researchobject__ro-crate-py-102

{
  "status": "ok",
  "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",
  "start_line": 60,
  "end_line": 100,
  "total_lines": 141,
  "is_truncated": false
}

{
  "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 1, in <module>\nImportError: cannot import name 'ROcrate' from 'rocrate.rocrate' (/workspace/rocrate/rocrate.py)\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 1, in <module>\nImportError: cannot import name 'ROcrate' from 'rocrate.rocrate' (/workspace/rocrate/rocrate.py)\n",
    "exit_code": 1
  }
}

{
  "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",
  "start_line": 1,
  "end_line": 150,
  "total_lines": 585,
  "is_truncated": true
}

{
  "status": "ok",
  "stdout": "Caught expected error: '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": "    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": 341,
  "end_line": 360,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "330:    def resolve_id(self, id_):\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "rocrate/rocrate.py",
  "content": "    def resolve_id(self, id_):\n        if not is_url(id_):\n            id_ = urljoin(self.arcp_base_uri, id_)  # also does path normalization\n        return id_.rstrip(\"/\")\n\n    def get_entities(self):\n        return self.__entity_map.values()\n\n    def _get_root_jsonld(self):",
  "start_line": 330,
  "end_line": 338,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "46:def is_url(string):\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "rocrate/utils.py",
  "content": "    if (isinstance(list_or_other, collections.Sequence)\n        and not isinstance(list_or_other, str)):  # FIXME: bytes?\n        return list_or_other\n    return [list_or_other]\n\n\ndef is_url(string):\n    parts = urlsplit(string)\n    return all((parts.scheme, parts.netloc, parts.path))\n\n\ndef iso_now():\n    return datetime.now(timezone.utc).replace(microsecond=0).isoformat()\n\n\ndef subclasses(cls):\n    \"\"\"\\\n    Recursively iterate through all subclasses (direct and indirect) of cls.\n\n    Subclasses appear before their parent classes, but ordering is otherwise\n    undefined. For instance, if Cat and Dog are subclasses of Pet and Beagle",
  "start_line": 40,
  "end_line": 60,
  "total_lines": 80,
  "is_truncated": false
}

{
  "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 11, in <module>\n  File \"/workspace/rocrate/model/entity.py\", line 81, in __getitem__\n    deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\n  File \"/workspace/rocrate/model/entity.py\", line 81, in <listcomp>\n    deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\nTypeError: 'NoneType' object is not subscriptable\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 11, in <module>\n  File \"/workspace/rocrate/model/entity.py\", line 81, in __getitem__\n    deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\n  File \"/workspace/rocrate/model/entity.py\", line 81, in <listcomp>\n    deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\nTypeError: 'NoneType' object is not subscriptable\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\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\n\n    def update(self):\n        raise NotImplementedError\n\n    def __iter__(self):\n        return iter(self._jsonld)\n\n    def __len__(self):\n        return len(self._jsonld)\n\n    def __contains__(self, key):\n        return key in self._jsonld\n\n    def __eq__(self, other):\n        if not isinstance(other, Entity):\n            return NotImplemented\n        return self.id == other.id and self._jsonld == other._jsonld\n\n    @property\n    def type(self):\n        return self._jsonld['@type']\n\n    # @property\n    # def types(self)-> List[str]:\n        # return tuple(as_list(self.get(\"@type\", \"Thing\")))\n\n    @property\n    def datePublished(self):\n        d = self.get('datePublished')\n        return d if not d else isoparse(d)\n\n    @datePublished.setter\n    def datePublished(self, value):\n        try:\n            value = value.isoformat()\n        except AttributeError:\n            pass\n        self['datePublished'] = value\n\n    def delete(self):\n        self.crate.delete(self)",
  "start_line": 1,
  "end_line": 141,
  "total_lines": 141,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "rocrate/model/entity.py:76:    def __getitem__(self, key):\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": "None value: None (Expected: None)\nString value: Some Category (Expected: Some Category)\nDict with @id: Resolved Entity (Expected: Resolved Entity)\nDict without @id: {'key': 'val'} (Expected: {'key': 'val'})\nList with None: [None, 'Resolved Entity'] (Expected: [None, 'Resolved Entity'])\nList with mix: [None, 'string', 'Resolved Entity', {'other': 'val'}] (Expected: [None, 'string', 'Resolved Entity', {'other': 'val'}])\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": "no tests found\n",
  "stderr": "grep: tests/: No such file or directory\n",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "./examples/read_test_metadata.py\n./test\n./test/test_cli.py\n./test/test_model.py\n./test/test_api.py\n./test/test_read.py\n./test/test_readwrite.py\n./test/test_write.py\n./test/test_test_metadata.py\n./test/test_utils.py\n./test/conftest.py\n./test/test-data\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\n17 passed, 1 warning in 0.13s\n",
  "stderr": "",
  "exit_code": 0
}