def last_result_by_first_point_by_patient():
res_by_pat = {}
for res in db(
(db.patient.sample_set_id == db.sample_set_membership.sample_set_id) &
(db.sample_set_membership.sequence_file_id == db.sequence_file.id)
& (db.results_file.sequence_file_id == db.sequence_file.id)
).select( #groupby=db.patient.id,
orderby=db.patient.id | db.sequence_file.sampling_date
| ~db.results_file.run_date):
if args.filter:
if not vidjil_utils.advanced_filter([
res.patient.first_name, res.patient.last_name,
res.patient.info
], args.filter):
continue
if args.creator:
if res.patient.creator != args.creator:
continue
# Remeber only the first element
if not str(res.patient.id) in res_by_pat:
res_by_pat[str(res.patient.id)] = (res, res.sequence_file)
for pat in res_by_pat:
yield res_by_pat[pat]
def index():
if auth.is_admin():
query = db((db.results_file.sequence_file_id == db.sequence_file.id)
& (db.sequence_file.id ==
db.sample_set_membership.sequence_file_id)
& (db.sample_set_membership.sample_set_id ==
db.patient.sample_set_id)
& (db.results_file.config_id == db.config.id)).select(
orderby=~db.results_file.run_date)
for row in query:
if row.results_file.scheduler_task_id is None:
row.status = ''
else:
row.status = db.scheduler_task[
row.results_file.scheduler_task_id].status
pass
##sort result
reverse = False
if request.vars["reverse"] == "true":
reverse = True
if request.vars["sort"] == "name":
query = query.sort(lambda row: row.patient.last_name,
reverse=reverse)
elif request.vars["sort"] == "run_date":
query = query.sort(lambda row: row.results_file.run_date,
reverse=reverse)
elif request.vars["sort"] == "config":
query = query.sort(lambda row: row.config.name, reverse=reverse)
elif request.vars["sort"] == "patient":
query = query.sort(lambda row: row.patient.last_name,
reverse=reverse)
elif request.vars["sort"] == "status":
query = query.sort(lambda row: row.status, reverse=reverse)
elif "sort" in request.vars and request.vars["sort"] != "":
query = query.sort(
lambda row: row.sequence_file[request.vars["sort"]],
reverse=reverse)
##filter
##filter
if "filter" not in request.vars:
request.vars["filter"] = ""
for row in query:
row.string = [
row.sequence_file.filename, row.config.name,
row.patient.last_name, row.patient.first_name,
row.sequence_file.producer,
str(row.results_file.run_date), row.status
]
query = query.find(lambda row: vidjil_utils.advanced_filter(
row.string, request.vars["filter"]))
return dict(query=query, reverse=reverse)
def filter(self, filter_str, data):
for row in data:
row['string'] = [
row['last_name'], row['first_name'], row['confs'],
row['groups'],
str(row['birth']),
str(row['info'])
]
return filter(
lambda row: vidjil_utils.advanced_filter(row['string'], filter_str
), data)
def index():
if auth.is_admin():
query = db(
(db.results_file.sequence_file_id==db.sequence_file.id)
& (db.sequence_file.id==db.sample_set_membership.sequence_file_id)
& (db.sample_set_membership.sample_set_id==db.patient.sample_set_id)
& (db.results_file.config_id==db.config.id)
).select(
orderby = ~db.results_file.run_date
)
for row in query :
if row.results_file.scheduler_task_id is None :
row.status = ''
else:
row.status = db.scheduler_task[row.results_file.scheduler_task_id ].status
pass
##sort result
reverse = False
if request.vars["reverse"] == "true" :
reverse = True
if request.vars["sort"] == "name" :
query = query.sort(lambda row : row.patient.last_name, reverse=reverse)
elif request.vars["sort"] == "run_date" :
query = query.sort(lambda row : row.results_file.run_date, reverse=reverse)
