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 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 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 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 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):
"""
2009-11-11
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, 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 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 findAccessions(cls, condition=None, extra_tables=None):
"""
2009-4-19
add argument 'extra_tables'
2009-4-14
become classmethod
2009-4-3
find accession with name exact matching name, nativename, stockparent or alias
"""
if condition:
condition = 'where %s'%condition
else:
condition = ""
table_str = '%s v'%cls.ecotype_central_view
if extra_tables:
table_str += ', %s'%extra_tables
rows = model.db.metadata.bind.execute("select v.* from %s %s"%\
(table_str, condition))
# dictionary to test whether one ecotype is in one dataset
if getattr(model, 'ecotype_id_set_2010', None)==None: #this lead to faster access next time. mysteriously, every call to self.ecotype_id_set_2010 (property) would lead to its execution everytime. no reference is stored.
model.ecotype_id_set_2010 = cls.ecotype_id_set_2010()
model.ecotype_id_set_384 = cls.ecotype_id_set_384()
model.ecotype_id_set_perlegen = cls.ecotype_id_set_perlegen()
model.ecotype_id_set_250k = cls.ecotype_id_set_250k()
model.ecotype_id_set_250k_in_pipeline = cls.ecotype_id_set_250k_in_pipeline()
dataset_name2ecotype_id_set = {'2010': model.ecotype_id_set_2010,
'384': model.ecotype_id_set_384,
'perlegen': model.ecotype_id_set_perlegen,
'250k': model.ecotype_id_set_250k}
#3rd finally construct the full data and turn it into json
column_name_type_ls = [("ecotypeid", ("number", "Ecotype ID")), ("tg_ecotypeid", ("number", "Unique Ecotype ID")), \
("name", ("string","Name")), \
("nativename", ("string","Native Name")), ("alias", ("string","Alias")), \
("stockparent",("string", "Stock Parent")), ("haplo_group_id",("string", "149SNP Haplo-Group")), \
("2010",("string", "2010")), \
("384",("string", "384")), \
("perlegen",("string", "perlegen")), \
("250k",("string", "250k")), \
("latitude",("number", "Latitude")), ("longitude",("number", "Longitude")), \
("geographic_integrity",("string", "Geographic Info Quality")),\
("site_name", ("string", "Collection Site")), ("country", ("string", "Country")),\
("collector", ("string", "Collector")), ("collectiondate", ("date", "Collection Date"))]
description = dict(column_name_type_ls)
return_ls = []
for row in rows:
entry = dict()
for column_name_type in column_name_type_ls:
column_name = column_name_type[0]
column_type = column_name_type[1][0]
if column_type=='string':
default_value = ''
elif column_type =='number':
default_value = -1
elif column_type=='date':
default_value = datetime.date(2050, 1, 1)
else:
default_value = None
if column_name == 'collector':
column_value = '%s %s'%(row.firstname, row.surname)
elif column_name == '2010' or column_name=='384' or column_name=='perlegen' or column_name=='250k':
if row.tg_ecotypeid in dataset_name2ecotype_id_set[column_name]:
column_value = 'yes'
elif column_name=='250k' and row.tg_ecotypeid in model.ecotype_id_set_250k_in_pipeline:
column_value = 'in pipeline'
else:
column_value = 'no'
elif column_name=='haplo_group_id':
column_value = getattr(row, column_name, default_value)
#haplo_group_name = model.Stock.HaploGroup.get(column_value).short_name
if column_value:
column_value = "<a href=%s target='_blank'>%s</a>"%(h.url_for(controller="Accession", action='haploGroup', id=column_value), column_value)
else:
column_value = getattr(row, column_name, default_value)
entry[column_name] = column_value
return_ls.append(entry)
data_table = gviz_api.DataTable(description)
data_table.LoadData(return_ls)
column_ls = [row[0] for row in column_name_type_ls]
json_result = data_table.ToJSon(columns_order=column_ls) #ToJSonResponse only works with google.visualization.Query
response.headers['Content-Type'] = 'application/json'
return json_result