source: trunk/www/common/annotations/list_annotations.jsp @ 8083

<%-- $Id: list_annotations.jsp 8083 2022-10-20 12:56:36Z nicklas $
  ------------------------------------------------------------------
  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.Permission"
  import="net.sf.basedb.core.AnnotationType"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.Project"
  import="net.sf.basedb.core.AnnotationSet"
  import="net.sf.basedb.core.Annotation"
  import="net.sf.basedb.core.Annotatable"
  import="net.sf.basedb.core.AnnotatableProxy"
  import="net.sf.basedb.core.Unit"
  import="net.sf.basedb.core.Nameable"
  import="net.sf.basedb.core.Subtypable"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.BioPlate"
  import="net.sf.basedb.core.BioPlateType"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.RawBioAssay"
  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.core.query.Restrictions"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.snapshot.AnnotationSetSnapshot"
  import="net.sf.basedb.core.snapshot.AnnotationSnapshot"
  import="net.sf.basedb.core.snapshot.SnapshotManager"
  import="net.sf.basedb.core.snapshot.ProjectFilter"
  import="net.sf.basedb.core.snapshot.AnnotationTypeFilter"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.NameableComparator"
  import="net.sf.basedb.util.units.UnitConverter"
  import="net.sf.basedb.util.formatter.Formatter"
  import="net.sf.basedb.util.formatter.PrefixSuffixFormatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.util.filter.Filter"
  import="net.sf.basedb.util.filter.AllOfFilter"
  import="java.util.Arrays"
  import="java.util.Collections"
  import="java.util.ArrayList"
  import="java.util.List"
  import="java.util.Set"
  import="java.util.HashSet"
  import="java.util.TreeSet"
  import="java.util.Map"
  import="java.util.HashMap"
  import="java.util.Date"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>

<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final Item itemType = Item.valueOf(request.getParameter("item_type"));
final int itemId = Values.getInt(request.getParameter("item_id"));
final float scale = Base.getScale(sc);
final DbControl dc = sc.newDbControl(":List annotations");

Set<AnnotationType> annotationTypes = null;
Set<AnnotationType> protocolParameters = null;
Map<AnnotationType, AnnotationSnapshot> existing = null;

boolean hasProjectSpecificAnnotationType = false;
AnnotationTypeFilter annotationTypeFilter = null;
Filter<AnnotationSnapshot> projectFilter = null;

try
{
  final Annotatable item = (Annotatable)itemType.getById(dc, itemId);
  final boolean writePermission = item.hasPermission(Permission.RESTRICTED_WRITE);
  final SnapshotManager manager = new SnapshotManager();
  
  ItemQuery<AnnotationType> annotationTypeQuery = null;
  String message = null;
  boolean isProxy = item instanceof AnnotatableProxy;

  // Load all annotation types that are possible for this item type
  if (isProxy)
  {
    AnnotatableProxy proxy = (AnnotatableProxy)item;
    annotationTypeQuery = Base.getAnnotationTypesQuery(proxy);
    message = proxy.getAnnotationMessage();
  }
  else
  {
    annotationTypeQuery = Base.getAnnotationTypesQuery(itemType, false);
  }
  annotationTypes = new TreeSet<AnnotationType>(new NameableComparator<>(false));
  annotationTypes.addAll(annotationTypeQuery.list(dc));

  final AnnotationSetSnapshot snapshot = item.isAnnotated() ? 
      manager.getSnapshot(dc, item.getAnnotationSet().getId()) : null;
  List<AnnotationSnapshot> inheritedAnnotations = null;
  if (snapshot != null)
  {
    // Load the existing primary and inherited annotations
    existing = new HashMap<AnnotationType, AnnotationSnapshot>();
    inheritedAnnotations = new ArrayList<AnnotationSnapshot>();
    for (AnnotationSnapshot a : manager.findAnnotations(dc, snapshot, null, true))
    {
      AnnotationType at = a.getAnnotationType(dc);
      if (a.getSource() == Annotation.Source.PRIMARY)
      {
        existing.put(a.getAnnotationType(dc), a);
        hasProjectSpecificAnnotationType |= at.getProjectAnnotations();
      }
      else
      {
        inheritedAnnotations.add(a);
      }
    }
    Collections.sort(inheritedAnnotations, AnnotationSnapshot.sortByAnnotationType(dc));
    annotationTypes.addAll(existing.keySet());
  }
  
  if (hasProjectSpecificAnnotationType)
  {
    manager.setAllProjects();
    annotationTypeFilter = new AnnotationTypeFilter();
    projectFilter = new AllOfFilter<>(Arrays.asList(annotationTypeFilter, new ProjectFilter(dc)));
  }
  
