further changes per review

ErykKul · May 10, 2023 · 89ec230 · 89ec230
1 parent 12e5e96
commit 89ec230
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Showing 18 changed files with 73 additions and 79 deletions.
diff --git a/modules/dataverse-spi-export-demo/pom.xml b/modules/dataverse-spi-export-demo/pom.xml
@@ -8,49 +8,42 @@
         <groupId>edu.harvard.iq</groupId>
         <artifactId>dataverse-parent</artifactId>
         <version>${revision}</version>
-        <relativePath>../../modules/dataverse-parent</relativePath>
+        <relativePath>../dataverse-parent</relativePath>
     </parent>
 
-    <artifactId>dataverse-example-exporter</artifactId>
-    <version>0.0.1</version>
+    <groupId>io.gdcc</groupId>
+    <artifactId>dataverse-spi-export-examples</artifactId>
+    <version>1.0.0</version>
     <packaging>jar</packaging>
 
     <properties>
     </properties>
 
     <dependencies>
         <dependency>
-            <groupId>edu.harvard.iq</groupId>
-            <artifactId>dataverse-exporter-spi</artifactId>
-            <version>0.0.1</version>
+            <groupId>io.gdcc</groupId>
+            <artifactId>dataverse-spi</artifactId>
+            <version>1.0.0</version>
         </dependency>
-        <!--
-        https://mvnrepository.com/artifact/com.google.auto.service/auto-service -->
-        <dependency>
+       <dependency>
             <groupId>com.google.auto.service</groupId>
             <artifactId>auto-service</artifactId>
             <version>1.0.1</version>
         </dependency>
-
         <dependency>
-            <groupId>jakarta.platform</groupId>
-            <artifactId>
-                jakarta.jakartaee-api</artifactId>
-            <version>${jakartaee-api.version}</version>
-            <scope>
-                provided</scope>
+            <groupId>jakarta.json</groupId>
+            <artifactId>jakarta.json-api</artifactId>
+            <scope>provided</scope>
+            <!-- no version here as managed by parent -->
         </dependency>
         <dependency>
-            <groupId>org.glassfish</groupId>
-            <artifactId>
-                jakarta.json</artifactId>
+            <groupId>jakarta.ws.rs</groupId>
+            <artifactId>jakarta.ws.rs-api</artifactId>
             <scope>provided</scope>
-            <!-- no version here as managed by Payara BOM above! -->
+            <!-- no version here as managed by parent -->
         </dependency>
     </dependencies>
     <build>
-        <sourceDirectory>
-            src/main/java</sourceDirectory>
         <plugins>
             <plugin>
                 <artifactId>maven-compiler-plugin</artifactId>

diff --git a/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/Exporter.java b/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/Exporter.java
@@ -2,7 +2,6 @@
 
 import java.io.OutputStream;
 import java.util.Locale;
-import javax.ws.rs.core.MediaType;
 
 public interface Exporter {
 
@@ -16,7 +15,7 @@ public interface Exporter {
 
     void exportDataset(ExportDataProvider dataProvider, OutputStream outputStream) throws ExportException;
 
-    String getProviderName();
+    String getFormatName();
 
     String getDisplayName(Locale locale);
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DCTermsExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DCTermsExporter.java
@@ -24,7 +24,7 @@ public class DCTermsExporter implements XMLExporter {
 
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return "dcterms";
     }
 
@@ -39,7 +39,7 @@ public void exportDataset(ExportDataProvider dataProvider, OutputStream outputSt
         try {
             DublinCoreExportUtil.datasetJson2dublincore(dataProvider.getDatasetJson(), outputStream, DublinCoreExportUtil.DC_FLAVOR_DCTERMS);
         } catch (XMLStreamException xse) {
-            throw new ExportException("Caught XMLStreamException performing DCTERMS export");
+            throw new ExportException("Caught XMLStreamException performing DCTERMS export", xse);
         }
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DDIExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DDIExporter.java
@@ -32,7 +32,7 @@ public class DDIExporter implements XMLExporter {
     public static final String PROVIDER_NAME = "ddi";
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return PROVIDER_NAME;
     }
 
