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From: William P. <wil...@ya...> - 2010-04-01 21:18:43
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Thanks Youjun, the javascript doesn't seem to be responding here: http://130.132.27.212:8080/treebase-web/search/study/trees.html?id=264 bp On Apr 1, 2010, at 4:13 PM, youjun guo wrote: > Hi, Guys, > > These javascrpt work on my server and I expect they will also work on treebase.org: > > function openPhylowidget(tree_id) > { > var realURL = "http://www.phylowidget.org/full/?tree='http://"+location.host+"${url}"+"TB2:Tr"+tree_id+"'"; > window.open(realURL,'myplwidget') > } > > and then > > <a href="javascript:void(0)" onClick="openPhylowidget(${tree.id}"> > > Code was submitted to sourceforge and need a re-deployment to see the change. > > Thank you for all of you, have a good good Friday. > > Youjun > > On Thu, Apr 1, 2010 at 10:46 AM, Hilmar Lapp <hl...@ne...> wrote: > > On Apr 1, 2010, at 10:16 AM, Jon Auman wrote: > >> A little php code inserted in the javascript could get the host dynamically: > > Just a note, you don't need PHP for this. JavaScript can give you the server name directly. The PHP code would be wrong, as it executes server-side, not browser-side. > > -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel William H. Piel Associate Director for Evolutionary Informatics Peabody 401, Yale University 170 Whitney Ave. New Haven CT 06511 (203) 436-4957 wil...@ya... |
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From: Hilmar L. <hl...@ne...> - 2010-04-01 21:15:34
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Youjun - doesn't this also mean that we are not using a locally modified version of PhyloWidget anymore? -hilmar On Apr 1, 2010, at 5:13 PM, youjun guo wrote: > Hi, Guys, > > These javascrpt work on my server and I expect they will also work > on treebase.org: > > function openPhylowidget(tree_id) > { > var realURL = "http://www.phylowidget.org/full/?tree='http:// > "+location.host+"${url}"+"TB2:Tr"+tree_id+"'"; > window.open(realURL,'myplwidget') > } > > and then > > <a href="javascript:void(0)" onClick="openPhylowidget(${tree.id}"> > > Code was submitted to sourceforge and need a re-deployment to see > the change. > > Thank you for all of you, have a good good Friday. > > Youjun > > On Thu, Apr 1, 2010 at 10:46 AM, Hilmar Lapp <hl...@ne...> > wrote: > > On Apr 1, 2010, at 10:16 AM, Jon Auman wrote: > >> A little php code inserted in the javascript could get the host >> dynamically: > > Just a note, you don't need PHP for this. JavaScript can give you > the server name directly. The PHP code would be wrong, as it > executes server-side, not browser-side. > > -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: youjun g. <you...@ya...> - 2010-04-01 21:14:01
|
Hi, Guys, These javascrpt work on my server and I expect they will also work on treebase.org: function openPhylowidget(tree_id) { var realURL = "http://www.phylowidget.org/full/?tree='http:// "+location.host+"${url}"+"TB2:Tr"+tree_id+"'"; window.open(realURL,'myplwidget') } and then <a href="javascript:void(0)" onClick="openPhylowidget(${tree.id}"> Code was submitted to sourceforge and need a re-deployment to see the change. Thank you for all of you, have a good good Friday. Youjun On Thu, Apr 1, 2010 at 10:46 AM, Hilmar Lapp <hl...@ne...> wrote: > > On Apr 1, 2010, at 10:16 AM, Jon Auman wrote: > > A little php code inserted in the javascript could get the host > dynamically: > > > Just a note, you don't need PHP for this. JavaScript can give you the > server name directly. The PHP code would be wrong, as it executes > server-side, not browser-side. > > -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: Hilmar L. <hl...@ne...> - 2010-04-01 21:13:39
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On Apr 1, 2010, at 4:54 PM, Vladimir Gapeyev wrote: > Alternatively, if the developer does not care about proper > functioning of PURLs, he can use tb2/BasePurl=http://localhost:8080/treebase-web/phylows/ Exactly - whether PURLs function or not is mostly under the control of the folks who operate purl.org, otherwise it's just a redirect, so you might as well use your local server right away. > Finally, I have changed several JSP pages that had "http://purl.org/phylo/treebase/phylows > ...." urls hardwired so that they instead look up the tb2/PurlBase > parameter. However, I used <%= ... %>, so someone more > knowledgeable might want to adjust that syntax. The value of these parameters is application-wide, right? So, wouldn't the easiest way be to have a class that sets these as application context parameters from JNDI and gets executed when the application is loaded? Or is this the way you implemented it? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Vladimir G. <vga...@ne...> - 2010-04-01 20:54:58
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With the today's fix of the PURLs issue, treebase-dev now again functions properly (without jumps to production). That is, we can go back to testing new WAR versions on treebase-dev before enabling them on production. Bill, Youjun, for the next week or so, please specify whether you want a new build & deployment on development, on production, or both. My task for the next week is to set up automatic build & deployment on treebase-dev, triggered by SVN commits. After this, you will only need to tell us when a development build that you are happy with should be moved on production. --Vladimir |
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From: Vladimir G. <vla...@du...> - 2010-04-01 20:54:53
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On Apr 1, 2010, at 10:05 AM, William Piel wrote: >> On Apr 1, 2010, at 9:11 AM, William Piel wrote: >> >>> Rather than a PURL, how about just hard-coding "www.treebase.org"? >>> (do we have a parameter init file where this can be stored?) As of rev 664, I introduced a JNDI parameter tb2/SiteUrl for this purpose. See src/main/webapp/META-INF/context.xml.example for usage. These is also a convenience method, org.cipres.treebase.TreebaseUtil.getSiteUrl() to look it up. --Vladimir |
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From: Vladimir G. <vga...@ne...> - 2010-04-01 20:54:46
|
As of rev 664, treebase-web.war expects two more parameters to be
supplied by Tomcat via JNDI:
tb2/BasePurl - is now used instead of a parameter that used to be
in treebase.properties
tb2/SiteUrl - as requested earlier today, to be used to implement
redirects to phylowidget.org
Anyone who runs their own instance, should add these parameters into
their src/main/webapp/META-INF/context.xml.example or $CATALINA_HOME/
cong/Catalina/localhost/treebase-web.xml, see src/main/webapp/META-INF/
context.xml.example for an example.
