diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 33 |
1 files changed, 19 insertions, 14 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 633f7545..015b2623 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -22,6 +22,8 @@ from __future__ import print_function, division +from flask import Flask, g + from htmlgen import HTMLgen2 as HT import webqtlConfig @@ -31,25 +33,28 @@ from pprint import pformat as pf # Used by create_database to instantiate objects DS_NAME_MAP = {} -def create_dataset(db_conn, dataset_name): - cursor = db_conn.cursor() - cursor.execute(""" +def create_dataset(dataset_name): + #cursor = db_conn.cursor() + print("dataset_name:", dataset_name) + + dataset_type = g.db.execute(""" SELECT DBType.Name FROM DBList, DBType WHERE DBList.Name = %s and DBType.Id = DBList.DBTypeId - """, (dataset_name)) - print("dataset_name:", dataset_name) - dataset_type = cursor.fetchone()[0] - print("dataset_type:", pf(dataset_type)) + """, (dataset_name)).fetchone().Name + + #dataset_type = cursor.fetchone()[0] + print("[blubber] dataset_type:", pf(dataset_type)) dataset_ob = DS_NAME_MAP[dataset_type] #dataset_class = getattr(data_set, dataset_ob) - + print("dataset_ob:", dataset_ob) print("DS_NAME_MAP:", pf(DS_NAME_MAP)) dataset_class = globals()[dataset_ob] - return dataset_class(dataset_name, db_conn) + return dataset_class(dataset_name) + class DataSet(object): """ @@ -58,12 +63,12 @@ class DataSet(object): """ - def __init__(self, name, db_conn): + def __init__(self, name): assert name self.name = name - self.db_conn = db_conn - self.cursor = self.db_conn.cursor() + #self.db_conn = db_conn + #self.cursor = self.db_conn.cursor() self.id = None self.type = None self.group = None @@ -271,7 +276,7 @@ class GenotypeDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - def get_trait_info(self, trait_list): + def get_trait_info(self, trait_list, species=None): for this_trait in trait_list: if not this_trait.haveinfo: this_trait.retrieveInfo() @@ -355,7 +360,7 @@ class MrnaAssayDataSet(DataSet): ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = "%s" - ''' % self.db_conn.escape_string(self.name) + ''' % g.db.escape_string(self.name) def check_confidentiality(self): |