def get_custom_data():
from subprocess import Popen, PIPE, STDOUT
if not auth.user :
res = {"redirect" : URL('default', 'user', args='login', scheme=True, host=True)} #TODO _next
return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
error = ""
samples = []
if not "custom" in request.vars :
error += "no file selected, "
else:
samples = request.vars['custom'] if type(request.vars['custom']) is not str else [request.vars['custom']]
if not samples:
error += "incorrect query, need at least one sample"
else:
for id in samples:
log.debug("id = '%s'" % str(id))
sequence_file_id = db.results_file[id].sequence_file_id
sample_set_id = db((db.sample_set_membership.sequence_file_id == sequence_file_id)
).select(db.sample_set_membership.sample_set_id).first().sample_set_id
if not auth.can_view_sample_set(sample_set_id):
error += "you do not have permission to consult this element ("+str(sample_set_id)+")"
if error == "" :
try:
data = custom_fuse(samples)
except IOError, error:
return error_message(str(error))
generic_info = "Compare samples" if len(samples) > 1 else "Sample %s" % samples[0]
data["sample_name"] = generic_info
data["dataFileName"] = generic_info
data["info"] = generic_info
data["samples"]["original_names"] = []
data["samples"]["timestamp"] = []
data["samples"]["info"] = []
data["samples"]["commandline"] = []
for id in samples:
sequence_file_id = db.results_file[id].sequence_file_id
sample_set = db((db.sequence_file.id == sequence_file_id)
& (db.sample_set_membership.sequence_file_id == db.sequence_file.id)
& (db.sample_set.id == db.sample_set_membership.sample_set_id)
& (db.sample_set.sample_type.belongs([defs.SET_TYPE_PATIENT, defs.SET_TYPE_RUN, defs.SET_TYPE_GENERIC]))
).select(db.sample_set.id, db.sample_set.sample_type).first()
patient_run = db(db[sample_set.sample_type].sample_set_id == sample_set.id).select().first()
config_id = db.results_file[id].config_id
name = vidjil_utils.anon_ids([patient_run.id])[0] if sample_set.sample_type == defs.SET_TYPE_PATIENT else patient_run.name
filename = db.sequence_file[sequence_file_id].filename
data["samples"]["original_names"].append(name + "_" + filename)
data["samples"]["timestamp"].append(str(db.sequence_file[sequence_file_id].sampling_date))
data["samples"]["info"].append(db.sequence_file[sequence_file_id].info)
data["samples"]["commandline"].append(db.config[config_id].command)
log.info("load custom data #TODO log db")
return gluon.contrib.simplejson.dumps(data, separators=(',',':'))
def get_names(self):
'''Returns the names of all the sample sets.
The function returns a dictionary whose keys are sample set
IDs and value is the name.
The number of queries is constant (which is true only if
permissions have been cached: anon_ids checks for permission)
'''
results = {}
for stype in self.sample_types:
stype_ids = self.get_sample_type_ids(stype)
if stype == defs.SET_TYPE_PATIENT:
patient_ids = db(
db[stype].sample_set_id.belongs(stype_ids)).select(
db[stype].id, db[stype].sample_set_id)
names = vidjil_utils.anon_ids([p.id for p in patient_ids])
for i, p_id in enumerate(patient_ids):
results[p_id.sample_set_id] = names[i]
else:
set_names = db(
db[stype].sample_set_id.belongs(stype_ids)).select(
db[stype].sample_set_id, db[stype].name)
for s in set_names:
results[s.sample_set_id] = s.name
return results
def get_names(self):
'''Returns the names of all the sample sets.
The function returns a dictionary whose keys are sample set
IDs and value is the name.
The number of queries is constant (which is true only if
permissions have been cached: anon_ids checks for permission)
'''
results = {}
for stype in self.sample_types:
stype_ids = self.get_sample_type_ids(stype)
if stype == defs.SET_TYPE_PATIENT:
patient_ids = db(db[stype].sample_set_id.belongs(stype_ids)).select(db[stype].id, db[stype].sample_set_id)
names = vidjil_utils.anon_ids([p.id for p in patient_ids])
for i, p_id in enumerate(patient_ids):
results[p_id.sample_set_id] = names[i]
else:
set_names = db(db[stype].sample_set_id.belongs(stype_ids)).select(db[stype].sample_set_id, db[stype].name)
for s in set_names:
results[s.sample_set_id] = s.name
return results
def get_custom_data():
from subprocess import Popen, PIPE, STDOUT
if not auth.user :
res = {"redirect" : URL('default', 'user', args='login', scheme=True, host=True)} #TODO _next
return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
error = ""
if not "custom" in request.vars :
error += "no file selected, "
else:
if type(request.vars['custom']) is not list or len(request.vars['custom']) < 2:
error += "you must select several files."
