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workflow
representation
Commits
e8222be6
Commit
e8222be6
authored
Dec 09, 2019
by
payno
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Merge branch 'test_moml' into 'master'
Test moml Closes
#6
See merge request
!1
parents
1ba331cc
cb2098be
Changes
6
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6 changed files
with
138 additions
and
14 deletions
+138
-14
.gitignore
.gitignore
+53
-0
doc/scheme_uml_class_diag.dia
doc/scheme_uml_class_diag.dia
+0
-0
doc/scheme_uml_class_diag.png
doc/scheme_uml_class_diag.png
+0
-0
scheme/link.py
scheme/link.py
+2
-2
scheme/node.py
scheme/node.py
+23
-1
scheme/scheme.py
scheme/scheme.py
+60
-11
No files found.
.gitignore
0 → 100644
View file @
e8222be6
# Build files
build
dist
ESRF_Orange3_Add_on.egg-info
Orange/version.py
doc/build
*.so
*.pyd
*.pyc
MANIFEST
# Cython generated files
__pycache__
# Editor files
.idea
.idea/*
*~
.project
.pydevproject
.settings/*
.DS_Store
# Windows temp files
Thumbs.db
# PyLint, Coverage reports
.pylint_cache/*
htmlcov/*
# Tmp files
*tmp
tmp*
*.edf
*.info
*.cfg
*.xml
*.db
*.tar.bz2
dataset/
datasets/
*.egg-info*
# notebook checkpoints
*.ipynb_checkpoints/
# notebook nbconvert
*.nbconvert.ipynb
# octave files
octave-workspace
doc/scheme_uml_class_diag.dia
View file @
e8222be6
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doc/scheme_uml_class_diag.png
View replaced file @
1ba331cc
View file @
e8222be6
40.8 KB
|
W:
|
H:
44.6 KB
|
W:
|
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2-up
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Onion skin
scheme/link.py
View file @
e8222be6
...
...
@@ -61,8 +61,8 @@ class Link(object):
_JSON_SINK_NODE_ID
=
'sink_node_id'
_JSON_LINK_ID
=
'link_id'
def
__init__
(
self
,
source_node
,
sink_node
,
source_channel
,
sink_channel
,
id
=
None
):
def
__init__
(
self
,
source_node
,
sink_node
,
source_channel
=
'default'
,
sink_channel
=
'default'
,
id
=
None
):
self
.
id
=
get_next_link_free_id
()
if
id
is
None
else
id
if
isinstance
(
source_node
,
int
):
self
.
source_node_id
=
source_node
...
...
scheme/node.py
View file @
e8222be6
...
...
@@ -86,6 +86,7 @@ class Node(object):
_JSON_PROCESS_PT
=
'process_pt'
_JSON_ID
=
'id'
_JSON_PROPERTIES
=
'properties'
_JSON_ERROR_HANDLER
=
'error_handler'
def
__init__
(
self
,
processing_pt
,
id
=
None
,
properties
=
None
,
error_handler
=
None
):
...
...
@@ -209,11 +210,19 @@ class Node(object):
:return: json description of the node
:rtype: dict
"""
re
turn
{
re
s
=
{
self
.
_JSON_PROCESS_PT
:
self
.
process_pt
,
self
.
_JSON_ID
:
self
.
id
,
self
.
_JSON_PROPERTIES
:
self
.
properties
,
}
res
.
update
(
self
.
_get_error_handler_json
())
return
res
def
_get_error_handler_json
(
self
):
error_handler_json
=
self
.
_error_handler
.
to_json
()
if
self
.
_error_handler
else
{}
return
{
self
.
_JSON_ERROR_HANDLER
:
error_handler_json
,
}
@
staticmethod
def
from_json
(
json_data
):
...
...
@@ -264,3 +273,16 @@ class WorkflowException(Exception):
self
.
errorMessage
=
msg
self
.
data
=
data
self
.
traceBack
=
traceBack
class
ErrorHandler
(
Node
):
'''
TODO
'''
def
__init__
(
self
,
processing_pt
,
id
=
None
,
properties
=
None
):
super
(
ErrorHandler
,
self
).
__init__
(
processing_pt
=
processing_pt
,
id
=
id
,
properties
=
properties
,
error_handler
=
None
)
def
_get_error_handler_json
(
self
):
return
{}
\ No newline at end of file
scheme/scheme.py
View file @
e8222be6
...
...
@@ -36,6 +36,7 @@ import pprint
import
base64
import
pickle
import
logging
import
typing
from
.node
import
Node
from
.link
import
Link
from
ast
import
literal_eval
...
