#24 EML 2.2.0 updates

- Change description type from List to String, use DocBook
- Update IPT EML template, use DocBook for description, introduction, gettingStarted, acknowledgements
- Update EmlFactory and tests

gbif-metadata-profile-eml/src/main/java/org/gbif/metadata/eml/ipt/EmlFactory.java

@@ -32,20 +32,58 @@
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.StringWriter;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.apache.commons.beanutils.MethodUtils;
 import org.apache.commons.digester3.Digester;
 import org.apache.commons.digester3.NodeCreateRule;
+import org.apache.commons.lang3.StringUtils;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.xml.sax.SAXException;
 
+import com.sun.org.apache.xml.internal.serialize.OutputFormat;
+import com.sun.org.apache.xml.internal.serialize.XMLSerializer;
+
 /**
  * This class is considered a utility for testing but should be migrated to the source when stable, as this is an EML
  * Model Factory based on the Apache Commons Digester and will be used when importing DwC-A.
  */
 public class EmlFactory {
 
+  // Define pairs of DocBook tags. MUST MATCH HTML tags!
+  private static final String[] DOCBOOK_TAGS = {
+      "<section>", "</section>",
+      "<title>", "</title>",
+      "<para>", "</para>",
+      "<itemizedlist>", "</itemizedlist>",
+      "<listitem>", "</listitem>",
+      "<orderedlist>", "</orderedlist>",
+      "<emphasis>", "</emphasis>",
+      "<subscript>", "</subscript>",
+      "<superscript>", "</superscript>",
+      "<literalLayout>", "</literalLayout>"
+  };
+
+  // Define pairs of HTML tags. MUST MATCH DocBook tags!
+  private static final String[] HTML_TAGS = {
+      "<div>", "</div>",
+      "<h1>", "</h1>",
+      "<p>", "</p>",
+      "<ul>", "</ul>",
+      "<li>", "</li>",
+      "<ol>", "</ol>",
+      "<b>", "</b>",
+      "<sub>", "</sub>",
+      "<sup>", "</sup>",
+      "<pre>", "</pre>"
+  };
+
   /**
    * Uses rule based parsing to read the EML XML and build the EML model.
    * Note the following: - Metadata provider rules are omitted on the assumption that the provider is the same as the
@@ -89,9 +127,11 @@ public static Eml build(InputStream xml)
 
     digester.addBeanPropertySetter("eml/dataset/language", "language");
 
-    // descriptions, broken into multiple paragraphs
-    digester.addCallMethod("eml/dataset/abstract/para", "addDescriptionPara", 1);
-    digester.addCallParam("eml/dataset/abstract/para", 0);
+    // DocBook description, gettingStarted, introduction, acknowledgements
+    digester.addRule("eml/dataset/abstract", new SetSerializedNodeRule("setDescription", "abstract"));
+    digester.addRule("eml/dataset/gettingStarted", new SetSerializedNodeRule("setGettingStarted", "gettingStarted"));
+    digester.addRule("eml/dataset/introduction", new SetSerializedNodeRule("setIntroduction", "introduction"));
+    digester.addRule("eml/dataset/acknowledgements", new SetSerializedNodeRule("setAcknowledgements", "acknowledgements"));
 
     digester.addBeanPropertySetter("eml/dataset/additionalInfo/para", "additionalInfo");
     digester.addRule("eml/dataset/intellectualRights/para", new NodeCreateRule(Node.ELEMENT_NODE));
@@ -468,4 +508,71 @@ private static void addJGTICuratorialIUnit(Digester digester) {
     // JGTICuratorialIUnit to the list in
     // EML
   }
+
+  // Converter to literal XML (DocBook) ant then to HTML
+  public static class SetSerializedNodeRule extends NodeCreateRule {
+
+    private String method;
+    private String wrapperElement;
+
+    public SetSerializedNodeRule() throws ParserConfigurationException {
+      super(Node.ELEMENT_NODE);
+    }
+
+    public SetSerializedNodeRule(String method, String wrapperElement)
+        throws ParserConfigurationException {
+      this.method = method;
+      this.wrapperElement = wrapperElement;
+    }
+
+    @Override
+    public void end(String namespace, String name) throws Exception {
+      Element nodeToSerialize = super.getDigester().pop();
+      String serializedNode = serializeNode(nodeToSerialize);
+      invokeMethodOnTopOfStack(method, serializedNode);
+    }
+
+    protected String serializeNode(Element nodeToSerialize) throws Exception {
+      String htmlOutput;
+
+      try (StringWriter writer = new StringWriter()) {
+        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+        DocumentBuilder builder = factory.newDocumentBuilder();
+        Document doc = builder.newDocument();
+        OutputFormat format = new OutputFormat(doc);
+        format.setOmitXMLDeclaration(true);
+        XMLSerializer serializer = new XMLSerializer(writer, format);
+        serializer.serialize(nodeToSerialize);
+
+        String serializedDocBookXml = writer.getBuffer().toString();
+        String unwrappedDocBookXml = unwrapParentTag(serializedDocBookXml);
+        htmlOutput = convertDocBookToHtml(unwrappedDocBookXml);
+      }
+
+      return htmlOutput;
+    }
+
+    private String unwrapParentTag(String str) {
+      return StringUtils.replaceEach(
+          str,
+          new String[] {"<" + wrapperElement + ">", "</" + wrapperElement + ">"},
+          new String[] {"", ""});
+    }
+
+    private String convertDocBookToHtml(String docbookXmlString) {
+      // Replace links
+      String docBookXmlStringWithLinksReplaces =
+          docbookXmlString.replaceAll(
+              "<ulink\\s+url=\"(.*?)\">\\s*<citetitle>(.*?)</citetitle>\\s*</ulink>",
+              "<a href=\"$1\">$2</a>");
+
+      // Perform replacements
+      return StringUtils.replaceEach(docBookXmlStringWithLinksReplaces, DOCBOOK_TAGS, HTML_TAGS);
+    }
+
+    protected void invokeMethodOnTopOfStack(String methodName, String param) throws Exception {
+      Object objOnTopOfStack = getDigester().peek();
+      MethodUtils.invokeExactMethod(objOnTopOfStack, methodName, param);
+    }
+  }
 }

