def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
ifVerified = fd.formdata.getvalue('ifVerified')
status = fd.formdata.getvalue('status')
if ifVerified != 'GN@UTHSC':
heading = "Error page"
detail = ["You are NoT verified as administrator."]
self.error(heading=heading,detail=detail)
return
else:
if status == 'input':
self.dict['body'] = self.genInputPage()
self.dict['title'] = 'Delete Phenotype Trait Input Page'
if status == 'check':
PublishFreeze_Name = fd.formdata.getvalue('PublishFreeze_Name')
traitID = fd.formdata.getvalue('traitID')
self.dict['body'] = self.checkInputPage(PublishFreeze_Name, traitID)
self.dict['title'] = 'Delete Phenotype Trait Check Input Page'
if status == 'delete':
PublishFreeze_Name = fd.formdata.getvalue('PublishFreeze_Name')
traitID = fd.formdata.getvalue('traitID')
self.dict['body'] = self.deleteResultPage(PublishFreeze_Name, traitID)
self.dict['title'] = 'Delete Phenotype Trait Result Page'
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 __init__(self, fd):
templatePage.__init__(self)
if not self.updMysql():
return
try:
user = fd.formdata.getvalue('user')
password = fd.formdata.getvalue('password')
newpassword = fd.formdata.getvalue('newpassword')
retypepassword = fd.formdata.getvalue('retypepassword')
except:
user = ''
if newpassword != retypepassword:
result = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('The new passwords you just entered are inconsistent. Please try it again',color='black'))
elif user and password and newpassword:
try:
encrypt_password = webqtlUtil.authUser(user,password,self.cursor)[3]
if encrypt_password:
self.cursor.execute("""update User set password=SHA(%s) where name=%s""",(newpassword,user))
result = HT.Blockquote(HT.Font('Change Result: ',color='green'),HT.Font('You have succesfully changed your password. You may continue to use WebQTL.',color='black'))
else:
result = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('You entered wrong user name or password. Please try it again.',color='black'))
except:
result = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('User database is not ready yet. Try again later.',color='black'))
else:
result = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('No user name or password or new password was entered, Please try it again.',color='black'))
result.__setattr__("class","subtitle")
self.dict['title'] = 'Change Password Result'
self.dict['body'] = HT.TD(result,colspan=2,height=200,width="100%",bgColor='#eeeeee')
def __init__(self, fd=None):
templatePage.__init__(self, fd)
if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
pass
else:
heading = "Editing Info"
detail = ["You don't have the permission to modify this file"]
self.error(heading=heading,detail=detail,error="Error")
return
cursor = webqtlDatabaseFunction.getCursor()
if (not cursor):
return
Id=self.trimValue(fd.formdata.getvalue('Id'))
GN_AccesionId=self.trimValue(fd.formdata.getvalue('GN_AccesionId'))
InfoPageName=self.trimValue(fd.formdata.getvalue('InfoPageName'))
DatasetId=self.trimValue(fd.formdata.getvalue('DatasetId'))
if Id=='-1':
sharingInfoObject = SharingInfo2.SharingInfo2(GN_AccesionId, InfoPageName)
GN_AccessionId,InfoPageName,info = sharingInfoObject.getInfo()
if info:
heading = "Editing Info"
detail = ["The new dataset info record is duplicate."]
self.error(heading=heading, detail=detail, error="Error")
return
sql = """INSERT INTO InfoFiles SET GN_AccesionId=%s, InfoPageName=%s, DatasetId=%s"""
cursor.execute(sql, tuple([GN_AccesionId, InfoPageName, DatasetId]))
infoupdate="This record has been succesfully added."
else:
sql = """UPDATE InfoFiles SET GN_AccesionId=%s, InfoPageName=%s, DatasetId=%s WHERE Id=%s"""
cursor.execute(sql, tuple([GN_AccesionId, InfoPageName, DatasetId, Id]))
infoupdate="This record has been succesfully updated."
sharingInfoObject = SharingInfo2.SharingInfo2(GN_AccesionId, InfoPageName)
sharingInfoObject.getInfo()
sharingInfoObject.getDatasetsList()
self.dict['body'] = sharingInfoObject.getBody(infoupdate=infoupdate)
def __init__(self, fd):
templatePage.__init__(self, fd)
collectionName = '%s_Select' % fd.RISet
try:
preSelection = fd.input_session_data[collectionName]
preSelection = list(string.split(preSelection,','))
except:
preSelection = []
for item in preSelection:
if not item:
preSelection.remove(item)
if preSelection:
self.content_type = 'application/txt'
self.content_disposition = 'attachment; filename=%s' % (fd.RISet+'_export-%s.txt' % time.strftime("%y-%m-%d-%H-%M"))
self.attachment += fd.RISet+"\n"
for item in preSelection:
self.attachment += item+"\n"
else:
heading = 'Export Collection'
detail = ['This collection is empty. No trait could be exported.']
