Linode has alerted a few times since last night that the CPU usage on CGSpace (linode18) was high despite me increasing the alert threshold last week from 250% to 275%—I might need to increase it again!
Linode has alerted a few times since last night that the CPU usage on CGSpace (linode18) was high despite me increasing the alert threshold last week from 250% to 275%—I might need to increase it again!
<li>Linode has alerted a few times since last night that the CPU usage on CGSpace (linode18) was high despite me increasing the alert threshold last week from 250% to 275%—I might need to increase it again!</li>
<li>The Solr statistics the past few months have been very high and I was wondering if the web server logs also showed an increase</li>
<li>There were just over 3 million accesses in the nginx logs last month:</li>
</ul>
<pre><code># time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Jan/2019"
3018243
real 0m19.873s
user 0m22.203s
sys 0m1.979s
</code></pre>
<ul>
<li>Normally I’d say this was very high, but <ahref="/cgspace-notes/2018-02/">about this time last year</a> I remember thinking the same thing when we had 3.1 million…</li>
<li>I will have to keep an eye on this to see if there is some error in Solr…</li>
<li>Atmire sent their <ahref="https://github.com/ilri/DSpace/pull/407">pull request to re-enable the Metadata Quality Module (MQM) on our <code>5_x-dev</code> branch</a> today
<ul>
<li>I will test it next week and send them feedback</li>
<li>Another alert from Linode about CGSpace (linode18) this morning, here are the top IPs in the web server logs before, during, and after that time:</li>
<li><code>45.5.184.2</code> is CIAT and <code>85.25.237.71</code> is the new Linguee bot that I first noticed a few days ago</li>
<li>I will increase the Linode alert threshold from 275 to 300% because this is becoming too much!</li>
<li>I tested the Atmire Metadata Quality Module (MQM)’s duplicate checked on the some <ahref="https://dspacetest.cgiar.org/handle/10568/81268">WLE items</a> that I helped Udana with a few months ago on DSpace Test (linode19) and indeed it found many duplicates!</li>
<li><code>45.5.184.2</code> is CIAT, <code>70.32.83.92</code> and <code>205.186.128.185</code> are Macaroni Bros harvesters for CCAFS I think</li>
<li><code>195.201.104.240</code> is a new IP address in Germany with the following user agent:</li>
</ul>
<pre><code>Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:62.0) Gecko/20100101 Firefox/62.0
</code></pre>
<ul>
<li>This user was making 20–60 requests per minute this morning… seems like I should try to block this type of behavior heuristically, regardless of user agent!</li>
<li>This user was making requests to <code>/browse</code>, which is not currently under the existing rate limiting of dynamic pages in our nginx config
<ul>
<li>I <ahref="https://github.com/ilri/rmg-ansible-public/commit/36dfb072d6724fb5cdc81ef79cab08ed9ce427ad">extended the existing <code>dynamicpages</code> (12/m) rate limit to <code>/browse</code> and <code>/discover</code></a> with an allowance for bursting of up to five requests for “real” users</li>
<li>Generate a list of CTA subjects from CGSpace for Peter:</li>
</ul>
<pre><code>dspace=# \copy (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=124 GROUP BY text_value ORDER BY COUNT DESC) to /tmp/cta-subjects.csv with csv header;
<li>This morning there was another alert from Linode about the high load on CGSpace (linode18), here are the top IPs in the web server logs before, during, and after that time:</li>
<li>At this rate I think I just need to stop paying attention to these alerts—DSpace gets thrashed when people use the APIs properly and there’s nothing we can do to improve REST API performance!</li>
<li>Perhaps I just need to keep increasing the Linode alert threshold (currently 300%) for this host?</li>
