Add ChEBI web service converter

[Copilot]

Adds a new ChEBI converter backed by the ChEBI REST API, exposing chemical entity lookups and cross-identifier conversions.

Changes

MSMetaEnhancer/libs/converters/web/ChEBI.py

• Two API endpoints used:
  • /search?query=...&searchCategory={CHEBI_NAME|INCHI_KEY|INCHI|SMILES}&maximumResults=10&stars=ALL
  • /chemicalentity/{chebiId}
• 25 conversion methods covering all pairwise combinations of: chebiid, compound_name, inchikey, inchi, smiles, formula
• Dynamically registered via create_top_level_conversion_methods, consistent with existing converters

MSMetaEnhancer/libs/converters/web/__init__.py

• ChEBI added to __all__ and imported alongside existing converters

tests/test_ChEBI.py

• Tests for service availability, key conversion round-trips (chebiid ↔ inchikey, etc.), raw response format validation, and get_conversion_functions() output

Example usage:

converters = ["ChEBI"]
jobs = [("chebiid", "inchikey"), ("inchikey", "chebiid"), ("compound_name", "smiles")]
await app.annotate_spectra(converters=converters, jobs=jobs)

• Fixes Add new ChEBI service #182

[hechth]

@copilot use CHEBI:60888 for the testing entity - the results can be found here: https://www.ebi.ac.uk/chebi/CHEBI:60888

[Copilot]

@copilot use CHEBI:60888 for the testing entity - the results can be found here: https://www.ebi.ac.uk/chebi/CHEBI:60888

Updated the test entity to CHEBI:60888 (caffeine) with its corresponding InChIKey RYYVLZVUVIJVGH-UHFFFAOYSA-N in commit Use CHEBI:60888 as test entity in test_ChEBI.py.

[hechth]

@copilot I think your API url is wrong - the query to search for the chebi ID is https://www.ebi.ac.uk/chebi/backend/api/public/compound/CHEBI:60888/

also add a test for the name search function using the name "bapta" as can be seen in this url: https://www.ebi.ac.uk/chebi/backend/api/public/es_search/?term=bapta&page=1&size=15

[Copilot]

@copilot I think your API url is wrong - the query to search for the chebi ID is https://www.ebi.ac.uk/chebi/backend/api/public/compound/CHEBI:60888/

also add a test for the name search function us...

Fixed in the latest commit. The endpoints are now:

• ChEBI ID lookup: public/compound/{chebiId}/
• Name/InChIKey/InChI/SMILES search: public/es_search/?term={term}&page=1&size=15

Also added test_compound_name_to_chebiid using "bapta" as the search term.

[hechth]

@copilot add "InChI=1S/C22H24N2O10/c25-19(26)11-23(12-20(27)28)15-5-1-3-7-17(15)33-9-10-34-18-8-4-2-6-16(18)24(13-21(29)30)14-22(31)32/h1-8H,9-14H2,(H,25,26)(H,27,28)(H,29,30)(H,31,32)" as inchi for the tests and also add Iupac name "2,2',2'',2'''-[ethane-1,2-diylbis(oxy-2,1-phenylenenitrilo)]tetraacetic acid" - also the iupac name should be usable as input and output if that is allowed by the api

[Copilot]

@copilot add "InChI=1S/C22H24N2O10/c25-19(26)11-23(12-20(27)28)15-5-1-3-7-17(15)33-9-10-34-18-8-4-2-6-16(18)24(13-21(29)30)14-22(31)32/h1-8H,9-14H2,(H,25,26)(H,27,28)(H,29,30)(H,31,32)" as inchi for t...

Done. Added in the latest commit:

• INCHI constant set to "InChI=1S/C22H24N2O10/..." and assertion in test_chebiid_to_inchi
• IUPAC_NAME constant set to "2,2',2'',2'''-[ethane-1,2-diylbis(oxy-2,1-phenylenenitrilo)]tetraacetic acid"
• iupac_name is now extracted from synonyms (entity endpoint, where type == "IUPAC NAME") and from iupac_names list (es_search _source)
• All six pairwise conversions involving iupac_name are registered (e.g. iupac_name → chebiid, chebiid → iupac_name, etc.) — the from_iupac_name method uses the same es_search endpoint as the other search-based methods
• New integration tests: test_chebiid_to_iupac_name, test_inchi_to_chebiid, test_iupac_name_to_chebiid