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Add notes for 2021-11-08
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@ -36,7 +36,7 @@ I started processing those (about 411,000 records):
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"/>
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<meta name="generator" content="Hugo 0.88.1" />
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<meta name="generator" content="Hugo 0.89.2" />
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@ -132,8 +132,8 @@ I started processing those (about 411,000 records):
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
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</code></pre><ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ chrt -b <span style="color:#ae81ff">0</span> dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t <span style="color:#ae81ff">12</span> -c statistics-2015
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</code></pre></div><ul>
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<li>AReS went down when the <code>renew-letsencrypt</code> service stopped the <code>angular_nginx</code> container in the pre-update hook and failed to bring it back up
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<ul>
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<li>I ran all system updates on the host and rebooted it and AReS came back up OK</li>
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@ -179,18 +179,18 @@ $ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=tru
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<ul>
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<li>First the 2010 core:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o statistics-2010.json -k uid
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$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
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$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:*</query></delete>"
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</code></pre><ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ chrt -b <span style="color:#ae81ff">0</span> ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o statistics-2010.json -k uid
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$ chrt -b <span style="color:#ae81ff">0</span> ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
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$ curl -s <span style="color:#e6db74">"http://localhost:8081/solr/statistics-2010/update?softCommit=true"</span> -H <span style="color:#e6db74">"Content-Type: text/xml"</span> --data-binary <span style="color:#e6db74">"<delete><query>*:*</query></delete>"</span>
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</code></pre></div><ul>
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<li>Judging by the DSpace logs all these cores had a problem starting up in the last month:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console"># grep -rsI "Unable to create core" [dspace]/log/dspace.log.2020-* | grep -o -E "statistics-[0-9]+" | sort | uniq -c
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console"># grep -rsI <span style="color:#e6db74">"Unable to create core"</span> <span style="color:#f92672">[</span>dspace<span style="color:#f92672">]</span>/log/dspace.log.2020-* | grep -o -E <span style="color:#e6db74">"statistics-[0-9]+"</span> | sort | uniq -c
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24 statistics-2010
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24 statistics-2015
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18 statistics-2016
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6 statistics-2018
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</code></pre><ul>
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</code></pre></div><ul>
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<li>The message is always this:</li>
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</ul>
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<pre tabindex="0"><code>org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error CREATEing SolrCore 'statistics-2016': Unable to create core [statistics-2016] Caused by: Lock obtain timed out: NativeFSLock@/[dspace]/solr/statistics-2016/data/index/write.lock
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@ -223,9 +223,9 @@ $ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=tru
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<ul>
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<li>There are apparently 1,700 locks right now:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ psql -c <span style="color:#e6db74">'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;'</span> | wc -l
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1739
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</code></pre><h2 id="2020-12-08">2020-12-08</h2>
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</code></pre></div><h2 id="2020-12-08">2020-12-08</h2>
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<ul>
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<li>Atmire sent some instructions for using the DeduplicateValuesProcessor
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<ul>
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@ -341,17 +341,17 @@ Caused by: org.apache.http.TruncatedChunkException: Truncated chunk ( expected s
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<ul>
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<li>I can see it in the <code>openrxv-items-final</code> index:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*' | json_pp
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||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-final/_count?q=*'</span> | json_pp
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{
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"_shards" : {
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"failed" : 0,
