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Merge pull request #191 from simleo/add_action
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Add method to add actions to the crate
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elichad authored Sep 10, 2024
2 parents 1419ddc + 7ca4ebc commit 352deab
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16 changes: 16 additions & 0 deletions rocrate/rocrate.py
Original file line number Diff line number Diff line change
Expand Up @@ -556,6 +556,22 @@ def add_test_definition(
self.metadata.extra_terms.update(TESTING_EXTRA_TERMS)
return definition

def add_action(self, instrument, identifier=None, object=None, result=None, properties=None):
if properties is None:
properties = {}
if "@type" not in properties:
properties["@type"] = "CreateAction"
action = self.add(ContextEntity(self, identifier, properties=properties))
action["instrument"] = instrument
if "name" not in properties:
action.name = action.id.lstrip("#")
if object:
action["object"] = object
if result:
action["result"] = result
self.root_dataset.append_to("mentions", action)
return action

def add_jsonld(self, jsonld):
"""Add a JSON-LD dictionary as a contextual entity to the RO-Crate.
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79 changes: 79 additions & 0 deletions test/test_wrroc.py
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@@ -0,0 +1,79 @@
# Copyright 2019-2024 The University of Manchester, UK
# Copyright 2020-2024 Vlaams Instituut voor Biotechnologie (VIB), BE
# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from rocrate.rocrate import ROCrate
from rocrate.model import ContextEntity, SoftwareApplication


def test_add_action(tmpdir):
crate = ROCrate()
instrument = SoftwareApplication(crate)
crate.add(instrument)
f_in_name = "f_in"
f_in_path = tmpdir / f_in_name
with open(f_in_path, "wt") as f:
f.write("IN\n")
f_in = crate.add_file(f_in_path)
f_out_name = "f_out"
f_out_path = tmpdir / f_out_name
with open(f_out_path, "wt") as f:
f.write("OUT\n")
f_out = crate.add_file(f_out_path)
param = crate.add(ContextEntity(crate, "#param", properties={
"@type": "PropertyValue",
"name": "param_name",
"value": "param_value",
}))
create_action = crate.add_action(
instrument,
object=[f_in, param],
result=[f_out],
properties={
"name": f"Run 1 of {instrument.id}",
"startTime": "2018-10-25T15:46:35.211153",
"endTime": "2018-10-25T15:46:43.020168",
}
)
assert create_action.type == "CreateAction"
create_actions = crate.get_by_type("CreateAction")
assert crate.root_dataset.get("mentions") == create_actions
assert create_actions == [create_action]
assert create_action.get("instrument") is instrument
assert create_action.get("object") == [f_in, param]
assert create_action.get("result") == [f_out]
assert create_action.get("name") == f"Run 1 of {instrument.id}"
assert create_action.get("startTime") == "2018-10-25T15:46:35.211153"
assert create_action.get("endTime") == "2018-10-25T15:46:43.020168"

activate_action = crate.add_action(
instrument,
object=[f_out],
properties={
"@type": "ActivateAction",
"name": f"Run 2 of {instrument.id}",
"endTime": "2018-10-25T16:48:41.021563",
}
)
assert activate_action.type == "ActivateAction"
assert crate.root_dataset.get("mentions") == [create_action, activate_action]
assert activate_action.get("instrument") is instrument
assert activate_action.get("object") == [f_out]
assert "result" not in activate_action
assert activate_action.get("name") == f"Run 2 of {instrument.id}"
assert activate_action.get("endTime") == "2018-10-25T16:48:41.021563"

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