BioAssaySetExporter should request 'r' for reading Projects

[Jari Häkkinen]

I am running rev 4527 on trunk.

Setting use permission to yes will make BioAssaySetExporter to add a stacktrace (see sample below) in the end of the exported file if the plug-in has no 'r' on projects.

net.sf.basedb.core.PermissionDeniedException: Permission denied: Not allowed to read Project[id=2; name=MergeBioAssay test]
	at net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110)
	at net.sf.basedb.core.DbControl.getItem(DbControl.java:813)
	at net.sf.basedb.core.DbControl.loadItem(DbControl.java:698)
	at net.sf.basedb.core.Project.getById(Project.java:132)
	at net.sf.basedb.core.DbControl.commit(DbControl.java:330)
	at net.sf.basedb.core.plugin.AbstractExporterPlugin.doExport(AbstractExporterPlugin.java:188)
	at net.sf.basedb.core.PluginResponse.downloadImmediately(PluginResponse.java:181)
	at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:602)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:337)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:70)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:286)
	at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:844)
	at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
	at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:447)
	at java.lang.Thread.run(Thread.java:637)

[Jari Häkkinen]

The same is true for Base1PluginExecuter. Has something changed in trunk regarding permissions and plug-ins? I upgraded to latest trunk a couple of hours ago, before that Base1PluginEecuter worked for men, but now I had to add 'r' on Projects since use permissions is set to true.

[Jari Häkkinen]

Raw data importer and Formula intensity calculator have the same issue.

[Nicklas Nordborg]

Seems like a side-effect of a bad implementation of #1112.