def checkLogedIn(self):
if request.POST.get('username'):
if request.POST.get('username') == request.cookies.get("usernameCIS3210"):
return render("/manageUsers.mako")
else:
response.set_cookie("usernameCIS3210" , request.cookies.get("usernameCIS3210"), max_age= -1)
return render("/login.mako")
else:
response.set_cookie("usernameCIS3210" , request.cookies.get("usernameCIS3210"), max_age= -1)
return render("/login.mako")
def index(self, id=None):
"""
2009-2-19
snp context
snp annotation
snp frequency
geographic distribution colored by phenotype
which accession has which allele
phenotype distribution stratified according to allele
significant associations (top 1k) in other phenotypes
"""
# Return a rendered template
# return render('/template.mako')
# or, Return a response
self.readInRequestParams(request, c)
start_pos = c.position-40000
stop_pos = c.position+40000
track_id = '%s_%s_%s'%(c.call_method_id, c.phenotype_method_id, c.analysis_method_id)
c.gbrowseLink = config['app_conf']['GBrowseURL']%(start_pos, stop_pos, c.chromosome)+track_id+"-"+track_id+"_SNP"
phenotype_method = model.Stock_250kDB.PhenotypeMethod.get(c.phenotype_method_id)
c.pageTitle = "SNP chromosome %s position %s Phenotype %s %s"%\
(c.chromosome, c.position, c.phenotype_method_id, phenotype_method.short_name)
#return render('/snp.html')
return render('/SNP.html')
def index(self):
# Return a rendered template
# return render('/template.mako')
# or, Return a response
# return 'Hello World'
c.find250kAccessionsURL = h.url_for(controller="Accession", action="find250kAccessions", id=None)
return render('/Accession.html')
def index(self):
# Return a rendered template
#return render('/main.mako')
# or, return a string
if request.cookies.get( 'username' ):
return redirect(url('/dashboard'))
else:
return render('/index.mako')
def index(self):
#c.call_method_ls = DisplayresultsController.getCallMethodLsJson()
c.callMethodLsURL = h.url_for(controller="DisplayResults", action="getCallMethodLsJson", id=None)
#c.gene_list_ls = DisplayresultsgeneController.getGeneListTypeLsGivenTypeAndPhenotypeMethodAndAnalysisMethodJson()
c.geneListLsURL = h.url_for(controller="DisplayResultsGene", action="getGeneListTypeLsGivenTypeAndPhenotypeMethodAndAnalysisMethodJson", id=None)
c.callMethodOnChangeURL = h.url_for(controller="DisplayResults", action="getPhenotypeMethodLsJson", id=None)
c.haplotypeImgURL = h.url_for(controller='HaplotypeView', action='getPlot', id=None)
return render('/HaplotypeView.html')
def login(self):
sql = 'SELECT * FROM users WHERE BINARY username = "******" AND BINARY password = "******";'
cur.execute(sql)
row = cur.fetchone()
if row:
response.set_cookie("usernameCIS3210" , request.POST.get('userName'), max_age=180*24*3600)
return json.dumps({'code': render("/manageUsers.mako")})
else:
return json.dumps({'error':'Authentication error.'})
def index(self):
# Return a rendered template
#return render('/dashboard.mako')
# or, return a string
if request.cookies.get('username'):
c.test = 'cool'
return render('/dashboard.mako')
else:
return redirect(url('/'))
def contact(self):
if request.method == 'POST':
redirect_url = self._process_contact()
redirect(redirect_url)
log1.info ('Generating a form ...')
