Merge branch 'eml-2.2.0'

pom.xml

@@ -9,7 +9,7 @@
   </parent>
 
   <artifactId>ipt</artifactId>
-  <version>3.0.7-SNAPSHOT</version>
+  <version>3.1.0-SNAPSHOT</version>
   <packaging>war</packaging>
 
   <name>IPT</name>
@@ -43,7 +43,7 @@
     <gbif-api.version>1.16.13</gbif-api.version>
     <gbif-common.version>0.60</gbif-common.version>
     <gbif-doi.version>2.21</gbif-doi.version>
-    <gbif-metadata-profile.version>2.2</gbif-metadata-profile.version>
+    <gbif-metadata-profile.version>2.3</gbif-metadata-profile.version>
     <gbif-parsers.version>0.67</gbif-parsers.version>
     <gbif-httputils.version>1.4</gbif-httputils.version>
 

src/main/java/org/gbif/ipt/action/BaseAction.java

@@ -192,7 +192,7 @@ public String getRequestURL() {
           .replaceQueryParam("request_locale")
           .build().toString();
     } catch (RuntimeException e) {
-      LOG.warn("Failed to reconstruct requestURL from " + req.getRequestURL(), e);
+      LOG.warn("Failed to reconstruct requestURL from {}. Error: {}", req.getRequestURL(), e.getMessage());
     }
     return getBaseURL();
   }

src/main/java/org/gbif/ipt/action/manage/MetadataAction.java

@@ -362,14 +362,25 @@ public void prepare() {
 
         // update frequencies list, derived from XML vocabulary, and displayed in drop-down on basic metadata page
         frequencies = new LinkedHashMap<>();
-        frequencies.putAll(vocabManager.getI18nVocab(Constants.VOCAB_URI_UPDATE_FREQUENCIES, getLocaleLanguage(), false));
-
+        // temporary fix: remove "unkown" from vocabulary
+        vocabManager.getI18nVocab(Constants.VOCAB_URI_UPDATE_FREQUENCIES, getLocaleLanguage(), false)
+          .entrySet()
+          .stream()
+          .filter(p -> !"unkown".equals(p.getKey()))
+          .forEach(p -> frequencies.put(p.getKey(), p.getValue()));
 
         // sanitize intellectualRights - pre-v2.2 text was manually entered and may have characters that break js
         if (getEml().getIntellectualRights() != null) {
           getEml().setIntellectualRights(removeNewlineCharacters(getEml().getIntellectualRights()));
         }
 
+        // Public, published occurrence resources have a distribution download URL
+        if (CoreRowType.OCCURRENCE.toString().equalsIgnoreCase(resource.getCoreType())
+            && resource.isPublished()
+            && resource.isPubliclyAvailable()) {
+          resource.getEml().setDistributionDownloadUrl(cfg.getBaseUrl() + "/archive.do?r=" + resource.getShortname());
+        }
+
         // populate agent vocabularies
         loadAgentVocabularies();
 
@@ -397,10 +408,6 @@ public void prepare() {
         }
 
         if (isHttpPost()) {
-          resource.getEml().getDescription().clear();
-          resource.getEml().getContacts().clear();
-          resource.getEml().getCreators().clear();
-          resource.getEml().getMetadataProviders().clear();
           resource.getEml().setIntellectualRights(null);
 
           // publishing organisation, if provided must match organisation
@@ -415,6 +422,17 @@ public void prepare() {
         }
         break;
 
+      case CONTACTS_SECTION:
+        // populate agent vocabularies
+        loadAgentVocabularies();
+        if (isHttpPost()) {
+          resource.getEml().getContacts().clear();
+          resource.getEml().getCreators().clear();
+          resource.getEml().getMetadataProviders().clear();
+          resource.getEml().getAssociatedParties().clear();
+        }
+        break;
+
       case GEOGRAPHIC_COVERAGE_SECTION:
         if (isHttpPost()) {
           resource.getEml().getGeospatialCoverages().clear();
@@ -443,19 +461,13 @@ public void prepare() {
         }
         break;
 
-      case PARTIES_SECTION:
-        // populate agent vocabularies
-        loadAgentVocabularies();
-        if (isHttpPost()) {
-          resource.getEml().getAssociatedParties().clear();
-        }
-        break;
-
       case PROJECT_SECTION:
         // populate agent vocabularies
         loadAgentVocabularies();
         if (isHttpPost()) {
           resource.getEml().getProject().getPersonnel().clear();
+          resource.getEml().getProject().getAwards().clear();
+          resource.getEml().getProject().getRelatedProjects().clear();
         }
         break;
 
