source: branches/3.4-stable/www/views/physicalbioassays/index.jsp @ 6715

Last change on this file since 6715 was 6715, checked in by Nicklas Nordborg, 7 years ago

Fixes #1918: Can't export the derived bioassays column in physical bioassays list

Add '%' to the registration of data loader and formatter so that the names matches the filter expression.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 17.9 KB
Line 
1<%-- $Id: index.jsp 6715 2015-02-04 11:42:44Z nicklas $
2  ------------------------------------------------------------------
3  Copyright (C) 2005 Nicklas Nordborg, Gregory Vincic
4  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
5
6  This file is part of BASE - BioArray Software Environment.
7  Available at http://base.thep.lu.se/
8
9  BASE is free software; you can redistribute it and/or
10  modify it under the terms of the GNU General Public License
11  as published by the Free Software Foundation; either version 3
12  of the License, or (at your option) any later version.
13
14  BASE is distributed in the hope that it will be useful,
15  but WITHOUT ANY WARRANTY; without even the implied warranty of
16  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
17  GNU General Public License for more details.
18
19  You should have received a copy of the GNU General Public License
20  along with BASE. If not, see <http://www.gnu.org/licenses/>.
21  ------------------------------------------------------------------
22
23  @author Nicklas
24  @version 2.0
25--%>
26<%@ page pageEncoding="UTF-8" session="false"
27  import="net.sf.basedb.core.SessionControl"
28  import="net.sf.basedb.core.DbControl"
29  import="net.sf.basedb.core.Item"
30  import="net.sf.basedb.core.Include"
31  import="net.sf.basedb.core.PhysicalBioAssay"
32  import="net.sf.basedb.core.ArraySlide"
33  import="net.sf.basedb.core.BioMaterialEvent"
34  import="net.sf.basedb.core.BioMaterialEventSource"
35  import="net.sf.basedb.core.Extract"
36  import="net.sf.basedb.core.Protocol"
37  import="net.sf.basedb.core.Hardware"
38  import="net.sf.basedb.core.ItemSubtype"
39  import="net.sf.basedb.core.DerivedBioAssay"
40  import="net.sf.basedb.core.ItemQuery"
41  import="net.sf.basedb.core.ItemResultIterator"
42  import="net.sf.basedb.core.Permission"
43  import="net.sf.basedb.core.ItemContext"
44  import="net.sf.basedb.core.MultiPermissions"
45  import="net.sf.basedb.core.OwnedItem"
46  import="net.sf.basedb.core.PermissionDeniedException"
47  import="net.sf.basedb.core.ItemAlreadyExistsException"
48  import="net.sf.basedb.core.query.Hql"
49  import="net.sf.basedb.core.query.Orders"
50  import="net.sf.basedb.core.query.Restrictions"
51  import="net.sf.basedb.core.query.Expressions"
52  import="net.sf.basedb.util.RemovableUtil"
53  import="net.sf.basedb.util.ShareableUtil"
54  import="net.sf.basedb.util.OwnableUtil"
55  import="net.sf.basedb.clients.web.Base"
56  import="net.sf.basedb.clients.web.WebException"
57  import="net.sf.basedb.util.Values"
58  import="net.sf.basedb.clients.web.util.HTML"
59  import="net.sf.basedb.util.formatter.Formatter"
60  import="net.sf.basedb.util.formatter.NameableFormatter"
61  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
62  import="net.sf.basedb.clients.web.plugins.ItemQueryLoader"
63  import="net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter"
64  import="net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay"
65  import="net.sf.basedb.core.plugin.GuiContext"
66  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
67  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
68  import="net.sf.basedb.clients.web.extensions.JspContext"
69  import="net.sf.basedb.clients.web.extensions.edit.EditUtil"
70  import="net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer"
71  import="net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer"
72  import="net.sf.basedb.clients.web.extensions.list.ListColumnUtil"
73  import="java.util.Enumeration"
74  import="java.util.Set"
75  import="java.util.HashSet"
76  import="java.util.List"
77  import="java.util.ArrayList"
78  import="java.util.Collections"
79  import="java.util.Date"
80%>
81<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
82<%!
