source: trunk/www/views/formulas/view_formula.jsp @ 5939

<%-- $Id: view_formula.jsp 5939 2012-01-30 14:42:18Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
  Copyright (C) 2007 Nicklas Nordborg, Martin Svensson

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
  of the License, or (at your option) any later version.

  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with BASE. If not, see <http://www.gnu.org/licenses/>.
  ------------------------------------------------------------------

  @author Nicklas
  @version 2.0
--%>
<%@ page pageEncoding="UTF-8" session="false"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.SystemItems"
  import="net.sf.basedb.core.Group"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.MultiPermissions"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.Formula"
  import="net.sf.basedb.core.Coloring"
  import="net.sf.basedb.core.User"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.PluginDefinition"
  import="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.core.plugin.Plugin"
  import="net.sf.basedb.core.Project"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.ChangeHistoryUtil"
  import="net.sf.basedb.clients.web.PermissionUtil"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.formatter.Formatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
  import="net.sf.basedb.clients.web.extensions.JspContext"
  import="net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer"
  import="net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="java.util.Date"
  import="java.util.Collections"
  import="java.util.List"
  import="java.util.Map"
  import="java.util.Set"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
<%@ taglib prefix="ext" uri="/WEB-INF/extensions.tld" %>
<%!
  private static final Item itemType = Item.FORMULA;
  private static final GuiContext guiContext = new GuiContext(itemType, GuiContext.Type.ITEM);
%>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
final int itemId = cc.getId();
final String tab = Values.getString(request.getParameter("tab"), "properties");
final float scale = Base.getScale(sc);
final DbControl dc = sc.newDbControl();
try
{
  Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
  Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);

  String title = null;
  final Formula formula = Formula.getById(dc, itemId);
  final RawDataType rawDataType = formula.getRawDataType();
  final List<String> expressions = formula.getFormulas();
  final Coloring coloring = formula.getColoring();
  
  final boolean writePermission = formula.hasPermission(Permission.WRITE);
  final boolean deletePermission = formula.hasPermission(Permission.DELETE);
  final boolean sharePermission = formula.hasPermission(Permission.SET_PERMISSION);
  final boolean setOwnerPermission = formula.hasPermission(Permission.SET_OWNER);
  final boolean isRemoved = formula.isRemoved();
  final boolean isUsed = isRemoved && formula.isUsed();
  final boolean deletePermanentlyPermission = deletePermission && !isUsed;
  final boolean isOwner = formula.isOwner();
  JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, guiContext, formula);
  ExtensionsInvoker invoker = ToolbarUtil.useExtensions(jspContext);
  %>
  <base:page title="<%=title%>">
  <base:head scripts="table.js,tabcontrol.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css">
    <ext:scripts context="<%=jspContext%>" />
    <ext:stylesheets context="<%=jspContext%>" />
    <script language="JavaScript">
    function editItem()
    {
      Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, true);
    }
    function shareItem()
    {
      Main.openPopup('index.jsp?ID=<%=ID%>&cmd=ShareItem&item_id=<%=itemId%>', 'ShareFormula', 600, 400);
    }
    function deleteItem()
    {
      location.replace('index.jsp?ID=<%=ID%>&cmd=DeleteItem&item_id=<%=itemId%>');
    }
    function restoreItem()
    {
      location.replace('index.jsp?ID=<%=ID%>&cmd=RestoreItem&item_id=<%=itemId%>');
    }
    function deleteItemPermanently()
    {
      Main.deleteItemPermanently('<%=ID%>', true, '<%=itemType.name()%>', <%=itemId%>, '&callback=itemDeleted');
    }
    function itemDeleted()
    {
      Main.listItems('<%=ID%>', '<%=itemType.name()%>');
    }
    function showUsingItems()
    {
      Main.showUsingItems('<%=ID%>', '<%=itemType.name()%>', <%=itemId%>);
    }
    function setOwner()
    {
      Main.openPopup('index.jsp?ID=<%=ID%>&cmd=SetOwnerOfItem&item_id=<%=itemId%>', 'SetOwnerOfItem', 450, 300);
    }
    function runPlugin(cmd)
    {
      Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&item_id=<%=itemId%>', 'RunPlugin'+cmd, 750, 500);
    }
    function switchTab(tabControlId, tabId)
    {
      if (TabControl.isActive(tabControlId, tabId)) return;
      if (tabId == 'history' && tabId != '<%=tab%>')
      {
        location.href = 'index.jsp?ID=<%=ID%>&cmd=ViewItem&item_id=<%=itemId%>&tab='+tabId;
      }
      else
      {
        TabControl.setActiveTab(tabControlId, tabId);
      }
    }
    </script>
  </base:head>
  <base:body>
    <p:path><p:pathelement
      title="Formulas" href="<%="index.jsp?ID="+ID%>" 
      /><p:pathelement title="<%=HTML.encodeTags(formula.getName())%>"
      /></p:path>
    