Regarding the PURLs, you should also go to www.purl.org, register a
new PURL that redirects to your server, and put this PURL into tb2/
BasePurl in your Tomcat config. This configuration only works with a
Treebase server that is addressable from the outside world, i.e. it
does not work from a personal developer server that runs at localhost
(unless you run your own PURL service at localhost, I guess...).
Alternatively, if the developer does not care about proper functioning
of PURLs, he can use tb2/BasePurl=http://localhost:8080/treebase-web/phylows/
Here are the values of tb2/BasePurl that are will be used on the
instances at NESCent:
production: http://purl.org/phylo/treebase/phylows/
staging: http://purl.org/phylo/treebase/stage/phylows/
development: http://purl.org/phylo/treebase/dev/phylows/
So far, we have deployed this version (664) on *development* only.
Finally, I have changed several JSP pages that had "http://purl.org/phylo/treebase/phylows
...." urls hardwired so that they instead look up the tb2/PurlBase
parameter. However, I used <%= ... %>, so someone more knowledgeable
might want to adjust that syntax.
--Vladimir
|
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From: Hilmar L. <hl...@ne...> - 2010-04-01 14:46:29
|
On Apr 1, 2010, at 10:16 AM, Jon Auman wrote: > A little php code inserted in the javascript could get the host > dynamically: Just a note, you don't need PHP for this. JavaScript can give you the server name directly. The PHP code would be wrong, as it executes server-side, not browser-side. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Jon A. <jon...@du...> - 2010-04-01 14:17:00
|
Bill, This is disk space issue. The tomcat log was growing very large as it is currently logging every single query. I am currently working on: 1) excluding all application messages from catalina.out. There is a a separate treebase.log for this, which is properly rotated. 2) get catalina.out into log rotation (not straightforward, most scenarios require a tomcat restart) 3) disk space monitoring checks submitted to nagios. Anyways, for the moment, I've moved the old tomcat log and started a new one, which freed up 4 GB of space. -Jon On Apr 1, 2010, at 9:42 AM, William Piel wrote: > > Hi Jon, > > Is this a RAM outage or a disc space issue? > > "No space left on device at org.apache.commons.fileupload.FileUploadBase.parseRequest" > > bp > > > > Begin forwarded message: > >> From: "Torbjørn Ekrem via RT" <bu...@tr...> >> Date: April 1, 2010 8:31:41 AM CDT >> To: undisclosed-recipients: ; >> Subject: [[treebase-bugs] #7718] error message when submitting nexus file >> Reply-To: bu...@tr... >> >> >> Thu Apr 01 09:31:40 2010: Request 7718 was acted upon. >> Transaction: Ticket created by Tor...@vm... >> Queue: Treebase-bugs >> Subject: error message when submitting nexus file >> Owner: Nobody >> Requestors: Tor...@vm... >> Status: new >> Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7718 > >> >> >> Hi, >> >> I tried to upload a nexus-file that is successfully parsed in Mesquite today, >> and got the below error message. Is there anything that I might have overlooked >> or is this perhaps a bug. The file is not very large (about 270 kb) and include >> taxa, characters and trees blocks. >> >> Best regards, >> Torbjørn >> >> -- >> Dr. Torbjørn Ekrem >> Systematikk og evolusjonsgruppa >> NTNU Vitenskapsmuseet >> Seksjon for naturhistorie >> 7491 Trondheim >> >> Systematics and Evolution Group >> Museum of Natural History and Archaeology >> Norwegian University of Science and Technology >> NO-7491 Trondheim, Norway >> >> Tel: +47 73 59 78 12 >> Email: Tor...@vm...Web: www.ntnu.no/~torbjoe >> Uncaught Exception Encountered >> >> >> org.springframework.web.multipart.MultipartException: Could not parse multipart >> servlet request; nested exception is >> org.apache.commons.fileupload.FileUploadBase$IOFileUploadException: Processing >> of multipart/form-data request failed. No space left on device Caused by: >> org.apache.commons.fileupload.FileUploadBase$IOFileUploadException: Processing >> of multipart/form-data request failed. No space left on device at >> org.apache.commons.fileupload.FileUploadBase.parseRequest(FileUploadBase.java:359) >> at >> org.apache.commons.fileupload.servlet.ServletFileUpload.parseRequest(ServletFileUpload.java:126) >> at >> org.cipres.treebase.web.controllers.AjaxMultipartResolver.resolveMultipart(AjaxMultipartResolver.java:35) >> at >> org.springframework.web.servlet.DispatcherServlet.checkMultipart(DispatcherServlet.java:980) >> at >> org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:834) >> at >> org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) >> at >> org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) >> at >> org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) >> at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at >> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) >> at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at >> org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90) >> at >> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) >> at >> org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) >> at >> com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) >> at >> org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) >> at >> org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) >> at >> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) >> at >> org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) >> at >> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) >> at >> org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) >> at >> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) >> at >> org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) >> at >> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) >> at >> org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) >> at >> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) >> at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) >> at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) >> at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> at >> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) >> at >> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) >> at >> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) >> at >> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) >> at >> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) >> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) >> at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) >> at >> org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) >> at >> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) >> at >> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) >> at >> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) >> at java.lang.Thread.run(Thread.java:636) Caused by: java.io.IOException: No >> space left on device at java.io.FileOutputStream.writeBytes(Native Method) at >> java.io.FileOutputStream.write(FileOutputStream.java:297) at >> org.apache.commons.io.output.ByteArrayOutputStream.writeTo(ByteArrayOutputStream.java:217) >> at >> org.apache.commons.io.output.DeferredFileOutputStream.thresholdReached(DeferredFileOutputStream.java:124) >> at >> org.apache.commons.io.output.ThresholdingOutputStream.checkThreshold(ThresholdingOutputStream.java:220) >> at >> org.apache.commons.io.output.ThresholdingOutputStream.write(ThresholdingOutputStream.java:127) >> at org.apache.commons.fileupload.util.Streams.copy(Streams.java:101) at >> org.apache.commons.fileupload.util.Streams.copy(Streams.java:64) at >> org.apache.commons.fileupload.FileUploadBase.parseRequest(FileUploadBase.java:354) >> ... 56 more Cookies: >> itemToHighlight=[http%3A//www.treebase.org/treebase-web/user/uploadFile.html] >> JSESSIONID=[4159496F4E66A78FD91DB3E51F4833F3] >> > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: William P. <wil...@ya...> - 2010-04-01 14:16:52
|
On Apr 1, 2010, at 8:51 AM, Vladimir Gapeyev wrote: > Meanwhile, would you prefer to revert production to the previous build, or leave it as is? uhmm... well, I don't want to lose Youjun's fix that allows for deletion of trees. Can we revert to just the changes to the phylowidget links without disturbing other advances? (or just comment out the phylowidget links with a "temporarily unavailable" hover-over message) bp |
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From: Jon A. <jon...@du...> - 2010-04-01 14:16:46
|
A little php code inserted in the javascript could get the host dynamically: Of course, that means we've now added yet another framework to the app, but php is already enabled on the apache server. <script language="Javascript"> var hostName = <?= $_SERVER['SERVER_NAME'] ?> </script> -Jon On Apr 1, 2010, at 10:05 AM, William Piel wrote: > > On Apr 1, 2010, at 8:40 AM, Hilmar Lapp wrote: > >> On Apr 1, 2010, at 9:11 AM, William Piel wrote: >> >>> Rather than a PURL, how about just hard-coding "www.treebase.org"? >>> (do we have a parameter init file where this can be stored?) >> >> >> That's possible, but I'd do that only as a last resort, because it >> would be different between dev/staging/production deployments. >> >> -hilmar > > If using javascript, it would have to change links like this: > > http://www.phylowidget.org/full/?tree='http://localhost:8080/treebase-web/tree_for_phylowidget/TB2:Tr300' > > to this: > > http://www.phylowidget.org/full/?tree='http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr300' > > on two different pages. This page: > > http://www.treebase.org/treebase-web/search/treeSearch.html > > and this page: > > http://www.treebase.org/treebase-web/search/study/trees.html?id=2344 > > bp > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: William P. <wil...@ya...> - 2010-04-01 14:06:03
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On Apr 1, 2010, at 8:40 AM, Hilmar Lapp wrote: > On Apr 1, 2010, at 9:11 AM, William Piel wrote: > >> Rather than a PURL, how about just hard-coding "www.treebase.org"? >> (do we have a parameter init file where this can be stored?) > > > That's possible, but I'd do that only as a last resort, because it > would be different between dev/staging/production deployments. > > -hilmar If using javascript, it would have to change links like this: http://www.phylowidget.org/full/?tree='http://localhost:8080/treebase-web/tree_for_phylowidget/TB2:Tr300' to this: http://www.phylowidget.org/full/?tree='http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr300' on two different pages. This page: http://www.treebase.org/treebase-web/search/treeSearch.html and this page: http://www.treebase.org/treebase-web/search/study/trees.html?id=2344 bp |
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From: Vladimir G. <vla...@du...> - 2010-04-01 13:53:55
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I currently work on moving the PURL prefix from treebase.properties into the Tomcat config, so that we can have back a properly functioning development instance. Since I am already into that, I will as well create a new JNDI parameter, say tb2/HostUrl, to hold the server name (like "www.treebase.org"). I hope to be done by the end of the day. Meanwhile, would you prefer to revert production to the previous build, or leave it as is? --VG On Apr 1, 2010, at 9:11 AM, William Piel wrote: > > Whatever works is fine by me... let's fix and redeploy, seeing as > the production is broken. > > The path needs to be full, not relative, and while Javascript can do > just about anything -- it wouldn't be an easy solution. > > Rather than a PURL, how about just hard-coding "www.treebase.org"? > (do we have a parameter init file where this can be stored?) > > bp > > > On Mar 31, 2010, at 8:07 PM, Hilmar Lapp wrote: > >> Do you need an absolute path that includes the server name, i.e., >> does a relative path not suffice? If you do need a full path, does >> that have to be generated server-side or can that also be done in >> JavaScript (which will yield the correct server name). >> >> -hilmar >> >> On Mar 31, 2010, at 8:02 PM, youjun guo wrote: >> >>> Bill, >>> >>> In treebase.org the server name in the phylowidget redirect url >>> return "localhost:8080" because we have a Apache server in front >>> of Tomcat, and Apache addressed the Tomact work this way. >>> >>> I think we have to use purl this time. >>> >>> Youjun > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: William P. <wil...@ya...> - 2010-04-01 13:42:36