83  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,itemSubtype,extracts,arraySlide,description");
84  private static final Item itemType = Item.PHYSICALBIOASSAY;
85 
86  private static void registerExportUtils(ItemContext cc)
87  {
88    // Register formatters
89    cc.setObject("export.formatter.&creationEvent.sources(bioMaterial.name)", new BioMaterialEventSourceFormatter());
90    cc.setObject("export.formatter.&rootDerivedBioAssays(%name)", new NameableFormatter());
91   
92    // Register dataloaders
93    String bioassayParameter = "bioassay";
94    cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ParentBioMaterialEventSourceLoaderFromBioAssay());
95
96    ItemQuery<DerivedBioAssay> dbasQuery = DerivedBioAssay.getQuery();
97    dbasQuery.include(cc.getInclude());
98    dbasQuery.join(Hql.innerJoin("physicalBioAssays", "pba"));
99    dbasQuery.restrict(Restrictions.eq(Hql.alias("pba"), Expressions.parameter(bioassayParameter)));
100    dbasQuery.restrict(Restrictions.eq(Hql.property("root"), Expressions.bool(true)));
101    dbasQuery.order(Orders.asc(Hql.property("name")));
102    cc.setObject("export.dataloader.&rootDerivedBioAssays(%name)", new ItemQueryLoader(dbasQuery, bioassayParameter));
103  }
104%>
105<%
106final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
107final String ID = sc.getId();
108final String cmd = request.getParameter("cmd");
109final String root = request.getContextPath()+"/";
110final String mode = request.getParameter("mode");
111final String callback = request.getParameter("callback");
112final String itemId = request.getParameter("item_id");
113final String listPage = "list_bioassays.jsp?ID="+ID
114  +(mode == null ? "" : "&mode="+mode)
115  +(callback == null ? "" : "&callback="+callback)
116  +(itemId == null ? "" : "&item_id="+itemId);
117final String viewPage = "view_bioassay.jsp?ID="+ID;
118final String editPage = "edit_bioassay.jsp?ID="+ID;
119
120String forward = null;
121String redirect = null;
122String message = null;
123DbControl dc = null;
124
125try
126{
127  if (cmd == null || "List".equals(cmd))
128  {
129    // Display the list page without updatinging the current context
130    Base.getAndSetCurrentContext(sc, itemType, null, defaultContext, true);
131    redirect = listPage;
132  }
133  else if ("UpdateContext".equals(cmd))
134  {
135    // Display the list page after updating the current context from the request parameters
136    Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
137    redirect = listPage;
138  }
139  else if ("LoadContext".equals(cmd))
140  {
141    // Display the list page after loading a saved context
142    int contextId = Values.getInt(request.getParameter("context"));
143    Base.loadContext(sc, contextId, defaultContext);
144    redirect = listPage;
145  }
146
147  else if ("ViewItem".equals(cmd))
148  {
149    // Display the view page for a single item
150    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
151    forward = viewPage;
152  }
153  else if ("EditItem".equals(cmd))
154  {
155    // Display the edit page for a single item (should be opened in a popup)
156    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
157    redirect = editPage;
158  }
159  else if ("NewItem".equals(cmd))
160  {
161    // Display the edit page for a new item (should be opened in a popup)
162    if (!sc.hasPermission(Permission.CREATE, itemType))
163    {
164      throw new PermissionDeniedException(Permission.CREATE, itemType.toString());
165    }
166    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
167    cc.setId(0);
168    forward = editPage;
169  }
170  else if ("UpdateItem".equals(cmd))
171  {
172    // Update the properties on an item (will close the popup)
173    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext);
174    final int maxRecent = Base.getMaxRecent(sc);
175    dc = sc.newDbControl();
176    PhysicalBioAssay pba = (PhysicalBioAssay)cc.getObject("item");
177    BioMaterialEvent creationEvent = null;
178    if (pba == null)
179    {
180      pba = PhysicalBioAssay.getNew(dc);
181      creationEvent = pba.getCreationEvent();
182      message = "Physical bioassay created";
183      dc.saveItem(pba);
184    }
185    else
186    {
187      creationEvent = pba.getCreationEvent();
188      dc.reattachItem(pba, false);
189      dc.reattachItem(creationEvent, false);
190      message = "Physical bioassay updated";
191    }
192    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(Item.PHYSICALBIOASSAY), pba);
193    ExtensionsInvoker invoker = EditUtil.useOnSaveExtensions(jspContext);
194    try
195    {
196      pba.setName(Values.getStringOrNull(request.getParameter("name")));
197      pba.setDescription(Values.getStringOrNull(request.getParameter("description")));
198      pba.setSize(Values.getInt(request.getParameter("size"), 1));
199
200      int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
201      ItemSubtype subtype = null;
202      if (subtypeId >= 0) // < 0 = denied or unchanged
