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-rw-r--r--wqflask/base/data_set.py74
1 files changed, 38 insertions, 36 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4953e728..f75447f6 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -51,6 +51,9 @@ from maintenance import get_group_samplelists
from MySQLdb import escape_string as escape
from pprint import pformat as pf
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
# Used by create_database to instantiate objects
# Each subclass will add to this
DS_NAME_MAP = {}
@@ -59,7 +62,7 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
- print("dataset_type is:", dataset_type)
+ logger.debug("dataset_type is:", dataset_type)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
@@ -73,7 +76,7 @@ class Dataset_Types(object):
with open(file_name, 'r') as fh:
data = json.load(fh)
- print("*" * 70)
+ logger.debug("*" * 70)
for species in data['datasets']:
for group in data['datasets'][species]:
for dataset_type in data['datasets'][species][group]:
@@ -98,7 +101,7 @@ def create_datasets_list():
result = Redis.get(key)
if result:
- print("Cache hit!!!")
+ logger.debug("Cache hit!!!")
datasets = pickle.loads(result)
else:
@@ -113,7 +116,7 @@ def create_datasets_list():
for result in g.db.execute(query).fetchall():
#The query at the beginning of this function isn't necessary here, but still would
#rather just reuse it
- #print("type: {}\tname: {}".format(dataset_type, result.Name))
+ #logger.debug("type: {}\tname: {}".format(dataset_type, result.Name))
dataset = create_dataset(result.Name, dataset_type)
datasets.append(dataset)
@@ -133,7 +136,7 @@ def create_in_clause(items):
def mescape(*items):
"""Multiple escape"""
escaped = [escape(str(item)) for item in items]
- #print("escaped is:", escaped)
+ #logger.debug("escaped is:", escaped)
return escaped
@@ -152,12 +155,12 @@ class Markers(object):
marker['Mb'] = float(marker['Mb'])
self.markers = markers
- #print("self.markers:", self.markers)
+ #logger.debug("self.markers:", self.markers)
def add_pvalues(self, p_values):
- print("length of self.markers:", len(self.markers))
- print("length of p_values:", len(p_values))
+ logger.debug("length of self.markers:", len(self.markers))
+ logger.debug("length of p_values:", len(p_values))
if type(p_values) is list:
# THIS IS only needed for the case when we are limiting the number of p-values calculated
@@ -178,10 +181,10 @@ class Markers(object):
elif type(p_values) is dict:
filtered_markers = []
for marker in self.markers:
- #print("marker[name]", marker['name'])
- #print("p_values:", p_values)
+ #logger.debug("marker[name]", marker['name'])
+ #logger.debug("p_values:", p_values)
if marker['name'] in p_values:
- #print("marker {} IS in p_values".format(i))
+ #logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
@@ -192,7 +195,7 @@ class Markers(object):
marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
filtered_markers.append(marker)
#else:
- #print("marker {} NOT in p_values".format(i))
+ #logger.debug("marker {} NOT in p_values".format(i))
#self.markers.remove(marker)
#del self.markers[i]
self.markers = filtered_markers
@@ -204,7 +207,7 @@ class HumanMarkers(Markers):
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
- #print("splat:", splat)
+ #logger.debug("splat:", splat)
if len(specified_markers) > 0:
if splat[1] in specified_markers:
marker = {}
@@ -220,7 +223,7 @@ class HumanMarkers(Markers):
marker['Mb'] = float(splat[3]) / 1000000
self.markers.append(marker)
- #print("markers is: ", pf(self.markers))
+ #logger.debug("markers is: ", pf(self.markers))
def add_pvalues(self, p_values):
@@ -237,7 +240,7 @@ class DatasetGroup(object):
"""
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
- #print("DATASET NAME2:", dataset.name)
+ #logger.debug("DATASET NAME2:", dataset.name)
self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
if self.name == 'BXD300':
self.name = "BXD"
@@ -245,7 +248,7 @@ class DatasetGroup(object):
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
- #print("parents/f1s: {}:{}".format(self.parlist, self.f1list))
