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Merged in jmchilton/galaxy-central-fork-1 (pull request #621)

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Workflow API: Replace preferred usage terminology in the API (s/usage/invocation)
This commit is contained in:
John Chilton
2015-01-05 15:59:02 -05:00
parent 630287500d ec62c5417c
commit 0e597573d9
2 changed files with 83 additions and 34 deletions
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lib/galaxy/webapps/galaxy/api/workflows.py
+29 -28
View File
@@ -372,9 +372,9 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHis
return item
@expose_api
def workflow_request( self, trans, workflow_id, payload, **kwd ):
def invoke( self, trans, workflow_id, payload, **kwd ):
"""
POST /api/workflows/{encoded_workflow_id}/usage
POST /api/workflows/{encoded_workflow_id}/invocations
Schedule the workflow specified by `workflow_id` to run.
"""
@@ -398,10 +398,11 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHis
return self.encode_all_ids( trans, workflow_invocation.to_dict(), recursive=True )
@expose_api
def workflow_usage(self, trans, workflow_id, **kwd):
def index_invocations(self, trans, workflow_id, **kwd):
"""
GET /api/workflows/{workflow_id}/usage
Get the list of the workflow usage
GET /api/workflows/{workflow_id}/invocations
Get the list of the workflow invocations
:param workflow_id: the workflow id (required)
:type workflow_id: str
@@ -416,53 +417,53 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHis
return out
@expose_api
def workflow_usage_contents(self, trans, workflow_id, usage_id, **kwd):
def show_invocation(self, trans, workflow_id, invocation_id, **kwd):
"""
GET /api/workflows/{workflow_id}/usage/{usage_id}
Get detailed description of workflow usage
GET /api/workflows/{workflow_id}/invocation/{invocation_id}
Get detailed description of workflow invocation
:param workflow_id: the workflow id (required)
:type workflow_id: str
:param workflow_id: the workflow id (required)
:type workflow_id: str
:param usage_id: the usage id (required)
:type usage_id: str
:param invocation_id: the invocation id (required)
:type invocation_id: str
:raises: exceptions.MessageException, exceptions.ObjectNotFound
"""
decoded_workflow_invocation_id = self.__decode_id( trans, usage_id )
decoded_workflow_invocation_id = self.__decode_id( trans, invocation_id )
workflow_invocation = self.workflow_manager.get_invocation( trans, decoded_workflow_invocation_id )
if workflow_invocation:
return self.__encode_invocation( trans, workflow_invocation )
return None
@expose_api
def cancel_workflow_invocation(self, trans, workflow_id, usage_id, **kwd):
def cancel_invocation(self, trans, workflow_id, invocation_id, **kwd):
"""
DELETE /api/workflows/{workflow_id}/usage/{usage_id}
DELETE /api/workflows/{workflow_id}/invocation/{invocation_id}
Cancel the specified workflow invocation.
:param workflow_id: the workflow id (required)
:type workflow_id: str
:param usage_id: the usage id (required)
:type usage_id: str
:param invocation_id: the usage id (required)
:type invocation_id: str
:raises: exceptions.MessageException, exceptions.ObjectNotFound
"""
decoded_workflow_invocation_id = self.__decode_id( trans, usage_id )
decoded_workflow_invocation_id = self.__decode_id( trans, invocation_id )
workflow_invocation = self.workflow_manager.cancel_invocation( trans, decoded_workflow_invocation_id )
return self.__encode_invocation( trans, workflow_invocation )
@expose_api
def workflow_invocation_step(self, trans, workflow_id, usage_id, step_id, **kwd):
def invocation_step(self, trans, workflow_id, invocation_id, step_id, **kwd):
"""
GET /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}
GET /api/workflows/{workflow_id}/invocation/{invocation_id}/steps/{step_id}
:param workflow_id: the workflow id (required)
:type workflow_id: str
:param workflow_id: the workflow id (required)
:type workflow_id: str
:param usage_id: the usage id (required)
:type usage_id: str
:param invocation_id: the invocation id (required)
:type invocation_id: str
:param step_id: encoded id of the WorkflowInvocationStep (required)
:type step_id: str
@@ -480,9 +481,9 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHis
return self.__encode_invocation_step( trans, invocation_step )
@expose_api
def workflow_invocation_step_update(self, trans, workflow_id, usage_id, step_id, payload, **kwd):
def update_invocation_step(self, trans, workflow_id, invocation_id, step_id, payload, **kwd):
"""
PUT /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}
PUT /api/workflows/{workflow_id}/invocation/{invocation_id}/steps/{step_id}
Update state of running workflow step invocation - still very nebulous
but this would be for stuff like confirming paused steps can proceed
etc....
@@ -491,8 +492,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHis
:param workflow_id: the workflow id (required)
:type workflow_id: str
:param usage_id: the usage id (required)
:type usage_id: str
:param invocation_id: the usage id (required)
:type invocation_id: str
:param step_id: encoded id of the WorkflowInvocationStep (required)
:type step_id: str
lib/galaxy/webapps/galaxy/buildapp.py
+54 -6
View File
@@ -227,14 +227,62 @@ def populate_api_routes( webapp, app ):
webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) )
# Deprecated in favor of POST /api/workflows with shared_workflow_id in payload.
webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) )
webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET']))
webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET']))
webapp.mapper.connect( 'cancel_workflow_invocation', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='cancel_workflow_invocation', conditions=dict(method=['DELETE']))
webapp.mapper.connect( 'workflow_invocation_step', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step', conditions=dict(method=['GET']))
webapp.mapper.connect( 'workflow_invocation_step_update', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step_update', conditions=dict(method=['PUT']))
# API refers to usages and invocations - these mean the same thing but the
# usage routes should be considered deprecated.
invoke_names = {
"invocations": "",
"usage": "_deprecated",
}
for noun, suffix in invoke_names.iteritems():
name = "%s%s" % (noun, suffix)
webapp.mapper.connect(
'list_workflow_%s' % name,
'/api/workflows/{workflow_id}/%s' % noun,
controller='workflows',
action='index_invocations',
conditions=dict(method=['GET'])
)
webapp.mapper.connect( 'workflow_request', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_request', conditions=dict( method=['POST'] ) )
webapp.mapper.connect(
'workflow_%s_contents' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}' % noun,
controller='workflows',
action='show_invocation',
conditions=dict(method=['GET'])
)
webapp.mapper.connect(
'cancel_workflow_%s' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}' % noun,
controller='workflows',
action='cancel_invocation',
conditions=dict(method=['DELETE'])
)
webapp.mapper.connect(
'workflow_%s_step' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun,
controller='workflows',
action='invocation_step',
conditions=dict(method=['GET'])
)
webapp.mapper.connect(
'workflow_%s_step_update' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun,
controller='workflows',
action='update_invocation_step',
conditions=dict(method=['PUT'])
)
webapp.mapper.connect(
'workflow_%s' % name,
'/api/workflows/{workflow_id}/%s' % noun,
controller='workflows',
action='invoke',
conditions=dict( method=['POST'] )
)
# ============================
# ===== AUTHENTICATE API =====
# ============================