gbif-metadata-profile-eml/src/main/java/org/gbif/metadata/eml/ipt/model/Eml.java

@@ -37,6 +37,7 @@
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
+import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
@@ -56,6 +57,34 @@ public class Eml implements Serializable {
 
   private static final Logger LOG = LoggerFactory.getLogger(Eml.class);
 
+  // Define pairs of DocBook tags. MUST MATCH HTML tags!
+  private static final String[] DOCBOOK_TAGS = {
+      "<section>", "</section>",
+      "<title>", "</title>",
+      "<para>", "</para>",
+      "<itemizedlist>", "</itemizedlist>",
+      "<listitem>", "</listitem>",
+      "<orderedlist>", "</orderedlist>",
+      "<emphasis>", "</emphasis>",
+      "<subscript>", "</subscript>",
+      "<superscript>", "</superscript>",
+      "<literalLayout>", "</literalLayout>"
+  };
+
+  // Define pairs of HTML tags. MUST MATCH DocBook tags!
+  private static final String[] HTML_TAGS = {
+      "<div>", "</div>",
+      "<h1>", "</h1>",
+      "<p>", "</p>",
+      "<ul>", "</ul>",
+      "<li>", "</li>",
+      "<ol>", "</ol>",
+      "<b>", "</b>",
+      "<sub>", "</sub>",
+      "<sup>", "</sup>",
+      "<pre>", "</pre>"
+  };
+
   private static final Pattern PACKAGED_ID_PATTERN = Pattern.compile("/v([0-9]+(\\.\\d+)?)$");
   private static final char SEMICOLON = ';';
   private static final char COMMA = ',';
@@ -77,7 +106,7 @@ public class Eml implements Serializable {
   /**
    * Description, composed of one or more paragraphs.
    */
-  private List<String> description = new ArrayList<>();
+  private String description;
 
   /**
    * This is not in the GBIF extended metadata document, but seems like a sensible placeholder that can be used to
@@ -244,6 +273,11 @@ public class Eml implements Serializable {
    */
   private List<MaintenanceChange> maintenanceChangeHistory = new ArrayList<>();
 
+  /**
+   * Current change of maintenance update frequency.
+   */
+  private MaintenanceChange currentMaintenanceChange;
+
   /**
    * The 'creator' element provides the full name of the person, organization, or position who created the resource.
    * The list of creators for a resource represent the people and organizations who should be cited for the resource.
@@ -738,6 +772,14 @@ public void setMaintenanceChangeHistory(List<MaintenanceChange> maintenanceChang
     this.maintenanceChangeHistory = maintenanceChangeHistory;
   }
 
+  public MaintenanceChange getCurrentMaintenanceChange() {
+    return currentMaintenanceChange;
+  }
+
+  public void setCurrentMaintenanceChange(MaintenanceChange currentMaintenanceChange) {
+    this.currentMaintenanceChange = currentMaintenanceChange;
+  }
+
   public List<Agent> getCreators() {
     return creators;
   }
@@ -849,7 +891,7 @@ public String getCreatorName() {
     return null;
   }
 
-  public List<String> getDescription() {
+  public String getDescription() {
     return getAbstract();
   }
 
@@ -901,15 +943,6 @@ public void addAlternateIdentifier(String alternateIdentifier) {
     alternateIdentifiers.add(alternateIdentifier);
   }
 