self.error(heading=heading,detail=detail)
def __init__(self, fd, snpId):
templatePage.__init__(self, fd)
snpCols = "snpname, chromosome, mb, domain, rs, function, type, majorAllele, majorCount, minorAllele, minorCount, class, flanking5, flanking3, blatScore, sourceId, gene, ncbi".split(", ")
#get the details from the database if search the SNP variants by the "gene/snp" field
if snpId:
self.openMysql()
mysqlField = ['snpname','rs', 'chromosome', 'mb', 'function', 'type', 'class', 'flanking5', 'flanking3', 'blatscore', 'domain', 'gene', 'ncbi']
query = """
SELECT
%s, c.Name,b.*
from
SnpAll a, SnpPattern b, SnpSource c
where
a.Id =%s AND a.Id = b.SnpId AND a.SourceId =c.Id
""" % (string.join(mysqlField, ", "), snpId)
self.cursor.execute(query)
results = self.cursor.fetchone()
result =results[:14]
mysqlField.append('sourceName')
snpDict = {}
for i, item in enumerate(result):
snpDict[mysqlField[i]] = item
alleleList =results[15:]
objSnpBrowserPage =snpBrowserPage(fd)
flag =0
majAllele,minAllele,majAlleleCount,minAlleleCount= objSnpBrowserPage.getMajMinAlleles(alleleList,flag)
snpDict['majorAllele'] = majAllele
snpDict['minorAllele'] = minAllele
snpDict['majorCount'] = majAlleleCount
snpDict['minorCount'] = minAlleleCount
else:
return
# Creates the table for the SNP data
snpTable = HT.TableLite(border=0, cellspacing=5, cellpadding=3, Class="collap")
for item in snpCols:
thisTR = HT.TR(HT.TD(snpBrowserUtils.columnNames[item], Class="fs14 fwb ffl b1 cw cbrb", NOWRAP = 1))
if item in ('flanking5', 'flanking3'):
seq0 = snpDict[item]
seq = ""
i = 0
if seq0:
while i < len(seq0):
seq += seq0[i:i+5] + " "
i += 5
thisTR.append(HT.TD(HT.Span(seq, Class="code", Id="green"), Class='fs13 b1 cbw c222'))
elif item in snpDict.keys() and snpDict[item]:
thisTR.append(HT.TD(snpDict[item], Class='fs13 b1 cbw c222'))
else:
thisTR.append(HT.TD("", Class='fs13 b1 cbw c222'))
snpTable.append(thisTR)
self.dict['body'] = HT.TD(HT.Paragraph("Details for %s" % snpDict['snpname'], Class="title"), HT.Blockquote(snpTable))
self.dict['title'] = "Details for %s" % snpDict['snpname']
def __init__(self, fd, formdata, cookies):
templatePage.__init__(self, fd)
if not self.openMysql():
return
if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:
pass
else:
heading = "Upload File"
detail = ["You don't have the permission to upload file to the server."]
self.error(heading=heading,detail=detail)
return
self.cursor.close()
file1 = self.save_uploaded_file (formdata, 'imgName1')
file2 = self.save_uploaded_file (formdata, 'imgName2')
file3 = self.save_uploaded_file (formdata, 'imgName3')
file4 = self.save_uploaded_file (formdata, 'imgName4')
file5 = self.save_uploaded_file (formdata, 'imgName5')
i = 0
uploaded = []
for filename in (file1, file2, file3, file4, file5):
if filename:
i += 1
uploaded.append(filename)
if i == 0:
heading = "Upload File"
detail = ["No file was selected, no file uploaded."]
