Work for gbif/rs.gbif.org#138

matching-ws/Dockerfile

@@ -9,17 +9,33 @@ ARG CLB_URL=""
 ARG CLB_USER=""
 ARG CLB_PASSWORD=""
 ENV CLB_API_URL="https://api.checklistbank.org"
-ENV BACKEND_BRANCH="matching-ws"
+ARG GIT_BRANCH=""
 
-# Clone the backend repository
-RUN rm -Rf backend
-RUN git clone https://github.com/CatalogueOfLife/backend.git
+# Local builds - run from root of backend
+COPY .. /app/backend
 WORKDIR /app/backend
-RUN git checkout $BACKEND_BRANCH
+
+# Run a script to validate the arguments
+#RUN if [ -z "$GIT_BRANCH" ]; then \
+#        echo "Error: GIT_BRANCH is not set." >&2; \
+#        exit 1; \
+#    fi
+
+# Clone the backend repository
+#RUN rm -Rf backend
+#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
+
 # 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)"
 
@@ -38,12 +54,6 @@ RUN if [ -n "$CLB_DATASET_ID" ]; then \
         echo "{}" > /app/backend/dataset.json; \
     fi
 
-# 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 verify
-
 # Copy the executable JAR file from the builder image to the new image
 FROM openjdk:11
 

matching-ws/README.md

@@ -58,10 +58,9 @@ mvn clean install spring-boot:repackage
 ### Software only
 To build a software only docker image, run the following command from the root directory of this module (backend/matching-ws):
 ```bash
-docker buildx build \
---platform linux/amd64 . -t matching-ws:v1 
+docker buildx build --platform linux/amd64 . -t matching-ws:1.0-SNAPSHOT
 ```
-For this image to be of use, an lucene index must be pre-generated and mounted as a docker
+For this image to be of use, a lucene index must be pre-generated and mounted as a docker
 volume with the docker container.
 
