Re: [base] Sample annotation error(s) ??
Thanks for the rapid response! I managed to sort the second problem out, it seems that an increase in the memory allocated to Tomcat solved it...all samples are now found! With regards to the termination of my session when working on the main Samples page (with +/- 85 annotation fields visible). I've looked at the Tomcat log, but I'm not to sure what to look for. The log data is included at the end of this msg (first bit is generated when I navigate to the Samples page, 2nd bit is generated when I try and open any window from this page) below. I've tried to do some diagnostics and the problem seems to be related to the number of annotation fields visible in the main view. As soon as I reduce the number of annotation columns to 62 everything works fine. Having looked at why 63 fields seem to produce some limit I found that the URL being passed to backend (URL in address bar of error page) seems to be truncated (with the cmd function, which is Import in this case, being truncated as impo (see below). The Web interface also generates an error saying Invalid command: The command Impo is not recognised as a valid command. (Screenshot can be sent.) http://xx.xx.xx/base2/biomaterials/samples/index.jsp?rowsperpage=10presetselector=filter%3ASTRING%3Aname=%25WBA%25.plasmafilter%3ASTRING%3AexternalId=filter%3AFLOAT%3AoriginalQuantity=filter%3AFLOAT%3AremainingQuantity=filter%3ASTRING%3AcreationEvent.protocol.name=filter%3ADATE%3AcreationEvent.eventDate=filter%3ADATE%3AcreationEvent.entryDate=filter%3ABOOLEAN%3Apooled=filter%3ASTRING%3Aowner.name=filter%3ASTRING%3Adescription=permission=filter%3ADOUBLE%3A%2337=filter%3ADOUBLE%3A%2338=filter%3ADOUBLE%3A%2336=filter%3ADOUBLE%3A%2386=filter%3ADOUBLE%3A%2385=filter%3ADOUBLE%3A%2384=filter%3ADOUBLE%3A%2350=filter%3ADOUBLE%3A%2349=filter%3ADOUBLE%3A%2348=filter%3ADOUBLE%3A%2376=filter%3ADOUBLE%3A%2377=filter%3ADOUBLE%3A%2375=filter%3ADOUBLE%3A%2379=filter%3ADOUBLE%3A%2380=filter%3ADOUBLE%3A%2378=filter%3ADOUBLE%3A%2356=filter%3ADOUBLE%3A%2355=filter%3ADOUBLE%3A%2354=filter%3ADOUBLE%3A%2390=filter%3ADOUBLE%3A%2391=filter%3ADOUBLE%3A%2389=filter%3A DOUBLE%3A%2358=filter%3ADOUBLE%3A%2359=filter%3ADOUBLE%3A%2357=filter%3ADOUBLE%3A%2362=filter%3ADOUBLE%3A%2361=filter%3ADOUBLE%3A%2360=filter%3ADOUBLE%3A%2365=filter%3ADOUBLE%3A%2364=filter%3ADOUBLE%3A%2363=filter%3ADOUBLE%3A%2368=filter%3ADOUBLE%3A%2367=filter%3ADOUBLE%3A%2366=filter%3ADOUBLE%3A%2370=filter%3ADOUBLE%3A%2371=filter%3ADOUBLE%3A%2369=filter%3ADOUBLE%3A%2322=filter%3ADOUBLE%3A%2323=filter%3ADOUBLE%3A%2321=filter%3ADOUBLE%3A%2328=filter%3ADOUBLE%3A%2329=filter%3ADOUBLE%3A%2327=filter%3ADOUBLE%3A%2325=filter%3ADOUBLE%3A%2326=filter%3ADOUBLE%3A%2324=filter%3ADOUBLE%3A%2331=filter%3ADOUBLE%3A%2332=filter%3ADOUBLE%3A%2330=filter%3ADOUBLE%3A%2334=filter%3ADOUBLE%3A%2335=filter%3ADOUBLE%3A%2333=filter%3ADOUBLE%3A%2340=filter%3ADOUBLE%3A%2341=filter%3ADOUBLE%3A%2339=filter%3ADOUBLE%3A%2343=filter%3ADOUBLE%3A%2344=filter%3ADOUBLE%3A%2342=filter%3ADOUBLE%3A%2352=filter%3ADOUBLE%3A%2353=filter%3ADOUBLE%3A%2351=filter%3ADOUBLE%3A%237 3=filter%3ADOUBLE%3A%2374=filter%3ADOUBLE%3A%2372=rowsperpage=10ID=4721ceb93fa55a04cmd=Impo As soon as the annotation fields are increased to 64, I get an error saying that Im no longer logged in or that BASE has been restarted. I presume this is because the ID= bit is being truncated? At 62 annotation fields, the Import screen activated without any problems and the URL in the address bar is: http://xx.xx.xx/base2/common/import/index.jsp?ID=bf0b70ec121da201cmd=SelectPluginitem_type=SAMPLEcontext_type=LISTtitle=Import+sample Any ideas as to how to get around this problem will be greatly appreciated!! TOMCAT LOG #1 [Navigating to Samples view] org.apache.jsp.biomaterials.samples.index_jsp._jspService(index_jsp.java:85) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at
Re: [base] Sample annotation error(s) ??