+ #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list))
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
@@ -257,7 +260,7 @@ class DatasetGroup(object):
self.markers = HumanMarkers(self.name, markers)
def get_markers(self):
- #print("self.species is:", self.species)
+ #logger.debug("self.species is:", self.species)
if self.species == "human":
marker_class = HumanMarkers
else:
@@ -267,10 +270,10 @@ class DatasetGroup(object):
def datasets(self):
key = "group_dataset_menu:v2:" + self.name
- print("key is2:", key)
+ logger.debug("key is2:", key)
dataset_menu = []
- print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
- print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
+ logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
+ logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
results = g.db.execute('''
(SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
FROM PublishFreeze,InbredSet
@@ -317,7 +320,7 @@ class DatasetGroup(object):
break
if tissue_already_exists:
- #print("dataset_menu:", dataset_menu[i]['datasets'])
+ #logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(dict(tissue=tissue_name,
@@ -343,18 +346,18 @@ class DatasetGroup(object):
def get_samplelist(self):
key = "samplelist:v2:" + self.name
- #print("key is:", key)
+ #logger.debug("key is:", key)
#with Bench("Loading cache"):
result = Redis.get(key)
if result:
- #print("Sample List Cache hit!!!")
- #print("Before unjsonifying {}: {}".format(type(result), result))
+ #logger.debug("Sample List Cache hit!!!")
+ #logger.debug("Before unjsonifying {}: {}".format(type(result), result))
self.samplelist = json.loads(result)
- #print(" type: ", type(self.samplelist))
- #print(" self.samplelist: ", self.samplelist)
+ #logger.debug(" type: ", type(self.samplelist))
+ #logger.debug(" self.samplelist: ", self.samplelist)
else:
- print("Cache not hit")
+ logger.debug("Cache not hit")
genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
@@ -364,7 +367,7 @@ class DatasetGroup(object):
self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
else:
self.samplelist = None
- print("Sample list: ",self.samplelist)
+ logger.debug("Sample list: ",self.samplelist)
Redis.set(key, json.dumps(self.samplelist))
Redis.expire(key, 60*5)
@@ -482,7 +485,7 @@ class DataSet(object):
""" % (query_args)).fetchone()
except TypeError:
- print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
+ logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
def get_trait_data(self, sample_list=None):
@@ -549,10 +552,10 @@ class DataSet(object):
""".format(*mescape(self.type, self.type, self.type, self.type,
self.name, dataset_type, self.type, self.type, dataset_type))
- #print("trait data query: ", query)
+ #logger.debug("trait data query: ", query)
results = g.db.execute(query).fetchall()
- #print("query results:", results)
+ #logger.debug("query results:", results)
trait_sample_data.append(results)
trait_count = len(trait_sample_data[0])
@@ -571,7 +574,7 @@ class PhenotypeDataSet(DataSet):
def setup(self):
- #print("IS A PHENOTYPEDATASET")
+ #logger.debug("IS A PHENOTYPEDATASET")
# Fields in the database table
self.search_fields = ['Phenotype.Post_publication_description',
@@ -967,7 +970,7 @@ class MrnaAssayDataSet(DataSet):
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
- #print("query is:", pf(query))
+ #logger.debug("query is:", pf(query))
result = g.db.execute(query).fetchone()
@@ -1046,7 +1049,7 @@ class MrnaAssayDataSet(DataSet):
Strain.Name
""" % (escape(trait), escape(self.name))
results = g.db.execute(query).fetchall()
- #print("RETRIEVED RESULTS HERE:", results)
+ #logger.debug("RETRIEVED RESULTS HERE:", results)
return results
@@ -1130,7 +1133,7 @@ class TempDataSet(DataSet):
def geno_mrna_confidentiality(ob):
dataset_table = ob.type + "Freeze"
- #print("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
+ #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = %%s''' % (dataset_table)
@@ -1145,4 +1148,3 @@ def geno_mrna_confidentiality(ob):
if confidential:
return True
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 01:42:22 +0000