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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
ng6
Commits
9e758030
Commit
9e758030
authored
Apr 15, 2019
by
Celine Noirot
Browse files
directory in db start again with a /
parent
71c0f556
Changes
8
Hide whitespace changes
Inline
Side-by-side
src/ng6/analysis.py
View file @
9e758030
...
...
@@ -105,7 +105,7 @@ class Analysis (Component):
"""
# The directories structure into ng6
DIRECTORIES_STRUCTURE
=
"analyze
/
"
DIRECTORIES_STRUCTURE
=
"analyze"
ANALYSIS_CONFIG_FILE_NAME
=
"analysis.cfg"
def
__init__
(
self
,
name
=
""
,
description
=
""
,
software
=
""
,
...
...
@@ -183,7 +183,7 @@ class Analysis (Component):
break
directory_name
=
uuid
.
uuid4
().
hex
[:
9
]
self
.
directory
=
os
.
path
.
join
(
ng6conf
.
get_space_directory
(
self
.
space_id
),
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
self
.
directory
=
"/"
+
os
.
path
.
join
(
ng6conf
.
get_space_directory
(
self
.
space_id
),
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
# first create the output directory
if
not
os
.
path
.
isdir
(
self
.
output_directory
):
...
...
@@ -649,7 +649,7 @@ class Analysis (Component):
Return the full path of the analysis directory into the save dir
"""
ng6conf
=
NG6ConfigReader
()
return
os
.
path
.
join
(
ng6conf
.
get_save_directory
()
,
self
.
directory
)
return
ng6conf
.
get_save_directory
()
+
self
.
directory
def
__get_work_directory
(
self
):
...
...
@@ -657,7 +657,7 @@ class Analysis (Component):
Return the full path of the analysis directory into the work dir
"""
ng6conf
=
NG6ConfigReader
()
return
os
.
path
.
join
(
ng6conf
.
get_work_directory
()
,
self
.
directory
)
return
ng6conf
.
get_work_directory
()
+
self
.
directory
@
staticmethod
...
...
src/ng6/run.py
View file @
9e758030
...
...
@@ -41,7 +41,7 @@ class Run(object):
"""
# The directories structure into ng6
DIRECTORIES_STRUCTURE
=
"run
/
"
DIRECTORIES_STRUCTURE
=
"run"
SEQUENCERS
=
[
"454"
,
"454 GS FLX Titanium"
,
"454 GS FLX+"
,
"454 GS FLX XL+"
,
"HiSeq 2000"
,
"MiSeq"
]
def
__init__
(
self
,
name
,
date
,
species
,
data_nature
,
type
,
description
,
sequencer
,
space_id
=
"default"
,
id
=
None
):
...
...
@@ -82,15 +82,19 @@ class Run(object):
uniq
=
False
directory_name
=
uuid
.
uuid4
().
hex
[:
9
]
while
True
:
save_dir
=
os
.
path
.
join
(
ng6conf
.
get_save_directory
(),
ng6conf
.
get_space_directory
(
self
.
space_id
),
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
work_dir
=
os
.
path
.
join
(
ng6conf
.
get_work_directory
(),
ng6conf
.
get_space_directory
(
self
.
space_id
),
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
save_dir
=
os
.
path
.
join
(
ng6conf
.
get_save_directory
(),
\
ng6conf
.
get_space_directory
(
self
.
space_id
),
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
work_dir
=
os
.
path
.
join
(
ng6conf
.
get_work_directory
(),
ng6conf
.
get_space_directory
(
self
.
space_id
),
\
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
print
(
work_dir
)
print
(
os
.
path
.
isdir
(
work_dir
))
if
not
os
.
path
.
isdir
(
save_dir
)
and
not
os
.
path
.
isdir
(
work_dir
):
break
directory_name
=
uuid
.
uuid4
().
hex
[:
9
]
# Then make directories
work_dir
=
os
.
path
.
join
(
ng6conf
.
get_work_directory
(),
ng6conf
.
get_space_directory
(
self
.
space_id
),
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
os
.
makedirs
(
work_dir
,
0o751
)
self
.
directory
=
os
.
path
.
join
(
ng6conf
.
get_space_directory
(
self
.
space_id
),
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
self
.
directory
=
"/"
+
os
.
path
.
join
(
ng6conf
.
get_space_directory
(
self
.
space_id
),
self
.
