Merge pull request #1387 from NCEAS/dev-2.11

Dev 2.11 second merge

Author: taojing2002

build.xml

@@ -342,7 +342,7 @@
 		<property name="eml2_0_1-schema-tag" value="RELEASE_EML_2_0_1" />
 		<property name="eml2_1_0-schema-tag" value="RELEASE_EML_2_1_0" />
 		<property name="eml2_1_1-schema-tag" value="RELEASE_EML_2_1_1" />
-		<property name="eml2_2_0-schema-tag" value="BRANCH_EML_2_2" />
+		<property name="eml2_2_0-schema-tag" value="RELEASE_EML_2_2_0" />
 		<!--<property name="eml2-style-tag" value="RELEASE_EML_UTILS_1_0_7" />-->
 
 

lib/metacat.properties

@@ -774,5 +774,5 @@ solr.collectionName=collection1
 #solr.systeminfo.urlappendix=/admin/system
 #Solr-home for the http solr server is used to store some files. It can be not really solr home.
 #solr.homeDir=/var/metacat/solr-home
-solr.query.appned.include.archived.name=archived
-solr.query.append.incldue.archived.value=-archived:*fake
+solr.query.append.includeArchived.name=archived
+solr.query.append.includeArchived.value=-archived:*fake

metacat-index/src/main/java/edu/ucsb/nceas/metacat/index/ApplicationController.java

@@ -163,8 +163,8 @@ private void initializeSharedConfiguration() {
             }
 
         }
-        queryIncludeArchivedParaName = Settings.getConfiguration().getString("solr.query.appned.include.archived.name");
-        queryIncludeArchivedParaValue = Settings.getConfiguration().getString("solr.query.append.incldue.archived.value");
+        queryIncludeArchivedParaName = Settings.getConfiguration().getString("solr.query.append.includeArchived.name");
+        queryIncludeArchivedParaValue = Settings.getConfiguration().getString("solr.query.append.includeArchived.value");
     }
 
     /**
@@ -326,7 +326,7 @@ public void run() {
      */
     public static String getIncludeArchivedQueryParaName() {
         if(queryIncludeArchivedParaName == null) {
-            queryIncludeArchivedParaName = Settings.getConfiguration().getString("solr.query.appned.include.archived.name");
+            queryIncludeArchivedParaName = Settings.getConfiguration().getString("solr.query.append.includeArchived.name");
         }
         return queryIncludeArchivedParaName;
     }
@@ -337,7 +337,7 @@ public static String getIncludeArchivedQueryParaName() {
      */
     public static String getIncludeArchivedQueryParaValue() {
         if(queryIncludeArchivedParaValue == null) {
-            queryIncludeArchivedParaValue = Settings.getConfiguration().getString("solr.query.append.incldue.archived.value");
+            queryIncludeArchivedParaValue = Settings.getConfiguration().getString("solr.query.append.includeArchived.value");
         }
         return queryIncludeArchivedParaValue;
     }

metacat-index/src/main/java/edu/ucsb/nceas/metacat/index/annotation/EmlAnnotationSubprocessor.java

@@ -25,16 +25,15 @@
 import org.dataone.cn.indexer.XmlDocumentUtility;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.w3c.dom.Document;
+
 /**
- * A subprocessor that extracts semantic annotations from EML records and
- * materializes the superclass hierarchy for all extracted concepts using a
- * pre-defined set of ontologies. It is very similar to a
- * BaseXPathDocumentSubprocessor but a bit different in that it post-processes
- * results from the usual ISolrDoc.getFields() instead of mergingn them asi-s.
+ * Extracts semantic annotations from EML records and materializes the
+ * superclass hierarchy for all extracted concepts using a pre-defined set of
+ * ontologies. It is very similar to a BaseXPathDocumentSubprocessor but a bit
+ * different in that it post-processes results from the usual
+ * ISolrDoc.getFields() instead of mergingn them asi-s.
  *
- * User: Mecum
- * Date: 2019/02/05
- * Time: 4:57 PM
+ * User: Mecum Date: 2019/02/05 Time: 4:57 PM
  *
  */
 public class EmlAnnotationSubprocessor implements IDocumentSubprocessor {
@@ -131,7 +130,7 @@ public Map<String, SolrDoc> processDocument(String identifier, Map<String, SolrD
     /**
      * Merge updates with existing solr documents
      *
-     * @param indexDocument
+     * @param indexDocument The index document to merge processed fields with
      * @return
      * @throws IOException
      * @throws EncoderException

metacat-index/src/main/java/edu/ucsb/nceas/metacat/index/annotation/OntologyModelService.java

