Merge branch 'master' into dev_jdk8

gbif · Jun 10, 2024 · e8c0be0 · e8c0be0
2 parents 6e5e7e8 + 9daea0d
commit e8c0be0
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Showing 15 changed files with 28 additions and 22 deletions.
diff --git a/api/pom.xml b/api/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>vocabulary-parent</artifactId>
     <groupId>org.gbif.vocabulary</groupId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

diff --git a/core/pom.xml b/core/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <groupId>org.gbif.vocabulary</groupId>
     <artifactId>vocabulary-parent</artifactId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
 
   <artifactId>core</artifactId>

diff --git a/model/pom.xml b/model/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <groupId>org.gbif.vocabulary</groupId>
     <artifactId>vocabulary-parent</artifactId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
 
   <artifactId>model</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -11,7 +11,7 @@
   <groupId>org.gbif.vocabulary</groupId>
   <artifactId>vocabulary-parent</artifactId>
   <packaging>pom</packaging>
-  <version>1.0.8-SNAPSHOT</version>
+  <version>1.0.9-SNAPSHOT</version>
 
   <modules>
     <module>core</module>

diff --git a/tools/pom.xml b/tools/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>vocabulary-parent</artifactId>
     <groupId>org.gbif.vocabulary</groupId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

diff --git a/vocabulary-cli/pom.xml b/vocabulary-cli/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>vocabulary-parent</artifactId>
     <groupId>org.gbif.vocabulary</groupId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

diff --git a/vocabulary-importer/README.md b/vocabulary-importer/README.md
@@ -94,12 +94,10 @@ This tool can be run via command line by sending these params:
 * *--csvDelimiter, -d  (Optional)*
 
     Delimiter of the CSV files for concepts and hidden labels. If not specified it uses a comma (",").
-    Note that some delimiters may need to be escaped for Java, e.g.: \\\\|
 
 * *--listDelimiter, -ld (Optional)*
 
-    Delimiter to specify multiple values in the alternative labels. If not specified it uses a pipe ("|").
-    Note that some delimiters may need to be escaped for Java, e.g.: \\\\|
+    Delimiter to specify multiple values in the alternative labels. If not specified it uses a pipe ("|")
 
 * *--apiUrl, -a*
 

diff --git a/vocabulary-importer/pom.xml b/vocabulary-importer/pom.xml
@@ -3,12 +3,12 @@
   <parent>
     <groupId>org.gbif.vocabulary</groupId>
     <artifactId>vocabulary-parent</artifactId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 
   <artifactId>vocabulary-importer</artifactId>
-  <version>1.0.8-SNAPSHOT</version>
+  <version>1.0.9-SNAPSHOT</version>
 
   <properties>
     <main.basedir>${project.parent.basedir}</main.basedir>

diff --git a/vocabulary-importer/src/main/java/org/gbif/vocabulary/importer/Fields.java b/vocabulary-importer/src/main/java/org/gbif/vocabulary/importer/Fields.java
@@ -28,5 +28,5 @@ public class Fields {
   static final String TAGS = "TAGS";
 
   static final List<String> CONCEPT_FIELDS =
-      Arrays.asList(CONCEPT, PARENT, SAME_AS_URIS, EXTERNAL_DEFINITIONS);
+      Arrays.asList(CONCEPT, PARENT, SAME_AS_URIS, EXTERNAL_DEFINITIONS, TAGS);
 }
diff --git a/vocabulary-importer/src/main/java/org/gbif/vocabulary/importer/VocabularyImporter.java b/vocabulary-importer/src/main/java/org/gbif/vocabulary/importer/VocabularyImporter.java
@@ -46,6 +46,7 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.function.Function;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -566,7 +567,8 @@ private ConceptData parseConceptFields(
     if (headersIndexes.containsKey(SAME_AS_URIS)
         && !Strings.isNullOrEmpty(values[headersIndexes.get(SAME_AS_URIS)])) {
       Set<URI> sameAsUris = new HashSet<>();
-      String[] urisValues = values[headersIndexes.get(SAME_AS_URIS)].split(listDelimiter);
+      String[] urisValues =
+          values[headersIndexes.get(SAME_AS_URIS)].split(Pattern.quote(listDelimiter));
       for (String uri : urisValues) {
         try {
           sameAsUris.add(URI.create(uri.trim()));
@@ -582,7 +584,8 @@ private ConceptData parseConceptFields(
     if (headersIndexes.containsKey(EXTERNAL_DEFINITIONS)
         && !Strings.isNullOrEmpty(values[headersIndexes.get(SAME_AS_URIS)])) {
       Set<URI> externalDefinitions = new HashSet<>();
-      String[] externalDefsValues = values[headersIndexes.get(SAME_AS_URIS)].split(listDelimiter);
+      String[] externalDefsValues =
+          values[headersIndexes.get(SAME_AS_URIS)].split(Pattern.quote(listDelimiter));
       for (String definition : externalDefsValues) {
         try {
           externalDefinitions.add(URI.create(definition.trim()));
@@ -597,7 +600,7 @@ private ConceptData parseConceptFields(
     // tags
     if (headersIndexes.containsKey(TAGS)
         && !Strings.isNullOrEmpty(values[headersIndexes.get(TAGS)])) {
-      String[] tagsValues = values[headersIndexes.get(TAGS)].split(listDelimiter);
+      String[] tagsValues = values[headersIndexes.get(TAGS)].split(Pattern.quote(listDelimiter));
       conceptData.tags =
           Arrays.stream(tagsValues)
               .filter(s -> !Strings.isNullOrEmpty(s))
@@ -628,7 +631,7 @@ private static List<Label> parseAlternativeLabels(
     List<Label> alternativeLabels = new ArrayList<>();
     alternativeLabelsIndexes.forEach(
         (lang, index) ->
-            Stream.of(values[index].split(listDelimiter))
+            Stream.of(values[index].split(Pattern.quote(listDelimiter)))
                 .filter(s -> !s.isEmpty())
                 .map(String::trim)
                 .forEach(