@@ -51,7 +51,7 @@ public void exportDataset(ExportDataProvider dataProvider, OutputStream outputSt
             DdiExportUtil.datasetJson2ddi(dataProvider.getDatasetJson(), dataProvider.getDatasetFileDetails(),
                     outputStream);
         } catch (XMLStreamException xse) {
-            throw new ExportException("Caught XMLStreamException performing DDI export");
+            throw new ExportException("Caught XMLStreamException performing DDI export", xse);
         }
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DataCiteExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DataCiteExporter.java
@@ -10,7 +10,7 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.IOException;
 import java.io.OutputStream;
-import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.util.Locale;
 
 /**
@@ -27,7 +27,7 @@ public class DataCiteExporter implements XMLExporter {
     public static final String NAME = "Datacite";
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return NAME;
     }
 
@@ -41,9 +41,9 @@ public String getDisplayName(Locale locale) {
     public void exportDataset(ExportDataProvider dataProvider, OutputStream outputStream) throws ExportException {
         try {
             String xml = dataProvider.getDataCiteXml();
-            outputStream.write(xml.getBytes(Charset.forName("utf-8")));
+            outputStream.write(xml.getBytes(StandardCharsets.UTF_8));
         } catch (IOException e) {
-            throw new ExportException("Caught IOException performing DataCite export");
+            throw new ExportException("Caught IOException performing DataCite export", e);
         }
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DublinCoreExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DublinCoreExporter.java
@@ -23,7 +23,7 @@
 public class DublinCoreExporter implements XMLExporter {
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return "oai_dc";
     }
 
@@ -41,7 +41,7 @@ public void exportDataset(ExportDataProvider dataProvider, OutputStream outputSt
             DublinCoreExportUtil.datasetJson2dublincore(dataProvider.getDatasetJson(), outputStream,
                     DublinCoreExportUtil.DC_FLAVOR_OAI);
         } catch (XMLStreamException xse) {
-            throw new ExportException("Caught XMLStreamException performing DC export");
+            throw new ExportException("Caught XMLStreamException performing DC export", xse);
         }
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java b/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java
@@ -40,6 +40,7 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.ServiceConfigurationError;
 import java.util.ServiceLoader;
 import java.util.Set;
@@ -66,17 +67,21 @@ private ExportService() {
          * Step 1 - find the EXPORTERS dir and add all jar files there to a class loader
          */
         List<URL> jarUrls = new ArrayList<URL>();
-        Path exporterDir = Paths.get(JvmSettings.EXPORTERS_DIRECTORY.lookup());
-        try (DirectoryStream<Path> stream = Files.newDirectoryStream(exporterDir)) {
-            for (Path path : stream) {
-                if (!Files.isDirectory(path)) {
-                    logger.fine("Adding  " + path.toUri().toURL());
-                    //This is the syntax required to indicate a jar file from which classes should be loaded (versus a class file). 
+        Optional<String> exportPathSetting = JvmSettings.EXPORTERS_DIRECTORY.lookupOptional(String.class);
+        if (exportPathSetting.isPresent()) {
+            Path exporterDir = Paths.get(exportPathSetting.get());
+            // Get all JAR files from the configured directory
+            try (DirectoryStream<Path> stream = Files.newDirectoryStream(exporterDir, "*.jar")) {
+                // Using the foreach loop here to enable catching the URI/URL exceptions
+                for (Path path : stream) {
+                    logger.log(Level.FINE, "Adding {0}", path.toUri().toURL());
+                    // This is the syntax required to indicate a jar file from which classes should
+                    // be loaded (versus a class file).
                     jarUrls.add(new URL("jar:" + path.toUri().toURL() + "!/"));
                 }
+            } catch (IOException e) {
+                logger.warning("Problem accessing external Exporters: " + e.getLocalizedMessage());
             }
-        } catch (IOException e) {
-            logger.warning("Problem accessing external Exporters: " + e.getLocalizedMessage());
         }
         URLClassLoader cl = URLClassLoader.newInstance(jarUrls.toArray(new URL[0]), this.getClass().getClassLoader());
 