elif request.vars["sort"] == "config" :
query = query.sort(lambda row : row.config.name, reverse=reverse)
elif request.vars["sort"] == "patient" :
query = query.sort(lambda row : row.patient.last_name, reverse=reverse)
elif request.vars["sort"] == "status" :
query = query.sort(lambda row : row.status, reverse=reverse)
elif "sort" in request.vars and request.vars["sort"] != "":
query = query.sort(lambda row : row.sequence_file[request.vars["sort"]], reverse=reverse)
##filter
##filter
if "filter" not in request.vars :
request.vars["filter"] = ""
for row in query :
row.string = [row.sequence_file.filename, row.config.name, row.patient.last_name, row.patient.first_name, row.sequence_file.producer, str(row.results_file.run_date), row.status]
query = query.find(lambda row : vidjil_utils.advanced_filter(row.string,request.vars["filter"]) )
return dict(query = query,
reverse=reverse)
def last_fused_by_patient():
fused_by_patient = {}
for res in db((db.patient.id == db.fused_file.patient_id)).select(orderby=db.patient.id|~db.fused_file.fuse_date):
if args.config:
if args.config != res.fused_file.config_id:
continue
if args.filter:
if not vidjil_utils.advanced_filter([res.patient.first_name,res.patient.last_name,res.patient.info], args.filter):
continue
if args.creator:
if res.patient.creator != args.creator:
continue
# Remeber only the first element
if not str(res.patient.id) in fused_by_patient:
fused_by_patient[str(res.patient.id)] = True
yield (res, res.fused_file)
def last_result_by_file():
for seq in db(db.sequence_file).select():
print "===", "seq-%d" % seq.id, "\t", seq.sampling_date, "\t", seq.filename, seq.data_file
res_with_file = []
for res in db((db.results_file.sequence_file_id == seq.id)).select(orderby=db.results_file.run_date):
print " ", "sched-%d" % res.results_file.scheduler_task_id, "\t", res.results_file.run_date, "\t", res.results_file.data_file
if args.filter:
if not vidjil_utils.advanced_filter([res.patient.first_name,res.patient.last_name,res.patient.info], args.filter):
continue
if res.results_file.data_file:
res_with_file += [res]
if not res_with_file:
continue
# Takes the last result
yield (res_with_file[-1], seq)
def last_result_by_first_point_by_patient():
res_by_pat = {}
for res in db((db.patient.sample_set_id == db.sample_set_membership.sample_set_id) & (db.sample_set_membership.sequence_file_id == db.sequence_file.id)
& (db.results_file.sequence_file_id == db.sequence_file.id)).select(#groupby=db.patient.id,
orderby=db.patient.id|db.sequence_file.sampling_date|~db.results_file.run_date):
if args.filter:
if not vidjil_utils.advanced_filter([res.patient.first_name,res.patient.last_name,res.patient.info], args.filter):
continue
if args.creator:
if res.patient.creator != args.creator:
continue
# Remeber only the first element
if not str(res.patient.id) in res_by_pat:
res_by_pat[str(res.patient.id)] = (res, res.sequence_file)
for pat in res_by_pat:
yield res_by_pat[pat]
def last_fused_by_patient():
fused_by_patient = {}
for res in db((db.patient.id == db.fused_file.patient_id)).select(
orderby=db.patient.id | ~db.fused_file.fuse_date):
if args.config:
if args.config != res.fused_file.config_id:
continue
if args.filter:
if not vidjil_utils.advanced_filter([
res.patient.first_name, res.patient.last_name,
res.patient.info
], args.filter):
continue
if args.creator:
if res.patient.creator != args.creator:
continue
# Remeber only the first element
if not str(res.patient.id) in fused_by_patient:
fused_by_patient[str(res.patient.id)] = True
