researchobject__ro-crate-py-102

{
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  "filepath": "rocrate/model/entity.py",
  "content": "            return clsName\n        return \"Thing\"\n\n    def canonical_id(self):\n        return self.crate.resolve_id(self.id)\n\n    def __hash__(self):\n        return hash(self.canonical_id())\n\n    def _empty(self):\n        val = {\n            \"@id\": self.id,\n            \"@type\": self._default_type\n        }\n        return val\n\n    def __getitem__(self, key):\n        v = self._jsonld[key]\n        if isinstance(v, str) or key.startswith(\"@\"):\n            return v\n        values = v if isinstance(v, list) else [v]\n        deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\n        return deref_values if isinstance(v, list) else deref_values[0]\n\n    def __setitem__(self, key: str, value):\n        if key.startswith(\"@\"):\n            raise KeyError(f\"cannot set '{key}'\")\n        values = value if isinstance(value, list) else [value]\n        ref_values = [{\"@id\": _.id} if isinstance(_, Entity) else _ for _ in values]\n        self._jsonld[key] = ref_values if isinstance(value, list) else ref_values[0]\n\n    def __delitem__(self, key: str):\n        if key.startswith(\"@\"):\n            raise KeyError(f\"cannot delete '{key}'\")\n        del self._jsonld[key]\n\n    def popitem(self):\n        raise NotImplementedError\n\n    def clear(self):\n        raise NotImplementedError",
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{
  "status": "ok",
  "filepath": "rocrate/rocrate.py",
  "content": "#!/usr/bin/env python\n\n# Copyright 2019-2021 The University of Manchester, UK\n# Copyright 2020-2021 Vlaams Instituut voor Biotechnologie (VIB), BE\n# Copyright 2020-2021 Barcelona Supercomputing Center (BSC), ES\n# Copyright 2020-2021 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n#     http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, software\n# distributed under the License is distributed on an \"AS IS\" BASIS,\n# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n\nimport errno\nimport json\nimport os\nimport uuid\nimport zipfile\nimport atexit\nimport shutil\nimport tempfile\n\nfrom collections import OrderedDict\nfrom pathlib import Path\nfrom urllib.parse import urljoin\n\nfrom .model.contextentity import ContextEntity\nfrom .model.entity import Entity\nfrom .model.root_dataset import RootDataset\nfrom .model.data_entity import DataEntity\nfrom .model.file_or_dir import FileOrDir\nfrom .model.file import File\nfrom .model.dataset import Dataset\nfrom .model.metadata import Metadata, LegacyMetadata, TESTING_EXTRA_TERMS, metadata_class\nfrom .model.preview import Preview\nfrom .model.testdefinition import TestDefinition\nfrom .model.computationalworkflow import ComputationalWorkflow, galaxy_to_abstract_cwl\nfrom .model.computerlanguage import ComputerLanguage, get_lang\nfrom .model.testinstance import TestInstance\nfrom .model.testservice import TestService, get_service\nfrom .model.softwareapplication import SoftwareApplication, get_app, PLANEMO_DEFAULT_VERSION\nfrom .model.testsuite import TestSuite\n\nfrom .utils import is_url, subclasses, get_norm_value\n\n\ndef read_metadata(metadata_path):\n    \"\"\"\\\n    Read an RO-Crate metadata file.\n\n    Return a tuple of two elements: the context; a dictionary that maps entity\n    ids to the entities themselves.\n    \"\"\"\n    with open(metadata_path) as f:\n        metadata = json.load(f)\n    try:\n        context = metadata['@context']\n        graph = metadata['@graph']\n    except KeyError:\n        raise ValueError(f\"{metadata_path} must have a @context and a @graph\")\n    return context, {_[\"@id\"]: _ for _ in graph}\n\n\ndef pick_type(json_entity, type_map, fallback=None):\n    try:\n        t = json_entity[\"@type\"]\n    except KeyError:\n        raise ValueError(f'entity {json_entity[\"@id\"]!r} has no @type')\n    types = {_.strip() for _ in set(t if isinstance(t, list) else [t])}\n    for name, c in type_map.items():\n        if name in types:\n            return c\n    return fallback\n\n\nclass ROCrate():\n\n    def __init__(self, source=None, gen_preview=False, init=False):\n        self.__entity_map = {}\n        self.default_entities = []\n        self.data_entities = []\n        self.contextual_entities = []\n        # TODO: add this as @base in the context? At least when loading\n        # from zip\n        self.uuid = uuid.uuid4()\n        self.arcp_base_uri = f\"arcp://uuid,{self.uuid}/\"\n        self.preview = None\n        if gen_preview:\n            self.add(Preview(self))\n        if not source:\n            # create a new ro-crate\n            self.add(RootDataset(self), Metadata(self))\n        elif init:\n            self.