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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