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genotoul-bioinfo
jflow
Commits
7af1b803
Commit
7af1b803
authored
May 07, 2014
by
Jerome Mariette
Browse files
ok for a laod + a process workflow
parent
de5c3aa0
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/jflow/workflow.py
View file @
7af1b803
...
...
@@ -91,7 +91,7 @@ class Workflow(threading.Thread):
except
:
self
.
engine_arguments
=
None
try
:
# Add config information
self
.
name
,
self
.
description
,
self
.
parameters
=
self
.
_get_from_config
()
self
.
name
,
self
.
description
,
self
.
parameters
=
self
.
_get_from_config
(
self
.
parameters_section
)
except
:
raise
IOError
(
self
.
__class__
.
__name__
+
" workflow property file not found or invalid."
)
...
...
@@ -123,15 +123,16 @@ class Workflow(threading.Thread):
del
odict
[
'_Thread__stderr'
]
return
odict
def
get_parameters_per_groups
(
self
):
parameters
,
parameters_order
=
{},
[]
for
param
in
self
.
parameters
:
def
get_parameters_per_groups
(
self
,
parameters_section
=
"parameters"
):
name
,
description
,
parameters
=
self
.
_get_from_config
(
parameters_section
)
pgparameters
,
parameters_order
=
{},
[]
for
param
in
parameters
:
if
param
.
group
not
in
parameters_order
:
parameters_order
.
append
(
param
.
group
)
if
parameters
.
has_key
(
param
.
group
):
parameters
[
param
.
group
].
append
(
param
)
if
pg
parameters
.
has_key
(
param
.
group
):
pg
parameters
[
param
.
group
].
append
(
param
)
else
:
parameters
[
param
.
group
]
=
[
param
]
return
[
parameters
,
parameters_order
]
pg
parameters
[
param
.
group
]
=
[
param
]
return
[
pg
parameters
,
parameters_order
]
def
get_exec_path
(
self
,
software
):
exec_path
=
self
.
jflow_config_reader
.
get_exec
(
software
)
...
...
@@ -330,15 +331,15 @@ class Workflow(threading.Thread):
extended_args
[
param
.
name
]
=
param
.
default
return
extended_args
def
_get_from_config
(
self
):
def
_get_from_config
(
self
,
parameters_section
):
reader
=
ConfigParser
()
reader
.
read
(
self
.
_get_property_path
())
parameters
,
param_order
=
[],
[]
try
:
params
,
sub_order
,
excludes
,
hash_params
=
{},
{},
[],
{}
# first grab all parameters name
for
param
in
reader
.
items
(
self
.
parameters_section
):
cvalue
=
reader
.
get
(
self
.
parameters_section
,
param
[
0
])
for
param
in
reader
.
items
(
parameters_section
):
cvalue
=
reader
.
get
(
parameters_section
,
param
[
0
])
cparam
=
param
[
0
].
split
(
"."
)[
0
]
ckey
=
"."
.
join
(
param
[
0
].
split
(
"."
)[
1
:])
if
len
(
ckey
.
split
(
"."
))
>
1
:
...
...
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