source: branches/3.6-stable/www/common/annotations/inherit.jsp @ 6975

<%-- $Id: inherit.jsp 6975 2015-10-08 06:11:11Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg
  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
  Copyright (C) 2007 Nicklas Nordborg

  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/>.
  ------------------------------------------------------------------

  This page is used to display and modify the attributes of
  the of a news item

  @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.Type"
  import="net.sf.basedb.core.BasicItem"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.Annotatable"
  import="net.sf.basedb.core.AnnotationSet"
  import="net.sf.basedb.core.Annotation"
  import="net.sf.basedb.core.RawBioAssay"
  import="net.sf.basedb.core.PhysicalBioAssay"
  import="net.sf.basedb.core.DerivedBioAssay"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.Nameable"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.AnnotationType"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.util.AnnotationUtil"
  import="net.sf.basedb.core.Subtypable"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.util.Tree"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.util.formatter.Formatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="java.util.List"
  import="java.util.Set"
  import="java.util.HashSet"
  import="java.util.Map"
  import="java.util.HashMap"
  import="org.json.simple.JSONArray"
  import="org.json.simple.JSONObject"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
private void loadParents(DbControl dc, Set<AnnotationSet> parentAnnotations, Set<Annotatable> parentItems, Annotatable current)
{
  Set<Annotatable> parents = AnnotationUtil.getAllAnnotatableParentItems(dc, current, null);
  for (Annotatable parent : parents)
  {
    if (parent != null && parentItems.add(parent))
    {
      if (parent.hasPermission(Permission.USE) && parent.isAnnotated())
      {
        parentAnnotations.add(parent.getAnnotationSet());
      }
    }
  }
}

JSONArray generateJoustTree(Set<AnnotationSet> parentAnnotations, Set<AnnotationSet> nonParents, Set<Annotation> inheritedAnnotations)
{
  String itemIcon = "Annotatable";
  String annotationIcon = "Annotation";
  String parameterIcon = "Parameter";
  String nonParentIcon = "NonParent";
  JSONArray json = new JSONArray();
  
  for (AnnotationSet as : parentAnnotations)
  {
    Annotatable item = null;
    String itemType = as.getItemType().toString();
    try
    {
      item = as.getItem();
    }
    catch (PermissionDeniedException ex)
    {}
    if (item instanceof Subtypable)
    {
      try
      {
        ItemSubtype subtype = ((Subtypable)item).getItemSubtype();
        if (subtype != null) itemType = subtype.getName();
      }
      catch (PermissionDeniedException ex)
      {}
    }
    
    String icon = nonParents.contains(as) ? nonParentIcon : itemIcon;
    
    String joustId = "as-"+as.getId();
    String input = "<input type=\"checkbox\""+
      " name=\""+joustId+"\">";
    String name = item == null ? "<i>- denied -</i>" : 
      HTML.encodeTags(((Nameable)item).getName()) + " <span class=\"itemsubtype\">(" + itemType + ")</span>";
    
    ItemQuery<Annotation> query = as.getAnnotations(Annotation.Source.PRIMARY);
    query.restrict(Restrictions.eq(Hql.property("annotationType.disableInheritance"), Expressions.bool(false)));
    List<Annotation> annotations = query.list(as.getDbControl());
    if (annotations.size() == 0) continue; // With the next AnnotationSet/item
      
    JSONObject jsonJoust = null;

    SessionControl sc = as.getSessionControl();
    for (Annotation a : annotations)
    {
      Formatter formatter = FormatterFactory.getAnnotationFormatter(sc, a, null);
      boolean inherited = inheritedAnnotations != null && inheritedAnnotations.contains(a);
      if (inherited) continue;
      
      if (jsonJoust == null)
      {
        jsonJoust = newJoustEntry(null, icon, input+name, joustId);
        jsonJoust.put("isOpen", 1);
        jsonJoust.put("type", "annotation-set");
        jsonJoust.put("externalId", as.getId());
        json.add(jsonJoust);
      }
      
