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{"receipt_id":"agent1-2","seq":2,"branch_id":"agent1","kind":"command","cmd":"grep -n \"test_entity_in_properties\" test/test_model.py","path":null,"exit_code":0,"stdout_tail":"518:def test_entity_in_properties(tmpdir):\n","stderr_tail":"","stdout_sha256":"d2063bf2555dac9a19f1e220b4301e01b429316fea66a9d297cca5bd9b5109c4","log_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/logs/agent1/agent1-2.log","tree_digest":null,"tree_download_s":null,"started_at":"2026-10-03T17:49:04.508895Z","duration_s":0.002956,"timed_out":false,"image_before":"dff22d89-f125-4275-8509-dff59fcf1321","image_after":"4f0130c2-6468-470d-86ca-925e8e128320","junit":null,"diff":null,"patch_sha256":null,"dropped_paths":[],"snapshot_sha":null}
{"receipt_id":"agent1-3","seq":3,"branch_id":"agent1","kind":"write","cmd":"/opt/receipts-a5374cfe06f7479695c0a0fa8e37965f/bin/busybox sh -c 'mkdir -p /ro-crate-py/rocrate/model && cp /opt/receipts-a5374cfe06f7479695c0a0fa8e37965f/incoming/3820ea184a0e1cf651bcd5efa34bd3ae848458c79dacdea374015c4ece34fe26 /ro-crate-py/rocrate/model/entity.py'","path":"rocrate/model/entity.py","exit_code":0,"stdout_tail":"","stderr_tail":"","stdout_sha256":"3820ea184a0e1cf651bcd5efa34bd3ae848458c79dacdea374015c4ece34fe26","log_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/logs/agent1/agent1-3.log","tree_digest":null,"tree_download_s":null,"started_at":"2026-10-03T17:49:10.854822Z","duration_s":0.0050550000000000005,"timed_out":false,"image_before":"4f0130c2-6468-470d-86ca-925e8e128320","image_after":"0ff5e8fc-604d-470b-b79d-bbce6c89462f","junit":null,"diff":null,"patch_sha256":null,"dropped_paths":[],"snapshot_sha":null}
{"receipt_id":"agent1-4","seq":4,"branch_id":"agent1","kind":"command","cmd":"/opt/receipts-4aed21f8d81c48629274f4dd05798937/bin/busybox mkdir -p /opt/receipts/reports && python -I /opt/receipts-4aed21f8d81c48629274f4dd05798937/receipts_pytest.py test/test_model.py::test_entity_in_properties -v -o junit_family=xunit1 -p no:cacheprovider -rA --continue-on-collection-errors --junitxml=/opt/receipts/reports/agent1-4.xml","path":null,"exit_code":1,"stdout_tail":"============================= test session starts ==============================\nplatform linux -- Python 3.10.19, pytest-9.0.2, pluggy-1.6.0 -- /usr/local/bin/python\nrootdir: /ro-crate-py\nconfigfile: setup.cfg\ncollecting ... collected 1 item\n\ntest/test_model.py::test_entity_in_properties FAILED                     [100%]\n\n=================================== FAILURES ===================================\n__________________________ test_entity_in_properties ___________________________\n\ntmpdir = PosixPath('/tmp/pytest-of-root/pytest-2/test_entity_in_properties0')\n\n    def test_entity_in_properties(tmpdir):\n        file_id = \"data.csv\"\n        file_path = tmpdir / file_id\n        with open(file_path, \"wt\") as fout:\n            fout.write(\"DATA\\n\")\n        crate = ROCrate()\n        alice_id = \"https://orcid.org/0000-0000-0000-0000\"\n        bob_id = \"https://orcid.org/0000-0000-0000-0001\"\n        alice = crate.add(Person(crate, alice_id, properties={\n            \"name\": \"Alice Doe\",\n            \"affiliation\": \"University of Flatland\",\n        }))\n        bob = crate.add(Person(crate, bob_id, properties={\n            \"name\": \"Bob Doe\",\n            \"affiliation\": \"University of Flatland\",\n        }))\n        data = crate.add_file(file_path, properties={\n            \"name\": \"Data file\",\n            \"encodingFormat\": \"text/csv\",\n            \"author\": [alice, bob],\n        })\n        authors = data[\"author\"]\n        assert len(authors) == 2\n        assert authors[0] is alice\n        assert authors[1] is bob\n    \n>       book = crate.add(ContextEntity(crate, \"#44cats\", properties={\n            \"@type\": \"Book\",\n            \"name\": \"44 Cats\",\n            \"author\": alice,\n        }))\n\ntest/test_model.py:544: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \nrocrate/model/contextentity.py:35: in __init__\n    super(ContextEntity, self).