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Hi Jon, Is this a RAM outage or a disc space issue? "No space left on device at org.apache.commons.fileupload.FileUploadBase.parseRequest" bp Begin forwarded message: > From: "Torbjørn Ekrem via RT" <bu...@tr...> > Date: April 1, 2010 8:31:41 AM CDT > To: undisclosed-recipients: ; > Subject: [[treebase-bugs] #7718] error message when submitting nexus file > Reply-To: bu...@tr... > > > Thu Apr 01 09:31:40 2010: Request 7718 was acted upon. > Transaction: Ticket created by Tor...@vm... > Queue: Treebase-bugs > Subject: error message when submitting nexus file > Owner: Nobody > Requestors: Tor...@vm... > Status: new > Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7718 > > > > Hi, > > I tried to upload a nexus-file that is successfully parsed in Mesquite today, > and got the below error message. Is there anything that I might have overlooked > or is this perhaps a bug. The file is not very large (about 270 kb) and include > taxa, characters and trees blocks. > > Best regards, > Torbjørn > > -- > Dr. Torbjørn Ekrem > Systematikk og evolusjonsgruppa > NTNU Vitenskapsmuseet > Seksjon for naturhistorie > 7491 Trondheim > > Systematics and Evolution Group > Museum of Natural History and Archaeology > Norwegian University of Science and Technology > NO-7491 Trondheim, Norway > > Tel: +47 73 59 78 12 > Email: Tor...@vm...Web: www.ntnu.no/~torbjoe > Uncaught Exception Encountered > > > org.springframework.web.multipart.MultipartException: Could not parse multipart > servlet request; nested exception is > org.apache.commons.fileupload.FileUploadBase$IOFileUploadException: Processing > of multipart/form-data request failed. No space left on device Caused by: > org.apache.commons.fileupload.FileUploadBase$IOFileUploadException: Processing > of multipart/form-data request failed. No space left on device at > org.apache.commons.fileupload.FileUploadBase.parseRequest(FileUploadBase.java:359) > at > org.apache.commons.fileupload.servlet.ServletFileUpload.parseRequest(ServletFileUpload.java:126) > at > org.cipres.treebase.web.controllers.AjaxMultipartResolver.resolveMultipart(AjaxMultipartResolver.java:35) > at > org.springframework.web.servlet.DispatcherServlet.checkMultipart(DispatcherServlet.java:980) > at > org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:834) > at > org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) > at > org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) > at > org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at > javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) > at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at > org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90) > at > org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) > at > org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) > at > com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) > at > org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) > at > org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) > at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) > at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) > at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) > at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) > at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) > at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) > at java.lang.Thread.run(Thread.java:636) Caused by: java.io.IOException: No > space left on device at java.io.FileOutputStream.writeBytes(Native Method) at > java.io.FileOutputStream.write(FileOutputStream.java:297) at > org.apache.commons.io.output.ByteArrayOutputStream.writeTo(ByteArrayOutputStream.java:217) > at > org.apache.commons.io.output.DeferredFileOutputStream.thresholdReached(DeferredFileOutputStream.java:124) > at > org.apache.commons.io.output.ThresholdingOutputStream.checkThreshold(ThresholdingOutputStream.java:220) > at > org.apache.commons.io.output.ThresholdingOutputStream.write(ThresholdingOutputStream.java:127) > at org.apache.commons.fileupload.util.Streams.copy(Streams.java:101) at > org.apache.commons.fileupload.util.Streams.copy(Streams.java:64) at > org.apache.commons.fileupload.FileUploadBase.parseRequest(FileUploadBase.java:354) > ... 56 more Cookies: > itemToHighlight=[http%3A//www.treebase.org/treebase-web/user/uploadFile.html] > JSESSIONID=[4159496F4E66A78FD91DB3E51F4833F3] > |
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From: Hilmar L. <hl...@ne...> - 2010-04-01 13:40:22
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On Apr 1, 2010, at 9:11 AM, William Piel wrote: > Rather than a PURL, how about just hard-coding "www.treebase.org"? > (do we have a parameter init file where this can be stored?) That's possible, but I'd do that only as a last resort, because it would be different between dev/staging/production deployments. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-04-01 13:11:39
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Whatever works is fine by me... let's fix and redeploy, seeing as the production is broken. The path needs to be full, not relative, and while Javascript can do just about anything -- it wouldn't be an easy solution. Rather than a PURL, how about just hard-coding "www.treebase.org"? (do we have a parameter init file where this can be stored?) bp On Mar 31, 2010, at 8:07 PM, Hilmar Lapp wrote: > Do you need an absolute path that includes the server name, i.e., does a relative path not suffice? If you do need a full path, does that have to be generated server-side or can that also be done in JavaScript (which will yield the correct server name). > > -hilmar > > On Mar 31, 2010, at 8:02 PM, youjun guo wrote: > >> Bill, >> >> In treebase.org the server name in the phylowidget redirect url return "localhost:8080" because we have a Apache server in front of Tomcat, and Apache addressed the Tomact work this way. >> >> I think we have to use purl this time. >> >> Youjun |
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From: Hilmar L. <hl...@ne...> - 2010-04-01 01:07:18
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Do you need an absolute path that includes the server name, i.e., does a relative path not suffice? If you do need a full path, does that have to be generated server-side or can that also be done in JavaScript (which will yield the correct server name). -hilmar On Mar 31, 2010, at 8:02 PM, youjun guo wrote: > Bill, > > In treebase.org the server name in the phylowidget redirect url > return "localhost:8080" because we have a Apache server in front of > Tomcat, and Apache addressed the Tomact work this way. > > I think we have to use purl this time. > > Youjun > > > > > On Wed, Mar 31, 2010 at 4:46 PM, Jon Auman <jon...@du...