Changeset 5698

Timestamp:

Aug 15, 2011, 1:57:00 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #597: Subtypes of items

Implemented linking of item subtypes and data file types so that we can show/hide the suitable file types when editing an item.

This should more or less complete the item subtype feature. I'll keep the ticket open a little longer in case something pops up.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/DataFileType.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Install.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/ItemSubtype.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DataFileTypeData.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/data/ItemSubtypeData.java (modified) (2 diffs)
• www/admin/itemsubtypes/edit_subtype.jsp (modified) (11 diffs)
• www/admin/itemsubtypes/index.jsp (modified) (2 diffs)
• www/admin/itemsubtypes/list_subtypes.jsp (modified) (4 diffs)
• www/admin/itemsubtypes/view_subtype.jsp (modified) (2 diffs)
• www/common/datafiles/list_files.jsp (modified) (6 diffs)
• www/common/datafiles/select_files.jsp (modified) (9 diffs)
• www/include/scripts/platforms.js (modified) (2 diffs)
• www/views/derivedbioassays/edit_bioassay.jsp (modified) (6 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -1058 +1058 @@
   /**
     Get a query that returns all data file types for a specific
-    platform/variant that can be used on a given item type. If an item
+    platform/variant/subtype that can be used on a given item type. If an item
     is specified the query will also return data file types that
     already are present in the item's file set even if those 
@@ -1066 +1066 @@
     @param platform The platform to get file types for, or null
     @param variant The platform variant to get file types for, or null
+    @param subtype The item subtype to get the file types for, or null
     @return An <code>ItemQuery</code> object
-    @since 2.5
-  */
-  public static ItemQuery<DataFileType> getDataFileTypes(Item itemType, FileStoreEnabled item, Platform platform, PlatformVariant variant)
+    @since 3.0
+  */
+  public static ItemQuery<DataFileType> getDataFileTypes(Item itemType, FileStoreEnabled item, Platform platform, PlatformVariant variant, ItemSubtype subtype)
   {
     ItemQuery<DataFileType> q = DataFileType.getQuery();
@@ -1103 +1104 @@
     }
     
+    // Restrict on item subtype
+    Restriction onSubtype = null;
+    if (subtype != null)
+    {
+      onSubtype = Restrictions.eq(Hql.alias("its"), Hql.entity(subtype));
+      q.join(Hql.leftJoin("itemSubtypes", "its"));
+    }
+    
     // Also include file types already present for item
     Restriction onItem = null;
@@ -1112 +1121 @@
     }
     
-    // full = onItem || (onItemType && onPlatform)
+    // full = onItem || (onItemType && onPlatform && onSubtype)
     Restriction full = onItemType;
     if (onPlatform != null) full = Restrictions.and(full, onPlatform);
+    if (onSubtype != null) full = Restrictions.and(full, onSubtype);
     if (onItem != null) full = Restrictions.or(full, onItem);
     

trunk/src/core/net/sf/basedb/core/DataFileType.java

@@ -560 +560 @@
 
   /**
+    Get a query returning the item subtypes that files of this type
+    can be used on. The query should only be used if the main item
+    type {@link #getItemType()} is a {@link Subtypable} item.
+    @return A query
+    @since 3.0
+  */
+  public ItemQuery<ItemSubtype> getItemSubtypes()
+  {
+    ItemQuery<ItemSubtype> query = ItemSubtype.getQuery(null);
+    query.joinPermanent(Hql.innerJoin("dataFileTypes", Item.DATAFILETYPE.getAlias()));
+    query.restrictPermanent(
+      Restrictions.eq(
+        Hql.alias(Item.DATAFILETYPE.getAlias()), 
+        Hql.entity(this)
+    ));
+    return query;
+  }
+  
+  /**
     Check if there is at least one extension that claims to support 
     validation of files of this type. The extensions are not actually

