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genotoul-bioinfo
jflow
Commits
f1028f5b
Commit
f1028f5b
authored
Sep 23, 2015
by
Jerome Mariette
Browse files
from python2 to python3 > ok from command line
parent
9474bb02
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/jflow/workflows_manager.py
View file @
f1028f5b
...
...
@@ -41,7 +41,7 @@ class WorkflowsManager(object):
def
__init__
(
self
):
self
.
config_reader
=
JFlowConfigReader
()
if
not
os
.
path
.
isdir
(
self
.
get_output_directory
()):
os
.
makedirs
(
self
.
get_output_directory
(),
0751
)
os
.
makedirs
(
self
.
get_output_directory
(),
0
o
751
)
self
.
dump_file
=
os
.
path
.
join
(
self
.
get_output_directory
(),
self
.
WORKFLOWS_DUMP_FILE_NAME
)
self
.
ids_file
=
os
.
path
.
join
(
self
.
get_output_directory
(),
self
.
IDS_FILE_NAME
)
...
...
@@ -49,7 +49,7 @@ class WorkflowsManager(object):
WorkflowsManager
.
lock_workflows_file
.
acquire
()
# first load the existing workflows
try
:
wdfh
=
open
(
self
.
dump_file
)
wdfh
=
open
(
self
.
dump_file
,
"rb"
)
workflows_dump
=
pickle
.
load
(
wdfh
)
wdfh
.
close
()
except
:
...
...
@@ -59,7 +59,7 @@ class WorkflowsManager(object):
workflows_dump
[
utils
.
get_nb_string
(
workflow
.
id
)]
=
{
"dump_path"
:
workflow
.
dump_path
,
"object"
:
workflow
.
minimize
()}
# and save them
wdfh
=
open
(
self
.
dump_file
,
"w"
)
wdfh
=
open
(
self
.
dump_file
,
"w
b
"
)
pickle
.
dump
(
workflows_dump
,
wdfh
)
wdfh
.
close
()
WorkflowsManager
.
lock_workflows_file
.
release
()
...
...
@@ -78,13 +78,14 @@ class WorkflowsManager(object):
if
issubclass
(
obj
,
jflow
.
workflow
.
Workflow
)
and
obj
.
__name__
!=
jflow
.
workflow
.
Workflow
.
__name__
:
for
function
in
functions
:
# check if the workflow has the requested methode
for
ifunction
in
inspect
.
getmembers
(
obj
,
predicate
=
inspect
.
ismethod
):
# inspect.ismethod has been changed for inspect.isfunction in Python3
for
ifunction
in
inspect
.
getmembers
(
obj
,
predicate
=
inspect
.
isfunction
):
if
ifunction
[
0
]
==
function
:
# try to build the workflow
try
:
wf_instances
.
append
(
obj
(
function
=
function
))
wf_methodes
.
append
(
function
)
except
:
pass
#
try:
wf_instances
.
append
(
obj
(
function
=
function
))
wf_methodes
.
append
(
function
)
#
except: pass
return
[
wf_instances
,
wf_methodes
]
def
rerun_workflow
(
self
,
workflow_id
):
...
...
@@ -119,7 +120,7 @@ class WorkflowsManager(object):
from
jflow.workflow
import
Workflow
WorkflowsManager
.
lock_workflows_file
.
acquire
()
try
:
awfh
=
open
(
self
.
dump_file
)
awfh
=
open
(
self
.
dump_file
,
"rb"
)
all_workflows_dump
=
pickle
.
load
(
awfh
)
awfh
.
close
()
except
:
...
...
@@ -137,7 +138,7 @@ class WorkflowsManager(object):
logging
.
getLogger
(
"jflow"
).
debug
(
"Workflow #"
+
rworkflow_id
+
" connot be retrieved in the available workflows!"
)
raise
Exception
(
"Workflow #"
+
rworkflow_id
+
" connot be retrieved in the available workflows!"
)
# and save them
awfh
=
open
(
self
.
dump_file
,
"w"
)
awfh
=
open
(
self
.
dump_file
,
"w
b
"
)
pickle
.
dump
(
all_workflows_dump
,
awfh
)
awfh
.
close
()
WorkflowsManager
.
lock_workflows_file
.
release
()
...
...
@@ -157,7 +158,7 @@ class WorkflowsManager(object):
from
jflow.workflow
import
Workflow
workflows
=
[]
try
:
awfh
=
open
(
self
.
dump_file
)
awfh
=
open
(
self
.
dump_file
,
"rb"
)
workflows_dump
=
pickle
.
load
(
awfh
)
awfh
.
close
()
except
:
...
...
@@ -191,12 +192,12 @@ class WorkflowsManager(object):
def
get_workflow
(
self
,
workflow_id
):
rworkflow_id
=
utils
.
get_nb_string
(
workflow_id
)
try
:
wdfh
=
open
(
self
.
dump_file
)
wdfh
=
open
(
self
.
dump_file
,
"rb"
)
workflows_dump
=
pickle
.
load
(
wdfh
)
wdfh
.
close
()
except
:
workflows_dump
=
{}
if
workflow
s_dump
.
has_key
(
r
workflow
_id
)
:
if
r
workflow
_id
in
workflow
s_dump
:
workflow_dump
=
open
(
workflows_dump
[
rworkflow_id
][
"dump_path"
],
"rb"
)
workflow
=
pickle
.
load
(
workflow_dump
)
workflow_dump
.
close
()
...
...
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