self.error(heading=heading,detail=detail)
return
else:
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
imgTbl = HT.TableLite(border=0, width = "90%",cellspacing=2, cellpadding=2, align="Center")
imgTbl.append(HT.TR(HT.TD("Thumbnail", width="%30", align='center',Class="colorBlue"),
HT.TD("URL", width="%60",Class="colorBlue", align='center')))
for item in uploaded:
img = HT.Image("/images/upload/" + item, border = 0, width=80)
#url = "%s/images/upload/" % webqtlConfig.PORTADDR + item
#url = HT.Href(text=url, url = url, Class='normalsize', target="_blank")
url2 = "/images/upload/" + item
url2 = HT.Href(text=url2, url = url2, Class='normalsize', target="_blank")
imgTbl.append(HT.TR(HT.TD(img, width="%30", align='center',Class="colorWhite"),
#HT.TD(url, HT.BR(), 'OR', HT.BR(), url2, width="%60",Class="colorWhite", align='center')))
HT.TD(url2, width="%60",Class="colorWhite", align='center')))
intro = HT.Paragraph('A total of %d files are uploaded' % i)
TD_LR.append( HT.Center(intro) )
TD_LR.append( imgTbl )
self.dict['body'] = str(TD_LR)
def __init__(self,fd):
templatePage.__init__(self, fd)
filename = self.session("Genome Association Result", "Computing Genome Association Results")
webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename)
os.system("%s %swebqtlCmdLine.py markerRegression %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
self.redirection = url
def __init__(self, fd=None):
templatePage.__init__(self, fd)
if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
pass
else:
heading = "Adding Info"
detail = ["You don't have the permission to add new dataset"]
self.error(heading=heading,detail=detail,error="Error")
return
self.dict['body'] = SharingBody.sharinginfoedit_body_string % ("Add new dataset", "-1", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "")
def __init__(self, fd=None):
templatePage.__init__(self, fd)
if not self.openMysql():
return
if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
pass
else:
heading = "Editing Info"
detail = ["You don't have the permission to list the datasets"]
self.error(heading=heading,detail=detail,error="Error")
return
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
query = """select InfoPageName,GN_AccesionId,InfoPageTitle,Progreso from InfoFiles order by Id"""
self.cursor.execute(query)
result = self.cursor.fetchall()
heading = HT.Paragraph('Dataset Table', Class="title")
newrecord = HT.Href(text="New Record", url="/webqtl/main.py?FormID=sharinginfoadd")
info = "Click the accession id to view the dataset info. Click the dataset name to edit the dataset info."
datasetTable = HT.TableLite(border=0, cellpadding=0, cellspacing=0, Class="collap", width="100%")
tableHeaderRow = HT.TR()
tableHeaderRow.append(HT.TD("InfoPageName", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
tableHeaderRow.append(HT.TD("Accession Id", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
tableHeaderRow.append(HT.TD("Dataset name", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
tableHeaderRow.append(HT.TD("Progress", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
tableHeaderRow.append(HT.TD("Operation", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
datasetTable.append(tableHeaderRow)
for one_row in result:
InfoPageName,Accession_Id,InfoPage_title,Progress = one_row
datasetRow = HT.TR()
datasetRow.append(HT.TD(HT.Href(text="%s" % InfoPageName, url="/webqtl/main.py?FormID=sharinginfo&InfoPageName=%s" % InfoPageName, Class='fs12 fwn'), Class="fs12 fwn b1 c222"))
datasetRow.append(HT.TD(HT.Href(text="GN%s" % Accession_Id, url="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=%s" % Accession_Id, Class='fs12 fwn'), Class="fs12 fwn b1 c222"))
datasetRow.append(HT.TD("%s" % InfoPage_title, Class="fs12 fwn b1 c222"))
datasetRow.append(HT.TD("%s" % Progress, Class='fs12 fwn b1 c222'))
operation_edit = HT.Href(text="Edit", url="/webqtl/main.py?FormID=sharinginfoedit&InfoPageName=%s" % InfoPageName)
operation_delete = HT.Href(text="Delete", onClick="deleteRecord('%s'); return false;" % InfoPageName)
operation = HT.TD(Class="fs12 fwn b1 c222", align="center")
operation.append(operation_edit)
operation.append(" ")
operation.append(operation_delete)
datasetRow.append(operation)
datasetTable.append(datasetRow)
TD_LR.append(heading, HT.P(), newrecord, HT.P(), datasetTable)
js1 = """ <script language="javascript" type="text/javascript">
function deleteRecord(InfoPageName){
question = confirm("Are you sure you want to delete the dataset info record (InfoPageName="+InfoPageName+")?")
