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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/search/TextSearchPage.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/search/TextSearchPage.py')
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1 files changed, 536 insertions, 0 deletions
diff --git a/web/webqtl/search/TextSearchPage.py b/web/webqtl/search/TextSearchPage.py
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+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import string
+import os
+import cPickle
+from math import *
+
+import reaper
+from htmlgen import HTMLgen2 as HT
+
+from base import admin
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+from base.webqtlDataset import webqtlDataset
+from base.webqtlTrait import webqtlTrait
+from utility.THCell import THCell
+from utility.TDCell import TDCell
+from utility import webqtlUtil
+
+
+
+class TextSearchPage(templatePage):
+ maxReturn = 200
+
+ def __init__(self, fd):
+
+ templatePage.__init__(self, fd)
+
+ if not self.openMysql():
+ return
+
+ # updated by NL, deleted jquery here, move it to dhtml.js
+ self.dict['js1'] = ''
+
+ species_list = [] #List of species (mouse, rat, human), with the selected species listed first
+
+ input_species = string.strip(string.lower(fd.formdata.getfirst('species', "mouse"))) #XZ, Oct 28, 2009: I changed the default species to mouse.
+ species_list.append(input_species)
+ #Create list of species (mouse, rat, human) with the species the user selected first
+ for species in ["mouse","rat","human"]:
+ if species not in species_list:
+ species_list.append(species)
+
+ ADMIN_tissue_alias = admin.ADMIN_tissue_alias
+
+ tissue = string.strip(string.lower(fd.formdata.getfirst('tissue', "")))
+ if tissue:
+ try:
+ rev_ADMIN_tissue_alias = {}
+ for key in ADMIN_tissue_alias.keys():
+ rev_ADMIN_tissue_alias[key] = key
+ for alias in ADMIN_tissue_alias[key]:
+ rev_ADMIN_tissue_alias[alias.upper()] = key
+ tissue = rev_ADMIN_tissue_alias[tissue.upper()]
+ except:
+ tissue = "UNKNOWN"
+
+ #possibly text output
+ txtOutput = [] #ZS: if format=text
+ all_species_dataset_count = 0 #XZ: count of datasets across all species; used in the opening text of the page
+ all_species_trait_count = 0 #XZ: count of records across all species; used in opening text of the page and text file (if format = text)
+
+ #div containing the tabs (species_container), the tabs themselves (species_tab_list, which is inserted into species_tabs), and the table (species_table) containing both the tissue and results tables for each tab
+ species_container = HT.Div(id="species_tabs", Class="tab_container") #Div that will contain tabs for mouse/rat/human species; each tab contains a table with the result count for each tissue group
+ species_tab_list = [HT.Href(text="%s" % species_list[0].capitalize(), url="#species1"), HT.Href(text="%s" % species_list[1].capitalize(), url="#species2"), HT.Href(text="%s" % species_list[2].capitalize(), url="#species3")]
+ species_tabs = HT.List(species_tab_list, Class="tabs")
+ species_table = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
+
+ for i in range(len(species_list)):
+ species_container_table = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") #ZS: Table containing both the tissue record count and trait record tables as cells; this fixes a display issue in some browsers that places the tables side by side instead of top/bottom
+
+ species = species_list[i]
+ ADMIN_search_dbs = admin.ADMIN_search_dbs[species]
+ this_species_dataset_count = 0 #XZ: count of the datasets containing results for this species
+ this_species_trait_count = 0 #XZ: count of the trait records for this species
+
+ div = HT.Div(id="species%s" % (i+1), Class="tab_content")
+ tab_container = HT.Span() #ZS: Contains species_container_table within the species' tab
+
+ tissuePageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
+ tissue_tblobj = {} # object used to create the table listing the results for each tissue
+ tissue_tblobj['header'] = self.getTissueTableHeader() # creates header for table listing results for selected tissue
+
+ traitPageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
