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Add notes for 2018-01-10

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Alan Orth 2018-01-10 09:39:16 +02:00
parent 13460b8466
commit 727c761af4
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
3 changed files with 197 additions and 8 deletions
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92
content/post/2018-01.md
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@ -281,3 +281,95 @@ org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError:
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv;
COPY 4515
```
## 2018-01-10
- I looked to see what happened to this year's Solr statistics sharding task that should have run on 2018-01-01 and of course it failed:
```
Moving: 81742 into core statistics-2010
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2010
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2010
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2243)
at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
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: org.apache.http.client.ClientProtocolException
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
... 10 more
Caused by: org.apache.http.client.NonRepeatableRequestException: Cannot retry request with a non-repeatable request entity. The cause lists the reason the original request failed.
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:659)
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:487)
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
... 14 more
Caused by: java.net.SocketException: Connection reset
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:115)
at java.net.SocketOutputStream.write(SocketOutputStream.java:155)
at org.apache.http.impl.io.AbstractSessionOutputBuffer.flushBuffer(AbstractSessionOutputBuffer.java:159)
at org.apache.http.impl.io.AbstractSessionOutputBuffer.write(AbstractSessionOutputBuffer.java:179)
at org.apache.http.impl.io.ChunkedOutputStream.flushCacheWithAppend(ChunkedOutputStream.java:124)
at org.apache.http.impl.io.ChunkedOutputStream.write(ChunkedOutputStream.java:181)
at org.apache.http.entity.InputStreamEntity.writeTo(InputStreamEntity.java:132)
at org.apache.http.entity.HttpEntityWrapper.writeTo(HttpEntityWrapper.java:89)
at org.apache.http.impl.client.EntityEnclosingRequestWrapper$EntityWrapper.writeTo(EntityEnclosingRequestWrapper.java:108)
at org.apache.http.impl.entity.EntitySerializer.serialize(EntitySerializer.java:117)
at org.apache.http.impl.AbstractHttpClientConnection.sendRequestEntity(AbstractHttpClientConnection.java:265)
at org.apache.http.impl.conn.ManagedClientConnectionImpl.sendRequestEntity(ManagedClientConnectionImpl.java:203)
at org.apache.http.protocol.HttpRequestExecutor.doSendRequest(HttpRequestExecutor.java:236)
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:121)
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:685)
... 16 more
```
- DSpace Test has the same error but with creating the 2017 core:
```
Moving: 2243021 into core statistics-2017
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2017
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2017
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2243)
at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
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: org.apache.http.client.ClientProtocolException
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
... 10 more
```
- There is interesting documentation about this on the DSpace Wiki: https://wiki.duraspace.org/display/DSDOC5x/SOLR+Statistics+Maintenance#SOLRStatisticsMaintenance-SolrShardingByYear
- I'm looking to see maybe if we're hitting the issues mentioned in [DS-2212](https://jira.duraspace.org/browse/DS-2212) that were apparently fixed in DSpace 5.2
- I can apparently search for records in the Solr stats core that have an empty `owningColl` field using this in the Solr admin query: `-owningColl:*`
- On CGSpace I see 48,000,000 records that have an `owningColl` field and 34,000,000 that don't:
```
$ http 'http://localhost:3000/solr/statistics/select?q=owningColl%3A*&wt=json&indent=true' | grep numFound
"response":{"numFound":48476327,"start":0,"docs":[
$ http 'http://localhost:3000/solr/statistics/select?q=-owningColl%3A*&wt=json&indent=true' | grep numFound
"response":{"numFound":34879872,"start":0,"docs":[
```
- Linode continues to test mitigations for Meltdown and Spectre: https://blog.linode.com/2018/01/03/cpu-vulnerabilities-meltdown-spectre/
- I rebooted DSpace Test to see if the kernel will be updated (currently Linux 4.14.12-x86_64-linode92)... nope.
- It looks like Linode will reboot the KVM hosts later this week, though

103
public/2018-01/index.html
View File

@ -92,7 +92,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
<meta property="article:published_time" content="2018-01-02T08:35:54-08:00"/>
<meta property="article:modified_time" content="2018-01-09T09:44:16&#43;01:00"/>
<meta property="article:modified_time" content="2018-01-09T10:02:52&#43;01:00"/>
@ -194,9 +194,9 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
"@type": "BlogPosting",
"headline": "January, 2018",
"url": "https://alanorth.github.io/cgspace-notes/2018-01/",
"wordCount": "1250",
"wordCount": "1602",
"datePublished": "2018-01-02T08:35:54-08:00",
"dateModified": "2018-01-09T09:44:16&#43;01:00",
"dateModified": "2018-01-09T10:02:52&#43;01:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -565,6 +565,103 @@ sys 3m14.890s
COPY 4515
</code></pre>
<h2 id="2018-01-10">2018-01-10</h2>
<ul>
<li>I looked to see what happened to this year&rsquo;s Solr statistics sharding task that should have run on 2018-01-01 and of course it failed:</li>
</ul>
<pre><code>Moving: 81742 into core statistics-2010
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2010
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2010
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2243)
at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
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: org.apache.http.client.ClientProtocolException
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
... 10 more
Caused by: org.apache.http.client.NonRepeatableRequestException: Cannot retry request with a non-repeatable request entity. The cause lists the reason the original request failed.