 
@@ -87,6 +86,14 @@ docker buildx build \
 --build-arg CLB_PASSWORD=****
 ```
 
+### Local docker builds for development purposes
+
+For local development, the following command can be used to build a docker image.
+Run this from the root of the cloned copy of the `backend` repository:
+```bash
+docker build -f matching-ws/Dockerfile . -t matching-local-build
+```
+
 ## Running docker image
 
 Pre-built Docker images can be pulled from the Docker repository at docker.gbif.org and run as follows:

matching-ws/pom.xml

@@ -17,8 +17,7 @@
       <spring-boot.version>2.7.18</spring-boot.version>
       <lombok.version>1.18.22</lombok.version>
       <spotless-maven-plugin.version>2.43.0</spotless-maven-plugin.version>
-      <gbif-api.version>1.6.0</gbif-api.version>
-      <logback.version>1.2.11</logback.version>
+      <logback.version>1.4.5</logback.version>
       <mybatis-spring-boot.version>2.3.1</mybatis-spring-boot.version>
       <gbif-common.version>0.60</gbif-common.version>
       <jackson.version>2.17.0</jackson.version>
@@ -79,6 +78,10 @@
       <artifactId>spring-boot-starter</artifactId>
       <version>${spring-boot.version}</version>
       <exclusions>
+        <exclusion>
+          <groupId>org.apache.logging.log4j</groupId>
+          <artifactId>log4j-to-slf4j</artifactId>
+        </exclusion>
         <exclusion>
           <groupId>ch.qos.logback</groupId>
           <artifactId>logback-classic</artifactId>
@@ -146,22 +149,34 @@
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-api</artifactId>
+      <version>1.7.36</version>
     </dependency>
+<!--    <dependency>-->
+<!--      <groupId>org.slf4j</groupId>-->
+<!--      <artifactId>slf4j-simple</artifactId>-->
+<!--      <version>2.0.12</version>-->
+<!--    </dependency>-->
+<!--    <dependency>-->
+<!--      <groupId>org.slf4j</groupId>-->
+<!--      <artifactId>jul-to-slf4j</artifactId>-->
+<!--      <version>2.0.6</version>-->
+<!--    </dependency>-->
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-classic</artifactId>
-      <version>${logback.version}</version>
+      <version>1.2.13</version>
     </dependency>
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-core</artifactId>
-      <version>${logback.version}</version>
+      <version>1.2.13</version>
     </dependency>
     <dependency>
       <groupId>org.mybatis.spring.boot</groupId>
       <artifactId>mybatis-spring-boot-starter</artifactId>
       <version>${mybatis-spring-boot.version}</version>
     </dependency>
+    <!-- enable for dev -->
 <!--    <dependency>-->
 <!--      <groupId>org.springframework.boot</groupId>-->
 <!--      <artifactId>spring-boot-devtools</artifactId>-->
@@ -291,6 +306,8 @@
         </configuration>
         <executions>
           <execution>
+            <id>repackage</id>
+            <phase>package</phase>
             <goals>
               <goal>repackage</goal>
             </goals>

matching-ws/src/main/java/life/catalogue/matching/MatchingApplication.java

@@ -19,6 +19,7 @@
 import org.springframework.context.annotation.Profile;
 
 import java.text.NumberFormat;
+import java.util.Optional;
 
 /**
  * Main application class for the matching-ws module.
@@ -41,36 +42,46 @@ public MatchingApplication(MatchingService matchingService) {
 
   @Override
   public void run(ApplicationArguments args) {
-    APIMetadata metadata = matchingService.getIndexMetadata();
-    LOG.info("Web services started. Index size: {} taxa, size on disk: {}",
-      NumberFormat.getInstance().format(metadata.getMainIndex().getNameUsageCount()),
-      metadata.getMainIndex().getSizeInMB() > 0 ? NumberFormat.getInstance().format(metadata.getMainIndex().getSizeInMB()) + "MB" : "unknown"
-    );
+
+    Optional<APIMetadata> metadata = matchingService.getIndexMetadata();
+    if (metadata.isEmpty()) {
+      LOG.error("No main index found. Cannot start web services");
+      return;
+    }
+
+    metadata.ifPresent(m -> {
+      LOG.info("Web services started. Index size: {} taxa, size on disk: {}",
+      NumberFormat.getInstance().format(
+        m.getMainIndex().getNameUsageCount()),
+        m.getMainIndex().getSizeInMB() > 0 ? NumberFormat.getInstance().format(m.getMainIndex().getSizeInMB()) + "MB" : "unknown");
+    });
   }
 
   @Bean
   public OpenAPI customOpenAPI() {
-    APIMetadata metadata = matchingService.getIndexMetadata();
-    String title = metadata.getMainIndex().getDatasetTitle() != null ?
-      metadata.getMainIndex().getDatasetTitle() + " Matching Service API" :
-      "COL Matching Service API";
-    String description = "API for matching scientific names to taxa in the checklist" +
-      (metadata.getMainIndex().getDatasetTitle() != null ? " " + metadata.getMainIndex().getDatasetTitle() : "");
-
-    OpenAPI openAPI = new OpenAPI()
-      .info(new Info()
-        .title(title)
-        .description(description)
-        .version(version)
-        .license(new License()
-          .name(licence)
-          .url(licenceUrl)));
-
-    if (metadata.getMainIndex().getDatasetKey() != null) {
-      openAPI.externalDocs(new ExternalDocumentation()
-        .description(metadata.getMainIndex().getDatasetTitle())
-        .url("https://checklistbank.org/dataset/" + metadata.getMainIndex().getDatasetKey()));
-    }
+    Optional<APIMetadata> metadata = matchingService.getIndexMetadata();
+    OpenAPI openAPI = new OpenAPI();
+    metadata.ifPresent(m -> {
+      String title = m.getMainIndex().getDatasetTitle() != null ?
+        m.getMainIndex().getDatasetTitle() + " Matching Service API" :
+        "COL Matching Service API";
+      String description = "API for matching scientific names to taxa in the checklist" +
+        (m.getMainIndex().getDatasetTitle() != null ? " " + m.getMainIndex().getDatasetTitle() : "");
+
+          openAPI.info(new Info()
+          .title(title)
+          .description(description)
+          .version(version)
+          .license(new License()
+            .name(licence)
