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Alan Orth
2021-09-13 16:21:16 +03:00
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@ -44,7 +44,7 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
"/>
<meta name="generator" content="Hugo 0.87.0" />
<meta name="generator" content="Hugo 0.88.1" />
@ -153,16 +153,16 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;cgspace-account&quot; -W &quot;(sAMAccountName=otheraccounttoquery)&quot;
<pre tabindex="0"><code class="language-console" data-lang="console">$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;cgspace-account&quot; -W &quot;(sAMAccountName=otheraccounttoquery)&quot;
</code></pre><h2 id="2021-04-04">2021-04-04</h2>
<ul>
<li>Check the index aliases on AReS Explorer to make sure they are sane before starting a new harvest:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
</code></pre><ul>
<li>Then set the <code>openrxv-items-final</code> index to read-only so we can make a backup:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
{&quot;acknowledged&quot;:true}%
$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-backup
{&quot;acknowledged&quot;:true,&quot;shards_acknowledged&quot;:true,&quot;index&quot;:&quot;openrxv-items-final-backup&quot;}%
@ -181,7 +181,7 @@ $ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Conte
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ ./ilri/fix-metadata-values.py -i /tmp/2021-04-01-ISSNs.csv -db dspace -u dspace -p 'fuuu' -f cg.issn -t 'correct' -m 253
<pre tabindex="0"><code class="language-console" data-lang="console">$ ./ilri/fix-metadata-values.py -i /tmp/2021-04-01-ISSNs.csv -db dspace -u dspace -p 'fuuu' -f cg.issn -t 'correct' -m 253
</code></pre><ul>
<li>For now I only fixed obvious errors like &ldquo;1234-5678.&rdquo; and &ldquo;e-ISSN: 1234-5678&rdquo; etc, but there are still lots of invalid ones which need more manual work:
<ul>
@ -196,7 +196,7 @@ $ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Conte
<ul>
<li>The AReS Explorer harvesting from yesterday finished, and the results look OK, but actually the Elasticsearch indexes are messed up again:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
{
&quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {}
@ -218,7 +218,7 @@ $ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Conte
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ ~/dspace63/bin/dspace metadata-export -i 10568/80100 -f /tmp/rtb.csv
<pre tabindex="0"><code class="language-console" data-lang="console">$ ~/dspace63/bin/dspace metadata-export -i 10568/80100 -f /tmp/rtb.csv
$ csvcut -c 'id,dcterms.issued,dcterms.issued[],dcterms.issued[en_US]' /tmp/rtb.csv | \
sed '1d' | \
csvsql --no-header --no-inference --query 'SELECT a AS id,COALESCE(b, &quot;&quot;)||COALESCE(c, &quot;&quot;)||COALESCE(d, &quot;&quot;) AS issued FROM stdin' | \
@ -257,13 +257,13 @@ $ csvcut -c 'id,dcterms.issued,dcterms.issued[],dcterms.issued[en_US]' /tmp/rtb.