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:659)
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:487)
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
... 14 more
Caused by: java.net.SocketException: Connection reset
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:115)
at java.net.SocketOutputStream.write(SocketOutputStream.java:155)
at org.apache.http.impl.io.AbstractSessionOutputBuffer.flushBuffer(AbstractSessionOutputBuffer.java:159)
at org.apache.http.impl.io.AbstractSessionOutputBuffer.write(AbstractSessionOutputBuffer.java:179)
at org.apache.http.impl.io.ChunkedOutputStream.flushCacheWithAppend(ChunkedOutputStream.java:124)
at org.apache.http.impl.io.ChunkedOutputStream.write(ChunkedOutputStream.java:181)
at org.apache.http.entity.InputStreamEntity.writeTo(InputStreamEntity.java:132)
at org.apache.http.entity.HttpEntityWrapper.writeTo(HttpEntityWrapper.java:89)
at org.apache.http.impl.client.EntityEnclosingRequestWrapper$EntityWrapper.writeTo(EntityEnclosingRequestWrapper.java:108)
at org.apache.http.impl.entity.EntitySerializer.serialize(EntitySerializer.java:117)
at org.apache.http.impl.AbstractHttpClientConnection.sendRequestEntity(AbstractHttpClientConnection.java:265)
at org.apache.http.impl.conn.ManagedClientConnectionImpl.sendRequestEntity(ManagedClientConnectionImpl.java:203)
at org.apache.http.protocol.HttpRequestExecutor.doSendRequest(HttpRequestExecutor.java:236)
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:121)
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:685)
... 16 more
</code></pre>
<ul>
<li>DSpace Test has the same error but with creating the 2017 core:</li>
</ul>
<pre><code>Moving: 2243021 into core statistics-2017
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2017
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2017
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2243)
at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
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: org.apache.http.client.ClientProtocolException
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
... 10 more
</code></pre>
<ul>
<li>There is interesting documentation about this on the DSpace Wiki: <a href="https://wiki.duraspace.org/display/DSDOC5x/SOLR+Statistics+Maintenance#SOLRStatisticsMaintenance-SolrShardingByYear">https://wiki.duraspace.org/display/DSDOC5x/SOLR+Statistics+Maintenance#SOLRStatisticsMaintenance-SolrShardingByYear</a></li>
<li>I&rsquo;m looking to see maybe if we&rsquo;re hitting the issues mentioned in <a href="https://jira.duraspace.org/browse/DS-2212">DS-2212</a> that were apparently fixed in DSpace 5.2</li>
<li>I can apparently search for records in the Solr stats core that have an empty <code>owningColl</code> field using this in the Solr admin query: <code>-owningColl:*</code></li>
<li>On CGSpace I see 48,000,000 records that have an <code>owningColl</code> field and 34,000,000 that don&rsquo;t:</li>
</ul>
<pre><code>$ http 'http://localhost:3000/solr/statistics/select?q=owningColl%3A*&amp;wt=json&amp;indent=true' | grep numFound
&quot;response&quot;:{&quot;numFound&quot;:48476327,&quot;start&quot;:0,&quot;docs&quot;:[
$ http 'http://localhost:3000/solr/statistics/select?q=-owningColl%3A*&amp;wt=json&amp;indent=true' | grep numFound
&quot;response&quot;:{&quot;numFound&quot;:34879872,&quot;start&quot;:0,&quot;docs&quot;:[
</code></pre>
<ul>
<li>Linode continues to test mitigations for Meltdown and Spectre: <a href="https://blog.linode.com/2018/01/03/cpu-vulnerabilities-meltdown-spectre/">https://blog.linode.com/2018/01/03/cpu-vulnerabilities-meltdown-spectre/</a></li>
<li>I rebooted DSpace Test to see if the kernel will be updated (currently Linux 4.14.12-x86_64-linode92)&hellip; nope.</li>
<li>It looks like Linode will reboot the KVM hosts later this week, though</li>
</ul>

10
public/sitemap.xml
View File

@ -4,7 +4,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/2018-01/</loc>
<lastmod>2018-01-09T09:44:16+01:00</lastmod>
<lastmod>2018-01-09T10:02:52+01:00</lastmod>
</url>
<url>
@ -144,7 +144,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2018-01-09T09:44:16+01:00</lastmod>
<lastmod>2018-01-09T10:02:52+01:00</lastmod>
<priority>0</priority>
</url>
@ -155,7 +155,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2018-01-09T09:44:16+01:00</lastmod>
<lastmod>2018-01-09T10:02:52+01:00</lastmod>
<priority>0</priority>
</url>
@ -167,13 +167,13 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/post/</loc>
<lastmod>2018-01-09T09:44:16+01:00</lastmod>
<lastmod>2018-01-09T10:02:52+01:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
<lastmod>2018-01-09T09:44:16+01:00</lastmod>
<lastmod>2018-01-09T10:02:52+01:00</lastmod>
<priority>0</priority>
</url>