diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 36 |
1 files changed, 26 insertions, 10 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 58f08ae7..017c6052 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -436,7 +436,7 @@ class DataSet(object): except TypeError: print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - + def get_trait_data(self): self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list query = """ @@ -470,11 +470,18 @@ class DataSet(object): # method=method, # returnNumber=returnNumber) + if self.type == "Publish": + dataset_type = "Phenotype" + else: + dataset_type = self.type temp = ['T%s.value' % item for item in sample_ids_step] - query = "SELECT {}.Name,".format(escape(self.type)) + if self.type == "Publish": + query = "SELECT {}XRef.Id,".format(escape(self.type)) + else: + query = "SELECT {}.Name,".format(escape(dataset_type)) data_start_pos = 1 query += string.join(temp, ', ') - query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type, + query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type, self.type, self.type)) @@ -484,13 +491,22 @@ class DataSet(object): and T{}.StrainId={}\n """.format(*mescape(self.type, item, item, self.type, item, item)) - query += """ - WHERE {}XRef.{}FreezeId = {}Freeze.Id - and {}Freeze.Name = '{}' - and {}.Id = {}XRef.{}Id - order by {}.Id - """.format(*mescape(self.type, self.type, self.type, self.type, - self.name, self.type, self.type, self.type, self.type)) + if self.type == "Publish": + query += """ + WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId + and {}Freeze.Name = '{}' + and {}.Id = {}XRef.PhenotypeId + order by {}.Id + """.format(*mescape(self.type, self.type, self.type, self.name, + dataset_type, self.type, dataset_type )) + else: + query += """ + WHERE {}XRef.{}FreezeId = {}Freeze.Id + and {}Freeze.Name = '{}' + and {}.Id = {}XRef.{}Id + order by {}.Id + """.format(*mescape(self.type, self.type, self.type, self.type, + self.name, dataset_type, self.type, self.type, dataset_type)) results = g.db.execute(query).fetchall() trait_sample_data.append(results) |