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genotoul-bioinfo
jflow
Commits
da2cc6b6
Commit
da2cc6b6
authored
May 12, 2017
by
Floreal Cabanettes
Browse files
Use get_command function to get program name
parent
0203c77b
Changes
2
Hide whitespace changes
Inline
Side-by-side
src/jflow/component.py
View file @
da2cc6b6
...
...
@@ -51,7 +51,10 @@ class Component(object):
self
.
output_directory
=
None
self
.
description
=
None
self
.
config_reader
=
JFlowConfigReader
()
self
.
prg_name
=
self
.
get_prg_name
()
try
:
self
.
prg_name
=
self
.
get_command
()
except
NotImplementedError
:
self
.
prg_name
=
self
.
__class__
.
__name__
self
.
version
=
self
.
get_version
()
if
isinstance
(
self
.
version
,
bytes
):
self
.
version
=
self
.
version
.
decode
()
...
...
src/jflow/workflow.py
View file @
da2cc6b6
...
...
@@ -611,18 +611,18 @@ class Workflow(threading.Thread):
descriptions
=
self
.
get_description_per_components
()
idx
=
1
for
component
,
program
in
programs
.
items
():
name
=
component
[:
component
.
index
(
"."
)]
component
=
str
(
idx
)
+
". "
name
=
component
component
_str
=
str
(
idx
)
+
". "
if
component
in
descriptions
and
descriptions
[
component
]
is
not
None
:
component
+=
descriptions
[
component
]
component
_str
+=
descriptions
[
component
]
else
:
component
+=
name
component
+=
":
\n
"
component
+=
"
\t
- Program: {0}
\n
"
.
format
(
program
[
"name"
])
component
+=
"
\t
- Version: {0}
\n
"
.
format
(
program
[
"version"
])
component
+=
"
\t
- Parameters: {0}
\n
"
.
format
(
", "
.
join
(
program
[
"parameters"
])
component
_str
+=
name
component
_str
+=
":
\n
"
component
_str
+=
"
\t
- Program: {0}
\n
"
.
format
(
program
[
"name"
])
component
_str
+=
"
\t
- Version: {0}
\n
"
.
format
(
program
[
"version"
])
component
_str
+=
"
\t
- Parameters: {0}
\n
"
.
format
(
", "
.
join
(
program
[
"parameters"
])
if
len
(
program
[
"parameters"
])
>
0
else
"None"
)
print
(
component
)
print
(
component
_str
)
idx
+=
1
def
get_description_per_components
(
self
):
...
...
@@ -644,7 +644,7 @@ class Workflow(threading.Thread):
version
=
current_component
.
version
if
version
:
program
=
{
"name"
:
current_component
.
get_
prg_name
()
,
"name"
:
current_component
.
prg_name
,
"version"
:
version
,
"parameters"
:
[]
}
...
...
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