def find_control_file(self,rep,default=None):
'''Attempts to find an appropriate control file.'''
# TODO Make more generic and move to dxencode.py when needed.
(AUTHID,AUTHPW,SERVER) = dxencode.processkey(self.server_key)
if 'controls' not in rep:
return None
for file_key in rep['controls']:
if isinstance(file_key,list):
file_key = file_key[0]
file_obj = dxencode.enc_lookup_json(file_key,self.server_key,frame='embedded')
rep_id = file_obj["replicate"]['@id']
rep_obj = dxencode.enc_lookup_json(rep_id,self.server_key,frame='embedded')
exp_id = rep_obj['experiment']['@id'].split('/')[2]
rep_tech = "rep%s_%s" % \
(rep_obj['biological_replicate_number'], rep_obj['technical_replicate_number'])
control_root = self.psv['control_path']
# Cheating:
if self.proj_name == "scratchPad" and self.psv['control_path'] == self.CONTROL_ROOT_FOLDER:
control_root = "/lrna"
path_n_glob = control_root + exp_id + '/' + rep_tech + '/' + self.CONTROL_FILE_GLOB
target_folder = dxencode.find_folder(exp_id + '/' + rep_tech,self.project,control_root)
#print "Target found [%s]" % target_folder
if target_folder != None:
path_n_glob = target_folder + '/' + self.CONTROL_FILE_GLOB
fid = dxencode.find_file(path_n_glob,self.proj_id,multiple=False,recurse=False)
if fid != None:
return dxencode.file_path_from_fid(fid)
if default != None:
return default
#print json.dumps(rep,indent=4)
print "Unable to find control in search of %s" % rep['controls']
sys.exit(1)
def find_control_file(self,rep,default=None):
'''Attempts to find an appropriate control file.'''
# TODO Make more generic and move to dxencode.py when needed.
(AUTHID,AUTHPW,SERVER) = dxencode.processkey(self.server_key)
for file_key in rep['controls']:
url = '%s%s/?format=json&frame=embedded' % (SERVER,file_key)
#print '-- ' + AUTHID + " " + AUTHPW + " " + SERVER + " " + url
try:
response = dxencode.encoded_get(url, AUTHID, AUTHPW)
file_obj = response.json()
except:
print "URL to control [%s] returned ?" % url
print response
sys.exit(1)
#print json.dumps(response,indent=4)
rep_id = file_obj["replicate"]['@id']
url = '%s%s/?format=json&frame=embedded' % (SERVER,rep_id)
try:
response = dxencode.encoded_get(url, AUTHID, AUTHPW)
rep_obj = response.json()
except:
print "URL to replicate [%s] returned ?" % url
print response
sys.exit(1)
exp_id = rep_obj['experiment'].split('/')[2]
rep_tech = "rep%s_%s" % \
(rep_obj['biological_replicate_number'], rep_obj['technical_replicate_number'])
# default by cheating
if self.proj_name == dxencode.PRODUCTION_PROJECT:
control_root = "/long-RNA-seq/runs/"
else:
control_root = self.CONTROL_ROOT_FOLDER
path_n_glob = control_root + exp_id + '/' + rep_tech + '/' + self.CONTROL_FILE_GLOB
target_folder = dxencode.find_folder(exp_id + '/' + rep_tech,self.project,control_root)
#print "Target found [%s]" % target_folder
if target_folder != None:
path_n_glob = target_folder + '/' + self.CONTROL_FILE_GLOB
fid = dxencode.find_file(path_n_glob,self.proj_id,multiple=False,recurse=False)
if fid != None:
return dxencode.file_path_from_fid(fid)
if default != None:
return default
print "Unable to find control in search of %s" % rep['controls']
sys.exit(1)