trunk/src/core/net/sf/basedb/core/Install.java

@@ -489 +489 @@
       
       // Derived bioassay set subtypes
-      createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.SCAN, 
+      ItemSubtypeData scan = createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.SCAN, 
         "Scan", "A hybridization that has been scanned to produce one or more images.", 
         hybridization, scanner, scanningProtocol, labeledExtract);
-      createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.SEQUENCED,
+      ItemSubtypeData sequenced = createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.SEQUENCED,
         "Sequenced", "A flow cell that has been sequenced.", 
         flowCell, sequencer, sequencingProtocol, library);
-      createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.ASSEMBLY, 
+      ItemSubtypeData assembly = createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.ASSEMBLY, 
         "Assembly", "A data set of sequences that has been aligned against a reference database", 
         alignmentSoftware, library);
@@ -849 +849 @@
         DataFileType.SAM, "Sequence Alignment/Map",
         "SAM format is a generic format for storing large nucleotide sequence alignments.",
-        Item.DERIVEDBIOASSAY, "sam", alignedType
+        Item.DERIVEDBIOASSAY, "sam", alignedType, assembly
       );
       DataFileTypeData bamFile = createDataFileType(
         DataFileType.BAM, "Compressed Sequence Alignment/Map",
         "BAM format is a BGZF-compressed SAM file.",
-        Item.DERIVEDBIOASSAY, "bam", alignedType
+        Item.DERIVEDBIOASSAY, "bam", alignedType, assembly
       );
       DataFileTypeData scanImageFile = createDataFileType(
         DataFileType.MICROARRAY_IMAGE, "Microarray image",
         "Scanned image from a microarray slide.",
-        Item.DERIVEDBIOASSAY, "tif", imageType
+        Item.DERIVEDBIOASSAY, "tif", imageType, scan
       );
       
@@ -2593 +2593 @@
   private static DataFileTypeData createDataFileType(
     String externalId, String name, String description,
-    Item itemType, String extension, ItemSubtypeData genericType)
+    Item itemType, String extension, ItemSubtypeData genericType, 
+    ItemSubtypeData... itemSubtypes)
     throws BaseException
   {
@@ -2613 +2614 @@
       {
         log.info("createDataFileType: EXISTS [externalId="+externalId+"]");
+        if (itemSubtypes != null)
+        {
+          for (ItemSubtypeData itemSubtype : itemSubtypes)
+          {
+            fileType.getItemSubtypes().add(itemSubtype);
+          }
+        }
         HibernateUtil.commit(tx);
       }
@@ -2625 +2633 @@
         fileType.setGenericType(genericType);
   
+        if (itemSubtypes != null)
+        {
+          for (ItemSubtypeData itemSubtype : itemSubtypes)
+          {
+            fileType.getItemSubtypes().add(itemSubtype);
+          }
+        }
+        
         HibernateUtil.saveData(session, fileType);
         HibernateUtil.commit(tx);

trunk/src/core/net/sf/basedb/core/ItemSubtype.java

@@ -525 +525 @@
   
   /**
+    Get a query returning the data file types that have been
+    associated with this subtype. The association is only used
+    for main item types that implemented the 
+    {@link FileStoreEnabled} interface.
+    @return A query
+  */
+  public ItemQuery<DataFileType> getDataFileTypes()
+  {
+    ItemQuery<DataFileType> query = DataFileType.getQuery();
+    query.joinPermanent(Hql.innerJoin("itemSubtypes", Item.ITEMSUBTYPE.getAlias()));
+    query.restrictPermanent(
+      Restrictions.eq(
+        Hql.alias(Item.ITEMSUBTYPE.getAlias()), 
+        Hql.entity(this)
+    ));
+    return query;
+  }
+  
+  /**
+    Checks if the given data file type is associated with this subtype or not.
+    @param fileType The file type to check
+    @return TRUE if the file type is associated, FALSE if not
+  */
+  public boolean isAssociatedDataFileType(DataFileType fileType)
+  {
+    return getData().getDataFileTypes().contains(fileType.getData());
+  }
+  
+  /**
+    Add a data file type as an associated file type. The data file type
+    must use the same main item type as this subtype.
+    @param fileType The file type to associate (required)
+  */
+  public void addAssociatedDataFileType(DataFileType fileType)
+  {
+    checkPermission(Permission.WRITE);
+    if (fileType == null) throw new InvalidUseOfNullException("fileType");
+    if (fileType.getItemType() != getMainItemType())
+    {
+      throw new InvalidDataException("The file type is not used for " + getMainItemType() + ": " + fileType.getName());
+    }
+    getData().getDataFileTypes().add(fileType.getData());
+  }
+  
+  /**
+    Remove the association between this subtype and the given data file type. 
+    If the file type is not associated nothing happens.
+    @param fileType The file type to remove
+  */
+  public void removeAssociatedDataFileType(DataFileType fileType)
+  {
+    checkPermission(Permission.WRITE);
+    if (fileType != null)
+    {
+      getData().getDataFileTypes().remove(fileType.getData());
+    }
+  }
+  
+  /**
     Helper method for implementing the {@link Subtypable#setItemSubtype(ItemSubtype)}
     method.