+ trait_tblobj = {} # object used to create the table listing the trait results for each tissue
+ trait_tblobj['header'] = self.getTraitTableHeader() # creates header for table listing trait results for selected tissue
+
+ tissue_tblobj['body'], trait_tblobj['body'], this_species_dataset_count, this_species_trait_count, this_species_txtOutput = self.createTableBodies(fd, species, tissue, ADMIN_search_dbs)
+
+ if species == input_species:
+ txtOutput = this_species_txtOutput
+
+ filename1 = webqtlUtil.genRandStr("Search_") #filename for tissue table object
+ tissue_objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename1), 'wb')
+ cPickle.dump(tissue_tblobj, tissue_objfile)
+ tissue_objfile.close()
+
+ tissue_sortby = self.getTissueSortByValue() # sets how the tissue table should be sorted by default
+ tissue_div = HT.Div(webqtlUtil.genTableObj(tblobj=tissue_tblobj, file=filename1, sortby=tissue_sortby, tableID = "tissue_sort%s" % (i+1), addIndex = "1"), Id="tissue_sort%s" % (i+1))
+
+ tissuePageTable.append(HT.TR(HT.TD(" ")))
+ tissuePageTable.append(HT.TR(HT.TD(tissue_div)))
+ tissuePageTable.append(HT.TR(HT.TD(" ")))
+ species_container_table.append(HT.TR(HT.TD(tissuePageTable)), HT.TR(HT.TD(" ")))
+
+
+ filename2 = webqtlUtil.genRandStr("Search_") #filename for trait table object
+ trait_objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename2), 'wb')
+ cPickle.dump(trait_tblobj, trait_objfile)
+ trait_objfile.close()
+
+ trait_sortby = self.getTraitSortByValue() # sets how the trait table should be sorted by default
+ trait_div = HT.Div(webqtlUtil.genTableObj(tblobj=trait_tblobj, file=filename2, sortby=trait_sortby, tableID = "results_sort%s" % (i+1), addIndex = "0"), Id="results_sort%s" % (i+1))
+
+ traitPageTable.append(HT.TR(HT.TD(" ")))
+ traitPageTable.append(HT.TR(HT.TD(trait_div)))
+ traitPageTable.append(HT.TR(HT.TD(" ")))
+ species_container_table.append(HT.TR(HT.TD(traitPageTable)), HT.TR(HT.TD(" ")))
+
+ if this_species_trait_count == 0:
+ tab_container.append(HT.Div("No records retrieved for this species.", align="left", valign="top", style="font-size:42"))
+ else:
+ tab_container.append(species_container_table)
+
+ all_species_dataset_count += this_species_dataset_count
+ all_species_trait_count += this_species_trait_count
+
+ div.append(tab_container)
+ species_table.append(HT.TR(HT.TD(div)))
+
+ species_container.append(species_table)
+
+
+
+
+ if fd.returnFmt != 'text': #if the format is not 'text'
+ self.dict['title'] = 'Search Results'
+ TD_LR = HT.TD(height=100,width="100%",bgColor='#fafafa',valign="top")
+ pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") # Table containing all of the page's elements (opening text, form); in some browers the elements arrange themselves horizontally if you don't put them into a table, so this fixes that problem
+
+ formTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="100%",border=0) # Table containing all of the form's elements (tabs, option buttons); used to correct the same issue mentioned in pageTable's comment
+
+ mainForm = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
+ hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet}
+ hddn['incparentsf1']='ON'
+ for key in hddn.keys():
+ mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+
+ #Add to collection, select all, invert selection, and deselect all ("reset") buttons
+ addselect = HT.Href(url="#redirect", Class="add_traits")
+ addselect_img = HT.Image("/images/add_collection1_final.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;")
+ addselect.append(addselect_img)
+ selectall = HT.Href(url="#redirect", onClick="checkAll(document.getElementsByName('showDatabase')[0]);")
+ selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
+ selectall.append(selectall_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)
+ reset = HT.Href(url="#redirect", onClick="checkNone(document.getElementsByName('showDatabase')[0]); return false;")
+ reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
+ reset.append(reset_img)
+
+ #Table with select, deselect, invert, etc. It is used for the results table.
+ optionsTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="20%",border=0)
+ optionsRow = HT.TR(HT.TD(selectall, width="25%"), HT.TD(reset, width="25%"), HT.TD(selectinvert, width="25%"), HT.TD(addselect, width="25%"))
+ labelsRow = HT.TR(HT.TD(" "*2,"Select", width="25%"), HT.TD(" ","Deselect", width="25%"), HT.TD(" "*3,"Invert", width="25%"), HT.TD(" "*4,"Add", width="25%"))
+ optionsTable.append(HT.TR(HT.TD(" ")), optionsRow, labelsRow)
+
+ if fd.geneName:
+ searchType = "gene name " + fd.geneName
+ elif fd.refseq:
+ searchType = "RefSeq accession number " + fd.refseq
+ elif fd.genbankid:
+ searchType = "Genbank ID " + fd.genbankid
+ elif fd.geneid:
+ searchType = "Gene ID " + fd.geneid
+ else:
+ searchType = ""
+
+ SearchText = HT.Span("You searched for the %s in GeneNetwork." % searchType, HT.BR(),
+ "We queried %s expression datasets across %s species and listed the results" % (all_species_dataset_count, len(species_list)), HT.BR(),
+ "below. A total of %s records that may be of interest to you were found. The" % all_species_trait_count, HT.BR(),
+ "top table lists the number of results found for each relevant tissue, and the", HT.BR(),
+ "bottom gives a basic summary of each result. To study one of the results, click", HT.BR(),
+ "its Record ID. More detailed information is also available for each result's group", HT.BR() ,
+ "and dataset. To switch between species, click the tab with the corresponding", HT.BR(),
+ "label.", HT.BR(), HT.BR(),
+ "Please visit the links to the right to learn more about the variety of features", HT.BR(),
+ "available within GeneNetwork.")
+
+ LinkText = HT.Span()
+
+ mainLink = HT.Href(url="/webqtl/main.py", text = "Main Search Page", target="_blank")
+ homeLink = HT.Href(url="/home.html", text = "What is GeneNetwork?", target="_blank")
+ tourLink = HT.Href(url="/tutorial/WebQTLTour/", text = "Tour of GeneNetwork (20-40 min)", target="_blank")
+ faqLink = HT.Href(url="/faq.html", text = "Frequently Asked Questions", target="_blank")
+ glossaryLink = HT.Href(url="/glossary.html", text = "Glossary of terms used throughout GeneNetwork", target="_blank")
+
+ LinkText.append(mainLink, HT.BR(), homeLink, HT.BR(), tourLink, HT.BR(), faqLink, HT.BR(), glossaryLink)
+
+ formTable.append(HT.TR(HT.TD(species_tabs, species_container)), HT.TR(HT.TD(optionsTable)))
+ mainForm.append(formTable)
+
+
+ if fd.geneName:
+ SearchHeading = HT.Paragraph('Search Results for gene name ', fd.geneName)
+ elif fd.refseq:
+ SearchHeading = HT.Paragraph('Search Results for RefSeq accession number ', fd.refseq)
+ elif fd.genbankid:
+ SearchHeading = HT.Paragraph('Search Results for Genbank ID ', fd.genbankid)
+ elif fd.geneid:
+ SearchHeading = HT.Paragraph('Search Results for Gene ID ', fd.geneid)
+ else:
+ SearchHeading = HT.Paragraph('')
+
+ SearchHeading.__setattr__("class","title")
+
+ pageTable.append(HT.TR(HT.TD(SearchText, width=600), HT.TD(LinkText, align="left", valign="top")), HT.TR(HT.TD(" ", colspan=2)), HT.TR(HT.TD(mainForm, colspan=2)))
+ TD_LR.append(SearchHeading, pageTable)
+ self.dict['body'] = TD_LR
+ else:
+ if len(txtOutput) == 0:
+ self.output = "##No records were found for this species. \n"
+ else:
+ self.output = "##A total of %d records were returned. \n" % all_species_trait_count
+ newOutput = []
+ strainLists = {}
+ for item in txtOutput:
+ tissueGrp, thisTrait = item
+ RISet = thisTrait.riset
+ if strainLists.has_key(RISet):
+ thisStrainlist = strainLists[RISet]
+ else:
+ thisGenotype = reaper.Dataset()
+ thisGenotype.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
+ if thisGenotype.type == "riset":
+ _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[RISet]
+ thisGenotype = thisGenotype.add(Mat=_mat, Pat=_pat, F1=_f1)
+ thisStrainlist = list(thisGenotype.prgy)
