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<?xml version="1.0" encoding="UTF-8" ?> |
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<!-- |
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$Id$ |
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|
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Copyright (C) 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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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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<extensions |
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xmlns="http://base.thep.lu.se/extensions.xsd" |
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id-base="net.sf.basedb.clients.web." |
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> |
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<about> |
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<version></version> |
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<name>Web client extensions points and extensions</name> |
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<description> |
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This file defines extension points and extensions for |
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the web client. The extensions are only loaded when BASE |
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starts up as a web server. |
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</description> |
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<copyright>BASE development team</copyright> |
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<email>basedb-users@lists.sourceforge.net</email> |
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<url>https://base.thep.lu.se/</url> |
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</about> |
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|
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<plugin-definition |
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id="SimpleExport"> |
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<about> |
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<name>Table exporter</name> |
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<description> |
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Export all table listings in the web interface as tab-separated |
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text files or as XML. This plugin only works from within the web |
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client, since it depends on context and table information. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.clients.web.plugins.SimpleExport</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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<property name="immediate-execution">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<extension-point |
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id="menu.extensions" |
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> |
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<action-class>net.sf.basedb.clients.web.extensions.menu.MenuItemAction</action-class> |
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<name>Menu: extensions</name> |
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<description> |
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Extension point for adding extensions to the 'Extensions' menu. |
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Extensions should provide MenuItemAction instances. The rendering |
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is internal and extensions can't use their own rendering factories. |
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The context will only include information about the currently logged |
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in user, not information about the current page that is displayed. |
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The reason for this is that the rendered menu is cached as a string |
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in the user session. The menu is not updated on every page request. |
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As of BASE 3.3, this extension point also support custom scripts and |
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stylesheets. |
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</description> |
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</extension-point> |
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|
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<extension-point |
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id="bioassayset.list.tools" |
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> |
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<action-class>net.sf.basedb.clients.web.extensions.toolbar.ButtonAction</action-class> |
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<renderer-factory override="true"> |
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<factory-class>net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory</factory-class> |
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</renderer-factory> |
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<name>Bioassay set: Tools</name> |
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<description> |
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Extension point for the Tools column in the bioassayset tree |
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view of an experiment. Extensions should provide ActionButton |
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instances. The default renderer factory is CompactButtonRendererFactory, |
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but this can be overridden by the extensions. Note that the tree |
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contains items of more than one type: BioAssaySet, Transformation and |
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ExtraValue. The JspContext.getItem() can return any one of those |
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types. |
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</description> |
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</extension-point> |
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|
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<extension-point |
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id="bioassayset.overviewplots" |
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> |
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<action-class>net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction</action-class> |