if (question != "0"){
window.open("/webqtl/main.py?FormID=sharinginfodelete&InfoPageName="+InfoPageName, "_self");
}
}
</script>"""
self.dict['js1'] = js1
self.dict['body'] = str(TD_LR)
def __init__(self, fd):
templatePage.__init__(self, fd)
# get mysql connection, if not, show error
if not self.openMysql():
heading = "Geno Updating"
detail = ["Can't connect to MySQL server"]
self.error(heading=heading,detail=detail)
return
self.dict['title'] = 'Geno Updating'
# status is the switch, direct what's the next step
try:
status = fd.formdata.getvalue('status')
except:
status = ''
if fd.formdata.getvalue('submit')=='Clear':
status=''
if not status: # show
self.dict['body']=self.showSelectionPage()
elif status=='search' or status == 'addNewMarker':
InbredSetName = fd.formdata.getvalue('InbredSetName')
Chr = fd.formdata.getvalue('Chr')
if not InbredSetName:
self.dict['body']= "Please select the population."
return
elif not Chr:
self.dict['body']= "Please input Chr."
return
else:
self.dict['body']=self.showAllMarkers (InbredSetName, Chr, fd)
elif status == 'editMarkerTable':
self.dict['body'] = self.editMarkerTable(fd)
elif status == 'checkMarkerHasBeenInGroup': # check if there is anything changed.
InbredSetName = fd.formdata.getvalue('InbredSetName')
Marker = fd.formdata.getvalue('Name')
self.dict['body'] = self.checkMarkerHasBeenInGroup (InbredSetName, Marker, fd)
elif status=='changeMarker': #insert new marker
InbredSetName = fd.formdata.getvalue('InbredSetName')
self.dict['body']=self.changeMarker(InbredSetName, fd)
else: #this part is used to test, the proceduce won't come here in normal cycle
HTTable = HT.TableLite(border=0, cellspacing=1, cellpadding=1,align="center")
for key in fd.formdata.keys():
HTTable.append(HT.TR(HT.TD(key), HT.TD(':'), HT.TD(fd.formdata.getvalue(key))))
self.dict['body'] = HTTable
def __init__(self,fd):
self.theseTraits = []
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
templatePage.__init__(self, fd)
if not self.openMysql():
return
self.searchResult = fd.formdata.getvalue('searchResult', [])
if type("1") == type(self.searchResult):
self.searchResult = [self.searchResult]
for item in self.searchResult:
try:
thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
thisTrait.retrieveInfo(QTL=1)
if thisTrait.db.type == "ProbeSet":
self.theseTraits.append(thisTrait)
except:
pass
if self.theseTraits:
pass
else:
templatePage.__init__(self, fd)
heading = 'GCAT'
detail = ['You need to select at least one microarray trait to submit to GCAT.']
self.error(heading=heading,detail=detail)
return
geneSymbolList = self.getGeneSymbolList()
geneSymbolSet = set(geneSymbolList)
if ( len(geneSymbolSet) < 500 ):
temp = '+'.join(geneSymbolSet)
GCATurl = "http://binf1.memphis.edu/gcat/?organism=mouse&subset=all&year=2010&geneInput=%s" % temp
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout( 'window.location = "%s"', 2000 );
</SCRIPT>
""" % GCATurl
TD_LR.append(HT.Paragraph("Your selection of %d genes is being submitted to GCAT" % len(geneSymbolSet), Class="cr fs16 fwb", align="Center"))
else:
TD_LR.append(HT.Paragraph("Your selection of %d genes exceeds the limit of 500. Please reduce your gene number to below the limit." % len(geneSymbolSet), Class="cr fs16 fwb", align="Center"))
self.dict['body'] = TD_LR
def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.updMysql():
return
fd.incparentsf1 = 1
if not fd.genotype:
fd.readGenotype()
fd.strainlist = fd.f1list + fd.strainlist
fd.readData()
if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:
pass
else:
heading = "Add to Published Database"
detail = ["You don't have the permission to modify this database"]
self.error(heading=heading,detail=detail,error="Error")
return
self.cursor.execute("""
SelecT
PublishFreeze.Name
from
PublishFreeze, InbredSet
where
PublishFreeze.InbredSetId = InbredSet.Id AND
InbredSet.Name = '%s'""" % fd.RISet)
try:
self.db = webqtlDataset(self.cursor.fetchone()[0], self.cursor)
except:
heading = "Add to Published Database"
detail = ["The published database you requested has not been established"]
self.error(heading=heading,detail=detail,error="Error")
return
