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genotoul-bioinfo
jflow
Commits
aa57aef7
Commit
aa57aef7
authored
Nov 18, 2014
by
Frédéric Escudié
Browse files
No commit message
No commit message
parent
46687289
Changes
3
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Side-by-side
src/jflow/component.py
View file @
aa57aef7
...
...
@@ -67,12 +67,10 @@ class Component(object):
required
=
False
,
flag
=
None
,
group
=
"default"
,
display_name
=
None
,
add_to
=
None
):
new_param
=
InputFile
(
name
,
help
,
flag
=
flag
,
file_format
=
file_format
,
default
=
default
,
type
=
type
,
required
=
required
,
group
=
group
,
display_name
=
display_name
)
# store where the parameter is coming from
new_param
.
component_nameid
=
self
.
get_nameid
()
if
issubclass
(
default
.
__class__
,
LinkTraceback
):
new_param
.
parent_component_nameid
=
default
.
component_nameid
new_param
.
parent_component_nameid
=
[
default
.
component_nameid
]
# if this input should be added to a particular parameter
if
add_to
:
try
:
...
...
@@ -102,13 +100,13 @@ class Component(object):
if
issubclass
(
default
.
__class__
,
list
):
for
idx
,
val
in
enumerate
(
default
):
if
issubclass
(
val
.
__class__
,
LinkTraceback
):
new_param
[
idx
].
parent_component_nameid
=
val
.
component_nameid
new_param
[
idx
].
parent_component_nameid
=
[
val
.
component_nameid
]
new_param
.
parent_component_nameid
.
append
(
val
.
component_nameid
)
else
:
new_param
.
parent_component_nameid
.
append
(
None
)
else
:
if
issubclass
(
default
.
__class__
,
LinkTraceback
):
new_param
[
0
].
parent_component_nameid
=
default
.
component_nameid
new_param
[
0
].
parent_component_nameid
=
[
default
.
component_nameid
]
new_param
.
parent_component_nameid
.
append
(
default
.
component_nameid
)
else
:
new_param
.
parent_component_nameid
.
append
(
None
)
...
...
src/jflow/parameter.py
View file @
aa57aef7
...
...
@@ -374,14 +374,14 @@ class AbstractParameter(object):
class
LinkTraceback
(
object
):
def
__init__
(
self
,
component_nameid
=
None
,
parent_component_nameid
=
[]
):
def
__init__
(
self
,
component_nameid
=
None
,
parent_component_nameid
=
None
):
self
.
component_nameid
=
component_nameid
self
.
parent_component_nameid
=
parent_component_nameid
self
.
parent_component_nameid
=
[]
if
parent_component_nameid
==
None
else
parent_component_nameid
class
AbstractIOFile
(
LinkTraceback
):
def
__init__
(
self
,
file_format
=
"any"
,
component_nameid
=
None
,
parent_component_nameid
=
[]
):
def
__init__
(
self
,
file_format
=
"any"
,
component_nameid
=
None
,
parent_component_nameid
=
None
):
LinkTraceback
.
__init__
(
self
,
component_nameid
,
parent_component_nameid
)
self
.
file_format
=
file_format
...
...
@@ -990,10 +990,10 @@ class OutputFilesEndsWith(DynamicOutput):
for
file
in
os
.
listdir
(
self
.
output_directory
):
if
file
.
endswith
(
self
.
end_str
)
and
self
.
include
:
output_files
.
append
(
IOFile
(
os
.
path
.
join
(
self
.
output_directory
,
file
),
self
.
file_format
,
self
.
component_nameid
,
None
)
)
self
.
component_par
ent_nameid
.
append
(
None
)
self
.
parent_compon
ent_nameid
.
append
(
None
)
elif
not
file
.
endswith
(
self
.
end_str
)
and
not
self
.
include
:
output_files
.
append
(
IOFile
(
os
.
path
.
join
(
self
.
output_directory
,
file
),
self
.
file_format
,
self
.
component_nameid
,
None
)
)
self
.
component_par
ent_nameid
.
append
(
None
)
self
.
parent_compon
ent_nameid
.
append
(
None
)
list
.
__init__
(
self
,
output_files
)
...
...
@@ -1022,8 +1022,8 @@ class OutputFilesPattern(DynamicOutput):
for
file
in
os
.
listdir
(
self
.
output_directory
):
if
self
.
include
and
re
.
search
(
self
.
pattern
,
file
)
is
not
None
:
output_files
.
append
(
IOFile
(
os
.
path
.
join
(
self
.
output_directory
,
file
),
self
.
file_format
,
self
.
component_nameid
,
None
)
)
self
.
component_par
ent_nameid
.
append
(
None
)
self
.
parent_compon
ent_nameid
.
append
(
None
)
elif
not
self
.
include
and
re
.
search
(
self
.
pattern
,
file
)
is
None
:
output_files
.
append
(
IOFile
(
os
.
path
.
join
(
self
.
output_directory
,
file
),
self
.
file_format
,
self
.
component_nameid
,
None
)
)
self
.
component_par
ent_nameid
.
append
(
None
)
self
.
parent_compon
ent_nameid
.
append
(
None
)
return
list
.
__init__
(
self
,
output_files
)
\ No newline at end of file
src/jflow/workflow.py
View file @
aa57aef7
...
...
@@ -346,12 +346,12 @@ class Workflow(threading.Thread):
for
ioparameter
in
cpt
.
__dict__
.
values
():
if
issubclass
(
ioparameter
.
__class__
,
InputFile
):
if
ioparameter
.
parent_component_nameid
!=
None
:
try
:
gr
.
add_edge
((
ioparameter
.
parent_component_nameid
,
ioparameter
.
component_nameid
))
try
:
gr
.
add_edge
((
ioparameter
.
parent_component_nameid
[
0
]
,
ioparameter
.
component_nameid
))
except
:
pass
if
issubclass
(
ioparameter
.
__class__
,
InputFileList
):
for
iofile
in
ioparameter
:
if
iofile
.
parent_component_nameid
!=
None
:
try
:
gr
.
add_edge
((
iofile
.
parent_component_nameid
,
ioparameter
.
component_nameid
))
for
parent
in
ioparameter
.
parent_component_nameid
:
if
parent
!=
None
:
try
:
gr
.
add_edge
((
parent
,
ioparameter
.
component_nameid
))
except
:
pass
return
gr
...
...
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