> wrote: > I've redeployed and bumped the timeout to 15 minutes. > -jon > > On Mar 31, 2010, at 3:29 PM, William Piel wrote: > >> >> Hi all, >> >> Can we do a new build on production? (and dev or stage, if you have >> time) >> >> Youjun recently fixed the delete-tree function, and that will be >> useful for this guy's issue (see below). Also Youjun fixed the >> MacFirefox-PhyloWidget problem on the browse side of the equation. >> For that, we now pass the tree to the latest version of phylowidget >> stored on the phylowidget.org website (which doesn't have a problem >> with Mac-Firefox). >> >> We still have a problem with MacFirefox-PhyloWidget on the Submit >> side, but that can't be solved just by pointing to the latest copy >> on phylowidget.org because we have made custom changes to the code >> (for saving rerooted trees back the database). >> >> Finally, Michael Pirie's problem (below) seems to be the result of >> a time-out on headless-Mesquite ingest. Can we increase the time >> allotted to this process so as to avoid the time-out? (And, I >> should mention that when I deleted his extra matrix, I also got a >> proxy-timeout problem -- but when I came back to the submission, >> the matrix had been deleted. So again, the functions appear to go >> to completion eventually even though the browser shows a proxy >> error. If we could avoid the timeout, it would be better). >> >> Bill >> >> >> >> On Mar 31, 2010, at 3:18 PM, William Piel wrote: >> >>> Dear Michael Pirie: >>> >>> I think that the proxy error came from a time-out because the >>> parser was taking too long to commit the inserts (e.g. 298 x 11810 >>> = 3,519,380 inserts, not including all the other bits) -- but the >>> inserts happened anyway despite the time-out. And it looks like >>> you backed-up and re-clicked, so there were two matrices and two >>> sets of trees. I deleted one of the matrices -- but I don't want >>> to delete the extra set of trees until we've done a rebuild on our >>> deployment (we recently fixed some code having to do with deleting >>> trees). By tomorrow, feel free to delete the extra set of trees. >>> >>> So everything looks okay, despite the fact that the ingest did a >>> time-out on you. I'm going to suggest that our server gets reset >>> to allow for longer ingest times. >>> >>> regards, >>> >>> Bill >>> >>> >>> On Mar 31, 2010, at 10:54 AM, Michael D. Pirie via RT wrote: >>> >>>> >>>> Wed Mar 31 10:54:10 2010: Request 7708 was acted upon. >>>> Transaction: Ticket created by mp...@su... >>>> Queue: Treebase-help >>>> Subject: File upload problem submission 10367 >>>> Owner: Nobody >>>> Requestors: mp...@su... >>>> Status: new >>>> Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7708 > >>>> >>>> >>>> Dear Sir/Madam, >>>> I get the following error when attempting to upload a file to my >>>> submission 10367: >>>> >>>> >>>> Proxy Error >>>> >>>> The proxy server received an invalid response from an upstream >>>> server. >>>> The proxy server could not handle the request POST >>>> /treebase-web/user/uploadFile.html. >>>> >>>> Reason: Error reading from remote server >>>> >>>> Apache/2.2.3 (CentOS) Server at www.treebase.org Port 80 >>>> >>>> >>>> I'm attaching a zipped copy of the file - would it be possible to >>>> add >>>> this for me? >>>> Thanks and best wishes, >>>> >>>> -- >>>> Dr Michael D. Pirie >>>> Department of Biochemistry >>>> University of Stellenbosch >>>> Private Bag X1, MATIELAND 7602 >>>> Stellenbosch, Western Cape >>>> South Africa >>>> >>>> Tel: +27-21-8085841 >>>> Fax: +27-21-8085863 >>>> >>>> >>>> >>>> <TreeBASE 10367.zip> >>> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: youjun g. <you...@ya...> - 2010-04-01 00:02:44
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Bill, In treebase.org the server name in the phylowidget redirect url return "localhost:8080" because we have a Apache server in front of Tomcat, and Apache addressed the Tomact work this way. I think we have to use purl this time. Youjun On Wed, Mar 31, 2010 at 4:46 PM, Jon Auman <jon...@du...> wrote: > I've redeployed and bumped the timeout to 15 minutes. > -jon > > On Mar 31, 2010, at 3:29 PM, William Piel wrote: > > > Hi all, > > Can we do a new build on production? (and dev or stage, if you have time) > > Youjun recently fixed the delete-tree function, and that will be useful for > this guy's issue (see below). Also Youjun fixed the MacFirefox-PhyloWidget > problem on the browse side of the equation. For that, we now pass the tree > to the latest version of phylowidget stored on the phylowidget.org website > (which doesn't have a problem with Mac-Firefox). > > We still have a problem with MacFirefox-PhyloWidget on the Submit side, but > that can't be solved just by pointing to the latest copy on > phylowidget.org because we have made custom changes to the code (for > saving rerooted trees back the database). > > Finally, Michael Pirie's problem (below) seems to be the result of a > time-out on headless-Mesquite ingest. Can we increase the time allotted to > this process so as to avoid the time-out? (And, I should mention that when I > deleted his extra matrix, I also got a proxy-timeout problem -- but when I > came back to the submission, the matrix had been deleted. So again, the > functions appear to go to completion eventually even though the browser > shows a proxy error. If we could avoid the timeout, it would be better). > > Bill > > > > On Mar 31, 2010, at 3:18 PM, William Piel wrote: > > Dear Michael Pirie: > > > I think that the proxy error came from a time-out because the parser was > taking too long to commit the inserts (e.g. 298 x 11810 = 3,519,380 inserts, > not including all the other bits) -- but the inserts happened anyway despite > the time-out. And it looks like you backed-up and re-clicked, so there were > two matrices and two sets of trees. I deleted one of the matrices -- but I > don't want to delete the extra set of trees until we've done a rebuild on > our deployment (we recently fixed some code having to do with deleting > trees). By tomorrow, feel free to delete the extra set of trees. > > > So everything looks okay, despite the fact that the ingest did a time-out > on you. I'm going to suggest that our server gets reset to allow for longer > ingest times. > > > regards, > > > Bill > > > > On Mar 31, 2010, at 10:54 AM, Michael D. Pirie via RT wrote: > > > > Wed Mar 31 10:54:10 2010: Request 7708 was acted upon. > > Transaction: Ticket created by mp...@su... > > Queue: Treebase-help > > Subject: File upload problem submission 10367 > > Owner: Nobody > > Requestors: mp...@su... > > Status: new > > Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7708 > > > > > Dear Sir/Madam, > > I get the following error when attempting to upload a file to my > > submission 10367: > > > > Proxy Error > > > The proxy server received an invalid response from an upstream server. > > The proxy server could not handle the request POST > > /treebase-web/user/uploadFile.html. > > > Reason: Error reading from remote server > > > Apache/2.2.3 (CentOS) Server at www.treebase.org Port 80 > > > > I'm attaching a zipped copy of the file - would it be possible to add > > this for me? > > Thanks and best wishes, > > > -- > > Dr Michael D. Pirie > > Department of Biochemistry > > University of Stellenbosch > > Private Bag X1, MATIELAND 7602 > > Stellenbosch, Western Cape > > South Africa > > > Tel: +27-21-8085841 > > Fax: +27-21-8085863 > > > > > <TreeBASE 10367.zip> > > > > > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: Jon A. <jon...@du...> - 2010-03-31 20:46:52
