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Atomised usage for matching-ws #1375

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merged 2 commits into from
Nov 5, 2024
Merged

Atomised usage for matching-ws #1375

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c79d73f
Fixes for:
djtfmartin Nov 5, 2024
addadde
Merge branch 'master' into feature/include_atomised_usage_pr
mdoering Nov 5, 2024
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9 changes: 3 additions & 6 deletions matching-ws/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -27,14 +27,11 @@ RUN git clone https://github.com/CatalogueOfLife/backend.git
WORKDIR /app/backend
RUN git checkout $GIT_BRANCH

# Build all the CLB modules
RUN mvn clean install package -DskipTests

# Build the Maven project and create a exec file
WORKDIR /app/backend/matching-ws

# Run tests - full backend tests require additional services (e.g. ES)
RUN mvn clean install package
# Build all the CLB modules
RUN mvn clean install package -DskipTests -DskipITs

# Store git commit id and log
RUN curl -o /app/backend/git.json -H "Accept: application/vnd.github+json" "https://api.github.com/repos/catalogueoflife/backend/commits/$(git rev-parse HEAD)"
Expand Down Expand Up @@ -106,4 +103,4 @@ RUN chown -R $USER:$USER /opt/gbif/$APP_ARTIFACT
USER $USER
EXPOSE $SERVER_PORT

CMD java $JVM_OPTIONS -jar app.jar --server.port=$SERVER_PORT --working.dir=/opt/gbif/$APP_ARTIFACT --mode=RUN --spring.cloud.bootstrap.location=/opt/gbif/$APP_ARTIFACT/bootstrap.yaml
CMD java $JVM_OPTIONS -jar app.jar --server.port=$SERVER_PORT --working.dir=/opt/gbif/$APP_ARTIFACT/ --mode=RUN --spring.cloud.bootstrap.location=/opt/gbif/$APP_ARTIFACT/bootstrap.yaml
9 changes: 1 addition & 8 deletions matching-ws/pom.xml
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Expand Up @@ -15,6 +15,7 @@
<java.version>11</java.version>
<lucene.version>9.10.0</lucene.version>
<spring-boot.version>2.7.18</spring-boot.version>
<spring-cloud.version>2021.0.9</spring-cloud.version>
<lombok.version>1.18.22</lombok.version>
<spotless-maven-plugin.version>2.43.0</spotless-maven-plugin.version>
<logback.version>1.2.13</logback.version>
Expand Down Expand Up @@ -355,14 +356,6 @@
<artifactId>logstash-logback-encoder</artifactId>
<version>${logstash-logback.version}</version>
</dependency>
<!-- enable for dev -->
<!-- <dependency>-->
<!-- <groupId>org.springframework.boot</groupId>-->
<!-- <artifactId>spring-boot-devtools</artifactId>-->
<!-- <version>${spring-boot.version}</version>-->
<!-- <scope>runtime</scope>-->
<!-- <optional>true</optional>-->
<!-- </dependency>-->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-configuration-processor</artifactId>
Expand Down
5 changes: 3 additions & 2 deletions matching-ws/src/main/java/life/catalogue/matching/MatchingApplication.java
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Expand Up @@ -87,7 +87,7 @@ public void run(ApplicationArguments args) {
}

private void initialiseWebapp() {
Optional<APIMetadata> metadata = matchingService.getAPIMetadata(false);
Optional<APIMetadata> metadata = matchingService.getAPIMetadata(true);
if (metadata.isEmpty()) {
log.error("No main index found. Cannot start web services");
return;
Expand Down Expand Up @@ -136,7 +136,8 @@ private void runIndexingIfRequired(ApplicationArguments args) throws Exception {
indexingService.indexIdentifiers(id);
}

log.info("Indexing completed");
matchingService.getAPIMetadata(true);
log.info("Indexing ready");
}

private ExecutionMode getMode(ApplicationArguments args) {
Expand Down
48 changes: 11 additions & 37 deletions matching-ws/src/main/java/life/catalogue/matching/controller/MatchController.java
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Expand Up @@ -15,6 +15,7 @@
import java.util.stream.Collectors;
import life.catalogue.matching.model.*;
import life.catalogue.matching.service.MatchingService;
import life.catalogue.matching.util.IUCNUtils;
import lombok.AllArgsConstructor;
import lombok.Builder;
import lombok.Data;
Expand Down Expand Up @@ -112,9 +113,13 @@ public NameUsageMatch matchOldPaths(
HttpServletRequest response) {
return matchV2(
usageKey,
taxonID,taxonConceptID,scientificNameID,
scientificName2, scientificName,
authorship, authorship2,
taxonID,
taxonConceptID,
scientificNameID,
scientificName2,
scientificName,
authorship,
authorship2,
genericName,
specificEpithet,
infraspecificEpithet,
Expand Down Expand Up @@ -677,15 +682,15 @@ public Map<String, Object> iucnRedListV1(@PathVariable(value = "usageKey", requi
return Map.of();
}
NameUsageMatch.Status status = statusList.get(0);
String formatted = formatIucn(status.getStatus());
String formatted = IUCNUtils.formatIucn(status.getStatus());
if (formatted == null || formatted.isEmpty()) {
return Map.of();
}

String scientificName = match.getAcceptedUsage() != null ? match.getAcceptedUsage().getCanonicalName() : match.getUsage().getCanonicalName();

try {
IUCN iucn = IUCN.valueOf(formatted); // throws IllegalArgumentException if not found
IUCNUtils.IUCN iucn = IUCNUtils.IUCN.valueOf(formatted); // throws IllegalArgumentException if not found
watch.stop();
log("v1/species/iucnRedListCategory", usageKey, watch);
return Map.of(
Expand All @@ -695,7 +700,7 @@ public Map<String, Object> iucnRedListV1(@PathVariable(value = "usageKey", requi
"taxonomicStatus", NameUsageMatchV1.TaxonomicStatusV1.convert(
match.getDiagnostics().getStatus()),
"iucnTaxonID", status.getSourceId(),
"code", iucn.code
"code", iucn.getCode()
);
} catch (IllegalArgumentException e) {
log.error("IUCN category not found: {}", formatted, e);
Expand Down Expand Up @@ -757,37 +762,6 @@ private static void addIfNotNull(StringJoiner joiner, Object value) {
}
}

String formatIucn(String original){
if (original == null) {
return null;
}
// Trim the string
String trimmed = original.trim();
// Convert to uppercase
String uppercased = trimmed.toUpperCase();
// Replace any whitespace with a single underscore
return uppercased.replaceAll("\\s+", "_");
}

enum IUCN {
EXTINCT("EX"),
EXTINCT_IN_THE_WILD("EW"),
CRITICALLY_ENDANGERED ("CR"),
ENDANGERED ("EN"),
VULNERABLE ("VU"),
NEAR_THREATENED ("NT"),
CONSERVATION_DEPENDENT ("CD"),
LEAST_CONCERN ("LC"),
DATA_DEFICIENT ("DD"),
NOT_EVALUATED ("NE");

private final String code;

IUCN(String code) {
this.code = code;
}
}

@Data
@Builder
@NoArgsConstructor
Expand Down
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