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vidjil
vidjil
Commits
5a4af716
Commit
5a4af716
authored
Sep 24, 2019
by
Mathieu Giraud
Browse files
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Merge branch 'feature-s/3899-hidden-results' into 'dev'
Hide some results Closes #3899 See merge request
!477
parents
b57898a6
d7bd8fbe
Pipeline
#95183
passed with stages
in 9 minutes and 18 seconds
Changes
7
Pipelines
1
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Inline
Side-by-side
Showing
7 changed files
with
18 additions
and
3 deletions
+18
-3
server/web2py/applications/vidjil/controllers/default.py
server/web2py/applications/vidjil/controllers/default.py
+1
-0
server/web2py/applications/vidjil/controllers/results_file.py
...er/web2py/applications/vidjil/controllers/results_file.py
+1
-0
server/web2py/applications/vidjil/controllers/run.py
server/web2py/applications/vidjil/controllers/run.py
+3
-1
server/web2py/applications/vidjil/controllers/sample_set.py
server/web2py/applications/vidjil/controllers/sample_set.py
+6
-2
server/web2py/applications/vidjil/models/db.py
server/web2py/applications/vidjil/models/db.py
+1
-0
server/web2py/applications/vidjil/models/results_file.py
server/web2py/applications/vidjil/models/results_file.py
+1
-0
server/web2py/applications/vidjil/models/task.py
server/web2py/applications/vidjil/models/task.py
+5
-0
No files found.
server/web2py/applications/vidjil/controllers/default.py
View file @
5a4af716
...
...
@@ -313,6 +313,7 @@ def get_data():
&
(
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
.
hidden
==
False
)
&
(
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
)
...
...
server/web2py/applications/vidjil/controllers/results_file.py
View file @
5a4af716
...
...
@@ -20,6 +20,7 @@ def index():
&
(
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
)
&
(
db
.
results_file
.
hidden
==
False
)
).
select
(
orderby
=
~
db
.
results_file
.
run_date
)
...
...
server/web2py/applications/vidjil/controllers/run.py
View file @
5a4af716
...
...
@@ -59,7 +59,8 @@ def info():
).
select
(
left
=
db
.
results_file
.
on
(
(
db
.
results_file
.
sequence_file_id
==
db
.
sequence_file
.
id
)
&
(
db
.
results_file
.
config_id
==
str
(
config_id
)
)
&
(
db
.
results_file
.
config_id
==
str
(
config_id
))
&
(
db
.
results_file
.
hidden
==
False
)
),
orderby
=
db
.
sequence_file
.
id
|~
db
.
results_file
.
run_date
)
...
...
@@ -79,6 +80,7 @@ def info():
left
=
db
.
results_file
.
on
(
(
db
.
results_file
.
sequence_file_id
==
db
.
sequence_file
.
id
)
&
(
db
.
results_file
.
config_id
==
str
(
config_id
)
)
&
(
db
.
results_file
.
hidden
==
False
)
)
)
...
...
server/web2py/applications/vidjil/controllers/sample_set.py
View file @
5a4af716
...
...
@@ -99,7 +99,8 @@ def index():
).
select
(
left
=
db
.
results_file
.
on
(
(
db
.
results_file
.
sequence_file_id
==
db
.
sequence_file
.
id
)
&
(
db
.
results_file
.
config_id
==
str
(
config_id
)
)
&
(
db
.
results_file
.
config_id
==
str
(
config_id
))
&
(
db
.
results_file
.
hidden
==
False
)
),
orderby
=
db
.
sequence_file
.
id
|~
db
.
results_file
.
run_date
)
...
...
@@ -118,7 +119,8 @@ def index():
).
select
(
left
=
db
.
results_file
.
on
(
(
db
.
results_file
.
sequence_file_id
==
db
.
sequence_file
.
id
)
&
(
db
.
results_file
.
config_id
==
str
(
config_id
)
)
&
(
db
.
results_file
.
config_id
==
str
(
config_id
))
&
(
db
.
results_file
.
hidden
==
False
)
)
)
...
...
@@ -311,6 +313,7 @@ def result_files():
(
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
!=
None
)
&
(
db
.
results_file
.
hidden
==
False
)
&
config_query
)
...
...
@@ -600,6 +603,7 @@ def custom():
&
(
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
()
...
...
server/web2py/applications/vidjil/models/db.py
View file @
5a4af716
...
...