__init_from_tree(source, gen_preview=gen_preview)\n        else:\n            source = self.__read(source, gen_preview=gen_preview)\n        # in the zip case, self.source is the extracted dir\n        self.source = source\n\n    def __init_from_tree(self, top_dir, gen_preview=False):\n        top_dir = Path(top_dir)\n        if not top_dir.is_dir():\n            raise NotADirectoryError(errno.ENOTDIR, f\"'{top_dir}': not a directory\")\n        self.add(RootDataset(self), Metadata(self))\n        for root, dirs, files in os.walk(top_dir):\n            root = Path(root)\n            for name in dirs:\n                source = root / name\n                self.add_dataset(source, source.relative_to(top_dir))\n            for name in files:\n                source = root / name\n                if source == top_dir / Metadata.BASENAME or source == top_dir / LegacyMetadata.BASENAME:\n                    continue\n                if source != top_dir / Preview.BASENAME:\n                    self.add_file(source, source.relative_to(top_dir))\n                elif not gen_preview:\n                    self.add(Preview(self, source))\n\n    def __read(self, source, gen_preview=False):\n        source = Path(source)\n        if not source.exists():\n            raise FileNotFoundError(errno.ENOENT, f\"'{source}' not found\")\n        if zipfile.is_zipfile(source):\n            zip_path = tempfile.mkdtemp(prefix=\"rocrate_\")\n            atexit.register(shutil.rmtree, zip_path)\n            with zipfile.ZipFile(source, \"r\") as zf:\n                zf.extractall(zip_path)\n            source = Path(zip_path)\n        metadata_path = source / Metadata.BASENAME\n        if not metadata_path.is_file():\n            metadata_path = source / LegacyMetadata.BASENAME\n        if not metadata_path.is_file():\n            raise ValueError(f\"Not a valid RO-Crate: missing {Metadata.BASENAME}\")\n        _, entities = read_metadata(metadata_path)\n        self.__read_data_entities(entities, source, gen_preview)\n        self.__read_contextual_entities(entities)\n        return source\n\n    def find_root_entity_id(self, entities):\n        \"\"\"Find Metadata file and Root Data Entity in RO-Crate.\n\n        Returns a tuple of the @id identifiers (metadata, root)\n        \"\"\"\n        # Note that for all cases below we will deliberately",
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}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "/workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  import pkg_resources\nTraceback (most recent call last):\n  File \"<stdin>\", line 5, in <module>\nTypeError: Entity.__init__() got an unexpected keyword argument 'id'\n",
  "details": {
    "stdout": "",
    "stderr": "/workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  import pkg_resources\nTraceback (most recent call last):\n  File \"<stdin>\", line 5, in <module>\nTypeError: Entity.__init__() got an unexpected keyword argument 'id'\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "filepath": "rocrate/model/entity.py",
  "content": "#!/usr/bin/env python\n\n# Copyright 2019-2021 The University of Manchester, UK\n# Copyright 2020-2021 Vlaams Instituut voor Biotechnologie (VIB), BE\n# Copyright 2020-2021 Barcelona Supercomputing Center (BSC), ES\n# Copyright 2020-2021 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n#     http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, software\n# distributed under the License is distributed on an \"AS IS\" BASIS,\n# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n\nimport uuid\nfrom collections.abc import MutableMapping\n\nfrom dateutil.parser import isoparse\nfrom .. import vocabs\n\n\nclass Entity(MutableMapping):\n\n    def __init__(self, crate, identifier=None, properties=None):\n        self.crate = crate\n        if identifier:\n            self.id = self.format_id(identifier)\n        else:\n            self.id = \"#%s\" % uuid.uuid4()\n        if properties:\n            empty = self._empty()\n            empty.update(properties)\n            self._jsonld = empty\n        else:\n            self._jsonld = self._empty()\n\n    # Format the given ID with rules appropriate for this type.\n    # For example, Dataset (directory) data entities SHOULD end with /\n    def format_id(self, identifier):\n        return str(identifier)\n\n    def __repr__(self):\n        return \"<%s %s>\" % (self.id, self.type)\n\n    def properties(self):\n        return self._jsonld\n\n    def as_jsonld(self):\n        return self._jsonld\n\n    @property\n    def _default_type(self):\n        clsName = self.__class__.__name__\n        if clsName in vocabs.RO_CRATE[\"@context\"]:\n            return clsName",