@@ -506,9 +518,9 @@ public void prepare() {
 
   @Override
   public String save() throws Exception {
-    // before saving, the minimum amount of mandatory metadata must have been provided, and ALL metadata sections must
-    // be valid, otherwise an error is displayed
-    if (emlValidator.areAllSectionsValid(this, resource)) {
+    // before saving, the minimum amount of mandatory metadata must have been provided, and the current metadata section
+    // must be valid, otherwise an error is displayed
+    if (emlValidator.isSectionValid(this, resource, section)) {
       // Save metadata information (eml.xml)
       resourceManager.saveEml(resource);
       // save date metadata was last modified
@@ -520,6 +532,12 @@ public String save() throws Exception {
       // progress to next section, since save succeeded
       switch (section) {
         case BASIC_SECTION:
+          next = MetadataSection.CONTACTS_SECTION;
+          break;
+        case CONTACTS_SECTION:
+          next = MetadataSection.ACKNOWLEDGEMENTS_SECTION;
+          break;
+        case ACKNOWLEDGEMENTS_SECTION:
           next = MetadataSection.GEOGRAPHIC_COVERAGE_SECTION;
           break;
         case GEOGRAPHIC_COVERAGE_SECTION:
@@ -529,12 +547,12 @@ public String save() throws Exception {
           next = MetadataSection.TEMPORAL_COVERAGE_SECTION;
           break;
         case TEMPORAL_COVERAGE_SECTION:
+          next = MetadataSection.ADDITIONAL_DESCRIPTION_SECTION;
+          break;
+        case ADDITIONAL_DESCRIPTION_SECTION:
           next = MetadataSection.KEYWORDS_SECTION;
           break;
         case KEYWORDS_SECTION:
-          next = MetadataSection.PARTIES_SECTION;
-          break;
-        case PARTIES_SECTION:
           next = MetadataSection.PROJECT_SECTION;
           break;
         case PROJECT_SECTION:
@@ -689,7 +707,7 @@ public String getResourceHasCore() {
 
   /**
    * On the basic metadata page, this map populates the update frequencies dropdown. The map is derived from the
-   * vocabulary {@link -linkoffline http://rs.gbif.org/vocabulary/eml/update_frequency.xml}.
+   * vocabulary <a href="http://rs.gbif.org/vocabulary/eml/update_frequency.xml">http://rs.gbif.org/vocabulary/eml/update_frequency.xml</a>.
    *
    * @return update frequencies map
    */
@@ -859,7 +877,7 @@ private void loadAgentVocabularies() {
       Agent current = new Agent();
       current.setFirstName(getCurrentUser().getFirstname());
       current.setLastName(getCurrentUser().getLastname());
-      current.setEmail(getCurrentUser().getEmail());
+      current.setEmail(Collections.singletonList(getCurrentUser().getEmail()));
 
       // contacts list
       Agent firstContact = null;

src/main/java/org/gbif/ipt/action/manage/OverviewAction.java

@@ -96,10 +96,10 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.UUID;
-import java.util.stream.Stream;
 
 import javax.annotation.Nullable;
 import javax.validation.constraints.NotNull;
+import javax.xml.parsers.ParserConfigurationException;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -1252,6 +1252,14 @@ public void prepare() {
 
       usableSpace = cfg.getDataDir().getDataDirUsableSpace();
       freeDiscSpaceReadable = org.apache.commons.io.FileUtils.byteCountToDisplaySize(usableSpace);
+
+      if (resource.isPublished()
+          && resource.getEml() != null
+          && resource.getEml().getProject() != null
+          && resource.getEml().getProject().getTitle() != null
+          && resource.getEml().getProject().getPersonnel().isEmpty()) {
+        addActionWarning(getText("validation.personnel.now.required"));
+      }
     }
   }
 
