source: trunk/www/biomaterials/biosources/list_biosources.jsp @ 7605

<%-- $Id: list_biosources.jsp 7605 2019-02-26 10:10:15Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
  Copyright (C) 2007 Johan Enell, 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.BioSource"
  import="net.sf.basedb.core.Sample"
  import="net.sf.basedb.core.AnnotationType"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.AnnotationSet"
  import="net.sf.basedb.core.Annotation"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.ItemResultIterator"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.Nameable"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.PluginDefinition"
  import="net.sf.basedb.core.Type"
  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.query.Orders"
  import="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.core.plugin.Plugin"
  import="net.sf.basedb.core.snapshot.AnnotationLoaderUtil"
  import="net.sf.basedb.core.snapshot.AnnotationTypeFilter"
  import="net.sf.basedb.core.snapshot.AnnotationSnapshot"
  import="net.sf.basedb.core.snapshot.AnnotationSetSnapshot"
  import="net.sf.basedb.core.snapshot.SnapshotManager"
  import="net.sf.basedb.util.Enumeration"
  import="net.sf.basedb.util.ShareableUtil"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.ModeInfo"
  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.ButtonAction" 
  import="net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil"
  import="net.sf.basedb.clients.web.extensions.list.ListColumnAction"
  import="net.sf.basedb.clients.web.extensions.list.ListColumnUtil"
  import="net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="net.sf.basedb.util.Values"
  import="java.util.Iterator"
  import="java.util.Date"
  import="java.util.List"
  import="java.util.Map"
  import="java.util.ArrayList"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
<%@ taglib prefix="ext" uri="/WEB-INF/extensions.tld" %>
<%!
  private static final Item itemType = Item.BIOSOURCE;
  private static final GuiContext guiContext = new GuiContext(itemType, GuiContext.Type.LIST);
%>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, Permission.DENIED, itemType);
final String ID = sc.getId();
final boolean createPermission = sc.hasPermission(Permission.CREATE, itemType);
final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);

final ModeInfo mode = ModeInfo.get(request.getParameter("mode"));
final String callback = request.getParameter("callback");
final String title = mode.generateTitle("biosource", "biosources");
final DbControl dc = sc.newDbControl();
ItemResultIterator<BioSource> bioSources = null;
List<AnnotationLoaderUtil> annotationLoaders = new ArrayList<AnnotationLoaderUtil>();
try
{
  final ItemQuery<AnnotationType> annotationTypeQuery = Base.getAnnotationTypesQuery(itemType);
  SnapshotManager manager = new SnapshotManager();
  ProjectSpecificInfoFilter psInfo = new ProjectSpecificInfoFilter();
  for (AnnotationType at : annotationTypeQuery.list(dc))
  {
    annotationLoaders.add(new AnnotationLoaderUtil(dc, manager, at));
  }
  final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);

  final ItemQuery<Sample> sampleQuery = Sample.getQuery();
  sampleQuery.include(cc.getInclude());
  sampleQuery.restrict(Restrictions.eq(Hql.property("parent"), Expressions.parameter("bioSource")));
  sampleQuery.order(Orders.asc(Hql.property("name")));
  final boolean createSamplePermission = sc.hasPermission(Permission.CREATE, Item.SAMPLE);

  Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
  try
  {
    final ItemQuery<BioSource> query = Base.getConfiguredQuery(dc, cc, true, BioSource.getQuery(), mode);
    bioSources = query.iterate(dc);
  }
  catch (Throwable t)
  {
    cc.setMessage(t.getMessage());
    t.printStackTrace();
  }
  int numListed = 0;
  Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
  JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, guiContext, null);
  ExtensionsInvoker<ButtonAction> invoker = ToolbarUtil.useExtensions(jspContext);
  ExtensionsInvoker<ListColumnAction<BioSource,?>> columnsInvoker = ListColumnUtil.useExtensions(jspContext);
  %>
  <base:page title="<%=title==null ? "Biosources" : title%>" type="<%=mode.getPageType()%>" id="list-page">
  <base:head scripts="table.js,~biosources.js" styles="table.css,toolbar.css">
    <ext:scripts context="<%=jspContext%>" />
    <ext:stylesheets context="<%=jspContext%>" />
  </base:head>
  
  <base:body >