  "start_line": 1,
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  "total_lines": 141,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "Caught expected TypeError: 'NoneType' object is not subscriptable\n",
  "stderr": "/workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  import pkg_resources\n",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "341:    def dereference(self, entity_id, default=None):\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "rocrate/rocrate.py",
  "content": "\n    def dereference(self, entity_id, default=None):\n        canonical_id = self.resolve_id(entity_id)\n        return self.__entity_map.get(canonical_id, default)\n\n    get = dereference\n\n    def add_file(\n            self,\n            source=None,\n            dest_path=None,\n            fetch_remote=False,\n            validate_url=True,\n            properties=None\n    ):\n        return self.add(File(\n            self,\n            source=source,\n            dest_path=dest_path,\n            fetch_remote=fetch_remote,\n            validate_url=validate_url,",
  "start_line": 340,
  "end_line": 360,
  "total_lines": 585,
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}

{
  "status": "ok",
  "stdout": "rocrate/model/entity.py:81:        deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\nrocrate/rocrate.py:309:        rval = self.dereference(\"test\")\nrocrate/rocrate.py:316:        rval = self.dereference(\"examples\")\nrocrate/rocrate.py:341:    def dereference(self, entity_id, default=None):\nrocrate/rocrate.py:345:    get = dereference\nrocrate/rocrate.py:426:                e = self.dereference(e)\nrocrate/rocrate.py:465:                if not self.dereference(str(rel)):\nrocrate/rocrate.py:582:            suite = self.dereference(suite)\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "rocrate/model/entity.py",
  "occurrences": 1,
  "strategy": "exact",
  "diff": "--- a/rocrate/model/entity.py\n+++ b/rocrate/model/entity.py\n@@ -75,10 +75,13 @@\n \n     def __getitem__(self, key):\n         v = self._jsonld[key]\n-        if isinstance(v, str) or key.startswith(\"@\"):\n+        if v is None or isinstance(v, str) or key.startswith(\"@\"):\n             return v\n         values = v if isinstance(v, list) else [v]\n-        deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\n+        deref_values = [\n+            self.crate.dereference(_[\"@id\"], _[\"@id\"]) if isinstance(_, dict) and \"@id\" in _ else _\n+            for _ in values\n+        ]\n         return deref_values if isinstance(v, list) else deref_values[0]\n \n     def __setitem__(self, key: str, value):\n",
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "Value of name: None\n",
  "stderr": "/workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  import pkg_resources\n",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "Value of names: ['Name 1', None, 'Name 3']\n",
  "stderr": "/workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  import pkg_resources\n",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "",
  "stderr": "/workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  import pkg_resources\n",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "383:    def add(self, *entities):\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "rocrate/rocrate.py",
  "content": "\n    add_directory = add_dataset\n\n    def add(self, *entities):\n        \"\"\"\\\n        Add one or more entities to this RO-Crate.\n\n        If an entity with the same (canonical) id is already present in the\n        crate, it will be replaced (as in Python dictionaries).\n\n        Note that, according to the specs, \"The RO-Crate Metadata JSON @graph\n        MUST NOT list multiple entities with the same @id; behaviour of\n        consumers of an RO-Crate encountering multiple entities with the same\n        @id is undefined\". In practice, due to the replacement semantics, the\n        entity for a given id is the last one added to the crate with that id.\n        \"\"\"\n        for e in entities:\n            key = e.canonical_id()\n            if isinstance(e, RootDataset):\n                self.root_dataset = e\n            if isinstance(e, (Metadata, LegacyMetadata)):",