yield (res, res.fused_file)
def last_result_by_file():
for seq in db(db.sequence_file).select():
print "===", "seq-%d" % seq.id, "\t", seq.sampling_date, "\t", seq.filename, seq.data_file
res_with_file = []
for res in db((db.results_file.sequence_file_id == seq.id)).select(
orderby=db.results_file.run_date):
print " ", "sched-%d" % res.results_file.scheduler_task_id, "\t", res.results_file.run_date, "\t", res.results_file.data_file
if args.filter:
if not vidjil_utils.advanced_filter([
res.patient.first_name, res.patient.last_name,
res.patient.info
], args.filter):
continue
if res.results_file.data_file:
res_with_file += [res]
if not res_with_file:
continue
# Takes the last result
yield (res_with_file[-1], seq)
def index():
start = time.time()
if not auth.user:
res = {
"redirect":
URL('default',
'user',
args='login',
scheme=True,
host=True,
vars=dict(
_next=URL('patient', 'index', scheme=True, host=True)))
}
return gluon.contrib.simplejson.dumps(res, separators=(',', ':'))
isAdmin = auth.is_admin()
##retrieve patient list
query = db(
auth.vidjil_accessible_query(PermissionEnum.read.value,
db.patient)).select(
db.patient.ALL,
orderby=~db.patient.id)
auth.load_permissions(PermissionEnum.admin.value, 'patient')
auth.load_permissions(PermissionEnum.anon.value, 'patient')
result = {}
for i, row in enumerate(query):
result[row.id] = {
"id": int(row.id),
"sample_set_id": int(row.sample_set_id),
"last_name": row.last_name,
"first_name": row.first_name,
"has_permission": auth.can_modify_patient(row.id),
"anon_allowed": auth.can_view_patient_info(row.id),
"birth": row.birth,
"info": row.info,
"creator": row.creator,
"confs": "",
"conf_list": [],
"conf_id_list": [-1],
"most_used_conf": "",
"groups": "",
"group_list": [],
"file_count": 0,
"size": 0
}
patient_ids = result.keys()
query1 = db((db.patient.creator == db.auth_user.id)
& (db.patient.id.belongs(patient_ids))).select(
db.patient.id, db.auth_user.last_name)
for i, row in enumerate(query1):
result[row.patient.id]['creator'] = row.auth_user.last_name
query2 = db(
(db.patient.sample_set_id == db.sample_set.id)
& (db.sample_set_membership.sample_set_id == db.sample_set.id)
& (db.sequence_file.id == db.sample_set_membership.sequence_file_id)
& (db.patient.id.belongs(patient_ids))).select(
db.patient.id, db.sequence_file.size_file)
for i, row in enumerate(query2):
result[row.patient.id]['file_count'] += 1
result[row.patient.id]['size'] += row.sequence_file.size_file
query3 = db((db.patient.sample_set_id == db.fused_file.sample_set_id)
& (db.fused_file.config_id == db.config.id)
& (auth.vidjil_accessible_query(
PermissionEnum.read_config.value, db.config)
| auth.vidjil_accessible_query(
PermissionEnum.admin_config.value, db.config))
& (db.patient.id.belongs(patient_ids))).select(
db.patient.id, db.config.name, db.config.id,
db.fused_file.fused_file)
for i, row in enumerate(query3):
result[row.patient.id]['conf_list'].append({
'id':
row.config.id,
'name':
row.config.name,
'fused_file':
row.fused_file.fused_file
})
#result[row.patient.id]['conf_list'].append(row.config.name)
result[row.patient.id]['conf_id_list'].append(row.config.id)
query4 = db(((db.patient.id == db.auth_permission.record_id)
| (db.auth_permission.record_id == 0))
& (db.auth_permission.table_name == 'patient')
& (db.auth_permission.name == PermissionEnum.access.value)
& (db.auth_group.id == db.auth_permission.group_id)
& (db.patient.id.belongs(patient_ids))).select(
db.patient.id, db.auth_group.role)
for i, row in enumerate(query4):
result[row.patient.id]['group_list'].append(