trunk/src/core/net/sf/basedb/core/data/DataFileTypeData.java

@@ -22 +22 @@
 package net.sf.basedb.core.data;
 
+import java.util.HashSet;
 import java.util.Set;
 
@@ -138 +139 @@
   }
   
+  private Set<ItemSubtypeData> itemSubtypes;
+  /**
+    The subtypes that this file type can be used with.
+
+    @hibernate.set table="`DataFileItemSubTypes`" lazy="true"
+    @hibernate.collection-key column="`datafiletype_id`"
+    @hibernate.collection-many-to-many column="`itemsubtype_id`" class="net.sf.basedb.core.data.ItemSubtypeData"
+  */
+  public Set<ItemSubtypeData> getItemSubtypes()
+  {
+    if (itemSubtypes == null) itemSubtypes = new HashSet<ItemSubtypeData>();
+    return itemSubtypes;
+  }
+  void setItemSubtypes(Set<ItemSubtypeData> itemSubtypes)
+  {
+    this.itemSubtypes = itemSubtypes;
+  }
+  
   private ItemSubtypeData genericType;
   /**

trunk/src/core/net/sf/basedb/core/data/ItemSubtypeData.java

@@ -24 +24 @@
 import java.util.Date;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
@@ -171 +172 @@
   }
   
+  private Set<DataFileTypeData> dataFileTypes;
+  /**
+    This is the inverse end. See {@link DataFileTypeData#getItemSubtypes()}.
+
+    @hibernate.set table="`DataFileItemSubTypes`" lazy="true"
+    @hibernate.collection-key column="`itemsubtype_id`"
+    @hibernate.collection-many-to-many column="`datafiletype_id`" class="net.sf.basedb.core.data.DataFileTypeData"
+  */
+  public Set<DataFileTypeData> getDataFileTypes()
+  {
+    if (dataFileTypes == null) dataFileTypes = new HashSet<DataFileTypeData>();
+    return dataFileTypes;
+  }
+  void setDataFileTypes(Set<DataFileTypeData> dataFileTypes)
+  {
+    this.dataFileTypes = dataFileTypes;
+  }
+
   
 }

trunk/www/admin/itemsubtypes/edit_subtype.jsp

@@ -32 +32 @@
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.Metadata"
+  import="net.sf.basedb.core.FileStoreEnabled"
+  import="net.sf.basedb.core.DataFileType"
+  import="net.sf.basedb.core.ItemQuery"
+  import="net.sf.basedb.core.Include"
+  import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.util.HTML"
@@ -57 +63 @@
   String title = null;
   ItemSubtype subtype = null;
-
+  ItemQuery<DataFileType> fileTypesQuery = null;
+  
   if (itemId == 0)
   {
@@ -69 +76 @@
     title = "Edit item subtype -- " + HTML.encodeTags(subtype.getName());
     subtype.checkPermission(Permission.WRITE);
+    fileTypesQuery = subtype.getDataFileTypes();
   }
   
@@ -78 +86 @@
   %>
   <base:page type="popup" title="<%=title%>">
-  <base:head scripts="tabcontrol.js" styles="tabcontrol.css">
+  <base:head scripts="tabcontrol.js,linkitems.js" styles="tabcontrol.css">
     <ext:scripts context="<%=jspContext%>" />
     <ext:stylesheets context="<%=jspContext%>" />
@@ -101 +109 @@
       if (TabControl.validateActiveTab('settings'))
       {
+        frm.addedFileTypes.value = Link.getActionIds(1, 'F').join(',');
+        frm.removedFileTypes.value = Link.getActionIds(-1, 'F').join(',');
         frm.submit();
       }
@@ -117 +127 @@
       }
       %>
+      initFileTypes();
       mainItemOnChange();
     }
     
