def _metadata(self):
s = {}
s["age"] = Helpers.sanitize(Helpers.getOrUnknown(self.exp.age_display))
s["sex"] = Helpers.getOrUnknown(self.exp.donor_sex)
s["accession"] = self.exp.encodeID
s["description"] = Helpers.sanitize(self._desc())
s["donor"] = self.exp.donor_id
s["view"] = self.view
return s
def _subgroups(self):
s = {}
s["donor"] = Helpers.getOrUnknown(self.exp.donor_id)
s["assay"] = Helpers.getOrUnknown(self.stateType)
s["label"] = Helpers.getOrUnknown(self.exp.tf)
s["biosample"] = Helpers.getOrUnknown(self.exp.biosample_term_name)
s["age"] = 'a' + Helpers.sanitize(Helpers.getOrUnknown(self.exp.age_display))
s["view"] = self.exp.encodeID
self.presentation = {}
self.presentation["label"] = (s["label"],
Helpers.html_escape(Helpers.getOrUnknown(self.exp.tf)))
self.presentation["assay"] = (s["assay"], s["assay"])
self.presentation["donor"] = (s["donor"], s["donor"])
self.presentation["age"] = (s["age"],
Helpers.html_escape(Helpers.getOrUnknown(self.exp.age_display)))
self.presentation["view"] = (s["view"], s["view"])
self.presentation["biosample"] = (s["biosample"], s["biosample"])
self.presentation["sex"] = ('', '')
self.presentation["age_sex"] = ('', '')
self.presentation["target_label"] = (s["assay"], s["assay"])
self.presentation["biosample_summary"] = (s["biosample"], s["biosample"])
self.presentation["tissue"] = self.presentation["biosample"]
return s
def _subgroups(self):
assay = self.exp.assay_term_name
if "RNA-seq" == assay:
assay = self.exp.assay_title
target_label = ' '.join([self.exp.assay_term_name, self.exp.target, self.exp.label]).strip()
s = {}
s["donor"] = Helpers.getOrUnknown(self.exp.donor_id)
s["assay"] = Helpers.getOrUnknown(assay)
s["label"] = Helpers.getOrUnknown(self.exp.tf)
s["target_label"] = Helpers.getOrUnknown(target_label)
s["biosample"] = Helpers.getOrUnknown(self.exp.biosample_term_name)
s["biosample_summary"] = Helpers.getOrUnknown(self.exp.biosample_summary).encode('ascii', 'ignore').decode('ascii')
s["age"] = 'a' + Helpers.sanitize(Helpers.getOrUnknown(self.exp.age_display))
s["sex"] = Helpers.getOrUnknown(self.exp.donor_sex)
age_sex = ' '.join([e for e in [self.exp.age_display, self.exp.donor_sex] if e]).strip()
s["age_sex"] = Helpers.getOrUnknown(age_sex)
s["view"] = self.view
self.presentation["label"] = (s["label"],
Helpers.html_escape(Helpers.getOrUnknown(self.exp.tf)))
self.presentation["assay"] = (s["assay"], s["assay"])
self.presentation["donor"] = (s["donor"], s["donor"])
self.presentation["target_label"] = (s["target_label"], s["target_label"])
self.presentation["age"] = (s["age"],
Helpers.html_escape(Helpers.getOrUnknown(self.exp.age_display)))
self.presentation["view"] = (s["view"], s["view"])
self.presentation["sex"] = (s["sex"], s["sex"])
self.presentation["age_sex"] = (s["age_sex"], s["age_sex"])
self.presentation["biosample"] = (s["biosample"], s["biosample"])
self.presentation["biosample_summary"] = (s["biosample_summary"], s["biosample_summary"])
self.presentation["tissue"] = self.presentation["biosample"]
return s