203      {
204        if (subtypeId > 0) subtype = ItemSubtype.getById(dc, subtypeId);
205        pba.setItemSubtype(subtype);
206        if (subtype != null) cc.setRecent(subtype, maxRecent);
207      }
208     
209      int arraySlideId = Values.getInt(request.getParameter("arrayslide_id"), -1);
210      if (arraySlideId >= 0) // < 0 = denied or unchanged
211      {
212        ArraySlide slide = arraySlideId == 0 ? null : ArraySlide.getById(dc, arraySlideId);
213        pba.setArraySlide(slide);
214      }
215      Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
216      creationEvent.setEventDate(dateFormatter.parseString(Values.getStringOrNull(request.getParameter("event_date"))));
217      int protocolId = Values.getInt(request.getParameter("protocol_id"), -1);
218      if (protocolId >= 0) // < 0 = denied or unchanged
219      {
220        Protocol pt = protocolId == 0 ? null : Protocol.getById(dc, protocolId);
221        creationEvent.setProtocol(pt);
222        if (pt != null) cc.setRecent(pt, subtype, maxRecent);
223      }
224     
225      //Hardware
226      int hardwareId = Values.getInt(request.getParameter("hardware_id"), -1);
227      if (hardwareId >= 0) // < 0 denied or unchanged
228      {
229        Hardware hw = hardwareId == 0 ? null : Hardware.getById(dc, hardwareId);
230        creationEvent.setHardware(hw);
231        if (hw != null) cc.setRecent(hw, subtype, maxRecent);
232      }
233     
234      // Extracts
235      String[] modifiedExtracts = Values.getString(request.getParameter("+EXTRACT")).split(",");
236      for (int i = 0; i < modifiedExtracts.length; ++i)
237      {
238        int extractId = Values.getInt(modifiedExtracts[i], -1);
239        if (extractId != -1) 
240        {
241          Extract e = Extract.getById(dc, extractId);
242          String[] extra = request.getParameter("EXTRACT."+extractId).split(":");
243          Float usedQuantity = Values.getFloat(extra[0], null);
244          int position = extra.length > 1 ? Values.getInt(extra[1], 1) : 1;
245          BioMaterialEventSource evtSrc = creationEvent.addSource(e);
246          evtSrc.setUsedQuantity(usedQuantity);
247          evtSrc.setPosition(position);
248        }
249      }
250      String[] removedExtracts = Values.getString(request.getParameter("-EXTRACT")).split(",");
251      for (int i = 0; i < removedExtracts.length; ++i)
252      {
253        int extractId = Values.getInt(removedExtracts[i], -1);
254        if (extractId != -1) creationEvent.removeSource(Extract.getById(dc, extractId));
255      }
256     
257      // Annotations tab
258      Base.updateAnnotations(dc, pba, pba, request);
259     
260      // OnSave extensions
261      invoker.render(OnSaveRenderer.ON_SAVE);
262      dc.commit();
263      invoker.render(OnSaveRenderer.ON_COMMIT);
264    }
265    catch (Exception ex)
266    {
267      invoker.render(OnSaveRenderer.onRollback(ex));
268      throw ex;
269    }
270    finally
271    {
272      cc.removeObject("item");
273    }
274  }
275  else if ("DeleteItem".equals(cmd))
276  {
277    // Delete a single item and then return to the view page
278    dc = sc.newDbControl();
279    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
280    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), true);
281    dc.commit();
282    redirect = viewPage;
283  }
284  else if ("DeleteItems".equals(cmd))
285  {
286    // Delete all selected items on the list page
287    dc = sc.newDbControl();
288    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
289    int numTotal = cc.getSelected().size();
290    int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), true);
291    dc.commit();
292    if (numTotal != numRemoved)
293    {
294      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be deleted, because you have no DELETE permission";
295    }
296    redirect = listPage;
297  }
298  else if ("RestoreItem".equals(cmd))
299  {
300    // Restore a single item and then return to the view page
301    dc = sc.newDbControl();
302    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
303    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), false);
304    dc.commit();
305    redirect = viewPage;
306  }
307  else if ("RestoreItems".equals(cmd))
308  {
309    // Restore all selected items on the list page
310    dc = sc.newDbControl();
311    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
312    int numTotal = cc.getSelected().size();
313    int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), false);
314    dc.commit();
315    if (numTotal != numRemoved)
316    {
317      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be restored, because you have no WRITE permission";
318    }
319    redirect = listPage;
320  }
321  else if ("ShareItem".equals(cmd))
322  {
323    // Display a popup window for sharing a single item
324    dc = sc.newDbControl();
325    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