</code></pre></div><ul>
<li>Then I submitted the file three times (changing the page parameter):</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp &gt; /tmp/page1.json
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp &gt; /tmp/page1.json
$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp &gt; /tmp/page2.json
$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp &gt; /tmp/page3.json
</code></pre><ul>
<li>Then I extracted the views and downloads in the most ridiculous way:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ grep views /tmp/page*.json | grep -o -E '[0-9]+$' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
<pre tabindex="0"><code class="language-console" data-lang="console">$ grep views /tmp/page*.json | grep -o -E '[0-9]+$' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
30364
$ grep downloads /tmp/page*.json | grep -o -E '[0-9]+,' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
9100
@ -290,16 +290,16 @@ $ grep downloads /tmp/page*.json | grep -o -E '[0-9]+,' | sed 's/,//' | xargs |
</ul>
</li>
</ul>
<pre><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
<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
12413
</code></pre><ul>
<li>The system journal shows thousands of these messages in the system journal, this is the first one:</li>
</ul>
<pre><code class="language-console" data-lang="console">Apr 06 07:52:13 linode18 tomcat7[556]: Apr 06, 2021 7:52:13 AM org.apache.tomcat.jdbc.pool.ConnectionPool abandon
<pre tabindex="0"><code class="language-console" data-lang="console">Apr 06 07:52:13 linode18 tomcat7[556]: Apr 06, 2021 7:52:13 AM org.apache.tomcat.jdbc.pool.ConnectionPool abandon
</code></pre><ul>
<li>Around that time in the dspace log I see nothing unusual, but maybe these?</li>
</ul>
<pre><code class="language-console" data-lang="console">2021-04-06 07:52:29,409 INFO com.atmire.dspace.cua.CUASolrLoggerServiceImpl @ Updating : 200/127 docs in http://localhost:8081/solr/statistics
<pre tabindex="0"><code class="language-console" data-lang="console">2021-04-06 07:52:29,409 INFO com.atmire.dspace.cua.CUASolrLoggerServiceImpl @ Updating : 200/127 docs in http://localhost:8081/solr/statistics
</code></pre><ul>
<li>(BTW what is the deal with the &ldquo;200/127&rdquo;? I should send a comment to Atmire)
<ul>
@ -308,7 +308,7 @@ $ grep downloads /tmp/page*.json | grep -o -E '[0-9]+,' | sed 's/,//' | xargs |
</li>
<li>I restarted the PostgreSQL and Tomcat services and now I see less connections, but still WAY high:</li>
</ul>
<pre><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
<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
3640
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
2968
@ -318,7 +318,7 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
<li>After ten minutes or so it went back down&hellip;</li>
<li>And now it&rsquo;s back up in the thousands&hellip; I am seeing a lot of stuff in dspace log like this:</li>
</ul>
<pre><code class="language-console" data-lang="console">2021-04-06 11:59:34,364 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717951
<pre tabindex="0"><code class="language-console" data-lang="console">2021-04-06 11:59:34,364 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717951
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717952
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717953
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717954
@ -354,17 +354,17 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
<li>I had a meeting with Peter and Abenet about CGSpace TODOs</li>
<li>CGSpace went down again and the PostgreSQL locks are through the roof:</li>
</ul>
<pre><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
<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
12154
</code></pre><ul>
<li>I don&rsquo;t see any activity on REST API, but in the last four hours there have been 3,500 DSpace sessions:</li>
</ul>
<pre><code class="language-console" data-lang="console"># grep -a -E '2021-04-06 (13|14|15|16|17):' /home/cgspace.cgiar.org/log/dspace.log.2021-04-06 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
<pre tabindex="0"><code class="language-console" data-lang="console"># grep -a -E '2021-04-06 (13|14|15|16|17):' /home/cgspace.cgiar.org/log/dspace.log.2021-04-06 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
3547
</code></pre><ul>
<li>I looked at the same time of day for the past few weeks and it seems to be a normal number of sessions:</li>
</ul>
<pre><code class="language-console" data-lang="console"># for file in /home/cgspace.cgiar.org/log/dspace.log.2021-0{3,4}-*; do grep -a -E &quot;2021-0(3|4)-[0-9]{2} (13|14|15|16|17):&quot; &quot;$file&quot; | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l; done
<pre tabindex="0"><code class="language-console" data-lang="console"># for file in /home/cgspace.cgiar.org/log/dspace.log.2021-0{3,4}-*; do grep -a -E &quot;2021-0(3|4)-[0-9]{2} (13|14|15|16|17):&quot; &quot;$file&quot; | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l; done
...
3572
4085
@ -390,7 +390,7 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
</code></pre><ul>
<li>What about total number of sessions per day?</li>
</ul>
<pre><code class="language-console" data-lang="console"># for file in /home/cgspace.cgiar.org/log/dspace.log.2021-0{3,4}-*; do echo &quot;$file:&quot;; grep -a -o -E 'session_id=[A-Z0-9]{32}' &quot;$file&quot; | sort | uniq | wc -l; done
<pre tabindex="0"><code class="language-console" data-lang="console"># for file in /home/cgspace.cgiar.org/log/dspace.log.2021-0{3,4}-*; do echo &quot;$file:&quot;; grep -a -o -E 'session_id=[A-Z0-9]{32}' &quot;$file&quot; | sort | uniq | wc -l; done
...