-    var related = new Array();
-    var nameToValue = new Array();
+    function initFileTypes()
+    {
+      var frm = document.forms['subtype'];
+      var fileTypes = frm.fileTypes;
+      <%
+      if (fileTypesQuery != null)
+      {
+        fileTypesQuery.include(Include.ALL);
+        fileTypesQuery.order(Orders.asc(Hql.property("name")));
+        for (DataFileType fileType : fileTypesQuery.list(dc))
+        {
+          %>
+          Link.addNewItem(fileTypes, new Item('F', <%=fileType.getId()%>, '<%=HTML.javaScriptEncode(fileType.getName())%>'));
+          <%
+        }
+      }
+      %>
+    }
+    
+    var itemInfo = new Array();
     <%
     for (Item item : subtypableItems)
@@ -131 +160 @@
       }
       %>
-      related['<%=item.name()%>'] = '<%=tmp%>';
-      nameToValue['<%=item.name()%>'] = <%=item.getValue()%>;
+      var info = new Object();
+      info.value = <%=item.getValue()%>;
+      info.related = '<%=tmp%>';
+      info.fileStoreEnabled = <%=FileStoreEnabled.class.isAssignableFrom(item.getItemClass()) ? "true" : "false"%>;
+      itemInfo['<%=item.name()%>'] = info;
       <%
     }
     %>
     
-    function mainItemOnChange()
+    function getCurrentMainItemType()
     {
       var frm = document.forms['subtype'];
@@ -153 +185 @@
         <%
       }
+      %>
+      return mainType;
+    }
+    
+    function mainItemOnChange()
+    {
+      var mainType = getCurrentMainItemType();
+      <%
       for (Item item : subtypableItems)
       {
         %>
-        Main.showHide('section.<%=item.name()%>', related[mainType].indexOf('<%=item.name()%>') >= 0)
+        Main.showHide('section.<%=item.name()%>', itemInfo[mainType].related.indexOf('<%=item.name()%>') >= 0)
         <%
       }
       %>
-      Main.showHide('section.none', related[mainType] == '')
+      Main.showHide('section.none', itemInfo[mainType].related == '')
+      if (itemInfo[mainType].fileStoreEnabled)
+      {
+        Main.show('filetypes.enabled');
+        Main.hide('filetypes.disabled');
+      }
+      else
+      {
+        Main.show('filetypes.disabled');
+        Main.hide('filetypes.enabled');
+        document.getElementById('filetypes.disabled').innerHTML = 'The selected main item type (' + mainType + ') has not support for attaching data files.';
+      }
     }
     
@@ -169 +220 @@
       lastList = frm['related.'+itemType];
       var url = 'index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&title=Select+related+subtype&callback=setRelatedCallback';
-      url += '&resetTemporary=1&tmpfilter:INT:itemType=' + nameToValue[itemType];
+      url += '&resetTemporary=1&tmpfilter:INT:itemType=' + itemInfo[itemType].value;
       if (lastList.length > 1) 
       {
@@ -189 +240 @@
       list.selectedIndex = 1;
     }
+    function addFileTypesOnClick()
+    {
+      var frm = document.forms['subtype'];
+      var itemType = getCurrentMainItemType();
+      var ids = Link.getListIds(frm.fileTypes, 'F');
+      var excludes = ids.join(',');
+      var url = '../../admin/datafiletypes/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple&callback=addFileTypeCallback';
+      url += '&resetTemporary=1&tmpfilter:INT:itemType=' + itemInfo[itemType].value;
+      url += "&exclude="+excludes;
+      Main.openPopup(url, 'AddFileTypes', 1000, 700);
+    }
+    function addFileTypeCallback(fileTypeId, name)
+    {
+      var item = Link.getItem('F', fileTypeId);
+      if (!item) item = new Item('F', fileTypeId, name);
+      Link.addItem(document.forms['subtype'].fileTypes, item);
+    }
+    function removeFileTypesOnClick()
+    {
+      Link.removeSelected(document.forms['subtype'].fileTypes);
+    }
+
     </script>
   </base:head>
@@ -273 +346 @@
       <div align=right>&nbsp;<i><base:icon image="required.gif" /> = required information</i></div>
     </t:tab>
+    <t:tab
+      id="filetypes"
+      title="File types">
+      <div id="filetypes.enabled">
+      <table class="form" cellspacing=0>
+      <tr valign="top">
+        <td class="prompt">File types</td>
+        <td>
+          <table border="0" cellspacing="0" cellpadding="0">
+          <tr valign="top">
+          <td>
+            <select name="fileTypes" size="10" multiple style="width: 20em;">
+            </select>
+            <input type="hidden" name="addedFileTypes" value="">
+            <input type="hidden" name="removedFileTypes" value="">
+          </td>
+          <td>
+            <table border="0">
+            <tr><td width="150"><base:button 
+              onclick="addFileTypesOnClick()" 
+              title="Add file types&hellip;" 
+              tooltip="Add file types"
+              /></td></tr>
+            <tr><td width="150"><base:button 
+              onclick="removeFileTypesOnClick()" 
+              title="Remove" 
+              tooltip="Remove the selected file types"
+            /></td></tr>
+            </table>
+          </td>
+          </tr>
+          </table>
+        </td>
+      </tr>
+      </table>
+      </div>
+      <div id="filetypes.disabled" style="display: none;">
+      
+      </div>
+    </t:tab>
     </t:tabcontrol>
 