    <t:tabcontrol 
      id="main" 
      subclass="content mastertabcontrol" 
      active="<%=tab%>" switch="switchTab" remember="false">
    <t:tab id="properties" title="Properties">
      <div>
      <table class="fullform bottomborder">
      <tr>
        <th class="itemstatus">
          <base:icon 
            image="shared.gif" 
            visible="<%=formula.isShared()%>"
            tooltip="This item is shared to other users, groups and/or projects"
          />
          <base:icon 
            image="deleted.gif"
            onclick="deleteItemPermanently()"
            tooltip="This item has been flagged for deletion. Click to delete it now."
            enabled="<%=deletePermanentlyPermission %>"
            visible="<%=isRemoved%>" 
          />
          <base:icon image="used.gif" 
            onclick="showUsingItems()"
            tooltip="This item is used by other items and can't be permanently deleted. Show the items that are using this one"
            visible="<%=isRemoved && isUsed%>" />
        </th>
        <td style="padding: 0px;">
          <tbl:toolbar subclass="bottomborder">
            <tbl:button 
              disabled="<%=writePermission ? false : true%>" 
              image="edit.gif" 
              onclick="editItem()" 
              title="Edit&hellip;" 
              tooltip="<%=writePermission ? "Edit this formula" : "You do not have permission to edit this formula"%>" 
            />
            <tbl:button 
              disabled="<%=deletePermission ? false : true%>" 
              image="delete.gif" 
              onclick="deleteItem()" 
              title="Delete"
              visible="<%=!formula.isRemoved()%>"
              tooltip="<%=deletePermission ? "Delete this formula" : "You do not have permission to delete this formula"%>" 
            />
            <tbl:button 
              disabled="<%=writePermission ? false : true%>" 
              image="restore.gif" 
              onclick="restoreItem()" 
              title="Restore"
              visible="<%=formula.isRemoved()%>"
              tooltip="<%=writePermission ? "Restore this formula" : "You do not have permission to restore this formula"%>" 
            />
            <tbl:button 
              disabled="<%=sharePermission ? false : true%>"
              image="share.gif"
              onclick="shareItem()" 
              title="Share&hellip;" 
              tooltip="<%=sharePermission ? "Share this formula to other user, groups and projects" : "You do not have permission to share this formula"%>"
            />
            <tbl:button 
              disabled="<%=setOwnerPermission ? false : true%>"
              image="take_ownership.png"
              onclick="setOwner()" 
              title="Set owner&hellip;"
              tooltip="<%=setOwnerPermission ? "Change owner of this item" : "You do not have permission to change ownership of this item"%>"
            />
            <tbl:button 
              image="import.gif" 
              onclick="runPlugin('ImportItem')" 
              title="Import&hellip;" 
              tooltip="Import data" 
              visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
            />
            <tbl:button 
              image="export.gif" 
              onclick="runPlugin('ExportItem')" 
              title="Export&hellip;" 
              tooltip="Export data" 
              visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
            />
            <tbl:button 
              image="runplugin.gif" 
              onclick="runPlugin('RunPlugin')" 
              title="Run plugin&hellip;" 
              tooltip="Run a plugin" 
              visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
            />
            <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
              wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/>
            <tbl:button
              image="help.png"
              onclick="<%="Main.openHelp('" + ID +"', 'formula.view.properties')"%>"
              title="Help&hellip;"
              tooltip="Get help about this page"
            />
          </tbl:toolbar>
        </td>
      </tr>
      <tr>
        <th>Name</th>
        <td><%=HTML.encodeTags(formula.getName())%></td>
      </tr>
      <tr>
        <th>Registered</th>
        <td><%=dateFormatter.format(formula.getEntryDate())%></td>
      </tr>
      <tr>
        <th>Type</th>
        <td><%=formula.getFormulaType()%></td>
      </tr>
      <tr>
        <th>Value type</th>
        <td><%=formula.getValueType() == null ? "<i>- unknown -</i>" : formula.getValueType()%></td>
      </tr>
      <tr>
        <th>Parser</th>
        <td><%=formula.getParser()%></td>
      </tr>
      <tr>
        <th>Raw data type</th>
        <td><%=rawDataType == null ? "<i>- none -</i>" : HTML.encodeTags(rawDataType.getName())%></td>
      </tr>
      <tr>
        <th>Channels</th>
        <td><%=formula.getChannels()%></td>
      </tr>
      <tr class="big">
        <th>Expressions</th>
        <td>
          <%
          for (int i = 0; i < expressions.size(); ++i)
          {
            %>
            <%=(i+1) + ": " + HTML.encodeTags(expressions.get(i))%><br>
            <%
          }
          %>
        </td>
      </tr>
      <tr>
        <th>Avg. method</th>
        <td><%=formula.getAverageMethod().toString()%></td>
      </tr>
      <tr>
        <th>Source intensity transform</th>
        <td><%=formula.getSourceIntensityTransform() == null ? "<i>- any -</i>" : formula.getSourceIntensityTransform().toString()%></td>
      </tr>
      <tr>
        <th>Result intensity transform</th>
        <td><%=formula.getResultIntensityTransform() == null ? "<i>- any -</i>" : formula.getResultIntensityTransform().toString()%></td>
      </tr>
      <tr>
        <th>Use coloring</th>
        <td>
          <%=coloring.isUsingColors() ? "yes" : "no"%>
          <%
          if (coloring.isUsingColors())
          {
            %>
            <b>Range</b> 
            [<%=Values.formatNumber(coloring.getMinValue(), 2)%>,
            <%=Values.formatNumber(coloring.getMidValue(), 2)%>,
            <%=Values.formatNumber(coloring.getMaxValue(), 2)%>]
            <b>Logarithmic</b> <%=coloring.isLogarithmic() ? "yes" : "no" %>
            <%
          }
          %>
        </td>
      </tr>
      <tr>
        <th>Owner</th>
        <td><base:propertyvalue item="<%=formula%>" property="owner" /></td>
      </tr>
      <tr>
        <th>Permissions</th>
        <td><%=PermissionUtil.getFullPermissionNames(formula)%></td>
      </tr>
      <tr>
        <th>Description</th>
        <td><%=HTML.niceFormat(formula.getDescription())%></td>
      </tr>
      </table>
      </div>
      