<li>Peter sent me corrections and deletions for the CTA subjects and as usual, there were encoding errors with some accentsÁ in his file</li>
<li>In other news, it seems that the GREL syntax regarding booleans changed in OpenRefine recently, so I need to update some expressions like the one I use to detect encoding errors to use <code>toString()</code>:</li>
</ul>
<pre><code>or(
isNotNull(value.match(/.*\uFFFD.*/)),
isNotNull(value.match(/.*\u00A0.*/)),
isNotNull(value.match(/.*\u200A.*/)),
isNotNull(value.match(/.*\u2019.*/)),
isNotNull(value.match(/.*\u00b4.*/)),
isNotNull(value.match(/.*\u007e.*/))
).toString()
</code></pre>
<ul>
<li>Testing the corrections for sixty-five items and sixteen deletions using my <ahref="https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897">fix-metadata-values.py</a> and <ahref="https://gist.github.com/alanorth/bd7d58c947f686401a2b1fadc78736be">delete-metadata-values.py</a> scripts:</li>
<li>Peter had marked several terms with <code>||</code> to indicate multiple values in his corrections so I will have to go back and do those manually:</li>
<li>So it seems that the load issue comes from the REST API, not the XMLUI</li>
<li>I could probably rate limit the REST API, or maybe just keep increasing the alert threshold so I don’t get alert spam (this is probably the correct approach because it seems like the REST API can keep up with the requests and is returning HTTP 200 status as far as I can tell)</li>
<li>Bosede from IITA sent a message that a colleague is having problems submitting to some collections in their community:</li>
</ul>
<pre><code>Authorization denied for action WORKFLOW_STEP_1 on COLLECTION:1056 by user 1759
</code></pre>
<ul>
<li>Collection 1056 appears to be <ahref="https://cgspace.cgiar.org/handle/10568/68741">IITA Posters and Presentations</a> and I see that its workflow step 1 (Accept/Reject) is empty:</li>
</ul>
<p><imgsrc="/cgspace-notes/2019/02/iita-workflow-step1-empty.png"alt="IITA Posters and Presentations workflow step 1 empty"/></p>
<ul>
<li>IITA editors or approvers should be added to that step (though I’m curious why nobody is in that group currently)</li>
<li>CGNET said these servers were discontinued in 2018-01 and that I should use <ahref="https://docs.microsoft.com/en-us/exchange/mail-flow-best-practices/how-to-set-up-a-multifunction-device-or-application-to-send-email-using-office-3">Office 365</a></li>
</ul>
<h2id="2019-02-08">2019-02-08</h2>
<ul>
<li>I re-configured CGSpace to use the email/password for cgspace-support, but I get this error when I try the <code>test-email</code> script:</li>
</ul>
<pre><code>Error sending email:
- Error: com.sun.mail.smtp.SMTPSendFailedException: 530 5.7.57 SMTP; Client was not authenticated to send anonymous mail during MAIL FROM [AM6PR10CA0028.EURPRD10.PROD.OUTLOOK.COM]
</code></pre>
<ul>
<li>I tried to log into Outlook 365 with the credentials but I think the ones I have must be wrong, so I will ask ICT to reset the password</li>
<li>Linode sent another alert about CGSpace (linode18) CPU load this morning, here are the top IPs in the web server XMLUI and API logs before, during, and after that time:</li>
<li>I think I need to increase the Linode alert threshold from 300 to 350% now so I stop getting some of these alerts—it’s becoming a bit of <em>the boy who cried wolf</em> because it alerts like clockwork twice per day!</li>
<li>Add my Python- and shell-based metadata workflow helper scripts as well as the environment settings for pipenv to our DSpace repository (<ahref="https://github.com/ilri/DSpace/pull/408">#408</a>) so I can track changes and distribute them more formally instead of just keeping them <ahref="https://github.com/ilri/DSpace/wiki/Scripts">collected on the wiki</a></li>
<li>Started adding IITA research theme (<code>cg.identifier.iitatheme</code>) to CGSpace
<ul>