trunk/www/admin/itemsubtypes/index.jsp

@@ -29 +29 @@
   import="net.sf.basedb.core.Include"
   import="net.sf.basedb.core.ItemSubtype"
+  import="net.sf.basedb.core.DataFileType"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.Permission"
@@ -171 +172 @@
         }
       }
+
+      String[] removeFileTypes = Values.getString(request.getParameter("removedFileTypes")).split(",");
+      for (int i = 0; i < removeFileTypes.length; ++i)
+      {
+        int fileTypeId = Values.getInt(removeFileTypes[i], -1);
+        if (fileTypeId != -1) subtype.removeAssociatedDataFileType(DataFileType.getById(dc, fileTypeId));
+      }
       
+      String[] addFileTypes = Values.getString(request.getParameter("addedFileTypes")).split(",");
+      for (int i = 0; i < addFileTypes.length; ++i)
+      {
+        int fileTypeId = Values.getInt(addFileTypes[i], -1);
+        if (fileTypeId != -1) subtype.addAssociatedDataFileType(DataFileType.getById(dc, fileTypeId));
+      }
+
       cc.removeAllTemporaryFilters();
       

trunk/www/admin/itemsubtypes/list_subtypes.jsp

@@ -28 +28 @@
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemSubtype"
+  import="net.sf.basedb.core.DataFileType"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.Include"
@@ -98 +99 @@
   relatedQuery.include(cc.getInclude());
   
+  final ItemQuery<DataFileType> fileTypesQuery = DataFileType.getQuery();
+  fileTypesQuery.include(cc.getInclude());
+  fileTypesQuery.join(Hql.innerJoin("itemSubtypes", "ist"));
+  fileTypesQuery.restrict(Restrictions.eq(Hql.alias("ist"), Expressions.parameter("subtype")));
+  fileTypesQuery.order(Orders.asc(Hql.property("name"))); 
+
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
   try
@@ -272 +279 @@
         exportable="true"
       />      
+      <tbl:columndef
+        id="dataFileTypes"
+        title="File types"
+        property="&dataFileTypes(name)"
+        datatype="string"
+        filterable="true"
+        exportable="true"
+      />
       <tbl:columndef 
         id="description"
@@ -457 +472 @@
                   %>
                 </tbl:cell>
+                <tbl:cell column="dataFileTypes">
+                  <%
+                  fileTypesQuery.setParameter("subtype", itemId, Type.INT);
+                  String separator = "";
+                  for (DataFileType dft : fileTypesQuery.list(dc))
+                  {
+                    out.write(separator);
+                    if (mode.hasPropertyLink())
+                    {
+                      out.write(Base.getLinkedName(ID, dft, false, mode.hasEditLink()));
+                    }
+                    else
+                    {
+                      out.write(HTML.encodeTags(dft.getName()));
+                    }
+                    separator = ", ";
+                  }
+                  %>
+                </tbl:cell>
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
               </tbl:row>

trunk/www/admin/itemsubtypes/view_subtype.jsp

@@ -34 +34 @@
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.ItemSubtype"
+  import="net.sf.basedb.core.DataFileType"
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.PluginDefinition"
@@ -313 +314 @@
       %>
 