/home/cgspace.cgiar.org/log/dspace.log.2021-03-28:
11784
@ -421,7 +421,7 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
</li>
<li>The locks in PostgreSQL shot up again&hellip;</li>
</ul>
<pre><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
<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
3447
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
3527
@ -440,7 +440,7 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
<ul>
<li>While looking at the nginx logs I see that MEL is trying to log into CGSpace&rsquo;s REST API and delete items:</li>
</ul>
<pre><code class="language-console" data-lang="console">34.209.213.122 - - [06/Apr/2021:03:50:46 +0200] &quot;POST /rest/login HTTP/1.1&quot; 401 727 &quot;-&quot; &quot;MEL&quot;
<pre tabindex="0"><code class="language-console" data-lang="console">34.209.213.122 - - [06/Apr/2021:03:50:46 +0200] &quot;POST /rest/login HTTP/1.1&quot; 401 727 &quot;-&quot; &quot;MEL&quot;
34.209.213.122 - - [06/Apr/2021:03:50:48 +0200] &quot;DELETE /rest/items/95f52bf1-f082-4e10-ad57-268a76ca18ec/metadata HTTP/1.1&quot; 401 704 &quot;-&quot; &quot;-&quot;
</code></pre><ul>
<li>I see a few of these per day going back several months
@ -450,7 +450,7 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
</li>
<li>Also annoying, I see tons of what look like penetration testing requests from Qualys:</li>
</ul>
<pre><code class="language-console" data-lang="console">2021-04-04 06:35:17,889 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:no DN found for user &quot;'&gt;&lt;qss a=X158062356Y1_2Z&gt;
<pre tabindex="0"><code class="language-console" data-lang="console">2021-04-04 06:35:17,889 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:no DN found for user &quot;'&gt;&lt;qss a=X158062356Y1_2Z&gt;
2021-04-04 06:35:17,889 INFO org.dspace.authenticate.PasswordAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:authenticate:attempting password auth of user=&quot;'&gt;&lt;qss a=X158062356Y1_2Z&gt;
2021-04-04 06:35:17,890 INFO org.dspace.app.xmlui.utils.AuthenticationUtil @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:email=&quot;'&gt;&lt;qss a=X158062356Y1_2Z&gt;, realm=null, result=2
2021-04-04 06:35:18,145 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:auth:attempting trivial auth of user=was@qualys.com
@ -464,19 +464,19 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
</li>
<li>10PM and the server is down again, with locks through the roof:</li>
</ul>
<pre><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
<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
12198
</code></pre><ul>
<li>I see that there are tons of PostgreSQL connections getting abandoned today, compared to very few in the past few weeks:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ journalctl -u tomcat7 --since=today | grep -c 'ConnectionPool abandon'
<pre tabindex="0"><code class="language-console" data-lang="console">$ journalctl -u tomcat7 --since=today | grep -c 'ConnectionPool abandon'
1838
$ journalctl -u tomcat7 --since=2021-03-20 --until=2021-04-05 | grep -c 'ConnectionPool abandon'
3
</code></pre><ul>
<li>I even restarted the server and connections were low for a few minutes until they shot back up:</li>
</ul>
<pre><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
<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
13
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
8651
@ -488,12 +488,12 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
<li>I had to go to bed and I bet it will crash and be down for hours until I wake up&hellip;</li>
<li>What the hell is this user agent?</li>
</ul>
<pre><code>54.197.119.143 - - [06/Apr/2021:19:18:11 +0200] &quot;GET /handle/10568/16499 HTTP/1.1&quot; 499 0 &quot;-&quot; &quot;GetUrl/1.0 wdestiny@umich.edu (Linux)&quot;
<pre tabindex="0"><code>54.197.119.143 - - [06/Apr/2021:19:18:11 +0200] &quot;GET /handle/10568/16499 HTTP/1.1&quot; 499 0 &quot;-&quot; &quot;GetUrl/1.0 wdestiny@umich.edu (Linux)&quot;
</code></pre><h2 id="2021-04-07">2021-04-07</h2>
<ul>
<li>CGSpace was still down from last night of course, with tons of database locks:</li>