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"skipped" : 0,
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"successful" : 1,
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"total" : 1
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"_shards" : {
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"failed" : 0,
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"skipped" : 0,
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"successful" : 1,
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"total" : 1
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},
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"count" : 299922
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"count" : 299922
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}
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</code></pre><ul>
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</code></pre></div><ul>
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<li>I filed a bug on OpenRXV: <a href="https://github.com/ilri/OpenRXV/issues/64">https://github.com/ilri/OpenRXV/issues/64</a></li>
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<li>For now I will try to delete the index and start a re-harvest in the Admin UI:</li>
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</ul>
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@ -371,8 +371,8 @@ $ curl -XDELETE http://localhost:9200/openrxv-items-temp
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</ul>
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</li>
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||||
</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= > SELECT * FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-[0-9]{2}-*';
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</code></pre><h2 id="2020-12-14">2020-12-14</h2>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">localhost/dspace63= > SELECT * FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-[0-9]{2}-*';
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||||
</code></pre></div><h2 id="2020-12-14">2020-12-14</h2>
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||||
<ul>
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||||
<li>The re-harvesting finished last night on AReS but there are no records in the <code>openrxv-items-final</code> index
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||||
<ul>
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||||
@ -380,44 +380,44 @@ $ curl -XDELETE http://localhost:9200/openrxv-items-temp
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||||
</ul>
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||||
</li>
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||||
</ul>
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||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*' | json_pp
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp/_count?q=*'</span> | json_pp
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||||
{
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||||
"count" : 99992,
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||||
"_shards" : {
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||||
"skipped" : 0,
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||||
"total" : 1,
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||||
"failed" : 0,
|
||||
"successful" : 1
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||||
"count" : 99992,
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||||
"_shards" : {
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||||
"skipped" : 0,
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||||
"total" : 1,
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||||
"failed" : 0,
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||||
"successful" : 1
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||||
}
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||||
}
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||||
</code></pre><ul>
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||||
</code></pre></div><ul>
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||||
<li>I’m going to try to <a href="https://www.elastic.co/guide/en/elasticsearch/reference/master/indices-clone-index.html">clone</a> the temp index to the final one…
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<ul>
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<li>First, set the <code>openrxv-items-temp</code> index to block writes (read only) and then clone it to <code>openrxv-items-final</code>:</li>
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</ul>
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||||
</li>
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||||
</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": true}}'</span>
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$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
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{"acknowledged":true,"shards_acknowledged":true,"index":"openrxv-items-final"}
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$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
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||||
</code></pre><ul>
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||||
{"acknowledged":true,"shards_acknowledged":true,"index":"openrxv-items-final"}
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||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": false}}'</span>
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||||
</code></pre></div><ul>
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||||
<li>Now I see that the <code>openrxv-items-final</code> index has items, but there are still none in AReS Explorer UI!</li>
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||||
</ul>
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||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'</span>