+ strainLists[RISet] = thisStrainlist
+ thisTrait.retrieveData(strainlist=thisStrainlist)
+ thisData = []
+ for item in thisStrainlist:
+ if thisTrait.data.has_key(item): thisData.append(thisTrait.data[item].val)
+ else: thisData.append(None)
+ newOutput.append(["Structure", "Database", "ProbeSetID", "Cross"] + thisStrainlist)
+ newOutput.append([tissueGrp, '"%s"' % thisTrait.db.fullname, thisTrait.name, RISet]+map(str,thisData))
+ newOutput = webqtlUtil.asymTranspose(newOutput)
+ for item in newOutput:
+ self.output += string.join(item, "\t") + "\n"
+
+
+ def createTableBodies(self, fd, species, tissue, ADMIN_search_dbs):
+
+ this_species_txtOutput = []
+
+ #priority GeneName > refseq > genbankid
+ this_species_trait_count = 0 #count of all traits in this species
+ this_species_dataset_count = 0 #Number of datasets in this species
+ row_count = 0 #Index number used in the first row of the trait table
+ trait_tblobj_body = [] #body of table with the results themselves;
+ tissue_tblobj_body = [] #body of table with the number of results for each tissue group
+ className = "fs12 fwn b1 c222"
+
+ for i, tissueGrp in enumerate(ADMIN_search_dbs.keys()):
+ if tissue and tissue.upper() != tissueGrp.upper():
+ continue
+ dbNames = ADMIN_search_dbs[tissueGrp]
+
+ tissue_tr = [] #Table row for tissue group
+ tissue_tr.append(TDCell(HT.TD('', Class=className)))
+ tissue_tr.append(TDCell(HT.TD(tissueGrp.capitalize(), Class=className), tissueGrp, tissueGrp)) #Append cell with tissue name to row
+
+ this_tissue_record_count = 0 #Count of the results for each tissue
+ for dbName in dbNames:
+ this_species_dataset_count += 1
+ thisDB = webqtlDataset(dbName, self.cursor)
+
+ if fd.geneName:
+ if fd.searchAlias:
+ self.cursor.execute("""SELECT ProbeSet.Name
+ FROM
+ ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSetFreeze.Name = "%s" AND
+ ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+ MATCH (ProbeSet.symbol, alias) AGAINST ("+%s" IN BOOLEAN MODE) AND
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneName))
+ else:
+ self.cursor.execute("""SELECT ProbeSet.Name
+ FROM
+ ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSetFreeze.Name = "%s" AND
+ ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+ ProbeSet.symbol = "%s" AND
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneName))
+ elif fd.refseq:
+
+ # XZ, Oct/08/2009: Search for RefSeq ID is kind of tricky. One probeset can have multiple RefseqIDs that are delimited by ' /// ' (currently).
+ # So I have to use 'like' instead of '=' in SQL query. But user search with one short string, for example 'NM_1', it will return thousands of results.
+ # To prevent this, I set the restriction that the length of input Refseq ID must be at least 9 characters. Otherwise, do NOT start searching.
+ # Even with the restriction of input RefSeqID, I'm still worried about the 'like' in SQL query. My concern is in future, there might be RefSeqIDs with
+ # 10 characters whose first 9 characters are the same as the existing ones. So I decide to further check the result. We should also consider that the
+ # RefSeqID in database may have version number such as "NM_177938.2". If the input RefSeqID is 'NM_177938', it should be matched. I think we should get rid of the version number in database.
+
+ if len(fd.refseq) < 9:
+ if fd.returnFmt != 'text':
+ heading = "Search Result"
+ detail = ["The RefSeq ID that you inputed is less than 9 characters. GeneNetwork thinks it is not a legitimate RefSeq ID and did not do the search. Please try to use a RefSeq ID with at least 9 characters."]
+ self.error(heading=heading,detail=detail,error="Not Found")
+ else:
+ self.output = "#The gene name or IDs you submitted did not match any record in the databases available. You may try different gene names or tissue type."