  // Load the possible protocol parameters
  Protocol protocol = null;
  boolean readProtocol = true;
  try
  {
    protocol = item.getProtocol();
  }
  catch (PermissionDeniedException ex)
  {
    readProtocol = false;
  }
  ItemQuery<AnnotationType> parameterQuery = Base.getProtocolParametersQuery(protocol);
  if (parameterQuery != null)
  {
    protocolParameters = new HashSet<AnnotationType>(parameterQuery.list(dc));
    annotationTypes.removeAll(protocolParameters);
  }
  
  // Load the current subtype
  // NOTE! User may have selected a different subtype in the form than what is
  // currently saved so if a subtype_id is sent in the request we use that
  String selectedCategoryName = null;
  try
  {
    ItemSubtype subtype = null;
    if (item instanceof Subtypable)
    {
      subtype = ((Subtypable)item).getItemSubtype();
    }
    else if (item instanceof BioPlate)
    {
      BioPlateType bpt = ((BioPlate)item).getBioPlateType();
      subtype = bpt.getItemSubtype();
      if (subtype == null) selectedCategoryName = bpt.getName();
    }
    else if (item instanceof RawBioAssay)
    {
      RawDataType rdt = ((RawBioAssay)item).getRawDataType();
      selectedCategoryName = rdt.getName();
    }
    if (subtype != null) selectedCategoryName = subtype.getName();
  }
  catch (PermissionDeniedException ex)
  {}
  Set<AnnotationType> annotationTypesInCategory = new HashSet<AnnotationType>();
  if (selectedCategoryName != null)
  {
    ItemQuery<AnnotationType> query = AnnotationType.getQuery(item.getType());
    query.setIncludes(Include.ALL);
    query.join(Hql.innerJoin("categories", "ct"));
    query.restrict(Restrictions.eq(Hql.property("ct", "name"), Expressions.string(selectedCategoryName)));
    annotationTypesInCategory.addAll(query.list(dc));
  }
  Formatter<Date> dateTimeFormatter = FormatterFactory.getDateTimeFormatter(sc);
  String projectValuesTitle = "<div class=\"project-values\"><div>Project values</div><div></div><div></div><div class=\"last-modified\">Last modified</div></div>";
  %>
  <base:page type="iframe" id="list-annotations">
  <base:head scripts="~list.js" styles="table.css">
  <style>
    #annotations-data.all
    {}
    
    #annotations-data.values .novalues
    {
      display: none;
    }
    
    #annotations-data.category .nocategory
    {
      display: none;
    }
    
    .edit-annotation
    {
      float: right;
    }
    
    .project-values
    {
      display: grid;
      grid-template-columns: 1fr 1fr 18px 12em;
    }
    
    .project-values div
    {
      padding: 1px 2px;
      border-bottom-width: 1px;
      border-bottom-style: dotted;
    }
    
    /* Remove borders on last row */
    .project-values div:nth-last-child(-n+4)
    {
      border-bottom-width: 0;
    }
    
    .project-values .default-value
    {
      font-style: italic;
    }
    
    .project-values .current-value::before 
    {
      font-weight: bold;
      content: '›';
      margin-right: 2px;
    }

    .project-values .other-value::before 
    {
      font-weight: bold;
      content: '›';
      color: transparent;
      margin-right: 2px;
    }
    
    /* Span accross first 2 columns */
    .project-values .no-default
    {
      font-style: italic;
      grid-column-start: 1;
      grid-column-end: 3;
    }
    
