diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rwxr-xr-x | wqflask/base/trait.py | 52 |
1 files changed, 33 insertions, 19 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 58bed865..ff80795c 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -53,7 +53,8 @@ class GeneralTrait(object): self.pvalue = None self.mean = None self.num_overlap = None - + self.strand_probe = None + self.symbol = None if kw.get('fullname'): name2 = value.split("::") @@ -250,14 +251,7 @@ class GeneralTrait(object): # Todo: is this necessary? If not remove self.data.clear() - if self.dataset.group.parlist: - all_samples_ordered = (self.dataset.group.parlist + - self.dataset.group.f1list + - self.dataset.group.samplelist) - elif self.dataset.group.f1list: - all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist - else: - all_samples_ordered = self.dataset.group.samplelist + all_samples_ordered = self.dataset.group.all_samples_ordered() if results: for item in results: @@ -297,7 +291,7 @@ class GeneralTrait(object): PublishFreeze.Id = %s """ % (self.name, self.dataset.id) - print("query is:", query) + print("query is:", query) trait_info = g.db.execute(query).fetchone() #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name @@ -336,10 +330,10 @@ class GeneralTrait(object): trait_info = g.db.execute(query).fetchone() #print("trait_info is: ", pf(trait_info)) else: #Temp type - query = """SELECT %s FROM %s WHERE Name = %s - """ % (string.join(self.dataset.display_fields,','), - self.dataset.type, self.name) - trait_info = g.db.execute(query).fetchone() + query = """SELECT %s FROM %s WHERE Name = %s""" + trait_info = g.db.execute(query, + (string.join(self.dataset.display_fields,','), + self.dataset.type, self.name)).fetchone() if trait_info: self.haveinfo = True @@ -422,6 +416,8 @@ class GeneralTrait(object): if result: self.locus_chr = result[0] self.locus_mb = result[1] + else: + self.locus = self.locus_chr = self.locus_mb = "" else: self.locus = self.locus_chr = self.locus_mb = "" else: @@ -533,12 +529,27 @@ class GeneralTrait(object): return setDescription @property + def name_header_fmt(self): + '''Return a human-readable name for use in page header''' + if self.dataset.type == 'ProbeSet': + return self.symbol + elif self.dataset.type == 'Geno': + return self.name + elif self.dataset.type == 'Publish': + return self.post_publication_abbreviation + else: + return "unnamed" + + @property def description_fmt(self): '''Return a text formated description''' - if self.description: - formatted = self.description - if self.probe_target_description: - formatted += "; " + self.probe_target_description + if self.dataset.type == 'ProbeSet': + if self.description: + formatted = self.description + if self.probe_target_description: + formatted += "; " + self.probe_target_description + elif self.dataset.type == 'Publish': + formatted = self.post_publication_description else: formatted = "Not available" return formatted.capitalize() @@ -549,6 +560,9 @@ class GeneralTrait(object): if self.alias: alias = string.replace(self.alias, ";", " ") alias = string.join(string.split(alias), ", ") + else: + alias = 'Not available' + return alias @@ -649,4 +663,4 @@ def get_sample_data(): # jsonable_sample_data[sample] = trait_ob.data[sample].value # #return jsonable_sample_data -
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