Update to newest GBIF API, and GBIF common for bugfix with CSV sorting.

pom.xml

@@ -48,10 +48,10 @@
     <dwc-api.version>1.17</dwc-api.version>
     <dwca-io.version>1.31</dwca-io.version>
     <freemarker.version>2.3.26-incubating</freemarker.version>
-    <gbif-api.version>0.56</gbif-api.version>
+    <gbif-api.version>0.62</gbif-api.version>
     <gbif-common-ws.version>0.41</gbif-common-ws.version>
-    <gbif-common.version>0.36</gbif-common.version>
-    <gbif-doi.version>1.5</gbif-doi.version>
+    <gbif-common.version>0.38</gbif-common.version>
+    <gbif-doi.version>1.7</gbif-doi.version>
     <gbif-metadata-profile.version>1.1.1</gbif-metadata-profile.version>
     <gbif-parsers.version>0.31</gbif-parsers.version>
     <gbif-registry.version>2.74</gbif-registry.version>
@@ -102,7 +102,7 @@
       <post>[email protected]</post>
       <subscribe>[email protected]</subscribe>
       <unsubscribe>[email protected]</unsubscribe>
-      <archive>http://lists.gbif.org/pipermail/ipt/</archive>
+      <archive>https://lists.gbif.org/pipermail/ipt/</archive>
     </mailingList>
   </mailingLists>
 
@@ -522,7 +522,7 @@
       <groupId>javax.validation</groupId>
       <artifactId>validation-api</artifactId>
       <version>${validation-api.version}</version>
-    </dependency>    
+    </dependency>
 
     <!-- Simple XML Parsing -->
     <dependency>

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

@@ -1215,8 +1215,8 @@ public synchronized void updateAlternateIdentifierForDOI() {
     if (doi != null) {
       // retrieve a list of the resource's alternate identifiers
       List<String> ids = eml.getAlternateIdentifiers();
-      if (identifierStatus.equals(IdentifierStatus.PUBLIC_PENDING_PUBLICATION) || identifierStatus
-        .equals(IdentifierStatus.PUBLIC)) {
+      if (identifierStatus.equals(IdentifierStatus.PUBLIC_PENDING_PUBLICATION) ||
+          identifierStatus.equals(IdentifierStatus.PUBLIC)) {
         // make sure the DOI always appears first
         List<String> reorderedList = Lists.newArrayList();
         reorderedList.add(doi.toString());
@@ -1232,8 +1232,8 @@ public synchronized void updateAlternateIdentifierForDOI() {
         }
         ids.addAll(reorderedList);
         log.debug("DOI=" + doi.toString() + " added to resource's list of alt ids as first element");
-      } else if (identifierStatus.equals(IdentifierStatus.UNAVAILABLE) || identifierStatus
-        .equals(IdentifierStatus.UNRESERVED)) {
+      } else if (identifierStatus.equals(IdentifierStatus.UNAVAILABLE) ||
+          identifierStatus.equals(IdentifierStatus.UNRESERVED)) {
         for (Iterator<String> iterator = ids.iterator(); iterator.hasNext(); ) {
           String id = iterator.next();
           // make sure a DOI that has been made unavailable, or that has been deleted, no longer appears in the list

src/main/java/org/gbif/ipt/service/manage/impl/SourceManagerImpl.java

@@ -32,7 +32,7 @@
 import org.gbif.ipt.service.manage.SourceManager;
 import org.gbif.utils.file.ClosableIterator;
 import org.gbif.utils.file.ClosableReportingIterator;
-import org.gbif.utils.file.csv.UnkownDelimitersException;
+import org.gbif.utils.file.csv.UnknownDelimitersException;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -96,7 +96,7 @@ public SqlColumnIterator(SqlSource source, int column, int limit) throws SQLExce
 
     /**
      * SqlColumnIterator constructor
-     * 
+     *
      * @param source of the sql data
      * @param column to inspect, zero based numbering as used in the dwc archives
      * @param sql statement to query in the sql source
@@ -306,16 +306,16 @@ private TextFileSource addTextFile(File file) throws ImportException {
       // anaylze individual files using the dwca reader
       Archive arch = ArchiveFactory.openArchive(file);
       copyArchiveFileProperties(arch.getCore(), src);
+    } catch (UnknownDelimitersException e) {
+      // this file is invalid
+      log.warn(e.getMessage());
+      throw new ImportException(e);
     } catch (IOException e) {
       log.warn(e.getMessage());
       throw new ImportException(e);
     } catch (UnsupportedArchiveException e) {
       // fine, cant read it with dwca library, but might still be a valid file for manual setup
       log.warn(e.getMessage());
-    } catch (UnkownDelimitersException e) {
-      // this file is invalid
-      log.warn(e.getMessage());
-      throw new ImportException(e);
     }
     return src;
   }