</ul>
<pre><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
<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
12168
</code></pre><ul>
<li>I restarted the server again and the locks came back</li>
@ -504,7 +504,7 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">2021-04-01 12:45:11,414 WARN org.dspace.workflowbasic.BasicWorkflowServiceImpl @ a.akwarandu@cgiar.org:session_id=2F20F20D4A8C36DB53D42DE45DFA3CCE:notifyGroupofTask:cannot email user group_id=aecf811b-b7e9-4b6f-8776-3d372e6a048b workflow_item_id=33085\colon; Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException\colon; 501 5.1.3 Invalid address
<pre tabindex="0"><code class="language-console" data-lang="console">2021-04-01 12:45:11,414 WARN org.dspace.workflowbasic.BasicWorkflowServiceImpl @ a.akwarandu@cgiar.org:session_id=2F20F20D4A8C36DB53D42DE45DFA3CCE:notifyGroupofTask:cannot email user group_id=aecf811b-b7e9-4b6f-8776-3d372e6a048b workflow_item_id=33085\colon; Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException\colon; 501 5.1.3 Invalid address
</code></pre><ul>
<li>The issue is not the named user above, but a member of the group&hellip;</li>
<li>And the group does have users with invalid email addresses (probably accounts created automatically after authenticating with LDAP):</li>
@ -513,7 +513,7 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
<ul>
<li>I extracted all the group IDs from recent logs that had users with invalid email addresses:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ grep -a -E 'email user group_id=\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' /home/cgspace.cgiar.org/log/dspace.log.* | grep -o -E '\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' | sort | uniq
<pre tabindex="0"><code class="language-console" data-lang="console">$ grep -a -E 'email user group_id=\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' /home/cgspace.cgiar.org/log/dspace.log.* | grep -o -E '\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' | sort | uniq
0a30d6ae-74a6-4eee-a8f5-ee5d15192ee6
1769137c-36d4-42b2-8fec-60585e110db7
203c8614-8a97-4ac8-9686-d9d62cb52acc
@ -565,12 +565,12 @@ fe800006-aaec-4f9e-9ab4-f9475b4cbdc3
</ul>
</li>
</ul>
<pre><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
<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
12070
</code></pre><ul>
<li>I restarted PostgreSQL and Tomcat and the locks go straight back up!</li>
</ul>
<pre><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
<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
13
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
986
@ -608,7 +608,7 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-backup
$ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
@ -616,18 +616,18 @@ $ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
</code></pre><ul>
<li>Then I updated all Docker containers and rebooted the server (linode20) so that the correct indexes would be created again:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
<pre tabindex="0"><code class="language-console" data-lang="console">$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
</code></pre><ul>
<li>Then I realized I have to clone the backup index directly to <code>openrxv-items-final</code>, and re-create the <code>openrxv-items</code> alias:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ curl -X PUT &quot;localhost:9200/openrxv-items-backup/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-backup/_clone/openrxv-items-final
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{&quot;actions&quot; : [{&quot;add&quot; : { &quot;index&quot; : &quot;openrxv-items-final&quot;, &quot;alias&quot; : &quot;openrxv-items&quot;}}]}'
</code></pre><ul>
<li>Now I see both <code>openrxv-items-final</code> and <code>openrxv-items</code> have the current number of items:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&amp;pretty'
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&amp;pretty'
{
&quot;count&quot; : 103373,
&quot;_shards&quot; : {
@ -672,24 +672,24 @@ $ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&amp;pretty'
<ul>
