curies

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Closes #87

cthoyt

References #103. This PR adds a ``w3c_validation`` flag to instantiation of a converter and to `Converter.expand()` that turns on W3C CURIE specification validation. For now, it's not a "true" implementation...

cthoyt

Handling of CURIEs that include square brackets don't conform to W3C specs and are incompatible with semantic web tools

1

There are some cases of bioregistry "CURIEs" allowing square brackets in the local id. This is questionable if we follow the (IMO frustratingly opaque) W3C specs. Here are some examples...

cmungall

Add tests for federated SPARQL queries between the curies mapping service and popular triplestores

1

Add tests to check if federated queries between the curies mapping service and popular triplestores properly work. Triplestores need to be deployed locally before running the tests with docker compose,...

vemonet

https://github.com/monarch-initiative/monarch-gene-mapping/pull/34#discussion_r1416026076

cthoyt

```python r1 = Record( prefix="geo", prefix_synonyms=["GEO"], uri_prefix="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", pattern="^G(PL|SM|SE|DS)\\d+$", ) r2 = Record( prefix="geogeo", uri_prefix="http://purl.obolibrary.org/obo/GEO_", pattern="^\\d{9}$" ) c1 = Converter([r1, r2]) remapping = {"GEO": "ncbi.geo", "geogeo": "GEO"} c2 = remap_curie_prefixes(c1, remapping)...

cthoyt

Improve configurability and documentation of Pandas utilities

1

References #63 This pull request does the following: - [x] Make strictness configurable for pandas expansion, compression, and standardization functions - [ ] When not strict, report a summary of...

cthoyt

It might be worth having a way to hash an EPM so they can be quickly indexed / compared for equality ``` def get_hash(self) -> str: import hashlib from operator...

cthoyt

Tests for remote federated services

1

I've excerpted this from #49 - this code tests public SPARQL interfaces are able to use the Bioregistry. I'm not sure if this belongs in this package, though ```python """Tests...

cthoyt

Add the following else clause: ```python elif subj_query is not None and obj_query is not None: if obj_query in self._expand_pair_all(subj_query): yield subj_query, pred_query, obj_query ```

cthoyt