src/main/java/org/gbif/ipt/task/GenerateDwca.java

@@ -1346,7 +1346,7 @@ private void applyTranslations(PropertyMapping[] inCols, String[] in, String[] r
         // use DOI for datasetID property?
         if (pm.getTerm().qualifiedName().equalsIgnoreCase(Constants.DWC_DATASET_ID) && doiUsedForDatasetId
             && doi != null) {
-          val = doi.toString();
+          val = doi.getDoiString();
         }
       }
       // add value to data file record

src/test/java/org/gbif/ipt/action/manage/OverviewActionIT.java

@@ -338,7 +338,7 @@ public void testDeleteReservedDoiWhenPreviousDoiExists() throws Exception {
     assertEquals(ORGANISATION_KEY, r.getDoiOrganisationKey());
     assertEquals(IdentifierStatus.PUBLIC, r.getIdentifierStatus());
     assertEquals(1, r.getEml().getAlternateIdentifiers().size()); // alternate ids updated
-    assertEquals("doi:10.5072/bclona1", r.getEml().getAlternateIdentifiers().get(0));
+    assertEquals("10.5072/bclona1", r.getEml().getAlternateIdentifiers().get(0));
     assertEquals("https://doi.org/10.5072/bclona1", r.getEml().getCitation().getIdentifier()); // citation id reset to previous DOI
     assertTrue(r.isAlreadyAssignedDoi());
     LOG.info("Existing DOI was deleted successfully");

src/test/java/org/gbif/ipt/model/ResourceTest.java

@@ -685,7 +685,7 @@ public void testUpdateAlternateIdentifierForDOICase1() {
     r.updateAlternateIdentifierForDOI();
 
     assertEquals(1, r.getEml().getAlternateIdentifiers().size());
-    assertEquals("doi:10.5072/case1", r.getEml().getAlternateIdentifiers().get(0));
+    assertEquals("10.5072/case1", r.getEml().getAlternateIdentifiers().get(0));
   }
 
   /**
@@ -707,7 +707,7 @@ public void testUpdateAlternateIdentifierForDOICase2() {
     r.updateAlternateIdentifierForDOI();
 
     assertEquals(3, r.getEml().getAlternateIdentifiers().size());
-    assertEquals("doi:10.5072/case2", r.getEml().getAlternateIdentifiers().get(0));
+    assertEquals("10.5072/case2", r.getEml().getAlternateIdentifiers().get(0));
     assertEquals("alt-id-1", r.getEml().getAlternateIdentifiers().get(1));
     assertEquals("alt-id-2", r.getEml().getAlternateIdentifiers().get(2));
   }
@@ -732,7 +732,7 @@ public void testUpdateAlternateIdentifierForDOICase3() {
     r.updateAlternateIdentifierForDOI();
 
     assertEquals(3, r.getEml().getAlternateIdentifiers().size());
-    assertEquals("doi:10.5072/case3", r.getEml().getAlternateIdentifiers().get(0));
+    assertEquals("10.5072/case3", r.getEml().getAlternateIdentifiers().get(0));
     assertEquals("alt-id-1", r.getEml().getAlternateIdentifiers().get(1));
     assertEquals("doi:10.5077/other", r.getEml().getAlternateIdentifiers().get(2));
   }
@@ -747,16 +747,18 @@ public void testUpdateAlternateIdentifierForDOICase4() {
     r.setDoi(new DOI("10.5072/case4"));
     r.setIdentifierStatus(IdentifierStatus.UNAVAILABLE);
 
-    r.getEml().getAlternateIdentifiers().add("doi:10.5072/case4");
-    r.getEml().getAlternateIdentifiers().add("doi:10.5077/other");
+    r.getEml().getAlternateIdentifiers().add("10.5072/case4");
+    r.getEml().getAlternateIdentifiers().add("10.5077/other");
     assertEquals(2, r.getEml().getAlternateIdentifiers().size());
-    assertEquals("doi:10.5072/case4", r.getEml().getAlternateIdentifiers().get(0));
-    assertEquals("doi:10.5077/other", r.getEml().getAlternateIdentifiers().get(1));
+    assertEquals("10.5072/case4", r.getEml().getAlternateIdentifiers().get(0));
+    assertEquals("10.5077/other", r.getEml().getAlternateIdentifiers().get(1));
 
     r.updateAlternateIdentifierForDOI();
 
+    System.out.println(r.getEml().getAlternateIdentifiers());
+
     assertEquals(1, r.getEml().getAlternateIdentifiers().size());
-    assertEquals("doi:10.5077/other", r.getEml().getAlternateIdentifiers().get(0));
+    assertEquals("10.5077/other", r.getEml().getAlternateIdentifiers().get(0));
   }
 
   /**