+      <%
+      ItemQuery<DataFileType> fileTypeQuery = subtype.getDataFileTypes();
+      fileTypeQuery.include(Include.ALL);
+      fileTypeQuery.order(Orders.asc(Hql.property("name")));
+      ItemResultList<DataFileType> fileTypes = fileTypeQuery.list(dc);
+      if (fileTypes.size() == 0)
+      {
+        %>
+        <h4>File types associated with this subtype</h4>
+        There are no file types (or, you don't have permission to view them).
+        <%
+      }
+      else
+      {
+        %>
+        <base:section 
+          id="fileTypes" 
+          title="<%="File types associated with this subtype (" + fileTypes.size() + ")"%>"
+          context="<%=cc%>"
+          >       
+          <tbl:table
+            id="fileTypes"
+            clazz="itemlist"
+            columns="all"
+            >
+            <tbl:columndef 
+              id="name"
+              title="Name"
+            />
+            <tbl:columndef 
+              id="extension"
+              title="File extension"
+            />
+            <tbl:columndef 
+              id="description"
+              title="Description"
+            />
+            <tbl:data>
+              <tbl:columns>
+              </tbl:columns>
+              <tbl:rows>
+              <%
+              for (DataFileType fileType : fileTypes)
+              {
+                %>
+                <tbl:row>
+                  <tbl:cell column="name"><base:icon 
+                      image="deleted.gif" 
+                      tooltip="This item has been scheduled for deletion" 
+                      visible="<%=fileType.isRemoved()%>"
+                    /><%=Base.getLinkedName(ID, fileType, false, true)%></tbl:cell>
+                  <tbl:cell column="extension"><%=HTML.encodeTags(fileType.getExtension()) %></tbl:cell>
+                  <tbl:cell column="description"><%=HTML.encodeTags(fileType.getDescription())%></tbl:cell>
+                </tbl:row>
+                <%
+              }
+              %>
+              </tbl:rows>
+            </tbl:data>
+          </tbl:table>
+        </base:section>
+        <%
+      }
+      %>
+
+
       <jsp:include page="../../common/anytoany/list_anytoany.jsp">
         <jsp:param name="ID" value="<%=ID%>" />

trunk/www/common/datafiles/list_files.jsp

@@ -23 +23 @@
   @version 2.0
 --%>
+<%@page import="net.sf.basedb.core.Subtypable"%>
+<%@page import="net.sf.basedb.core.ItemSubtype"%>
 <%@ page pageEncoding="UTF-8" session="false"
   import="net.sf.basedb.core.SessionControl"
@@ -101 +103 @@
   Platform platform = null;
   PlatformVariant variant = null;
+  ItemSubtype subtype = null;
   try
   {
@@ -108 +111 @@
   catch (Throwable t)
   {}
+  if (item instanceof Subtypable)
+  {
+    try
+    {
+      subtype = ((Subtypable)item).getItemSubtype();
+    }
+    catch (Throwable t)
+    {}
+  }
   
   // Load member file types
@@ -175 +187 @@
       catch (Throwable t)
       {}
+    }
+  }
+  
+  // Load subtype-related file types
+  if (subtype != null)
+  {
+    ItemQuery<DataFileType> query = subtype.getDataFileTypes();
+    for (DataFileType dft : query.list(dc))
+    {
+      if (!existing.contains(dft))
+      {
+        members.add(new DataFile(dft, null, null));
+      }
     }
   }
@@ -255 +280 @@
             PlatformFileType pft = platformFileTypes.get(dft);
             boolean isRequired = pft == null ? false : pft.isRequired();
-            boolean isPartOfPlatform = pft != null;
+            boolean isPartOfPlatform = pft != null || (subtype != null && subtype.isAssociatedDataFileType(dft));
             String icon = null;
             if (member == null)
@@ -273 +298 @@
                 icon = "error.gif";
               }
-              else if (!isPartOfPlatform && platform != null)
+              else if (!isPartOfPlatform)
               {
                 icon = "warning.gif";
-                validationMessage = "This file is not part of the <i>" + HTML.encodeTags(platform.getName()) + "</i> platform";
+                if (platform != null)
+                {
+                  validationMessage = "This file is not part of the <i>" + HTML.encodeTags(platform.getName()) + "</i> platform";
+                }
+                else if (subtype != null)
+                {
+                  validationMessage = "This file is not part of the <i>" + HTML.encodeTags(subtype.getName()) + "</i> subtype";
+                }
               }
               else if (Boolean.TRUE.equals(validFile))