|
||||
{
|
||||
"count" : 99992,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
"count" : 99992,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
}
|
||||
}
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>The api logs show this from last night after the harvesting:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">[Nest] 92 - 12/13/2020, 1:58:52 PM [HarvesterService] Starting Harvest
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">[Nest] 92 - 12/13/2020, 1:58:52 PM [HarvesterService] Starting Harvest
|
||||
[Nest] 92 - 12/13/2020, 10:50:20 PM [FetchConsumer] OnGlobalQueueDrained
|
||||
[Nest] 92 - 12/13/2020, 11:00:20 PM [PluginsConsumer] OnGlobalQueueDrained
|
||||
[Nest] 92 - 12/13/2020, 11:00:20 PM [HarvesterService] reindex function is called
|
||||
@ -426,16 +426,16 @@ $ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H
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at IncomingMessage.emit (events.js:326:22)
|
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at endReadableNT (_stream_readable.js:1223:12)
|
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at processTicksAndRejections (internal/process/task_queues.js:84:21)
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>But I’m not sure why the frontend doesn’t show any data despite there being documents in the index…</li>
|
||||
<li>I talked to Moayad and he reminded me that OpenRXV uses an alias to point to temp and final indexes, but the UI actually uses the <code>openrxv-items</code> index</li>
|
||||
<li>I cloned the <code>openrxv-items-final</code> index to <code>openrxv-items</code> index and now I see items in the explorer UI</li>
|
||||
<li>The PDF report was broken and I looked in the API logs and saw this:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">(node:94) UnhandledPromiseRejectionWarning: Error: Error: Could not find soffice binary
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">(node:94) UnhandledPromiseRejectionWarning: Error: Error: Could not find soffice binary
|
||||
at ExportService.downloadFile (/backend/dist/export/services/export/export.service.js:51:19)
|
||||
at processTicksAndRejections (internal/process/task_queues.js:97:5)
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>I installed <code>unoconv</code> in the backend api container and now it works… but I wonder why this changed…</li>
|
||||
<li>Skype with Abenet and Peter to discuss AReS that will be shown to ILRI scientists this week
|
||||
<ul>
|
||||
@ -487,10 +487,10 @@ $ query-json '.items | length' /tmp/policy2.json
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": true}}'</span>
|
||||
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-2020-12-14
|
||||
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
|
||||
</code></pre><h2 id="2020-12-15">2020-12-15</h2>
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": false}}'</span>
|
||||
</code></pre></div><h2 id="2020-12-15">2020-12-15</h2>
|
||||
<ul>
|
||||
<li>After the re-harvest last night there were 200,000 items in the <code>openrxv-items-temp</code> index again
|
||||
<ul>
|
||||
@ -499,36 +499,36 @@ $ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H
|
||||
</li>
|
||||
<li>I checked the 1,534 fixes in Open Refine (had to fix a few UTF-8 errors, as always from Peter’s CSVs) and then applied them using the <code>fix-metadata-values.py</code> script:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ ./fix-metadata-values.py -i /tmp/2020-10-28-fix-1534-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t 'correct' -m 3
|
||||
$ ./delete-metadata-values.py -i /tmp/2020-10-28-delete-2-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -m 3
|
||||
</code></pre><ul>
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ ./fix-metadata-values.py -i /tmp/2020-10-28-fix-1534-Authors.csv -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -f dc.contributor.author -t <span style="color:#e6db74">'correct'</span> -m <span style="color:#ae81ff">3</span>
|
||||
$ ./delete-metadata-values.py -i /tmp/2020-10-28-delete-2-Authors.csv -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -f dc.contributor.author -m <span style="color:#ae81ff">3</span>
|
||||
</code></pre></div><ul>
|
||||
<li>Since I was re-indexing Discovery anyways I decided to check for any uppercase AGROVOC and lowercase them:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">dspace=# BEGIN;
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">dspace=# BEGIN;
|
||||
BEGIN
|
||||
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=57 AND text_value ~ '[[:upper:]]';
|
||||
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=57 AND text_value ~ '[[:upper:]]';
|
||||
UPDATE 406
|
||||
dspace=# COMMIT;
|
||||
COMMIT
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>I also updated the Font Awesome icon classes for version 5 syntax:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">dspace=# BEGIN;
|
||||
dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, 'fa fa-rss','fas fa-rss', 'g') WHERE text_value LIKE '%fa fa-rss%';
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">dspace=# BEGIN;
|
||||
dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, 'fa fa-rss','fas fa-rss', 'g') WHERE text_value LIKE '%fa fa-rss%';
|
||||
UPDATE 74
|
||||
dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, 'fa fa-at','fas fa-at', 'g') WHERE text_value LIKE '%fa fa-at%';
|
||||
dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, 'fa fa-at','fas fa-at', 'g') WHERE text_value LIKE '%fa fa-at%';
|
||||
UPDATE 74
|
||||
dspace=# COMMIT;
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>Then I started a full Discovery re-index:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m"
|
||||
$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
|
||||
|
||||
real 265m11.224s
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ export JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Dfile.encoding=UTF-8 -Xmx512m"</span>
|
||||