status = fd.formdata.getvalue('curStatus')
if status == 'insertResult':
newRecord = self.readForm(fd)
if not newRecord:
return
else:
self.insertResultPage(fd, newRecord)
elif status == 'insertCheck':
newRecord = self.readForm(fd)
if not newRecord:
return
else:
self.insertCheckPage(fd, newRecord)
else:
self.dispFormPage(fd)
def __init__(self,fd):
templatePage.__init__(self, fd)
filename = self.session("QTL Heatmap", "Computing QTL Heatmap")
webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename)
os.system("%s %swebqtlCmdLine.py heatmap %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
self.redirection = url
def __init__(self,fd):
templatePage.__init__(self, fd)
filename = self.session("Generate Report v2", "Generating Report v2. Please be Patient")
webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename)
os.system("%s %swebqtlCmdLine.py genreport2 %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
self.redirection = url
def __init__(self,fd):
templatePage.__init__(self, fd)
filename = self.session("Partial Correlation", "Partial Correlation in Progress")
webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename)
os.system("%s %swebqtlCmdLine.py partialCorrelation %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
self.redirection = url
def __init__(self, fd=None):
templatePage.__init__(self, fd)
if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
pass
else:
heading = "Editing Info"
detail = ["You don't have the permission to edit this dataset"]
self.error(heading=heading,detail=detail,error="Error")
return
GN_AccessionId = fd.formdata.getvalue('GN_AccessionId')
InfoPageName = fd.formdata.getvalue('InfoPageName')
sharingInfoObject = SharingInfo2.SharingInfo2(GN_AccessionId, InfoPageName)
GN_AccessionId,InfoPageName,info = sharingInfoObject.getInfo()
self.dict['body'] = SharingBody.sharinginfoedit_body_string % (info[9], info[22], info[21], info[22], info[29], info[28], info[30], info[32], info[23], info[24], info[25], info[26], info[27], info[13], info[18], info[14], info[15], info[16], info[19], info[20], info[17], info[1], info[9], info[10], info[12], info[11], info[3], info[2], info[6], info[7], info[4], info[8], info[5], info[0], info[32], info[32], info[32])
def __init__(self, fd=None):
templatePage.__init__(self, fd)
GN_AccessionId = fd.formdata.getvalue('GN_AccessionId')
InfoPageName = fd.formdata.getvalue('InfoPageName')
cursor = webqtlDatabaseFunction.getCursor()
if InfoPageName and not GN_AccessionId:
sql = "select GN_AccesionId from InfoFiles where InfoPageName = %s"
cursor.execute(sql, InfoPageName)
GN_AccessionId = cursor.fetchone()
url = webqtlConfig.CGIDIR + "main.py?FormID=sharinginfo&GN_AccessionId=%s" % GN_AccessionId
self.redirection = url
else:
sharingInfoObject = SharingInfo.SharingInfo(GN_AccessionId, InfoPageName)
self.dict['body'] = sharingInfoObject.getBody(infoupdate="")
def __init__(self,fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
searchResult = fd.formdata.getvalue('searchResult')
if not searchResult:
heading = 'BNW'
detail = ['You need to select at least one trait.']
self.error(heading=heading, detail=detail)
return
if type("1") == type(searchResult):
searchResult = string.split(searchResult, '\t')
fd.incparentsf1 = 1
if not fd.genotype:
fd.readGenotype()
strainlist = fd.f1list + fd.strainlist
valuesList = []
formvalue = ''
for item in searchResult:
#
thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
thisTrait.retrieveData(strainlist=strainlist)
values = thisTrait.exportData(strainlist)
valuesList.append(values)
#
item = item.replace("Geno::", "_")
item = item.replace("Publish::", "_")
item = item.replace("::", "_")
formvalue += item
formvalue += ','
valuesList = zip(*valuesList)
formvalue = formvalue[:-1]
formvalue += ';'
for row in valuesList:
hasNone = False
for cell in row:
if not cell:
hasNone = True
break
if hasNone:
continue
formvalue += ','.join(str(cell) for cell in row)
formvalue += ';'
self.dict['body'] = BNWPage.body % formvalue
return
def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
if not fd.genotype:
fd.readGenotype()
self.searchResult = []
self.genSelection(fd=fd)