    .last-modified
    {
      white-space: nowrap;
      border-left-width: 1px;
      border-left-style: dotted;
    }
  </style>
  </base:head>
  <base:body>
    <%
    if (message != null)
    {
      %>
      <div class="messagecontainer note"><%=message%></div>
      <%
    }
    %>
    <base:section
      id="primaryAnnotations"
      title="<%="Primary annotations (" + annotationTypes.size() + ")"%>"
      >
      <%
      int allWithValues = 0;
      int allOfCategory = 0;
      if (annotationTypes.size() == 0)
      {
        %>
        <div class="messagecontainer note">
        No annotation types has been defined for this type of item 
        (or you don't have permission to view them).
        </div>
        <%
      }
      else
      {
        %>
        <tbl:table
          id="annotations"
          columns="all"
          stickyheaders="<%=null%>"
          >
          <tbl:columndef 
            id="annotation"
            title="Annotation"
          />
          <tbl:columndef 
            id="values"
            title="<%=hasProjectSpecificAnnotationType ? "Current values" : "Values" %>"
          />
          <tbl:columndef
            id="projectValues"
            title="<%=projectValuesTitle%>"
            tooltip="Project values"
            show="<%=hasProjectSpecificAnnotationType ? "always" : "never" %>"
            style="padding: 0;"
          />
          <tbl:columndef
            id="lastModified"
            title="Last modified"
            formatter="<%=dateTimeFormatter%>"
            show="<%=hasProjectSpecificAnnotationType ? "never" : "always" %>"
          />
          <tbl:columndef 
            id="description"
            title="Description"
          />
          <tbl:data id="annotations-data">
            <tbl:headers>
              <tbl:headerrow>
                <tbl:header colspan="5" subclass="bottomborder" style="padding: 5px;">
                  <b>View:</b> 
                  <%
                  if (selectedCategoryName != null)
                  {
                    %>
                    <label><input type="radio" name="view" id="view_category" value="category" checked>All of <i><%=HTML.encodeTags(selectedCategoryName)%></i> category</label> (<span id="allOfCategory">?</span>)
                    <%
                  }
                  %>
                  <label><input type="radio" name="view" id="view_values" value="values" <%=selectedCategoryName == null ? "checked" : ""%>>All with values</label> (<span id="allWithValues">?</span>)
                  <label><input type="radio" name="view" id="view_all" value="all">All annotations</label> (<%=annotationTypes.size()%>)
                </tbl:header>
              </tbl:headerrow>
              <tbl:headerrow>
                <tbl:columnheaders />
              </tbl:headerrow>
            </tbl:headers>
            <tbl:rows>
            <%
            for (AnnotationType at : annotationTypes)
            {
              // Permission for creating a new annotation
              boolean annotatePermission = writePermission & at.hasPermission(Permission.USE);
              AnnotationSnapshot a = existing != null ? existing.get(at) : null;
              List<?> values = null;
              Formatter<Object> formatter = null;
              boolean projectSpecific = false;
              if (a != null)
              {
                Annotation ann = a.getThisAnnotation(dc);
                // Permission on this annotation
                annotatePermission = ann.hasPermission(Permission.WRITE);
                values = a.getActualValues(ann.getUnitConverter(null), ann.getValueType());
                formatter = FormatterFactory.getAnnotationFormatter(sc, ann, null);
                projectSpecific = a.getProjectId() != 0;
              }
              if (values != null || !at.isRemoved())
              {
                String rowClass = "";
                if (values == null || values.size() == 0) 
                {
                  rowClass += " novalues";
                }
                else
                {
                  allWithValues++;
                }
                if (!annotationTypesInCategory.contains(at)) 
                {
                  rowClass += " nocategory";
                }
                else
                {
                  allOfCategory++;
                }
                %>
                <tbl:row subclass="<%=rowClass%>">
                  <tbl:cell column="annotation"><base:icon 
                    image="deleted.png" 
                    tooltip="This item has been scheduled for deletion" 
                    visible="<%=at.isRemoved()%>"
                    /><%=Base.getLinkedName(ID, at, false, true)%></tbl:cell>
                  <tbl:cell column="values" clazz="<%=projectSpecific ? "cell ps-annotation" : "cell" %>" disableOverflowCheck="true">
                    <%=values == null || values.size() == 0 ? "<i>- no values -</i>" : Values.getString(values, ", ", true, formatter)%>
                    <base:icon image="<%=a==null?"edit_create.png":"edit.png" %>" subclass="edit-annotation auto-init link" 