Thanks! The analysis is excellent and the information is just what we needed. The problem is that there is a limit on how long an URL can be. This is different from browser to browser. It can also be affected by what the server can handle and if there are any proxys the request is passing through. If found this link which has investigated some limitations: http://www.boutell.com/newfaq/misc/urllength.html If you are using IE this would explain why the URL gets truncated. Obviously the problem needs to be fixed on the BASE side. We should not generate URLs that are as long as this. In the meantime I see only two possible workarounds: 1) Don't display too many columns. The limit of 62 may become lower if you are filtering since the filter string(s) will also be added to the URL. 2) Try to use Firefox instead. This option will of course only work if the web server, proxies, etc. also supports longer URLs. /Nicklas Johan van Heerden wrote: Thanks for the rapid response! I managed to sort the second problem out, it seems that an increase in the memory allocated to Tomcat solved it...all samples are now found! With regards to the termination of my session when working on the main Samples page (with +/- 85 annotation fields visible). I've looked at the Tomcat log, but I'm not to sure what to look for. The log data is included at the end of this msg (first bit is generated when I navigate to the Samples page, 2nd bit is generated when I try and open any window from this page) below. I've tried to do some diagnostics and the problem seems to be related to the number of annotation fields visible in the main view. As soon as I reduce the number of annotation columns to 62 everything works fine. Having looked at why 63 fields seem to produce some limit I found that the URL being passed to backend (URL in address bar of error page) seems to be truncated (with the cmd function, which is “Import” in this case, being truncated as impo (see below). The Web interface also generates an error saying Invalid command: The command Impo is not recognised as a valid command. (Screenshot can be sent.) http://xx.xx.xx/base2/biomaterials/samples/index.jsp?rowsperpage=10presetselector=filter%3ASTRING%3Aname=%25WBA%25.plasmafilter%3ASTRING%3AexternalId=filter%3AFLOAT%3AoriginalQuantity=filter%3AFLOAT%3AremainingQuantity=filter%3ASTRING%3AcreationEvent.protocol.name=filter%3ADATE%3AcreationEvent.eventDate=filter%3ADATE%3AcreationEvent.entryDate=filter%3ABOOLEAN%3Apooled=filter%3ASTRING%3Aowner.name=filter%3ASTRING%3Adescription=permission=filter%3ADOUBLE%3A%2337=filter%3ADOUBLE%3A%2338=filter%3ADOUBLE%3A%2336=filter%3ADOUBLE%3A%2386=filter%3ADOUBLE%3A%2385=filter%3ADOUBLE%3A%2384=filter%3ADOUBLE%3A%2350=filter%3ADOUBLE%3A%2349=filter%3ADOUBLE%3A%2348=filter%3ADOUBLE%3A%2376=filter%3ADOUBLE%3A%2377=filter%3ADOUBLE%3A%2375=filter%3ADOUBLE%3A%2379=filter%3ADOUBLE%3A%2380=filter%3ADOUBLE%3A%2378=filter%3ADOUBLE%3A%2356=filter%3ADOUBLE%3A%2355=filter%3ADOUBLE%3A%2354=filter%3ADOUBLE%3A%2390=filter%3ADOUBLE%3A%2391=filter%3ADOUBLE%3A%2389=filter%3A