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<%-- $Id$ |
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------------------------------------------------------------------ |
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Copyright (C) 2006 Nicklas Nordborg |
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|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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|
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This file is part of BASE. |
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|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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------------------------------------------------------------------ |
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|
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@author Nicklas |
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@version 2.0 |
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--%> |
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<%@ page pageEncoding="UTF-8" session="false" |
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import="net.sf.basedb.core.SessionControl" |
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import="net.sf.basedb.core.DbControl" |
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import="net.sf.basedb.core.Item" |
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import="net.sf.basedb.core.Include" |
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import="net.sf.basedb.core.Experiment" |
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import="net.sf.basedb.core.BioAssaySet" |
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import="net.sf.basedb.core.ExtraValue" |
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import="net.sf.basedb.core.User" |
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import="net.sf.basedb.core.Path" |
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import="net.sf.basedb.core.ItemQuery" |
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import="net.sf.basedb.core.ItemResultIterator" |
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import="net.sf.basedb.core.Permission" |
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import="net.sf.basedb.core.ItemContext" |
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import="net.sf.basedb.core.MultiPermissions" |
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import="net.sf.basedb.core.PermissionDeniedException" |
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import="net.sf.basedb.core.ItemAlreadyExistsException" |
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import="net.sf.basedb.core.query.Restriction" |
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import="net.sf.basedb.util.RemovableUtil" |
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import="net.sf.basedb.util.ShareableUtil" |
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import="net.sf.basedb.util.BioAssaySetFilterUtil" |
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import="net.sf.basedb.util.DynamicFilter" |
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import="net.sf.basedb.util.IncludeExcludeFilter" |
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import="net.sf.basedb.clients.web.Base" |
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import="net.sf.basedb.clients.web.WebException" |
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import="net.sf.basedb.util.Values" |
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import="net.sf.basedb.clients.web.util.HTML" |
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import="java.util.Enumeration" |
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import="java.util.Set" |
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import="java.util.HashSet" |
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import="java.util.List" |
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import="java.util.LinkedList" |
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import="java.util.Collections" |
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import="java.util.Arrays" |
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%> |
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<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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<%! |
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private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,transformation,spots,reporters,date,tools"); |
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private static final Item itemType = Item.EXTRAVALUE; |
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%> |
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<% |
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final int experimentId = Values.getInt(request.getParameter("experiment_id")); |
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final SessionControl sc = Base.getExistingSessionControl(pageContext, true); |
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final String ID = sc.getId(); |
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final String cmd = request.getParameter("cmd"); |
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final String root = request.getContextPath()+"/"; |
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final String mode = request.getParameter("mode"); |
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final String callback = request.getParameter("callback"); |
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final String itemId = request.getParameter("item_id"); |
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|
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final String viewPage = "view_extravalue.jsp?ID="+ID+"&experiment_id="+experimentId; |
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if (experimentId > 0) sc.getCurrentContext(Item.EXPERIMENT).setId(experimentId); |
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|
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String forward = null; |
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String redirect = null; |
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String message = null; |
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DbControl dc = null; |
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|
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try |
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{ |
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if ("ViewItem".equals(cmd)) |
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{ |
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// Display the view page for a single item |
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ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext); |
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forward = viewPage; |
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} |
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else if ("DeleteItem".equals(cmd)) |
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{ |
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// Delete a single item and then return to the view page |
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dc = sc.newDbControl(":Delete "+itemType); |
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ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext); |
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BioAssaySet bas = ExtraValue.getById(dc, cc.getId()).getBioAssaySet(); |
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RemovableUtil.delete(dc, itemType, Collections.singleton(cc.getId())); |
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dc.commit(); |
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redirect = "../bioassaysets/index.jsp?ID="+ID+"&cmd=ViewItem&item_id="+bas.getId(); |
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} |
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else if ("ExportItem".equals(cmd)) |
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{ |
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// Run an export plugin in single-item context |
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ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext); |
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redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+bioassay+set"; |
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} |
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else if ("ImportItem".equals(cmd)) |
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{ |
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// Run an import plugin in single-item context |
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ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext); |
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redirect = "../../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+bioassay+set"; |
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} |
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else if ("RunPlugin".equals(cmd)) |
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{ |
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// Run a plugin in single-item context |
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ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext); |
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redirect = "../../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=OTHER&title=Run+plugin"; |
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} |
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else if ("RunAnalysisPlugin".equals(cmd)) |
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{ |
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// Run an analysis plugin in single-item context |
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ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext); |
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redirect = "../../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=ANALYZE&title=Run+analysis+plugin"; |
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} |
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else |
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{ |
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throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd); |
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} |
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} |
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finally |
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{ |
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if (dc != null) dc.close(); |
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} |
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|
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if (forward != null) |
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{ |
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sc.setSessionSetting("alert-message", message); |
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pageContext.forward(forward); |
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} |
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else if (redirect != null) |
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{ |
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sc.setSessionSetting("alert-message", message); |
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response.sendRedirect(redirect); |
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} |
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else if (message == null) |
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{ |
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response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0"); |
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} |
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else |
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{ |
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response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message)); |
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} |
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%> |
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|