                      data-auto-init="edit-annotation" 
                      data-annotation="<%=a!=null ? a.getThisAnnotationId() : 0 %>"
                      data-annotation-type="<%=at.getId()%>"
                      data-item-type="<%=itemType.name()%>" 
                      data-item-id="<%=itemId %>"
                      tooltip="<%=a==null?"Create this annotation":"Modify the values of this annotation"%>"
                      visible="<%=annotatePermission %>"
                    />
                  </tbl:cell>
                  <tbl:cell column="projectValues" disableOverflowCheck="true" style="padding:0;">
                    <div class="project-values">
                    <%
                    if (at.getProjectAnnotations())
                    {
                      annotationTypeFilter.setAnnotationType(at);
                      List<AnnotationSnapshot> projectValues = manager.findAnnotations(dc, snapshot, projectFilter, false);
                      projectValues.sort(AnnotationSnapshot.sortByProject(dc, true));
                      int numValues = projectValues.size();
                      if (numValues == 0 || projectValues.get(0).getProjectId() != 0)
                      {
                        %>
                        <div class="no-default"><%=numValues > 0 ? "No default value":""%></div>
                        <div><base:icon image="edit_create.png" subclass="edit-annotation auto-init link" 
                            data-auto-init="edit-annotation" 
                            data-annotation="0"
                            data-annotation-type="<%=at.getId()%>"
                            data-project="0"
                            data-item-type="<%=itemType.name()%>" 
                            data-item-id="<%=itemId %>"
                            tooltip="Create a default value"
                            visible="<%=annotatePermission %>"
                          /></div>
                        <div class="last-modified"></div>
                        <%
                      }
                      if (numValues > 0)
                      {
                        for (AnnotationSnapshot pv : projectValues)
                        {
                          boolean isDefault = pv.getProjectId() == 0;
                          boolean isCurrent = pv == a;
                          Annotation ann = pv.getThisAnnotation(dc);
                          values = pv.getActualValues(ann.getUnitConverter(null), ann.getValueType());
                          formatter = FormatterFactory.getAnnotationFormatter(sc, ann, null);
                          if (numValues > 1)
                          {
                            %>
                            <div class="<%=isCurrent?"current-value":"other-value"%><%=isDefault ? " default-value":""%>"><%=isDefault ? "Default" : pv.getProject(dc).getName() %></div>
                            <div><%=Values.getString(values, ", ", true, formatter) %></div>
                            <%
                          }
                          else
                          {
                            %>
                            <div></div><div></div>
                            <%
                          }
                          %>
                          <div><base:icon image="edit.png" subclass="edit-annotation auto-init link" 
                              data-auto-init="edit-annotation" 
                              data-annotation="<%=pv.getThisAnnotationId()%>"
                              data-annotation-type="<%=at.getId()%>"
                              data-project="<%=pv.getProjectId()%>"
                              data-item-type="<%=itemType.name()%>" 
                              data-item-id="<%=itemId %>"
                              tooltip="<%=isDefault ? "Modify the default value" : "Modify the value in this project"%>"
                              visible="<%=annotatePermission %>"
                            /></div>
                          <div class="last-modified"><%=dateTimeFormatter.format(pv.getThisLastUpdate())%></div>
                          <%
                        }
                      }
                    }
                    else if (a != null)
                    {
                      %>
                      <div></div><div></div><div></div>
                      <div class="last-modified"><%=dateTimeFormatter.format(a.getThisLastUpdate())%></div>
                      <%
                    }
                    %>
                    </div>
                  </tbl:cell>
                  <tbl:cell column="lastModified" value="<%=a == null ? null : a.getThisLastUpdate() %>" />
                  <tbl:cell column="description"><%=HTML.encodeTags(at.getDescription())%></tbl:cell>
                </tbl:row>
                <%
              }
            }
            %>
            </tbl:rows>
          </tbl:data>
        </tbl:table>
        <%
      }
      %>
      <div id="annotations-stat" class="datacontainer"
        data-all-with-values="<%=allWithValues %>"
        data-all-of-category="<%=allOfCategory%>"
      ></div>
    </base:section>

