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Update notes for 2019-03-15

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Alan Orth 2019-03-15 15:29:11 +02:00
parent 2807f179ba
commit bd7570e9f8
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
3 changed files with 266 additions and 8 deletions
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126
content/posts/2019-03.md
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@ -182,4 +182,130 @@ $ grep -oE '201[89]' /tmp/*.csv | sort -u
- Run all system updates and reboot linode20
- Follow up with Felix from Earlham to see if he's done testing DSpace Test with COPO so I can re-sync the server from CGSpace
## 2019-03-15
- CGSpace (linode18) has the blank page error again
- I'm not sure if it's related, but I see the following error in DSpace's log:
```
2019-03-15 14:09:32,685 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error -
java.sql.SQLException: Connection org.postgresql.jdbc.PgConnection@55ba10b5 is closed.
at org.apache.tomcat.dbcp.dbcp.DelegatingConnection.checkOpen(DelegatingConnection.java:398)
at org.apache.tomcat.dbcp.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:279)
at org.apache.tomcat.dbcp.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313)
at org.dspace.storage.rdbms.DatabaseManager.queryTable(DatabaseManager.java:220)
at org.dspace.authorize.AuthorizeManager.getPolicies(AuthorizeManager.java:612)
at org.dspace.content.crosswalk.METSRightsCrosswalk.disseminateElement(METSRightsCrosswalk.java:154)
at org.dspace.content.crosswalk.METSRightsCrosswalk.disseminateElement(METSRightsCrosswalk.java:300)
```
- Interestingly, I see a pattern of these errors increasing, with single and double digit numbers over the past month, but spikes of over 1,000 today, yesterday, and on 2019-03-08, which was exactly the first time we saw this blank page error recently
```
# grep -c 'SQL QueryTable Error' dspace.log.2019-0*
dspace.log.2019-02-01:6
dspace.log.2019-02-02:1
dspace.log.2019-02-03:0
dspace.log.2019-02-04:4
dspace.log.2019-02-05:4
dspace.log.2019-02-06:3
dspace.log.2019-02-07:0
dspace.log.2019-02-08:2
dspace.log.2019-02-09:0
dspace.log.2019-02-10:0
dspace.log.2019-02-11:1
dspace.log.2019-02-12:2
dspace.log.2019-02-13:1
dspace.log.2019-02-14:74
dspace.log.2019-02-15:47
dspace.log.2019-02-16:44
dspace.log.2019-02-17:37
dspace.log.2019-02-18:191
dspace.log.2019-02-19:51
dspace.log.2019-02-20:32
dspace.log.2019-02-21:64
dspace.log.2019-02-22:48
dspace.log.2019-02-23:32
dspace.log.2019-02-24:25
dspace.log.2019-02-25:53
dspace.log.2019-02-26:63
dspace.log.2019-02-27:28
dspace.log.2019-02-28:31
dspace.log.2019-03-01:29
dspace.log.2019-03-02:24
dspace.log.2019-03-03:41
dspace.log.2019-03-04:25
dspace.log.2019-03-05:48
dspace.log.2019-03-06:48
dspace.log.2019-03-07:42
dspace.log.2019-03-08:1781
dspace.log.2019-03-09:22
dspace.log.2019-03-10:23
dspace.log.2019-03-11:52
dspace.log.2019-03-12:474
dspace.log.2019-03-13:37
dspace.log.2019-03-14:924
dspace.log.2019-03-15:770
```
- There are not too many connections currently in PostgreSQL:
```
$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
6 dspaceApi
10 dspaceCli
15 dspaceWeb
```
- I didn't see anything interesting in the PostgreSQL logs, though this stack trace from the Tomcat logs (in the systemd journal) from earlier today *might* be related?