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<name>Bioassay set: Overview plots</name> |
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<description> |
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Extension point for overview plots for a bioassay set. The overview |
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plots are usually one pre-defined plot per bioassay. For example, |
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MA plots for 2-channel data. Extensions should provide OverviewPlotAction |
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instances. The rendering is internal and generates one <img> tag |
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for each plot. An extension is supposed to generate the image URL that |
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leads to a servlet that creates the actual image. We recommend that |
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images are cached. See the core plot servlet for details. |
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</description> |
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</extension-point> |
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|
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<extension-point |
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id="services" |
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> |
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<action-class>net.sf.basedb.clients.web.extensions.service.ServiceControllerAction</action-class> |
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<name>Services</name> |
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<description> |
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Extension point for services. A service is a piece of code that |
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is loaded when the BASE web server starts up. The service is then running |
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as long as the BASE web server is running. It is also possible to |
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manually stop and start services. This extension point is different from |
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most others in that it doesn't affects the visible interface. Since |
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services are loaded at startup time, this also means that the |
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context passed to ActionFactory methods doesn't have any user |
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information. However, the InvokationContext.getClientContext().getSessionControl() |
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returns a special SessionControl which gives the extension permission to impersonate |
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another user so that it can access the BASE database if needed. |
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There is also no meaning for extensions to specify a RendererFactory. |
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</description> |
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<error-handler-factory> |
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<factory-class>net.sf.basedb.util.extensions.LoggingErrorHandlerFactory</factory-class> |
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<parameters> |
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<rememberLast>true</rememberLast> |
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</parameters> |
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</error-handler-factory> |
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</extension-point> |
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|
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<extension-point |
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id="services.list.actions" |
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> |
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<action-class>net.sf.basedb.clients.web.extensions.toolbar.ButtonAction</action-class> |
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<renderer-factory override="true"> |
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<factory-class>net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory</factory-class> |
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</renderer-factory> |
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<name>Services: Actions</name> |
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<description> |
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Extension point for the Actions column in the Adminstrate->services list. |
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Extensions should provide ActionButton instances. The default renderer factory is |
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CompactButtonRendererFactory, but this can be overridden by the extensions. |
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The JspContext.getItem() method return the current ServiceControllerAction. |
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</description> |
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</extension-point> |
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|
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<extension-point |
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id="file-viewer" |
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> |
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<action-class>net.sf.basedb.clients.web.extensions.toolbar.ButtonAction</action-class> |
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<renderer-factory override="true"> |
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<factory-class>net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory</factory-class> |
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<parameters> |
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<button-tag>span</button-tag> |
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</parameters> |
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</renderer-factory> |
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<name>File viewer</name> |
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<description> |
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Extension point for adding actions after the "View" and "Download" actions |
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whenever a file item is displayed. Extensions should provide ActionButton |
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instances. The default renderer factory is CompactButtonRendererFactory, but |
