Changeset 5721

Timestamp:

Sep 6, 2011, 3:39:13 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #1604: Support for multiple files of the same type in a FileSet?

Added 'too many files' validation rule to the Item overview that links with the 'Allow multiple files' setting.

Location:

trunk

Files:

• src/core/net/sf/basedb/util/overview/OverviewUtil.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/Validator.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/validator/DataFileValidator.java (modified) (6 diffs)
• www/views/derivedbioassays/edit_bioassay.jsp (modified) (2 diffs)
• www/views/derivedbioassays/index.jsp (modified) (1 diff)

trunk/src/core/net/sf/basedb/util/overview/OverviewUtil.java

@@ -120 +120 @@
             Validator.DATAFILE_INVALID, Validator.DATAFILE_NOTVALIDATED,
             Validator.MISSING_DATAFILE, Validator.DATAFILE_NOTPLATFORM,
+            Validator.DATAFILE_TOOMANYFILES,
             Validator.DATAFILE_INVALID_ITEM, Validator.DENIED_DATAFILETYPE,
             Validator.DENIED_FILE

trunk/src/core/net/sf/basedb/util/overview/Validator.java

@@ -748 +748 @@
 
   /**
-    Validator rule that checks if all files required by the platform
-    are present or not. Default severity level is WARNING.
+    Validator rule that checks if a file is registered with
+    a platform/item subtype or not. Default severity level is WARNING.
   */
   public static final Validator DATAFILE_NOTPLATFORM = new Validator(
-      "datafile.notplatform", "File is not used by platform",
-      "Checks that all data files are used by the current platform.",
-      "File is not used by platform", Severity.WARNING
+      "datafile.notplatform", "File is not used by platform/subtype",
+      "Checks that all data files are used by the current platform/subtype.",
+      "File is not used by platform/subtype", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks if there are more than one file
+    of a file type that doesn't allow multiple files. Default 
+    severity level is WARNING.
+    @since 3.0
+  */
+  public static final Validator DATAFILE_TOOMANYFILES = new Validator(
+      "datafile.toomanyfiles", "Too many files",
+      "Checks if an item has too many files of a type that doesn't " +
+      "allow more than one file.",
+      "Too many files", Severity.WARNING
     );
   

trunk/src/core/net/sf/basedb/util/overview/validator/DataFileValidator.java

@@ -22 +22 @@
 package net.sf.basedb.util.overview.validator;
 
+import java.util.List;
+
 import net.sf.basedb.core.BasicItem;
 import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.File;
+import net.sf.basedb.core.FileSet;
 import net.sf.basedb.core.FileSetMember;
 import net.sf.basedb.core.FileStoreEnabled;
 import net.sf.basedb.core.ItemQuery;
-import net.sf.basedb.core.ItemResultIterator;
+import net.sf.basedb.core.ItemSubtype;
+import net.sf.basedb.core.ItemSubtypeFileType;
 import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.Platform;
 import net.sf.basedb.core.PlatformFileType;
 import net.sf.basedb.core.PlatformVariant;
-import net.sf.basedb.core.Type;
+import net.sf.basedb.core.Subtypable;
+import net.sf.basedb.core.UsableDataFileType;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
-import net.sf.basedb.core.query.Restriction;
 import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.util.overview.Fix;
@@ -58 +62 @@
   <li>File type doesn't match parent item type: {@link Validator#DATAFILE_INVALID_ITEM}
   <li>File type is not part of used platform: {@link Validator#DATAFILE_NOTPLATFORM}
+  <li>Too many files of a single-file file type: {@link Validator#DATAFILE_TOOMANYFILES}
   <li>Missing a required file: {@link Validator#MISSING_DATAFILE}
   </ul>
@@ -141 +146 @@
       }
 
-      // Check that the file type is part of the used platform/variant
+      // Check that the file type is part of the used platform/variant/subtype
       try
       {
@@ -161 +166 @@
             pvName = platform.getName();
           }
-          // TODO #1604
-          /*
-          if (platform.getFileType(fileType, variant) == null)
+          if (platform.getFileType(fileType, variant, false) == null)
           {
             context.createFailure(Validator.DATAFILE_NOTPLATFORM, node, 
@@ -172 +175 @@
               );
           }
-          */
+        }
+        else if (parentItem instanceof Subtypable)
+        {
+          ItemSubtype subtype = ((Subtypable)parentItem).getItemSubtype();
+          if (subtype != null)
+          {
+            if (subtype.getAssociatedDataFileType(fileType, false) == null)
+            {
+              context.createFailure(Validator.DATAFILE_NOTPLATFORM, node, 
+                  fileType.getName() + " can't be used with '" + subtype.getName() + "' subtype", 
+                  new Fix("Remove '" + fileType.getName() + "' from " + parentItem.getType().toString().toLowerCase(), 
+                    (BasicItem)parentItem, fileType),
+                  new Fix("Add '" + fileType.getName() +"' to '" + subtype.getName() + "' subtype", subtype, fileType)
+                );
+            }
+          }
         }
       }
@@ -197 +215 @@
     