```
SEVERE: Servlet.service() for servlet [spring] in context with path [] threw exception [org.springframework.web.util.NestedServletException: Request processing failed; nested exception is java.util.EmptyStackException] with root cause
java.util.EmptyStackException
at java.util.Stack.peek(Stack.java:102)
at java.util.Stack.pop(Stack.java:84)
at org.apache.cocoon.callstack.CallStack.leave(CallStack.java:54)
at org.apache.cocoon.servletservice.CallStackHelper.leaveServlet(CallStackHelper.java:85)
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:484)
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:443)
at org.apache.cocoon.servletservice.spring.ServletFactoryBean$ServiceInterceptor.invoke(ServletFactoryBean.java:264)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy90.service(Unknown Source)
at org.dspace.springmvc.CocoonView.render(CocoonView.java:113)
at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1180)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:950)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:778)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.rdf.negotiation.NegotiationFilter.doFilter(NegotiationFilter.java:59)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:494)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:104)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:234)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:1025)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1137)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:317)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
```
- For now I will just restart Tomcat...
<!-- vim: set sw=2 ts=2: -->

138
docs/2019-03/index.html
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@ -25,7 +25,7 @@ I think I will need to ask Udana to re-copy and paste the abstracts with more ca
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-03/" />
<meta property="article:published_time" content="2019-03-01T12:16:30&#43;01:00"/>
<meta property="article:modified_time" content="2019-03-14T20:18:29&#43;02:00"/>
<meta property="article:modified_time" content="2019-03-14T22:15:10&#43;02:00"/>
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="March, 2019"/>
@ -55,9 +55,9 @@ I think I will need to ask Udana to re-copy and paste the abstracts with more ca
"@type": "BlogPosting",
"headline": "March, 2019",
"url": "https://alanorth.github.io/cgspace-notes/2019-03/",
"wordCount": "1471",
"wordCount": "1790",
"datePublished": "2019-03-01T12:16:30&#43;01:00",
"dateModified": "2019-03-14T20:18:29&#43;02:00",
"dateModified": "2019-03-14T22:15:10&#43;02:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -352,6 +352,138 @@ done
<li>Follow up with Felix from Earlham to see if he&rsquo;s done testing DSpace Test with COPO so I can re-sync the server from CGSpace</li>
</ul>
<h2 id="2019-03-15">2019-03-15</h2>
<ul>
<li>CGSpace (linode18) has the blank page error again</li>
<li>I&rsquo;m not sure if it&rsquo;s related, but I see the following error in DSpace&rsquo;s log:</li>
</ul>
<pre><code>2019-03-15 14:09:32,685 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error -
java.sql.SQLException: Connection org.postgresql.jdbc.PgConnection@55ba10b5 is closed.
at org.apache.tomcat.dbcp.dbcp.DelegatingConnection.checkOpen(DelegatingConnection.java:398)
at org.apache.tomcat.dbcp.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:279)
at org.apache.tomcat.dbcp.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313)
at org.dspace.storage.rdbms.DatabaseManager.queryTable(DatabaseManager.java:220)
at org.dspace.authorize.AuthorizeManager.getPolicies(AuthorizeManager.java:612)
at org.dspace.content.crosswalk.METSRightsCrosswalk.disseminateElement(METSRightsCrosswalk.java:154)
at org.dspace.content.crosswalk.METSRightsCrosswalk.disseminateElement(METSRightsCrosswalk.java:300)
</code></pre>
<ul>
<li>Interestingly, I see a pattern of these errors increasing, with single and double digit numbers over the past month, but spikes of over 1,000 today, yesterday, and on 2019-03-08, which was exactly the first time we saw this blank page error recently</li>
</ul>
