✨ Add parameter validation

[Zethson]

Fixes #109

Before:

tissues = bt.Tissue.public(organism="Homo sapiens")
tissues

led to

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File /vol/data/miniconda3/envs/similarity-lamin/lib/python3.10/site-packages/bionty/models.py:394, in BioRecord.public(cls, organism, source)
    393 try:
--> 394     return getattr(bionty_base, cls.__name__)(
    395         organism=organism, source=source_name, version=version
    396     )
    397 except (AttributeError, ValueError):

File /vol/data/miniconda3/envs/similarity-lamin/lib/python3.10/site-packages/bionty/base/entities/_tissue.py:26, in Tissue.__init__(self, organism, source, version, **kwargs)
     19 def __init__(
     20     self,
     21     organism: Optional[Literal["all"]] = None,
   (...)
     24     **kwargs,
     25 ) -> None:
---> 26     super().__init__(
     27         source=source,
     28         version=version,
     29         organism=organism,
     30         include_id_prefixes={"uberon": ["UBERON"]},
     31         include_rel="part_of",
     32         **kwargs,
     33     )

File /vol/data/miniconda3/envs/similarity-lamin/lib/python3.10/site-packages/bionty/base/_public_ontology.py:73, in PublicOntology.__init__(self, source, version, organism, include_id_prefixes, include_rel)
     72 # search in all available sources to get url and md5
---> 73 self._source_record = self._match_sources(
     74     self._all_sources,
     75     source=source,
     76     version=version,
     77     organism=organism,
     78 )
     80 self._organism = self._source_record["organism"]

File /vol/data/miniconda3/envs/similarity-lamin/lib/python3.10/site-packages/bionty/base/_public_ontology.py:230, in PublicOntology._match_sources(self, ref_sources, source, version, organism)
    229 if row.shape[0] == 0:
--> 230     raise ValueError(
    231         f"No source is available with {kwargs}\nCheck"
    232         " `.display_available_sources()`"
    233     )
    234 return row.to_dict(orient="records")[0]

ValueError: No source is available with {'organism': 'Homo sapiens'}
Check `.display_available_sources()`

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
Cell In[31], line 1
----> 1 tissues = bt.Tissue.public(organism="Homo sapiens")
      2 tissues

File /vol/data/miniconda3/envs/similarity-lamin/lib/python3.10/site-packages/bionty/models.py:409, in BioRecord.public(cls, organism, source)
    407             kwargs["organism"] = organism
    408     source = Source.filter(**kwargs).first()
--> 409 return StaticReference(source)

File /vol/data/miniconda3/envs/similarity-lamin/lib/python3.10/site-packages/bionty/models.py:35, in StaticReference.__init__(self, source_record)
     32 def __init__(self, source_record: Source) -> None:
     33     self._source_record = source_record
     34     super().__init__(
---> 35         source=source_record.name,
     36         version=source_record.version,
     37         organism=source_record.organism,
     38     )

AttributeError: 'NoneType' object has no attribute 'name'

After:

{
	"name": "ValueError",
	"message": "Invalid organism: Homo sapiens. Must be one of: all",
	"stack": "---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[3], line 1
----> 1 tissues = bt.Tissue.public(organism=\"Homo sapiens\")
      2 tissues

File ~/PycharmProjects/bionty/bionty/models.py:399, in BioRecord.public(cls, organism, source)
    395     return getattr(bionty_base, cls.__name__)(
    396         organism=organism, source=source_name, version=version
    397     )
    398 except InvalidParamError as e:
--> 399     raise ValueError(str(e)) from None
    400 except (AttributeError, ValueError):
    401     if source is None:

ValueError: Invalid organism: 'Homo sapiens'. Must be one of: 'all'"
}

[github-actions]

🚀 Deployed on https://66e871bfda90374c2041807f--bionty-kyow.netlify.app

[falexwolf]

This header is awesome!

But what is the after state? Is there an equally succinct way of phrasing it? :D

[falexwolf]

If this equates type annotation checks, why not used typechecked or pydantic?

I assume it's because there is more going on.

Small note re naming: param in lamindb has a special meaning akin to feature. When we talk about plain Python function args, we say args aligned with Google-style docstrings.

[falexwolf]

(Should at some point update the "Paramters" header and replace it with "Arguments".

[falexwolf]

Great PR!

Not so important: Why do we use Optional instead of | None here?