trunk/www/common/datafiles/select_files.jsp

@@ -40 +40 @@
   import="net.sf.basedb.core.PlatformFileType"
   import="net.sf.basedb.core.DataFileType"
+  import="net.sf.basedb.core.Subtypable"
+  import="net.sf.basedb.core.ItemSubtype"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.Include"
@@ -70 +72 @@
 final int platformId = Values.getInt(request.getParameter("platform_id"), -1);
 final int variantId = Values.getInt(request.getParameter("variant_id"), -1);
+final int itemSubtypeId = Values.getInt(request.getParameter("itemsubtype_id"), -1);
 final ItemContext cc = sc.getCurrentContext(itemType);
 
@@ -84 +87 @@
   }
 
-  // Get the current platform/variant 
+  // Get the current platform/variant/itemsubtype
   // -- if not submitted in URL use values from current item
   PlatformVariant variant = null;
   Platform platform = null;
+  ItemSubtype itemSubtype = null;
   boolean deniedPlatform = false;
   try
   {
+    if (itemSubtypeId > 0)
+    {
+      itemSubtype = ItemSubtype.getById(dc, itemSubtypeId);
+    }
+    else if (item instanceof Subtypable)
+    {
+      itemSubtype = ((Subtypable)item).getItemSubtype();
+    }
     if (variantId > 0)
     {
@@ -113 +125 @@
   // Query to load data file types for specific itemType/platform/variant
   final ItemQuery<DataFileType> fileTypeQuery = 
-    Base.getDataFileTypes(itemType, item, platform, variant);
+    Base.getDataFileTypes(itemType, item, platform, variant, itemSubtype);
   List<DataFileType> fileTypes = fileTypeQuery.list(dc);
   
@@ -203 +215 @@
     if (fileTypes.size() == 0)
     {
+      String what = "";
+      if (platform != null)
+      {
+        what = "'" + HTML.encodeTags(platform.getName()) + "' platform";
+      }
+      else if (itemSubtype != null)
+      {
+        what = "'" + HTML.encodeTags(itemSubtype.getName()) + "' subtype";
+      }
       %>
       <div class="error">
-        The <%=platform == null ? "" : "'" + HTML.encodeTags(platform.getName()) + "'" %>
-        platform doesn't define any file types for <%=itemType.toString() %>
-        items.
+        The <%=what%> doesn't define any file types for 
+        <%=itemType.toString() %> items.
       </div>
       <%
@@ -233 +253 @@
         // If file type is not registered with a variant, also check if it is inherited from platform
         if (pft == null && variant != null) pft = platform.getFileType(dft, null);
-        boolean isPartOfPlatform = pft != null;
+        boolean isPartOfPlatform = pft != null || (itemSubtype != null && itemSubtype.isAssociatedDataFileType(dft));
         boolean isRequired = pft == null ? false : pft.isRequired();
         FileSetMember member = fileSet == null || !fileSet.hasMember(dft) ?
@@ -270 +290 @@
         %>
         <tr>
-          <td class="prompt"><%=HTML.encodeTags(dft.getName())%>
+          <td class="prompt "><%=HTML.encodeTags(dft.getName())%>
           <%
           if (!isPartOfPlatform && !deniedPlatform)
@@ -276 +296 @@
             hasNonPlatformFiles = true;
             %>
-            <base:icon image="warning.gif" tooltip="This file is not part of the platform" />
+            <base:icon image="warning.gif" tooltip="This file is not part of the platform/subtype" />
             <%
           }
@@ -339 +359 @@
       </table>
       <%
-      if (platform != null && hasNonPlatformFiles)
-      {
-        %>
-        <div align="right">
-        <base:icon image="warning.gif" /> 
-        = The file type is not part of the <i><%=HTML.encodeTags(platform.getName())%></i> platform
-        </div>
-        <%
-      }
-      %>
-      <%
+      if (hasNonPlatformFiles)
+      {
+        if (platform != null)
+        {
+          %>
+          <div align="right">
+          <base:icon image="warning.gif" /> 
+          = The file type is not part of the <i><%=HTML.encodeTags(platform.getName())%></i> platform
+          </div>
+          <%
+        }
+        else if (itemSubtype != null)
+        {
+          %>
+          <div align="right">
+          <base:icon image="warning.gif" /> 
+          = The file type is not part of the <i><%=HTML.encodeTags(itemSubtype.getName())%></i> subtype
+          </div>
+          <%
+        }
+      }
     }
     %>