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this can be overridden by the extensions. The JspContext.getCurrentItem() method |
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return a FileViewerContext instance. This object can be used to retrieve information |
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about the current file, but also about the surrounding context, for example, |
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if the file is in a "Data files" list for another item. |
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</description> |
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</extension-point> |
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|
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<extension-point |
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id="overview.info-details"> |
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<action-class>net.sf.basedb.clients.web.extensions.section.SectionAction</action-class> |
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<name>Item overview - node information</name> |
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<description> |
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Extension point for including more information about the currently selected node |
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in the overview. The information is displayed as a section in the right pane. |
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This extension point supports custom javascript and stylesheet, but rendering |
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is internal. The JspContext is populated with the current 'Node' object from the |
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overview which can be used to retreive more information. |
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</description> |
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</extension-point> |
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|
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<extension-point |
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id="login-form"> |
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<action-class>net.sf.basedb.clients.web.extensions.login.LoginFormAction</action-class> |
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<name>Login form customization</name> |
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<description> |
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Extension point for customizing the login form. Makes it possible to change login |
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and/or password prompts, help texts, etc. Since there is only one login form, |
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only the first extension found for this extension point is used. |
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</description> |
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</extension-point> |
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|
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<extension-point |
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id="global-skin"> |
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<action-class>net.sf.basedb.clients.web.extensions.skin.SkinAction</action-class> |
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<name>Skins</name> |
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<description> |
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Extension point for GUI customizations. Extensions should implement |
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the SkinAction interface, which can be used to set the favicon and |
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add custom data to a hidden div tag on the page. Most work is expected |
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to be done by stylesheets and/or scripts added to the JspContext |
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instance passed to factory via the prepareContext method. |
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</description> |
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</extension-point> |
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|
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<extension-point |
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id="start-page"> |
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<action-class>net.sf.basedb.clients.web.extensions.startpage.StartPageAction</action-class> |
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<name>Start page</name> |
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<description> |
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Extension point for selecting the start page that is displayed |
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after a user has logged in to BASE. Extensions should implement |
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the StartPageAction interface. Use the BASE › Preferences menu |
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to select the start page. This extension point doesn't use any |
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custom scripts or stylesheets. |
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</description> |
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</extension-point> |
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|
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<!-- |
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More extension points: |
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In addition to the extension points in this file, the web |
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01 Apr 11 |
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client also defines a lot of other extension points that are |
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01 Apr 11 |
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registered programmatically. For more information see |
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Extensions -> Installed extensions in the web client interface. |
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|
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* Toolbar extension points: Adds buttons to toolbars in |
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list and single-item view pages. |
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* Edit dialog: Adds extra tabs to edit dialogs |
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01 Apr 11 |
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* OnSave: Add callback functionality when saving from an edit dialog |
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--> |
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|