@@ -1652,7 +1660,7 @@ public String replaceEml() {
       LOG.error("Failed to replace EML", e);
       addActionError(getText("manage.overview.failed.replace.eml"));
       return ERROR;
-    } catch (SAXException e) {
+    } catch (SAXException | ParserConfigurationException e) {
       LOG.error("Failed to create EML validator", e);
       addActionError(getText("manage.overview.failed.replace.eml.validator"));
       return ERROR;

src/main/java/org/gbif/ipt/action/portal/ResourceAction.java

@@ -899,15 +899,27 @@ private boolean isValidAgent(Agent agent) {
    */
   private boolean agentsMatch(Agent agent1, Agent agent2) {
     boolean namesMatch = false;
-    boolean emailsMatch;
+    boolean emailsMatch = false;
     boolean positionsMatch;
 
     if (agent1.getFullName() != null && agent2.getFullName() != null) {
       namesMatch = agent1.getFullName().equals(agent2.getFullName());
     }
 
     if (agent1.getEmail() != null && agent2.getEmail() != null) {
-      emailsMatch = agent1.getEmail().equalsIgnoreCase(agent2.getEmail());
+      emailsMatch = true;
+      if (agent1.getEmail().size() != agent2.getEmail().size()) {
+        emailsMatch = false;
+      } else {
+        for (int i = 0; i < agent1.getEmail().size(); i++) {
+          String email1 = agent1.getEmail().get(i);
+          String email2 = agent2.getEmail().get(i);
+          if (!email1.equalsIgnoreCase(email2)) {
+            emailsMatch = false;
+            break;
+          }
+        }
+      }
     } else {
       emailsMatch = true;
     }

src/main/java/org/gbif/ipt/config/Constants.java

@@ -127,6 +127,9 @@ public final class Constants {
   public static final Set<String> GBIF_SUPPORTED_LICENSES;
   public static final Set<String> GBIF_SUPPORTED_LICENSES_CODES;
 
+  public static final String EML_2_1_1_SCHEMA = "eml://ecoinformatics.org/eml-2.1.1";
+  public static final String EML_2_2_0_SCHEMA = "https://eml.ecoinformatics.org/eml-2.2.0";
+
   static {
     Set<String> licencesInternal = new HashSet<>();
     licencesInternal.add("http://creativecommons.org/publicdomain/zero/1.0/legalcode");

src/main/java/org/gbif/ipt/model/Resource.java

@@ -1464,7 +1464,12 @@ public String generateResourceCitation(@NotNull BigDecimal version, @NotNull URI
 
     // make list of verified agents (having first and last name)
     Set<String> verifiedAuthorList = new LinkedHashSet<>();
-    Stream.of(getEml().getCreators(), getEml().getMetadataProviders())
+
+    List<Agent> suitableAssociatedParties = getEml().getAssociatedParties().stream()
+        .filter(p -> "originator".equalsIgnoreCase(p.getRole()) || "metadataProvider".equalsIgnoreCase(p.getRole()))
+        .collect(Collectors.toList());
+
+    Stream.of(getEml().getCreators(), getEml().getMetadataProviders(), suitableAssociatedParties)
         .flatMap(Collection::stream)
         .map(this::getCitationAgentName)
         .filter(StringUtils::isNotEmpty)

src/main/java/org/gbif/ipt/model/voc/MetadataSection.java

@@ -21,9 +21,12 @@
  */
 public enum MetadataSection {
   BASIC_SECTION("basic"),
+  CONTACTS_SECTION("contacts"),
+  ACKNOWLEDGEMENTS_SECTION("acknowledgements"),
   GEOGRAPHIC_COVERAGE_SECTION ("geocoverage"),
   TAXANOMIC_COVERAGE_SECTION ("taxcoverage"),
   TEMPORAL_COVERAGE_SECTION ("tempcoverage"),
+  ADDITIONAL_DESCRIPTION_SECTION("additionalDescription"),
   PROJECT_SECTION ("project"),
   METHODS_SECTION ("methods"),
   CITATIONS_SECTION ("citations"),

src/main/java/org/gbif/ipt/service/manage/ResourceManager.java

@@ -43,6 +43,7 @@
 import java.util.concurrent.ThreadPoolExecutor;
 
 import javax.annotation.Nullable;
+import javax.xml.parsers.ParserConfigurationException;
 
 import org.apache.commons.collections4.ListValuedMap;
 import org.xml.sax.SAXException;
@@ -421,7 +422,7 @@ Resource create(String shortname, String type, File dwca, User creator, BaseActi
    * @param emlFile
    * @param validate
    */
-  void replaceEml(Resource resource, File emlFile, boolean validate) throws SAXException, IOException, InvalidEmlException, ImportException;
+  void replaceEml(Resource resource, File emlFile, boolean validate) throws SAXException, ParserConfigurationException, IOException, InvalidEmlException, ImportException;
 
   /**
    * Replace the datapackage metadata file in a resource by the provided file