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I've redeployed and bumped the timeout to 15 minutes. -jon On Mar 31, 2010, at 3:29 PM, William Piel wrote: > > Hi all, > > Can we do a new build on production? (and dev or stage, if you have time) > > Youjun recently fixed the delete-tree function, and that will be useful for this guy's issue (see below). Also Youjun fixed the MacFirefox-PhyloWidget problem on the browse side of the equation. For that, we now pass the tree to the latest version of phylowidget stored on the phylowidget.org website (which doesn't have a problem with Mac-Firefox). > > We still have a problem with MacFirefox-PhyloWidget on the Submit side, but that can't be solved just by pointing to the latest copy on phylowidget.org because we have made custom changes to the code (for saving rerooted trees back the database). > > Finally, Michael Pirie's problem (below) seems to be the result of a time-out on headless-Mesquite ingest. Can we increase the time allotted to this process so as to avoid the time-out? (And, I should mention that when I deleted his extra matrix, I also got a proxy-timeout problem -- but when I came back to the submission, the matrix had been deleted. So again, the functions appear to go to completion eventually even though the browser shows a proxy error. If we could avoid the timeout, it would be better). > > Bill > > > > On Mar 31, 2010, at 3:18 PM, William Piel wrote: > >> Dear Michael Pirie: >> >> I think that the proxy error came from a time-out because the parser was taking too long to commit the inserts (e.g. 298 x 11810 = 3,519,380 inserts, not including all the other bits) -- but the inserts happened anyway despite the time-out. And it looks like you backed-up and re-clicked, so there were two matrices and two sets of trees. I deleted one of the matrices -- but I don't want to delete the extra set of trees until we've done a rebuild on our deployment (we recently fixed some code having to do with deleting trees). By tomorrow, feel free to delete the extra set of trees. >> >> So everything looks okay, despite the fact that the ingest did a time-out on you. I'm going to suggest that our server gets reset to allow for longer ingest times. >> >> regards, >> >> Bill >> >> >> On Mar 31, 2010, at 10:54 AM, Michael D. Pirie via RT wrote: >> >>> >>> Wed Mar 31 10:54:10 2010: Request 7708 was acted upon. >>> Transaction: Ticket created by mp...@su... >>> Queue: Treebase-help >>> Subject: File upload problem submission 10367 >>> Owner: Nobody >>> Requestors: mp...@su... >>> Status: new >>> Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7708 > >>> >>> >>> Dear Sir/Madam, >>> I get the following error when attempting to upload a file to my >>> submission 10367: >>> >>> >>> Proxy Error >>> >>> The proxy server received an invalid response from an upstream server. >>> The proxy server could not handle the request POST >>> /treebase-web/user/uploadFile.html. >>> >>> Reason: Error reading from remote server >>> >>> Apache/2.2.3 (CentOS) Server at www.treebase.org Port 80 >>> >>> >>> I'm attaching a zipped copy of the file - would it be possible to add >>> this for me? >>> Thanks and best wishes, >>> >>> -- >>> Dr Michael D. Pirie >>> Department of Biochemistry >>> University of Stellenbosch >>> Private Bag X1, MATIELAND 7602 >>> Stellenbosch, Western Cape >>> South Africa >>> >>> Tel: +27-21-8085841 >>> Fax: +27-21-8085863 >>> >>> >>> >>> <TreeBASE 10367.zip> >> > > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: William P. <wil...@ya...> - 2010-03-31 19:29:17
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Hi all, Can we do a new build on production? (and dev or stage, if you have time) Youjun recently fixed the delete-tree function, and that will be useful for this guy's issue (see below). Also Youjun fixed the MacFirefox-PhyloWidget problem on the browse side of the equation. For that, we now pass the tree to the latest version of phylowidget stored on the phylowidget.org website (which doesn't have a problem with Mac-Firefox). We still have a problem with MacFirefox-PhyloWidget on the Submit side, but that can't be solved just by pointing to the latest copy on phylowidget.org because we have made custom changes to the code (for saving rerooted trees back the database). Finally, Michael Pirie's problem (below) seems to be the result of a time-out on headless-Mesquite ingest. Can we increase the time allotted to this process so as to avoid the time-out? (And, I should mention that when I deleted his extra matrix, I also got a proxy-timeout problem -- but when I came back to the submission, the matrix had been deleted. So again, the functions appear to go to completion eventually even though the browser shows a proxy error. If we could avoid the timeout, it would be better). Bill On Mar 31, 2010, at 3:18 PM, William Piel wrote: > Dear Michael Pirie: > > I think that the proxy error came from a time-out because the parser was taking too long to commit the inserts (e.g. 298 x 11810 = 3,519,380 inserts, not including all the other bits) -- but the inserts happened anyway despite the time-out. And it looks like you backed-up and re-clicked, so there were two matrices and two sets of trees. I deleted one of the matrices -- but I don't want to delete the extra set of trees until we've done a rebuild on our deployment (we recently fixed some code having to do with deleting trees). By tomorrow, feel free to delete the extra set of trees. > > So everything looks okay, despite the fact that the ingest did a time-out on you. I'm going to suggest that our server gets reset to allow for longer ingest times. > > regards, > > Bill > > > On Mar 31, 2010, at 10:54 AM, Michael D. Pirie via RT wrote: > >> >> Wed Mar 31 10:54:10 2010: Request 7708 was acted upon. >> Transaction: Ticket created by mp...@su... >> Queue: Treebase-help >> Subject: File upload problem submission 10367 >> Owner: Nobody >> Requestors: mp...@su... >> Status: new >> Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7708 > >> >> >> Dear Sir/Madam, >> I get the following error when attempting to upload a file to my >> submission 10367: >> >> >> Proxy Error >> >> The proxy server received an invalid response from an upstream server. >> The proxy server could not handle the request POST >> /treebase-web/user/uploadFile.html. >> >> Reason: Error reading from remote server >> >> Apache/2.2.3 (CentOS) Server at www.treebase.org Port 80 >> >> >> I'm attaching a zipped copy of the file - would it be possible to add >> this for me? >> Thanks and best wishes, >> >> -- >> Dr Michael D. Pirie >> Department of Biochemistry >> University of Stellenbosch >> Private Bag X1, MATIELAND 7602 >> Stellenbosch, Western Cape >> South Africa >> >> Tel: +27-21-8085841 >> Fax: +27-21-8085863 >> >> >> >> <TreeBASE 10367.zip> > |