$ time chrt -b <span style="color:#ae81ff">0</span> ionice -c2 -n7 nice -n19 dspace index-discovery -b
|
||||
<span style="color:#960050;background-color:#1e0010">
|
||||
</span><span style="color:#960050;background-color:#1e0010"></span>real 265m11.224s
|
||||
user 171m29.141s
|
||||
sys 2m41.097s
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>Udana sent a report that the WLE approver is experiencing the same issue Peter highlighted a few weeks ago: they are unable to save metadata edits in the workflow</li>
|
||||
<li>Yesterday Atmire responded about the owningComm and owningColl duplicates in Solr saying they didn’t see any anymore…
|
||||
<ul>
|
||||
@ -544,31 +544,31 @@ sys 2m41.097s
|
||||
<ul>
|
||||
<li>After the Discovery re-indexing finished on CGSpace I prepared to start re-harvesting AReS by making sure the <code>openrxv-items-temp</code> index was empty and that the backup index I made yesterday was still there:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp?pretty'</span>
|
||||
{
|
||||
"acknowledged" : true
|
||||
"acknowledged" : true
|
||||
}
|
||||
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
|
||||
$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'</span>
|
||||
{
|
||||
"count" : 0,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
"count" : 0,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
}
|
||||
}
|
||||
$ curl -s 'http://localhost:9200/openrxv-items-2020-12-14/_count?q=*&pretty'
|
||||
$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-2020-12-14/_count?q=*&pretty'</span>
|
||||
{
|
||||
"count" : 99992,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
"count" : 99992,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
}
|
||||
}
|
||||
</code></pre><h2 id="2020-12-16">2020-12-16</h2>
|
||||
</code></pre></div><h2 id="2020-12-16">2020-12-16</h2>
|
||||
<ul>
|
||||
<li>The harvesting on AReS finished last night so this morning I manually cloned the <code>openrxv-items-temp</code> index to <code>openrxv-items</code>
|
||||
<ul>
|
||||
@ -576,32 +576,32 @@ $ curl -s 'http://localhost:9200/openrxv-items-2020-12-14/_count?q=*&pretty'
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'</span>
|
||||
{
|
||||
"count" : 100046,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
"count" : 100046,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
}
|
||||
}
|
||||
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
||||
$ curl -XDELETE 'http://localhost:9200/openrxv-items?pretty'
|
||||
$ curl -s -X POST "http://localhost:9200/openrxv-items-temp/_clone/openrxv-items?pretty"
|
||||
$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": true}}'</span>
|
||||
$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items?pretty'</span>
|
||||
$ curl -s -X POST <span style="color:#e6db74">"http://localhost:9200/openrxv-items-temp/_clone/openrxv-items?pretty"</span>
|
||||
$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items/_count?q=*&pretty'</span>
|
||||
{
|
||||
"count" : 100046,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
"count" : 100046,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
}
|
||||
}
|
||||
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
|
||||
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
|
||||
</code></pre><ul>
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": false}}'</span>
|
||||
$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp?pretty'</span>
|
||||
</code></pre></div><ul>
|
||||
<li>Interestingly <a href="https://hdl.handle.net/10568/110447">the item</a> that we noticed was duplicated now only appears once</li>
|
||||
<li>The <a href="https://hdl.handle.net/10568/110133">missing item</a> is still missing</li>
|
||||
<li>Jane Poole noticed that the “previous page” and “next page” buttons are not working on AReS
|
||||
@ -611,16 +611,16 @@ $ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
|
||||
</li>
|
||||
<li>Generate a list of submitters and approvers active in the last months using the Provenance field on CGSpace:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ psql -h localhost -U postgres dspace -c "SELECT text_value FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-(06|07|08|09|10|11|12)-*'" > /tmp/provenance.txt
|
||||
$ grep -o -E 'by .*)' /tmp/provenance.txt | grep -v -E "( on |checksum)" | sed -e 's/by //' -e 's/ (/,/' -e 's/)//' | sort | uniq > /tmp/recent-submitters-approvers.csv
|
||||
</code></pre><ul>
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ psql -h localhost -U postgres dspace -c <span style="color:#e6db74">"SELECT text_value FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-(06|07|08|09|10|11|12)-*'"</span> > /tmp/provenance.txt
|
||||
$ grep -o -E <span style="color:#e6db74">'by .*)'</span> /tmp/provenance.txt | grep -v -E <span style="color:#e6db74">"( on |checksum)"</span> | sed -e <span style="color:#e6db74">'s/by //'</span> -e <span style="color:#e6db74">'s/ (/,/'</span> -e <span style="color:#e6db74">'s/)//'</span> | sort | uniq > /tmp/recent-submitters-approvers.csv
|
||||
</code></pre></div><ul>
|
||||
<li>Peter wanted it to send some mail to the users…</li>
|
||||
</ul>
|
||||
<h2 id="2020-12-17">2020-12-17</h2>
|
||||
<ul>
|
||||
<li>I see some errors from CUA in our Tomcat logs:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">Thu Dec 17 07:35:27 CET 2020 | Query:containerItem:b049326a-0e76-45a8-ac0c-d8ec043a50c6
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">Thu Dec 17 07:35:27 CET 2020 | Query:containerItem:b049326a-0e76-45a8-ac0c-d8ec043a50c6
|
||||
Error while updating
|
||||
java.lang.UnsupportedOperationException: Multiple update components target the same field:solr_update_time_stamp
|
||||
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1155)
|
||||
@ -628,7 +628,7 @@ java.lang.UnsupportedOperationException: Multiple update components target the s
|
||||
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1140)
|
||||
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1129)
|
||||
...
