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Update notes for 2017-12-19

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Alan Orth 2017-12-19 18:33:19 +02:00
parent cfc88fc491
commit b6f2841ca7
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
4 changed files with 202 additions and 14 deletions
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90
content/post/2017-12.md
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@ -529,4 +529,94 @@ $ cp ~/dspace/lib/postgresql-9.1-901-1.jdbc4.jar /usr/local/opt/tomcat@7/libexec
- a `<ResourceLink>` defined in each web application's context XML - a `<ResourceLink>` defined in each web application's context XML
- unset the `db.url`, `db.username`, and `db.password` parameters in dspace.cfg - unset the `db.url`, `db.username`, and `db.password` parameters in dspace.cfg
- set the `db.jndi` in dspace.cfg to the name specified in the web application context - set the `db.jndi` in dspace.cfg to the name specified in the web application context
- After adding the `Resource` to _server.xml_ on Ubuntu I get this in Catalina's logs:
```
SEVERE: Unable to create initial connections of pool.
java.sql.SQLException: org.postgresql.Driver
...
Caused by: java.lang.ClassNotFoundException: org.postgresql.Driver
```
- The username and password are correct, but maybe I need to copy the fucking lib there too?
- I tried installing Ubuntu's `libpostgresql-jdbc-java` package but Tomcat still can't find the class
- Let me try to symlink the lib into Tomcat's libs:
```
# ln -sv /usr/share/java/postgresql.jar /usr/share/tomcat7/lib
```
- Now Tomcat starts but the localhost container has errors:
```
SEVERE: Exception sending context initialized event to listener instance of class org.dspace.app.util.DSpaceContextListener
java.lang.AbstractMethodError: Method org/postgresql/jdbc3/Jdbc3ResultSet.isClosed()Z is abstract
```
- Could be a version issue or something since the Ubuntu package provides 9.2 and DSpace's are 9.1...
- Let me try to remove it and copy in DSpace's:
```
# rm /usr/share/tomcat7/lib/postgresql.jar
# cp [dspace]/webapps/xmlui/WEB-INF/lib/postgresql-9.1-901-1.jdbc4.jar /usr/share/tomcat7/lib/
```
- Wow, I think that actually works...
- I wonder if I could get the JDBC driver from postgresql.org instead of relying on the one from the DSpace build: https://jdbc.postgresql.org/
- I notice our version is 9.1-901, which isn't even available anymore! The latest in the archived versions is 9.1-903
- Also, since I commented out all the db parameters in DSpace.cfg, how does the command line `dspace` tool work?
- Let's try the upstream JDBC driver first:
```
# rm /usr/share/tomcat7/lib/postgresql-9.1-901-1.jdbc4.jar
# wget https://jdbc.postgresql.org/download/postgresql-42.1.4.jar -O /usr/share/tomcat7/lib/postgresql-42.1.4.jar
```
- DSpace command line fails unless db settings are present in dspace.cfg:
```
$ dspace database info
Caught exception:
java.sql.SQLException: java.lang.ClassNotFoundException:
at org.dspace.storage.rdbms.DataSourceInit.getDatasource(DataSourceInit.java:171)
at org.dspace.storage.rdbms.DatabaseManager.initDataSource(DatabaseManager.java:1438)
at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:81)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
Caused by: java.lang.ClassNotFoundException:
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.dspace.storage.rdbms.DataSourceInit.getDatasource(DataSourceInit.java:41)
... 8 more
```
- And in the logs:
```
2017-12-19 18:26:56,971 ERROR org.dspace.storage.rdbms.DatabaseManager @ Error retrieving JNDI context: jdbc/dspace
javax.naming.NoInitialContextException: Need to specify class name in environment or system property, or as an applet parameter, or in an application resource file: java.naming.factory.initial
at javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:662)
at javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:313)
at javax.naming.InitialContext.getURLOrDefaultInitCtx(InitialContext.java:350)
at javax.naming.InitialContext.lookup(InitialContext.java:417)
at org.dspace.storage.rdbms.DatabaseManager.initDataSource(DatabaseManager.java:1413)
at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:81)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
2017-12-19 18:26:56,983 INFO org.dspace.storage.rdbms.DatabaseManager @ Unable to locate JNDI dataSource: jdbc/dspace
2017-12-19 18:26:56,983 INFO org.dspace.storage.rdbms.DatabaseManager @ Falling back to creating own Database pool
