diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 46 |
1 files changed, 31 insertions, 15 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1520b180..89bbf03d 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -46,7 +46,7 @@ from pprint import pformat as pf DS_NAME_MAP = {} def create_dataset(dataset_name): - print("dataset_name:", dataset_name) + #print("dataset_name:", dataset_name) query = """ SELECT DBType.Name @@ -71,7 +71,7 @@ def create_dataset(dataset_name): def mescape(*items): """Multiple escape""" escaped = [escape(item) for item in items] - print("escaped is:", escaped) + #print("escaped is:", escaped) return escaped @@ -235,6 +235,7 @@ class DataSet(object): self.retrieve_other_names() self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype + self.group.read_genotype_file() self.species = species.TheSpecies(self) @@ -624,17 +625,34 @@ class MrnaAssayDataSet(DataSet): return trait_data def get_trait_data(self): + import pdb + pdb.set_trace() + #samplelist = [] + #samplelist += self.group.samplelist + #samplelist += self.group.parlist + #samplelist += self.group.f1list + #self.samplelist = samplelist + + self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list + sample_ids = [] - for sample in self.group.samplelist: - query = """ - SELECT Strain.Id FROM Strain, Species - WHERE Strain.Name = '{}' - and Strain.SpeciesId=Species.Id - and Species.name = '{}' - """.format(*mescape(sample, self.group.species)) - this_id = g.db.execute(query).fetchone()[0] - sample_ids.append('%d' % this_id) - print("sample_ids size: ", len(sample_ids)) + + where_clause = "" + for sample in self.samplelist: + if len(where_clause): + where_clause += " or " + where_clause += """'{}'""".format(*mescape(sample)) + + query = """ + SELECT Strain.Id, Strain.Name FROM Strain, Species + WHERE Strain.Name = '{}' + and Strain.SpeciesId=Species.Id + and Species.name = '{}' + """.format(*mescape(where_clause, self.group.species)) + result = g.db.execute(query).fetchall() + + print("[blueberry] result is:", pf(result)) + #sample_ids.append('%d' % this_id) # MySQL limits the number of tables that can be used in a join to 61, # so we break the sample ids into smaller chunks @@ -642,7 +660,6 @@ class MrnaAssayDataSet(DataSet): n = len(sample_ids) / chunk_count if len(sample_ids) % chunk_count: n += 1 - print("n: ", n) #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId #tempTable = None #if GeneId and db.type == "ProbeSet": @@ -681,10 +698,9 @@ class MrnaAssayDataSet(DataSet): order by {}.Id """.format(*mescape(self.type, self.type, self.type, self.type, self.name, self.type, self.type, self.type, self.type)) - print("query: ", query) results = g.db.execute(query).fetchall() trait_sample_data.append(results) - + trait_count = len(trait_sample_data[0]) self.trait_data = collections.defaultdict(list) # put all of the separate data together into a dictionary where the keys are |