def __init__(self):
"""Create a dictionary of samples where the value is set to Geno,
Publish or ProbeSet. E.g.
{'AD-cases-controls-MyersGeno': 'Geno',
'AD-cases-controls-MyersPublish': 'Publish',
'AKXDGeno': 'Geno',
'AXBXAGeno': 'Geno',
'AXBXAPublish': 'Publish',
'Aging-Brain-UCIPublish': 'Publish',
'All Phenotypes': 'Publish',
'B139_K_1206_M': 'ProbeSet',
'B139_K_1206_R': 'ProbeSet' ...
"""
self.datasets = {}
if USE_GN_SERVER:
data = menu_main()
else:
file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
with open(file_name, 'r') as fh:
data = json.load(fh)
for species in data['datasets']:
for group in data['datasets'][species]:
for dataset_type in data['datasets'][species][group]:
for dataset in data['datasets'][species][group][
dataset_type]:
short_dataset_name = dataset[1]
if dataset_type == "Phenotypes":
new_type = "Publish"
elif dataset_type == "Genotypes":
new_type = "Geno"
else:
new_type = "ProbeSet"
self.datasets[short_dataset_name] = new_type
# Set LOG_LEVEL_DEBUG=5 to see the following:
logger.debugf(5, "datasets", self.datasets)
def __init__(self):
"""Create a dictionary of samples where the value is set to Geno,
Publish or ProbeSet. E.g.
{'AD-cases-controls-MyersGeno': 'Geno',
'AD-cases-controls-MyersPublish': 'Publish',
'AKXDGeno': 'Geno',
'AXBXAGeno': 'Geno',
'AXBXAPublish': 'Publish',
'Aging-Brain-UCIPublish': 'Publish',
'All Phenotypes': 'Publish',
'B139_K_1206_M': 'ProbeSet',
'B139_K_1206_R': 'ProbeSet' ...
"""
self.datasets = {}
if USE_GN_SERVER:
data = menu_main()
else:
file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
with open(file_name, 'r') as fh:
data = json.load(fh)
for species in data['datasets']:
for group in data['datasets'][species]:
for dataset_type in data['datasets'][species][group]:
for dataset in data['datasets'][species][group][dataset_type]:
short_dataset_name = dataset[1]
if dataset_type == "Phenotypes":
new_type = "Publish"
elif dataset_type == "Genotypes":
new_type = "Geno"
else:
new_type = "ProbeSet"
self.datasets[short_dataset_name] = new_type
# Set LOG_LEVEL_DEBUG=5 to see the following:
logger.debugf(5,"datasets",self.datasets)