else:
for id in request.vars["custom"] :
log.debug("id = '%s'" % str(id))
sequence_file_id = db.results_file[id].sequence_file_id
patient_id = db((db.sample_set_membership.sequence_file_id == sequence_file_id)
& (db.patient.sample_set_id == db.sample_set_membership.sample_set_id)
).select(db.patient.id).first()
if not auth.can_view_patient(patient_id):
error += "you do not have permission to consult this patient ("+str(patient_id)+")"
if error == "" :
try:
data = custom_fuse(request.vars["custom"])
except IOError, error:
return error_message(str(error))
data["dataFileName"] = "Compare patients"
data["info"] = "Compare patients"
data["samples"]["original_names"] = []
data["samples"]["timestamp"] = []
data["samples"]["info"] = []
data["samples"]["commandline"] = []
for id in request.vars["custom"] :
sequence_file_id = db.results_file[id].sequence_file_id
sample_set = db((db.sequence_file.id == sequence_file_id)
& (db.sample_set_membership.sequence_file_id == db.sequence_file.id)
& (db.sample_set.id == db.sample_set_membership.sample_set_id)
& (db.sample_set.sample_type.belongs(['patient', 'run']))
).select(db.sample_set.id, db.sample_set.sample_type).first()
patient_run = db(db[sample_set.sample_type].sample_set_id == sample_set.id).select().first()
config_id = db.results_file[id].config_id
name = vidjil_utils.anon_ids(patient_run.id) if sample_set.sample_type == 'patient' else patient_run.name
filename = db.sequence_file[sequence_file_id].filename
data["samples"]["original_names"].append(name + "_" + filename)
data["samples"]["timestamp"].append(str(db.sequence_file[sequence_file_id].sampling_date))
data["samples"]["info"].append(db.sequence_file[sequence_file_id].info)
data["samples"]["commandline"].append(db.config[config_id].command)
return gluon.contrib.simplejson.dumps(data, separators=(',',':'))
def get_data():
from subprocess import Popen, PIPE, STDOUT
if not auth.user :
res = {"redirect" : URL('default', 'user', args='login', scheme=True, host=True,
vars=dict(_next=URL('default', 'get_data', scheme=True, host=True,
vars=dict(sample_set_id = request.vars["sample_set_id"],
config =request.vars["config"]))
)
)}
return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
error = ""
if "patient" in request.vars :
request.vars["sample_set_id"] = db.patient[request.vars["patient"]].sample_set_id
download = False
if "filename" in request.vars:
download = True
if "run" in request.vars :
request.vars["sample_set_id"] = db.run[request.vars["run"]].sample_set_id
if not "sample_set_id" in request.vars or request.vars['sample_set_id'] is None:
error += "id sampleset file needed, "
else :
if not auth.can_view_sample_set(request.vars["sample_set_id"]):
error += "you do not have permission to consult this sample_set ("+str(request.vars["sample_set_id"])+")"
if not "config" in request.vars:
error += "id config needed, "
sample_set = db.sample_set[request.vars["sample_set_id"]]
query = db( ( db.fused_file.sample_set_id == request.vars["sample_set_id"])
& ( db.fused_file.config_id == request.vars["config"] )
).select(db.fused_file.ALL).first()
if query is not None:
fused_file = defs.DIR_RESULTS+'/'+query.fused_file
sequence_file_list = query.sequence_file_list
if not 'fused_file' in locals():
error += "file not found"
if error == "" :
f = open(fused_file, "r")
data = gluon.contrib.simplejson.loads(f.read())
f.close()
patient_name = ""
run_name = ""
config_name = db.config[request.vars["config"]].name
command = db.config[request.vars["config"]].command
log_reference_id = request.vars["sample_set_id"]
if (sample_set.sample_type == defs.SET_TYPE_GENERIC) :
for row in db( db.generic.sample_set_id == request.vars["sample_set_id"] ).select() :
log_reference_id = row.id
generic_name = db.generic[row.id].name
data["dataFileName"] = generic_name + " (" + config_name + ")"
data["info"] = db.generic[row.id].info
data["generic_id"] = row.id
data["sample_name"] = generic_name
data["group_id"] = get_set_group(row.sample_set_id)
if (sample_set.sample_type == defs.SET_TYPE_PATIENT):
for row in db( db.patient.sample_set_id == request.vars["sample_set_id"] ).select() :
log_reference_id = row.id
patient_name = vidjil_utils.anon_ids([row.id])[0]
data["dataFileName"] = patient_name + " (" + config_name + ")"