@@ -93,12 +98,12 @@ private ExportService() {
          * providerName may be processed before or after external ones.
          */
         loader.forEach(exp -> {
-            String formatName = exp.getProviderName();
+            String formatName = exp.getFormatName();
             // If no entry for this providerName yet or if it is an external exporter
             if (!exporterMap.containsKey(formatName) || exp.getClass().getClassLoader().equals(cl)) {
                 exporterMap.put(formatName, exp);
             }
-            logger.fine("SL: " + exp.getProviderName() + " from " + exp.getClass().getCanonicalName()
+            logger.log(Level.FINE, "SL: " + exp.getFormatName() + " from " + exp.getClass().getCanonicalName()
                     + " and classloader: " + exp.getClass().getClassLoader().getClass().getCanonicalName());
         });
     }
@@ -116,7 +121,7 @@ public List<String[]> getExportersLabels() {
         exporterMap.values().forEach(exp -> {
             String[] temp = new String[2];
             temp[0] = exp.getDisplayName(BundleUtil.getCurrentLocale());
-            temp[1] = exp.getProviderName();
+            temp[1] = exp.getFormatName();
             retList.add(temp);
         });
         return retList;
@@ -248,10 +253,10 @@ public void exportAllFormats(Dataset dataset) throws ExportException {
                 throw new ExportException("No released version for dataset " + dataset.getGlobalId().toString());
             }
             ExportDataProvider dataProvider = new InternalExportDataProvider(releasedVersion);
-            
+
             for (Exporter e : exporterMap.values()) {
-                String formatName = e.getProviderName();
-                
+                String formatName = e.getFormatName();
+
                 cacheExport(dataset, dataProvider, formatName, e);
             }
             // Finally, if we have been able to successfully export in all available
@@ -272,7 +277,7 @@ public void clearAllCachedFormats(Dataset dataset) throws IOException {
         try {
 
             for (Exporter e : exporterMap.values()) {
-                String formatName = e.getProviderName();
+                String formatName = e.getFormatName();
                 clearCachedExport(dataset, formatName);
             }
 
@@ -293,7 +298,8 @@ public void exportFormat(Dataset dataset, String formatName) throws ExportExcept
             if (e != null) {
                 DatasetVersion releasedVersion = dataset.getReleasedVersion();
                 if (releasedVersion == null) {
-                    throw new ExportException("No published version found during export. " + dataset.getGlobalId().toString());
+                    throw new ExportException(
+                            "No published version found during export. " + dataset.getGlobalId().toString());
                 }
                 InternalExportDataProvider dataProvider = new InternalExportDataProvider(releasedVersion);
                 cacheExport(dataset, dataProvider, formatName, e);
@@ -303,15 +309,13 @@ public void exportFormat(Dataset dataset, String formatName) throws ExportExcept
                 throw new ExportException("Exporter not found");
             }
         } catch (IllegalStateException e) {
-            // IllegalStateException can potentially mean very different, and 
+            // IllegalStateException can potentially mean very different, and
             // unexpected things. An exporter attempting to get a single primitive
-            // value from a fieldDTO that is in fact a Multiple and contains a 
+            // value from a fieldDTO that is in fact a Multiple and contains a
             // json vector (this has happened, for example, when the code in the
-            // DDI exporter was not updated following a metadata fieldtype change), 
+            // DDI exporter was not updated following a metadata fieldtype change),
             // will result in IllegalStateException.
-            throw new ExportException("IllegalStateException caught when exporting " 
-                    + formatName 
-                    + " for dataset "
+            throw new ExportException("IllegalStateException caught when exporting " + formatName + " for dataset "
                     + dataset.getGlobalId().toString()
                     + "; may or may not be due to a mismatch between an exporter code and a metadata block update. "
                     + e.getMessage());
@@ -331,12 +335,12 @@ public Exporter getExporter(String formatName) throws ExportException {
     // in a file in the dataset directory / container based on its DOI:
     private void cacheExport(Dataset dataset, ExportDataProvider dataProvider, String format, Exporter exporter)
             throws ExportException {
-        boolean tempFileUsed = false;
-        File tempFile = null;
         OutputStream outputStream = null;
-
-        StorageIO<Dataset> storageIO = null;
         try {
+            boolean tempFileUsed = false;
+            File tempFile = null;
+            StorageIO<Dataset> storageIO = null;
+
             // With some storage drivers, we can open a WritableChannel, or OutputStream
             // to directly write the generated metadata export that we want to cache;
             // Some drivers (like Swift) do not support that, and will give us an