    <h1><%=title==null ? "Biosources" : title%></h1>
    <div class="content">
      <tbl:table 
        id="biosources" 
        columns="<%=cc.getSetting("columns")%>"
        sortby="<%=cc.getSortProperty()%>" 
        direction="<%=cc.getSortDirection()%>"
        action="index.jsp"
        sc="<%=sc%>"
        item="<%=itemType%>"
        filterrows="<%=cc.getFilterRows()%>"
        subclass="fulltable"
      >
      <tbl:hidden 
        name="mode" 
        value="<%=mode.getName()%>" 
      />
      <tbl:hidden 
        name="callback" 
        value="<%=callback%>" 
        skip="<%=callback == null%>" 
      />
      <tbl:columndef 
        id="name"
        property="name"
        datatype="string"
        title="Name"
        sortable="true" 
        filterable="true"
        exportable="true"
        show="always" 
      />
      <tbl:columndef 
        id="itemSubtype"
        property="itemSubtype"
        sortproperty="itemSubtype.name"
        exportproperty="itemSubtype.name:string"
        datatype="int"
        enumeration="<%=Enumeration.fromItems(subtypesQuery.list(dc), "-none-")%>"
        title="Type"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
         id="id"
        clazz="uniquecol"
         property="id"
         datatype="int"
         title="ID"
         sortable="true" 
         filterable="true"
         exportable="true"
      />
      <tbl:columndef 
        id="externalId"
        property="externalId"
        datatype="string"
        title="External id"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="entryDate"
        property="entryDate"
        datatype="date"
        title="Registered"
        sortable="true" 
        filterable="true"
        exportable="true"
        formatter="<%=dateFormatter%>"
      />
      <tbl:columndef
        id="samples"
        title="Samples"
        property="&children(name)"
        datatype="string"
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="owner"
        property="owner.name"
        datatype="string"
        title="Owner"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="description"
        property="description"
        datatype="string"
        title="Description" 
        sortable="true" 
        filterable="true" subclass="foobar"
        exportable="true"
      />      
      <tbl:columndef
        id="itemList"
        property="§itemLists"
        datatype="int"
        title="Item list"
        filterable="true"
        enumeration="<%=Base.getItemListsEnum(dc, itemType, cc.getInclude())%>"
        multiple="false"
      />
      <%
      for (AnnotationLoaderUtil loader : annotationLoaders)
      {
        AnnotationType at = loader.getAnnotationType();
        Enumeration<String, String> annotationEnum = null;
        Formatter<Object> formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
        if (at.isEnumeration())
        {
          annotationEnum = new Enumeration<String, String>();
          if (!at.getDisplayAsList()) annotationEnum.add("", "-none-");
          List<?> values = at.getValues();
          for (Object value : values)
          {
            String encoded = formatter.format(value);
            annotationEnum.add(encoded, encoded);
          }
        }
        %>
        <tbl:columndef 
          id="<%="at"+at.getId()%>"
          title="<%=HTML.encodeTags(at.getName())+" [A]"%>" 
          property="<%="#"+at.getId()%>"
          annotation="true"
          datatype="<%=at.getValueType().getStringValue()%>"
          enumeration="<%=annotationEnum%>"
          smartenum="<%=at.getDisplayAsList() %>"
          sortable="<%=at.getMultiplicity() == 1%>" 
          filterable="true" 
          exportable="true"
          formatter="<%=formatter%>"
          unit="<%=at.getDefaultUnit()%>"
        />
        <%
      }
      %>
      <tbl:columndef
        id="permission"
        title="Permission"
      />
      <tbl:columndef
        id="sharedTo"
        title="Shared to"
        filterable="true"
        filterproperty="!sharedTo.name"
        datatype="string"
      />
      <tbl:columndef 
        id="xt-columns" 
        extensions="<%=columnsInvoker%>" 
        jspcontext="<%=jspContext%>" 
      />
      <div class="panelgroup bg-filled-50 bottomborder">
        <tbl:toolbar
          visible="<%=mode.hasToolbar()%>"
          subclass="bottomborder"
          >
          <tbl:button 
            id="btnNewItem"
