def info(sample_set_id):
sample_type = db.sample_set[request.vars["id"]].sample_type
if sample_type == "patient" :
patient = db((db.patient.sample_set_id == request.vars["id"])).select()[0]
name = vidjil_utils.anon_names(patient.id, patient.first_name, patient.last_name)
return dict(name = name,
filename = name,
label = patient.id_label + " (" + str(patient.birth) + ")",
info = patient.info
)
if sample_type == "run" :
run = db((db.run.sample_set_id == request.vars["id"])).select()[0]
return dict(name = "run : " + run.name + " (" + str(run.run_date) + ")",
filename = "run : " + run.name + "_" + str(run.run_date),
label = run.id_label + " (" + str(run.run_date) + ")",
info = run.info
)
return dict(name = "sample_set : " +db.sample_set[request.vars["id"]].sample_type,
filename = "sample_set_" + request.vars["id"],
label = "",
info = ""
)
def info():
next_patient()
patient = db.patient[request.vars["id"]]
sample_set_id = patient.sample_set_id
if request.vars["config_id"] and request.vars["config_id"] != "-1" and request.vars["config_id"] != "None":
config_id = long(request.vars["config_id"])
patient_name = vidjil_utils.anon_names(patient.id, patient.first_name, patient.last_name)
config_name = db.config[request.vars["config_id"]].name
fused = db((db.fused_file.sample_set_id == sample_set_id) & (db.fused_file.config_id == config_id))
analysis = db(db.analysis_file.sample_set_id == sample_set_id).select(orderby=~db.analysis_file.analyze_date)
config = True
fused_count = fused.count()
fused_file = fused.select()
fused_filename = patient_name + "_" + config_name + ".data"
analysis_count = len(analysis)
analysis_file = analysis
analysis_filename = patient_name + ".analysis"
else:
config_id = -1
config = False
fused_count = 0
fused_file = ""
fused_filename = ""
analysis_count = 0
analysis_file = ""
analysis_filename = ""
if config:
query = []
query2 = db(
(db.sequence_file.id == db.sample_set_membership.sequence_file_id)
& (db.sample_set_membership.sample_set_id == db.patient.sample_set_id)
& (db.patient.id == request.vars["id"])
).select(
left=db.results_file.on(
(db.results_file.sequence_file_id == db.sequence_file.id)
& (db.results_file.config_id == str(config_id))
),
orderby=db.sequence_file.id | ~db.results_file.run_date,
)
previous = -1
for row in query2:
if row.sequence_file.id != previous:
query.append(row)
previous = row.sequence_file.id
else:
query = db(
(db.sequence_file.id == db.sample_set_membership.sequence_file_id)
& (db.sample_set_membership.sample_set_id == db.patient.sample_set_id)
& (db.patient.id == request.vars["id"])
).select(
left=db.results_file.on(
(db.results_file.sequence_file_id == db.sequence_file.id)
& (db.results_file.config_id == str(config_id))
)
)
log.debug("patient (%s)" % request.vars["id"])
if auth.can_view_patient(request.vars["id"]):
return dict(
query=query,
patient=patient,
birth=vidjil_utils.anon_birth(request.vars["id"], auth.user.id),
config_id=config_id,
fused_count=fused_count,
fused_file=fused_file,
fused_filename=fused_filename,
analysis_count=analysis_count,
analysis_file=analysis_file,
analysis_filename=analysis_filename,
config=config,
)
else:
res = {"message": ACCESS_DENIED}
log.error(res)
return gluon.contrib.simplejson.dumps(res, separators=(",", ":"))
def get_name(self, data, anon=None):
return vidjil_utils.anon_names(data['sample_set_id'], data['first_name'], data['last_name'], anon)
def custom():
start = time.time()
if request.vars["config_id"] and request.vars["config_id"] != "-1" :
config_id = long(request.vars["config_id"])
config_name = db.config[request.vars["config_id"]].name
config = True
else:
request.vars["config_id"] = -1
config_id = -1
config_name = None
config = False
if "custom_list" not in request.vars :
request.vars["custom_list"] = []
if type(request.vars["custom_list"]) is str :
request.vars["custom_list"] = [request.vars["custom_list"]]
myGroupBy = None
helper = None
if request.vars["id"] and auth.can_view_sample_set(request.vars["id"]):
sample_set = db.sample_set[request.vars["id"]]
factory = ModelFactory()
helper = factory.get_instance(type=sample_set.sample_type)