<li>13,000 requests in the last two months from a user with user agent <code>SomeRandomText</code>, for example:</li>
</ul>
<pre><code class="language-console" data-lang="console">84.33.2.97 - - [06/Apr/2021:06:25:13 +0200] &quot;GET /bitstream/handle/10568/77776/CROP%20SCIENCE.jpg.jpg HTTP/1.1&quot; 404 10890 &quot;-&quot; &quot;SomeRandomText&quot;
<pre tabindex="0"><code class="language-console" data-lang="console">84.33.2.97 - - [06/Apr/2021:06:25:13 +0200] &quot;GET /bitstream/handle/10568/77776/CROP%20SCIENCE.jpg.jpg HTTP/1.1&quot; 404 10890 &quot;-&quot; &quot;SomeRandomText&quot;
</code></pre><ul>
<li>I purged them:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ ./ilri/check-spider-hits.sh -f /tmp/agents.txt -p
<pre tabindex="0"><code class="language-console" data-lang="console">$ ./ilri/check-spider-hits.sh -f /tmp/agents.txt -p
Purging 13159 hits from SomeRandomText in statistics
Total number of bot hits purged: 13159
</code></pre><ul>
<li>I noticed there were 78 items submitted in the hour before CGSpace crashed:</li>
</ul>
<pre><code class="language-console" data-lang="console"># grep -a -E '2021-04-06 0(6|7):' /home/cgspace.cgiar.org/log/dspace.log.2021-04-06 | grep -c -a add_item
<pre tabindex="0"><code class="language-console" data-lang="console"># grep -a -E '2021-04-06 0(6|7):' /home/cgspace.cgiar.org/log/dspace.log.2021-04-06 | grep -c -a add_item
78
</code></pre><ul>
<li>Of those 78, 77 of them were from Udana</li>
<li>Compared to other mornings (0 to 9 AM) this month that seems to be pretty high:</li>
</ul>
<pre><code class="language-console" data-lang="console"># for num in {01..13}; do grep -a -E &quot;2021-04-$num 0&quot; /home/cgspace.cgiar.org/log/dspace.log.2021-04-$num | grep -c -a
<pre tabindex="0"><code class="language-console" data-lang="console"># for num in {01..13}; do grep -a -E &quot;2021-04-$num 0&quot; /home/cgspace.cgiar.org/log/dspace.log.2021-04-$num | grep -c -a
add_item; done
32
0
@ -723,7 +723,7 @@ Total number of bot hits purged: 13159
</li>
<li>Create a test account for Rafael from Bioversity-CIAT to submit some items to DSpace Test:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p 'fuuuuuuuu'
<pre tabindex="0"><code class="language-console" data-lang="console">$ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p 'fuuuuuuuu'
</code></pre><ul>
<li>I added the account to the Alliance Admins account, which is should allow him to submit to any Alliance collection
<ul>
@ -735,12 +735,12 @@ Total number of bot hits purged: 13159
<ul>
<li>Update all containers on AReS (linode20):</li>
</ul>
<pre><code class="language-console" data-lang="console">$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
<pre tabindex="0"><code class="language-console" data-lang="console">$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
</code></pre><ul>
<li>Then run all system updates and reboot the server</li>
<li>I learned a new command for Elasticsearch:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl http://localhost:9200/_cat/indices
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl http://localhost:9200/_cat/indices
yellow open openrxv-values ChyhGwMDQpevJtlNWO1vcw 1 1 1579 0 537.6kb 537.6kb
yellow open openrxv-items-temp PhV5ieuxQsyftByvCxzSIw 1 1 103585 104372 482.7mb 482.7mb
yellow open openrxv-shared J_8cxIz6QL6XTRZct7UBBQ 1 1 127 0 115.7kb 115.7kb
@ -754,7 +754,7 @@ yellow open users M0t2LaZhSm2NrF5xb64dnw 1 1 2 0 1
</code></pre><ul>
<li>Somehow the <code>openrxv-items-final</code> index only has a few items and the majority are in <code>openrxv-items-temp</code>, via the <code>openrxv-items</code> alias (which is in the temp index):</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&amp;pretty'
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&amp;pretty'
{
&quot;count&quot; : 103585,
&quot;_shards&quot; : {
@ -767,7 +767,7 @@ yellow open users M0t2LaZhSm2NrF5xb64dnw 1 1 2 0 1
</code></pre><ul>
<li>I found a cool tool to help with exporting and restoring Elasticsearch indexes:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
<pre tabindex="0"><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
...
