, thisTrait.db.name.upper())) + + #XZ: Trait ID column + if thisTrait.cellid: + tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.cellid,url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, thisTrait.db.name, thisTrait.name, thisTrait.cellid), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.cellid), thisTrait.cellid)) + else: + tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name)) + + #XZ: Symbol column and Description column + if (thisTrait.db.type == "Publish"): + AbbreviationString = "--" + if (thisTrait.post_publication_abbreviation != None): + AbbreviationString = thisTrait.post_publication_abbreviation + PhenotypeString = thisTrait.post_publication_description + if thisTrait.confidential: + if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): + if thisTrait.pre_publication_abbreviation: + AbbreviationString = thisTrait.pre_publication_abbreviation + else: + AbbreviationString = "--" + PhenotypeString = thisTrait.pre_publication_description + + if AbbreviationString == "--": + tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) + else: + tr.append(TDCell(HT.TD(AbbreviationString, Class=className), AbbreviationString, AbbreviationString.upper())) + + tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper())) + + + elif (thisTrait.db.type == "ProbeSet" or thisTrait.db.type == "Temp"): + description_string = str(thisTrait.description).strip() + if (thisTrait.db.type == "ProbeSet"): + if (thisTrait.symbol != None): + if thisTrait.geneid: + symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % thisTrait.geneid, Class="font_black fs12 fwn") + else: + symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % thisTrait.symbol, Class="font_black fs12 fwn") + tr.append(TDCell(HT.TD(symbolurl, align="left", Class="fs12 fwn b1 c222 fsI"), thisTrait.symbol, thisTrait.symbol)) + else: + tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) + target_string = str(thisTrait.probe_target_description).strip() + + description_display = '' + + if len(description_string) > 1 and description_string != 'None': + description_display = description_string + else: + description_display = thisTrait.symbol + + if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None': + description_display = description_display + '; ' + target_string.strip() + + description_string = description_display + else: + tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) + tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string)) + else: + if (thisTrait.name != None): + tr.append(TDCell(HT.TD(thisTrait.name, Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name)) + else: + tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) + tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) + + #XZ: Location column + if (thisTrait.db.type == "Publish"): + tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) + else: + if thisTrait.db.type == "ProbeSet" and thisTrait.cellid: + EnsemblProbeSetID = thisTrait.name + if '_at' in thisTrait.name: + EnsemblProbeSetID = thisTrait.name[0:thisTrait.name.index('_at')+3] + + #These tables (Ensembl) were created by Xusheng Wang in 2010 and are mm9 (so they'll need to be changed at some point to be mm10. + self.cursor.execute(''' + SELECT EnsemblProbeLocation.* + FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze, ProbeSetFreeze + WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and + GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and + ProbeSetFreeze.Id=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id group by Chr, Start, End''' + ,(thisTrait.cellid, EnsemblProbeSetID, thisTrait.db.id)) + LocationFields = self.cursor.fetchall() + + Chr='' + Mb='' + Start='' + End='' + if (len(LocationFields)>=1): + Chr,Start,End,Strand,MisMatch,ProbeId = map(self.nullRecord,LocationFields[0]) + Start /= 1000000.0 + End /= 1000000.0 + Mb = Start + if (len(LocationFields)>1): + self.cursor.execute(''' + SELECT ProbeSet.Chr, ProbeSet.Mb FROM ProbeSet, ProbeFreeze, ProbeSetFreeze + WHERE ProbeSet.ChipId=ProbeFreeze.ChipId and ProbeSet.Name=%s and ProbeSetFreeze.Id=%s and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id''' + ,(thisTrait.name, thisTrait.db.id)) + ProbeSetChr, ProbeSetMb = map(self.nullRecord,self.cursor.fetchall()[0]) + + self.cursor.execute(''' + SELECT EnsemblProbeLocation.*, ABS(EnsemblProbeLocation.Start/1000000-%s) as Mb + FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze + WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and + GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and + EnsemblProbeLocation.Chr=%s and ProbeSetFreezeId=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id order by Mb limit 1''' + ,(ProbeSetMb, thisTrait.cellid, EnsemblProbeSetID, ProbeSetChr, thisTrait.db.id)) + NewLocationFields = self.cursor.fetchall() + if (len(NewLocationFields)>0): + Chr,Start,End,Strand,MisMatch,ProbeId,Mb = map(self.nullRecord,NewLocationFields[0]) + Start /= 1000000.0 + End /= 1000000.0 + Mb = Start + + #ZS: trait_location_value is used for sorting + trait_location_repr = "--" + trait_location_value = 1000000 + + if Chr and Mb: + try: + trait_location_value = int(Chr)*1000 + Mb + except: + if Chr.upper() == "X": + trait_location_value = 20*1000 + Mb + else: + trait_location_value = ord(str(Chr).upper()[0])*1000 + Mb + + trait_location_repr = "Chr%s: %.6f" % (Chr, float(Mb) ) + + tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value)) + + else: + + #ZS: trait_location_value is used for sorting + trait_location_repr = "--" + trait_location_value = 1000000 + + if hasattr(thisTrait, 'chr') and hasattr(thisTrait, 'mb') and thisTrait.chr and thisTrait.mb: + try: + trait_location_value = int(thisTrait.chr)*1000 + thisTrait.mb + except: + if thisTrait.chr.upper() == "X": + trait_location_value = 20*1000 + thisTrait.mb + else: + trait_location_value = ord(str(thisTrait.chr).upper()[0])*1000 + thisTrait.mb + + trait_location_repr = "Chr%s: %.6f" % (thisTrait.chr, float(thisTrait.mb) ) + + tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value)) + + #XZ: Mean column + if (thisTrait.db.type == "ProbeSet"): + if thisTrait.cellid: + mean = -10000.0 + try: + thisTrait.retrieveData() + mean, median, var, stdev, sem, N = reaper.anova(thisTrait.exportInformative()[1]) + except: + pass + repr = '%2.3f' % mean + mean = '%2.2f' % mean + tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean)) + else: + self.cursor.execute(""" + select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet + where ProbeSetXRef.ProbeSetFreezeId = %d and + ProbeSet.Id = ProbeSetXRef.ProbeSetId and + ProbeSet.Name = '%s' + """ % (thisTrait.db.id, thisTrait.name)) + result = self.cursor.fetchone() + if result: + if result[0]: + mean = result[0] + else: + mean=0 + else: + mean = 0 + + #XZ, 06/05/2009: It is neccessary to turn on nowrap + repr = "%2.3f" % mean + tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean)) + + elif (thisTrait.db.type == "Publish"): + self.cursor.execute(""" + select count(PublishData.value), sum(PublishData.value) from PublishData, PublishXRef, PublishFreeze + where PublishData.Id = PublishXRef.DataId and + PublishXRef.Id = %s and + PublishXRef.InbredSetId = PublishFreeze.InbredSetId and + PublishFreeze.Id = %d + """ % (thisTrait.name, thisTrait.db.id)) + result = self.cursor.fetchone() + + if result: + if result[0] and result[1]: + mean = result[1]/result[0] + else: + mean = 0 + else: + mean = 0 + + repr = "%2.3f" % mean + tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean)) + else: + tr.append(TDCell(HT.TD("--", Class=className, align='left', nowrap='ON'),"--", 0)) + + #Number of cases + n_cases_value = 0 + n_cases_repr = "--" + if (thisTrait.db.type == "Publish"): + self.cursor.execute(""" + select count(PublishData.value) from PublishData, PublishXRef, PublishFreeze + where PublishData.Id = PublishXRef.DataId and + PublishXRef.Id = %s and + PublishXRef.InbredSetId = PublishFreeze.InbredSetId and + PublishFreeze.Id = %d + """ % (thisTrait.name, thisTrait.db.id)) + result = self.cursor.fetchone() + + if result: + if result[0]: + n_cases_value = result[0] + n_cases_repr = result[0] + + if (n_cases_value == "--"): + tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value)) + else: + tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value)) + + elif (thisTrait.db.type == "ProbeSet"): + self.cursor.execute(""" + select count(ProbeSetData.value) from ProbeSet, ProbeSetXRef, ProbeSetData, ProbeSetFreeze + where ProbeSet.Name='%s' and + ProbeSetXRef.ProbeSetId = ProbeSet.Id and + ProbeSetXRef.DataId = ProbeSetData.Id and + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and + ProbeSetFreeze.Name = '%s' + """ % (thisTrait.name, thisTrait.db.name)) + result = self.cursor.fetchone() + + if result: + if result[0]: + n_cases_value = result[0] + n_cases_repr = result[0] + if (n_cases_value == "--"): + tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value)) + else: + tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value)) + + elif (thisTrait.db.type == "Geno"): + self.cursor.execute(""" + select count(GenoData.value) from GenoData, GenoXRef, GenoFreeze, Geno, Strain + where Geno.SpeciesId = %s and Geno.Name='%s' and + GenoXRef.GenoId = Geno.Id and + GenoXRef.DataId = GenoData.Id and + GenoXRef.GenoFreezeId = GenoFreeze.Id and + GenoData.StrainId = Strain.Id and + GenoFreeze.Name = '%s' + """ % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, thisTrait.db.riset), thisTrait.name, thisTrait.db.name)) + result = self.cursor.fetchone() + + if result: + if result[0]: + n_cases_value = result[0] + n_cases_repr = result[0] + if (n_cases_value == "--"): + tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value)) + else: + tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value)) + + else: + tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value)) + + #XZ: Max LRS column and Max LRS Location column + if (thisTrait.db.type != "Geno"): + #LRS and its location + LRS_score_repr = '--' + LRS_score_value = 0 + LRS_location_repr = '--' + LRS_location_value = 1000000 + LRS_flag = 1 + + #Max LRS and its Locus location + if hasattr(thisTrait, 'lrs') and hasattr(thisTrait, 'locus') and thisTrait.lrs and thisTrait.locus: + self.cursor.execute(""" + select Geno.Chr, Geno.Mb from Geno, Species + where Species.Name = '%s' and + Geno.Name = '%s' and + Geno.SpeciesId = Species.Id + """ % (species, thisTrait.locus)) + result = self.cursor.fetchone() + + if result: + if result[0] and result[1]: + LRS_Chr = result[0] + LRS_Mb = result[1] + + #XZ: LRS_location_value is used for sorting + try: + LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb) + except: + if LRS_Chr.upper() == 'X': + LRS_location_value = 20*1000 + float(LRS_Mb) + else: + LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb) + + + LRS_score_repr = '%3.1f' % thisTrait.lrs + LRS_score_value = thisTrait.lrs + LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) ) + LRS_flag = 0 + + tr.append(TDCell(HT.TD(LRS_score_repr, Class=className, align='right', nowrap="on"), LRS_score_repr, LRS_score_value)) + tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value)) + + if LRS_flag: + tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value)) + tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value)) + else: + tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 0)) + tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 1000000)) + + tblobj_body.append(tr) + + return tblobj_body + + def getSortByValue(self): + + sortby = ("pv", "up") + + return sortby + + def nullRecord(self,x): + if x or x == 0: + return x + else: + return "" + |