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authorBonfaceKilz2020-07-23 02:44:42 +0300
committerBonfaceKilz2020-07-24 03:47:44 +0300
commit1a0380b9f778600f4ed0838a2dfaf4fc3d7bc768 (patch)
tree42d178b0f79be5b60e3f6803df2359442aa84ab3 /wqflask/base/data_set.py
parent87fd995209aba0df1f95c1d5d5dd7eefd60d0906 (diff)
downloadgenenetwork2-1a0380b9f778600f4ed0838a2dfaf4fc3d7bc768.tar.gz
Inject redis instance into DatasetType class
* wqflask/base/data_set.py(DatasetType): - Rename Redis instance to r to avoid confusion and name collisions - Inject the redis instance into Dataset_Types class to make it easier to test - Rename Dataset_Types class to DatasetType class
Diffstat (limited to 'wqflask/base/data_set.py')
-rw-r--r--wqflask/base/data_set.py38
1 files changed, 19 insertions, 19 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index f9705a22..21ace006 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -49,8 +49,8 @@ import cPickle as pickle
import itertools
from redis import Redis
-Redis = Redis()
+r = Redis()
logger = getLogger(__name__)
@@ -74,9 +74,9 @@ def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_n
return dataset_class(dataset_name, get_samplelist)
-class Dataset_Types(object):
+class DatasetType:
- def __init__(self):
+ def __init__(self, redis_instance):
"""Create a dictionary of samples where the value is set to Geno,
Publish or ProbeSet. E.g.
@@ -91,9 +91,9 @@ Publish or ProbeSet. E.g.
'B139_K_1206_R': 'ProbeSet' ...
"""
+ self.redis_instance = redis_instance
self.datasets = {}
-
- data = Redis.get("dataset_structure")
+ data = redis_instance.get("dataset_structure")
if data:
self.datasets = json.loads(data)
else: # ZS: I don't think this should ever run unless Redis is emptied
@@ -115,7 +115,7 @@ Publish or ProbeSet. E.g.
except:
pass
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ redis_instance.set("dataset_structure", json.dumps(self.datasets))
# Set LOG_LEVEL_DEBUG=5 to see the following:
logger.debugf(5, "datasets", self.datasets)
@@ -134,7 +134,7 @@ Publish or ProbeSet. E.g.
results = g.db.execute(mrna_expr_query).fetchall()
if len(results):
self.datasets[name] = "ProbeSet"
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ redis_instance.set("dataset_structure", json.dumps(self.datasets))
return self.datasets[name]
group_name = name.replace("Publish", "")
@@ -148,7 +148,7 @@ Publish or ProbeSet. E.g.
results = g.db.execute(pheno_query).fetchall()
if len(results):
self.datasets[name] = "Publish"
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ redis_instance.set("dataset_structure", json.dumps(self.datasets))
return self.datasets[name]
# ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary
@@ -160,7 +160,7 @@ Publish or ProbeSet. E.g.
results = g.db.execute(other_pheno_query).fetchall()
if len(results):
self.datasets[name] = "Publish"
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ redis_instance.set("dataset_structure", json.dumps(self.datasets))
return self.datasets[name]
geno_query = """
@@ -175,7 +175,7 @@ Publish or ProbeSet. E.g.
results = g.db.execute(geno_query).fetchall()
if len(results):
self.datasets[name] = "Geno"
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
return self.datasets[name]
# ZS: It shouldn't ever reach this
@@ -185,13 +185,13 @@ Publish or ProbeSet. E.g.
# Do the intensive work at startup one time only
-Dataset_Getter = Dataset_Types()
+Dataset_Getter = DatasetType(r)
def create_datasets_list():
if USE_REDIS:
key = "all_datasets"
- result = Redis.get(key)
+ result = r.get(key)
if result:
logger.debug("Redis cache hit")
@@ -215,8 +215,8 @@ def create_datasets_list():
datasets.append(dataset)
if USE_REDIS:
- Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*60)
+ r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
+ r.expire(key, 60*60)
return datasets
@@ -431,7 +431,7 @@ class DatasetGroup(object):
result = None
key = "samplelist:v3:" + self.name
if USE_REDIS:
- result = Redis.get(key)
+ result = r.get(key)
if result is not None:
self.samplelist = json.loads(result)
@@ -446,8 +446,8 @@ class DatasetGroup(object):
self.samplelist = None
if USE_REDIS:
- Redis.set(key, json.dumps(self.samplelist))
- Redis.expire(key, 60*5)
+ r.set(key, json.dumps(self.samplelist))
+ r.expire(key, 60*5)
def all_samples_ordered(self):
result = []
@@ -558,8 +558,8 @@ def datasets(group_name, this_group=None):
datasets=[(dataset, dataset_short)]))
if USE_REDIS:
- Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*5)
+ r.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
+ r.expire(key, 60*5)
if this_group != None:
this_group._datasets = dataset_menu