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<extension |
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id="password-login-form" |
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extends="net.sf.basedb.clients.web.login-form" |
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> |
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<about> |
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<name>Password login form</name> |
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<description> |
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The regular username+password login form. This is disabled by |
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default, but need to be enabled when installing an external |
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authentication manager that is optional. |
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</description> |
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</about> |
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<index>99</index> |
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<action-factory> |
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<factory-class>net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory</factory-class> |
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</action-factory> |
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</extension> |
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|
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<extension |
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id="bioassayset.overviewplots.maplot" |
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01 Apr 11 |
nicklas |
257 |
extends="net.sf.basedb.clients.web.bioassayset.overviewplots" |
5601 |
01 Apr 11 |
nicklas |
258 |
> |
5601 |
01 Apr 11 |
nicklas |
259 |
<index>1</index> |
5601 |
01 Apr 11 |
nicklas |
260 |
<about> |
5601 |
01 Apr 11 |
nicklas |
261 |
<name>MA/Correction factor plots</name> |
5601 |
01 Apr 11 |
nicklas |
262 |
<description> |
5601 |
01 Apr 11 |
nicklas |
263 |
Generates MA and correction factor plots for |
5601 |
01 Apr 11 |
nicklas |
264 |
2-channel data. |
5601 |
01 Apr 11 |
nicklas |
265 |
</description> |
5601 |
01 Apr 11 |
nicklas |
266 |
</about> |
5601 |
01 Apr 11 |
nicklas |
267 |
<action-factory> |
5601 |
01 Apr 11 |
nicklas |
268 |
<factory-class> |
5601 |
01 Apr 11 |
nicklas |
269 |
net.sf.basedb.clients.web.extensions.plot.MAPlotFactory |
5601 |
01 Apr 11 |
nicklas |
270 |
</factory-class> |
5601 |
01 Apr 11 |
nicklas |
271 |
<parameters> |
5601 |
01 Apr 11 |
nicklas |
272 |
<width>400</width> |
5601 |
01 Apr 11 |
nicklas |
273 |
<height>300</height> |
5601 |
01 Apr 11 |
nicklas |
274 |
<plotServlet>/views/experiments/plotter/plot</plotServlet> |
5601 |
01 Apr 11 |
nicklas |
275 |
</parameters> |
5601 |
01 Apr 11 |
nicklas |
276 |
</action-factory> |
5601 |
01 Apr 11 |
nicklas |
277 |
</extension> |
5601 |
01 Apr 11 |
nicklas |
278 |
|
7757 |
27 Nov 19 |
nicklas |
279 |
<extension |
7757 |
27 Nov 19 |
nicklas |
280 |
id="view-and-download-file" |
7757 |
27 Nov 19 |
nicklas |
281 |
extends="net.sf.basedb.clients.web.file-viewer" |
7757 |
27 Nov 19 |
nicklas |
282 |
> |
7757 |
27 Nov 19 |
nicklas |
283 |
<index>1</index> |
7757 |
27 Nov 19 |
nicklas |
284 |
<about> |
7757 |
27 Nov 19 |
nicklas |
285 |
<name>View and download files</name> |
7757 |
27 Nov 19 |
nicklas |
286 |
<description> |
7757 |
27 Nov 19 |
nicklas |
287 |
Add view and download icons to all files. |
7757 |
27 Nov 19 |
nicklas |
288 |
</description> |
7757 |
27 Nov 19 |
nicklas |
289 |
</about> |
7757 |
27 Nov 19 |
nicklas |
290 |
<action-factory> |
7757 |
27 Nov 19 |
nicklas |
291 |
<factory-class> |
7757 |
27 Nov 19 |
nicklas |
292 |
net.sf.basedb.clients.web.extensions.fileviewer.ViewAndDownloadActionFactory |
7757 |
27 Nov 19 |
nicklas |
293 |
</factory-class> |
7757 |
27 Nov 19 |
nicklas |
294 |
</action-factory> |
7757 |
27 Nov 19 |
nicklas |
295 |
</extension> |
6052 |
23 Apr 12 |
nicklas |
296 |
|
7764 |
04 Feb 20 |
nicklas |
297 |
<extension |
7840 |
31 Aug 20 |
nicklas |
298 |
id="related-item-columns"> |
7773 |
17 Feb 20 |
nicklas |
299 |
<extends> |
7773 |
17 Feb 20 |
nicklas |
300 |
<ref index="2">net.sf.basedb.clients.web.listcolumn.rawbioassay</ref> |
7773 |
17 Feb 20 |
nicklas |
301 |
<ref index="2">net.sf.basedb.clients.web.listcolumn.derivedbioassay</ref> |
7773 |
17 Feb 20 |
nicklas |
302 |
<ref index="2">net.sf.basedb.clients.web.listcolumn.physicalbioassay</ref> |
7773 |
17 Feb 20 |
nicklas |
303 |
<ref index="2">net.sf.basedb.clients.web.listcolumn.extract</ref> |
7773 |
17 Feb 20 |
nicklas |
304 |
<ref index="2">net.sf.basedb.clients.web.listcolumn.sample</ref> |
7842 |
01 Sep 20 |
nicklas |
305 |
<ref index="2">net.sf.basedb.clients.web.listcolumn.biosource</ref> |
7773 |
17 Feb 20 |
nicklas |
306 |
</extends> |
7764 |
04 Feb 20 |
nicklas |
307 |
<about> |
7840 |
31 Aug 20 |
nicklas |
308 |
<name>Parent/child item data</name> |
7764 |
04 Feb 20 |
nicklas |
309 |
<description> |
7840 |
31 Aug 20 |
nicklas |
310 |
Display and export data from parent and child items. |
7764 |
04 Feb 20 |
nicklas |
311 |
</description> |
7764 |
04 Feb 20 |
nicklas |
312 |
</about> |
7764 |
04 Feb 20 |
nicklas |
313 |
<action-factory> |
7764 |
04 Feb 20 |
nicklas |
314 |
<factory-class> |
7840 |
31 Aug 20 |
nicklas |
315 |
net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory |
7764 |
04 Feb 20 |
nicklas |
316 |
</factory-class> |
7764 |
04 Feb 20 |
nicklas |
317 |
</action-factory> |
7764 |
04 Feb 20 |
nicklas |
318 |
</extension> |
7850 |
14 Oct 20 |
nicklas |
319 |
|
7850 |
14 Oct 20 |
nicklas |
320 |
<extension |
7850 |
14 Oct 20 |
nicklas |
321 |
id="linked-item-columns"> |
7850 |
14 Oct 20 |
nicklas |
322 |
<extends> |
7850 |
14 Oct 20 |
nicklas |
323 |
<ref index="2">net.sf.basedb.clients.web.listcolumn.all</ref> |
7850 |
14 Oct 20 |
nicklas |
324 |
</extends> |
7850 |
14 Oct 20 |
nicklas |
325 |
<about> |
7850 |
14 Oct 20 |
nicklas |
326 |
<name>Custom links</name> |
7850 |
14 Oct 20 |
nicklas |
327 |
<description> |
7850 |
14 Oct 20 |
nicklas |
328 |
Display and export data from custom linked items. |
7850 |
14 Oct 20 |
nicklas |
329 |
</description> |
7850 |
14 Oct 20 |
nicklas |
330 |
</about> |
7850 |
14 Oct 20 |
nicklas |
331 |
<action-factory> |
7850 |
14 Oct 20 |
nicklas |
332 |
<factory-class> |
7850 |
14 Oct 20 |
nicklas |
333 |
net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory |
7850 |
14 Oct 20 |
nicklas |
334 |
</factory-class> |
7850 |
14 Oct 20 |
nicklas |
335 |
</action-factory> |
7850 |
14 Oct 20 |
nicklas |
336 |
</extension> |
7850 |
14 Oct 20 |
nicklas |
337 |
|
7850 |
14 Oct 20 |
nicklas |
338 |
|
5601 |
01 Apr 11 |
nicklas |
339 |
</extensions> |