q = ((auth.vidjil_accessible_query(PermissionEnum.read_config.value, db.config))
& (db.sample_set.id == request.vars["id"])
& (db.sample_set_membership.sample_set_id == db.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.data_file != '')
& (db.config.id==db.results_file.config_id)
)
else:
q = ((auth.vidjil_accessible_query(PermissionEnum.read.value, db.patient)
| auth.vidjil_accessible_query(PermissionEnum.read.value, db.run)
| auth.vidjil_accessible_query(PermissionEnum.read.value, db.generic))
& (auth.vidjil_accessible_query(PermissionEnum.read_config.value, db.config))
& (db.sample_set_membership.sample_set_id == db.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.data_file != '')
& (db.config.id==db.results_file.config_id)
)
myGroupBy = db.sequence_file.id|db.patient.id|db.run.id|db.generic.id|db.results_file.config_id
query = db(q).select(
db.patient.id, db.patient.info, db.patient.first_name, db.patient.last_name,
db.run.id, db.run.info, db.run.name,
db.generic.id, db.generic.info, db.generic.name,
db.results_file.id, db.results_file.config_id, db.sequence_file.sampling_date,
db.sequence_file.pcr, db.config.name, db.results_file.run_date, db.results_file.data_file, db.sequence_file.filename,
db.sequence_file.data_file, db.sequence_file.id, db.sequence_file.info,
db.sequence_file.size_file,
left = [
db.patient.on(db.patient.sample_set_id == db.sample_set.id),
db.run.on(db.run.sample_set_id == db.sample_set.id),
db.generic.on(db.generic.sample_set_id == db.sample_set.id)
],
orderby = db.sequence_file.id|db.results_file.run_date,
groupby = myGroupBy
)
##filter
if "filter" not in request.vars :
request.vars["filter"] = ""
for row in query :
row.checked = False
if (str(row.results_file.id) in request.vars["custom_list"]) :
row.checked = True
if row.patient.id is not None:
row.names = vidjil_utils.anon_names(row.patient.id, row.patient.first_name, row.patient.last_name)
info = row.patient.info
elif row.run.id is not None:
row.names = row.run.name
info = row.run.info
elif row.generic.id is not None:
row.names = row.generic.name
info = row.generic.info
row.string = [row.names, row.sequence_file.filename, str(row.sequence_file.sampling_date), str(row.sequence_file.pcr), str(row.config.name), str(row.results_file.run_date), info]
query = query.find(lambda row : ( vidjil_utils.advanced_filter(row.string,request.vars["filter"]) or row.checked) )
if config :
query = query.find(lambda row : ( row.results_file.config_id==config_id or (str(row.results_file.id) in request.vars["custom_list"])) )
log.debug("sample_set/custom (%.3fs) %s" % (time.time()-start, request.vars["filter"]))
return dict(query=query,
config_id=config_id,
config=config,
helper=helper)
def get_name(self, data, anon=None):
return vidjil_utils.anon_names(data.id, data.first_name, data.last_name, anon)
def info():
next_patient()
patient = db.patient[request.vars["id"]]
sample_set_id = patient.sample_set_id
if request.vars["config_id"] and request.vars[
"config_id"] != "-1" and request.vars["config_id"] != "None":
config_id = long(request.vars["config_id"])
patient_name = vidjil_utils.anon_names(patient.id, patient.first_name,
patient.last_name)
config_name = db.config[request.vars["config_id"]].name
fused = db((db.fused_file.sample_set_id == sample_set_id)
& (db.fused_file.config_id == config_id))
analysis = db(db.analysis_file.sample_set_id == sample_set_id).select(
orderby=~db.analysis_file.analyze_date)
config = True
fused_count = fused.count()
fused_file = fused.select()
fused_filename = patient_name + "_" + config_name + ".data"
analysis_count = len(analysis)
analysis_file = analysis
analysis_filename = patient_name + ".analysis"
else:
config_id = -1
config = False
fused_count = 0
fused_file = ""
fused_filename = ""
analysis_count = 0
analysis_file = ""
analysis_filename = ""
if config:
query = []
query2 = db(
(db.sequence_file.id == db.sample_set_membership.sequence_file_id)
& (db.sample_set_membership.sample_set_id ==
db.patient.sample_set_id)
& (db.patient.id == request.vars["id"])).select(
left=db.results_file.on(
(db.results_file.sequence_file_id == db.sequence_file.id)
& (db.results_file.config_id == str(config_id))),