@@ -80,6 +80,12 @@ private void init() {
         }
     }
 
+    /**
+     * Perform expansion on a given term URI.
+     *
+     * @param uri The URI to expand
+     * @return A Map of String (field) <-> Set<String> expanded concepts
+     */
     protected Map<String, Set<String>> expandConcepts(String uri) {
         log.debug("expandConcepts " + uri);
         Map<String, Set<String>> conceptFields = new HashMap<String, Set<String>>();
@@ -168,6 +174,11 @@ public void setAltEntryList(Map<String, String> entryList) {
         altEntryList = entryList;
     }
 
+    /**
+     * Tell the OntologyModelService where to find ontologies by adding alternative
+     * entries to the OntDocumentManager with imports disabled. Processing of
+     * imports is a security risk so this is disabled explicitly.
+     */
     public void loadAltEntries() {
         log.debug("OntologyModelService - Loading altEntries of size " + altEntryList.size());
 

src/edu/ucsb/nceas/metacat/dataone/MNodeService.java

@@ -2127,9 +2127,11 @@ public Identifier publish(Session session, Identifier originalIdentifier) throws
             ObjectFormatIdentifier objFormatId = originalSystemMetadata.getFormatId();
             String formatId = objFormatId.getValue();
             //For all EML formats
-            if(formatId.indexOf("eml") == 0){
-                logMetacat.debug("~~~~~~~~~~~~~~~~~~~~~~MNodeService.publish - the object "+originalIdentifier.getValue()+" with format id "+formatId+" is an eml document.");
+            if(formatId.contains("ecoinformatics.org/eml")){
+                logMetacat.debug("~~~~~~~~~~~~~~~~~~~~~~MNodeService.publish - the object " + originalIdentifier.getValue() + " with format id " + formatId + " is an eml document.");
                 isEML = true;
+            } else {
+                logMetacat.debug("MNodeService.publish - the object " + originalIdentifier.getValue() + " with format id " + formatId + " is NOT an eml document.");
             }
 			InputStream originalObject = this.get(session, originalIdentifier);
 

test/edu/ucsb/nceas/metacat/dataone/RegisterDOITest.java

@@ -344,6 +344,11 @@ public void testPublishDOI() {
 	            // now publish it
 	            Identifier publishedIdentifier = MNodeService.getInstance(request).publish(session, pid);
 
+	            //check if the package id was updated
+	            InputStream emlObj = MNodeService.getInstance(request).get(session, publishedIdentifier);
+	            String emlStr = IOUtils.toString(emlObj, "UTF-8");
+	            assertTrue(emlStr.contains("packageId=\"" + publishedIdentifier.getValue() + "\""));
+	            
 	            // check for the metadata explicitly, using ezid service
 	            EZIDService ezid = new EZIDService(ezidServiceBaseUrl);
 	            ezid.login(ezidUsername, ezidPassword);
@@ -894,10 +899,35 @@ public void testPublishEML220() throws Exception {
         } while (metadata == null && count < 20);
         assertNotNull(metadata);
         String result = metadata.get(DOIService.DATACITE);
-        System.out.println("result is\n"+result);
         assertTrue(result.contains("EML Annotation Example"));
         assertTrue(result.contains("0000-0002-1209-5122"));
         assertTrue(result.contains("It can include multiple paragraphs"));
         content.close();
+        
+        //check if the package id was updated
+        InputStream emlObj = MNodeService.getInstance(request).get(session, publishedIdentifier);
+        String emlStr = IOUtils.toString(emlObj, "UTF-8");
+        assertTrue(emlStr.contains("packageId=\"" + publishedIdentifier.getValue() + "\""));
+        
+        //check the query
+        String query = "q=id:"+guid.getValue();
+        InputStream stream = MNodeService.getInstance(request).query(session, "solr", query);
+        String resultStr = IOUtils.toString(stream, "UTF-8");
+        do {
+            try {
+               if(resultStr.contains("funding")) {
+                   break;
+               }
+            } catch (Exception e) {
+                Thread.sleep(2000);
+            }
+            count++;
+        } while (metadata == null && count < 20);
+        assertTrue(resultStr.contains("<arr name=\"funding\">"));
+        assertTrue(resultStr.contains("<str>Funding is from a grant from the National Science Foundation.</str>"));
+        assertTrue(resultStr.contains("<arr name=\"funderName\">"));
+        assertTrue(resultStr.contains("<str>National Science Foundation</str>"));
+        assertTrue(resultStr.contains("<arr name=\"sem_annotation\"><str>http://purl.dataone.org/odo/ECSO_00000512</str>"));
+        assertTrue(resultStr.contains("<str>http://purl.dataone.org/odo/ECSO_00000512</str>"));
     }
 }