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Include atomised name to avoid pipelines and other services reparsing…
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… the name

#1350
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@djtfmartin
djtfmartin committed Sep 6, 2024
1 parent c4b2f64 commit 1c7452b
Showing 1 changed file with 83 additions and 60 deletions.
143 changes: 83 additions & 60 deletions matching-ws/src/main/java/life/catalogue/matching/service/IndexingService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -862,78 +862,44 @@ protected static Document toDoc(NameUsage nameUsage) {
Rank rank = Rank.valueOf(nameUsage.getRank());

Optional<String> optCanonical = Optional.empty();
ParsedName pn = null;

try {
NomCode nomCode = null;
if (!StringUtils.isEmpty(nameUsage.getNomenclaturalCode())) {
nomCode = NomCode.valueOf(nameUsage.getNomenclaturalCode());
}

ParsedName pn = null;
if (StringUtils.isBlank(nameUsage.getAuthorship())) {
pn = NameParsers.INSTANCE.parse(nameUsage.getScientificName(), rank, nomCode);
} else{
pn = NameParsers.INSTANCE.parse(nameUsage.getScientificName() + " " + nameUsage.getAuthorship(), rank, nomCode);
}

StoredParsedName storedParsedName = new StoredParsedName();
storedParsedName.setAbbreviated(pn.isAbbreviated());
storedParsedName.setAutonym(pn.isAutonym());
storedParsedName.setBinomial(pn.isBinomial());
storedParsedName.setCandidatus(pn.isCandidatus());
storedParsedName.setCultivarEpithet(pn.getCultivarEpithet());
storedParsedName.setDoubtful(pn.isDoubtful());
storedParsedName.setGenus(pn.getGenus());
storedParsedName.setUninomial(pn.getUninomial());
storedParsedName.setUnparsed(pn.getUnparsed());
storedParsedName.setTrinomial(pn.isTrinomial());
storedParsedName.setIncomplete(pn.isIncomplete());
storedParsedName.setIndetermined(pn.isIndetermined());
storedParsedName.setTerminalEpithet(pn.getTerminalEpithet());
storedParsedName.setInfragenericEpithet(pn.getInfragenericEpithet());
storedParsedName.setInfraspecificEpithet(pn.getInfraspecificEpithet());
storedParsedName.setExtinct(pn.isExtinct());
storedParsedName.setPublishedIn(pn.getPublishedIn());
storedParsedName.setSanctioningAuthor(pn.getSanctioningAuthor());
storedParsedName.setSpecificEpithet(pn.getSpecificEpithet());
storedParsedName.setPhrase(pn.getPhrase());
storedParsedName.setPhraseName(pn.isPhraseName());
storedParsedName.setVoucher(pn.getVoucher());
storedParsedName.setNominatingParty(pn.getNominatingParty());
storedParsedName.setNomenclaturalNote(pn.getNomenclaturalNote());
storedParsedName.setWarnings(pn.getWarnings());
if (pn.getBasionymAuthorship() != null) {
storedParsedName.setBasionymAuthorship(
StoredParsedName.StoredAuthorship.builder()
.authors(pn.getBasionymAuthorship().getAuthors())
.exAuthors(pn.getBasionymAuthorship().getExAuthors())
.year(pn.getBasionymAuthorship().getYear()).build()
);
}
if (pn.getCombinationAuthorship() != null) {
storedParsedName.setCombinationAuthorship(
StoredParsedName.StoredAuthorship.builder()
.authors(pn.getCombinationAuthorship().getAuthors())
.exAuthors(pn.getCombinationAuthorship().getExAuthors())
.year(pn.getCombinationAuthorship().getYear()).build()
);
}
storedParsedName.setType(pn.getType() != null ? pn.getType().name() : null);
storedParsedName.setNotho(pn.getNotho() != null ? pn.getNotho().name() : null);

// store the parsed name components in JSON
doc.add(new StoredField(
FIELD_PARSED_NAME_JSON,
MAPPER.writeValueAsString(storedParsedName))
);

