New sssom==0.3.42 breaks oaklib

[rly]

sssom==0.3.42 was released a few hours ago but breaks importing of oaklib.

In a clean python 3.11 environment on Mac M1:

$ pip install oaklib
$ python -c "import oaklib"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/rly/mambaforge/envs/test/lib/python3.11/site-packages/oaklib/__init__.py", line 7, in <module>
    from oaklib.interfaces import BasicOntologyInterface  # noqa:F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/rly/mambaforge/envs/test/lib/python3.11/site-packages/oaklib/interfaces/__init__.py", line 8, in <module>
    from oaklib.interfaces.text_annotator_interface import TextAnnotatorInterface
  File "/Users/rly/mambaforge/envs/test/lib/python3.11/site-packages/oaklib/interfaces/text_annotator_interface.py", line 22, in <module>
    from oaklib.utilities.lexical.lexical_indexer import create_or_load_lexical_index
  File "/Users/rly/mambaforge/envs/test/lib/python3.11/site-packages/oaklib/utilities/lexical/lexical_indexer.py", line 18, in <module>
    from sssom.context import get_default_metadata
ImportError: cannot import name 'get_default_metadata' from 'sssom.context' (/Users/rly/mambaforge/envs/test/lib/python3.11/site-packages/sssom/context.py)

In mapping-commons/sssom-py#421 it looks like get_default_metadata was removed from sssom/src/sssom/context.py but this function is used in oaklib/src/oaklib/utilities/lexical/lexical_indexer.py

It looks like oaklib should use instead:

from .typehints import Metadata
default_metadata = Metadata.default()

I think either oaklib should be updated with the above, or sssom should be updated to maintain the old get_default_metadata function while it is being deprecated.

[matentzn]

@rly thanks a ton.

This should not ever happen, I am not sure how I missed this but somehow I must have allowed a PR in sssom-py through that removes a method (which I would not do usually if I had my full mental capacity).

@hrshdhgd can you re-introduce that method in SSSOM, formally @deprecate it and make a new release? Also, before you make a release, can you run all the OAK tests with the new sssom version so we can be sure that nothing else has broken?

[cthoyt]

@hrshdhgd I will take care of it

[cthoyt]

Alternatively,

ontology-access-kit/src/oaklib/utilities/lexical/lexical_indexer.py

Lines 313 to 325 in 75940bf

	if meta is None:
	meta = get_default_metadata()
	if prefix_map:
	meta.prefix_map.update(
	{k: v for k, v in prefix_map.items() if k not in meta.prefix_map.keys()}
	)
	mapping_set_id = meta.metadata[MAPPING_SET_ID]
	license = meta.metadata[LICENSE]
	mset = MappingSet(mapping_set_id=mapping_set_id, mappings=mappings, license=license)
	# doc = MappingSetDocument(prefix_map=oi.prefix_map(), mapping_set=mset)
	doc = MappingSetDocument(prefix_map=meta.prefix_map, mapping_set=mset)
	msdf = to_mapping_set_dataframe(doc)

can all refactored to only use high-level functionality from sssom-py instead of duplicating its functionality for management of metadata/prefix maps

[cthoyt]

We yanked the 0.3.42 release, these breaking changes will get put into a 0.4.0 series and OAK will be updated to use the new code in #666

[rly]

Thanks for the update!