2017-12-19 18:26:56,992 WARN org.dspace.core.ConfigurationManager @ Warning: Number format error in property: db.maxconnections
2017-12-19 18:26:56,992 WARN org.dspace.core.ConfigurationManager @ Warning: Number format error in property: db.maxwait
2017-12-19 18:26:56,993 WARN org.dspace.core.ConfigurationManager @ Warning: Number format error in property: db.maxidle
```
- If I add the db values back to dspace.cfg the `dspace database info` command succeeds but the log still shows errors retrieving the JNDI connection
- Perhaps something to report to the dspace-tech mailing list when I finally send my comments

104
public/2017-12/index.html
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@ -23,7 +23,7 @@ The list of connections to XMLUI and REST API for today:
<meta property="article:published_time" content="2017-12-01T13:53:54&#43;03:00"/> <meta property="article:published_time" content="2017-12-01T13:53:54&#43;03:00"/>
<meta property="article:modified_time" content="2017-12-19T10:38:57&#43;02:00"/> <meta property="article:modified_time" content="2017-12-19T14:10:16&#43;02:00"/>
@ -56,9 +56,9 @@ The list of connections to XMLUI and REST API for today:
"@type": "BlogPosting", "@type": "BlogPosting",
"headline": "December, 2017", "headline": "December, 2017",
"url": "https://alanorth.github.io/cgspace-notes/2017-12/", "url": "https://alanorth.github.io/cgspace-notes/2017-12/",
"wordCount": "2915", "wordCount": "3342",
"datePublished": "2017-12-01T13:53:54&#43;03:00", "datePublished": "2017-12-01T13:53:54&#43;03:00",
"dateModified": "2017-12-19T10:38:57&#43;02:00", "dateModified": "2017-12-19T14:10:16&#43;02:00",
"author": { "author": {
"@type": "Person", "@type": "Person",
"name": "Alan Orth" "name": "Alan Orth"
@ -708,6 +708,104 @@ javax.naming.NameNotFoundException: Name [jdbc/dspace] is not bound in this Cont
<li>unset the <code>db.url</code>, <code>db.username</code>, and <code>db.password</code> parameters in dspace.cfg</li> <li>unset the <code>db.url</code>, <code>db.username</code>, and <code>db.password</code> parameters in dspace.cfg</li>
<li>set the <code>db.jndi</code> in dspace.cfg to the name specified in the web application context</li> <li>set the <code>db.jndi</code> in dspace.cfg to the name specified in the web application context</li>
</ul></li> </ul></li>
<li>After adding the <code>Resource</code> to <em>server.xml</em> on Ubuntu I get this in Catalina&rsquo;s logs:</li>
</ul>
<pre><code>SEVERE: Unable to create initial connections of pool.
java.sql.SQLException: org.postgresql.Driver
...
Caused by: java.lang.ClassNotFoundException: org.postgresql.Driver
</code></pre>
<ul>
<li>The username and password are correct, but maybe I need to copy the fucking lib there too?</li>
<li>I tried installing Ubuntu&rsquo;s <code>libpostgresql-jdbc-java</code> package but Tomcat still can&rsquo;t find the class</li>
<li>Let me try to symlink the lib into Tomcat&rsquo;s libs:</li>
</ul>
<pre><code># ln -sv /usr/share/java/postgresql.jar /usr/share/tomcat7/lib
</code></pre>
<ul>
<li>Now Tomcat starts but the localhost container has errors:</li>
</ul>
<pre><code>SEVERE: Exception sending context initialized event to listener instance of class org.dspace.app.util.DSpaceContextListener
java.lang.AbstractMethodError: Method org/postgresql/jdbc3/Jdbc3ResultSet.isClosed()Z is abstract
</code></pre>
<ul>
<li>Could be a version issue or something since the Ubuntu package provides 9.2 and DSpace&rsquo;s are 9.1&hellip;</li>
<li>Let me try to remove it and copy in DSpace&rsquo;s:</li>
</ul>
<pre><code># rm /usr/share/tomcat7/lib/postgresql.jar
# cp [dspace]/webapps/xmlui/WEB-INF/lib/postgresql-9.1-901-1.jdbc4.jar /usr/share/tomcat7/lib/
</code></pre>
<ul>
<li>Wow, I think that actually works&hellip;</li>
<li>I wonder if I could get the JDBC driver from postgresql.org instead of relying on the one from the DSpace build: <a href="https://jdbc.postgresql.org/">https://jdbc.postgresql.org/</a></li>
<li>I notice our version is 9.1-901, which isn&rsquo;t even available anymore! The latest in the archived versions is 9.1-903</li>
<li>Also, since I commented out all the db parameters in DSpace.cfg, how does the command line <code>dspace</code> tool work?</li>
<li>Let&rsquo;s try the upstream JDBC driver first:</li>
</ul>
<pre><code># rm /usr/share/tomcat7/lib/postgresql-9.1-901-1.jdbc4.jar
# wget https://jdbc.postgresql.org/download/postgresql-42.1.4.jar -O /usr/share/tomcat7/lib/postgresql-42.1.4.jar
</code></pre>
<ul>
<li>DSpace command line fails unless db settings are present in dspace.cfg:</li>
</ul>