diff --git a/vocabulary-lookup/pom.xml b/vocabulary-lookup/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>vocabulary-parent</artifactId>
     <groupId>org.gbif.vocabulary</groupId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

diff --git a/vocabulary-rest-ws-client/pom.xml b/vocabulary-rest-ws-client/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>vocabulary-parent</artifactId>
     <groupId>org.gbif.vocabulary</groupId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

diff --git a/vocabulary-rest-ws/pom.xml b/vocabulary-rest-ws/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <groupId>org.gbif.vocabulary</groupId>
     <artifactId>vocabulary-parent</artifactId>
-    <version>1.0.8-SNAPSHOT</version>
+    <version>1.0.9-SNAPSHOT</version>
   </parent>
 
   <artifactId>vocabulary-rest-ws</artifactId>

diff --git a/vocabulary-rest-ws/src/main/java/org/gbif/vocabulary/restws/Application.java b/vocabulary-rest-ws/src/main/java/org/gbif/vocabulary/restws/Application.java
@@ -63,7 +63,11 @@
   RequestHeaderParamUpdateFilter.class
 })
 @ComponentScan(
-    basePackages = {"org.gbif.vocabulary.restws", "org.gbif.ws.remoteauth"},
+    basePackages = {
+      "org.gbif.vocabulary.restws",
+      "org.gbif.ws.remoteauth",
+      "org.gbif.ws.server.interceptor"
+    },
     excludeFilters = {@ComponentScan.Filter(type = FilterType.ASSIGNABLE_TYPE)})
 @EnableConfigurationProperties({
   ExportConfig.class,

diff --git a/vocabulary-rest-ws/src/main/java/org/gbif/vocabulary/restws/resources/TagResource.java b/vocabulary-rest-ws/src/main/java/org/gbif/vocabulary/restws/resources/TagResource.java
@@ -13,6 +13,7 @@
  */
 package org.gbif.vocabulary.restws.resources;
 
+import org.gbif.api.annotation.Trim;
 import org.gbif.api.model.common.paging.Pageable;
 import org.gbif.api.model.common.paging.PagingResponse;
 import org.gbif.vocabulary.model.Tag;
@@ -97,7 +98,7 @@ public Tag getTag(@PathVariable("name") String tagName) {
   @Docs.DefaultUnsuccessfulReadResponses
   @Docs.DefaultUnsuccessfulWriteResponses
   @PostMapping
-  public Tag create(@RequestBody Tag tag) {
+  public Tag create(@RequestBody @Trim Tag tag) {
     int key = tagService.create(tag);
     return tagService.get(key);
   }
@@ -115,7 +116,7 @@ public Tag create(@RequestBody Tag tag) {
   @Docs.DefaultUnsuccessfulReadResponses
   @Docs.DefaultUnsuccessfulWriteResponses
   @PutMapping("{name}")
-  public Tag update(@PathVariable("name") String tagName, @RequestBody Tag tag) {
+  public Tag update(@PathVariable("name") String tagName, @RequestBody @Trim Tag tag) {
     Tag oldTag = tagService.getByName(tagName);
     checkArgument(oldTag != null, "Tag not found for name " + tagName);
     checkArgument(