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genotoul-bioinfo
jflow
Commits
954672ca
Commit
954672ca
authored
Dec 05, 2014
by
Ibouniyamine Nabihoudine
Browse files
No commit message
No commit message
parent
1dc1e730
Changes
2
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Inline
Side-by-side
src/jflow/parameter.py
View file @
954672ca
...
...
@@ -757,16 +757,10 @@ class InputDirectory(StrParameter, LinkTraceback):
StrParameter
.
__init__
(
self
,
name
,
help
,
flag
=
flag
,
default
=
default
,
type
=
"inputdirectory"
,
choices
=
choices
,
required
=
required
,
group
=
group
,
display_name
=
display_name
,
cmd_format
=
cmd_format
,
argpos
=
argpos
)
def
prepare
_input_directory
(
self
,
input
):
def
prepare
(
self
,
input
):
if
input
==
None
:
return
None
try
:
is_local
=
os
.
path
.
isdir
(
input
)
except
:
is_local
=
False
if
not
is_local
:
jflow_config_reader
=
JFlowConfigReader
()
new_path
=
os
.
path
.
join
(
jflow_config_reader
.
get_tmp_directory
(),
input
)
if
is_local
:
new_path
=
os
.
path
.
abspath
(
input
)
return
new_path
return
os
.
path
.
abspath
(
input
)
class
AbstractInputFile
(
AbstractIOFile
):
"""
...
...
@@ -853,7 +847,7 @@ class InputFile(StrParameter, AbstractInputFile):
else
:
ctype
=
self
.
get_type
()
return
create_test_function
(
ctype
)
def
prepare
_input_file
(
self
,
input
):
def
prepare
(
self
,
input
):
if
input
==
None
:
return
None
# handle url inputs
...
...
@@ -951,7 +945,7 @@ class InputFileList(ParameterList, AbstractInputFile):
else
:
ctype
=
self
.
get_type
()
return
create_test_function
(
ctype
)
def
prepare
_input_files
(
self
,
inputs
):
def
prepare
(
self
,
inputs
):
path2test
=
_copy
.
deepcopy
(
inputs
)
new_vals
=
list
()
if
not
path2test
.
__class__
.
__name__
==
"list"
:
...
...
src/jflow/workflow.py
View file @
954672ca
...
...
@@ -307,7 +307,7 @@ class Workflow(threading.Thread):
elif
parameter
.
__class__
==
InputFileList
:
if
value
==
""
:
value
=
[]
# from GUI
iovalues
=
[]
prepared_files
=
parameter
.
prepare
_input_files
(
value
)
prepared_files
=
parameter
.
prepare
(
value
)
for
file
in
prepared_files
:
iovalues
.
append
(
IOFile
(
file
,
parameter
.
file_format
,
parameter
.
linkTrace_nameid
,
None
))
new_param
=
InputFileList
(
parameter
.
name
,
parameter
.
help
,
file_format
=
parameter
.
file_format
,
default
=
iovalues
,
...
...
@@ -316,14 +316,14 @@ class Workflow(threading.Thread):
new_param
.
linkTrace_nameid
=
parameter
.
linkTrace_nameid
elif
parameter
.
__class__
==
InputFile
:
if
value
==
""
:
value
=
None
# from GUI
prepared_file
=
parameter
.
prepare
_input_file
(
value
)
prepared_file
=
parameter
.
prepare
(
value
)
new_param
=
InputFile
(
parameter
.
name
,
parameter
.
help
,
file_format
=
parameter
.
file_format
,
default
=
prepared_file
,
type
=
parameter
.
type
,
choices
=
parameter
.
choices
,
required
=
parameter
.
required
,
flag
=
parameter
.
flag
,
group
=
parameter
.
group
,
display_name
=
parameter
.
display_name
)
new_param
.
linkTrace_nameid
=
parameter
.
linkTrace_nameid
elif
parameter
.
__class__
==
InputDirectory
:
if
value
==
""
:
value
=
None
# from GUI
prepared_directory
=
parameter
.
prepare
_input_directory
(
value
)
prepared_directory
=
parameter
.
prepare
(
value
)
new_param
=
InputDirectory
(
parameter
.
name
,
parameter
.
help
,
default
=
prepared_directory
,
choices
=
parameter
.
choices
,
required
=
parameter
.
required
,
flag
=
parameter
.
flag
,
group
=
parameter
.
group
,
display_name
=
parameter
.
display_name
)
...
...
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