DOUBLE%3A%2358=filter%3ADOUBLE%3A%2359=filter%3ADOUBLE%3A%2357=filter%3ADOUBLE%3A%2362=filter%3ADOUBLE%3A%2361=filter%3ADOUBLE%3A%2360=filter%3ADOUBLE%3A%2365=filter%3ADOUBLE%3A%2364=filter%3ADOUBLE%3A%2363=filter%3ADOUBLE%3A%2368=filter%3ADOUBLE%3A%2367=filter%3ADOUBLE%3A%2366=filter%3ADOUBLE%3A%2370=filter%3ADOUBLE%3A%2371=filter%3ADOUBLE%3A%2369=filter%3ADOUBLE%3A%2322=filter%3ADOUBLE%3A%2323=filter%3ADOUBLE%3A%2321=filter%3ADOUBLE%3A%2328=filter%3ADOUBLE%3A%2329=filter%3ADOUBLE%3A%2327=filter%3ADOUBLE%3A%2325=filter%3ADOUBLE%3A%2326=filter%3ADOUBLE%3A%2324=filter%3ADOUBLE%3A%2331=filter%3ADOUBLE%3A%2332=filter%3ADOUBLE%3A%2330=filter%3ADOUBLE%3A%2334=filter%3ADOUBLE%3A%2335=filter%3ADOUBLE%3A%2333=filter%3ADOUBLE%3A%2340=filter%3ADOUBLE%3A%2341=filter%3ADOUBLE%3A%2339=filter%3ADOUBLE%3A%2343=filter%3ADOUBLE%3A%2344=filter%3ADOUBLE%3A%2342=filter%3ADOUBLE%3A%2352=filter%3ADOUBLE%3A%2353=filter%3ADOUBLE%3A%2351=filter%3ADOUBLE%3A%237 3=filter%3ADOUBLE%3A%2374=filter%3ADOUBLE%3A%2372=rowsperpage=10ID=4721ceb93fa55a04cmd=Impo As soon as the annotation fields are increased to 64, I get an error saying that I’m no longer logged in or that BASE has been restarted. I presume this is because the “ID=” bit is being truncated? At 62 annotation fields, the Import screen activated without any problems and the URL in the address bar is: http://xx.xx.xx/base2/common/import/index.jsp?ID=bf0b70ec121da201cmd=SelectPluginitem_type=SAMPLEcontext_type=LISTtitle=Import+sample Any ideas as to how to get around this problem will be greatly appreciated!! - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___
Re: [base] Sample annotation error(s) ??
Johan van Heerden wrote: Hi all, I've been experiencing strange problems (BASE V2.4.5) with sample annotations. The first problem seems to be related to a limit on the number of annotation fields allowed (I'm not sure if there is a limit?). I have been trying to attach non-array type data to samples as annotations. Specifically, I have 83 annotation fields per sample. I managed to create all annotation types without any hitches, but as soon as I go to the Samples page and try to initiate any other action (e.g. importing of annotation data) from this page I get a msg saying that I'm not logged in, OR that the server has been restarted. I've manage to avoid this problem, however, if I reduce the number of annotation fields to somewhere 50 (I haven't determined the exact limit yet). Any ideas why this should happen? There is no special limit. Have you checked Tomcat's logfile for any error messages? The message about being logged out is typical when an unexpected error happens during the page generation befor the session ID has been written to the output. You have not actually been logged out. Going back to the previous page would allow you to continue working. The second problem relates to the annotation importer (this might be related to the first). Once I've reduced the number of annotation fields to enable me to initialise the importer wizard, I manage to start the importing of data, but keep on getting a msg saying that: Item not found: Sample[name=T10656.b1.WBA.plasma] on line 2: T10656.b1.WBA.pla... I've tried to create simpler sample entries (i.e. Not seperated by .), but this generates the same error msg. I've previously had this working, which leaves me somewhat baffled? Any ideas? The samples must exists before running the annotation importer. If they do, make sure that you set the options where the annotation importer should look for them (owned by you, in the current projects, etc...) /Nicklas - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