c.csrf_token_field = secure_form.auth_token_hidden_field()
c.errors = session.get('contactform.errors', None)
c.values = session.get('contactform.values', {})
return render('contactform/contact.html')
def results(self):
log.info ('Viewing poll results')
db_session = model.Session()
q1 = db_session.query(model.Vote.vote, model.func.count(model.Vote.vote)).group_by(model.Vote.vote)
c.vote_freqs = q1.all()
q2 = db_session.query(model.Vote)
c.vote_count = q2.count()
db_session.close()
return render('poll/results.html')
def index(self):
# Return a rendered template
#return render('/dashboard.mako')
# or, return a string
if request.cookies.get( 'username' ):
c.test='cool';
return render('/dashboard.mako')
else:
return redirect(url('/'))
def trend(self, id=None):
"""
2009-5-3
"""
c.trendDataURL = h.url_for(controller='Phenotype', action='getTrendData', id=None)
c.trendAnnotationDataURL = h.url_for(controller='Phenotype', action='getTrendAnnotationData', id=None)
c.multiPhenotypeDataURL = h.url_for(controller='Phenotype', action='getMultiPhenotypeData', id=None,\
call_method_id=int(config['app_conf']['good_call_method_id']))
return render('/PhenotypeTrend.html')
def haploGroup(self, id=None):
"""
2009-4-5
server end to return haplotype group json data structure
"""
if id is None:
id = 1
c.haplo_group_id = id
c.getHaploGroupURL = h.url_for(controller="Accession", action="getHaploGroup", id=id)
return render('/HaploGroup.html')
def index(self):
"""
2009-11-30
"""
# Return a rendered template
# return render('/template.mako')
# or, Return a response
c.getCallMethodLsJsonURL = h.url_for(controller="associationoverlap", action="getCallMethodLsJson")
c.getOverlappingDataAcrossPhenotypesURL = h.url_for(controller="associationoverlap", action="getOverlappingDataAcrossPhenotypes")
c.getNoOfTopSNPsLsJsonURL = h.url_for(controller="associationoverlap", action="getNoOfTopSNPsLsJson")
return render("AssociationOverlap.html")
def form(self, id=None):
"""
2009-1-30
"""
if id is None:
id = request.params.get('id', 1)
defaults = {'call_method_id': id,
"remove_old_plots":"on"}
c.call_method_ls = self.getCallMethodLs()
c.call_method_ls.insert(0, [0, u'Please Choose ...'])
html = render('/display_results_form.html')
return htmlfill.render(html, defaults)
def test_render(self):
''' An example of using Pylons globals after the test request
has been completed.
'''
response = self.app.get(url(controller='greet', action='index'))
self._setup_template_context()
self._setup_request_globals(response)
from pylons import tmpl_context as c
c.author = 'Foo'
c.maintainer = 'Boo'
markup = render('greet/index-1.html', extra_vars={ 'foo': 'bar' })
self._teardown_request_globals()
self._teardown_template_context()
def index(self):
"""
2009-11-11
add c.getPhenotypeURL
2009-10-8
first try to get the call_method_id from the URL parameters. if it's null, use the published_call_method_id instead.
2009-7-2
update c.displayResultsGeneURL to h.url_for(controller="DisplayResultsGene", action='showResultsGeneForOnePhenotype')
"""
# Return a rendered template
# return render('/template.mako')
# or, Return a response
c.call_method_id = request.params.get('call_method_id', config['app_conf']['published_call_method_id'])
c.getPhenotypeCategoryLsURL = h.url_for(controller="DisplayResults", action="getPhenotypeCategoryLs")
c.getPhenotypeTableDataURL = h.url_for(controller="DisplayResults", action="getPhenotypeTableData")
c.getGWAURL = h.url_for(controller="DisplayResults", action="showGWA")
c.getPhenotypeURL = h.url_for(controller='Phenotype')
c.displayResultsGeneURL = h.url_for(controller="DisplayResultsGene", action='showResultsGeneForOnePhenotype')
return render("GWASPhenotypes.html")
def index(self):
''' Display a directory listing '''
relpath = request.params.get('path', '/')
relpath = re.sub(r'[\.]+', ".", relpath)
abspath = os.path.join (STORAGE_ROOT_DIR, relpath.strip(' /'))
if not os.path.isdir(abspath):
abort (400, detail=u'The path (%s) does not map to a directory' %(abspath))
listing = []
for f in os.listdir(abspath):
pf = os.path.join (abspath, f)
is_dir = os.path.isdir(pf)
is_file = os.path.isfile(pf)
if (is_dir or is_file):
sf = os.stat(pf)
target = None
if is_dir:
target = url(controller='storage', action='index',
path = relpath.strip(' /') + '/' + f)
else:
target = url(controller='storage', action='file',
path = relpath.strip(' /') + '/' + f)
entry = dict(
is_dir = is_dir,
is_file = is_file,
name = f,
target = target,
size = sf.st_size,
created = datetime.fromtimestamp(sf.st_ctime),
modified = datetime.fromtimestamp(sf.st_mtime))
listing.append (entry)
c.storage_index = {
'listing': listing,
'path': relpath,
'upload_url': url(controller='storage', action='upload_handle')
}
return render('storage/index.html')
pass
def index(self, id=None):
"""
2009-4-6
display a summary page given a phenotype id
"""