    <%
    if (protocolParameters != null)
    {
      %>
      <base:section 
        id="parameterSection" 
        title="<%="Protocol parameters for " + HTML.encodeTags(protocol.getName()) + 
          " (" + protocolParameters.size() + ")"%>"
        >
        <%
        if (protocolParameters.size() == 0)
        {
          %>
          <div class="messagecontainer note">
          No protocol parameters has been defined for the protocol 
          <%=Base.getLinkedName(ID, protocol, !readProtocol, true)%> 
          (or you don't have permission to view them).
          </div>
          <%
        }
        else
        {
          %>
          <tbl:table
            id="parameters"
            columns="all"
            >
            <tbl:columndef 
              id="parameter"
              title="Parameter"
            />
            <tbl:columndef 
              id="values"
              title="<%=hasProjectSpecificAnnotationType ? "Current values" : "Values" %>"
            />
            <tbl:columndef
              id="projectValues"
              title="<%=projectValuesTitle%>"
              tooltip="Project values"
              show="<%=hasProjectSpecificAnnotationType ? "always" : "never" %>"
              style="padding: 0;"
            />
            <tbl:columndef
              id="lastModified"
              title="Last modified"
              formatter="<%=dateTimeFormatter%>"
              show="<%=hasProjectSpecificAnnotationType ? "never" : "always" %>"
            />
            <tbl:columndef 
              id="description"
              title="Description"
            />
            <tbl:data>
              <tbl:headers>
                <tbl:headerrow>
                  <tbl:columnheaders />
                </tbl:headerrow>
              </tbl:headers>
              <tbl:rows>
              <%
              for (AnnotationType at : protocolParameters)
              {
                // Permission for creating a new annotation
                boolean annotatePermission = writePermission & at.hasPermission(Permission.USE);
                AnnotationSnapshot a = existing != null ? existing.get(at) : null;
                List<?> values = null;
                Formatter<Object> formatter = null;
                boolean projectSpecific = false;
                if (a != null)
                {
                  Annotation ann = a.getThisAnnotation(dc);
                  // Permission on this annotation
                  annotatePermission = ann.hasPermission(Permission.WRITE);
                  values = a.getActualValues(ann.getUnitConverter(null), ann.getValueType());
                  formatter = FormatterFactory.getAnnotationFormatter(sc, ann, null);
                  projectSpecific = a.getProjectId() != 0;
                }
                if (values != null || !at.isRemoved())
                {
                  %>
                  <tbl:row>
                    <tbl:cell column="parameter"><base:icon 
                      image="deleted.png" 
                      tooltip="This item has been scheduled for deletion" 
                      visible="<%=at.isRemoved()%>"
                    /><%=Base.getLinkedName(ID, at, false, true)%></tbl:cell>
                    <tbl:cell column="values" clazz="<%=projectSpecific ? "cell ps-annotation" : "cell" %>" disableOverflowCheck="true">
                      <%=values == null || values.size() == 0 ? "<i>- no values -</i>" : Values.getString(values, ", ", true, formatter)%>
                      <base:icon image="<%=a==null?"edit_create.png":"edit.png" %>" subclass="edit-annotation auto-init link" 
                        data-auto-init="edit-annotation" 
                        data-annotation="<%=a!=null ? a.getThisAnnotationId() : 0 %>"
                        data-annotation-type="<%=at.getId()%>"
                        data-item-type="<%=itemType.name()%>" 
                        data-item-id="<%=itemId %>"
                        tooltip="<%=a==null?"Create this protocol parameter":"Modify the values of this protocol parameter"%>"
                        visible="<%=annotatePermission %>"
                      />
                    </tbl:cell>
                    <tbl:cell column="projectValues" disableOverflowCheck="true" style="padding:0;"> 
                      <div class="project-values">
                      <%
                      if (at.getProjectAnnotations())
                      {
                        annotationTypeFilter.setAnnotationType(at);
                        List<AnnotationSnapshot> projectValues = manager.findAnnotations(dc, snapshot, projectFilter, false);
                        projectValues.sort(AnnotationSnapshot.sortByProject(dc, true));
                        int numValues = projectValues.size();
                        if (numValues == 0 || projectValues.get(0).getProjectId() != 0)
                        {
                          %>
                          <div class="no-default"><%=numValues > 0 ? "No default value":""%></div>
                          <div><base:icon image="edit_create.png" subclass="edit-annotation auto-init link" 
                              data-auto-init="edit-annotation" 
                              data-annotation="0"
                              data-annotation-type="<%=at.getId()%>"
