Iridium

The metal Iridium is used to refine and enhance metal alloys. Similarly, this package provides an enhanced coating around the Invenio RDM APIs and is a central piece of the Ardiem platform.

It provides:

a lower-level Python API wrapping the public Invenio RDM backend APIs
a higher-level object-oriented convenience API (TODO)
a JSON Schema based concept of "dataset profiles" for Invenio records (TODO)
transparent support for storage and retrieval of additional validated metadata (TODO)

Development

This project uses Poetry for dependency management.

Clone this repository and run poetry install.

Run pre-commit install after cloning to enable pre-commit to enforce the required linting hooks.

Run pytest before merging your changes to make sure you did not break anything.

To generate documentation, run pdoc --html -o docs python_app_template.

To check coverage, use pytest --cov.

Acknowledgements

This project was developed at the Institute for Materials Data Science and Informatics (IAS-9) of the Jülich Research Center and funded by the Helmholtz Metadata Collaboration (HMC), an incubator-platform of the Helmholtz Association within the framework of the Information and Data Science strategic initiative.

$ poetry run pytest
================================================================================================================================================= test session starts =================================================================================================================================================
platform linux -- Python 3.9.2, pytest-6.2.5, py-1.11.0, pluggy-1.0.0
rootdir: /home/chriz/rz/code/invenio/repos/iridium/iridium, configfile: pyproject.toml
plugins: anyio-3.5.0, cov-3.0.0, dotenv-0.5.2
collected 14 items                                                                                                                                                                                                                                                                                                    

tests/test_api.py EEE                                                                                                                                                                                                                                                                                           [ 21%]
tests/test_generic.py ...                                                                                                                                                                                                                                                                                       [ 42%]
tests/test_inveniordm_api.py EEEEEE                                                                                                                                                                                                                                                                             [ 85%]
tests/test_utils.py ..                                                                                                                                                                                                                                                                                          [100%]

======================================================================================================================================================= ERRORS ========================================================================================================================================================
_________________________________________________________________________________________________________________________________________ ERROR at setup of test_vocab_query __________________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
____________________________________________________________________________________________________________________________________ ERROR at setup of test_readonly_fields_draft _____________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
________________________________________________________________________________________________________________________________________ ERROR at setup of test_create_record _________________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
_________________________________________________________________________________________________________________________________________ ERROR at setup of test_vocabularies _________________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
________________________________________________________________________________________________________________________________________ ERROR at setup of test_record_queries ________________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
__________________________________________________________________________________________________________________________________________ ERROR at setup of test_new_draft ___________________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
______________________________________________________________________________________________________________________________________ ERROR at setup of test_draft_from_record _______________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
_____________________________________________________________________________________________________________________________________ ERROR at setup of test_version_from_record ______________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
_________________________________________________________________________________________________________________________________________ ERROR at setup of test_access_links _________________________________________________________________________________________________________________________________________

    @pytest.fixture(scope="session")
    def rdm():
        """Return an low-level API instance configured from environment variables."""
        cl = InvenioRDMClient.from_env(verify=False)
    
        # clean up all drafts from possible previous unclean runs
        if cl.connected():
>           drafts = cl.query.records(user=True, q="is_published:false")

tests/conftest.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
iridium/inveniordm/__init__.py:202: in records
    res.parse_hits(Record)
iridium/inveniordm/models/query.py:135: in parse_hits
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/query.py:135: in <listcomp>
    self.hits.hits = [obj_cls.parse_obj(x) for x in self.hits.hits]  # type: ignore
iridium/inveniordm/models/base.py:66: in parse_obj
    return cast(cls, super().parse_obj(val, *args, **kwargs))
pydantic/main.py:578: in pydantic.main.BaseModel.parse_obj
    ???
iridium/inveniordm/models/base.py:29: in __init__
    super().__init__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   pydantic.error_wrappers.ValidationError: 1 validation error for Record
E   is_draft
E     extra fields not permitted (type=value_error.extra)