orderby=db.sequence_file.id | ~db.results_file.run_date)
previous = -1
for row in query2:
if row.sequence_file.id != previous:
query.append(row)
previous = row.sequence_file.id
else:
query = db(
(db.sequence_file.id == db.sample_set_membership.sequence_file_id)
& (db.sample_set_membership.sample_set_id ==
db.patient.sample_set_id)
& (db.patient.id == request.vars["id"])).select(
left=db.results_file.on(
(db.results_file.sequence_file_id == db.sequence_file.id)
& (db.results_file.config_id == str(config_id))))
log.debug('patient (%s)' % request.vars["id"])
if (auth.can_view('patient', request.vars["id"])):
return dict(query=query,
patient=patient,
birth=vidjil_utils.anon_birth(request.vars["id"],
auth.user.id),
config_id=config_id,
fused_count=fused_count,
fused_file=fused_file,
fused_filename=fused_filename,
analysis_count=analysis_count,
analysis_file=analysis_file,
analysis_filename=analysis_filename,
config=config)
else:
res = {"message": ACCESS_DENIED}
log.error(res)
return gluon.contrib.simplejson.dumps(res, separators=(',', ':'))
def get_name(self, data, anon=None):
return vidjil_utils.anon_names(data['sample_set_id'],
data['first_name'], data['last_name'],
anon)
def custom():
start = time.time()
if request.vars["config_id"] and request.vars["config_id"] != "-1" :
config_id = long(request.vars["config_id"])
config_name = db.config[request.vars["config_id"]].name
config = True
else:
request.vars["config_id"] = -1
config_id = -1
config_name = None
config = False
if "custom_list" not in request.vars :
request.vars["custom_list"] = []
if type(request.vars["custom_list"]) is str :
request.vars["custom_list"] = [request.vars["custom_list"]]
myGroupBy = None
if request.vars["id"] and auth.can_view_sample_set(request.vars["id"]):
q = ((auth.vidjil_accessible_query(PermissionEnum.read_config.value, db.config))
& (db.sample_set.id == request.vars["id"])
& (db.sample_set_membership.sample_set_id == db.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.data_file != '')
& (db.config.id==db.results_file.config_id)
)
else:
q = ((auth.vidjil_accessible_query(PermissionEnum.read.value, db.patient)
| auth.vidjil_accessible_query(PermissionEnum.read.value, db.run))
& (auth.vidjil_accessible_query(PermissionEnum.read_config.value, db.config))
& (db.sample_set_membership.sample_set_id == db.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.data_file != '')
& (db.config.id==db.results_file.config_id)
)
myGroupBy = db.sequence_file.id|db.patient.id|db.run.id|db.results_file.config_id
query = db(q).select(
db.patient.id, db.patient.info, db.patient.first_name, db.patient.last_name,
db.run.id, db.run.info, db.run.name,
db.results_file.id, db.results_file.config_id, db.sequence_file.sampling_date,
db.sequence_file.pcr, db.config.name, db.results_file.run_date, db.results_file.data_file, db.sequence_file.filename,
db.sequence_file.data_file, db.sequence_file.id, db.sequence_file.info,
db.sequence_file.size_file,
left = [
db.patient.on(db.patient.sample_set_id == db.sample_set.id),
db.run.on(db.run.sample_set_id == db.sample_set.id)
],
orderby = ~db.patient.id|db.sequence_file.id|db.results_file.run_date,
groupby = myGroupBy
)
##filter
if "filter" not in request.vars :
request.vars["filter"] = ""
for row in query :
row.checked = False
if (str(row.results_file.id) in request.vars["custom_list"]) :
row.checked = True
if row.patient.id is not None:
row.names = vidjil_utils.anon_names(row.patient.id, row.patient.first_name, row.patient.last_name)
info = row.patient.info
else:
row.names = row.run.name
info = row.run.info
row.string = [row.names, row.sequence_file.filename, str(row.sequence_file.sampling_date), str(row.sequence_file.pcr), str(row.config.name), str(row.results_file.run_date), info]
query = query.find(lambda row : ( vidjil_utils.advanced_filter(row.string,request.vars["filter"]) or row.checked) )
if config :
query = query.find(lambda row : ( row.results_file.config_id==config_id or (str(row.results_file.id) in request.vars["custom_list"])) )
log.debug("sample_set/custom (%.3fs) %s" % (time.time()-start, request.vars["filter"]))
return dict(query=query,
config_id=config_id,
config=config)