            disabled="<%=!createPermission%>" 
            image="new.png" 
            title="New&hellip;" 
            tooltip="<%=createPermission ? "Create new biosource" : "You do not have permission to create biosources"%>" 
          />
          <tbl:button 
            id="btnDeleteItems"
            image="delete.png"
            title="Delete" 
            tooltip="Delete the selected items" 
          />
          <tbl:button 
            id="btnRestoreItems"
            image="restore.png"
            title="Restore" 
            tooltip="Restore the selected (deleted) items"
          />
          <tbl:button 
            id="btnShareItems"
            image="share.png"
            title="Share&hellip;" 
            tooltip="Share the selected items"
          />
          <tbl:button 
            id="btnSetOwner"
            image="take_ownership.png"
            title="Set owner&hellip;"
            tooltip="Change owner of the selected items"
          />
          <tbl:button 
            id="btnColumns"
            image="columns.png" 
            title="Columns&hellip;" 
            tooltip="Show, hide and re-order columns" 
          />
          <tbl:button
            id="btnNewItemList"
            image="add.png"
            title="New item list&hellip;"
            tooltip="Create a new item list from matching biosources"
            visible="<%=sc.hasPermission(Permission.CREATE, Item.ITEMLIST)%>"
          />
          <tbl:button 
            id="btnImport"
            data-plugin-type="IMPORT"
            image="import.png" 
            title="Import&hellip;" 
            tooltip="Import data" 
            visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
          />
          <tbl:button 
            id="btnExport"
            data-plugin-type="EXPORT"
            image="export.png" 
            title="Export&hellip;" 
            tooltip="Export data" 
            visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
          />
          <tbl:button 
            id="btnRunPlugin"
            data-plugin-type="OTHER"
            image="runplugin.png" 
            title="Run plugin&hellip;" 
            tooltip="Run a plugin" 
            visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
          />
          <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
            wrapper="<%=new PrefixSuffixRenderer<ButtonAction>(jspContext, "<td>", "</td>") %>"/>
        </tbl:toolbar>
        <tbl:panel>
          <tbl:presetselector />
          <tbl:navigator
            page="<%=cc.getPage()%>" 
            rowsperpage="<%=cc.getRowsPerPage()%>" 
            totalrows="<%=bioSources == null ? 0 : bioSources.getTotalCount()%>" 
            visible="<%=mode.hasNavigator()%>"
          />
        </tbl:panel>
      </div>
      <tbl:data>
        <tbl:headers>
          <tbl:headerrow>
            <tbl:header colspan="3" />
            <tbl:columnheaders />
          </tbl:headerrow>
          <%
          int numFilters = cc.getNumPropertyFilters();
          int numRows = cc.getFilterRows();
          for (int filterNo = 0; filterNo < numRows; filterNo++)
          {
            boolean lastRow = filterNo == numRows-1;
            %>
            <tbl:headerrow>
              <tbl:header subclass="index" />
              <tbl:header 
                subclass="check" 
                visible="<%=mode.hasCheck()%>"
                ><base:icon 
                  subclass="link table-check"
                  image="check_uncheck.png" 
                  tooltip="Toggle all (use CTRL, ALT or SHIFT to check/uncheck)" 
                  visible="<%=lastRow%>"
                /></tbl:header>
              <tbl:header 
                subclass="check" 
                visible="<%=mode.hasRadio()%>"
                />
              <tbl:header 
                subclass="icons" 
                visible="<%=mode.hasIcons()%>"
                >
                <base:icon
                  subclass="link table-filter-row-action"
                  image="add.png"
                  tooltip="Add extra filter row"
                  visible="<%=lastRow%>"
                /><base:icon
                  subclass="link table-filter-row-action"
                  image="remove.png"
                  tooltip="Remove this filter row"
                  visible="<%=numRows > 1 || numFilters > 0 %>"
                  data-remove-row="<%=filterNo%>"