      AnnotationType at = a.getAnnotationType();
      String annotationName = at.getName();
      boolean isParameter = at.isProtocolParameter();

      joustId = "a-"+a.getId();
      String values = Values.getString(a.getValues(null), ", ", true, formatter);
      name = HTML.encodeTags(annotationName +
        " [" + Values.trimString(values, 20)+"]");
      input = "<input type=\"checkbox\""+
        " name=\""+joustId+"\""+
        (inherited ? " checked" : "")+
        ">";
      
      JSONObject jsonAnnotation = newJoustEntry(jsonJoust, isParameter ? parameterIcon : annotationIcon, input+name, joustId);
      jsonAnnotation.put("type", "annotation");
      jsonAnnotation.put("externalId", a.getId());
      jsonAnnotation.put("annotationType", HTML.encodeTags(annotationName));
      jsonAnnotation.put("values", HTML.encodeTags(values));
      jsonAnnotation.put("inherited", inherited ? 1 : 0);
      jsonAnnotation.put("modified", 0);
    }
  }
  return json;
}

JSONObject newJoustEntry(JSONObject jsonParent, String icon, String text, String id)
{
  JSONObject jsonJoust = new JSONObject();
  jsonJoust.put("icon", icon);
  jsonJoust.put("text", text);
  jsonJoust.put("id", id);
  if (jsonParent != null)
  {
    JSONArray jsonChildren = (JSONArray)jsonParent.get("children");
    if (jsonChildren == null)
    {
      jsonChildren = new JSONArray();
      jsonParent.put("children", jsonChildren);
    }
    jsonChildren.add(jsonJoust);
  }
  return jsonJoust;
}
%>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final float scale = Base.getScale(sc);
final Item itemType = Item.valueOf(request.getParameter("item_type"));
final int itemId = Values.getInt(request.getParameter("item_id"));

//final boolean standalone = Values.getBoolean(request.getParameter("standalone"));

final DbControl dc = sc.newDbControl();
ItemResultList<AnnotationType> annotationTypes = null;
try
{
  final Annotatable item = itemId == 0 ? null : (Annotatable)itemType.getById(dc, itemId);
  Set<AnnotationSet> parentAnnotations = new java.util.LinkedHashSet<AnnotationSet>();
  Set<Annotatable> parentItems = new HashSet<Annotatable>();
  Set<AnnotationSet> nonParents = new HashSet<AnnotationSet>();

  if (item != null)
  {
    // Get all annotated parents and their annotation sets
    loadParents(dc, parentAnnotations, parentItems, item);
  }

  String title = "Inherit annotations to " + 
    HTML.encodeTags((item instanceof Nameable ? ((Nameable)item).getName() : 
    (item == null ? " new item" : item.toString())));

  // Parent items may have been submitted by caller
  String[] parents = request.getParameterValues("parents");
  // Each parameter is ITEMTYPE:ID:ID:...
  if (parents != null)
  {
    for (String parent : parents)
    {
      String[] temp = parent.split(":");
      Item parentType = Item.valueOf(temp[0]);
      for (int i = 1; i < temp.length; ++i)
      {
        int parentId = Values.getInt(temp[i], -1);
        if (parentId != -1) 
        {
          Annotatable parentItem = (Annotatable)parentType.getById(dc, parentId);
          if (parentItems.add(parentItem))
          {
            // This is a new parent
            if (parentItem.hasPermission(Permission.USE) && parentItem.isAnnotated()) 
            {
              parentAnnotations.add(parentItem.getAnnotationSet());
            }
            loadParents(dc, parentAnnotations, parentItems, parentItem);
          }
        }
      }
    }
  }
  
  // Get the currently inherited annotations
  final AnnotationSet as = item != null && item.isAnnotated() ? item.getAnnotationSet() : null;
  Set<Annotation> inheritedAnnotations = null;
  
  if (as != null)
  {
    ItemQuery<Annotation> inheritedQuery = as.getAnnotations(null);
    inheritedQuery.restrict(
        Restrictions.neq(
          Hql.property("source"), 
          Expressions.integer(Annotation.Source.PRIMARY.ordinal())
      ));
    
