Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
genotoul-bioinfo
jflow
Commits
e099f690
Commit
e099f690
authored
Aug 12, 2014
by
Jerome Mariette
Browse files
make hierarchie OK
parent
22b46d74
Changes
2
Hide whitespace changes
Inline
Side-by-side
src/jflow/component.py
View file @
e099f690
...
...
@@ -82,6 +82,9 @@ class Component(object):
except
:
pass
# otherwise, add it to the class itself
else
:
new_param
.
component_nameid
=
self
.
get_nameid
()
if
default
.
__class__
.
__name__
==
"OutputFileList"
or
default
.
__class__
.
__name__
==
"OutputFile"
:
new_param
.
parent_component_nameid
=
default
.
component_nameid
self
.
params_order
.
append
(
name
)
self
.
__setattr__
(
name
,
new_param
)
...
...
@@ -119,6 +122,7 @@ class Component(object):
except
:
pass
# otherwise, add it to the class itself
else
:
new_param
.
component_nameid
=
self
.
get_nameid
()
self
.
params_order
.
append
(
name
)
self
.
__setattr__
(
name
,
new_param
)
...
...
src/jflow/parameter.py
View file @
e099f690
...
...
@@ -296,9 +296,11 @@ class AbstractParameter(object):
return
self
.
type
.
__name__
class
AbstractFile
(
object
):
class
AbstractIOFile
(
object
):
def
__init__
(
self
,
file_format
=
"any"
):
self
.
file_format
=
file_format
self
.
component_nameid
=
None
self
.
parent_component_nameid
=
None
...
...
@@ -384,7 +386,7 @@ class Parameter(str, AbstractParameter):
action
=
"store"
,
sub_parameters
=
sub_parameters
,
group
=
group
,
display_name
=
display_name
)
class
InputFile
(
Parameter
,
AbstractFile
):
class
InputFile
(
Parameter
,
Abstract
IO
File
):
def
__new__
(
self
,
name
,
help
,
file_format
=
"any"
,
default
=
""
,
type
=
"localfile"
,
choices
=
None
,
required
=
False
,
flag
=
None
,
group
=
"default"
,
display_name
=
None
):
...
...
@@ -401,12 +403,12 @@ class InputFile(Parameter, AbstractFile):
def
__init__
(
self
,
name
,
help
,
file_format
=
"any"
,
default
=
""
,
type
=
"localfile"
,
choices
=
None
,
required
=
False
,
flag
=
None
,
group
=
"default"
,
display_name
=
None
):
AbstractFile
.
__init__
(
self
,
file_format
)
Abstract
IO
File
.
__init__
(
self
,
file_format
)
Parameter
.
__init__
(
self
,
name
,
help
,
flag
=
flag
,
type
=
type
,
choices
=
choices
,
required
=
required
,
group
=
group
,
display_name
=
display_name
)
class
OutputFile
(
Parameter
,
AbstractFile
):
class
OutputFile
(
Parameter
,
Abstract
IO
File
):
def
__new__
(
self
,
name
,
help
,
file_format
=
"any"
,
default
=
""
,
choices
=
None
,
required
=
False
,
flag
=
None
,
group
=
"default"
,
display_name
=
None
):
...
...
@@ -414,7 +416,7 @@ class OutputFile(Parameter, AbstractFile):
def
__init__
(
self
,
name
,
help
,
file_format
=
"any"
,
default
=
""
,
choices
=
None
,
required
=
False
,
flag
=
None
,
group
=
"default"
,
display_name
=
None
):
AbstractFile
.
__init__
(
self
,
file_format
)
Abstract
IO
File
.
__init__
(
self
,
file_format
)
Parameter
.
__init__
(
self
,
name
,
help
,
flag
=
flag
,
type
=
"localfile"
,
choices
=
choices
,
required
=
required
,
group
=
group
,
display_name
=
display_name
)
...
...
@@ -432,7 +434,7 @@ class ParameterList(list, AbstractParameter):
return
list
.
__init__
(
self
,
default
)
class
InputFileList
(
ParameterList
,
AbstractFile
):
class
InputFileList
(
ParameterList
,
Abstract
IO
File
):
def
__init__
(
self
,
name
,
help
,
file_format
=
"any"
,
default
=
None
,
type
=
"localfile"
,
choices
=
None
,
required
=
False
,
flag
=
None
,
group
=
"default"
,
display_name
=
None
):
...
...
@@ -447,7 +449,7 @@ class InputFileList(ParameterList, AbstractFile):
raise
ValueError
(
"InputFile.__new__: wrong type provided: '"
+
type2test
+
"', this should be choosen between '"
+
"', '"
.
join
(
INPUTFILE_TYPES
)
+
"'"
)
AbstractFile
.
__init__
(
self
,
file_format
)
Abstract
IO
File
.
__init__
(
self
,
file_format
)
ParameterList
.
__init__
(
self
,
name
,
help
,
flag
=
flag
,
type
=
type
,
choices
=
choices
,
required
=
required
,
group
=
group
,
display_name
=
display_name
)
if
default
.
__class__
.
__name__
==
"str"
:
...
...
@@ -458,12 +460,12 @@ class InputFileList(ParameterList, AbstractFile):
return
list
.
__init__
(
self
,
default
)
class
OutputFileList
(
ParameterList
,
AbstractFile
):
class
OutputFileList
(
ParameterList
,
Abstract
IO
File
):
def
__init__
(
self
,
name
,
help
,
file_format
=
"any"
,
default
=
None
,
choices
=
None
,
required
=
False
,
flag
=
None
,
group
=
"default"
,
display_name
=
None
):
if
default
==
None
:
default
=
[]
AbstractFile
.
__init__
(
self
,
file_format
)
Abstract
IO
File
.
__init__
(
self
,
file_format
)
ParameterList
.
__init__
(
self
,
name
,
help
,
flag
=
flag
,
type
=
"localfile"
,
choices
=
choices
,
required
=
required
,
group
=
group
,
display_name
=
display_name
)
if
default
.
__class__
.
__name__
==
"str"
:
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment