def to_dict(self, input_connections):
# We are to the point where we need a content id for this. We got
# figure that out - short term we can load everything up as an
# in-memory tool and reference by the JSONLD ID I think. So workflow
# proxy should force the loading of a tool.
tool_proxy = cwl_tool_object_to_proxy(self.tool_references()[0])
from galaxy.tools.hash import build_tool_hash
tool_hash = build_tool_hash(tool_proxy.to_persistent_representation())
# We need to stub out null entries for things getting replaced by
# connections. This doesn't seem ideal - consider just making Galaxy
# handle this.
tool_state = {}
for input_name in input_connections.keys():
tool_state[input_name] = None
outputs = self.galaxy_workflow_outputs_list()
return {
"id": self._index,
"tool_hash": tool_hash,
"label": self.label,
"position": {"left": 0, "top": 0},
"type": "tool",
"annotation": self._workflow_proxy.cwl_object_to_annotation(self._step.tool),
"input_connections": input_connections,
"inputs": self.inputs_to_dicts(),
"workflow_outputs": outputs,
}
def to_dict(self, input_connections):
# We are to the point where we need a content id for this. We got
# figure that out - short term we can load everything up as an
# in-memory tool and reference by the JSONLD ID I think. So workflow
# proxy should force the loading of a tool.
tool_proxy = cwl_tool_object_to_proxy(self.tool_references()[0])
tool_hash = build_tool_hash(tool_proxy.to_persistent_representation())
# We need to stub out null entries for things getting replaced by
# connections. This doesn't seem ideal - consider just making Galaxy
# handle this.
tool_state = {}
for input_name in input_connections.keys():
tool_state[input_name] = None
outputs = self.galaxy_workflow_outputs_list()
return {
"id": self._index,
"tool_hash": tool_hash,
"label": self.label,
"position": {"left": 0, "top": 0},
"type": "tool",
"annotation": self._workflow_proxy.cwl_object_to_annotation(self._step.tool),
"input_connections": input_connections,
"inputs": self.inputs_to_dicts(),
"workflow_outputs": outputs,
}
def galaxy_id(self):
raw_id = self.id
tool_id = None
# don't reduce "search.cwl#index" to search
if raw_id and "#" not in raw_id:
tool_id = os.path.splitext(os.path.basename(raw_id))[0]
if not tool_id:
from galaxy.tools.hash import build_tool_hash
tool_id = build_tool_hash(self.to_persistent_representation())
assert tool_id
return tool_id
def galaxy_id(self):
raw_id = self.id
tool_id = None
# don't reduce "search.cwl#index" to search
if raw_id and "#" not in raw_id:
tool_id = os.path.splitext(os.path.basename(raw_id))[0]
if not tool_id:
from galaxy.tools.hash import build_tool_hash
tool_id = build_tool_hash(self.to_persistent_representation())
assert tool_id
return tool_id
def galaxy_id(self):
raw_id = self.id
if raw_id:
return os.path.splitext(os.path.basename(raw_id))[0]
else:
return build_tool_hash(self.to_persistent_representation())
