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",
  "start_line": 60,
  "end_line": 90,
  "total_lines": 141,
  "is_truncated": false
}

{
  "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\nTraceback (most recent call last):\n  File \"<stdin>\", line 24, in <module>\n  File \"/workspace/rocrate/model/entity.py\", line 77, in __getitem__\n    v = self._jsonld[key]\nKeyError: 'name'\n",
  "exit_code": 0
}

{
  "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,
  "end_line": 60,
  "total_lines": 141,
  "is_truncated": false
}

{
  "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\nTraceback (most recent call last):\n  File \"<stdin>\", line 24, 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": 0
}

{
  "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)",
  "start_line": 1,
  "end_line": 100,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "341:    def dereference(self, entity_id, default=None):\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):\n        self.root_dataset.properties()\n\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,",
  "start_line": 330,
  "end_line": 350,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "Error getting name: 'NoneType' object is not subscriptable\nError getting tags: string indices must be integers\nError getting related: string indices must be integers\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": "./rocrate/model/entity.py:81:        deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) for _ in values]\n./rocrate/rocrate.py:309:        rval = self.dereference(\"test\")\n./rocrate/rocrate.py:316:        rval = self.dereference(\"examples\")\n./rocrate/rocrate.py:341:    def dereference(self, entity_id, default=None):\n./rocrate/rocrate.py:345:    get = dereference\n./rocrate/rocrate.py:426:                e = self.dereference(e)\n./rocrate/rocrate.py:465:                if not self.dereference(str(rel)):\n./rocrate/rocrate.py:582:            suite = self.dereference(suite)\n./test/test_model.py:41:    root_dataset = crate.dereference('./')\n./test/test_model.py:43:    metadata_entity = crate.dereference(helpers.METADATA_FILE_NAME)\n./test/test_model.py:45:    preview_entity = crate.dereference(helpers.PREVIEW_FILE_NAME)\n./test/test_model.py:48:    # dereference added files\n./test/test_model.py:52:    dereference_file = crate.dereference(\"sample_file.txt\")\n./test/test_model.py:53:    assert file_returned is dereference_file\n./test/test_model.py:56:    assert crate.dereference(readme_url) is readme_entity\n./test/test_model.py:58:    # dereference nonexistent entity\n./test/test_model.py:59:    assert crate.dereference(f\"#{uuid.uuid4()}\") is None\n./test/test_model.py:60:    assert crate.dereference(f\"#{uuid.uuid4()}\", file_returned) is file_returned\n./test/test_model.py:81:        deref_entity = crate.dereference(id_)\n./test/test_model.py:123:    person_dereference = crate.dereference('#joe')\n./test/test_model.py:124:    assert person_dereference is new_person\n./test/test_model.py:125:    assert person_dereference.type == 'Person'\n./test/test_model.py:126:    person_prop = person_dereference.properties()\n./test/test_model.py:132:    person_dereference = crate.dereference(id_)\n./test/test_model.py:133:    assert person_dereference is new_person\n./test/test_model.py:193:    assert crate.dereference(john.id) is john\n./test/test_model.py:194:    assert crate.dereference(file_.id) is wf\n./test/test_model.py:243:    suite = crate.dereference(\"#test1\")\n./test/test_model.py:244:    definition = crate.dereference(def_path)\n./test/test_model.py:307:    person = crate.dereference(orcid)\n./test/test_api.py:29:    wf = wf_crate.dereference(wf_id)\n./test/test_api.py:32:    lang = wf_crate.dereference(\"#galaxy\")\n./test/test_api.py:65:    wf = wf_crate.dereference(wf_id)\n./test/test_api.py:67:    lang = wf_crate.dereference(\"#cwl\")\n./test/test_api.py:96:    wf = wf_crate.dereference(wf_id)\n./test/test_api.py:98:    lang = wf_crate.dereference(\"#galaxy\")\n./test/test_api.py:104:    assert wf_crate.dereference(extra_file1.name) is not None\n./test/test_api.py:105:    assert wf_crate.dereference(extra_file2.name) is not None\n./test/test_read.py:58:    root = crate.dereference('./')\n./test/test_read.py:65:    metadata = crate.dereference(helpers.METADATA_FILE_NAME)\n./test/test_read.py:76:    preview = crate.dereference(helpers.PREVIEW_FILE_NAME)\n./test/test_read.py:88:    main_wf = crate.dereference('test_galaxy_wf.ga')\n./test/test_read.py:96:    abs_wf = crate.dereference('abstract_wf.cwl')\n./test/test_read.py:102:    wf_author = crate.dereference('#joe')\n./test/test_read.py:109:    test_file = crate.dereference('test_file_galaxy.txt')\n./test/test_read.py:114:    remote_file = crate.dereference(_URL)\n./test/test_read.py:119:    examples_dataset = crate.dereference('examples/')\n./test/test_read.py:125:    