source: trunk/www/admin/protocols/edit_protocol.jsp @ 5631

<%-- $Id: edit_protocol.jsp 5631 2011-05-16 12:56:23Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg
  Copyright (C) 2006 Jari Häkkinen, 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.Item"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.AnnotationType"
  import="net.sf.basedb.core.File"
  import="net.sf.basedb.core.SystemItems"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
  import="net.sf.basedb.clients.web.extensions.JspContext"
  import="net.sf.basedb.clients.web.extensions.edit.EditUtil"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="java.util.List"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%
final Item itemType = Item.PROTOCOL;
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
final int itemId = cc.getId();
final String ID = sc.getId();
final float scale = Base.getScale(sc);
final DbControl dc = sc.newDbControl();
try
{
  String title = null;
  Protocol protocol = null;
  boolean readCurrentProtocolType = true;
  int currentProtocolTypeId = 0;
  boolean readCurrentFile = true;
  File currentFile = null;
  ItemQuery<AnnotationType> parameterQuery = null;

  // Load recently used items
  List<File> recentFiles = (List<File>)cc.getRecent(dc, Item.FILE);

  if (itemId == 0)
  {
    title = "Create protocol";

    currentProtocolTypeId = Values.getInt(request.getParameter("protocoltype_id"));
    if (currentProtocolTypeId == 0) 
    {
      int recentProtocolTypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
      currentProtocolTypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentProtocolTypeId);
    }
    cc.removeObject("item");
  }
  else
  {
    protocol = Protocol.getById(dc, itemId);
    parameterQuery = protocol.getParameters();
    cc.setObject("item", protocol);
    title = "Edit protocol -- " + HTML.encodeTags(protocol.getName());
    try
    {
      ItemSubtype pt = protocol.getItemSubtype();
      if (pt != null) currentProtocolTypeId = pt.getId();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentProtocolType = false;
    }
    try
    {
      currentFile = protocol.getFile();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentFile = false;
    }
  }
  if (protocol != null && !protocol.hasPermission(Permission.WRITE))
  {
    throw new PermissionDeniedException(Permission.WRITE, itemType.toString());
  }
  
  // Query to retrieve protocol types
  final ItemQuery<ItemSubtype> protocolTypeQuery = ItemSubtype.getQuery(itemType);
  protocolTypeQuery.include(Include.ALL);
  protocolTypeQuery.order(Orders.asc(Hql.property("name")));
  
  final String clazz = "class=\"text\"";
  final String requiredClazz = "class=\"text required\"";
  JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(itemType), protocol);
  ExtensionsInvoker invoker = EditUtil.useEditExtensions(jspContext);
  %>

  <base:page type="popup" title="<%=title%>">
  <base:head scripts="tabcontrol.js,annotations.js,linkitems.js,ajax.js,json2.js,subtypes.js" styles="tabcontrol.css">
    <ext:scripts context="<%=jspContext%>" />
    <ext:stylesheets context="<%=jspContext%>" />
    <script language="JavaScript">
    // Validate the "Protocol" tab
    function validateProtocol()
    {
      var frm = document.forms['protocol'];
      if (Main.trimString(frm.name.value) == '')
      {
        alert("You must enter a name");
        frm.name.focus();
        return false;
      }
      return true;
    }
    // Validate the "Parameters" tab
    function validateParameters()
    {
      return true;
    }

    // Submit the form
    function saveSettings()
    {
      var frm = document.forms['protocol'];
      if (TabControl.validateActiveTab('settings'))
      {
        if (annotationsLoaded) 
        {
          Annotations.addModifiedAnnotationsToForm(frames.annotations, frm);
        }
        frm.addedAnnotationTypes.value = Link.getActionIds(1, 'A').join(',');
        frm.removedAnnotationTypes.value = Link.getActionIds(-1, 'A').join(',');
        frm.submit();
      }
    }
    
    var annotationsLoaded = false;
    function switchTab(tabControlId, tabId)
    {
      if (TabControl.setActiveTab(tabControlId, tabId))
      {
        if (tabId == 'annotations' && !annotationsLoaded)
        {
          Annotations.loadAnnotateFrame(frames.annotations, '<%=ID%>', '<%=itemType.name()%>', <%=itemId%>);
          annotationsLoaded = true;
        }
      }
    }
    
    function browseOnClick()
    {
      var frm = document.forms['protocol'];
      var protocolType = Math.abs(frm.protocoltype_id[frm.protocoltype_id.selectedIndex].value);
      var relatedFileSubtype = ItemSubtype.getRelatedSubtype(protocolType, 'FILE', <%=SystemItems.getId(File.PROTOCOL)%>);
      var url = '../../filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&title=Select+protocol&callback=setFileCallback';
      url += '&resetTemporary=1&tmpfilter:INT:itemSubtype=' + relatedFileSubtype.id;
      if (frm.file_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.file_id[1].value));        
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectFile', 1000, 700);
    }
    function setFileCallback(id, path)
    {
      var frm = document.forms['protocol'];
      var list = frm.file_id;
      if (list.length < 2 || list[1].value == '0') // >
      {
        Forms.addListOption(list, 1, new Option());
      }
      list[1].value = id;
      list[1].text = path;
      list.selectedIndex = 1;
    }