326    MultiPermissions permissions = ShareableUtil.getMultiPermissions(dc, itemType, Collections.singleton(cc.getId()));
327    dc.close();
328    cc.setObject("MultiPermissions", permissions);
329    redirect = "../../common/share/share.jsp?ID="+ID+"&item_type="+itemType.name();
330  }
331  else if ("ShareItems".equals(cmd))
332  {
333    // Display a popup window for sharing all selected items on the list page
334    dc = sc.newDbControl();
335    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
336    MultiPermissions permissions = ShareableUtil.getMultiPermissions(dc, itemType, cc.getSelected());
337    dc.close();
338    cc.setObject("MultiPermissions", permissions);
339    redirect = "../../common/share/share.jsp?ID="+ID+"&item_type="+itemType.name();
340  }
341  else if ("SetOwnerOfItem".equals(cmd))
342  {
343    // Change owner of items selected on a list page
344    dc = sc.newDbControl();
345    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
346    OwnedItem item = (OwnedItem)itemType.getById(dc, cc.getId());
347    cc.setObject("OwnedItems", Collections.singleton(item));
348    redirect = "../../common/ownership/ownership.jsp?ID="+ID+"&item_type="+itemType.name();
349  }
350  else if ("SetOwnerOfItems".equals(cmd))
351  {
352    // Change owner of items selected on a list page
353    dc = sc.newDbControl();
354    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
355    Set<OwnedItem> items = new HashSet<OwnedItem>();
356    for (Integer id : cc.getSelected())
357    {
358      if (id != null) items.add((OwnedItem)itemType.getById(dc, id));
359    }
360    dc.close();
361    cc.setObject("OwnedItems", items);
362    redirect = "../../common/ownership/ownership.jsp?ID="+ID+"&item_type="+itemType.name();
363  }
364  else if ("ExportItems".equals(cmd))
365  {
366    // Run an export plugin in a list context
367    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
368    final ItemQuery<PhysicalBioAssay> query = PhysicalBioAssay.getQuery();
369    dc = sc.newDbControl();
370    cc.configureQuery(dc, query, true);
371    cc.setQuery(query);
372    registerExportUtils(cc);
373    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.list(itemType), null);
374    ExtensionsInvoker listInvoker = ListColumnUtil.useExtensions(jspContext);
375    listInvoker.render(new ListColumnExportRenderer(cc));
376    dc.close();
377    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+physical+bioassays";
378  }
379  else if ("ExportItem".equals(cmd))
380  {
381    // Run an export plugin in single-item context
382    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
383    registerExportUtils(cc);
384    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+physical+bioassay";
385  }
386  else if ("ImportItems".equals(cmd))
387  {
388    // Run an import plugin in a list context
389    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
390    final ItemQuery<PhysicalBioAssay> query = PhysicalBioAssay.getQuery();
391    dc = sc.newDbControl();
392    cc.configureQuery(dc, query, true);
393    dc.close();
394    cc.setQuery(query);
395    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+physical+bioassays";
396  }
397  else if ("ImportItem".equals(cmd))
398  {
399    // Run an import plugin in single-item context
400    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
401    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+physical+bioassay";
402  }
403  else if ("RunListPlugin".equals(cmd))
404  {
405    // Run another plugin in a list context
406    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
407    final ItemQuery<PhysicalBioAssay> query = PhysicalBioAssay.getQuery();
408    dc = sc.newDbControl();
409    cc.configureQuery(dc, query, true);
410    dc.close();
411    cc.setQuery(query);
412    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&main_type=OTHER&title=Run+plugin";
413  }
414  else if ("RunPlugin".equals(cmd))
415  {
416    // Run another plugin in single-item context
417    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
418    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=OTHER&title=Run+plugin";
419  }
420  else if ("NewMergedDerivedBioAssay".equals(cmd))
421  {
422    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
423    redirect = "../derivedbioassays/index.jsp?ID="+ID+"&cmd=NewItem&useParents=PHYISCALBIOASSAY";
424  }
425  else
426  {
427    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
428  }
429}
430finally
431{
432  if (dc != null) dc.close();
433}
434
435if (forward != null)
436{
437  sc.setSessionSetting("alert-message", message);
438  pageContext.forward(forward);
439}
440else if (redirect != null)
441{
442  sc.setSessionSetting("alert-message", message);
443  response.sendRedirect(redirect);
444}
445else if (message == null)
446{
447  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0");
448}
449else
450{
451  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message));
452}
453%>
454
Note: See TracBrowser for help on using the repository browser.