<pre><code># grep -c 'SQL QueryTable Error' dspace.log.2019-0*
dspace.log.2019-02-01:6
dspace.log.2019-02-02:1
dspace.log.2019-02-03:0
dspace.log.2019-02-04:4
dspace.log.2019-02-05:4
dspace.log.2019-02-06:3
dspace.log.2019-02-07:0
dspace.log.2019-02-08:2
dspace.log.2019-02-09:0
dspace.log.2019-02-10:0
dspace.log.2019-02-11:1
dspace.log.2019-02-12:2
dspace.log.2019-02-13:1
dspace.log.2019-02-14:74
dspace.log.2019-02-15:47
dspace.log.2019-02-16:44
dspace.log.2019-02-17:37
dspace.log.2019-02-18:191
dspace.log.2019-02-19:51
dspace.log.2019-02-20:32
dspace.log.2019-02-21:64
dspace.log.2019-02-22:48
dspace.log.2019-02-23:32
dspace.log.2019-02-24:25
dspace.log.2019-02-25:53
dspace.log.2019-02-26:63
dspace.log.2019-02-27:28
dspace.log.2019-02-28:31
dspace.log.2019-03-01:29
dspace.log.2019-03-02:24
dspace.log.2019-03-03:41
dspace.log.2019-03-04:25
dspace.log.2019-03-05:48
dspace.log.2019-03-06:48
dspace.log.2019-03-07:42
dspace.log.2019-03-08:1781
dspace.log.2019-03-09:22
dspace.log.2019-03-10:23
dspace.log.2019-03-11:52
dspace.log.2019-03-12:474
dspace.log.2019-03-13:37
dspace.log.2019-03-14:924
dspace.log.2019-03-15:770
</code></pre>
<ul>
<li>There are not too many connections currently in PostgreSQL:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
6 dspaceApi
10 dspaceCli
15 dspaceWeb
</code></pre>
<ul>
<li>I didn&rsquo;t see anything interesting in the PostgreSQL logs, though this stack trace from the Tomcat logs (in the systemd journal) from earlier today <em>might</em> be related?</li>
</ul>
<pre><code>SEVERE: Servlet.service() for servlet [spring] in context with path [] threw exception [org.springframework.web.util.NestedServletException: Request processing failed; nested exception is java.util.EmptyStackException] with root cause
java.util.EmptyStackException
at java.util.Stack.peek(Stack.java:102)
at java.util.Stack.pop(Stack.java:84)
at org.apache.cocoon.callstack.CallStack.leave(CallStack.java:54)
at org.apache.cocoon.servletservice.CallStackHelper.leaveServlet(CallStackHelper.java:85)
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:484)
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:443)
at org.apache.cocoon.servletservice.spring.ServletFactoryBean$ServiceInterceptor.invoke(ServletFactoryBean.java:264)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy90.service(Unknown Source)
at org.dspace.springmvc.CocoonView.render(CocoonView.java:113)
at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1180)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:950)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:778)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.rdf.negotiation.NegotiationFilter.doFilter(NegotiationFilter.java:59)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:494)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:104)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:234)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:1025)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1137)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:317)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
</code></pre>
<ul>
<li>For now I will just restart Tomcat&hellip;</li>
</ul>
<!-- vim: set sw=2 ts=2: -->

10
docs/sitemap.xml
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@ -4,7 +4,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/2019-03/</loc>
<lastmod>2019-03-14T20:18:29+02:00</lastmod>
<lastmod>2019-03-14T22:15:10+02:00</lastmod>
</url>
<url>
@ -214,7 +214,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2019-03-14T20:18:29+02:00</lastmod>
<lastmod>2019-03-14T22:15:10+02:00</lastmod>
<priority>0</priority>
</url>
@ -225,7 +225,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2019-03-14T20:18:29+02:00</lastmod>
<lastmod>2019-03-14T22:15:10+02:00</lastmod>
<priority>0</priority>
</url>
@ -237,13 +237,13 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
<lastmod>2019-03-14T20:18:29+02:00</lastmod>
<lastmod>2019-03-14T22:15:10+02:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
<lastmod>2019-03-14T20:18:29+02:00</lastmod>
<lastmod>2019-03-14T22:15:10+02:00</lastmod>
<priority>0</priority>
</url>