def create_datasets_list():
if USE_REDIS:
key = "all_datasets"
result = Redis.get(key)
if result:
logger.debug("Redis cache hit")
datasets = pickle.loads(result)
if result is None:
datasets = list()
with Bench("Creating DataSets object"):
type_dict = {'Publish': 'PublishFreeze',
'ProbeSet': 'ProbeSetFreeze',
'Geno': 'GenoFreeze'}
for dataset_type in type_dict:
query = "SELECT Name FROM {}".format(type_dict[dataset_type])
for result in fetchall(query):
#The query at the beginning of this function isn't
#necessary here, but still would rather just reuse
#it logger.debug("type: {}\tname:
#{}".format(dataset_type, result.Name))
dataset = create_dataset(result.Name, dataset_type)
datasets.append(dataset)
if USE_REDIS:
Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60*60)
return datasets
def create_datasets_list():
if USE_REDIS:
key = "all_datasets"
result = Redis.get(key)
if result:
logger.debug("Redis cache hit")
datasets = pickle.loads(result)
if result is None:
datasets = list()
with Bench("Creating DataSets object"):
type_dict = {'Publish': 'PublishFreeze',
'ProbeSet': 'ProbeSetFreeze',
'Geno': 'GenoFreeze'}
for dataset_type in type_dict:
query = "SELECT Name FROM {}".format(type_dict[dataset_type])
for result in fetchall(query):
#The query at the beginning of this function isn't
#necessary here, but still would rather just reuse
#it logger.debug("type: {}\tname:
#{}".format(dataset_type, result.Name))
dataset = create_dataset(result.Name, dataset_type)
datasets.append(dataset)
if USE_REDIS:
Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60*60)
return datasets
def datasets(group_name, this_group = None):
key = "group_dataset_menu:v2:" + group_name
logger.debug("key is2:", key)
dataset_menu = []
logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
the_results = fetchall('''
(SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
FROM PublishFreeze,InbredSet
WHERE PublishFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
and PublishFreeze.public > %s)
UNION
(SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
FROM GenoFreeze, InbredSet
WHERE GenoFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
and GenoFreeze.public > %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
and ProbeSetFreeze.public > %s
ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
''' % (group_name, webqtlConfig.PUBLICTHRESH,
group_name, webqtlConfig.PUBLICTHRESH,
"'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
#for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
for dataset_item in the_results:
tissue_name = dataset_item[0]
dataset = dataset_item[1]
dataset_short = dataset_item[2]
if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
else:
dataset_sub_menu = [item[1:] for item in dataset]
tissue_already_exists = False
tissue_position = None
for i, tissue_dict in enumerate(dataset_menu):
if tissue_dict['tissue'] == tissue_name:
tissue_already_exists = True
tissue_position = i
break
if tissue_already_exists:
#logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(dict(tissue=tissue_name,
datasets=[(dataset, dataset_short)]))
if USE_REDIS:
Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60*5)
if this_group != None:
this_group._datasets = dataset_menu
return this_group._datasets
else:
return dataset_menu
def datasets(group_name, this_group = None):
key = "group_dataset_menu:v2:" + group_name
logger.debug("key is2:", key)
dataset_menu = []
logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
the_results = fetchall('''
(SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
FROM PublishFreeze,InbredSet
WHERE PublishFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
and PublishFreeze.public > %s
and PublishFreeze.confidentiality < 1)
UNION
(SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
FROM GenoFreeze, InbredSet
WHERE GenoFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
and GenoFreeze.public > %s
and GenoFreeze.confidentiality < 1)
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
and ProbeSetFreeze.public > %s
and ProbeSetFreeze.confidentiality < 1
ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
''' % (group_name, webqtlConfig.PUBLICTHRESH,
group_name, webqtlConfig.PUBLICTHRESH,
"'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
#for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
for dataset_item in the_results:
tissue_name = dataset_item[0]
dataset = dataset_item[1]
dataset_short = dataset_item[2]
if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
else:
dataset_sub_menu = [item[1:] for item in dataset]
tissue_already_exists = False
tissue_position = None
for i, tissue_dict in enumerate(dataset_menu):
if tissue_dict['tissue'] == tissue_name:
tissue_already_exists = True
tissue_position = i
break
if tissue_already_exists:
#logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(dict(tissue=tissue_name,
datasets=[(dataset, dataset_short)]))
if USE_REDIS:
Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60*5)
if this_group != None:
this_group._datasets = dataset_menu
return this_group._datasets
else:
return dataset_menu
def datasets(group_name, this_group=None):
key = "group_dataset_menu:v2:" + group_name
logger.debug("key is2:", key)
dataset_menu = []
logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:",
webqtlConfig.PUBLICTHRESH)
logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:",
type(webqtlConfig.PUBLICTHRESH))
the_results = fetchall('''
(SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
FROM PublishFreeze,InbredSet
WHERE PublishFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
and PublishFreeze.public > %s
and PublishFreeze.confidentiality < 1
ORDER BY PublishFreeze.Id ASC)
UNION
(SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
FROM GenoFreeze, InbredSet
WHERE GenoFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
and GenoFreeze.public > %s
and GenoFreeze.confidentiality < 1)
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
and ProbeSetFreeze.public > %s
and ProbeSetFreeze.confidentiality < 1
ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
''' % (group_name, webqtlConfig.PUBLICTHRESH, group_name,
webqtlConfig.PUBLICTHRESH, "'" + group_name + "'",
webqtlConfig.PUBLICTHRESH))
sorted_results = sorted(the_results, key=lambda kv: kv[0])
pheno_inserted = False #ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
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:
#logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(
dict(tissue=tissue_name,
datasets=[(dataset, dataset_short)]))
if USE_REDIS:
Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60 * 5)
if this_group != None:
this_group._datasets = dataset_menu
return this_group._datasets
else:
return dataset_menu