row.auth_group.role.replace('user_', 'u'))
for key, row in result.iteritems():
row['most_used_conf'] = max(set(row['conf_id_list']),
key=row['conf_id_list'].count)
#row['confs'] = ", ".join(list(set(row['conf_list'])))
row['groups'] = ", ".join(
filter(lambda g: g != 'admin', set(row['group_list'])))
result = result.values()
##sort result
reverse = False
if request.vars["reverse"] == "true":
reverse = True
if request.vars["sort"] == "configs":
result = sorted(result, key=lambda row: row['confs'], reverse=reverse)
elif request.vars["sort"] == "groups":
result = sorted(result, key=lambda row: row['groups'], reverse=reverse)
elif request.vars["sort"] == "files":
result = sorted(result,
key=lambda row: row['file_count'],
reverse=reverse)
elif "sort" in request.vars:
result = sorted(result,
key=lambda row: vidjil_utils.prevent_none(
row[request.vars["sort"]], datetime.date.min),
reverse=reverse)
else:
result = sorted(result, key=lambda row: row['id'], reverse=not reverse)
##filter
if "filter" not in request.vars:
request.vars["filter"] = ""
for row in result:
row['string'] = [
row['last_name'], row['first_name'], row['confs'], row['groups'],
str(row['birth']),
str(row['info'])
]
result = filter(
lambda row: vidjil_utils.advanced_filter(row['string'], request.vars[
"filter"]), result)
log.debug("patient list (%.3fs) %s" %
(time.time() - start, request.vars["filter"]))
return dict(query=result, isAdmin=isAdmin, reverse=reverse)
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)
qq = (db.sample_set.id == request.vars["id"])
else:
qq = (auth.vidjil_accessible_query(PermissionEnum.read.value, db.sample_set))
myGroupBy = db.sequence_file.id|db.patient.id|db.run.id|db.generic.id|db.results_file.config_id
q = (qq
& (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))
group_ids = get_involved_groups()
##filter
if "filter" not in request.vars :
request.vars["filter"] = ""
search, tags = parse_search(request.vars["filter"])
left_join = [
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)
]
select = [
db.patient.id, db.patient.sample_set_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
]
if (tags is not None and len(tags) > 0):
q = filter_by_tags(q, 'sequence_file', tags)
count = db.tag.name.count()
select = select + [db.tag_ref.record_id,
db.tag_ref.table_name,
count]
query = db(q).select(
*select,
left = left_join,
orderby = db.sequence_file.id|db.results_file.run_date,
groupby = db.tag_ref.table_name|db.tag_ref.record_id,
having = count >= len(tags)
)
else:
query = db(q).select(
*select,
left = left_join,
orderby = db.sequence_file.id|db.results_file.run_date,
groupby = myGroupBy
)
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:
#TODO use helper.
row.names = vidjil_utils.display_names(row.patient.sample_set_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,search) 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"])) )
tag_decorator = TagDecorator(get_tag_prefix())
log.info("load compare list", extra={'user_id': auth.user.id, 'record_id': None, 'table_name': "results_file"})
log.debug("sample_set/custom (%.3fs) %s" % (time.time()-start, search))
return dict(query=query,
config_id=config_id,
config=config,
helper=helper,
tag_decorator=tag_decorator,
group_ids=group_ids)
def filter(self, filter_str, data):
keys = ['last_name', 'first_name', 'confs', 'groups', 'birth', 'info']
self.create_filter_string(data, keys)
return filter(
lambda row: vidjil_utils.advanced_filter(row['string'], filter_str
), data)
def showlog():
if auth.is_admin():