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>I sent the full stack to Atmire to investigate
|
||||
<ul>
|
||||
<li>I know we’ve had this “Multiple update components target the same field” error in the past with DSpace 5.x and Atmire said it was harmless, but would nevertheless be fixed in a future update</li>
|
||||
@ -636,10 +636,10 @@ java.lang.UnsupportedOperationException: Multiple update components target the s
|
||||
</li>
|
||||
<li>I was trying to export the ILRI community on CGSpace so I could update one of the ILRI author’s names, but it throws an error…</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ dspace metadata-export -i 10568/1 -f /tmp/2020-12-17-ILRI.csv
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ dspace metadata-export -i 10568/1 -f /tmp/2020-12-17-ILRI.csv
|
||||
Loading @mire database changes for module MQM
|
||||
Changes have been processed
|
||||
Exporting community 'International Livestock Research Institute (ILRI)' (10568/1)
|
||||
Exporting community 'International Livestock Research Institute (ILRI)' (10568/1)
|
||||
Exception: null
|
||||
java.lang.NullPointerException
|
||||
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:212)
|
||||
@ -654,14 +654,14 @@ java.lang.NullPointerException
|
||||
at java.lang.reflect.Method.invoke(Method.java:498)
|
||||
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
|
||||
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>I did it via CSV with <code>fix-metadata-values.py</code> instead:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ cat 2020-12-17-update-ILRI-author.csv
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ cat 2020-12-17-update-ILRI-author.csv
|
||||
dc.contributor.author,correct
|
||||
"Padmakumar, V.P.","Varijakshapanicker, Padmakumar"
|
||||
$ ./fix-metadata-values.py -i 2020-12-17-update-ILRI-author.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t 'correct' -m 3
|
||||
</code></pre><ul>
|
||||
"Padmakumar, V.P.","Varijakshapanicker, Padmakumar"
|
||||
$ ./fix-metadata-values.py -i 2020-12-17-update-ILRI-author.csv -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -f dc.contributor.author -t <span style="color:#e6db74">'correct'</span> -m <span style="color:#ae81ff">3</span>
|
||||
</code></pre></div><ul>
|
||||
<li>Abenet needed a list of all 2020 outputs from the Livestock CRP that were Limited Access
|
||||
<ul>
|
||||
<li>I exported the community from CGSpace and used <code>csvcut</code> and <code>csvgrep</code> to get a list:</li>
|
||||
@ -689,7 +689,7 @@ $ ./fix-metadata-values.py -i 2020-12-17-update-ILRI-author.csv -db dspace -u ds
|
||||
<ul>
|
||||
<li>The DeduplicateValuesProcessor has been running on DSpace Test since two days ago and it almost completed its second twelve-hour run, but crashed near the end:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">...
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">...
