1 files changed, 0 insertions, 124 deletions
diff --git a/wqflask/base/data_set/__init__.py b/wqflask/base/data_set/__init__.py
deleted file mode 100644
index 69eaab53..00000000
--- a/wqflask/base/data_set/__init__.py
+++ /dev/null
@@ -1,124 +0,0 @@
-"The data_set package ..."
-
-# builtins imports
-import json
-import pickle as pickle
-
-# 3rd-party imports
-from redis import Redis
-
-# local imports
-from .dataset import DataSet
-from base import webqtlConfig
-from utility.tools import get_setting, USE_REDIS
-from .datasettype import DatasetType
-from .tempdataset import TempDataSet
-from .datasetgroup import DatasetGroup
-from .utils import query_table_timestamp
-from .genotypedataset import GenotypeDataSet
-from .phenotypedataset import PhenotypeDataSet
-from .mrnaassaydataset import MrnaAssayDataSet
-from wqflask.database import database_connection
-
-# Used by create_database to instantiate objects
-# Each subclass will add to this
-
-DS_NAME_MAP = {
-    "Temp": "TempDataSet",
-    "Geno": "GenotypeDataSet",
-    "Publish": "PhenotypeDataSet",
-    "ProbeSet": "MrnaAssayDataSet"
-}
-
-def __dataset_type__(dataset_name):
-    """Get dataset type."""
-    if "Temp" in dataset_name:
-        return "Temp"
-    if "Geno" in dataset_name:
-        return "Geno"
-    if "Publish" in dataset_name:
-        return "Publish"
-    return "ProbeSet"
-
-def create_dataset(dataset_name, dataset_type=None,
-                   get_samplelist=True, group_name=None, redis_conn=Redis()):
-    dataset_type = dataset_type or __dataset_type__(dataset_name)
-
-    dataset_ob = DS_NAME_MAP[dataset_type]
-    dataset_class = globals()[dataset_ob]
-    if dataset_type == "Temp":
-        return dataset_class(dataset_name, get_samplelist, group_name)
-    else:
-        return dataset_class(dataset_name, get_samplelist)
-
-def datasets(group_name, this_group=None, redis_conn=Redis()):
-    key = "group_dataset_menu:v2:" + group_name
-    dataset_menu = []
-    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-        cursor.execute('''
-            (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
-            FROM PublishFreeze,InbredSet
-            WHERE PublishFreeze.InbredSetId = InbredSet.Id
-                and InbredSet.Name = '%s'
-            ORDER BY PublishFreeze.Id ASC)
-            UNION
-            (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
-            FROM GenoFreeze, InbredSet
-            WHERE GenoFreeze.InbredSetId = InbredSet.Id
-                and InbredSet.Name = '%s')
-            UNION
-            (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
-            FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
-            WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
-                and ProbeFreeze.TissueId = Tissue.Id
-                and ProbeFreeze.InbredSetId = InbredSet.Id
-                and InbredSet.Name like %s
-            ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
-            ''' % (group_name,
-                group_name,
-                "'" + group_name + "'"))
-        the_results = cursor.fetchall()
-
-    sorted_results = sorted(the_results, key=lambda kv: kv[0])
-
-    # ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
-    pheno_inserted = False
-    geno_inserted = False
-    for dataset_item in sorted_results:
-        tissue_name = dataset_item[0]
-        dataset = dataset_item[1]
-        dataset_short = dataset_item[2]
-        if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
-            if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'):
-                dataset_menu.insert(
-                    0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
-                pheno_inserted = True
-            elif pheno_inserted and tissue_name == '#GenoFreeze':
-                dataset_menu.insert(
-                    1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
-                geno_inserted = True
-            else:
-                dataset_menu.append(
-                    dict(tissue=None, datasets=[(dataset, dataset_short)]))
-        else:
-            tissue_already_exists = False
-            for i, tissue_dict in enumerate(dataset_menu):
-                if tissue_dict['tissue'] == tissue_name:
-                    tissue_already_exists = True
-                    break
-
-            if tissue_already_exists:
-                dataset_menu[i]['datasets'].append((dataset, dataset_short))
-            else:
-                dataset_menu.append(dict(tissue=tissue_name,
-                                         datasets=[(dataset, dataset_short)]))
-
-    if USE_REDIS:
-        redis_conn.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
-        redis_conn.expire(key, 60 * 5)
-
-    if this_group != None:
-        this_group._datasets = dataset_menu
-        return this_group._datasets
-    else:
-        return dataset_menu