  "start_line": 380,
  "end_line": 400,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "rocrate/rocrate.py",
  "content": "            if isinstance(e, (Metadata, LegacyMetadata)):\n                self.metadata = e\n            if isinstance(e, Preview):\n                self.preview = e\n            if isinstance(e, (RootDataset, Metadata, LegacyMetadata, Preview)):\n                self.default_entities.append(e)\n            elif hasattr(e, \"write\"):\n                self.data_entities.append(e)\n                if key not in self.__entity_map:\n                    self.root_dataset._jsonld.setdefault(\"hasPart\", [])\n                    self.root_dataset[\"hasPart\"] += [e]",
  "start_line": 400,
  "end_line": 410,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "rocrate/rocrate.py",
  "content": "                    self.root_dataset[\"hasPart\"] += [e]\n            else:\n                self.contextual_entities.append(e)\n            self.__entity_map[key] = e\n        return entities[0] if len(entities) == 1 else entities\n\n    def delete(self, *entities):\n        \"\"\"\\\n        Delete one or more entities from this RO-Crate.\n\n        Note that the crate could be left in an inconsistent state as a result",
  "start_line": 410,
  "end_line": 420,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "Value of mix: [<e1 Thing>, None, <e2 Thing>]\nAssertions passed!\n",
  "stderr": "/workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  import pkg_resources\n",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": ".................                                                        [100%]\n=============================== warnings summary ===============================\nrocrate/vocabs.py:21\n  /workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n    import pkg_resources\n\n-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html\n17 passed, 1 warning in 0.13s\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "...................                                                      [100%]\n=============================== warnings summary ===============================\nrocrate/vocabs.py:21\n  /workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n    import pkg_resources\n\n-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html\n19 passed, 1 warning in 0.19s\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": " M rocrate/model/entity.py\ndiff --git a/rocrate/model/entity.py b/rocrate/model/entity.py\nindex 826b564..7a13e9f 100644\n--- a/rocrate/model/entity.py\n+++ b/rocrate/model/entity.py\n@@ -75,10 +75,13 @@ class Entity(MutableMapping):\n \n     def __getitem__(self, key):\n         v = self._jsonld[key]\n-        if isinstance(v, str) or key.startswith(\"@\"):\n+        if v is None or isinstance(v, str) or key.startswith(\"@\"):\n             return v\n         values = v if isinstance(v, list) else [v]\n-        deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\n+        deref_values = [\n+            self.crate.dereference(_[\"@id\"], _[\"@id\"]) if isinstance(_, dict) and \"@id\" in _ else _\n+            for _ in values\n+        ]\n         return deref_values if isinstance(v, list) else deref_values[0]\n \n     def __setitem__(self, key: str, value):\n",
  "stderr": "",
  "exit_code": 0,
  "budget_warning": "Only 10 tool call(s) remaining (20/30 used). Finalize your edits and call submit_patch soon."
}

{
  "status": "ok",
  "stdout": ".................                                                        [100%]\n=============================== warnings summary ===============================\nrocrate/vocabs.py:21\n  /workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n    import pkg_resources\n\n-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html\n17 passed, 1 warning in 0.11s\n...................                                                      [100%]\n=============================== warnings summary ===============================\nrocrate/vocabs.py:21\n  /workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n    import pkg_resources\n\n-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html\n19 passed, 1 warning in 0.15s\n",
  "stderr": "/workspace/rocrate/vocabs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  import pkg_resources\n",
  "exit_code": 0,
  "budget_warning": "Only 9 tool call(s) remaining (21/30 used). Finalize your edits and call submit_patch soon."
}

{
  "status": "ok",
  "patch_size": 838,
  "files_changed": 1
}