     // Check that we have linked a file for all file types that
-    // are required by the platform
+    // are required by the platform and that the multiplicity setting
+    // is ok
     try
     {
       Platform platform = parentItem.getPlatform();
       PlatformVariant variant = parentItem.getVariant();
-      BasicItem pvItem = variant != null ? variant : platform;
-      if (platform == null) return;
-      
-      // Create a query that returns all required platform file types
-      ItemQuery<PlatformFileType> query = platform.getFileTypes(variant, variant == null);
-      query.join(Hql.innerJoin("dataFileType", "dft"));
-      query.restrict(
-        Restrictions.eq(
-          Hql.property("required"), 
-          Expressions.parameter("isRequired", true, Type.BOOLEAN)
-        )
-      );
-      query.restrict(
-        Restrictions.eq(
-          Hql.property("dft", "itemType"), 
-          Expressions.integer(parentNode.getItemType().getValue())
-        )
-      );
-      if (parentItem.hasFileSet())
-      {
-        // Add a restriction that filters out the files that we already have
-        Restriction myFileSet = Restrictions.eq(Hql.property("mbr", "fileSet.id"),
-            Hql.entity(parentItem.getFileSet()));
-        query.join(Hql.leftJoin("dft", "fileSetMembers", "mbr", myFileSet, false));
-        query.restrict(Restrictions.eq(Hql.alias("mbr"), null));
-      }
-      ItemResultIterator<PlatformFileType> it = query.iterate(dc);
-      while (it.hasNext())
-      {
-        PlatformFileType pft = it.next();
-        DataFileType dft = pft.getDataFileType();
-        context.createFailure(Validator.MISSING_DATAFILE, parentNode, 
-            "Missing '" + dft.getName() + "'", 
-            new Fix("Add '" + dft.getName() + "' to " + parentItem.getType().toString().toLowerCase(), 
-                (BasicItem)parentItem, dft),
-            new Fix("Remove 'Required' flag from '" + dft.getName() + "'", pvItem, dft)
-          );
+      BasicItem pvItem = null;
+      ItemSubtype subtype = parentItem instanceof Subtypable ? 
+          ((Subtypable)parentItem).getItemSubtype() : null;
+      // List for holding all file types defined by the platform or subtype
+      List<? extends UsableDataFileType> fileTypes = null;
+      if (platform != null)
+      {
+        pvItem = variant != null ? variant : platform;
+        // Create a query that returns all required platform file types
+        ItemQuery<PlatformFileType> query = platform.getFileTypes(variant, variant == null);
+        query.join(Hql.innerJoin("dataFileType", "dft"));
+        query.restrict(
+          Restrictions.eq(
+            Hql.property("dft", "itemType"), 
+            Expressions.integer(parentNode.getItemType().getValue())
+          )
+        );
+        fileTypes = query.list(dc);
+      }
+      if (subtype != null)
+      {
+        pvItem = subtype;
+        // Create a query that returns all required subtype file types
+        ItemQuery<ItemSubtypeFileType> query = subtype.getDataFileTypes();
+        query.join(Hql.innerJoin("dataFileType", "dft"));
+        query.restrict(
+          Restrictions.eq(
+            Hql.property("dft", "itemType"), 
+            Expressions.integer(parentNode.getItemType().getValue())
+          )
+        );
+        fileTypes = query.list(dc);
+      }
+      FileSet fs = parentItem.hasFileSet() ? parentItem.getFileSet() : null;
+      for (UsableDataFileType fileType : fileTypes)
+      {
+        DataFileType dft = fileType.getDataFileType();
+        int numMembers = fs == null ? 0 : fs.getNumMembers(dft);
+        if (fileType.isRequired() && numMembers == 0)
+        {
+          context.createFailure(Validator.MISSING_DATAFILE, parentNode, 
+              "Missing '" + dft.getName() + "'", 
+              new Fix("Add '" + dft.getName() + "' to " + parentItem.getType().toString().toLowerCase(), 
+                  (BasicItem)parentItem, dft),
+              new Fix("Remove 'Required' flag from '" + dft.getName() + "'", pvItem, dft)
+            );
+        }
+        if (!fileType.getAllowMultiple() && numMembers > 1)
+        {
+          context.createFailure(Validator.DATAFILE_TOOMANYFILES, parentNode, 
+              "Too many files: '" + dft.getName() + "'", 
+              new Fix("Remove '" + dft.getName() + "' from " + parentItem.getType().toString().toLowerCase(), 
+                  (BasicItem)parentItem, dft),
+              new Fix("Check 'Allow multiple files' on '" + dft.getName() + "'", pvItem, dft)
+            );
+        }
       }
     }

trunk/www/views/derivedbioassays/edit_bioassay.jsp

@@ -60 +60 @@
 final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
 final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
+final String tabId = Values.getString(request.getParameter("tab"), null);
 final int itemId = cc.getId();
 final String ID = sc.getId();
@@ -672 +673 @@
     <form action="index.jsp?ID=<%=ID%>" method="post" name="bioAssay" onsubmit="return false;">
     <input type="hidden" name="cmd" value="UpdateItem">
-
     <h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3>
     <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*370)+"px;"%>" 
-      position="bottom"  remember="<%=bioAssay != null%>" switch="switchTab"
+      position="bottom" active="<%=tabId%>" remember="<%=tabId == null && bioAssay != null%>" switch="switchTab"
       extensions="<%=invoker%>">
     <t:tab id="info" title="Bioassay" validate="validateBioAssay()" helpid="derivedbioassay.edit">

trunk/www/views/derivedbioassays/index.jsp

@@ -154 +154 @@
     // Display the edit page for a single item (should be opened in a popup)
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
-    redirect = editPage;
+    forward = editPage;
   }
   else if ("NewItem".equals(cmd))