ParsedName pn = NameParsers.INSTANCE.parse(nameUsage.getScientificName(), rank, nomCode);
// canonicalMinimal will construct the name without the hybrid marker and authorship
String canonical = NameFormatter.canonicalMinimal(pn);
optCanonical = Optional.ofNullable(canonical);
} catch (UnparsableNameException | JsonProcessingException | InterruptedException e) {
} catch (UnparsableNameException | InterruptedException e) {
// do nothing
log.debug("Unable to parse name to create canonical: {}", nameUsage.getScientificName());
} catch ( JsonProcessingException e) {
// do nothing
log.debug("Unable to parse name to create canonical: {}", nameUsage.getScientificName());
}

if (pn != null){
try {
// if there an authorship, reparse with it to get the component authorship parts
StoredParsedName storedParsedName = StringUtils.isBlank(nameUsage.getAuthorship()) ?
getStoredParsedName(pn) : constructParsedName(nameUsage, rank, nomCode);
// store the parsed name components in JSON
doc.add(new StoredField(
FIELD_PARSED_NAME_JSON,
MAPPER.writeValueAsString(storedParsedName))
);
} catch (UnparsableNameException | InterruptedException e) {
// do nothing
log.debug("Unable to parse name to create canonical: {}", nameUsage.getScientificName());
} catch ( JsonProcessingException e) {
// do nothing
log.debug("Unable to parse name to create canonical: {}", nameUsage.getScientificName());
}
}

final String canonical = optCanonical.orElse(nameUsage.getScientificName());

// use custom precision step as we do not need range queries and prefer to save memory usage
Expand Down Expand Up @@ -982,4 +948,61 @@ protected static Document toDoc(NameUsage nameUsage) {

return doc;
}

@NotNull
private static StoredParsedName constructParsedName(NameUsage nameUsage, Rank rank, NomCode nomCode) throws UnparsableNameException, InterruptedException {
ParsedName pn = !StringUtils.isBlank(nameUsage.getAuthorship()) ?
NameParsers.INSTANCE.parse(nameUsage.getScientificName() + " " + nameUsage.getAuthorship(), rank, nomCode)
: NameParsers.INSTANCE.parse(nameUsage.getScientificName(), rank, nomCode);
return getStoredParsedName(pn);
}

@NotNull
private static StoredParsedName getStoredParsedName(ParsedName pn) {
StoredParsedName storedParsedName = new StoredParsedName();
storedParsedName.setAbbreviated(pn.isAbbreviated());
storedParsedName.setAutonym(pn.isAutonym());
storedParsedName.setBinomial(pn.isBinomial());
storedParsedName.setCandidatus(pn.isCandidatus());
storedParsedName.setCultivarEpithet(pn.getCultivarEpithet());
storedParsedName.setDoubtful(pn.isDoubtful());
storedParsedName.setGenus(pn.getGenus());
storedParsedName.setUninomial(pn.getUninomial());
storedParsedName.setUnparsed(pn.getUnparsed());
storedParsedName.setTrinomial(pn.isTrinomial());
storedParsedName.setIncomplete(pn.isIncomplete());
storedParsedName.setIndetermined(pn.isIndetermined());
storedParsedName.setTerminalEpithet(pn.getTerminalEpithet());
storedParsedName.setInfragenericEpithet(pn.getInfragenericEpithet());
storedParsedName.setInfraspecificEpithet(pn.getInfraspecificEpithet());
storedParsedName.setExtinct(pn.isExtinct());
storedParsedName.setPublishedIn(pn.getPublishedIn());
storedParsedName.setSanctioningAuthor(pn.getSanctioningAuthor());
storedParsedName.setSpecificEpithet(pn.getSpecificEpithet());
storedParsedName.setPhrase(pn.getPhrase());
storedParsedName.setPhraseName(pn.isPhraseName());
storedParsedName.setVoucher(pn.getVoucher());
storedParsedName.setNominatingParty(pn.getNominatingParty());
storedParsedName.setNomenclaturalNote(pn.getNomenclaturalNote());
storedParsedName.setWarnings(pn.getWarnings());
if (pn.getBasionymAuthorship() != null) {
storedParsedName.setBasionymAuthorship(
StoredParsedName.StoredAuthorship.builder()
.authors(pn.getBasionymAuthorship().getAuthors())
.exAuthors(pn.getBasionymAuthorship().getExAuthors())
.year(pn.getBasionymAuthorship().getYear()).build()
);
}
if (pn.getCombinationAuthorship() != null) {
storedParsedName.setCombinationAuthorship(
StoredParsedName.StoredAuthorship.builder()
.authors(pn.getCombinationAuthorship().getAuthors())
.exAuthors(pn.getCombinationAuthorship().getExAuthors())
.year(pn.getCombinationAuthorship().getYear()).build()
);
}
storedParsedName.setType(pn.getType() != null ? pn.getType().name() : null);
storedParsedName.setNotho(pn.getNotho() != null ? pn.getNotho().name() : null);
return storedParsedName;
}
}

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