self.writeHTML(fd)
def __init__(self, fd):
templatePage.__init__(self, fd)
self.session_data_changed['user'] = '******'
self.session_data_changed['privilege'] = 'guest'
#self.cookie.append(myCookie('user',' ',0))
#self.cookie.append(myCookie('password',' ',0))
result = HT.Blockquote(HT.Font('Logout Result: ',color='green'),HT.Font('You have been succesfully logged out. ',color='black'))
result.__setattr__("class","subtitle")
self.dict['title'] = 'User Logoff Result'
self.dict['body'] = HT.TD(result,colspan=2,height=200,width="100%",bgColor='#eeeeee')
LOGIN = HT.Href(text = "Login",Class="small", target="_blank",url="account.html")
self.dict['login'] = LOGIN
def __init__(self, fd=None):
templatePage.__init__(self, fd)
if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
pass
else:
heading = "Deleting Info"
detail = ["You don't have the permission to delete this dataset"]
self.error(heading=heading,detail=detail,error="Error")
return
cursor = webqtlDatabaseFunction.getCursor()
if (not cursor):
return
GN_AccessionId = fd.formdata.getvalue('GN_AccessionId')
sql = "delete from InfoFiles where GN_AccesionId=%s"
cursor.execute(sql, GN_AccessionId)
re = cursor.fetchone()
self.dict['body'] = "Delete dataset info record (GN_AccesionId=%s) successfully." % GN_AccessionId
def __init__(self, fd):
templatePage.__init__(self, fd)
fd.formdata['remote_ip'] = fd.remote_ip
if not self.openMysql():
return
self.species = fd.formdata.getvalue("species", "mouse")
try:
self.startMb = float(fd.formdata.getvalue("startMb"))
except:
self.startMb = 10
try:
self.endMb = float(fd.formdata.getvalue("endMb"))
except:
self.endMb = self.startMb + 10
self.Chr = fd.formdata.getvalue("chromosome", "1")
self.xls = fd.formdata.getvalue("xls", "1")
try:
s1 = int(fd.formdata.getvalue("s1"))
s2 = int(fd.formdata.getvalue("s2"))
self.diffColDefault = self.diffCol = [s1, s2]
except:
self.diffColDefault = self.diffCol = []
if self.species != 'mouse':
self.diffColDefault = [2, 3]#default is B6 and D2 for other species
controlFrm, dispFields = self.genControlForm(fd)
geneTable, filename = self.genGeneTable(fd, dispFields)
infoTD = HT.TD(width=400, valign= "top")
infoTD.append(HT.Paragraph("Interval Analyst : Chr %s" % self.Chr, Class="title"),
HT.Strong("Species : "), self.species.title(), HT.BR(),
HT.Strong("Database : "), "UCSC %s" % self.speciesFreeze[self.species], HT.BR(),
HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(),
)
if filename:
infoTD.append(HT.BR(), HT.BR(), HT.Href(text="Download", url = "/tmp/" + filename, Class="normalsize")
, " output in MS excel format.")
mainTable = HT.TableLite(HT.TR(infoTD, HT.TD(controlFrm, Class="doubleBorder", width=400), HT.TD(" ", width="")), cellpadding=10)
mainTable.append(HT.TR(HT.TD(geneTable, colspan=3)))
self.dict['body'] = HT.TD(mainTable)
self.dict['title'] = "Interval Analyst"
def __init__(self, fd):
templatePage.__init__(self, fd)
fd.formdata['remote_ip'] = fd.remote_ip
if not self.openMysql():
return
self.species = fd.formdata.getvalue("species", "mouse")
try:
self.startMb = float(fd.formdata.getvalue("startMb"))
except:
self.startMb = 10
try:
self.endMb = float(fd.formdata.getvalue("endMb"))
except:
self.endMb = self.startMb + 10
self.Chr = fd.formdata.getvalue("chromosome", "1")
self.xls = fd.formdata.getvalue("xls", "1")
try:
s1 = int(fd.formdata.getvalue("s1"))
s2 = int(fd.formdata.getvalue("s2"))
self.diffColDefault = self.diffCol = [s1, s2]
except:
self.diffColDefault = self.diffCol = []
if self.species != 'mouse':
self.diffColDefault = [2, 3]#default is B6 and D2 for other species
controlFrm, dispFields = self.genControlForm(fd)
geneTable, filename = self.genGeneTable(fd, dispFields)
infoTD = HT.TD(width=400, valign= "top")
infoTD.append(HT.Paragraph("Interval Analyst : Chr %s" % self.Chr, Class="title"),
HT.Strong("Species : "), self.species.title(), HT.BR(),
HT.Strong("Database : "), "UCSC %s" % self.speciesFreeze[self.species], HT.BR(),
HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(),
)
if filename:
infoTD.append(HT.BR(), HT.BR(), HT.Href(text="Download", url = "/tmp/" + filename, Class="normalsize")
, " output in MS excel format.")