+ return
+ else:
+ sqlString = """SELECT ProbeSet.Id, ProbeSet.RefSeq_TranscriptId
+ FROM
+ ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSetFreeze.Name = "%s" AND
+ ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+ MATCH(ProbeSet.RefSeq_TranscriptId) AGAINST ("+%s" IN BOOLEAN MODE) AND
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.refseq)
+
+ self.cursor.execute(sqlString)
+
+ results = self.cursor.fetchall()
+ if results:
+ Id_of_really_matched_probeset = []
+
+ for one_result in results:
+ ProbeSet_Id, ProbeSet_RefSeq_TranscriptId = one_result
+ multiple_RefSeqId = string.split(string.strip(ProbeSet_RefSeq_TranscriptId), '///')
+ for one_RefSeqId in multiple_RefSeqId:
+ tokens = string.split( one_RefSeqId, '.' )
+ one_RefSeqId_without_versionNum = string.strip(tokens[0])
+ if one_RefSeqId_without_versionNum == fd.refseq:
+ Id_of_really_matched_probeset.append( ProbeSet_Id )
+ break
+
+ if Id_of_really_matched_probeset:
+ condition_string = " or ".join(["Id = %s" % one_ID for one_ID in Id_of_really_matched_probeset])
+ sqlString = """SELECT ProbeSet.Name from ProbeSet where (%s)""" % condition_string
+
+ self.cursor.execute(sqlString)
+ else:
+ pass
+
+ elif fd.genbankid:
+ self.cursor.execute("""SELECT ProbeSet.Name
+ FROM
+ ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSetFreeze.Name = "%s" AND
+ ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+ ProbeSet.GenbankId = "%s" AND
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.genbankid))
+ elif fd.geneid:
+ self.cursor.execute("""SELECT ProbeSet.Name
+ FROM
+ ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSetFreeze.Name = "%s" AND
+ ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+ ProbeSet.GeneId = "%s" AND
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneid))
+ else:
+ continue
+
+ results = self.cursor.fetchall()
+ if len(results) > 0:
+ this_tissue_record_count += len(results)
+ this_species_trait_count += this_tissue_record_count
+
+ for result in results:
+ _ProbeSetID = result[0]
+ thisTrait = webqtlTrait(db=thisDB, name=_ProbeSetID, cursor=self.cursor)
+ results_tr = []
+ trId = str(thisTrait)
+ _traitUrl = thisTrait.genHTML(dispFromDatabase=1)
+ _traitName = str(thisTrait)
+
+ #ZS: check box column
+ results_tr.append(TDCell(HT.TD(str(row_count+1), HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", align="right", Class=className), str(row_count+1), row_count+1))
+ row_count += 1
+
+ #ZS: Tissue column
+ results_tr.append(TDCell(HT.TD(tissueGrp.capitalize(), Class=className), tissueGrp, tissueGrp))
+
+ #ZS: Group column
+ risetUrl = HT.Href(text=thisTrait.riset, url="http://www.genenetwork.org/%sCross.html#%s" % (species, thisTrait.riset), target="_blank", Class=className)
+ results_tr.append(TDCell(HT.TD(risetUrl, Class=className), thisTrait.riset, thisTrait.riset))
+
+ #ZS: Dataset column
+ results_tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name,
+ target='_blank', Class="fs13 fwn non_bold"), Class=className), thisTrait.db.name.upper(), thisTrait.db.name.upper()))
+
+ #ZS: Trait ID column
+ results_tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % ('showDatabase', thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name))
+
+ #ZS: Symbol column and Description column
+ description_string = str(thisTrait.description).strip()
+ if (thisTrait.db.type == "ProbeSet"):
+ 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:
+ results_tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
+
+ results_tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string))
+
+ #XZ: 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) )
+
+ results_tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
+
+ #ZS: Mean column
+ 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
+
+ repr = "%2.3f" % mean
+ results_tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))
+ trait_tblobj_body.append(results_tr)
+
+ this_species_txtOutput.append([tissueGrp, thisTrait])
+
+
+ tissue_tr.append(TDCell(HT.TD(str(this_tissue_record_count), Class=className), str(this_tissue_record_count), this_tissue_record_count))
+ tissue_tblobj_body.append(tissue_tr)
+
+ self.output = "self.output"
+
+ return tissue_tblobj_body, trait_tblobj_body, this_species_dataset_count, this_species_trait_count, this_species_txtOutput
+
+
+ def getTissueSortByValue(self):
+
+ sortby = ("tissue_group", "up")
+
+ return sortby
+
+
+ def getTraitSortByValue(self):
+
+ sortby = ("tissue", "up")
+
+ return sortby
+
+
+ def getTissueTableHeader(self):
+
+ tblobj_header = []
+
+ className = "fs13 fwb ffl b1 cw cbrb"
+
+ tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0),
+ THCell(HT.TD('Tissue',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="tissue_group", idx=1),
+ THCell(HT.TD('Results', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="results", idx=2)]]
+
+ return tblobj_header
+
+ def getTraitTableHeader(self):
+
+ tblobj_header = []
+
+ className = "fs13 fwb ffl b1 cw cbrb"
+
+ tblobj_header = [[THCell(HT.TD('Index',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="index", idx=0),
+ THCell(HT.TD('Tissue',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="tissue", idx=1),
+ THCell(HT.TD('Group',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="group", idx=2),
+ THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=3),
+ THCell(HT.TD('Record ID', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=4),
+ THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=5),
+ THCell(HT.TD('Location', HT.BR(), 'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=6),
+ THCell(HT.TD('Mean', HT.BR(), 'Expr', HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=7)]]
+
+ return tblobj_header