Mica source plugin could be an Initialisable

Author: ymarcon

mica-core/src/main/java/org/obiba/mica/core/service/StudyTableSourceServiceRegistry.java

@@ -16,6 +16,7 @@
 import org.apache.commons.math3.util.Pair;
 import org.obiba.magma.NoSuchValueTableException;
 import org.obiba.magma.support.Disposables;
+import org.obiba.magma.support.Initialisables;
 import org.obiba.mica.core.source.ExcelTableSource;
 import org.obiba.mica.core.source.OpalTableSource;
 import org.obiba.mica.dataset.domain.StudyDataset;
@@ -92,13 +93,13 @@ private StudyTableSource makeStudyTableSourceInternal(StudyTableContext context,
     if (OpalTableSource.isFor(source)) {
       OpalTableSource tableSource = OpalTableSource.fromURN(source);
       tableSource.setStudyTableContext(context);
-      tableSource.initialise(opalService);
+      tableSource.setOpalService(opalService);
       return tableSource;
     }
     if (ExcelTableSource.isFor(source)) {
       ExcelTableSource tableSource = ExcelTableSource.fromURN(source);
       tableSource.setStudyTableContext(context);
-      tableSource.initialise(new AttachmentStream(context, tableSource.getPath()));
+      tableSource.setStudyTableFileStreamProvider(new AttachmentStreamProvider(context, tableSource.getPath()));
       return tableSource;
     }
     Optional<StudyTableSourceService> serviceOptional = pluginsService.getStudyTableSourceServices().stream()
@@ -108,20 +109,24 @@ private StudyTableSource makeStudyTableSourceInternal(StudyTableContext context,
       tableSource.setStudyTableContext(context);
       if (tableSource instanceof StudyTableFileSource) {
         StudyTableFileSource fileSource = (StudyTableFileSource)tableSource;
-        fileSource.initialise(new AttachmentStream(context, fileSource.getPath()));
+        fileSource.setStudyTableFileStreamProvider(new AttachmentStreamProvider(context, fileSource.getPath()));
       }
+      Initialisables.initialise(tableSource);
       return tableSource;
     }
     throw new NoSuchElementException("Missing study-table-source plugin to handle source: " + source);
   }
 
 
-  private class AttachmentStream implements StudyTableFileStream {
+  /**
+   * Get the input stream from an {@link AttachmentState} object.
+   */
+  private class AttachmentStreamProvider implements StudyTableFileStreamProvider {
 
     private final StudyTableContext context;
     private final String path;
 
-    private AttachmentStream(StudyTableContext context, String path) {
+    private AttachmentStreamProvider(StudyTableContext context, String path) {
       this.context = context;
       this.path = path;
     }

mica-core/src/main/java/org/obiba/mica/core/source/ExcelTableSource.java

@@ -17,7 +17,7 @@
 import org.obiba.magma.support.Initialisables;
 import org.obiba.mica.spi.source.AbstractStudyTableSource;
 import org.obiba.mica.spi.source.StudyTableFileSource;
-import org.obiba.mica.spi.source.StudyTableFileStream;
+import org.obiba.mica.spi.source.StudyTableFileStreamProvider;
 
 import javax.validation.constraints.NotNull;
 import java.util.List;
@@ -33,7 +33,7 @@ public class ExcelTableSource extends AbstractStudyTableSource implements StudyT
 
   private ExcelDatasource excelDatasource;
 
-  private StudyTableFileStream fileStream;
+  private StudyTableFileStreamProvider fileStreamProvider;
 
   public static boolean isFor(String source) {
     if (Strings.isNullOrEmpty(source) || !source.startsWith("urn:file:"))
@@ -84,15 +84,15 @@ public String getURN() {
   }
 
   @Override
-  public void initialise(StudyTableFileStream in) {
-    this.fileStream = in;
+  public void setStudyTableFileStreamProvider(StudyTableFileStreamProvider provider) {
+    this.fileStreamProvider = provider;
     // deferred init
     this.initialized = false;
   }
 
   private void ensureInitialized() {
     if (!initialized) {
-      excelDatasource = new ExcelDatasource(path, fileStream.getInputStream());
+      excelDatasource = new ExcelDatasource(path, fileStreamProvider.getInputStream());
       Initialisables.initialise(excelDatasource);
       initialized = true;
     }

mica-core/src/main/java/org/obiba/mica/core/source/OpalTableSource.java

@@ -117,7 +117,7 @@ public static String toTableName(String source) {
     return source.replace("urn:opal:", "");
   }
 
-  public void initialise(OpalService opalService) {
+  public void setOpalService(OpalService opalService) {
     this.opalService = opalService;
     this.opalUrl = getContext().getStudy().getOpal();
   }

mica-spi/src/main/java/org/obiba/mica/spi/source/StudyTableFileSource.java

@@ -10,8 +10,6 @@
 
 package org.obiba.mica.spi.source;
 
-import java.io.InputStream;
-
 /**
  * Study table is to be extracted from a file which path applies to the Mica's internal file system.
  */
@@ -25,10 +23,10 @@ public interface StudyTableFileSource extends StudyTableSource {
   String getPath();
 
   /**
-   * Initialise the source from the given input stream that represents the file content.
+   * Set the accessor to the input stream that represents the file content.
    *
-   * @param in
+   * @param provider
    */
-  void initialise(StudyTableFileStream in);
+  void setStudyTableFileStreamProvider(StudyTableFileStreamProvider provider);
 
 }

mica-spi/src/main/java/org/obiba/mica/spi/source/StudyTableFileStream.java mica-spi/src/main/java/org/obiba/mica/spi/source/StudyTableFileStreamProvider.java

@@ -12,7 +12,10 @@
 
 import java.io.InputStream;
 
-public interface StudyTableFileStream {
+/**
+ * Define an accessor to a file stream.
+ */
+public interface StudyTableFileStreamProvider {
 
   /**
    * Get the Mica file input stream on demand.