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From: William P. <wil...@ya...> - 2010-03-30 17:25:22
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The Firefox compatibility issue is still a problem, with some weird symptoms. If I'm in the office, I'm able to browser our local instance with PhyloWidget: http://130.132.27.212:8080/treebase-web/ But I cannot use PhyloWidget with the NESCent deployment. But if I'm at home, Firefox locks up when I try to access the 130.132.27.212 deployment. Perhaps this is because anything less than a super-fast connection causes some sort of collision in the various authentication/certification communication. (?) bp |
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From: Hilmar L. <hl...@ne...> - 2010-03-30 15:51:06
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You can look at http://demo.plhdb.org for an example. So yes, some kind of indicator of release, and an unequivocal identifier of the build that it was deployed from. -hilmar On Mar 30, 2010, at 9:39 AM, Rutger Vos wrote: > Sure, but maybe it's a starting point. Are we talking about the same > sort of principle where there is some point in the output produced by > the webapp where we (and other users) can see "release XXX, revision > YYY"? > > By the way, this would be nice to have both in html and in other > produced files, potentially. E.g. to diagnose the provenance of > inconsistencies in produced nexus/nexml/rdf. > > On Mon, Mar 29, 2010 at 11:06 PM, Hilmar Lapp <hl...@ne...> > wrote: >> Rutger - we really need a release identifier that is displayed, so >> users and >> everyone else can report it. A hidden svn revision will not solve >> this. >> >> -hilmar >> >> On Mar 29, 2010, at 6:00 PM, Rutger Vos wrote: >> >>> If you look in the html source of any page and you scroll all the >>> way >>> down to 'p class="footerLogo"' it will show the SVN revision of that >>> deployment. At least, this used to work back when MJD and I were >>> using >>> the 'publish' script, which used >>> >>> ${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/ >>> Version.java >>> as a little servlet to embed the SVN revision in the footer.jsp >>> (this >>> is done by deleting and then updating this version file). Perhaps >>> this >>> can be re-instated? >>> >>> On Mon, Mar 29, 2010 at 10:01 PM, Vladimir Gapeyev >>> <vla...@du...> wrote: >>>> >>>> On Mar 29, 2010, at 4:39 PM, Hilmar Lapp wrote: >>>> >>>> This should be in the tracker as a feature request already. Is it >>>> not? >>>> -hilmar >>>> On Mar 29, 2010, at 4:34 PM, Jon Auman wrote: >>>> >>>> I suggested to Vladimir last week that we should put a version and >>>> timestamp >>>> on the builds, like we do with nead.nescent.org. (ex. Version: >>>> 2.2.1 Built: 03/26/2010 12:43 PM ) >>>> Otherwise, how can we keep track of which version we are on? >>>> -Jon >>>> On Mar 29, 2010, at 4:31 PM, Hilmar Lapp wrote: >>>> >>>> I'll check and, if it is not there, will put a ticket for the >>>> suggestion, >>>> alongside tickets for a few other things we need to do here on the >>>> deployment side (restore the dev server; set up automatic builds, >>>> etc.). >>>> The 659 version will be deployed to production soon. >>>> --VG >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Download Intel® Parallel Studio Eval >>>> Try the new software tools for yourself. Speed compiling, find bugs >>>> proactively, and fine-tune applications for parallel performance. >>>> See why Intel Parallel Studio got high marks during beta. >>>> http://p.sf.net/sfu/intel-sw-dev >>>> _______________________________________________ >>>> Treebase-devel mailing list >>>> Tre...@li... >>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>> >>>> >>> >>> >>> >>> -- >>> Dr. Rutger A. Vos >>> School of Biological Sciences >>> Philip Lyle Building, Level 4 >>> University of Reading >>> Reading >>> RG6 6BX >>> United Kingdom >>> Tel: +44 (0) 118 378 7535 >>> http://www.nexml.org >>> http://rutgervos.blogspot.com >>> >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William H. P. <pi...@tr...> - 2010-03-30 15:46:27
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Apparently, compatibility with IE8 in the analysis section is still an issue. bp Begin forwarded message: > From: "Diego Salariato" <dsa...@da...> > Date: March 30, 2010 10:16:29 AM EDT > To: "'William Halliday Piel'" <pi...@tr...> > Subject: RE: I need help with my submission please (Submission ID 10349) > > I'm using IE 8.0.6001.18702 and Microsoft Windows XP professional 5.1.2600 > service pack 3, however I had the same problem with IE 8 and Windows vista. > The problem is that the input and output boxes don't show me any matrix or > tree available to assign in the analysis. Thank you a lot Bill!!! > > Diego > > -----Mensaje original----- > De: William Halliday Piel [mailto:pi...@tr...] > Enviado el: Martes, 30 de Marzo de 2010 11:04 > Para: Diego Salariato > Asunto: Re: I need help with my submission please (Submission ID 10349) > > > On Mar 30, 2010, at 7:48 AM, Diego Salariato wrote: > >> I need the treebase number urgently to insert in the final draft of our > paper. > > The permanent "number" is this whole string: > > http://purl.org/phylo/treebase/phylows/study/TB2:S10359 > > It serves a both a unique number/string and an URL that takes people > directly to your data. > > ... and it's now published (an anonymous user should be able to click on > this link and arrive at your data). > > Adding input and output items was not a problem for me -- can you tell me > what your browser & operating system is? We have been having some trouble > with IE 6 and 7, although we should be okay with IE 8. > > regards, > > Bill |
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From: Rutger V. <rut...@gm...> - 2010-03-30 13:39:45
|
Sure, but maybe it's a starting point. Are we talking about the same
sort of principle where there is some point in the output produced by
the webapp where we (and other users) can see "release XXX, revision
YYY"?