DIRECTORIES_STRUCTURE
,
directory_name
)
def
process_raw_files
(
self
,
total_size
,
total_seq
):
"""
...
...
@@ -370,21 +374,21 @@ class Run(object):
Return the full path of the run directory into the work dir
"""
ng6conf
=
NG6ConfigReader
()
return
os
.
path
.
join
(
ng6conf
.
get_work_directory
()
,
self
.
directory
)
return
ng6conf
.
get_work_directory
()
+
self
.
directory
def
get_work_directory
(
self
):
"""
Return the full path of the run directory into the work dir
"""
ng6conf
=
NG6ConfigReader
()
return
os
.
path
.
join
(
ng6conf
.
get_work_directory
()
,
self
.
directory
)
return
self
.
__
get_work_directory
()
def
__get_save_directory
(
self
):
"""
Return the full path of the run directory into the save dir
"""
ng6conf
=
NG6ConfigReader
()
return
os
.
path
.
join
(
ng6conf
.
get_save_directory
()
,
self
.
directory
)
return
ng6conf
.
get_save_directory
()
+
self
.
directory
@
staticmethod
def
get_from_id
(
id
):
...
...
ui/nG6/pi1/analyzes/Adaptorcleaner.tpl
View file @
9e758030
...
...
@@ -138,11 +138,11 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
block
name
=
download
}
{
if
$nb_files
!=
0
}
<p><ul>
{
$dir
=
$data_folder
|
cat
:
'/'
|
cat
:
$analyse.directory
}
{
$dir
=
$data_folder
|
cat
:
$analyse.directory
}
{
assign
var
=
"nb_files"
value
=
0
}
{
foreach
$dir
|
scandir
as
$file
}
{
if
$file
!=
"."
and
$file
!=
""
and
$file
!=
".."
and
(
$file
|
substr
:-
strlen
(
".png"
))
!=
".png"
}
{
$link
=((
'fileadmin'
|
cat
:
'/'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
$link
=((
'fileadmin'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
<li
class=
"filelist"
><a
href=
"
{
$link
}
"
>
{
$file
}
</a>
</li>
{
$nb_files
=
$nb_files
+
1
}
{/
if
}
...
...
ui/nG6/pi1/analyzes/AnalysisTemplate.tpl
View file @
9e758030
...
...
@@ -109,9 +109,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div
class=
"tab-pane fade"
id=
"downloads"
>
{
block
name
=
download
}
{
assign
var
=
"nb_files"
value
=
0
}
{
$dir
=
$data_folder
|
cat
:
'/'
|
cat
:
$analyse.directory
}
{
$dir
=
$data_folder
|
cat
:
$analyse.directory
}
{
foreach
$dir
|
scandir
as
$file
}
{
assign
var
=
"link"
value
=((
'fileadmin'
|
cat
:
'/'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
assign
var
=
"link"
value
=((
'fileadmin'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
if
$file
!=
"."
and
$file
!=
""
and
$file
!=
".."
and
(
$file
|
substr
:-
strlen
(
".png"
))
!=
".png"
and
!
is_dir
(
$link
)
}
{
$nb_files
=
$nb_files
+
1
}
{/
if
}
...
...
ui/nG6/pi1/analyzes/MothurOTU.tpl
View file @
9e758030
...
...
@@ -173,11 +173,11 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
block
name
=
download
}
{
if
$nb_files
!=
0
}
<p><ul>
{
$dir
=
$data_folder
|
cat
:
'/'
|
cat
:
$analyse.directory
}
{
$dir
=
$data_folder
|
cat
:
$analyse.directory
}
{
assign
var
=
"nb_files"
value
=
0
}
{
foreach
$dir
|
scandir
as
$file
}
{
if
$file
!=
"."
and
$file
!=
""
and
$file
!=
".."
and
(
$file
|
substr
:-
strlen
(
".png"
))
!=
".png"
}
{
$link
=((
'fileadmin'
|
cat
:
'/'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
$link
=((
'fileadmin'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
<li
class=
"filelist"
><a
href=
"
{
$link
}
"
>
{
$file
}
</a>
</li>
{
$nb_files
=
$nb_files
+
1
}
{/
if
}
...