test_dataset = crate.dereference('test/')\n./test/test_read.py:167:    assert crate.dereference(helpers.LEGACY_METADATA_FILE_NAME) is crate.metadata\n./test/test_read.py:170:    main_wf = crate.dereference('test_galaxy_wf.ga')\n./test/test_read.py:195:    assert crate.dereference(\"./\") is not None\n./test/test_read.py:196:    assert crate.dereference(helpers.METADATA_FILE_NAME) is not None\n./test/test_read.py:210:        assert isinstance(crate.dereference(p), File)\n./test/test_read.py:212:        assert isinstance(crate.dereference(p), Dataset)\n./test/test_read.py:235:    prev = crate.dereference(helpers.PREVIEW_FILE_NAME)\n./test/test_read.py:295:    examples_dataset = crate.dereference(name)\n./test/test_read.py:310:    test_file = crate.dereference(name)\n./test/test_read.py:355:        rc = crate.dereference(rc_id)\n./test/test_read.py:430:    entity = crate.dereference(id_)\n./test/test_readwrite.py:39:    upd_file = crate.dereference(upd_file_id)\n./test/test_write.py:150:        out_file = out_crate.dereference(file_.id)\n./test/test_write.py:153:        out_file = out_crate.dereference(url)\n./test/test_write.py:193:        out_dataset = out_crate.dereference(relpath)\n./test/test_write.py:198:        out_dataset = out_crate.dereference(url)\n./test/test_write.py:235:    assert file_ is crate.dereference(path.name)\n./test/test_write.py:242:    assert file_ is crate.dereference(path.name)\n./test/test_write.py:265:    assert crate.dereference(\"b\") is d1\n./test/test_write.py:267:    assert crate.dereference(\"a/b\") is d2\n./test/test_write.py:",
  "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@@ -78,7 +78,7 @@\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+        deref_values = [self.crate.dereference(_[\"@id\"], _[\"@id\"]) if isinstance(_, dict) and \"@id\" in _ else _ for _ in values]\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": "name: None\ntags: ['tag1', 'tag2']\nrelated: ['#entity2', 'just-a-string']\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",
  "filepath": "rocrate/rocrate.py",
  "content": "            properties=None\n    ):\n        return self.add(Dataset(\n            self,\n            source=source,\n            dest_path=dest_path,\n            fetch_remote=fetch_remote,\n            validate_url=validate_url,\n            properties=properties\n        ))\n\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": 370,
  "end_line": 400,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "rocrate/rocrate.py",
  "content": "                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": 401,
  "end_line": 410,
  "total_lines": 585,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "85:        self.__entity_map = {}\n336:        return self.__entity_map.values()\n343:        return self.__entity_map.get(canonical_id, default)\n408:                if key not in self.__entity_map:\n413:            self.__entity_map[key] = e\n449:            self.__entity_map.pop(e.canonical_id(), None)\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "",
  "details": {
    "stdout": "",
    "stderr": "",
    "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\"]) if isinstance(_, dict) and \"@id\" in _ else _ 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": "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' (/workspace/rocrate/__init__.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' (/workspace/rocrate/__init__.py)\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "filepath": "rocrate/__init__.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\n\"\"\"\nCreate/parse RO-Crate metadata.\n\nThis module intends to help create or parse\nRO-Crate metadata, see rocrate_\n\n.. _rocrate: https://w3id.org/ro/crate/\n\"\"\"\n\n__author__ = \", \".join((\n    'Bert Droesbeke',\n    'Ignacio Eguinoa',\n    'Alban Gaignard',\n    'Simone Leo',\n    'Luca Pireddu',\n    'Laura Rodríguez-Navas',\n    'Stian Soiland-Reyes'\n))\n__copyright__ = \"\"\"\\\nCopyright 2019-2021 The University of Manchester, UK\nCopyright 2021 Vlaams Instituut voor Biotechnologie (VIB), DE\nCopyright 2021 Barcelona Supercomputing Center (BSC), ES\nCopyright 2021 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT\n\"\"\"\n__license__ = (\"Apache License, version 2.0 \"\n               \"<https://www.apache.org/licenses/LICENSE-2.0>\")\n\n# for arcp scheme registration with urllib.parse\nimport arcp  # noqa\n\n# Convenience export of public functions/types\nfrom .model.metadata import Metadata  # noqa\nfrom ._version import __version__  # noqa",
  "start_line": 1,
  "end_line": 52,
  "total_lines": 52,
  "is_truncated": false
}

{
  "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)",
  "start_line": 1,
  "end_line": 100,
  "total_lines": 585,
  "is_truncated": false,
  "budget_warning": "Only 10 tool call(s) remaining (20/30 used). Finalize your edits and call submit_patch soon."
}