                              data-project="0"
                              data-item-type="<%=itemType.name()%>" 
                              data-item-id="<%=itemId %>"
                              tooltip="Create a default value"
                              visible="<%=annotatePermission %>"
                            /></div>
                          <div class="last-modified"></div>
                          <%
                        }
                        if (numValues > 0)
                        {
                          for (AnnotationSnapshot pv : projectValues)
                          {
                            boolean isDefault = pv.getProjectId() == 0;
                            boolean isCurrent = pv == a;
                            Annotation ann = pv.getThisAnnotation(dc);
                            values = pv.getActualValues(ann.getUnitConverter(null), ann.getValueType());
                            formatter = FormatterFactory.getAnnotationFormatter(sc, ann, null);
                            if (numValues > 1)
                            {
                              %>
                              <div class="<%=isCurrent?"current-value":"other-value"%><%=isDefault ? " default-value":""%>"><%=isDefault ? "Default" : pv.getProject(dc).getName() %></div>
                              <div><%=Values.getString(values, ", ", true, formatter) %></div>
                              <%
                            }
                            else
                            {
                              %>
                              <div></div><div></div>
                              <%
                            }
                            %>
                            <div><base:icon image="edit.png" subclass="edit-annotation auto-init link" 
                                data-auto-init="edit-annotation" 
                                data-annotation="<%=pv.getThisAnnotationId()%>"
                                data-annotation-type="<%=at.getId()%>"
                                data-project="<%=pv.getProjectId()%>"
                                data-item-type="<%=itemType.name()%>" 
                                data-item-id="<%=itemId %>"
                                tooltip="Modify the values of this protocol parameter"
                                visible="<%=annotatePermission %>"
                            /></div>
                            <div class="last-modified"><%=dateTimeFormatter.format(pv.getThisLastUpdate())%></div>
                            <%
                          }
                        }
                      }
                      else if (a != null)
                      {
                        %>
                        <div></div><div></div><div></div>
                        <div class="last-modified"><%=dateTimeFormatter.format(a.getThisLastUpdate())%></div>
                        <%
                      }
                      %>
                      </div>
                    </tbl:cell>
                    <tbl:cell column="lastModified" value="<%=a == null ? null : a.getThisLastUpdate() %>" />
                    <tbl:cell column="description"><%=HTML.encodeTags(at.getDescription())%></tbl:cell>
                  </tbl:row>
                  <%
                }
              }
              %>
              </tbl:rows>
            </tbl:data>
          </tbl:table>
          <%
        }
        %>
      </base:section>
      <%
    }
    if (!isProxy)
    {
      int numInherited = inheritedAnnotations == null ? 0 : inheritedAnnotations.size();
      %>
      <base:section 
        id="inherited"
        title="<%="Inherited annotations (" + numInherited + ")"%>"         
        >
        <%
        if (numInherited == 0)
        {
          %>
          <div class="messagecontainer note">
          No annotations are inherited by this item.
          (or you don't have permission to view them).
          </div>
          <%
        }
        else
        {
        %>
        <tbl:table
          id="inheritedAnnotations"
          columns="all"
          >
          <tbl:columndef 
            id="annotation"
            title="Annotation"
          />
          <tbl:columndef 
            id="values"
            title="Values"
          />
          <tbl:columndef 
            id="item"
            title="Parent item"
          />
          <tbl:columndef 
            id="note"
            title="Note"
          />
          <tbl:columndef
            id="lastModified"
            title="Last modified"
            formatter="<%=dateTimeFormatter %>"
          />
          <tbl:columndef 
            id="description"
            title="Description"
          />
          <tbl:data>
            <tbl:headers>
              <tbl:headerrow>
                <tbl:columnheaders />
              </tbl:headerrow>
            </tbl:headers>
            <tbl:rows>
            <%
            for (AnnotationSnapshot a : inheritedAnnotations)
            {
              boolean annotatePermission = a.hasPermission(dc, Permission.WRITE);
              AnnotationType at = a.getAnnotationType(dc);
              AnnotationSnapshot from = a.getInheritedFrom();
              