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/HtmlCodeBookExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/HtmlCodeBookExporter.java
@@ -25,7 +25,7 @@
 public class HtmlCodeBookExporter implements Exporter {
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return "html";
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/InternalExportDataProvider.java b/src/main/java/edu/harvard/iq/dataverse/export/InternalExportDataProvider.java
@@ -73,7 +73,6 @@ public JsonObject getDatasetORE() {
 
     @Override
     public String getDataCiteXml() {
-        // TODO Auto-generated method stub
         return DOIDataCiteRegisterService.getMetadataFromDvObject(
                 dv.getDataset().getGlobalId().asString(), new DataCitation(dv).getDataCiteMetadata(), dv.getDataset());
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java
@@ -22,7 +22,7 @@
 public class JSONExporter implements Exporter {
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return "dataverse_json";
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/OAI_DDIExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/OAI_DDIExporter.java
@@ -26,7 +26,7 @@
 public class OAI_DDIExporter implements XMLExporter {
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         // TODO: Consider adding this "short form" to the "Export Metadata" dropdown in the GUI.
         return "oai_ddi";
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java
@@ -37,7 +37,7 @@ public void exportDataset(ExportDataProvider dataProvider, OutputStream outputSt
 
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return NAME;
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/OpenAireExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/OpenAireExporter.java
@@ -23,7 +23,7 @@ public OpenAireExporter() {
     }
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return "oai_datacite";
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java
@@ -17,8 +17,8 @@
  * and available as an export format.
  * <p>
  * Do not make any backward incompatible changes unless it's absolutely
- * necessary and list them in the API Guide. The existing list is in the
- * "Native API" section.
+ * necessary and list them in the API Guide. The existing list is in the "Native
+ * API" section.
  * <p>
  * {@link SchemaDotOrgExporterTest} has most of the tests but
  * {@link DatasetVersionTest} has some as well. See
@@ -73,9 +73,8 @@ public class SchemaDotOrgExporter implements Exporter {
     public static final String NAME = "schema.org";
 
     @Override
-    public void exportDataset(ExportDataProvider dataProvider, OutputStream outputStream)
-            throws ExportException {
-                try {
+    public void exportDataset(ExportDataProvider dataProvider, OutputStream outputStream) throws ExportException {
+        try {
             outputStream.write(dataProvider.getDatasetSchemaDotOrg().toString().getBytes("UTF8"));
         } catch (IOException ex) {
             logger.info("IOException calling outputStream.write: " + ex);
@@ -88,7 +87,7 @@ public void exportDataset(ExportDataProvider dataProvider, OutputStream outputSt
     }
 
     @Override
-    public String getProviderName() {
+    public String getFormatName() {
         return NAME;
     }
 
@@ -99,7 +98,8 @@ public String getDisplayName(Locale locale) {
 
     @Override
     public Boolean isHarvestable() {
-        // Defer harvesting because the current effort was estimated as a "2": https://github.com/IQSS/dataverse/issues/3700
+        // Defer harvesting because the current effort was estimated as a "2":
+        // https://github.com/IQSS/dataverse/issues/3700
         return false;
     }