Deferred attachment stream extraction

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

@@ -78,7 +78,7 @@ private StudyTableSource makeStudyTableSourceInternal(StudyTableContext context,
     if (ExcelTableSource.isFor(source)) {
       ExcelTableSource tableSource = ExcelTableSource.fromURN(source);
       tableSource.setStudyTableContext(context);
-      tableSource.initialise(getFileInputStream(context, tableSource.getPath()));
+      tableSource.initialise(new AttachmentStream(context, tableSource.getPath()));
       return tableSource;
     }
     Optional<StudyTableSourceService> serviceOptional = pluginsService.getStudyTableSourceServices().stream()
@@ -88,43 +88,56 @@ private StudyTableSource makeStudyTableSourceInternal(StudyTableContext context,
       tableSource.setStudyTableContext(context);
       if (tableSource instanceof StudyTableFileSource) {
         StudyTableFileSource fileSource = (StudyTableFileSource)tableSource;
-        fileSource.initialise(getFileInputStream(context, fileSource.getPath()));
+        fileSource.initialise(new AttachmentStream(context, fileSource.getPath()));
       }
       return tableSource;
     }
     throw new NoSuchElementException("Missing study-table-source plugin to handle source: " + source);
   }
 
-  private InputStream getFileInputStream(StudyTableContext context, String path) {
-    String fullPath = path;
-    Optional<AttachmentState> attachmentState;
-    if (!fullPath.startsWith("/")) {
-      // not a full path, then it may be relative to the dataset's folder
-      fullPath = String.format("/%s-dataset/%s/%s", (context.getDataset() instanceof StudyDataset ? "collected" : "harmonized"), context.getDataset().getId(), path);
-      attachmentState = getAttachmentState(fullPath);
-      // not found, then try a path relative to the study's folder
-      if (!attachmentState.isPresent()) {
-        fullPath = String.format("/%s-study/%s/%s", (context.getStudy() instanceof Study ? "individual" : "harmonization"), context.getStudy().getId(), path);
+
+  private class AttachmentStream implements StudyTableFileStream {
+
+    private final StudyTableContext context;
+    private final String path;
+
+    private AttachmentStream(StudyTableContext context, String path) {
+      this.context = context;
+      this.path = path;
+    }
+
+    @Override
+    public InputStream getInputStream() {
+      String fullPath = path;
+      Optional<AttachmentState> attachmentState;
+      if (!fullPath.startsWith("/")) {
+        // not a full path, then it may be relative to the dataset's folder
+        fullPath = String.format("/%s-dataset/%s/%s", (context.getDataset() instanceof StudyDataset ? "collected" : "harmonized"), context.getDataset().getId(), path);
+        attachmentState = getAttachmentState(fullPath);
+        // not found, then try a path relative to the study's folder
+        if (!attachmentState.isPresent()) {
+          fullPath = String.format("/%s-study/%s/%s", (context.getStudy() instanceof Study ? "individual" : "harmonization"), context.getStudy().getId(), path);
+          attachmentState = getAttachmentState(fullPath);
+        }
+      } else {
         attachmentState = getAttachmentState(fullPath);
       }
-    } else {
-      attachmentState = getAttachmentState(fullPath);
-    }
-    if (attachmentState.isPresent()) {
-      return fileStoreService.getFile(attachmentState.get().getAttachment().getFileReference());
-    } else {
-      throw new NoSuchValueTableException("No value table at " + fullPath);
+      if (attachmentState.isPresent()) {
+        return fileStoreService.getFile(attachmentState.get().getAttachment().getFileReference());
+      } else {
+        throw new NoSuchValueTableException("No value table at " + fullPath);
+      }
     }
-  }
 
-  private Optional<AttachmentState> getAttachmentState(String fullPath) {
-    log.info("Reading study table from file: {}", fullPath);
-    Pair<String, String> pathName = FileSystemService.extractPathName(fullPath);
-    try {
-      AttachmentState state = fileSystemService.getAttachmentState(pathName.getKey(), pathName.getValue(), false);
-      return Optional.of(state);
-    } catch (Exception e) {
-      return Optional.empty();
+    private Optional<AttachmentState> getAttachmentState(String fullPath) {
+      log.info("Reading study table from file: {}", fullPath);
+      Pair<String, String> pathName = FileSystemService.extractPathName(fullPath);
+      try {
+        AttachmentState state = fileSystemService.getAttachmentState(pathName.getKey(), pathName.getValue(), false);
+        return Optional.of(state);
+      } catch (Exception e) {
+        return Optional.empty();
+      }
     }
   }
 

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

@@ -16,12 +16,10 @@
 import org.obiba.magma.datasource.excel.ExcelDatasource;
 import org.obiba.magma.support.Initialisables;
 import org.obiba.mica.spi.source.AbstractStudyTableSource;
-import org.obiba.mica.spi.source.IVariable;
 import org.obiba.mica.spi.source.StudyTableFileSource;
-import org.obiba.mica.web.model.Mica;
+import org.obiba.mica.spi.source.StudyTableFileStream;
 
 import javax.validation.constraints.NotNull;
-import java.io.InputStream;
 import java.util.List;
 
 public class ExcelTableSource extends AbstractStudyTableSource implements StudyTableFileSource {
@@ -35,6 +33,8 @@ public class ExcelTableSource extends AbstractStudyTableSource implements StudyT
 
   private ExcelDatasource excelDatasource;
 
+  private StudyTableFileStream fileStream;
+
   public static boolean isFor(String source) {
     if (Strings.isNullOrEmpty(source) || !source.startsWith("urn:file:"))
       return false;
@@ -84,12 +84,15 @@ public String getURN() {
   }
 
   @Override
-  public void initialise(InputStream in) {
-    excelDatasource = new ExcelDatasource(path, in);
+  public void initialise(StudyTableFileStream in) {
+    this.fileStream = in;
+    // deferred init
+    this.initialized = false;
   }
 
   private void ensureInitialized() {
     if (!initialized) {
+      excelDatasource = new ExcelDatasource(path, fileStream.getInputStream());
       Initialisables.initialise(excelDatasource);
       initialized = true;
     }

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

@@ -29,6 +29,6 @@ public interface StudyTableFileSource extends StudyTableSource {
    *
    * @param in
    */
-  void initialise(InputStream in);
+  void initialise(StudyTableFileStream in);
 
 }

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

@@ -0,0 +1,24 @@
+/*
+ * Copyright (c) 2022 OBiBa. All rights reserved.
+ *
+ * This program and the accompanying materials
+ * are made available under the terms of the GNU Public License v3.0.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.obiba.mica.spi.source;
+
+import java.io.InputStream;
+
+public interface StudyTableFileStream {
+
+  /**
+   * Get the Mica file input stream on demand.
+   *
+   * @return
+   */
+  InputStream getInputStream();
+
+}