Class ChemblCodeResolverImpl

java.lang.Object

ubic.gemma.core.ontology.chembl.ChemblCodeResolverImpl

All Implemented Interfaces:

ChemblCodeResolver

@Component
public class ChemblCodeResolverImpl
extends Object
implements ChemblCodeResolver

Resolves a trial code against ChEMBL's synonym table (GET {base}/chembl/api/data/molecule?molecule_synonyms__molecule_synonym__iexact=...).

Both positive and negative identifications are cached in the admin-evictable CACHE_NAME cache, so a repeatedly-submitted code — recognised or not — is sent upstream once. Transient failures are not cached and are never surfaced as errors; see ChemblCodeResolver.identify(String).

See Also:

• for why the fuzzy search endpoint is deliberately not used

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CACHE_NAME	Admin-evictable cache of code → ChemblCompound.

Constructor Summary

Constructors

Constructor	Description
ChemblCodeResolverImpl()

Method Summary

Modifier and Type	Method	Description
ChemblCompound	identify(String code)	Identify a code against ChEMBL.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

CACHE_NAME

public static final String CACHE_NAME

Admin-evictable cache of code → ChemblCompound. Registered in EhcacheConfig#APP_CACHES.

See Also:

• Constant Field Values

Constructor Details

ChemblCodeResolverImpl

public ChemblCodeResolverImpl()

Method Details

identify

@Nullable
public ChemblCompound identify(String code)

Description copied from interface: ChemblCodeResolver

Identify a code against ChEMBL.

Never throws for an unreachable or misbehaving ChEMBL: this is advisory enrichment sitting on a search path, and a naming authority being down is not a reason to fail a user's query. Failures are logged and reported as "not identified", and are NOT cached, so the next call retries.

Specified by:

identify in interface ChemblCodeResolver

Parameters:

code - the code as the submitter wrote it; separator spelling does not matter

Returns:

the identified compound, or null when ChEMBL has no exact synonym match, when the resolver is disabled, or when ChEMBL could not be reached