data["info"] = db.patient[row.id].info
data["patient_id"] = row.id
data["sample_name"] = patient_name
data["group_id"] = get_set_group(row.sample_set_id)
if (sample_set.sample_type == defs.SET_TYPE_RUN) :
for row in db( db.run.sample_set_id == request.vars["sample_set_id"] ).select() :
log_reference_id = row.id
run_name = db.run[row.id].name
data["dataFileName"] = run_name + " (" + config_name + ")"
data["info"] = db.run[row.id].info
data["run_id"] = row.id
data["sample_name"] = run_name
data["group_id"] = get_set_group(row.sample_set_id)
log_query = db( ( db.user_log.record_id == log_reference_id )
& ( db.user_log.table_name == sample_set.sample_type )
).select(db.user_log.ALL, orderby=db.user_log.created)
data["logs"] = []
for row in log_query:
data["logs"].append({'message': row.msg, 'created': str(row.created)})
## récupération des infos stockées sur la base de données
query = db( ( db.sample_set.id == request.vars["sample_set_id"] )
& ( db.sample_set.id == db.sample_set_membership.sample_set_id )
& ( db.sequence_file.id == db.sample_set_membership.sequence_file_id)
& ( db.results_file.sequence_file_id == db.sequence_file.id )
& ( db.results_file.config_id == request.vars["config"] )
).select(db.sequence_file.ALL,db.results_file.ALL, db.sample_set.id, orderby=db.sequence_file.id|~db.results_file.run_date)
query2 = {}
sequence_file_id = 0
for row in query :
if row.sequence_file.id != sequence_file_id :
query2[row.sequence_file.data_file]=row
sequence_file_id = row.sequence_file.id
data["sample_set_id"] = sample_set.id
data["config_name"] = config_name
data["samples"]["info"] = []
data["samples"]["timestamp"] = []
data["samples"]["sequence_file_id"] = []
data["samples"]["results_file_id"] = []
data["samples"]["config_id"] = []
data["samples"]["names"] = []
data["samples"]["db_key"] = []
data["samples"]["id"] = []
data["samples"]["patient_id"] = []
data["samples"]["sample_name"] = []
data["samples"]["run_id"] = []
for i in range(len(data["samples"]["original_names"])) :
o_n = data["samples"]["original_names"][i].split('/')[-1]
data["samples"]["original_names"][i] = data["samples"]["original_names"][i].split('/')[-1]
data["samples"]["config_id"].append(request.vars['config'])
data["samples"]["db_key"].append('')
data["samples"]["commandline"].append(command)
if o_n in query2:
row = query2[o_n]
data["samples"]["info"].append(row.sequence_file.info)
data["samples"]["timestamp"].append(str(row.sequence_file.sampling_date))
data["samples"]["sequence_file_id"].append(row.sequence_file.id)
data["samples"]["results_file_id"].append(row.results_file.id)
data["samples"]["names"].append(row.sequence_file.filename.split('.')[0])
data["samples"]["id"].append(row.sequence_file.id)
data["samples"]["patient_id"].append(get_patient_id(row.sequence_file.id))
data["samples"]["sample_name"].append(row.sequence_file.id)
data["samples"]["run_id"].append(row.sequence_file.id)
else :
data["samples"]["info"].append("this file has been deleted from the database, info relative to this sample are no longer available")
data["samples"]["timestamp"].append("None")
data["samples"]["sequence_file_id"].append("")
data["samples"]["results_file_id"].append("")
data["samples"]["names"].append("deleted")
data["samples"]["id"].append("")
log.debug("get_data (%s) c%s -> %s (%s)" % (request.vars["sample_set_id"], request.vars["config"], fused_file, "downloaded" if download else "streamed"))
log.info("load sample", extra={'user_id': auth.user.id, 'record_id': request.vars['sample_set_id'], 'table_name': 'sample_set'})
dumped_json = gluon.contrib.simplejson.dumps(data, separators=(',',':'))
if download:
return response.stream(StringIO.StringIO(dumped_json), attachment = True, filename = request.vars['filename'])
return dumped_json
else :
res = {"success" : "false",
"message" : "get_data (%s) c%s : %s " % (request.vars["sample_set_id"], request.vars["config"], error)}
log.error(res)
return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
def get_data():
from subprocess import Popen, PIPE, STDOUT
if not auth.user :
res = {"redirect" : URL('default', 'user', args='login', scheme=True, host=True,
vars=dict(_next=URL('default', 'get_data', scheme=True, host=True,
vars=dict(sample_set_id = request.vars["sample_set_id"],