mainTable = HT.TableLite(HT.TR(infoTD, HT.TD(controlFrm, Class="doubleBorder", width=400), HT.TD(" ", width="")), cellpadding=10)
mainTable.append(HT.TR(HT.TD(geneTable, colspan=3)))
self.dict['body'] = HT.TD(mainTable)
self.dict['title'] = "Interval Analyst"
def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.updMysql():
return
try:
user = fd.formdata.getvalue('user').strip()
password = fd.formdata.getvalue('password').strip()
except:
user = password = ''
if user and password:
try:
if user == password:
raise 'identError'
privilege, id, account_name, encrypt_password, grpName = webqtlUtil.authUser(user, password, self.cursor)
if encrypt_password:
self.session_data_changed['user'] = user
self.session_data_changed['privilege'] = privilege
self.cursor.execute("""update User set user_ip=%s,lastlogin=Now() where name=%s""",(fd.remote_ip,user))
myPage = IndexPage.IndexPage(fd)
self.dict['title'] = myPage.dict['title']
self.dict['body'] = myPage.dict['body']
self.dict['js1'] = myPage.dict['js1']
self.dict['js2'] = myPage.dict['js2']
return
else:
result = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('You entered wrong user name or password. Please try it again.',color='black'))
except 'identError':
result = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('User name and password are the same, modify you password before login.',color='black'))
except:
result = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('User database is not ready yet. Try again later.',color='black'))
else:
result = HT.Blockquote(HT.Font('Error: ',color='red'),HT.Font('No user name or password was entered, Please try it again.',color='black'))
result.__setattr__("class","subtitle")
self.dict['title'] = 'User Login Result'
self.dict['body'] = HT.TD(result,colspan=2,height=200,width="100%",bgColor='#eeeeee')
LOGOUT = HT.Href(text = "Logout",Class="small", target="_blank",url=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=userLogoff")
self.dict['login'] = LOGOUT
def __init__(self, fd):
templatePage.__init__(self, fd)
self.redirect_url = None # Set if you want a redirect
print("fd is:", pf(fd.__dict__))
# Todo: Need a [0] in line below????d
GN_AccessionId = fd.get('GN_AccessionId') # Used under search datasharing
InfoPageName = fd.get('database') # Might need to add a [0]
cursor = webqtlDatabaseFunction.getCursor()
if InfoPageName and not GN_AccessionId:
sql = "select GN_AccesionId from InfoFiles where InfoPageName = %s"
cursor.execute(sql, InfoPageName)
GN_AccessionId = cursor.fetchone()
self.redirect_url = urlparse.urljoin(webqtlConfig.ROOT_URL, "/data_sharing?GN_AccessionId=%s" % GN_AccessionId)
#self.redirect_url = flask.url_for('data_sharing', GN_AccessionId=GN_AccessionId[0])
print("set self.redirect_url")
#print("before redirect")
#return flask.redirect(url)
#print("after redirect")
else:
CauseError
def __init__(self,fd):
templatePage.__init__(self, fd)
shortName=fd.formdata.getfirst("shortTissueName", ',')
fullName=fd.formdata.getfirst("fullTissueName", ',')
shortNameList=[]
fullNameList=[]
if shortName:
shortNameList=shortName.split(',')
if fullName:
fullNameList=fullName.split(',')
tissueAbbrDict={}
for i, item in enumerate(shortNameList):
tissueAbbrDict[item]=fullNameList[i]
if tissueAbbrDict:
# Creates the table for the fullname and shortname of Tissue
tissueAbbrTable = HT.TableLite(border=1, cellspacing=5, cellpadding=3, Class="collap")
shortNameList = tissueAbbrDict.keys()
shortNameList.sort()
abbrHeaderStyle="fs14 fwb ffl"
abbrStyle="fs14 fwn ffl"
tissueAbbrTable.append(HT.TR(HT.TD('Abbr ', Class=abbrHeaderStyle, NOWRAP = 1),HT.TD('Full Name ', Class=abbrHeaderStyle, NOWRAP = 1)))
for item in shortNameList:
thisTR = HT.TR(HT.TD(item, Class=abbrStyle, NOWRAP = 1))
thisTR.append(HT.TD(tissueAbbrDict[item], Class=abbrStyle, NOWRAP = 1))
tissueAbbrTable.append(thisTR)
self.dict['body'] = HT.TD(HT.Paragraph("Tissue Abbreviation", Class="title"), HT.Blockquote(tissueAbbrTable))
self.dict['title'] = "Tissue Abbreviation"
else:
heading = "Tissue abbreviation"
detail = ["Cannot found Tissue Abbreviation. Please try again later."]
self.error(heading=heading,detail=detail)
return
def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.updMysql():
return
if not fd.genotype:
fd.readGenotype()
fd.strainlist = fd.f1list + fd.strainlist
fd.readData()
self.formdata = fd.formdata
self.dict['title'] = 'Data Updating'
try:
thisTrait = webqtlTrait(fullname=self.formdata.getvalue('fullname'), cursor=self.cursor)
thisTrait.retrieveInfo()
except:
heading = "Updating Database"
detail = ["The trait doesn't exist."]
