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 __init__(self):
self.args = self.get_args()
# expect graph of form (child, parent)
self.expected_graph = {
'unpaired': {},
'paired': {}
}
self.assay_term_name = ''
if self.args.test:
key = 'test'
else:
key = 'www'
(self.authid, self.authpw, self.server) = dxencode.processkey(key)
self.experiments = []
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)
#!/usr/bin/env python
import dxencode
import dxpy
import json
import requests
def patch(obs):
for fob in obs:
if fob['file_format'] == 'fastq' or fob['status'] == 'revoked':
continue
fn = fob['submitted_file_name']
folder = dxpy.describe(dxpy.find_one_data_object(name=fn.strip('/'), project='project-BQkYKg00F1GP55qQ9Qy00VP0')['id'])['folder']
newfn = folder+'/'+fn.strip('/')
print "Patch: %s with %s" % (fn, newfn)
res = requests.patch(srv+fob['@id'], auth=(id,pw), data=json.dumps({'submitted_file_name': newfn}),headers={'content-type': 'application/json'})
try:
res.raise_for_status()
print "Success"
except Exception, e:
print "Failed %s" % e
(id,pw,srv) = dxencode.processkey('www')
accs = dxencode.encoded_get(srv+'ENCSR000AEV', AUTHID=id, AUTHPW=pw).json()['original_files']
file_objs = [ dxencode.encoded_get(srv+acc, AUTHID=id, AUTHPW=pw).json() for acc in accs ]
patch(file_objs)
def run(self):
'''Runs recovery from start to finish using command line arguments.'''
args = self.get_args()
self.test = args.test
self.ignore = False
if args.ignore_properties:
print "Ignoring DXFile properties (will post to test server)"
self.ignore = args.ignore_properties
self.server_key = 'test' # mandated because option is dangerous
self.server_key = args.server
self.authid, self.authpw, self.server = dxencode.processkey(self.server_key)
if self.server_key == "www":
self.acc_prefix = "ENCFF"
self.proj_name = dxencode.env_get_current_project()
if self.proj_name == None or args.project != None:
self.proj_name = args.project
if self.proj_name == None:
print "Please enter a '--project' to run in."
sys.exit(1)
self.project = dxencode.get_project(self.proj_name)
self.proj_id = self.project.get_id()
print "== Running in project [%s] and will attempt recovery to the [%s] server ==" % \
(self.proj_name,self.server_key)
exp_count = 0
halted = 0
total_recovered = 0
for exp_id in args.experiments:
sys.stdout.flush() # Slow running job should flush to piped log
self.exp_id = exp_id
self.obj_cache["exp"] = {} # clear exp cache, which will hold exp specific wf_run and step_run objects
# 1) Lookup experiment type from encoded, based on accession
print "Working on %s..." % self.exp_id
self.exp = dxencode.get_exp(self.exp_id,must_find=True,key=self.server_key)
if self.exp == None or self.exp["status"] == "error":
print "Unable to locate experiment %s in encoded (%s)" % (self.exp_id, self.server_key)
continue
self.exp_type = dxencode.get_exp_type(self.exp_id,self.exp,self.EXPERIMENT_TYPES_SUPPORTED)
if self.exp_type == None:
continue
# 2) Locate the experiment accession named folder
# NOTE: genome and annotation are not known for this exp yet, so the umbrella folder is just based on exp_type
self.umbrella_folder = dxencode.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,self.exp_type)
self.exp_folder = dxencode.find_exp_folder(self.project,exp_id,self.umbrella_folder,warn=True)
if self.exp_folder == None:
continue
print "- Examining %s:%s for '%s' results..." % \
(self.proj_name, self.exp_folder, self.exp_type)
# 3) Given the experiment type, determine the expected results
self.pipeline = self.pipeline_specification(args,self.exp_type,self.exp_folder)
self.replicates = self.find_replicate_folders(self.exp_folder, verbose=args.verbose)
# 4) Given expected results locate any files (by glob) that should be posted for
# a) each single replicate (in replicate sub-folders named as reN_N/
# b) combined replicates in the experiment folder itself
files_expected = self.find_expected_files(self.exp_folder, self.replicates, verbose=args.verbose)
print "- Found %d files that are available in DX." % len(files_expected)
if len(files_expected) == 0:
continue
# 5) For each file that should be posted, determine if the file needs to be posted.
files_posted = self.find_posted_files(files_expected, test=self.test, verbose=args.verbose) #True)
print "- Found %d files that have been posted" % len(files_posted)
if len(files_posted) == 0:
continue
# 6) For each file that needs to be posted:
exp_count += 1
file_count = 0
recovery_count = 0
for (out_type,rep_tech,fid) in files_posted:
sys.stdout.flush() # Slow running job should flush to piped log
accession = self.found[fid]['accession']
file_name = dxencode.file_path_from_fid(fid)
if args.start_at != None:
if accession != args.start_at and not file_name.endswith(args.start_at):
continue
else:
print "- Starting at %s" % (file_name)
args.start_at = None
# a) discover all necessary dx information needed for post.
# b) gather any other information necessary from dx and encoded.
print "- Handle file %s %s" % (accession,dxencode.file_path_from_fid(fid))
payload = self.make_payload_obj(out_type,rep_tech,fid, verbose=args.verbose)
file_count += 1
# c) Update encoded database only if necessary.
if self.file_metadata_recovery(fid,payload,args.test,verbose=args.verbose):
recovery_count += 1
if args.files != 0 and file_count >= args.files: # Short circuit for test
print "- Just trying %d file(s) by request" % file_count
break
if not args.test:
print "- For %s Processed %d file(s), recovered %s" % (self.exp_id, file_count, recovery_count)
else:
print "- For %s Processed %d file(s), would recover %s" % (self.exp_id, file_count, recovery_count)
total_recovered += recovery_count
if not args.test:
print "Processed %d experiment(s), halted %d, recovered %d file(s)" % (exp_count, halted, total_recovered)
else:
print "Processed %d experiment(s), halted %d, would recover %d file(s)" % (exp_count, halted, total_recovered)
if halted == exp_count:
sys.exit(1)
print "(finished)"
for fob in obs:
if fob['file_format'] == 'fastq' or fob['status'] == 'revoked':
continue
fn = fob['submitted_file_name']
folder = dxpy.describe(
dxpy.find_one_data_object(
name=fn.strip('/'),
project='project-BQkYKg00F1GP55qQ9Qy00VP0')['id'])['folder']
newfn = folder + '/' + fn.strip('/')
print "Patch: %s with %s" % (fn, newfn)
res = requests.patch(srv + fob['@id'],
auth=(id, pw),
data=json.dumps({'submitted_file_name': newfn}),
headers={'content-type': 'application/json'})
try:
res.raise_for_status()
print "Success"
except Exception, e:
print "Failed %s" % e
(id, pw, srv) = dxencode.processkey('www')
accs = dxencode.encoded_get(srv + 'ENCSR000AEV', AUTHID=id,
AUTHPW=pw).json()['original_files']
file_objs = [
dxencode.encoded_get(srv + acc, AUTHID=id, AUTHPW=pw).json()
for acc in accs
]
patch(file_objs)