                />
              </tbl:header>
              <tbl:propertyfilter row="<%=filterNo%>" />
            </tbl:headerrow>
            <%
          }
          %>
        </tbl:headers>
        <tbl:rows>
          <%
          if (cc.getMessage() != null)
          {
            %>
            <tbl:panel subclass="bg-filled-50">
              <div class="messagecontainer error"><%=cc.getMessage()%></div>
            </tbl:panel>
            <%
            cc.setMessage(null);
          }
          int index = cc.getPage()*cc.getRowsPerPage();
          int selectedItemId = cc.getId();
          if (bioSources != null)
          {           
            while (bioSources.hasNext())
            {
              BioSource item = bioSources.next();
              int itemId = item.getId();
              boolean usePermission = item.hasPermission(Permission.USE);
              
              
              boolean deletePermission = item.hasPermission(Permission.DELETE);
              boolean sharePermission = item.hasPermission(Permission.SET_PERMISSION);
              boolean writePermission = item.hasPermission(Permission.WRITE);
              String tooltip = mode.isSelectionMode() ? 
                  "Select this item" : "View this item" + (writePermission ? " (use CTRL, ALT or SHIFT to edit)" : "");
              String name = HTML.encodeTags(item.getName());
              index++;
              numListed++;
              %>
              <tbl:row>
                <tbl:header 
                  clazz="index"
                  ><%=index%></tbl:header>
                <tbl:header 
                  clazz="check" 
                  visible="<%=mode.hasCheck()%>"
                  ><input 
                    type="checkbox" 
                    name="<%=itemId%>" 
                    value="<%=itemId%>" 
                    title="<%=name%>" 
                    <%=cc.getSelected().contains(itemId) ? "checked" : ""%> 
                  ></tbl:header>
                <tbl:header 
                  clazz="check" 
                  visible="<%=mode.hasRadio()%>"
                  ><input 
                    type="radio" 
                    name="item_id" 
                    value="<%=itemId%>" 
                    title="<%=name%>" 
                    <%=selectedItemId == itemId ? "checked" : ""%>
                  ></tbl:header>
                <tbl:header 
                  clazz="icons" 
                  visible="<%=mode.hasIcons()%>"
                  ><base:icon 
                    image="deleted.png"
                    id="<%="delete."+itemId %>"
                    subclass="<%=deletePermission ? "table-delete-item" : "disabled" %>"
                    data-item-id="<%=itemId%>"
                    tooltip="This item has been scheduled for deletion" 
                    visible="<%=item.isRemoved()%>"
                  /><base:icon 
                    image="shared.png" 
                    id="<%="share."+itemId %>"
                    subclass="<%=sharePermission ? "table-share-item" : "disabled" %>"
                    data-item-id="<%=itemId%>"
                    tooltip="This item is shared to other users, groups and/or projects" 
                    visible="<%=item.isShared()%>"
                  />&nbsp;</tbl:header>
                <tbl:cell column="name"><div 
                  class="link table-item"
                  data-item-id="<%=itemId%>"
                  data-no-edit="<%=writePermission ? 0 : 1 %>" 
                  tabindex="0"
                  title="<%=tooltip%>"><%=name%></div></tbl:cell>
                <tbl:cell column="id"><%=item.getId()%></tbl:cell>
                <tbl:cell column="itemSubtype"><base:propertyvalue 
                    item="<%=item%>" 
                    property="itemSubtype"
                    enableEditLink="<%=mode.hasEditLink()%>" 
                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
                  /></tbl:cell>
                <tbl:cell column="externalId"><%=HTML.encodeTags(item.getExternalId())%></tbl:cell>
                <tbl:cell column="samples">
                  <%
                  sampleQuery.setParameter("bioSource", itemId, Type.INT);
                  try
                  {
                    String separator = "";
                    for (Sample s : sampleQuery.list(dc))
                    {
                      out.write(separator);