-  /**
-   * Adds another paragraph to description.
-   *
-   * @param para paragraph
-   */
-  public void addDescriptionPara(String para) {
-    description.add(para);
-  }
-
   /**
    * Utility to add an agent to the creators list. This method was introduced to ease the Digester rules for parsing of
    * EML.
@@ -1064,7 +1097,7 @@ public void parseIntellectualRights(org.w3c.dom.Element element) {
     this.intellectualRights = paraXmlToHtml(xmlStr);
   }
 
-  public List<String> getAbstract() {
+  public String getAbstract() {
     return description;
   }
 
@@ -1076,7 +1109,7 @@ public String getPackageId() {
     return guid + "/v" + emlVersion.toPlainString();
   }
 
-  public void setAbstract(List<String> description) {
+  public void setAbstract(String description) {
     this.description = description;
   }
 
@@ -1088,7 +1121,7 @@ public void setCitation(String citation, String identifier) {
     this.citation = new Citation(citation, identifier);
   }
 
-  public void setDescription(List<String> description) {
+  public void setDescription(String description) {
     this.description = description;
   }
 
@@ -1445,4 +1478,31 @@ public String parseLicenseTitle() {
     }
     return licenseUrl;
   }
+
+  // Value with all HTML tags replaced by DocBook analogues
+  public String getDocBookField(String fieldName) {
+    String result = null;
+
+    try {
+      String value = BeanUtils.getProperty(this, fieldName);
+
+      if (value != null) {
+        result = replaceDocBookElements(value);
+      }
+    } catch (Exception e) {
+      // TODO log exception
+    }
+
+    return result;
+  }
+
+  private String replaceDocBookElements(String value) {
+    String htmlStringWithLinksReplaces =
+        value.replaceAll(
+            "<a\\s+href=\"(.*?)\">\\s*(.*?)\\s*</a>",
+            "<ulink url=\"$1\"><citetitle>$2</citetitle></ulink>");
+
+    // Perform replacements
+    return StringUtils.replaceEach(htmlStringWithLinksReplaces, HTML_TAGS, DOCBOOK_TAGS);
+  }
 }

gbif-metadata-profile-eml/src/main/resources/templates/eml-ipt.ftl

@@ -247,13 +247,11 @@
         </pubDate>
         <language>${eml.language!"en"}</language>
         <#-- A description of the resource -->
-        <#if (eml.abstract?size>0)>
+        <#if eml.abstract?has_content>
         <abstract>
-            <#list eml.abstract as p>
-            <#if p?has_content>
-            <para>${p}</para>
-            </#if>
-            </#list>
+            <#noescape>
+            ${eml.getDocBookField("description")}
+            </#noescape>
         </abstract>
         </#if>
         <#-- Zero or more sets of keywords and an associated thesaurus for each. -->
@@ -364,17 +362,17 @@
         </#if>
         <#if eml.introduction?has_content>
         <#noescape>
-        <introduction>${eml.introduction}</introduction>
+        <introduction>${eml.getDocBookField("introduction")}</introduction>
         </#noescape>
         </#if>
         <#if eml.gettingStarted?has_content>
         <#noescape>
-        <gettingStarted>${eml.gettingStarted}</gettingStarted>
+        <gettingStarted>${eml.getDocBookField("gettingStarted")}</gettingStarted>
         </#noescape>
         </#if>
         <#if eml.acknowledgements?has_content>
         <#noescape>
-        <acknowledgements>${eml.acknowledgements}</acknowledgements>
+        <acknowledgements>${eml.getDocBookField("acknowledgements")}</acknowledgements>
         </#noescape>
         </#if>
         <#if eml.updateFrequency??>

gbif-metadata-profile-eml/src/test/java/org/gbif/metadata/eml/ipt/EmlFactoryTest.java

@@ -204,7 +204,7 @@ public void testBuild() {
       assertEquals(cal.getTime(), eml.getPubDate());
 
       assertEquals("en_US", eml.getLanguage());
-      assertEquals("Specimens in jars.", eml.getAbstract().get(0));
+      assertEquals("<p>Specimens in jars.</p><p>Collected over years.</p><p>Still being curated.</p>", eml.getAbstract());
 
       // multiple KeywordSets tests
       assertNotNull(eml.getKeywords());

gbif-metadata-profile-eml/src/test/java/org/gbif/metadata/eml/ipt/EmlWriterTest.java

@@ -81,9 +81,7 @@ public void testRoundtrip() {
 
       assertFalse(eml.getDescription().isEmpty());
       assertFalse(eml2.getDescription().isEmpty());
-      assertEquals(eml2.getDescription().get(0), eml.getDescription().get(0));
-      assertEquals(eml2.getDescription().get(1), eml.getDescription().get(1));
-      assertEquals(eml2.getDescription().get(2), eml.getDescription().get(2));
+      assertEquals(eml2.getDescription(), eml.getDescription());
 
       assertNotNull(eml.getPubDate());
       assertEquals(eml2.getPubDate(), eml.getPubDate());