__init__(crate, identifier, properties)\nrocrate/model/entity.py:40: in __init__\n    self[key] = value\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\nself = <#44cats Thing>, key = '@type', value = 'Book'\n\n    def __setitem__(self, key: str, value):\n        if key.startswith(\"@\"):\n>           raise KeyError(f\"cannot set '{key}'\")\nE           KeyError: \"cannot set '@type'\"\n\nrocrate/model/entity.py:100: KeyError\n------------ generated xml file: /opt/receipts/reports/agent1-4.xml ------------\n=========================== short test summary info ============================\nFAILED test/test_model.py::test_entity_in_properties - KeyError: \"cannot set ...\n============================== 1 failed in 0.11s ===============================\n","stderr_tail":"","stdout_sha256":"9f9961d6d84aa7f9f6a748eda37797b5d48f809bbe50d0bdf188db7b0748b93a","log_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/logs/agent1/agent1-4.log","tree_digest":"4b597ac989b12b34dd95633163dda871be07824ff4c206cebeb30e41657d3417","tree_download_s":2.614628833020106,"started_at":"2026-10-03T17:49:13.279039Z","duration_s":0.856902,"timed_out":false,"image_before":"0ff5e8fc-604d-470b-b79d-bbce6c89462f","image_after":"f0fe00cb-6652-4760-b680-5f2dd25c04e0","junit":{"passed":[],"failed":["test/test_model.py::test_entity_in_properties"],"errors":[],"skipped":[],"collection_errors":[],"failure_text":{"test/test_model.py::test_entity_in_properties":"KeyError: \"cannot set '@type'\"\ntmpdir = PosixPath('/tmp/pytest-of-root/pytest-2/test_entity_in_properties0')\n\n    def test_entity_in_properties(tmpdir):\n        file_id = \"data.csv\"\n        file_path = tmpdir / file_id\n        with open(file_path, \"wt\") as fout:\n            fout.write(\"DATA\\n\")\n        crate = ROCrate()\n        alice_id = \"https://orcid.org/0000-0000-0000-0000\"\n        bob_id = \"https://orcid.org/0000-0000-0000-0001\"\n        alice = crate.add(Person(crate, alice_id, properties={\n            \"name\": \"Alice Doe\",\n            \"affiliation\": \"University of Flatland\",\n        }))\n        bob = crate.add(Person(crate, bob_id, properties={\n            \"name\": \"Bob Doe\",\n            \"affiliation\": \"University of Flatland\",\n        }))\n        data = crate.add_file(file_path, properties={\n            \"name\": \"Data file\",\n            \"encodingFormat\": \"text/csv\",\n            \"author\": [alice, bob],\n        })\n        authors = data[\"author\"]\n        assert len(authors) == 2\n        assert authors[0] is alice\n        assert authors[1] is bob\n    \n>       book = crate.add(ContextEntity(crate, \"#44cats\", properties={\n            \"@type\": \"Book\",\n            \"name\": \"44 Cats\",\n            \"author\": alice,\n        }))\n\ntest/test_model.py:544: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \nrocrate/model/contextentity.py:35: in __init__\n    super(ContextEntity, self).__init__(crate, identifier, properties)\nrocrate/model/entity.py:40: in __init__\n    self[key] = value\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\nself = <#44cats Thing>, key = '@type', value = 'Book'\n\n    def __setitem__(self, key: str, value):\n        if key.startswith(\"@\"):\n>           raise KeyError(f\"cannot set '{key}'\")\nE           KeyError: \"cannot set '@type'\"\n\nrocrate/model/entity.py:100: KeyError"}},"diff":null,"patch_sha256":null,"dropped_paths":[],"snapshot_sha":null}