lines = []
file = open(defs.DIR_LOG + request.vars["file"])
log_format = request.vars['format'] if 'format' in request.vars else ''
if log_format == 'raw':
return {'raw': ''.join(file.readlines()), 'format': log_format}
if "filter" not in request.vars:
request.vars["filter"] = ""
for row in reversed(file.readlines()):
parsed = False
if not vidjil_utils.advanced_filter([row], request.vars["filter"]):
continue
if log_format: # == 'vidjil'
# Parses lines such as
# [11889] 2015-02-01 12:01:28,367 INFO - default.py:312 1.23.45.67/user/Toto <Toto> xxxxx log message
# [11889] 2015-02-01 12:01:28,367 INFO - default.py:312 1.23.45.67 log message
# [11889] 2015-02-01 12:01:28,367 INFO - default.py:312 log message
line = {}
tmp = re.split('\t+| +', row)
if len(tmp) >= 7:
parsed = True
line["date"] = tmp[1]
line["date2"] = tmp[2].split(',')[0]
line["type"] = tmp[3]
line["file"] = vidjil_utils.log_links(tmp[5])
if tmp[6] != "Creating":
if len(tmp) < 9:
j = 0
parsed = False
elif '<' in tmp[8]:
line["user"] = tmp[8] + ' ' + tmp[7]
j = 9
else:
line["user"] = tmp[7]
j = 8
line["mes"] = " ".join(tmp[j:])
else:
line["user"] = ""
line["mes"] = " ".join(tmp[6:])
line["mes"] = line["mes"].replace(" at ", "\nat ")
line["mes"] = vidjil_utils.log_links(line["mes"])
if not parsed:
line = {
'mes': row,
'date': '',
'date2': '',
'user': '',
'type': '',
'file': ''
}
### Stores log line
lines.append(line)
if len(lines) >= MAX_LOG_LINES:
break
return {'lines': lines, 'format': log_format}
if link:
print "ln -s %s %s \t# %s" % (from_name, to_name, comments)
else:
print from_name
if args.sequences:
print "### Sequences"
for res in db(db.patient.sample_set_id == db.sample_set_membership.
sample_set_id) & (db.sample_set_membership.sequence_file_id
== db.sequence_file.id).select():
if args.filter:
if not vidjil_utils.advanced_filter([
res.patient.first_name, res.patient.last_name,
res.patient.info
], args.filter):
continue
if args.creator:
if res.patient.creator != args.creator:
continue
if args.original:
f = res.sequence_file.filename
else:
our_id += 1
f = "%5s.fa" % our_id
link(
"%s/%-20s" % (defs.DIR_SEQUENCES, res.sequence_file.data_file), f,
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 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)
qq = (db.sample_set.id == request.vars["id"])
else:
qq = (auth.vidjil_accessible_query(PermissionEnum.read.value, db.sample_set))
myGroupBy = db.sequence_file.id|db.patient.id|db.run.id|db.generic.id|db.results_file.config_id
q = (qq
& (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.results_file.hidden == False)
& (db.config.id==db.results_file.config_id))
group_ids = get_involved_groups()
##filter
if "filter" not in request.vars :
request.vars["filter"] = ""
search, tags = parse_search(request.vars["filter"])
left_join = [
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)
]
select = [
db.patient.id, db.patient.sample_set_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
]
if (tags is not None and len(tags) > 0):
q = filter_by_tags(q, 'sequence_file', tags)
count = db.tag.name.count()
select = select + [db.tag_ref.record_id,
db.tag_ref.table_name,
count]
query = db(q).select(
*select,
left = left_join,
orderby = db.sequence_file.id|db.results_file.run_date,
groupby = db.tag_ref.table_name|db.tag_ref.record_id,
having = count >= len(tags)
)
else:
query = db(q).select(
*select,
left = left_join,
orderby = db.sequence_file.id|db.results_file.run_date,
groupby = myGroupBy
)
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:
#TODO use helper.