trunk/www/include/scripts/platforms.js

@@ -31 +31 @@
 function PlatformsClass()
 {
-  this.loadDataFilesFrame = function(theFrame, ID, itemType, itemId, platformId, variantId)
+  this.loadDataFilesFrame = function(theFrame, ID, itemType, itemId, platformId, variantId, itemSubtypeId)
   {
     var url = getRoot()+'common/datafiles/select_files.jsp?ID='+ID;
@@ -37 +37 @@
     if (platformId != undefined && platformId != null) url += '&platform_id='+platformId;
     if (variantId != undefined && variantId != null) url += '&variant_id='+variantId;
+    if (itemSubtypeId != undefined && itemSubtypeId != null) url += '&itemsubtype_id='+itemSubtypeId;
     theFrame.location.href = url;
   }

trunk/www/views/derivedbioassays/edit_bioassay.jsp

@@ -318 +318 @@
     var parentsChanged = false;
     var protocolChanged = false;
+    var subtypeChanged = false;
     var dataFilesLoaded = false;
     function switchTab(tabControlId, tabId)
@@ -336 +337 @@
           parentsChanged = false;
         }
-        else if (tabId == 'datafiles' && (!dataFilesLoaded))
-        {
-          //var platform = Platforms.getSelectedPlatform(frm.platform);
-          //var variant = Platforms.getSelectedVariant(frm.platform);
-          Platforms.loadDataFilesFrame(frames.datafiles, '<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, 0, 0);
+        else if (tabId == 'datafiles' && (subtypeChanged || !dataFilesLoaded))
+        {
+          var subtypeId = ItemSubtype.getSubtypeId('bioAssay');
+          Platforms.loadDataFilesFrame(frames.datafiles, '<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, 0, 0, subtypeId);
           dataFilesLoaded = true;
+          subtypeChanged = false;
         }
       }
@@ -380 +381 @@
       var frm = document.forms['bioAssay'];
       var subtypeId = ItemSubtype.getSubtypeId('bioAssay');
+      subtypeChanged = true;
       var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'BIOASSAY', ['PROTOCOL', 'HARDWARE', 'SOFTWARE']);
       protocolChanged = ItemSubtype.updateRecentItemsInList(frm.protocol_id, recentInfo.PROTOCOL['recent']);
@@ -845 +847 @@
 
     <t:tab id="datafiles" title="Data files" helpid="datafiles.edit">
-      <iframe name="datafiles" id="idDatafiles" src="../../../common/datafiles/wait.jsp" 
+      <iframe name="datafiles" id="idDatafiles" src="../../common/datafiles/wait.jsp" 
         width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
         marginwidth=0 marginheight=0 scrolling="auto" style="overflow: visible"></iframe>
@@ -852 +854 @@
     <t:tab id="annotations" title="Annotations" 
       helpid="annotations.edit" tooltip="Enter values for annotations">
-      <iframe name="annotations" id="idAnnotations" src="../../../common/annotations/wait.jsp" 
+      <iframe name="annotations" id="idAnnotations" src="../../common/annotations/wait.jsp" 
         width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
         marginwidth=0 marginheight=0 scrolling="auto" style="overflow: visible"></iframe>
@@ -858 +860 @@
     
     <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
-      <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../../common/annotations/wait.jsp" 
+      <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp" 
         width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
         marginwidth=0 marginheight=0 scrolling="auto" style="overflow: visible"></iframe>