self.error(heading=heading,detail=detail,error="Error")
return
if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:
pass
else:
heading = "Updating Database"
detail = ["You don't have the permission to modify this trait"]
self.error(heading=heading,detail=detail,error="Error")
return
status = self.formdata.getvalue('curStatus')
if status == 'updateCheck': #XZhou: Check the change
self.updateCheckPage(fd, thisTrait)
elif status == 'updateResult': #XZhou: make the changes to database
self.updateResultPage(fd, thisTrait)
else: #XZhou: show info retrieved from database
self.dispTraitPage(fd, thisTrait)
def __init__(self, fd=None):
templatePage.__init__(self, fd)
GN_AccessionId1 = fd.formdata.getvalue('GN_AccessionId')
InfoPageName1 = fd.formdata.getvalue('InfoPageName')
sharingInfoObject = SharingInfo2.SharingInfo2(GN_AccessionId1, InfoPageName1)
GN_AccessionId2, InfoPageName2, info = sharingInfoObject.getInfo(create=True)
# ZS: This javascript is used to hide empty fields in the infofile page. It is here only because
# there are no other options due to the poor way in which all of this code is structured.
# When we finally use templates, it will be far easier to do this and javascript won't be necessary.
hideNoneJS = """
<script type="text/javascript">
$(window).load(function () {
empty_rows = $("table[name=infoTable]").find("tr").filter(function () {
return $.trim($(this).find('td').text()).length == 0;
});
empty_rows.each(function () {
$(this).hide();
$(this).prev().hide();
});
$("table[name=infoTable]").find("tr:contains('None')").each( function(){
$(this).hide();
$(this).prev().hide(); //hides the "title"/label for the field as well as its contents
});
});
</script>"""
self.dict['js1'] = hideNoneJS
if not GN_AccessionId1 and GN_AccessionId2:
url = webqtlConfig.CGIDIR + "main.py?FormID=sharinginfo&GN_AccessionId=%s" % GN_AccessionId2
self.redirection = url
else:
sharingInfoObject.getDatasetsList()
self.dict['body'] = sharingInfoObject.getBody(infoupdate="")
def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
if not fd.genotype:
fd.readGenotype()
self.importFile = fd.formdata.getvalue('importfile')
if not self.importFile:
templatePage.__init__(self, fd)
heading = 'Import Collection'
detail = ['The file you choose to import from doesn\'t exist.']
self.error(heading=heading,detail=detail)
return
self.importFile = string.split(self.importFile, '\n')
RISetLocate = 0
self.searchResult = []
for line in self.importFile:
if line and line[0] != '#':
if not RISetLocate:
RISetLocate = line
if RISetLocate != fd.RISet:
templatePage.__init__(self, fd)
heading = 'Import Collection'
detail = ['The file you choose to import from doesn\'t contain %s selection.' % fd.RISet]
self.error(heading=heading,detail=detail)
return
else:
self.searchResult.append(line)
if not self.searchResult:
templatePage.__init__(self, fd)
heading = 'Import Collection'
detail = ['The file you choose to import from is empty.']
self.error(heading=heading,detail=detail)
return
self.importMethod = fd.formdata.getvalue('importmethod')
if self.importMethod == 'replace':
checkPreSelection = 0
else:
checkPreSelection = 1
if self.genSelection(fd=fd, checkPreSelection = checkPreSelection):
self.writeHTML(fd)
def __init__(self,fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
searchResult = fd.formdata.getvalue('searchResult', [])
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
formODE = HT.Form(cgi="http://geneweaver.org/index.php?action=manage&cmd=importGeneSet", enctype='multipart/form-data', name='formODE', submit = HT.Input(type='hidden'))
hddnODE = {}
hddnODE['client'] = 'genenetwork'
hddnODE['species'] = "Mus musculus"
#hddnODE['idtype'] = chipName
hddnODE['list'] = string.join(searchResult, ",")
for key in hddnODE.keys():
formODE.append(HT.Input(name=key, value=hddnODE[key], type='hidden'))
TD_LR.append(formODE)
TD_LR.append(HT.Paragraph("Your selections of %d traits is being exported to the ODE" % len(searchResult), Class="cr fs16 fwb", align="Center"))
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout('document.formODE.submit()',1000);
</SCRIPT>
"""
self.dict['body'] = TD_LR