config =request.vars["config"]))
)
)}
return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
error = ""
if "patient" in request.vars :
request.vars["sample_set_id"] = db.patient[request.vars["patient"]].sample_set_id
download = False
if "filename" in request.vars:
download = True
if "run" in request.vars :
request.vars["sample_set_id"] = db.run[request.vars["run"]].sample_set_id
if not "sample_set_id" in request.vars or request.vars['sample_set_id'] is None:
error += "id sampleset file needed, "
else :
if not auth.can_view_sample_set(request.vars["sample_set_id"]):
error += "you do not have permission to consult this sample_set ("+str(request.vars["sample_set_id"])+")"
if not "config" in request.vars:
error += "id config needed, "
sample_set = db.sample_set[request.vars["sample_set_id"]]
query = db( ( db.fused_file.sample_set_id == request.vars["sample_set_id"])
& ( db.fused_file.config_id == request.vars["config"] )
).select(db.fused_file.ALL).first()
if query is not None:
fused_file = defs.DIR_RESULTS+'/'+query.fused_file
sequence_file_list = query.sequence_file_list
if not 'fused_file' in locals():
error += "file not found"
if error == "" :
f = open(fused_file, "r")
data = gluon.contrib.simplejson.loads(f.read())
f.close()
patient_name = ""
run_name = ""
config_name = db.config[request.vars["config"]].name
command = db.config[request.vars["config"]].command
log_reference_id = request.vars["sample_set_id"]
if (sample_set.sample_type == defs.SET_TYPE_GENERIC) :
for row in db( db.generic.sample_set_id == request.vars["sample_set_id"] ).select() :
log_reference_id = row.id
generic_name = db.generic[row.id].name
data["dataFileName"] = generic_name + " (" + config_name + ")"
data["info"] = db.generic[row.id].info
data["generic_id"] = row.id
data["sample_name"] = generic_name
data["group_id"] = get_set_group(row.sample_set_id)
if (sample_set.sample_type == defs.SET_TYPE_PATIENT):
for row in db( db.patient.sample_set_id == request.vars["sample_set_id"] ).select() :
log_reference_id = row.id
patient_name = vidjil_utils.anon_ids([row.id])[0]
data["dataFileName"] = patient_name + " (" + config_name + ")"
data["info"] = db.patient[row.id].info
data["patient_id"] = row.id
data["sample_name"] = patient_name
data["group_id"] = get_set_group(row.sample_set_id)
if (sample_set.sample_type == defs.SET_TYPE_RUN) :
for row in db( db.run.sample_set_id == request.vars["sample_set_id"] ).select() :
log_reference_id = row.id
run_name = db.run[row.id].name
data["dataFileName"] = run_name + " (" + config_name + ")"
data["info"] = db.run[row.id].info
data["run_id"] = row.id
data["sample_name"] = run_name
data["group_id"] = get_set_group(row.sample_set_id)
log_query = db( ( db.user_log.record_id == log_reference_id )
& ( db.user_log.table_name == sample_set.sample_type )
).select(db.user_log.ALL, orderby=db.user_log.created)
data["logs"] = []
for row in log_query:
data["logs"].append({'message': row.msg, 'created': str(row.created)})
## récupération des infos stockées sur la base de données
query = db( ( db.sample_set.id == request.vars["sample_set_id"] )
& ( db.sample_set.id == db.sample_set_membership.sample_set_id )
& ( db.sequence_file.id == db.sample_set_membership.sequence_file_id)
& ( db.results_file.sequence_file_id == db.sequence_file.id )
& ( db.results_file.config_id == request.vars["config"] )
).select(db.sequence_file.ALL,db.results_file.ALL, db.sample_set.id, orderby=db.sequence_file.id|~db.results_file.run_date)
query2 = {}
sequence_file_id = 0
for row in query :
if row.sequence_file.id != sequence_file_id :
query2[row.sequence_file.data_file]=row
sequence_file_id = row.sequence_file.id
data["sample_set_id"] = sample_set.id
data["config_name"] = config_name
data["samples"]["info"] = []
data["samples"]["timestamp"] = []
data["samples"]["sequence_file_id"] = []
data["samples"]["results_file_id"] = []
data["samples"]["config_id"] = []
data["samples"]["names"] = []
data["samples"]["db_key"] = []
data["samples"]["id"] = []
data["samples"]["patient_id"] = []
data["samples"]["sample_name"] = []
data["samples"]["run_id"] = []
for i in range(len(data["samples"]["original_names"])) :
o_n = data["samples"]["original_names"][i].split('/')[-1]