<pre><code>$ dspace database info
Caught exception:
java.sql.SQLException: java.lang.ClassNotFoundException:
at org.dspace.storage.rdbms.DataSourceInit.getDatasource(DataSourceInit.java:171)
at org.dspace.storage.rdbms.DatabaseManager.initDataSource(DatabaseManager.java:1438)
at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:81)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
Caused by: java.lang.ClassNotFoundException:
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.dspace.storage.rdbms.DataSourceInit.getDatasource(DataSourceInit.java:41)
... 8 more
</code></pre>
<ul>
<li>And in the logs:</li>
</ul>
<pre><code>2017-12-19 18:26:56,971 ERROR org.dspace.storage.rdbms.DatabaseManager @ Error retrieving JNDI context: jdbc/dspace
javax.naming.NoInitialContextException: Need to specify class name in environment or system property, or as an applet parameter, or in an application resource file: java.naming.factory.initial
at javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:662)
at javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:313)
at javax.naming.InitialContext.getURLOrDefaultInitCtx(InitialContext.java:350)
at javax.naming.InitialContext.lookup(InitialContext.java:417)
at org.dspace.storage.rdbms.DatabaseManager.initDataSource(DatabaseManager.java:1413)
at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:81)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
2017-12-19 18:26:56,983 INFO org.dspace.storage.rdbms.DatabaseManager @ Unable to locate JNDI dataSource: jdbc/dspace
2017-12-19 18:26:56,983 INFO org.dspace.storage.rdbms.DatabaseManager @ Falling back to creating own Database pool
2017-12-19 18:26:56,992 WARN org.dspace.core.ConfigurationManager @ Warning: Number format error in property: db.maxconnections
2017-12-19 18:26:56,992 WARN org.dspace.core.ConfigurationManager @ Warning: Number format error in property: db.maxwait
2017-12-19 18:26:56,993 WARN org.dspace.core.ConfigurationManager @ Warning: Number format error in property: db.maxidle
</code></pre>
<ul>
<li>If I add the db values back to dspace.cfg the <code>dspace database info</code> command succeeds but the log still shows errors retrieving the JNDI connection</li>
<li>Perhaps something to report to the dspace-tech mailing list when I finally send my comments</li>
</ul> </ul>

2
public/robots.txt
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@ -30,7 +30,7 @@ Disallow: /cgspace-notes/2015-12/
Disallow: /cgspace-notes/2015-11/ Disallow: /cgspace-notes/2015-11/
Disallow: /cgspace-notes/ Disallow: /cgspace-notes/
Disallow: /cgspace-notes/categories/ Disallow: /cgspace-notes/categories/
Disallow: /cgspace-notes/categories/notes/
Disallow: /cgspace-notes/tags/notes/ Disallow: /cgspace-notes/tags/notes/
Disallow: /cgspace-notes/categories/notes/
Disallow: /cgspace-notes/post/ Disallow: /cgspace-notes/post/
Disallow: /cgspace-notes/tags/ Disallow: /cgspace-notes/tags/

20
public/sitemap.xml
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@ -4,7 +4,7 @@
<url> <url>
<loc>https://alanorth.github.io/cgspace-notes/2017-12/</loc> <loc>https://alanorth.github.io/cgspace-notes/2017-12/</loc>
<lastmod>2017-12-19T10:38:57+02:00</lastmod> <lastmod>2017-12-19T14:10:16+02:00</lastmod>
</url> </url>
<url> <url>
@ -139,7 +139,7 @@
<url> <url>
<loc>https://alanorth.github.io/cgspace-notes/</loc> <loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2017-12-19T10:38:57+02:00</lastmod> <lastmod>2017-12-19T14:10:16+02:00</lastmod>
<priority>0</priority> <priority>0</priority>
</url> </url>
@ -148,27 +148,27 @@
<priority>0</priority> <priority>0</priority>
</url> </url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2017-12-19T14:10:16+02:00</lastmod>
<priority>0</priority>
</url>
<url> <url>
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc> <loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
<lastmod>2017-09-28T12:00:49+03:00</lastmod> <lastmod>2017-09-28T12:00:49+03:00</lastmod>
<priority>0</priority> <priority>0</priority>
</url> </url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2017-12-19T10:38:57+02:00</lastmod>
<priority>0</priority>
</url>
<url> <url>
<loc>https://alanorth.github.io/cgspace-notes/post/</loc> <loc>https://alanorth.github.io/cgspace-notes/post/</loc>
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<priority>0</priority> <priority>0</priority>
</url> </url>
<url> <url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc> <loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
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