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vidjil
vidjil
Commits
9813eefc
Commit
9813eefc
authored
May 14, 2016
by
Mathieu Giraud
Committed by
Vidjil Team
May 14, 2016
Browse files
models/task.py, controllers/{file,patient}.py: streamline log messages
parent
49c47f2e
Changes
3
Hide whitespace changes
Inline
Side-by-side
server/web2py/applications/vidjil/controllers/file.py
View file @
9813eefc
...
...
@@ -140,12 +140,14 @@ def add_form():
#add a default sample_set for this sequence file
id_sample_set
=
db
.
sample_set
.
insert
(
sample_type
=
"sequence_file"
)
ids_sample_set
=
[]
id_sample_set_membership
=
db
.
sample_set_membership
.
insert
(
sample_set_id
=
id_sample_set
,
sequence_file_id
=
id
)
#add sequence_file to a run sample_set
if
run_id
is
not
None
:
run_sample_set_id
=
db
.
run
[
run_id
].
sample_set_id
ids_sample_set
+=
[
run_sample_set_id
]
# for logging
id_sample_set_membership_run
=
db
.
sample_set_membership
.
insert
(
sample_set_id
=
run_sample_set_id
,
sequence_file_id
=
id
)
redirect_args
=
{
"id"
:
run_sample_set_id
}
...
...
@@ -153,13 +155,14 @@ def add_form():
#add sequence_file to a patient sample_set
if
patient_id
is
not
None
:
patient_sample_set_id
=
db
.
patient
[
patient_id
].
sample_set_id
ids_sample_set
+=
[
patient_sample_set_id
]
# for logging
id_sample_set_membership_patient
=
db
.
sample_set_membership
.
insert
(
sample_set_id
=
patient_sample_set_id
,
sequence_file_id
=
id
)
redirect_args
=
{
"id"
:
patient_sample_set_id
}
res
=
{
"file_id"
:
id
,
"message"
:
"file %s : upload started: %s"
%
(
id
,
request
.
vars
[
'filename'
]),
"message"
:
"
(%s)
file
{
%s
}
: upload started: %s"
%
(
','
.
join
(
map
(
str
,
ids_sample_set
)),
id
,
request
.
vars
[
'filename'
]),
"redirect"
:
"sample_set/index"
,
"args"
:
redirect_args
}
...
...
@@ -270,7 +273,7 @@ def edit_form():
error
+=
"date (wrong format), "
if
error
==
""
:
mes
=
"file
"
+
str
(
request
.
vars
[
'id'
]
)
+
" : "
mes
=
"file
{%s}: "
%
request
.
vars
[
'id'
]
filename
=
db
.
sequence_file
[
request
.
vars
[
'id'
]].
filename
if
request
.
vars
[
'filename'
]
!=
""
:
filename
=
request
.
vars
[
'filename'
]
...
...
@@ -305,7 +308,7 @@ def edit_form():
res
=
{
"file_id"
:
request
.
vars
[
"id"
],
"message"
:
"file %s: metadata saved"
%
request
.
vars
[
"id"
],
"message"
:
"file
{
%s
}
: metadata saved"
%
request
.
vars
[
"id"
],
"redirect"
:
"sample_set/index"
,
"args"
:
redirect_args
}
...
...
@@ -325,11 +328,7 @@ def upload():
error
+=
"no sequence file with this id"
if
not
error
:
patient_id
=
db
((
db
.
sequence_file
.
id
==
request
.
vars
[
"id"
])
&
(
db
.
sample_set_membership
.
sequence_file_id
==
db
.
sequence_file
.
id
)
&
(
db
.
patient
.
sample_set_id
==
db
.
sample_set_membership
.
sample_set_id
)
).
select
(
db
.
patient
.
id
).
first
()
mes
+=
" file %s (patient %s) "
%
(
db
.
sequence_file
[
request
.
vars
[
'id'
]].
filename
,
patient_id
[
'id'
])
mes
+=
" file {%s} "
%
(
request
.
vars
[
'id'
])
res
=
{
"message"
:
mes
+
"processing uploaded file"
,
"redirect"
:
"patient/info"
,
"args"
:
{
"id"
:
request
.
vars
[
'id'
]}
...
...
server/web2py/applications/vidjil/controllers/patient.py
View file @
9813eefc
...
...
@@ -326,7 +326,7 @@ def add_form():
res
=
{
"redirect"
:
"sample_set/index"
,
"args"
:
{
"id"
:
id_sample_set
},
"message"
:
patient
_name
+
":
patient
added"
}
"message"
:
"(%s)
patient
%s added"
%
(
id_sample_set
,
patient
_name
)
}
log
.
info
(
res
)
if
(
id
%
100
)
==
0
:
...
...
server/web2py/applications/vidjil/models/task.py
View file @
9813eefc
...
...
@@ -627,7 +627,7 @@ def schedule_pre_process(sequence_file_id, pre_process_id):
db
.
sequence_file
[
sequence_file_id
]
=
dict
(
pre_process_scheduler_task_id
=
task
.
id
)
res
=
{
"redirect"
:
"reload"
,
"message"
:
"
[
%s
]
(%s): process requested"
%
(
sequence_file_id
,
pre_process_id
)}
"message"
:
"
{
%s
}
(%s): process requested"
%
(
sequence_file_id
,
pre_process_id
)}
log
.
info
(
res
)
return
res
...
...
@@ -701,7 +701,7 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
stream
=
open
(
filepath
,
'rb'
)
except
IOError
:
print
"!!! Pre-process failed, no result file"
res
=
{
"message"
:
"
[
%s
]
p%s: 'pre_process' FAILED - %s"
%
(
sequence_file_id
,
pre_process_id
,
output_file
)}
res
=
{
"message"
:
"
{
%s
}
p%s: 'pre_process' FAILED - %s"
%
(
sequence_file_id
,
pre_process_id
,
output_file
)}
log
.
error
(
res
)
db
.
sequence_file
[
sequence_file_id
]
=
dict
(
pre_process_flag
=
"FAILED"
)
db
.
commit
()
...
...
@@ -726,7 +726,7 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
p
=
Popen
(
clean_cmd
,
shell
=
True
,
stdin
=
PIPE
,
stdout
=
PIPE
,
stderr
=
STDOUT
,
close_fds
=
True
)
p
.
wait
()
res
=
{
"message"
:
"
[
%s
]
p%s: 'pre_process' finished - %s"
%
(
sequence_file_id
,
pre_process_id
,
output_file
)}
res
=
{
"message"
:
"
{
%s
}
p%s: 'pre_process' finished - %s"
%
(
sequence_file_id
,
pre_process_id
,
output_file
)}
log
.
info
(
res
)
return
"SUCCESS"
...
...
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