    function init()
    {
      var frm = document.forms['protocol'];
      <%
      if (protocol == null)
      {
        %>
        frm.name.focus();
        frm.name.select();
        <%
      }
      if (parameterQuery != null)
      {
        %>
        var annotationTypes = frm.annotationTypes;
        <%
        parameterQuery.include(Include.ALL);
        parameterQuery.order(Orders.asc(Hql.property("name")));
        ItemResultList<AnnotationType> parameters = parameterQuery.list(dc);
        for (AnnotationType at : parameters)
        {
          %>
          Link.addNewItem(annotationTypes, new Item('A', <%=at.getId()%>, '<%=HTML.javaScriptEncode(at.getName())%>'));
          <%
        }
      }
      %>
    }
    function addAnnotationTypesOnClick()
    {
      var frm = document.forms['protocol'];
      var ids = Link.getListIds(frm.annotationTypes, 'A');
      var excludes = ids.join(',');
      var url = '../annotationtypes/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple&callback=addAnnotationTypeCallback';
      url += '&resetTemporary=1&tmpfilter:BOOLEAN:protocolParameter=true';
      url += "&exclude="+excludes;
      Main.openPopup(url, 'AddAnnotationTypes', 1000, 700);
    }
    function addAnnotationTypeCallback(annotationTypeId, name)
    {
      var item = Link.getItem('A', annotationTypeId);
      if (!item) item = new Item('A', annotationTypeId, name);
      Link.addItem(document.forms['protocol'].annotationTypes, item);
    }
    function removeAnnotationTypesOnClick()
    {
      Link.removeSelected(document.forms['protocol'].annotationTypes);
    }
    </script>
  </base:head>
  <base:body onload="init()">
    <p>
    <form action="index.jsp?ID=<%=ID%>" method="post" name="protocol" 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="<%=protocol != null%>" switch="switchTab"
      extensions="<%=invoker%>">
    <t:tab id="info" title="Protocol" validate="validateProtocol()" helpid="protocol.edit">
      <table class="form" cellspacing=0>
      <tr>
        <td class="prompt">Name</td>
        <td><input <%=requiredClazz%> type="text" name="name" 
          value="<%=HTML.encodeTags(protocol == null ? Values.getString(cc.getPropertyValue("name"), "New protocol") : protocol.getName())%>" 
          size="40" maxlength="<%=Protocol.MAX_NAME_LENGTH%>"></td>
      </tr>
      <tr valign="top">
        <td class="prompt">Type</td>
        <td colspan="2">
          <select name="protocoltype_id" 
            <%=!readCurrentProtocolType ? "disabled readonly class=\"disabled\"" : "class=\"required\""%>>
          <%
          if (!readCurrentProtocolType)
          {
            %>
            <option value="-1">- denied -
            <%
          }
          else
          {
            for (ItemSubtype protocolType : protocolTypeQuery.list(dc))
            {
              int id = protocolType.getId();
              if (id != currentProtocolTypeId && protocolType.isRemoved()) continue;
              %>
              <option value="<%=id == currentProtocolTypeId && protocol != null ? -id : id%>" 
                <%=id == currentProtocolTypeId ? "selected" : ""%>
                ><%=HTML.encodeTags(protocolType.getName())%>
              <%
            }
          }
          %>
          </select>
        </td>
      </tr>
      <tr>
        <td class="prompt">External ID</td>
        <td><input <%=clazz%> type="text" name="external_id" 
          value="<%=HTML.encodeTags(protocol == null ? Values.getString(cc.getPropertyValue("externalId"), "") : protocol.getExternalId())%>" 
          size="40" maxlength="<%=Protocol.MAX_EXTERNAL_ID_LENGTH%>"></td>
      </tr>
      <tr>
        <td class="prompt">File</td>
        <td>
          <base:select 
            id="file_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentFile%>"
            denied="<%=!readCurrentFile%>"
            recent="<%=recentFiles%>"
            newitem="<%=protocol == null%>"
            onselect="browseOnClick()"
          />
        </td>
      </tr>

      <tr valign=top>
        <td class="prompt">Description</td>
        <td nowrap>
          <textarea <%=clazz%> rows="4" cols="40" name="description" wrap="virtual"
            ><%=HTML.encodeTags(protocol == null ? cc.getPropertyValue("description") : protocol.getDescription())%></textarea>
          <a href="javascript:Main.zoom('Description', 'protocol', 'description')"
            title="Edit in larger window"><base:icon image="zoom.gif" /></a>
        </td>
      </tr>
      </table>
      <div align=right>&nbsp;<i><base:icon image="required.gif" /> = required information</i></div>
    </t:tab>
    
    <t:tab id="parameters" title="Parameters" 
      validate="validateParameters()" helpid="protocol.edit.parameters">
    <table class="form" cellspacing=0>
    
    <tr valign="top">
      <td><b>Annotation types</b>
        <table border="0" cellspacing="0" cellpadding="0">
        <tr valign="top">
        <td>
          <select name="annotationTypes" size="10" multiple style="width: 20em;">
          </select>
          <input type="hidden" name="addedAnnotationTypes" value="">
          <input type="hidden" name="removedAnnotationTypes" value="">
        </td>
        <td>
          <table border="0">
          <tr><td width="150"><base:button 
            onclick="addAnnotationTypesOnClick()" 
            title="Add annotation types&hellip;" 
            tooltip="Add annotation types"
            /></td></tr>
          <tr><td width="150"><base:button 
            onclick="removeAnnotationTypesOnClick()" 
            title="Remove" 
            tooltip="Remove the selected annotation types"
          /></td></tr>
          </table>
        </td>
        </tr>
        </table>
      </td>
    </tr>
    </table>
    </t:tab>
    
    <t:tab id="annotations" title="Annotations" 
      helpid="annotations.edit" tooltip="Enter values for annotations">
      <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>
    </t:tab>
    
    </t:tabcontrol>

    <table align="center">
    <tr>
      <td width="50%"><base:button onclick="saveSettings()" title="Save" /></td>
      <td width="50%"><base:button onclick="window.close()" title="Cancel" /></td>
    </tr>
    </table>
    </form>
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}
%>