row.names = vidjil_utils.display_names(row.patient.sample_set_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,search) 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"])) )
tag_decorator = TagDecorator(get_tag_prefix())
log.info("load compare list", extra={'user_id': auth.user.id, 'record_id': None, 'table_name': "results_file"})
log.debug("sample_set/custom (%.3fs) %s" % (time.time()-start, search))
classification = getConfigsByClassification()
return dict(query=query,
config_id=config_id,
config=config,
helper=helper,
tag_decorator=tag_decorator,
classification=classification,
group_ids=group_ids)
def index():
start = time.time()
if not auth.user :
res = {"redirect" : URL('default', 'user', args='login', scheme=True, host=True,
vars=dict(_next=URL('patient', 'index', scheme=True, host=True)))
}
return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
isAdmin = auth.is_admin()
##retrieve patient list
query = db(
auth.vidjil_accessible_query(PermissionEnum.read.value, db.patient)
).select(
db.patient.ALL,
orderby = ~db.patient.id
)
auth.load_permissions(PermissionEnum.admin.value, 'patient')
auth.load_permissions(PermissionEnum.anon.value, 'patient')
result = {}
for i, row in enumerate(query) :
result[row.id] = {
"id" :int(row.id),
"sample_set_id" : int(row.sample_set_id),
"last_name" : row.last_name,
"first_name" : row.first_name,
"has_permission" : auth.can_modify_patient(row.id),
"anon_allowed": auth.can_view_patient_info(row.id),
"birth" : row.birth,
"info" : row.info,
"creator" : row.creator,
"confs" : "",
"conf_list" : [],
"conf_id_list" : [-1],
"most_used_conf" : "",
"groups" : "",
"group_list" : [],
"file_count" : 0,
"size" : 0
}
keys = result.keys()
query1 = db(
db.patient.creator == db.auth_user.id
).select(
db.patient.id, db.auth_user.last_name
)
for i, row in enumerate(query1) :
if row.patient.id in keys :
result[row.patient.id]['creator'] = row.auth_user.last_name
query2 = db(
(db.patient.sample_set_id == db.sample_set.id)
&(db.sample_set_membership.sample_set_id == db.sample_set.id)
&(db.sequence_file.id == db.sample_set_membership.sequence_file_id)
).select(
db.patient.id, db.sequence_file.size_file
)
for i, row in enumerate(query2) :
if row.patient.id in keys :
result[row.patient.id]['file_count'] += 1
result[row.patient.id]['size'] += row.sequence_file.size_file
query3 = db(
(db.patient.sample_set_id == db.fused_file.sample_set_id) &
(db.fused_file.config_id == db.config.id) &
(auth.vidjil_accessible_query(PermissionEnum.read_config.value, db.config) | auth.vidjil_accessible_query(PermissionEnum.admin_config.value, db.config) )
).select(
db.patient.id, db.config.name, db.config.id, db.fused_file.fused_file
)
for i, row in enumerate(query3) :
if row.patient.id in keys :
result[row.patient.id]['conf_list'].append({'id': row.config.id, 'name': row.config.name, 'fused_file': row.fused_file.fused_file})
#result[row.patient.id]['conf_list'].append(row.config.name)
result[row.patient.id]['conf_id_list'].append(row.config.id)
query4 = db(
((db.patient.id == db.auth_permission.record_id) | (db.auth_permission.record_id == 0)) &
(db.auth_permission.table_name == 'patient') &
(db.auth_permission.name == PermissionEnum.access.value) &
(db.auth_group.id == db.auth_permission.group_id)
).select(
db.patient.id, db.auth_group.role
)
for i, row in enumerate(query4) :
if row.patient.id in keys :
result[row.patient.id]['group_list'].append(row.auth_group.role.replace('user_','u'))
for key, row in result.iteritems():
row['most_used_conf'] = max(set(row['conf_id_list']), key=row['conf_id_list'].count)
#row['confs'] = ", ".join(list(set(row['conf_list'])))
row['groups'] = ", ".join(filter(lambda g: g != 'admin', set(row['group_list'])))
result = result.values()