{"receipt_id":"agent1-5","seq":5,"branch_id":"agent1","kind":"write","cmd":"/opt/receipts-1c733aa0849d408c9a87c33583e93e08/bin/busybox sh -c 'mkdir -p /ro-crate-py/rocrate/model && cp /opt/receipts-1c733aa0849d408c9a87c33583e93e08/incoming/895d04cf48db14148a5c2468f9ae52256525053f18f34149ee27d45c9584303c /ro-crate-py/rocrate/model/entity.py'","path":"rocrate/model/entity.py","exit_code":0,"stdout_tail":"","stderr_tail":"","stdout_sha256":"895d04cf48db14148a5c2468f9ae52256525053f18f34149ee27d45c9584303c","log_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/logs/agent1/agent1-5.log","tree_digest":null,"tree_download_s":null,"started_at":"2026-10-03T17:49:21.580791Z","duration_s":0.004701,"timed_out":false,"image_before":"f0fe00cb-6652-4760-b680-5f2dd25c04e0","image_after":"4730bb46-2aaf-4cab-aa41-5fee66603035","junit":null,"diff":null,"patch_sha256":null,"dropped_paths":[],"snapshot_sha":null}
{"receipt_id":"agent1-6","seq":6,"branch_id":"agent1","kind":"command","cmd":"/opt/receipts-8beecd3e75a74eb8b11d20f33fddb807/bin/busybox mkdir -p /opt/receipts/reports && python -I /opt/receipts-8beecd3e75a74eb8b11d20f33fddb807/receipts_pytest.py test/test_model.py::test_entity_in_properties -v -o junit_family=xunit1 -p no:cacheprovider -rA --continue-on-collection-errors --junitxml=/opt/receipts/reports/agent1-6.xml","path":null,"exit_code":0,"stdout_tail":"============================= test session starts ==============================\nplatform linux -- Python 3.10.19, pytest-9.0.2, pluggy-1.6.0 -- /usr/local/bin/python\nrootdir: /ro-crate-py\nconfigfile: setup.cfg\ncollecting ... collected 1 item\n\ntest/test_model.py::test_entity_in_properties PASSED                     [100%]\n\n==================================== PASSES ====================================\n------------ generated xml file: /opt/receipts/reports/agent1-6.xml ------------\n=========================== short test summary info ============================\nPASSED test/test_model.py::test_entity_in_properties\n============================== 1 passed in 0.08s ===============================\n","stderr_tail":"","stdout_sha256":"288720ed3f3cde2f93d04d3a6912b69870786df38cb3f51d1722ed06a5f00892","log_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/logs/agent1/agent1-6.log","tree_digest":"d9d610563e781f8907ef084431e56aeadae3e3e491cad8df811f743b12ca0a9f","tree_download_s":2.8995487911161035,"started_at":"2026-10-03T17:49:24.028216Z","duration_s":0.8403970000000001,"timed_out":false,"image_before":"4730bb46-2aaf-4cab-aa41-5fee66603035","image_after":"db9c8c78-d5e0-43c2-85ec-8a067ce7e1c6","junit":{"passed":["test/test_model.py::test_entity_in_properties"],"failed":[],"errors":[],"skipped":[],"collection_errors":[],"failure_text":{}},"diff":null,"patch_sha256":null,"dropped_paths":[],"snapshot_sha":null}
{"receipt_id":"agent1-7","seq":7,"branch_id":"agent1","kind":"command","cmd":"/opt/receipts-bb2779218e824d6da49d97e98dab1f52/bin/busybox mkdir -p /opt/receipts/reports && python -I /opt/receipts-bb2779218e824d6da49d97e98dab1f52/receipts_pytest.py test/test_model.py --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning -o junit_family=xunit1 -p no:cacheprovider -rA --continue-on-collection-errors --junitxml=/opt/receipts/reports/agent1-7.xml","path":null,"exit_code":0,"stdout_tail":"============================= test session starts ==============================\ncollected 27 items\n\ntest/test_model.py ...........................                           [100%]\n\n==================================== PASSES ====================================\n------------ generated xml file: /opt/receipts/reports/agent1-7.xml ------------\n=========================== short test summary info ============================\nPASSED test/test_model.py::test_dereferencing\nPASSED test/test_model.py::test_dereferencing_equivalent_id[.foo]\nPASSED test/test_model.py::test_dereferencing_equivalent_id[foo.]\nPASSED test/test_model.py::test_dereferencing_equivalent_id[.foo/]\nPASSED test/test_model.py::test_dereferencing_equivalent_id[foo./]\nPASSED test/test_model.py::test_data_entities\nPASSED test/test_model.py::test_data_entities_perf\nPASSED test/test_model.py::test_remote_data_entities\nPASSED test/test_model.py::test_bad_data_entities\nPASSED test/test_model.py::test_contextual_entities\nPASSED test/test_model.py::test_contextual_entities_hash\nPASSED test/test_model.py::test_properties\nPASSED test/test_model.py::test_uuid\nPASSED test/test_model.py::test_update\nPASSED test/test_model.py::test_delete\nPASSED test/test_model.py::test_delete_refs\nPASSED test/test_model.py::test_delete_by_id\nPASSED test/test_model.py::test_self_delete\nPASSED test/test_model.py::test_entity_as_mapping\nPASSED test/test_model.py::test_wf_types\nPASSED test/test_model.py::test_append_to[False]\nPASSED test/test_model.py::test_append_to[True]\nPASSED test/test_model.py::test_get_by_type\nPASSED test/test_model.py::test_context\nPASSED test/test_model.py::test_add_no_duplicates\nPASSED test/test_model.py::test_immutable_id\nPASSED test/test_model.py::test_entity_in_properties\n============================== 27 passed in 0.43s ==============================\n","stderr_tail":"","stdout_sha256":"6aa755a47dd844868d2dcea4a01a0926d2564391eee84d9c4d671c6215c7c7c5","log_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/logs/agent1/agent1-7.log","tree_digest":"d9d610563e781f8907ef084431e56aeadae3e3e491cad8df811f743b12ca0a9f","tree_download_s":2.543890875065699,"started_at":"2026-10-03T17:49:31.002017Z","duration_s":0.984306,"timed_out":false,"image_before":"db9c8c78-d5e0-43c2-85ec-8a067ce7e1c6","image_after":"0aa549d9-e22c-45b2-8445-4f6950905ce1","junit":{"passed":["test/test_model.py::test_dereferencing","test/test_model.py::test_dereferencing_equivalent_id[.foo]","test/test_model.py::test_dereferencing_equivalent_id[foo.]","test/test_model.py::test_dereferencing_equivalent_id[.foo/]","test/test_model.py::test_dereferencing_equivalent_id[foo./]","test/test_model.py::test_data_entities","test/test_model.py::test_data_entities_perf","test/test_model.py::test_remote_data_entities","test/test_model.py::test_bad_data_entities","test/test_model.py::test_contextual_entities","test/test_model.py::test_contextual_entities_hash","test/test_model.py::test_properties","test/test_model.py::test_uuid","test/test_model.py::test_update","test/test_model.py::test_delete","test/test_model.py::test_delete_refs","test/test_model.py::test_delete_by_id","test/test_model.py::test_self_delete","test/test_model.py::test_entity_as_mapping","test/test_model.py::test_wf_types","test/test_model.py::test_append_to[False]","test/test_model.py::test_append_to[True]","test/test_model.py::test_get_by_type","test/test_model.py::test_context","test/test_model.py::test_add_no_duplicates","test/test_model.py::test_immutable_id","test/test_model.py::test_entity_in_properties"],"failed":[],"errors":[],"skipped":[],"collection_errors":[],"failure_text":{}},"diff":null,"patch_sha256":null,"dropped_paths":[],"snapshot_sha":null}