+            .url(licenceUrl)));
+
+      if (m.getMainIndex().getDatasetKey() != null) {
+        openAPI.externalDocs(new ExternalDocumentation()
+          .description(m.getMainIndex().getDatasetTitle())
+          .url("https://checklistbank.org/dataset/" + m.getMainIndex().getDatasetKey()));
+      }
+    });
 
     return openAPI;
   }

matching-ws/src/main/java/life/catalogue/matching/controller/IDController.java

@@ -19,8 +19,11 @@
 @RestController
 public class IDController {
 
-  @Autowired
-  MatchingService matchingService;
+  final MatchingService matchingService;
+
+  public IDController(MatchingService matchingService) {
+    this.matchingService = matchingService;
+  }
 
   @Operation(
     operationId = "idLookupByDataset",

matching-ws/src/main/java/life/catalogue/matching/controller/MatchController.java

@@ -1,7 +1,7 @@
 package life.catalogue.matching.controller;
 
-import static life.catalogue.matching.util.CleanupUtils.clean;
 import static life.catalogue.matching.service.MatchingService.first;
+import static life.catalogue.matching.util.CleanupUtils.*;
 
 import io.swagger.v3.oas.annotations.Hidden;
 import io.swagger.v3.oas.annotations.Operation;
@@ -23,7 +23,7 @@
 import life.catalogue.matching.service.MatchingService;
 import life.catalogue.parser.RankParser;
 import life.catalogue.parser.UnparsableException;
-import org.apache.commons.lang3.StringUtils;
+
 import org.gbif.nameparser.api.Rank;
 
 import org.springdoc.api.annotations.ParameterObject;
@@ -46,9 +46,7 @@
 @RestController
 public class MatchController implements ErrorController {
 
-  @Autowired
-  MatchingService matchingService;
-
+  private final MatchingService matchingService;
   private final ErrorAttributes errorAttributes;
 
   @Value("${v1.enabled:false}")
@@ -72,14 +70,14 @@ public Map<String, Object> error(WebRequest request) {
   }
 
   private boolean isTraceRequested(String traceRequested) {
-    return StringUtils.isNotBlank(traceRequested) &&
-      (traceRequested.equalsIgnoreCase("true") || traceRequested.equalsIgnoreCase("on"));
+    return "true".equalsIgnoreCase(traceRequested) || "on".equalsIgnoreCase(traceRequested);
   }
 
   @Autowired
-  public MatchController(ErrorAttributes errorAttributes) {
+  public MatchController(ErrorAttributes errorAttributes, MatchingService matchingService) {
     Assert.notNull(errorAttributes, "ErrorAttributes must not be null");
     this.errorAttributes = errorAttributes;
+    this.matchingService = matchingService;
   }
 
   private Map<String, Object> getErrorAttributes(WebRequest request) {
@@ -112,7 +110,7 @@ private Map<String, Object> getErrorAttributes(WebRequest request) {
   @GetMapping(
     value = {"v2/metadata"},
     produces = "application/json")
-  public APIMetadata metadata(){
+  public Optional<APIMetadata> metadata(){
     return matchingService.getIndexMetadata();
   }
 
@@ -397,6 +395,9 @@ public NameUsageMatch matchV2(
       produces = "application/json")
   public Object matchFlatV1(
       @RequestParam(value = "usageKey", required = false) String usageKey,
+      @RequestParam(value = "taxonID", required = false) String taxonID,
+      @RequestParam(value = "taxonConceptID", required = false) String taxonConceptID,
+      @RequestParam(value = "scientificNameID", required = false) String scientificNameID,
       @RequestParam(value = "name", required = false) String scientificName2,
       @RequestParam(value = "scientificName", required = false) String scientificName,
       @RequestParam(value = "authorship", required = false) String authorship2,
@@ -419,9 +420,9 @@ public Object matchFlatV1(
     Optional<NameUsageMatchFlatV1> optionalNameUsageMatchV1 = NameUsageMatchFlatV1.createFrom(
         matchingService.match(
             removeNulls(usageKey),
-            null,
-          null,
-          null,
+            removeNulls(taxonID),
+            removeNulls(taxonConceptID),
+            removeNulls(scientificNameID),
             first(removeNulls(scientificName), removeNulls(scientificName2)),
             first(removeNulls(authorship), removeNulls(authorship2)),
             removeNulls(genericName),
@@ -538,6 +539,9 @@ public Object matchFlatV1(
     produces = "application/json")
   public Object matchV1(
     @RequestParam(value = "usageKey", required = false) String usageKey,
+    @RequestParam(value = "taxonID", required = false) String taxonID,
+    @RequestParam(value = "taxonConceptID", required = false) String taxonConceptID,
+    @RequestParam(value = "scientificNameID", required = false) String scientificNameID,
     @RequestParam(value = "name", required = false) String scientificName2,
     @RequestParam(value = "scientificName", required = false) String scientificName,
     @RequestParam(value = "authorship", required = false) String authorship2,
@@ -559,10 +563,11 @@ public Object matchV1(
     classification.setClazz(response.getParameter("class"));
     Optional<NameUsageMatchV1> optionalNameUsageMatchV1 = NameUsageMatchV1.createFrom(
       matchingService.match(
+
         removeNulls(usageKey),
-        null,
-        null,
-        null,
+        removeNulls(taxonID),
+        removeNulls(taxonConceptID),
+        removeNulls(scientificNameID),
         first(removeNulls(scientificName), removeNulls(scientificName2)),
         first(removeNulls(authorship), removeNulls(authorship2)),
         removeNulls(genericName),
@@ -581,17 +586,6 @@ public Object matchV1(
     }
   }
 
-  public static String removeNulls(String value) {
-    if (value != null) {
-      value = StringUtils.trimToEmpty(value);
-      if (value.equalsIgnoreCase("null")) {
-        return null;
-      }
-      return value;
-    }
-    return null;
-  }
-
   private Rank parseRank(String value) {
     try {
       if (!Objects.isNull(value) && !value.isEmpty()) {
@@ -605,8 +599,4 @@ private Rank parseRank(String value) {
     }
     return null;
   }
-
-  private boolean bool(Boolean bool) {
-    return bool != null && bool;
-  }
 }