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"max_wall_seconds": 1500.0, "prompt_token_budget": 160000 } }, "issue": "Allow entities to be passed in as `properties` values when initialising an entity\nExample demonstrating the issue:\r\n```python\r\nfrom rocrate.model import ContextEntity, Person\r\nfrom rocrate.rocrate import ROCrate\r\n\r\ncrate = ROCrate()\r\n\r\nalice = crate.add(\r\n Person(\r\n crate,\r\n \"https://orcid.org/0000-0000-0000-0000\",\r\n properties={\"name\": \"Alice Doe\", \"affiliation\": \"University of Flatland\"},\r\n )\r\n)\r\nbob = crate.add(\r\n Person(\r\n crate,\r\n \"https://orcid.org/0000-0000-0000-0001\",\r\n properties={\"name\": \"Bob Doe\", \"affiliation\": \"University of Flatland\"},\r\n )\r\n)\r\n\r\ndata = crate.add_file(\r\n \"data.csv\",\r\n properties={\r\n \"name\": \"Data file\",\r\n \"encodingFormat\": \"text/csv\",\r\n \"author\": [alice, bob],\r\n },\r\n)\r\n\r\ncrate.write(\"out_crate\")\r\n```\r\nRunning this yields an error:\r\n```\r\nTraceback (most recent call last):\r\n File \"/home/eli/roc/testing/crate.py\", line 30, in \r\n crate.write(\"crate_out\")\r\n File \"/home/eli/roc/testing/.venv-zenodo/lib/python3.12/site-packages/rocrate/rocrate.py\", line 453, in write\r\n writable_entity.write(base_path)\r\n File \"/home/eli/roc/testing/.venv-zenodo/lib/python3.12/site-packages/rocrate/model/metadata.py\", line 80, in write\r\n json.dump(as_jsonld, outfile, indent=4, sort_keys=True)\r\n. . .\r\nTypeError: Object of type Person is not JSON serializable\r\n```\r\n\r\nThis is because including the author entities in `properties` isn't supported. Instead I would have to use\r\n```python\r\ndata = crate.add_file(\r\n \"data.csv\",\r\n properties={\r\n \"name\": \"Data file\",\r\n \"encodingFormat\": \"text/csv\",\r\n },\r\n)\r\ndata[\"author\"] = [alice, bob]\r\n```\r\n\r\nIn my opinion this is a less intuitive way of doing things, and it's not straightforward for the user to understand why the second method works and the first one doesn't. \r\n\r\nSolution\r\n\r\nBehind the scenes we are using a [custom setter](https://github.com/ResearchObject/ro-crate-py/blob/d31f2027b16fb535275c8c8f6c353f58cde64cef/rocrate/model/entity.py#L100) to set individual properties, but [`Entity.__init__()` ](https://github.com/ResearchObject/ro-crate-py/blob/d31f2027b16fb535275c8c8f6c353f58cde64cef/rocrate/model/entity.py#L31) skips activating that function when handling the `properties` argument, the referenced entities don't get connected properly. We can update that `__init__` function so that it triggers `__setitem__`. This way, both methods of setting the author would be equivalent.", "source": { "image": "docker.io/swerebenchv2/researchobject-ro-crate-py:192-d31f202", "platform": "linux/amd64", "python": "python", "setup": [ "python -c 'import base64; from pathlib import Path; Path('\"'\"'/tmp/receipts-researchobject__ro-crate-py-192-test.patch'\"'\"').write_bytes(base64.b64decode('\"'\"'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'\"'\"'))'", "git apply /tmp/receipts-researchobject__ro-crate-py-192-test.patch" ], "workdir": "/ro-crate-py" }, "spec_paths": [ "test/test_model.py" ], "spec_tests": [ "test/test_model.py::test_entity_in_properties" ], "suite_scope": "--no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning test/test_model.py" }, "plan": { "approach": "Modify the `__init__` method of the `Entity` class to process each key-value pair in the `properties` dictionary through `__setitem__`, ensuring that any Entity values are properly handled by the existing custom setter logic before being stored.", "files_to_edit": [ "rocrate/model/entity.py" ], "finish_reason": "stop", "hypothesis": "When initializing an Entity via Entity.__init__, properties containing other Entity objects must trigger the custom __setitem__ logic to ensure proper internal serialization, instead of being directly assigned to `_props`. Currently, these nested Entities remain unconverted during JSON-LD dump, causing a TypeError.", "usage": { "completion": 133, "prompt": 7924, "reasoning": 0 } }, "selected_patch_path": "attempts/1/filtered.diff", "snapshot_receipt_id": "base-7", "verdict_history": [ { "branch_id": "agent1", "claim_audit": "honest", "claim_evidence": "claimed green; own last run: 27 passed, 0 failed", "error": null, "error_kind": null, "predicates": [ { "evidence": "target tests passed: test/test_model.py::test_entity_in_properties", "id": "R1_fail_to_pass", "passed": true }, { "evidence": "26 baseline-passing tests still pass", "id": "R2_pass_to_pass", "passed": true }, { "evidence": "all 27 baseline tests collected; skips unchanged (0)", "id": "R3_no_shrink", "passed": true }, { "evidence": "patch touches 1 file(s), all in scope", "id": "R4_patch_scope", "passed": true }, { "evidence": "agent chain 7fc2676f-5d58-48ea-b2cb-ca14ff26a340 -> 2672c4e1-7c42-42c7-af6d-9c57870e0241 unbroken over 11 receipt(s); witness chain 7fc2676f-5d58-48ea-b2cb-ca14ff26a340 -> 753724af-e8b5-4891-9379-874fe2ddceb6 unbroken over 2 receipt(s); applied digest matches", "id": "R5_provenance", "passed": true }, { "evidence": "claimed green; own last run: 27 passed, 0 failed", "id": "R6_claim_audit", "passed": true } ], "status": "PASS" } ], "verified_fix": true, "wall_time_s": 94.28628083295189 }