      <jsp:include page="../../common/anytoany/list_anytoany.jsp">
        <jsp:param name="ID" value="<%=ID%>" />
        <jsp:param name="item_type" value="<%=itemType.name()%>" />
        <jsp:param name="item_id" value="<%=itemId%>" />
        <jsp:param name="title" value="Other items related to this formula" />
      </jsp:include>
      <jsp:include page="../../common/share/list_share.jsp">
        <jsp:param name="ID" value="<%=ID%>" />
        <jsp:param name="item_type" value="<%=itemType.name()%>" />
        <jsp:param name="item_id" value="<%=itemId%>" />
        <jsp:param name="title" value="Shared to" />
      </jsp:include>
    </t:tab>
    <t:tab id="history" title="Change history" 
      tooltip="Displays a log of all modifications made to this item"
      visible="<%=ChangeHistoryUtil.showChangeHistoryTab(sc)%>">
      <%
      if ("history".equals(tab))
      {
        %>
        <jsp:include page="../../common/history/frameset.jsp">
          <jsp:param name="source_type" value="<%=itemType.name()%>" />
          <jsp:param name="source_id" value="<%=itemId%>" />
          <jsp:param name="ID" value="<%=ID%>" />
        </jsp:include>
        <%
      }
      %>
    </t:tab>
    </t:tabcontrol>

  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}

%>