##sort result
reverse = False
if request.vars["reverse"] == "true" :
reverse = True
if request.vars["sort"] == "configs" :
result = sorted(result, key = lambda row : row['confs'], reverse=reverse)
elif request.vars["sort"] == "groups" :
result = sorted(result, key = lambda row : row['groups'], reverse=reverse)
elif request.vars["sort"] == "files" :
result = sorted(result, key = lambda row : row['file_count'], reverse=reverse)
elif "sort" in request.vars:
result = sorted(result, key = lambda row : row[request.vars["sort"]], reverse=reverse)
else:
result = sorted(result, key = lambda row : row['id'], reverse=not reverse)
##filter
if "filter" not in request.vars :
request.vars["filter"] = ""
for row in result :
row['string'] = [row['last_name'], row['first_name'], row['confs'], row['groups'], str(row['birth']), str(row['info'])]
result = filter(lambda row : vidjil_utils.advanced_filter(row['string'],request.vars["filter"]), result )
log.debug("patient list (%.3fs) %s" % (time.time()-start, request.vars["filter"]))
return dict(query = result,
isAdmin = isAdmin,
reverse = reverse)
def filter(self, filter_str, data):
keys = ['last_name', 'first_name', 'confs', 'groups', 'birth', 'info']
self.create_filter_string(data, keys)
return filter(lambda row : vidjil_utils.advanced_filter(row['string'], filter_str), data)
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)
def showlog():
if auth.is_admin():
lines = []
file = open(defs.DIR_LOG+request.vars["file"])
log_format = request.vars['format'] if 'format' in request.vars else ''
if log_format == 'raw':
return {'raw': ''.join(file.readlines()), 'format': log_format}
if "filter" not in request.vars :
request.vars["filter"] = ""
for row in reversed(file.readlines()) :
parsed = False
if not vidjil_utils.advanced_filter([row], request.vars["filter"]) :
continue
if log_format: # == 'vidjil'
# Parses lines such as
# [11889] 2015-02-01 12:01:28,367 INFO - default.py:312 1.23.45.67/user/Toto <Toto> xxxxx log message
# [11889] 2015-02-01 12:01:28,367 INFO - default.py:312 1.23.45.67 log message
# [11889] 2015-02-01 12:01:28,367 INFO - default.py:312 log message
line = {}
tmp = re.split('\t+| +', row)
if len(tmp) >= 7:
parsed = True
line["date"] = tmp[1]
line["date2"] = tmp[2].split(',')[0]
line["type"] = tmp[3]
line["file"] = vidjil_utils.log_links(tmp[5])
if tmp[6] != "Creating":
if len(tmp) < 9:
j = 0
parsed = False
elif '<' in tmp[8]:
line["user"] = tmp[8] + ' ' + tmp[7]
j = 9
else:
line["user"] = tmp[7]
j = 8
line["mes"] = " ".join(tmp[j:])
else:
line["user"] = ""
line["mes"] = " ".join(tmp[6:])
line["mes"] = line["mes"].replace(" at ", "\nat ")
line["mes"] = vidjil_utils.log_links(line["mes"])
if not parsed:
line = { 'mes': row, 'date': '', 'date2': '', 'user': '', 'type':'', 'file':''}
### Stores log line
lines.append(line)
if len(lines) >= MAX_LOG_LINES :
break
return {'lines': lines, 'format': log_format}
def patient_string(row):
return "u%s pat-%04d (%s %s) - %s" % (row.creator, row.id, row.first_name, row.last_name, row.info.replace('\n', ' '))
def link(from_name, to_name, comments, link):
if link:
print "ln -s %s %s \t# %s" % (from_name, to_name, comments)
else:
print from_name
if args.sequences:
print "### Sequences"
for res in db(db.patient.sample_set_id == db.sample_set_membership.sample_set_id) & (db.sample_set_membership.sequence_file_id == db.sequence_file.id).select():
if args.filter:
if not vidjil_utils.advanced_filter([res.patient.first_name,res.patient.last_name,res.patient.info], args.filter):
continue
if args.creator:
if res.patient.creator != args.creator:
continue
if args.original:
f = res.sequence_file.filename
else:
our_id += 1
f = "%5s.fa" % our_id
link("%s/%-20s" % (defs.DIR_SEQUENCES, res.sequence_file.data_file),
f,