data["samples"]["original_names"][i] = data["samples"]["original_names"][i].split('/')[-1]
data["samples"]["config_id"].append(request.vars['config'])
data["samples"]["db_key"].append('')
data["samples"]["commandline"].append(command)
if o_n in query2:
row = query2[o_n]
data["samples"]["info"].append(row.sequence_file.info)
data["samples"]["timestamp"].append(str(row.sequence_file.sampling_date))
data["samples"]["sequence_file_id"].append(row.sequence_file.id)
data["samples"]["results_file_id"].append(row.results_file.id)
data["samples"]["names"].append(row.sequence_file.filename.split('.')[0])
data["samples"]["id"].append(row.sequence_file.id)
data["samples"]["patient_id"].append(get_patient_id(row.sequence_file.id))
data["samples"]["sample_name"].append(row.sequence_file.id)
data["samples"]["run_id"].append(row.sequence_file.id)
else :
data["samples"]["info"].append("this file has been deleted from the database, info relative to this sample are no longer available")
data["samples"]["timestamp"].append("None")
data["samples"]["sequence_file_id"].append("")
data["samples"]["results_file_id"].append("")
data["samples"]["names"].append("deleted")
data["samples"]["id"].append("")
log.debug("get_data (%s) c%s -> %s (%s)" % (request.vars["sample_set_id"], request.vars["config"], fused_file, "downloaded" if download else "streamed"))
log.info("load sample", extra={'user_id': auth.user.id, 'record_id': request.vars['sample_set_id'], 'table_name': 'sample_set'})
dumped_json = gluon.contrib.simplejson.dumps(data, separators=(',',':'))
if download:
return response.stream(StringIO.StringIO(dumped_json), attachment = True, filename = request.vars['filename'])
return dumped_json
else :
res = {"success" : "false",
"message" : "get_data (%s) c%s : %s " % (request.vars["sample_set_id"], request.vars["config"], error)}
log.error(res)
return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
def get_custom_data():
from subprocess import Popen, PIPE, STDOUT
if not auth.user:
res = {
"redirect":
URL('default', 'user', args='login', scheme=True, host=True)
} #TODO _next
return gluon.contrib.simplejson.dumps(res, separators=(',', ':'))
error = ""
if not "custom" in request.vars:
error += "no file selected, "
else:
if type(request.vars['custom']) is not list or len(
request.vars['custom']) < 2:
error += "you must select several files."
else:
for id in request.vars["custom"]:
log.debug("id = '%s'" % str(id))
sequence_file_id = db.results_file[id].sequence_file_id
patient_id = db(
(db.sample_set_membership.sequence_file_id ==
sequence_file_id)
& (db.patient.sample_set_id ==
db.sample_set_membership.sample_set_id)).select(
db.patient.id).first()
if not auth.can_view_patient(patient_id):
error += "you do not have permission to consult this patient (" + str(
patient_id) + ")"
if error == "":
try:
data = custom_fuse(request.vars["custom"])
except IOError, error:
return error_message(str(error))
generic_info = "Compare sample sets"
data["sample_name"] = generic_info
data["dataFileName"] = generic_info
data["info"] = generic_info
data["samples"]["original_names"] = []
data["samples"]["timestamp"] = []
data["samples"]["info"] = []
data["samples"]["commandline"] = []
for id in request.vars["custom"]:
sequence_file_id = db.results_file[id].sequence_file_id
sample_set = db(
(db.sequence_file.id == sequence_file_id)
& (db.sample_set_membership.sequence_file_id ==
db.sequence_file.id)
& (db.sample_set.id == db.sample_set_membership.sample_set_id)
& (db.sample_set.sample_type.belongs(['patient', 'run']))
).select(db.sample_set.id, db.sample_set.sample_type).first()
patient_run = db(db[sample_set.sample_type].sample_set_id ==
sample_set.id).select().first()
config_id = db.results_file[id].config_id
name = vidjil_utils.anon_ids(
patient_run.id
) if sample_set.sample_type == 'patient' else patient_run.name
filename = db.sequence_file[sequence_file_id].filename
data["samples"]["original_names"].append(name + "_" + filename)
data["samples"]["timestamp"].append(
str(db.sequence_file[sequence_file_id].sampling_date))
data["samples"]["info"].append(
db.sequence_file[sequence_file_id].info)
data["samples"]["commandline"].append(db.config[config_id].command)
return gluon.contrib.simplejson.dumps(data, separators=(',', ':'))