Sun, 18 Apr 2021 06:27:07 GMT | Total Writes: 103585
@ -776,20 +776,20 @@ Sun, 18 Apr 2021 06:27:07 GMT | dump complete
<li>It took only two or three minutes to export everything&hellip;</li>
<li>I did a test to restore the index:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-test --type=mapping
<pre tabindex="0"><code class="language-console" data-lang="console">$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-test --type=mapping
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-test --limit 1000 --type=data
</code></pre><ul>
<li>So that&rsquo;s pretty cool!</li>
<li>I deleted the <code>openrxv-items-final</code> index and <code>openrxv-items-temp</code> indexes and then restored the mappings to <code>openrxv-items-final</code>, added the <code>openrxv-items</code> alias, and started restoring the data to <code>openrxv-items</code> with elasticdump:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{&quot;actions&quot; : [{&quot;add&quot; : { &quot;index&quot; : &quot;openrxv-items-final&quot;, &quot;alias&quot; : &quot;openrxv-items&quot;}}]}'
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
</code></pre><ul>
<li>AReS seems to be working fine аfter that, so I created the <code>openrxv-items-temp</code> index and then started a fresh harvest on AReS Explorer:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-temp&quot;
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-temp&quot;
</code></pre><ul>
<li>Run system updates on CGSpace (linode18) and run the latest Ansible infrastructure playbook to update the DSpace Statistics API, PostgreSQL JDBC driver, etc, and then reboot the system</li>
<li>I wasted a bit of time trying to get TSLint and then ESLint running for OpenRXV on GitHub Actions</li>
@ -798,13 +798,13 @@ $ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localh
<ul>
<li>The AReS harvesting last night seems to have completed successfully, but the number of results is strange:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
yellow open openrxv-items-temp kNUlupUyS_i7vlBGiuVxwg 1 1 103741 105553 483.6mb 483.6mb
yellow open openrxv-items-final HFc3uytTRq2GPpn13vkbmg 1 1 970 0 2.3mb 2.3mb
</code></pre><ul>
<li>The indices endpoint doesn&rsquo;t include the <code>openrxv-items</code> alias, but it is currently in the <code>openrxv-items-temp</code> index so the number of items is the same:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&amp;pretty'
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&amp;pretty'
{
&quot;count&quot; : 103741,
&quot;_shards&quot; : {
@ -821,7 +821,7 @@ yellow open openrxv-items-final HFc3uytTRq2GPpn13vkbmg 1 1 970 0
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ dspace test-email
<pre tabindex="0"><code class="language-console" data-lang="console">$ dspace test-email
...
Error sending email:
- Error: javax.mail.SendFailedException: Send failure (javax.mail.AuthenticationFailedException: 550 5.2.1 Mailbox cannot be accessed [PR0P264CA0280.FRAP264.PROD.OUTLOOK.COM]
@ -850,7 +850,7 @@ Error sending email:
</ul>
</li>
</ul>
<pre><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
<pre tabindex="0"><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
$ cp atmire-cua-update.xml-20210124-132112.old /home/dspacetest.cgiar.org/config/spring/api/atmire-cua-update.xml
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -r 100 -c statistics -t 12 -g
</code></pre><ul>
@ -869,7 +869,7 @@ $ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisti
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
<pre tabindex="0"><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
@ -883,13 +883,13 @@ $ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localh
<ul>
<li>The AReS harvest last night seems to have finished successfully and the number of items looks good:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
yellow open openrxv-items-temp H-CGsyyLTaqAj6-nKXZ-7w 1 1 0 0 283b 283b
yellow open openrxv-items-final ul3SKsa7Q9Cd_K7qokBY_w 1 1 103951 0 254mb 254mb
</code></pre><ul>
<li>And the aliases seem correct for once:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
...
&quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {
@ -904,7 +904,7 @@ yellow open openrxv-items-final ul3SKsa7Q9Cd_K7qokBY_w 1 1 103951 0 254mb
<li>That&rsquo;s 250 new items in the index since the last harvest!</li>
<li>Re-create my local Artifactory container because I&rsquo;m getting errors starting it and it has been a few months since it was updated:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ podman rm artifactory
<pre tabindex="0"><code class="language-console" data-lang="console">$ podman rm artifactory
$ podman pull docker.bintray.io/jfrog/artifactory-oss:latest
$ podman create --ulimit nofile=32000:32000 --name artifactory -v artifactory_data:/var/opt/jfrog/artifactory -p 8081-8082:8081-8082 docker.bintray.io/jfrog/artifactory-oss
$ podman start artifactory
@ -925,11 +925,11 @@ $ podman start artifactory
</li>
<li>I tried to delete all the Atmire SQL migrations:</li>
</ul>
<pre><code class="language-console" data-lang="console">localhost/dspace7b5= &gt; DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace7b5= &gt; DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';
</code></pre><ul>
<li>But I got an error when running <code>dspace database migrate</code>:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ ~/dspace7b5/bin/dspace database migrate
<pre tabindex="0"><code class="language-console" data-lang="console">$ ~/dspace7b5/bin/dspace database migrate
Database URL: jdbc:postgresql://localhost:5432/dspace7b5
Migrating database to latest version... (Check dspace logs for details)
@ -961,11 +961,11 @@ Detected applied migration not resolved locally: 6.0.2017.09.25
</code></pre><ul>
<li>I deleted those migrations:</li>
</ul>
<pre><code class="language-console" data-lang="console">localhost/dspace7b5= &gt; DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace7b5= &gt; DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
</code></pre><ul>
<li>Then when I ran the migration again it failed for a new reason, related to the configurable workflow:</li>
</ul>
<pre><code class="language-console" data-lang="console">Database URL: jdbc:postgresql://localhost:5432/dspace7b5
<pre tabindex="0"><code class="language-console" data-lang="console">Database URL: jdbc:postgresql://localhost:5432/dspace7b5
Migrating database to latest version... (Check dspace logs for details)
Migration exception:
java.sql.SQLException: Flyway migration error occurred
@ -993,12 +993,12 @@ Statement : UPDATE cwf_pooltask SET workflow_id='defaultWorkflow' WHERE workflo
</code></pre><ul>
<li>The <a href="https://wiki.lyrasis.org/display/DSDOC7x/Upgrading+DSpace">DSpace 7 upgrade docs</a> say I need to apply these previously optional migrations:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ ~/dspace7b5/bin/dspace database migrate ignored
<pre tabindex="0"><code class="language-console" data-lang="console">$ ~/dspace7b5/bin/dspace database migrate ignored
</code></pre><ul>
<li>Now I see all migrations have completed and DSpace actually starts up fine!</li>
<li>I will try to do a full re-index to see how long it takes:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ time ~/dspace7b5/bin/dspace index-discovery -b
<pre tabindex="0"><code class="language-console" data-lang="console">$ time ~/dspace7b5/bin/dspace index-discovery -b
...
~/dspace7b5/bin/dspace index-discovery -b 25156.71s user 64.22s system 97% cpu 7:11:09.94 total
</code></pre><ul>
@ -1012,7 +1012,7 @@ Statement : UPDATE cwf_pooltask SET workflow_id='defaultWorkflow' WHERE workflo
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ csvgrep -e 'windows-1252' -c 'Handle.net IDs' -i -m '10568/' ~/Downloads/Altmetric\ -\ Research\ Outputs\ -\ CGSpace\ -\ 2021-04-26.csv | csvcut -c DOI | sed '1d' &gt; /tmp/dois.txt
<pre tabindex="0"><code class="language-console" data-lang="console">$ csvgrep -e 'windows-1252' -c 'Handle.net IDs' -i -m '10568/' ~/Downloads/Altmetric\ -\ Research\ Outputs\ -\ CGSpace\ -\ 2021-04-26.csv | csvcut -c DOI | sed '1d' &gt; /tmp/dois.txt
$ ./ilri/doi-to-handle.py -i /tmp/dois.txt -o /tmp/handles.csv -db dspace63 -u dspace -p 'fuuu' -d
</code></pre><ul>
<li>He will Tweet them&hellip;</li>