...
@@ -47,15 +48,16 @@ class Scheme(object):
"""
class to define a workflow scheme from nodes and links
:param
list nodes:
:param
list links:
:param
typing.Iterable nodes: set of Node
:param
typing.Iterable list links: set of Link
"""
_JSON_DESCRIPTION
=
'description'
_JSON_TITLE
=
'title'
_JSON_NODES
=
'nodes'
_JSON_LINKS
=
'links'
def
__init__
(
self
,
nodes
=
None
,
links
=
None
,
description
=
None
,
title
=
None
):
def
__init__
(
self
,
nodes
:
typing
.
Iterable
=
None
,
links
:
typing
.
Iterable
=
None
,
description
:
str
=
None
,
title
:
str
=
None
):
self
.
_reset
(
nodes
=
nodes
,
links
=
links
,
description
=
description
,
title
=
title
)
...
...
@@ -116,19 +118,19 @@ class Scheme(object):
res
.
append
(
node
)
return
res
def
save_to
(
self
,
output_file
):
def
save_to
(
self
,
output_file
:
str
):
"""
Save the scheme as an xml formated file to `stream`
:param output_file: name of the output file.
:type: str
"""
if
output_file
.
lower
.
endswith
(
'.json'
):
if
output_file
.
lower
()
.
endswith
(
'.json'
):
self
.
save_as_json
(
output_file
)
else
:
self
.
save_as_xml
(
output_file
)
def
save_as_xml
(
self
,
output_file
):
def
save_as_xml
(
self
,
output_file
:
str
):
"""
save current scheme to a default xml format
...
...
@@ -139,7 +141,7 @@ class Scheme(object):
tree
.
write
(
output_file
)
def
save_as_json
(
self
,
output_file
):
def
save_as_json
(
self
,
output_file
:
str
):
"""
save current scheme to a default json format
...
...
@@ -203,6 +205,12 @@ class Scheme(object):
return
links
def
to_json
(
self
):
"""
Convert scheme to json
:return: json dict
:rtype: dict
"""
return
{
self
.
_JSON_DESCRIPTION
:
self
.
description
,
self
.
_JSON_TITLE
:
self
.
title
,
...
...
@@ -211,7 +219,15 @@ class Scheme(object):
}
@
staticmethod
def
from_json_file
(
json_file_path
):
def
from_json_file
(
json_file_path
:
str
):
"""
Create and load Scheme from a json file
:param str json_file_path: json file
:return: Scheme fitting the json description
:rtype: Scheme
:raises: ValueError if file not found or invalid
"""
scheme
=
Scheme
()
try
:
scheme
.
load_from_json_file
(
json_file_path
)
...
...
@@ -221,7 +237,7 @@ class Scheme(object):
else
:
return
scheme
def
load_from_json_file
(
self
,
json_file_path
):
def
load_from_json_file
(
self
,
json_file_path
:
str
):
"""
:param str json_file_path: path to the json file containing the scheme
...
...
@@ -437,14 +453,47 @@ class Scheme(object):
node
.
load_handlers
()
def
contains_control_nodes
(
nodes_list
):
class
SubScheme
(
Scheme
,
Node
):
"""
Define a sub-scheme of the workflow (or subworkflow). SubScheme are
as Scheme expect that they are not 'root'.
:param nodes: set of Node
:type: typing.Iterable
:param links: set of Node
:type: typing.Iterable
:param description: description of the subscheme
:type: str
:param error_handler: ErrorHandler
"""
def
__init__
(
self
,
nodes
:
typing
.
Iterable
,
links
:
typing
.
Iterable
,
description
:
str
=
None
,
error_handler
=
None
):
Node
.
__init__
(
self
,
processing_pt
=
None
,
error_handler
=
error_handler
)
Scheme
.
__init__
(
self
,
nodes
=
nodes
,
links
=
links
,
title
=
''
,
description
=
description
)
def
contains_control_nodes
(
nodes_list
:
typing
.
Iterable
):
"""
Return the list of the 'control' nodes.
:param typing.Iterable nodes_list:
:return:
"""
for
_node
in
nodes_list
:
if
_node
.
endless
or
contains_control_nodes
(
_node
.
upstream_nodes
):
return
True
return
False
def
loads
(
string
,
format
):
def
loads
(
string
:
str
,
format
:
str
)
->
object
:
"""load stream from the given format.
:param str string: stream to load
:param str format: format
:return: object contained in the stream
:rtype: object
"""
if
format
==
"literal"
:
return
literal_eval
(
string
)
elif
format
==
"json"
:
...
...
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