Merge pull request #148 from keeps/ap_alpha5_bugfixing

Bug fixing

src/main/java/org/roda/rodain/creation/BagitSipCreator.java

@@ -186,7 +186,7 @@ private long nodeSize(TreeNode node) throws IOException {
     Path nodePath = node.getPath();
     long result = 0;
     if (Files.isDirectory(nodePath)) {
-      for (TreeNode tn : node.getAllFiles().values()) {
+      for (TreeNode tn : node.getChildren().values()) {
         result += nodeSize(tn);
       }
     } else {
@@ -208,7 +208,7 @@ private void recCreateFiles(TreeNode node, Path dest) throws IOException {
     if (Files.isDirectory(nodePath)) {
       Path directory = dest.resolve(nodePath.getFileName().toString());
       new File(directory.toString()).mkdir();
-      for (TreeNode tn : node.getAllFiles().values()) {
+      for (TreeNode tn : node.getChildren().values()) {
         recCreateFiles(tn, directory);
       }
     } else {

src/main/java/org/roda/rodain/creation/EarkSipCreator.java

@@ -164,7 +164,7 @@ private void addFileToRepresentation(TreeNode tn, List<String> relativePath, IPR
       List<String> newRelativePath = new ArrayList<>(relativePath);
       newRelativePath.add(tn.getPath().getFileName().toString());
       // recursive call to all the node's children
-      for (TreeNode node : tn.getAllFiles().values()) {
+      for (TreeNode node : tn.getChildren().values()) {
         addFileToRepresentation(node, newRelativePath, rep);
       }
     } else {
@@ -182,7 +182,7 @@ private void addDocToZip(TreeNode tn, List<String> relativePath, SIP earkSip) {
       List<String> newRelativePath = new ArrayList<>(relativePath);
       newRelativePath.add(tn.getPath().getFileName().toString());
       // recursive call to all the node's children
-      for (TreeNode node : tn.getAllFiles().values()) {
+      for (TreeNode node : tn.getChildren().values()) {
         addDocToZip(node, newRelativePath, earkSip);
       }
     } else {

src/main/java/org/roda/rodain/inspection/InspectionPane.java

@@ -665,7 +665,8 @@ private void createContent() {
     HBox.setHgrow(space, Priority.ALWAYS);
 
     sipDocumentation = new SipDocumentationTreeView();
-
+    docsRoot = new SipContentDirectory(new TreeNode(Paths.get("")), null);
+    sipDocumentation.setRoot(docsRoot);
     toggleDocumentation = new ToggleButton();
     toggleDocumentation.setTooltip(new Tooltip(I18n.t("documentation")));
     Platform.runLater(() -> {
@@ -693,7 +694,9 @@ private void createContent() {
         }
       } else { // from the documentation to the representations
         toggleDocumentation.setTooltip(new Tooltip(I18n.t("documentation")));
+        dataBox.getChildren().clear();
         dataBox.getChildren().add(sipFiles);
+        content.setCenter(dataBox);
         content.setBottom(contentBottom);
       }
     });
@@ -827,6 +830,8 @@ protected Void call() throws Exception {
       sipRoot = newRoot;
       if (active) {
         sipFiles.setRoot(sipRoot);
+        dataBox.getChildren().clear();
+        dataBox.getChildren().add(sipFiles);
         content.setCenter(dataBox);
         content.setBottom(contentBottom);
       }
@@ -835,8 +840,7 @@ protected Void call() throws Exception {
   }
 
   private void createDocumentation(SipPreviewNode sip, boolean active) {
-    SipContentDirectory newRoot = new SipContentDirectory(new TreeNode(Paths.get("")), null);
-
+    docsRoot.getChildren().clear();
     if (active) {
       content.setCenter(loadingPane);
       content.setBottom(new HBox());
@@ -846,19 +850,21 @@ private void createDocumentation(SipPreviewNode sip, boolean active) {
       @Override
       protected Void call() throws Exception {
         for (TreeNode treeNode : sip.getSip().getDocumentation()) {
-          TreeItem<Object> startingItem = recCreateSipContent(treeNode, newRoot);
+          TreeItem<Object> startingItem = recCreateSipContent(treeNode, docsRoot);
           startingItem.setExpanded(true);
-          newRoot.getChildren().add(startingItem);
+          docsRoot.getChildren().add(startingItem);
         }
-        newRoot.sortChildren();
+        docsRoot.sortChildren();
         return null;
       }
     };
     docsTask.setOnSucceeded(event -> {
-      docsRoot = newRoot;
       if (active) {
-        sipDocumentation.setRoot(docsRoot);
         if (!docsRoot.getChildren().isEmpty()) {
+          if (!dataBox.getChildren().contains(sipDocumentation)) {
+            dataBox.getChildren().clear();
+            dataBox.getChildren().add(sipDocumentation);
+          }
           content.setCenter(dataBox);
           content.setBottom(docsBottom);
         } else {
@@ -867,6 +873,7 @@ protected Void call() throws Exception {
         }
       }
     });
+
     new Thread(docsTask).start();
   }
 