...
ui/nG6/pi1/analyzes/MothurOTUAnalysis.tpl
View file @
9e758030
...
...
@@ -249,9 +249,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div
class=
"tab-pane fade"
id=
"downloads"
>
{
block
name
=
download
}
{
assign
var
=
"nb_files"
value
=
0
}
{
$dir
=
$data_folder
|
cat
:
'/'
|
cat
:
$analyse.directory
}
{
$dir
=
$data_folder
|
cat
:
$analyse.directory
}
{
foreach
$dir
|
scandir
as
$file
}
{
assign
var
=
"link"
value
=((
'fileadmin'
|
cat
:
'/'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
assign
var
=
"link"
value
=((
'fileadmin'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
if
$file
!=
"."
and
$file
!=
""
and
$file
!=
".."
and
(
$file
|
substr
:-
strlen
(
".png"
))
!=
".png"
and
!
is_dir
(
$link
)
}
{
$nb_files
=
$nb_files
+
1
}
{/
if
}
...
...
@@ -263,7 +263,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
else
}
<ul>
{
foreach
$dir
|
scandir
as
$file
}
{
assign
var
=
"link"
value
=((
'fileadmin'
|
cat
:
'/'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
assign
var
=
"link"
value
=((
'fileadmin'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
if
$file
!=
"."
and
$file
!=
""
and
$file
!=
".."
and
(
$file
|
substr
:-
strlen
(
".png"
))
!=
".png"
and
!
is_dir
(
$link
)
}
<li
class=
"filelist"
><a
href=
"
{
$link
}
"
>
{
$file
}
</a>
</li>
{/
if
}
...
...
ui/nG6/pi1/analyzes/RunAssembly.tpl
View file @
9e758030
...
...
@@ -391,11 +391,11 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div
class=
"tab-pane fade"
id=
"downloads"
>
<ul>
{
$dir
=
$data_folder
|
cat
:
'/'
|
cat
:
$analyse.directory
}
{
$dir
=
$data_folder
|
cat
:
$analyse.directory
}
{
assign
var
=
"nb_files"
value
=
0
}
{
foreach
$dir
|
scandir
as
$file
}
{
if
$file
!=
"."
and
$file
!=
""
and
$file
!=
".."
and
(
$file
|
substr
:-
strlen
(
".png"
))
!=
".png"
}
{
$link
=((
'fileadmin'
|
cat
:
'/'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
$link
=((
'fileadmin'
|
cat
:
$analyse.directory
)|
cat
:
'/'
)|
cat
:
$file
}
<li
class=
"filelist"
><a
href=
"
{
$link
}
"
>
{
$file
}
</a>
</li>
{
$nb_files
=
$nb_files
+
1
}
{/
if
}
...
...
ui/nG6/pi1/run_view.tpl
View file @
9e758030
...
...
@@ -120,12 +120,12 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</div>
<div
class=
"tab-pane fade"
id=
"downloads"
>
{
$dir
=
$data_folder
|
cat
:
'/'
|
cat
:
$runs
[
key
(
$runs
)].
directory
}
{
$dir
=
$data_folder
|
cat
:
$runs
[
key
(
$runs
)].
directory
}
{
assign
var
=
"nb_files"
value
=
0
}
<ul>
{
foreach
$dir
|
scandir
as
$file
}
{
if
$file
!=
"."
and
$file
!=
""
and
$file
!=
".."
and
(
$file
|
substr
:-
strlen
(
".png"
))
!=
".png"
}
{
$link
=((
'fileadmin'
|
cat
:
'/'
|
cat
:
$runs
[
key
(
$runs
)].
directory
)|
cat
:
'/'
)|
cat
:
$file
}
{
$link
=((
'fileadmin'
|
cat
:
$runs
[
key
(
$runs
)].
directory
)|
cat
:
'/'
)|
cat
:
$file
}
<li
class=
"filelist"
><a
href=
"
{
$link
}
"
>
{
$file
}
</a>
<br
/></li>
{
$nb_files
=
$nb_files
+
1
}
{/
if
}
...
...
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