{"receipt_id":"agent1-8","seq":8,"branch_id":"agent1","kind":"write","cmd":"/opt/receipts-87eae704aec24ab7bba66b0645953402/bin/busybox sh -c 'mkdir -p /ro-crate-py && cp /opt/receipts-87eae704aec24ab7bba66b0645953402/incoming/efd7f2a7e8ffe1196026e9c0c8e4c27f6c34225d2161217963f01413e625fe20 /ro-crate-py/test_example.py'","path":"test_example.py","exit_code":0,"stdout_tail":"","stderr_tail":"","stdout_sha256":"efd7f2a7e8ffe1196026e9c0c8e4c27f6c34225d2161217963f01413e625fe20","log_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/logs/agent1/agent1-8.log","tree_digest":null,"tree_download_s":null,"started_at":"2026-10-03T17:49:41.206670Z","duration_s":0.005154000000000001,"timed_out":false,"image_before":"0aa549d9-e22c-45b2-8445-4f6950905ce1","image_after":"c7d6ce6e-3875-4a4f-b84a-48795d103106","junit":null,"diff":null,"patch_sha256":null,"dropped_paths":[],"snapshot_sha":null}
{"receipt_id":"agent1-9","seq":9,"branch_id":"agent1","kind":"command","cmd":"cd /ro-crate-py && python test_example.py","path":null,"exit_code":0,"stdout_tail":"Test successful - no error occurred!\nData entity author count: 2\nFirst author is Alice: True\nSecond author is Bob: True\n","stderr_tail":"","stdout_sha256":"34d99df57b4cab4d8f7ff1b3ffc8652d6aa353b3071c08e2f54f680e7269d92f","log_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/logs/agent1/agent1-9.log","tree_digest":null,"tree_download_s":null,"started_at":"2026-10-03T17:49:43.305356Z","duration_s":0.167502,"timed_out":false,"image_before":"c7d6ce6e-3875-4a4f-b84a-48795d103106","image_after":"02f62738-68e4-44b7-ac8c-9a14958c37ca","junit":null,"diff":null,"patch_sha256":null,"dropped_paths":[],"snapshot_sha":null}
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{"receipt_id":"agent1-11","seq":11,"branch_id":"agent1","kind":"diff","cmd":"compute patch in executor staging agent1-d27bb9635ea2492a9dcac887eaedce27: /opt/homebrew/Cellar/git/2.53.0/bin/git -c core.hooksPath=/dev/null -c core.attributesFile=/dev/null -c diff.external= -c core.quotePath=false add -A && /opt/homebrew/Cellar/git/2.53.0/bin/git -c core.hooksPath=/dev/null -c core.attributesFile=/dev/null -c diff.external= -c core.quotePath=false diff --cached --binary --no-ext-diff --no-textconv --no-renames ff027c7259db67c828a10567a821d55cfffd8f55","path":null,"exit_code":0,"stdout_tail":"diff --git a/rocrate/model/entity.py b/rocrate/model/entity.py\nindex c18096e..c07bc3d 100644\n--- a/rocrate/model/entity.py\n+++ b/rocrate/model/entity.py\n@@ -34,12 +34,13 @@ class Entity(MutableMapping):\n             self.__id = self.format_id(identifier)\n         else:\n             self.__id = f\"#{uuid.uuid4()}\"\n+        self._jsonld = self._empty()\n         if properties:\n-            empty = self._empty()\n-            empty.update(properties)\n-            self._jsonld = empty\n-        else:\n-            self._jsonld = self._empty()\n+            for key, value in properties.items():\n+                if key.startswith(\"@\"):\n+                    self._jsonld[key] = value\n+                else:\n+                    self[key] = value\n \n     @property\n     def id(self):\n","stderr_tail":"","stdout_sha256":"293a099712d64756141040e3a42cbaaefce617df27a739fe2d3043d592f9572c","log_path":null,"tree_digest":"d9d610563e781f8907ef084431e56aeadae3e3e491cad8df811f743b12ca0a9f","tree_download_s":1.8830838750582188,"started_at":"2026-10-03T17:49:54.109338Z","duration_s":0.030498999869450927,"timed_out":false,"image_before":"2672c4e1-7c42-42c7-af6d-9c57870e0241","image_after":"2672c4e1-7c42-42c7-af6d-9c57870e0241","junit":null,"diff":{"files":[{"path":"rocrate/model/entity.py","added":6,"deleted":5,"category":"source","status":"modified"}],"patch_sha256":"293a099712d64756141040e3a42cbaaefce617df27a739fe2d3043d592f9572c","patch_path":"~/dev/nebius-hackathon/pilot/v2-P/researchobject__ro-crate-py-192/runs/pilot-researchobject__ro-crate-py-192-ed0e4ed903/artifacts/agent1/agent1-11.patch"},"patch_sha256":"293a099712d64756141040e3a42cbaaefce617df27a739fe2d3043d592f9572c","dropped_paths":[],"snapshot_sha":"ff027c7259db67c828a10567a821d55cfffd8f55"}