@@ -1047,15 +1054,6 @@ public void update(SipPreviewNode sip) {
     boolean documentation = toggleDocumentation.isSelected();
     createContent(sip, !documentation);
     createDocumentation(sip, documentation);
-    if (documentation) {
-      if (docsRoot.getChildren().isEmpty()) {
-        content.setBottom(new HBox());
-      } else {
-        content.setBottom(docsBottom);
-      }
-    } else {
-      content.setBottom(contentBottom);
-    }
 
     center.getChildren().addAll(metadata, content);
     setCenter(center);
@@ -1139,8 +1137,10 @@ private void showMetadataHelp() {
   }
 
   private void updateTextArea(String content) {
-    metaText.replaceText(content);
-    metaText.setStyleSpans(0, XMLEditor.computeHighlighting(content));
+    Platform.runLater(() -> {
+      metaText.replaceText(content);
+      metaText.setStyleSpans(0, XMLEditor.computeHighlighting(content));
+    });
   }
 
   /**

src/main/java/org/roda/rodain/inspection/SipContentDirectory.java

@@ -105,7 +105,7 @@ public void skip() {
     TreeNode parentTreeNode = par.getTreeNode();
     parentTreeNode.remove(treeNode.getPath()); // remove this treeNode from the
     // parent
-    parentTreeNode.addAll(treeNode.getAllFiles()); // add this treeNode's
+    parentTreeNode.addAll(treeNode.getChildren()); // add this treeNode's
     // children to this node's
     // parent
     par.sortChildren();

src/main/java/org/roda/rodain/rules/Rule.java

@@ -179,7 +179,7 @@ public RuleTypes getAssocType() {
    * @see SipSingle
    */
   public TreeVisitor apply() {
-    sips = new HashMap<>();
+    sips = new ConcurrentHashMap<>();
     sipNodes = new ConcurrentHashMap<>();
     schemaNodes = Collections.synchronizedSet(new HashSet<>());
 

src/main/java/org/roda/rodain/rules/TreeNode.java

@@ -74,7 +74,7 @@ public Set<Path> getFullTreePathsAsPaths() {
   /**
    * @return The direct children of the TreeNode.
    */
-  public Map<String, TreeNode> getAllFiles() {
+  public Map<String, TreeNode> getChildren() {
     return files;
   }
 

src/main/java/org/roda/rodain/rules/sip/SipPerFile.java

@@ -1,22 +1,16 @@
 package org.roda.rodain.rules.sip;
 
-import org.apache.commons.io.FilenameUtils;
 import org.roda.rodain.core.PathCollection;
 import org.roda.rodain.rules.MetadataTypes;
 import org.roda.rodain.rules.TreeNode;
 import org.roda.rodain.rules.filters.ContentFilter;
-import org.roda.rodain.schema.DescObjMetadata;
 import org.roda.rodain.source.ui.items.SourceTreeItemState;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
 import java.io.IOException;
 import java.nio.file.*;
 import java.nio.file.attribute.BasicFileAttributes;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
 import java.util.Set;
 
 /**
@@ -28,8 +22,6 @@ public class SipPerFile extends SipPreviewCreator {
   private static final int UPDATEFREQUENCY = 500; // in milliseconds
   private long lastUIUpdate = 0;
 
-  private Map<String, Set<Path>> metadata;
-
   /**
    * Creates a new SipPreviewCreator where there's a new SIP created for each
    * visited file.
@@ -48,28 +40,6 @@ public class SipPerFile extends SipPreviewCreator {
   public SipPerFile(String id, Set<ContentFilter> filters, MetadataTypes metaType, Path metadataPath,
     String templateType, String templateVersion) {
     super(id, filters, metaType, metadataPath, templateType, templateVersion);
-    metadata = new HashMap<>();
-
-    if (metadataPath != null && metaType == MetadataTypes.DIFF_DIRECTORY) {
-      try {
-        Files.walkFileTree(metadataPath, new SimpleFileVisitor<Path>() {
-          @Override
-          public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
-            String key = FilenameUtils.removeExtension(file.getFileName().toString());
-            Set<Path> paths = metadata.get(key);
-            if (paths == null)
-              paths = new HashSet<>();
-            paths.add(file);
-            metadata.put(key, paths);
-            return FileVisitResult.CONTINUE;
-          }
-        });
-      } catch (AccessDeniedException e) {
-        log.info("Access denied to file", e);
-      } catch (IOException e) {
-        log.error("Error walking the file tree", e);
-      }
-    }
   }
 
   @Override
@@ -148,27 +118,8 @@ public void visitFile(Path path, BasicFileAttributes attrs) {
     if (filter(path) || cancelled)
       return;
 