# Return a rendered template
# return render('/template.mako')
# or, Return a response
c.phenotype_method_id = request.params.get('phenotype_method_id', id)
if c.phenotype_method_id:
c.phenotype_method_id = int(c.phenotype_method_id)
pm = model.Stock_250kDB.PhenotypeMethod.get(c.phenotype_method_id)
c.phenotype_method_short_name = pm.short_name
c.phenotype_method_description = pm.method_description
c.call_method_id = request.params.get('call_method_id', int(config['app_conf']['published_call_method_id']))
c.callInfoURL = h.url_for(controller='DisplayResults', action='fetchCallInfoData', id=None,\
phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.phenotypeHistImageURL = h.url_for(controller='DisplayResults', action='getPhenotypeHistImage', id=None, \
phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.callPhenotypeQQImageURL = h.url_for(controller='DisplayResults', action='getCallPhenotypeQQImage', id=None,\
phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.phenotypeHistogramDataURL = h.url_for(controller='Phenotype', action='getPhenotypeHistogramData', id=c.phenotype_method_id)
return render('/OnePhenotype.html')
def showGWA(self):
"""
2009-4-23
"""
c.phenotype_method_id = int(request.params.get('phenotype_method_id', 1))
c.call_method_id = int(request.params.get('call_method_id', config['app_conf']['published_call_method_id']))
c.phenotypeSummaryURL = h.url_for(controller="Phenotype", action=None, phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.GWABaseURL = h.url_for(controller='DisplayResults', action='fetchOne', phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.SNPBaseURL = h.url_for(controller='SNP', action=None, phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.getAnalysisMethodLsURL = h.url_for(controller='DisplayResults', action='getAnalysisMethodLsJson', phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
"""
# 2009-4-25 no way to pass this 2D (int, string) array to the template!
analysis_method_ls = self.getAnalysisMethodLs(c.call_method_id, c.phenotype_method_id)
c.analysis_method_ls = []
str_func = lambda x: '%s'%x
for analysis_method_entry in analysis_method_ls:
analysis_method_entry = map(str_func, analysis_method_entry)
c.analysis_method_ls.append('[' + ','.join(analysis_method_entry) + ']')
#c.analysis_method_ls.append(analysis_method_entry)
#c.analysis_method_ls = simplejson.dumps(c.analysis_method_ls)
c.analysis_method_ls = '[' + ','.join(c.analysis_method_ls) + ']'
"""
pm = model.Stock_250kDB.PhenotypeMethod.get(c.phenotype_method_id)
c.phenotype_method_short_name = pm.short_name
c.phenotype_method_description = pm.method_description
c.callInfoURL = h.url_for(controller='DisplayResults', action='fetchCallInfoData', id=None,\
phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.phenotypeHistImageURL = h.url_for(controller='DisplayResults', action='getPhenotypeHistImage', id=None, \
phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.callPhenotypeQQImageURL = h.url_for(controller='DisplayResults', action='getCallPhenotypeQQImage', id=None,\
phenotype_method_id=c.phenotype_method_id, call_method_id=c.call_method_id)
c.phenotypeHistogramDataURL = h.url_for(controller='Phenotype', action='getPhenotypeHistogramData', id=c.phenotype_method_id)
return render('/GWASOnePhenotype.html')
def vote(self):
if request.method == 'POST':
return self._vote_save()
log.info ('Generating a form to vote')
c.csrf_token_field = secure_form.auth_token_hidden_field()
return render('poll/vote.html')
def greet(self, id=None):
c.author = u'φουφουτος'
c.maintainer = u'λαλάκης'
markup = render('greet/index-1.html', extra_vars={ 'foo': 'Bazz'})
return markup
def index(self):
return render('/hello.mako')
def index(self):
# Return a rendered template
#return render('/hello.mako')
# or, return a string
#return 'Hello World'
return render('/hello.mako')
def index(self):
c.name = 'test' #这个参数可以传递到模版
c.person = meta.Session.query(Person).filter(Person.name == 'Mr Jones').first()
#result = conn.execute(s)
# Return a rendered template
return render('/hello.mako')
def index(self):
return render('/hello.mako')
def onePerson(self):
c.person = meta.Session.query(Person).filter(Person.name == 'Mr Jones').first()
return render('/onePerson.mako')
def logout(self):
response.set_cookie("usernameCIS3210" , request.cookies.get("usernameCIS3210"), max_age= -1)
return render("/login.mako")
def allPerson(self):
c.persons = meta.Session.query(Person)[0:2]
return render('/allPerson.mako')
def index(self):
# Return a rendered template
# return render('/template.mako')
# or, Return a response
c.motionChartFormActionURL = h.url_for(controller="utils", action="uploadForMotionChart");
return render('/Utils.html')
def index(self):
# Return a rendered template
#return render('/hello.mako')
# or, return a string
#return 'Hello World'
return render('/hello.mako')