By the way, this would be nice to have both in html and in other
produced files, potentially. E.g. to diagnose the provenance of
inconsistencies in produced nexus/nexml/rdf.
On Mon, Mar 29, 2010 at 11:06 PM, Hilmar Lapp <hl...@ne...> wrote:
> Rutger - we really need a release identifier that is displayed, so users and
> everyone else can report it. A hidden svn revision will not solve this.
>
> -hilmar
>
> On Mar 29, 2010, at 6:00 PM, Rutger Vos wrote:
>
>> If you look in the html source of any page and you scroll all the way
>> down to 'p class="footerLogo"' it will show the SVN revision of that
>> deployment. At least, this used to work back when MJD and I were using
>> the 'publish' script, which used
>>
>> ${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/Version.java
>> as a little servlet to embed the SVN revision in the footer.jsp (this
>> is done by deleting and then updating this version file). Perhaps this
>> can be re-instated?
>>
>> On Mon, Mar 29, 2010 at 10:01 PM, Vladimir Gapeyev
>> <vla...@du...> wrote:
>>>
>>> On Mar 29, 2010, at 4:39 PM, Hilmar Lapp wrote:
>>>
>>> This should be in the tracker as a feature request already. Is it not?
>>> -hilmar
>>> On Mar 29, 2010, at 4:34 PM, Jon Auman wrote:
>>>
>>> I suggested to Vladimir last week that we should put a version and
>>> timestamp
>>> on the builds, like we do with nead.nescent.org. (ex. Version:
>>> 2.2.1 Built: 03/26/2010 12:43 PM )
>>> Otherwise, how can we keep track of which version we are on?
>>> -Jon
>>> On Mar 29, 2010, at 4:31 PM, Hilmar Lapp wrote:
>>>
>>> I'll check and, if it is not there, will put a ticket for the suggestion,
>>> alongside tickets for a few other things we need to do here on the
>>> deployment side (restore the dev server; set up automatic builds, etc.).
>>> The 659 version will be deployed to production soon.
>>> --VG
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download Intel® Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev
>>> _______________________________________________
>>> Treebase-devel mailing list
>>> Tre...@li...
>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>>
>>>
>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> School of Biological Sciences
>> Philip Lyle Building, Level 4
>> University of Reading
>> Reading
>> RG6 6BX
>> United Kingdom
>> Tel: +44 (0) 118 378 7535
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>
--
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com
|
|
From: Hilmar L. <hl...@ne...> - 2010-03-29 22:06:34
|
Rutger - we really need a release identifier that is displayed, so
users and everyone else can report it. A hidden svn revision will not
solve this.
-hilmar
On Mar 29, 2010, at 6:00 PM, Rutger Vos wrote:
> If you look in the html source of any page and you scroll all the way
> down to 'p class="footerLogo"' it will show the SVN revision of that
> deployment. At least, this used to work back when MJD and I were using
> the 'publish' script, which used
> ${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/
> Version.java
> as a little servlet to embed the SVN revision in the footer.jsp (this
> is done by deleting and then updating this version file). Perhaps this
> can be re-instated?
>
> On Mon, Mar 29, 2010 at 10:01 PM, Vladimir Gapeyev
> <vla...@du...> wrote:
>>
>> On Mar 29, 2010, at 4:39 PM, Hilmar Lapp wrote:
>>
>> This should be in the tracker as a feature request already. Is it
>> not?
>> -hilmar
>> On Mar 29, 2010, at 4:34 PM, Jon Auman wrote:
>>
>> I suggested to Vladimir last week that we should put a version and
>> timestamp
>> on the builds, like we do with nead.nescent.org. (ex. Version:
>> 2.2.1 Built: 03/26/2010 12:43 PM )
>> Otherwise, how can we keep track of which version we are on?
>> -Jon
>> On Mar 29, 2010, at 4:31 PM, Hilmar Lapp wrote:
>>
>> I'll check and, if it is not there, will put a ticket for the
>> suggestion,
>> alongside tickets for a few other things we need to do here on the
>> deployment side (restore the dev server; set up automatic builds,
>> etc.).
>> The 659 version will be deployed to production soon.
>> --VG
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>>
>
>
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
===========================================================
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