diff --git a/lie_workflow/__init__.py b/mdstudio_workflow/__init__.py similarity index 93% rename from lie_workflow/__init__.py rename to mdstudio_workflow/__init__.py index 4fd9786..5037e4d 100644 --- a/lie_workflow/__init__.py +++ b/mdstudio_workflow/__init__.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__module__ = 'lie_workflow' +__module__ = 'mdstudio_workflow' __docformat__ = 'restructuredtext' __version__ = '{major:d}.{minor:d}'.format(major=1, minor=0) __author__ = 'Marc van Dijk' diff --git a/lie_workflow/schemas/endpoints/workflow_loop_task.v1.json b/mdstudio_workflow/schemas/endpoints/workflow_loop_task.v1.json similarity index 100% rename from lie_workflow/schemas/endpoints/workflow_loop_task.v1.json rename to mdstudio_workflow/schemas/endpoints/workflow_loop_task.v1.json diff --git a/lie_workflow/schemas/endpoints/workflow_python_task.v1.json b/mdstudio_workflow/schemas/endpoints/workflow_python_task.v1.json similarity index 100% rename from lie_workflow/schemas/endpoints/workflow_python_task.v1.json rename to mdstudio_workflow/schemas/endpoints/workflow_python_task.v1.json diff --git a/lie_workflow/schemas/endpoints/workflow_wamp_task.v1.json b/mdstudio_workflow/schemas/endpoints/workflow_wamp_task.v1.json similarity index 100% rename from lie_workflow/schemas/endpoints/workflow_wamp_task.v1.json rename to mdstudio_workflow/schemas/endpoints/workflow_wamp_task.v1.json diff --git a/lie_workflow/schemas/resources/task_template.json b/mdstudio_workflow/schemas/resources/task_template.json similarity index 100% rename from lie_workflow/schemas/resources/task_template.json rename to mdstudio_workflow/schemas/resources/task_template.json diff --git a/lie_workflow/schemas/resources/workflow_metadata_template.json b/mdstudio_workflow/schemas/resources/workflow_metadata_template.json similarity index 100% rename from lie_workflow/schemas/resources/workflow_metadata_template.json rename to mdstudio_workflow/schemas/resources/workflow_metadata_template.json diff --git a/lie_workflow/wamp_services.py b/mdstudio_workflow/wamp_services.py similarity index 93% rename from lie_workflow/wamp_services.py rename to mdstudio_workflow/wamp_services.py index 19178fa..523392c 100644 --- a/lie_workflow/wamp_services.py +++ b/mdstudio_workflow/wamp_services.py @@ -7,7 +7,7 @@ """ from autobahn import wamp -from lie_system import LieApplicationSession +from mdstudio_system import LieApplicationSession class WorkflowWampApi(LieApplicationSession): @@ -18,7 +18,7 @@ class WorkflowWampApi(LieApplicationSession): upon WAMP session setup """ - require_config = ['system', 'lie_db'] + require_config = ['system', 'mdstudio_db'] @wamp.register(u'liestudio.workflow.run') def retrieve_structures(self, workflow, session=None): diff --git a/lie_workflow/workflow_common.py b/mdstudio_workflow/workflow_common.py similarity index 99% rename from lie_workflow/workflow_common.py rename to mdstudio_workflow/workflow_common.py index ec30107..91fc130 100644 --- a/lie_workflow/workflow_common.py +++ b/mdstudio_workflow/workflow_common.py @@ -80,7 +80,7 @@ def validate_workflow(workflow): Validate the constructed workflow :param workflow: Workflow graph to validate - :type workflow: :lie_graph:GraphAxis + :type workflow: :graphit:GraphAxis :return: Validated or not :rtype: :py:bool diff --git a/lie_workflow/workflow_runner.py b/mdstudio_workflow/workflow_runner.py similarity index 99% rename from lie_workflow/workflow_runner.py rename to mdstudio_workflow/workflow_runner.py index d4e020a..3426b25 100644 --- a/lie_workflow/workflow_runner.py +++ b/mdstudio_workflow/workflow_runner.py @@ -4,8 +4,8 @@ import threading import random -from lie_workflow.workflow_common import WorkflowError, validate_workflow -from lie_workflow.workflow_spec import WorkflowSpec +from mdstudio_workflow.workflow_common import WorkflowError, validate_workflow +from mdstudio_workflow.workflow_spec import WorkflowSpec # Set twisted logger from twisted.logger import Logger @@ -136,7 +136,7 @@ def output_callback(self, output, tid): # No more new tasks if not next_task_nids: - + # Not finished but no active tasks anymore/breakpoint if not self.active_tasks and not self.is_completed: breakpoints = self.active_breakpoints @@ -197,7 +197,7 @@ def run_task(self, tid): if unfinished.status == 'failed': self.is_running = False break - + return # Run the task if status is 'ready' diff --git a/lie_workflow/workflow_spec.py b/mdstudio_workflow/workflow_spec.py similarity index 96% rename from lie_workflow/workflow_spec.py rename to mdstudio_workflow/workflow_spec.py index b6bb169..ce36bee 100644 --- a/lie_workflow/workflow_spec.py +++ b/mdstudio_workflow/workflow_spec.py @@ -18,12 +18,12 @@ from graphit.graph_py2to3 import to_unicode, prepaire_data_dict from graphit.graph_helpers import renumber_id -from lie_workflow import __version__ -from lie_workflow.workflow_common import WorkflowError -from lie_workflow.workflow_task_types import task_types, WORKFLOW_ORM +from mdstudio_workflow import __version__ +from mdstudio_workflow.workflow_common import WorkflowError +from mdstudio_workflow.workflow_task_types import task_types, WORKFLOW_ORM # Path to default workflow JSON schema part of the module -workflow_metadata_template = pkg_resources.resource_filename('lie_workflow', +workflow_metadata_template = pkg_resources.resource_filename('mdstudio_workflow', '/schemas/resources/workflow_metadata_template.json') @@ -35,7 +35,7 @@ class WorkflowSpec(object): tasks and the edges the connections between them. The Workflow class acts as manager collecting output from tasks and forwarding it to other tasks along the edges (push execution). - The `lie_workflow` DAG follows the workflow principles as described by the + The `mdstudio_workflow` DAG follows the workflow principles as described by the Workflow Patterns initiative supporting many but not all of the described patterns (http://www.workflowpatterns.com). diff --git a/lie_workflow/workflow_task_specs.py b/mdstudio_workflow/workflow_task_specs.py similarity index 100% rename from lie_workflow/workflow_task_specs.py rename to mdstudio_workflow/workflow_task_specs.py diff --git a/lie_workflow/workflow_task_types/__init__.py b/mdstudio_workflow/workflow_task_types/__init__.py similarity index 100% rename from lie_workflow/workflow_task_types/__init__.py rename to mdstudio_workflow/workflow_task_types/__init__.py diff --git a/lie_workflow/workflow_task_types/task_base_type.py b/mdstudio_workflow/workflow_task_types/task_base_type.py similarity index 98% rename from lie_workflow/workflow_task_types/task_base_type.py rename to mdstudio_workflow/workflow_task_types/task_base_type.py index ca123cd..182c48f 100644 --- a/lie_workflow/workflow_task_types/task_base_type.py +++ b/mdstudio_workflow/workflow_task_types/task_base_type.py @@ -17,7 +17,7 @@ from graphit.graph_py2to3 import prepaire_data_dict, PY_STRING from graphit.graph_io.io_jsonschema_format import read_json_schema -from lie_workflow.workflow_common import WorkflowError, collect_data, concat_dict +from mdstudio_workflow.workflow_common import WorkflowError, collect_data, concat_dict # Set twisted logger from twisted.logger import Logger @@ -42,7 +42,7 @@ def load_task_schema(schema_name): # Set 'directed' to True to import JSON schema as directed graph template_graph = GraphAxis(directed=True) - task_schema = pkg_resources.resource_filename('lie_workflow', '/schemas/endpoints/{0}'.format(schema_name)) + task_schema = pkg_resources.resource_filename('mdstudio_workflow', '/schemas/endpoints/{0}'.format(schema_name)) task_template = read_json_schema(task_schema, graph=template_graph, exclude_args=['title', 'description', 'schema_label']) task_node = task_template.query_nodes(key='task') @@ -259,7 +259,7 @@ def get_input(self, **kwargs): connected to it. The latter may be post-processed selecting and transforming data based on edge definitions. - lie_workflows are dynamic and therefore the `get_input` and `get_output` + mdstudio_workflows are dynamic and therefore the `get_input` and `get_output` methods are always called even if input/output was previously stored locally. diff --git a/lie_workflow/workflow_task_types/task_loop_type.py b/mdstudio_workflow/workflow_task_types/task_loop_type.py similarity index 97% rename from lie_workflow/workflow_task_types/task_loop_type.py rename to mdstudio_workflow/workflow_task_types/task_loop_type.py index f29007d..6597537 100644 --- a/lie_workflow/workflow_task_types/task_loop_type.py +++ b/mdstudio_workflow/workflow_task_types/task_loop_type.py @@ -8,7 +8,7 @@ from graphit.graph_utils.graph_utilities import edges_parent_to_subgraph from graphit.graph_combinatorial.graph_split_join_operations import graph_join -from lie_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema, edge_select_transform +from mdstudio_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema, edge_select_transform # Set twisted logger from twisted.logger import Logger diff --git a/lie_workflow/workflow_task_types/task_python_type.py b/mdstudio_workflow/workflow_task_types/task_python_type.py similarity index 98% rename from lie_workflow/workflow_task_types/task_python_type.py rename to mdstudio_workflow/workflow_task_types/task_python_type.py index cd8811c..29f286b 100644 --- a/lie_workflow/workflow_task_types/task_python_type.py +++ b/mdstudio_workflow/workflow_task_types/task_python_type.py @@ -11,7 +11,7 @@ from graphit.graph_mixin import NodeTools from graphit.graph_combinatorial.graph_split_join_operations import graph_join -from lie_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema +from mdstudio_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema # Set twisted logger from twisted.logger import Logger diff --git a/lie_workflow/workflow_task_types/task_wamp_type.py b/mdstudio_workflow/workflow_task_types/task_wamp_type.py similarity index 99% rename from lie_workflow/workflow_task_types/task_wamp_type.py rename to mdstudio_workflow/workflow_task_types/task_wamp_type.py index 44c07e4..9caf185 100644 --- a/lie_workflow/workflow_task_types/task_wamp_type.py +++ b/mdstudio_workflow/workflow_task_types/task_wamp_type.py @@ -22,8 +22,8 @@ from graphit.graph_io.io_jsonschema_format import read_json_schema from graphit.graph_io.io_pydata_format import write_pydata -from lie_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema -from lie_workflow.workflow_common import is_file, WorkflowError +from mdstudio_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema +from mdstudio_workflow.workflow_common import is_file, WorkflowError # Set twisted logger logging = Logger() @@ -469,7 +469,7 @@ def get_input(self, **kwargs): param_dict = write_pydata(request) # Remove all 'value' parameters with value None. - # TODO: These are left overs from lie_graph. + # TODO: These are left overs from graphit. def recursive_remove_none(d): for k, v in d.items():