pydantic/main.py:406: ValidationError
=============================================================================================================================================== short test summary info ===============================================================================================================================================
ERROR tests/test_api.py::test_vocab_query - pydantic.error_wrappers.ValidationError: 1 validation error for Record
ERROR tests/test_api.py::test_readonly_fields_draft - pydantic.error_wrappers.ValidationError: 1 validation error for Record
ERROR tests/test_api.py::test_create_record - pydantic.error_wrappers.ValidationError: 1 validation error for Record
ERROR tests/test_inveniordm_api.py::test_vocabularies - pydantic.error_wrappers.ValidationError: 1 validation error for Record
ERROR tests/test_inveniordm_api.py::test_record_queries - pydantic.error_wrappers.ValidationError: 1 validation error for Record
ERROR tests/test_inveniordm_api.py::test_new_draft - pydantic.error_wrappers.ValidationError: 1 validation error for Record
ERROR tests/test_inveniordm_api.py::test_draft_from_record - pydantic.error_wrappers.ValidationError: 1 validation error for Record
ERROR tests/test_inveniordm_api.py::test_version_from_record - pydantic.error_wrappers.ValidationError: 1 validation error for Record
ERROR tests/test_inveniordm_api.py::test_access_links - pydantic.error_wrappers.ValidationError: 1 validation error for Record
============================================================================================================================================= 5 passed, 9 errors in 1.90s =============================================================================================================================================

Looks like, there is an validation error. ;)

Maybe related: https://inveniordm.docs.cern.ch/releases/versions/version-v8.0.0/#my-dashboard

This also means we have changed the URL endpoint of the uploads page from `/uploads` to `/me/uploads` so that we can later add both `/me/communities` and `/me/requests`.

Edit: this seems to be an internal endpoint not an Rest-Api url-change.

Tests fail when running against invenioRDM-v8

opened by chriz-uniba 6

pdoc --html flag not available.

Maybe my setup is outdated but for me this command doesn't run through:

Error

https://github.com/Materials-Data-Science-and-Informatics/iridium/blob/4d357dc9d61aebfedd3c3e6a6b6451798c2c7122/README.md?plain=1#L92

$ pdoc --html -o docs iridium
usage: pdoc [-o DIR] [-d {google,numpy,restructuredtext}] [-e module=url] [--footer-text TEXT] [--logo URL] [--logo-link URL] [--math | --no-math] [--search | --no-search] [--show-source | --no-show-source] [-t DIR] [-h HOST] [-p PORT] [-n] [--help] [--version] [module ...]
pdoc: error: unrecognized arguments: --html

Setup

$ pdoc --version
pdoc: 8.3.0
Python: 3.9.2
Platform: Linux-5.10.0-11-amd64-x86_64-with-glibc2.31

Working command

$ pdoc -o docs iridium

Creates

.
├── index.html
├── iridium
│   ├── api.html
│   ├── generic.html
│   ├── inveniordm
│   │   ├── models
│   │   │   ├── base.html
│   │   │   ├── biblio.html
│   │   │   ├── query.html
│   │   │   └── technical.html
│   │   └── models.html
│   ├── inveniordm.html
│   ├── pprint.html
│   ├── query.html
│   ├── record.html
│   └── util.html
├── iridium.html
└── search.js

3 directories, 15 files

Do we need to fix the Readme, or do I need to fix my setup? If it is my setup, let me know what is needed (and maybe add this to the Readme, too). ;)

opened by chriz-uniba 1

Add new features added in v8
For example:

[ ] https://inveniordm.web.cern.ch//api/names - https://inveniordm.docs.cern.ch/customize/vocabularies/names/ - https://github.com/inveniosoftware/rfcs/blob/master/rfcs/rdm-0054-vocabulary-names.md#rest-api

If I find more, I will try to update this issue.
opened by chriz-uniba 0
Improvement of vocabulary-tests needed?

The tests for vocabularies provided here: https://github.com/Materials-Data-Science-and-Informatics/iridium/blob/4d357dc9d61aebfedd3c3e6a6b6451798c2c7122/tests/test_inveniordm_api.py#L23-L50

are only working on instances where the vocabularies aren't adjusted. For example, a freshly installed instance.

It is expected and wanted behaviour that vocabularies are adapted and changed: https://inveniordm.docs.cern.ch/customize/vocabularies/ Our instance, for example, has already some other subjects and we are working on different record-types.

I wonder whether the current tests need more improvement or whether we want to limit these tests down to a 'untouched' vocabularies folder and we expect the user to disable or adjust these tests for their own instances.

opened by chriz-uniba 1
Wrong documentation for delete method?

https://github.com/Materials-Data-Science-and-Informatics/iridium/blob/4d357dc9d61aebfedd3c3e6a6b6451798c2c7122/iridium/inveniordm/init.py#L223-L242

In line 236 I would expect some 'delete' information. Something like "Delete information about access link for record."?

opened by chriz-uniba 2