@@ -209,6 +209,7 @@ db.define_table('results_file',
Field
(
'config_id'
,
'reference config'
,
ondelete
=
'SET NULL'
),
Field
(
'run_date'
,
'datetime'
),
Field
(
'scheduler_task_id'
,
'integer'
),
Field
(
'hidden'
,
'boolean'
,
default
=
False
,
notnull
=
True
),
Field
(
'data_file'
,
'upload'
,
uploadfolder
=
defs
.
DIR_RESULTS
,
length
=
LENGTH_UPLOAD
,
autodelete
=
AUTODELETE
))
...
...
server/web2py/applications/vidjil/models/results_file.py
View file @
5a4af716
...
...
@@ -12,6 +12,7 @@ def get_last_results(sequence_file, config_ids=None):
select_on_config
=
db
.
results_file
.
config_id
.
belongs
(
config_ids
)
# First get the max run dates for the good result files
select_max_run
=
db
((
db
.
results_file
.
sequence_file_id
==
sequence_file
)
\
&
(
db
.
results_file
.
hidden
==
False
)
\
&
(
select_on_config
)).
_select
(
db
.
results_file
.
run_date
.
max
().
with_alias
(
'max'
),
groupby
=
db
.
results_file
.
config_id
)
...
...
server/web2py/applications/vidjil/models/task.py
View file @
5a4af716
...
...
@@ -62,6 +62,7 @@ def compute_contamination(sequence_file_id, results_file_id, config_id):
&
(
db
.
sequence_file
.
id
==
db
.
sample_set_membership
.
sequence_file_id
)
&
(
db
.
sequence_file
.
id
!=
sequence_file_id
[
i
])
&
(
db
.
results_file
.
sequence_file_id
==
db
.
sequence_file
.
id
)
&
(
db
.
results_file
.
hidden
==
False
)
&
(
db
.
results_file
.
config_id
==
config_id
[
i
]
)
).
select
(
db
.
sequence_file
.
ALL
,
db
.
results_file
.
ALL
,
db
.
sample_set
.
id
,
orderby
=
db
.
sequence_file
.
id
|~
db
.
results_file
.
run_date
)
...
...
@@ -104,6 +105,7 @@ def compute_extra(id_file, id_config, min_threshold):
result
=
{}
d
=
None
results_file
=
db
((
db
.
results_file
.
sequence_file_id
==
id_file
)
&
(
db
.
results_file
.
hidden
==
False
)
&
(
db
.
results_file
.
config_id
==
id_config
)
).
select
(
orderby
=~
db
.
results_file
.
run_date
).
first
()
filename
=
defs
.
DIR_RESULTS
+
results_file
.
data_file
...
...
@@ -148,6 +150,7 @@ def schedule_run(id_sequence, id_config, grep_reads=None):
ts
=
time
.
time
()
data_id
=
db
.
results_file
.
insert
(
sequence_file_id
=
id_sequence
,
run_date
=
datetime
.
datetime
.
fromtimestamp
(
ts
).
strftime
(
'%Y-%m-%d %H:%M:%S'
),
hidden
=
grep_reads
is
not
None
,
config_id
=
id_config
)
args
=
[
id_sequence
,
id_config
,
data_id
,
grep_reads
]
...
...
@@ -183,6 +186,7 @@ def schedule_fuse(sample_set_ids, config_ids):
row
=
db
((
db
.
sample_set_membership
.
sample_set_id
==
sample_set_id
)
&
(
db
.
sample_set_membership
.
sequence_file_id
==
db
.
results_file
.
sequence_file_id
)
&
(
db
.
results_file
.
config_id
==
config_id
)
&
(
db
.
results_file
.
hidden
==
False
)
).
select
(
db
.
sample_set_membership
.
sample_set_id
,
db
.
sample_set_membership
.
sequence_file_id
,
db
.
results_file
.
id
,
db
.
results_file
.
config_id
).
first
()
if
row
:
...
...
@@ -648,6 +652,7 @@ def run_fuse(id_file, id_config, id_data, sample_set_id, clean_before=True, clea
&
(
db
.
sample_set_membership
.
sequence_file_id
==
db
.
sequence_file
.
id
)
&
(
db
.
sample_set_membership
.
sample_set_id
==
sample_set_id
)
&
(
db
.
results_file
.
config_id
==
id_config
)
&
(
db
.
results_file
.
hidden
==
False
)
).
select
(
orderby
=
db
.
sequence_file
.
id
|~
db
.
results_file
.
run_date
)
query
=
[]
sequence_file_id
=
0
...
...
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