              // About this annotation
              String name = HTML.encodeTags(at.getName());
              String description = HTML.encodeTags(at.getDescription());
              Date lastModified = a.getThisLastUpdate();
              boolean isUpToDate = a.isUpToDate();
              
              // Which item are we inheriting from?
              Nameable fromItem = null;
              String fromType = null;
              boolean writeInherited = false;
              if (from != null)
              {
                fromType = from.getThisItemType().toString();
                if (lastModified == null)
                {
                  lastModified = from.getThisLastUpdate();
                }
                try
                {
                  fromItem = (Nameable)from.getThisItem(dc);
                  writeInherited = fromItem.hasPermission(Permission.WRITE);
                  if (fromItem instanceof Subtypable)
                  {
                    ItemSubtype subtype = ((Subtypable)fromItem).getItemSubtype();
                    if (subtype != null) fromType = subtype.getName();
                  }
                }
                catch (PermissionDeniedException ex)
                {}
              }
              
              // Values, units, etc.
              Formatter<Object> formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
              Unit unit = a.getActualUnit(dc);
              UnitConverter converter = null;
              if (unit != null)
              {
                converter = unit.getUnitConverter(at.getDefaultUnit());
                formatter = unit.getFormatter(formatter);
              }
              List<?> values = a.getActualValues(converter, at.getValueType());
              List<?> defaultValues = null;
              boolean projectSpecific = a.getProjectId() != 0;
              if (projectSpecific)
              {
                Annotation ann = a.getThisAnnotation(dc);
                if (ann.isOverridingDefault())
                {
                  Annotation defAnn = ann.getDefaultAnnotation();
                  Annotation defFrom = defAnn.getInheritedFrom();
                  defaultValues = defAnn.getSource() == Annotation.Source.CLONED ? defAnn.getValues() : defFrom.getValues();
                }
              }
              %>
              <tbl:row>
                <tbl:cell column="annotation"><%=Base.getLinkedName(ID, at, at == null, true)%></tbl:cell>
                <tbl:cell column="values" clazz="<%=projectSpecific ? "cell ps-annotation" : "cell" %>" disableOverflowCheck="true">
                  <%=values == null || values.size() == 0 ? 
                    "<i>- no values -</i>" : Values.getString(values, ", ", true, formatter)%>
                  <base:icon image="<%=isUpToDate ? "edit.png" : "edit-outofsync.png"%>" 
                    subclass="edit-annotation auto-init link" 
                    data-auto-init="edit-annotation" 
                    data-annotation="<%= a.getThisAnnotationId()%>"
                    data-annotation-type="<%=at.getId()%>"
                    data-item-type="<%=itemType.name()%>" 
                    data-item-id="<%=itemId %>"
                    tooltip="Modify the values of this annotation"
                    visible="<%=annotatePermission %>"
                  />
                </tbl:cell>
                <tbl:cell column="item"><%=from == null ? "<i>- missing -</i>" : Base.getLinkedName(ID, fromItem, fromItem == null, true)%><%=fromItem != null ? " <span class=\"itemsubtype\">("+fromType+")</span>" : ""%></tbl:cell>
                <tbl:cell column="note">
                  <%=a.getSource() == Annotation.Source.CLONED ? "Cloned" + (isUpToDate ? "; up-to-date" : "; modified") : "" %>
                    <%
                    if (projectSpecific && at.getProjectAnnotations())
                    {
                      %>
                      <%=defaultValues == null || defaultValues.size() == 0 ? "No default value" : "Default value: " + Values.getString(defaultValues, ", ", true, formatter)%>
                      <%
                    }
                    %>
                </tbl:cell>
                <tbl:cell column="lastModified" value="<%=lastModified %>"></tbl:cell>
                <tbl:cell column="description"><%=description%></tbl:cell>
              </tbl:row>
              <%
            }
            %>
            </tbl:rows>
          </tbl:data>
        </tbl:table>
        <%
      }
      %>
      </base:section>
      
      <%
    }
    %>
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}

%>