-    Path metaPath = getMetadataPath(path);
     TreeNode node = new TreeNode(path);
-    Set<TreeNode> files = new HashSet<>();
-    files.add(node);
-
-    DescObjMetadata dom = null;
-    if (metaType == MetadataTypes.TEMPLATE)
-      dom = new DescObjMetadata(metaType, templateType, templateVersion);
-    else if (metaPath != null)
-      dom = new DescObjMetadata(metaType, metaPath);
-
-    SipRepresentation rep = new SipRepresentation("rep1");
-    rep.setFiles(files);
-    Set<SipRepresentation> repSet = new HashSet<>();
-    repSet.add(rep);
-    SipPreview sipPreview = new SipPreview(path.getFileName().toString(), repSet, dom);
-    node.addObserver(sipPreview);
-
-    sips.add(sipPreview);
-    sipsMap.put(sipPreview.getId(), sipPreview);
-    added++;
+    createSip(path, node);
 
     long now = System.currentTimeMillis();
     if (now - lastUIUpdate > UPDATEFREQUENCY) {
@@ -177,52 +128,4 @@ else if (metaPath != null)
       lastUIUpdate = now;
     }
   }
-
-  private Path getMetadataPath(Path path) {
-    Path result;
-    switch (metaType) {
-      case SINGLE_FILE:
-        result = metadataPath;
-        break;
-      case DIFF_DIRECTORY:
-        result = getFileFromDir(path);
-        break;
-      case SAME_DIRECTORY:
-        result = searchMetadata(path);
-        break;
-      default:
-        return null;
-    }
-    return result;
-  }
-
-  private Path searchMetadata(Path sipPath) {
-    File dir = sipPath.toFile();
-    if (!dir.isDirectory())
-      dir = sipPath.getParent().toFile();
-
-    PathMatcher matcher = FileSystems.getDefault().getPathMatcher("glob:" + templateType);
-    File[] foundFiles = dir.listFiles((dir1, name) -> matcher.matches(Paths.get(name)));
-
-    if (foundFiles != null && foundFiles.length > 0) {
-      return foundFiles[0].toPath();
-    }
-    return null;
-  }
-
-  private Path getFileFromDir(Path path) {
-    String fileNameWithExtension = path.getFileName().toString();
-    String fileName = FilenameUtils.removeExtension(fileNameWithExtension);
-
-    Set<Path> paths = metadata.get(fileName);
-    Path result = null;
-    if (paths != null) {
-      for (Path p : paths) {
-        if (!p.getFileName().toString().equals(fileNameWithExtension))
-          result = p;
-
-      }
-    }
-    return result;
-  }
 }

src/main/java/org/roda/rodain/rules/sip/SipPerSelection.java

@@ -3,15 +3,11 @@
 import org.roda.rodain.rules.MetadataTypes;
 import org.roda.rodain.rules.TreeNode;
 import org.roda.rodain.rules.filters.ContentFilter;
-import org.roda.rodain.schema.DescObjMetadata;
 
-import java.io.File;
 import java.nio.file.FileSystems;
 import java.nio.file.Path;
 import java.nio.file.PathMatcher;
-import java.nio.file.Paths;
 import java.nio.file.attribute.BasicFileAttributes;
-import java.util.HashSet;
 import java.util.Set;
 
 /**
@@ -109,30 +105,6 @@ public void postVisitDirectory(Path path) {
     }
   }
 
-  private void createSip(Path path, TreeNode node) {
-    Path metaPath = getMetadataPath(path);
-    // create a new Sip
-    Set<TreeNode> files = new HashSet<>();
-    files.add(node);
-
-    DescObjMetadata metadata;
-    if (metaType == MetadataTypes.TEMPLATE)
-      metadata = new DescObjMetadata(metaType, templateType, templateVersion);
-    else
-      metadata = new DescObjMetadata(metaType, metaPath);
-
-    SipRepresentation rep = new SipRepresentation("rep1");
-    rep.setFiles(files);
-    Set<SipRepresentation> repSet = new HashSet<>();
-    repSet.add(rep);
-    SipPreview sipPreview = new SipPreview(path.getFileName().toString(), repSet, metadata);
-    node.addObserver(sipPreview);
-
-    sips.add(sipPreview);
-    sipsMap.put(sipPreview.getId(), sipPreview);
-    added++;
-  }
-
   /**
    * If the path is in the selected set of paths creates a new SIP using the
    * file, otherwise, adds the visited file to its parent.
@@ -155,30 +127,4 @@ public void visitFile(Path path, BasicFileAttributes attrs) {
       nodes.peekLast().add(path);
     }
   }
-
-  private Path getMetadataPath(Path sipPath) {
-    Path result = null;
-    if (metaType == MetadataTypes.SINGLE_FILE) {
-      result = metadataPath;
-    } else if (metaType == MetadataTypes.SAME_DIRECTORY) {
-      result = searchMetadata(sipPath);
-    }
-    return result;
-  }
-
-  private Path searchMetadata(Path sipPath) {
-    File dir = sipPath.toFile();
-    if (!dir.isDirectory())
-      dir = sipPath.getParent().toFile();
-
-    PathMatcher matcher = FileSystems.getDefault().getPathMatcher("glob:" + templateType);
-    File[] foundFiles = dir.listFiles((dir1, name) -> {
-      return matcher.matches(Paths.get(name));
-    });
-
-    if (foundFiles != null && foundFiles.length > 0) {
-      return foundFiles[0].toPath();
-    }
-    return null;
-  }
 }