                      if (mode.hasPropertyLink())
                      {
                        out.write(Base.getLinkedName(ID, s, false, mode.hasEditLink()));
                      }
                      else
                      {
                        out.write(HTML.encodeTags(s.getName()));
                      }
                      separator = ", ";
                    }
                  }
                  catch (Throwable t)
                  {
                    %>
                    <div class="error"><%=t.getMessage()%></div>
                    <%
                  }
                  %>
                  <base:icon
                    id="<%="newsample."+itemId%>"
                    image="add.png" 
                    subclass="auto-init"
                    data-auto-init="new-sample"
                    data-item-id="<%=itemId %>"
                    tooltip="Create new sample" 
                    visible="<%=mode.hasEditLink() && createSamplePermission && usePermission %>"
                  />
                </tbl:cell>
                <tbl:cell column="owner"
                  ><base:propertyvalue 
                    item="<%=item%>" 
                    property="owner"
                    enableEditLink="<%=mode.hasEditLink()%>" 
                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
                  /></tbl:cell>
                <tbl:cell column="entryDate" value="<%=item.getEntryDate()%>" />
                <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>               
                <%
                if (item.isAnnotated())
                {
                  AnnotationSetSnapshot snapshot = manager.getSnapshot(dc, item.getAnnotationSet().getId());
                  for (AnnotationLoaderUtil loader : annotationLoaders)
                  {
                    %>
                    <tbl:cell 
                      column="<%="at"+loader.getId()%>"
                      ><%
                      if (loader.find(snapshot, psInfo.reset())) 
                      {
                        %><tbl:cellvalue 
                          list="<%=loader.getValues()%>"
                          suffix="<%=loader.getUnitSymbol()%>"
                          clazz="<%=psInfo.overridesDefaultAnnotation() ? "ps-annotation" : null%>"
                        /><%
                      }
                      %></tbl:cell>
                    <%
                  }
                }
                %>
                <tbl:cell column="permission"><%=PermissionUtil.getShortPermissions(item)%></tbl:cell>
                <tbl:cell column="sharedTo">
                  <%
                  Iterator<Nameable> sharees = ShareableUtil.getSharedTo(dc, item).iterator();
                  while(sharees.hasNext())
                  {
                    Nameable n = sharees.next();
                    if (mode.hasPropertyLink())
                    {
                      out.write(Base.getLinkedName(ID, n, false, mode.hasEditLink()));
                    }
                    else
                    {
                      out.write(HTML.encodeTags(n.getName()));
                    }
                    out.write(sharees.hasNext() ? ", " : "");
                  }
                  %>
                </tbl:cell>
                <tbl:xt-cells dc="<%=dc%>" item="<%=item%>">
                  <tbl:cell column="xt-columns" />
                </tbl:xt-cells>
              </tbl:row>
              <%
              }
            }
            if (numListed == 0)
            {
              %>
              <tbl:panel subclass="bg-filled-50">
                <div class="messagecontainer note">
                <%=bioSources == null || bioSources.getTotalCount() == 0 ? "No biosources were found" : "No biosources on this page. Please select another page!" %>
                </div>
              </tbl:panel>
              <%
            }
          %>
        </tbl:rows>
      </tbl:data>
    </tbl:table>
    </div>

    <base:buttongroup subclass="dialogbuttons">
      <base:button id="btnOk" title="Ok" visible="<%=mode.hasOkButton()%>" />
      <base:button id="close" title="Cancel" visible="<%=mode.hasCancelButton()%>" />
      <base:button id="close" title="Close" visible="<%=mode.hasCloseButton()%>" />
    </base:buttongroup>
  </base:body>
  </base:page>
  <%
}
finally
{
  if (bioSources != null) bioSources.close();
  if (dc != null) dc.close();
}
%>