    // Ignore annotations marked for DELETE (so it is possible to re-select them)
    String d = request.getParameter("deleted");
    if (d != null)
    {
      Integer[] deleted = Values.getInt(d.split(","));
      if (deleted.length > 0)
      {
        inheritedQuery.restrict(Restrictions.not(Restrictions.in(Hql.property("id"), Expressions.parameter("deleted"))));
        inheritedQuery.setParameter("deleted", java.util.Arrays.asList(deleted), Type.INT);
      }
    }
        
    inheritedQuery.order(Orders.asc(Hql.property("annotationSet")));
    inheritedQuery.order(Orders.asc(Hql.property("annotationType.name")));
    inheritedAnnotations = new HashSet<Annotation>();
    for (Annotation a : inheritedQuery.list(dc))
    {
      a = a.getInheritedFrom();
      if (a != null)
      {
        inheritedAnnotations.add(a);
        AnnotationSet from = a.getAnnotationSet();
        if (!parentAnnotations.contains(from) && from.hasPermission(Permission.USE))
        {
          parentAnnotations.add(from);
          nonParents.add(from);
        }
      }
    }
  }
  JSONArray json = generateJoustTree(parentAnnotations, nonParents, inheritedAnnotations);
  %>
  <base:page type="popup" title="Inherit annotations">
  <base:head  scripts="joust-2.js,~inherit.js" styles="joust-2.css">
  <style>
  .selected .itemsubtype 
  {
    color: #E8E8E8;
  }
  </style>
  </base:head>
  <base:body>
    
  <h1><%=title%> <base:help helpid="annotations.inherit" /></h1>
  <div class="content bottomborder">
  
  <div id="page-data" class="datacontainer"
    data-callback="<%=HTML.encodeTags(request.getParameter("callback"))%>"
  ></div>
  
  <form name="annotations"> 
  <div class="absolutefull">
  
    <div class="absolutefull bg-filled-100 rightborder" style="width: 28em;">
    
      <div class="absolutefull bottomborder" style="height: 2em;">
      <%
      if (parentAnnotations.size() > 0) 
      {
        %>
        <table style="width: 100%;">
        <tr>
          <td style="padding-left: 4px; padding-right: 4px;"><base:icon image="filter.png"/></td>
          <td style="width: 100%; padding-top: 1px;">
            <input type="text" name="quickFilter" id="quickFilter" 
              class="auto-init" data-auto-init="focus"
              style="width: calc(100% - 10px);"
              title="Type to filter annotation types">
          </td>
        </table>
        <%
      }
      %>
      </div>
      <div class="absolutefull parameterlist" style="top: 2em; bottom: 3em;">
        <div id="joust" class="joust absolutefull"
          data-joust-tree="<%=HTML.encodeTags(json.toJSONString()) %>"
          >
          <%
          if (parentAnnotations.size() == 0) 
          {
            %>
            <div class="messagecontainer error" style="margin: 2em;">There are no parent items with annotations.</div>
            <%
          }
          %>
          <div id="noMatchingFilter" class="messagecontainer error" style="margin: 2em; display: none;">No annotations matches the filter.</div>
        </div>
      </div>
      
      <div class="absolutefull topborder" style="top: auto; bottom: 0px; height: 3em;">
        <table style="height: 100%; margin:auto;"><tr><td>
        <base:icon image="annotation.png" style="vertical-align: text-bottom;"/> = annotation
        <base:icon image="parameter.png" style="vertical-align: text-bottom;"/> = protocol parameter<br>
        <base:icon image="item-error.png" style="vertical-align: text-bottom;" /> = not a parent item
        </td></tr></table>
      </div>
    
    </div>
    
    <div class="absolutefull" style="left: 28em; padding: 1em;">
      <div id="annotationType" style="font-weight: bold;"></div>
      <div id="annotationValues"></div>
    </div>
  
  </div>
  </form>
  </div>

  <base:buttongroup subclass="dialogbuttons">
    <base:button id="btnClone" title="Clone" image="copy.png" data-clone="1" />
    <base:button id="btnInherit" title="Inherit" image="inherit.png" />
    <base:button id="close" title="Cancel" />
  </base:buttongroup>
  
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}
%>