|
||||
Run 1 — 100% — 8,230,000/8,239,228 docs — 39s — 9h 8m 31s
|
||||
Exception: Java heap space
|
||||
java.lang.OutOfMemoryError: Java heap space
|
||||
@ -725,7 +725,7 @@ java.lang.OutOfMemoryError: Java heap space
|
||||
at java.lang.reflect.Method.invoke(Method.java:498)
|
||||
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
|
||||
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>That was with a JVM heap of 512m</li>
|
||||
<li>I looked in Solr and found dozens of duplicates of each field again…
|
||||
<ul>
|
||||
@ -744,30 +744,30 @@ java.lang.OutOfMemoryError: Java heap space
|
||||
<li>The AReS harvest finished this morning and I moved the Elasticsearch index manually</li>
|
||||
<li>First, check the number of records in the temp index to make sure it seems complete and not with double data:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'</span>
|
||||
{
|
||||
"count" : 100135,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
"count" : 100135,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
}
|
||||
}
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>Then delete the old backup and clone the current items index as a backup:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-2020-12-14?pretty'
|
||||
$ curl -X PUT "localhost:9200/openrxv-items/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items-2020-12-14?pretty'</span>
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": true}}'</span>
|
||||
$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2020-12-21
|
||||
</code></pre><ul>
|
||||
</code></pre></div><ul>
|
||||
<li>Then delete the current items index and clone it from temp:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items?pretty'
|
||||
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items?pretty'</span>
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": true}}'</span>
|
||||
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items
|
||||
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
|
||||
</code></pre><h2 id="2020-12-22">2020-12-22</h2>
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": false}}'</span>
|
||||
</code></pre></div><h2 id="2020-12-22">2020-12-22</h2>
|
||||
<ul>
|
||||
<li>I finished getting the Swagger UI integrated into the dspace-statistics-api
|
||||
<ul>
|
||||
@ -810,10 +810,10 @@ $ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H
|
||||
</code></pre><ul>
|
||||
<li>I exported the 2012 stats from the year core and imported them to the main statistics core with solr-import-export-json:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics-2012 -a export -o statistics-2012.json -k uid
|
||||
$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
|
||||
$ curl -s "http://localhost:8081/solr/statistics-2012/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:*</query></delete>"
|
||||
</code></pre><ul>
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ chrt -b <span style="color:#ae81ff">0</span> ./run.sh -s http://localhost:8081/solr/statistics-2012 -a export -o statistics-2012.json -k uid
|
||||
$ chrt -b <span style="color:#ae81ff">0</span> ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
|
||||
$ curl -s <span style="color:#e6db74">"http://localhost:8081/solr/statistics-2012/update?softCommit=true"</span> -H <span style="color:#e6db74">"Content-Type: text/xml"</span> --data-binary <span style="color:#e6db74">"<delete><query>*:*</query></delete>"</span>
|
||||
</code></pre></div><ul>
|
||||
<li>I decided to do the same for the remaining 2011, 2014, 2017, and 2019 cores…</li>
|
||||
</ul>
|
||||
<h2 id="2020-12-29">2020-12-29</h2>
|
||||
@ -824,31 +824,31 @@ $ curl -s "http://localhost:8081/solr/statistics-2012/update?softCommit=tru
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items/_count?q=*&pretty'</span>
|
||||
{
|
||||
"count" : 100135,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
"count" : 100135,
|
||||
"_shards" : {
|
||||
"total" : 1,
|
||||
"successful" : 1,
|
||||
"skipped" : 0,
|
||||
"failed" : 0
|
||||
}
|
||||
}
|
||||
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
|
||||
$ curl -X PUT "localhost:9200/openrxv-items/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
||||
$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp?pretty'</span>
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": true}}'</span>
|
||||
$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2020-12-29
|
||||
$ curl -X PUT "localhost:9200/openrxv-items/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
|
||||
</code></pre><h2 id="2020-12-30">2020-12-30</h2>
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": false}}'</span>
|
||||
</code></pre></div><h2 id="2020-12-30">2020-12-30</h2>
|
||||
<ul>
|
||||
<li>The indexing on AReS finished so I cloned the <code>openrxv-items-temp</code> index to <code>openrxv-items</code> and deleted the backup index:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items?pretty'
|
||||
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
||||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items?pretty'</span>
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": true}}'</span>
|
||||
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items
|
||||
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
|
||||
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
|
||||
$ curl -XDELETE 'http://localhost:9200/openrxv-items-2020-12-29?pretty'
|
||||
</code></pre><!-- raw HTML omitted -->
|
||||
$ curl -X PUT <span style="color:#e6db74">"localhost:9200/openrxv-items-temp/_settings?pretty"</span> -H <span style="color:#e6db74">'Content-Type: application/json'</span> -d<span style="color:#e6db74">'{"settings": {"index.blocks.write": false}}'</span>
|
||||
$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp?pretty'</span>
|
||||
$ curl -XDELETE <span style="color:#e6db74">'http://localhost:9200/openrxv-items-2020-12-29?pretty'</span>
|
||||
</code></pre></div><!-- raw HTML omitted -->
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user