<li>I’m still waiting for feedback from IITA whether they actually want to use “SOCIAL SCIENCE & AGRIC BUSINESS” because it is listed as <ahref="http://www.iita.org/project-discipline/social-science-and-agribusiness/">“Social Science and Agribusiness”</a> on their website</li>
<li>Also, I think they want to do some mappings of items with existing subjects to these new themes</li>
</ul></li>
<li>Update ILRI author name style in the controlled vocabulary (Domelevo Entfellner, Jean-Baka) (<ahref="https://github.com/ilri/DSpace/pull/409">#409</a>)
<ul>
<li>I’m still waiting to hear from Bizuwork whether we’ll batch update all existing items with the old name style</li>
<li>Last week Hector Tobon from CCAFS asked me about the Creative Commons 3.0 Intergovernmental Organizations (IGO) license because it is not in the list of SPDX licenses
<li>Today I made <ahref="http://13.57.134.254/app/license_requests/15/">a request</a> to the <ahref="https://github.com/spdx/license-list-XML/blob/master/CONTRIBUTING.md">SPDX using their web form</a> to include this class of Creative Commons licenses](<ahref="https://wiki.creativecommons.org/wiki/Intergovernmental_Organizations">https://wiki.creativecommons.org/wiki/Intergovernmental_Organizations</a>)</li>
<li>Testing the <code>mail.server.disabled</code> property that I noticed in <code>dspace.cfg</code> recently
<ul>
<li>Setting it to true results in the following message when I try the <code>dspace test-email</code> helper on DSpace Test:</li>
</ul></li>
</ul>
<pre><code>Error sending email:
- Error: cannot test email because mail.server.disabled is set to true
</code></pre>
<ul>
<li>I’m not sure why I didn’t know about this configuration option before, and always maintained multiple configurations for development and production
<ul>
<li>I will modify the <ahref="https://github.com/ilri/rmg-ansible-public">Ansible DSpace role</a> to use this in its <code>build.properties</code> template</li>
</ul></li>
<li>I updated my local Sonatype nexus Docker image and had an issue with the volume for some reason so I decided to just start from scratch:</li>
<li>For some reason my <code>mvn package</code> for DSpace is not working now… I might go back to <ahref="https://mjanja.ch/2018/02/cache-maven-artifacts-with-artifactory/">using Artifactory for caching</a> instead:</li>
<li>Bosede from IITA said we can use “SOCIAL SCIENCE & AGRIBUSINESS” in their new IITA theme field to be consistent with other places they are using it</li>
<li>Run all system updates on DSpace Test (linode19) and reboot it</li>
<li>I notice that <ahref="https://jira.duraspace.org/browse/DS-3052">DSpace 6 has included a new JAR-based PDF thumbnailer based on PDFBox</a>, I wonder how good its thumbnails are and how it handles CMYK PDFs</li>
<li>On a similar note, I wonder if we could use the performance-focused <ahref="https://libvips.github.io/libvips/">libvps</a> and the third-party <ahref="https://github.com/codecitizen/jlibvips/">jlibvips Java library</a> in DSpace</li>
<li>Testing the <code>vipsthumbnail</code> command line tool with <ahref="https://cgspace.cgiar.org/handle/10568/51999">this CGSpace item that uses CMYK</a>:</li>
<li>Thinking about making “top items” endpoints in my <ahref="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a></li>
<li>I could use the following SQL queries very easily to get the top items by views or downloads:</li>
</ul>
<pre><code>dspacestatistics=# SELECT * FROM items WHERE views > 0 ORDER BY views DESC LIMIT 10;
dspacestatistics=# SELECT * FROM items WHERE downloads > 0 ORDER BY downloads DESC LIMIT 10;
</code></pre>
<ul>
<li>I’d have to think about what to make the REST API endpoints, perhaps: <code>/statistics/top/items?limit=10</code></li>
<li>But how do I do top items by views / downloads separately?</li>
<li>I re-deployed DSpace 6.3 locally to test the PDFBox thumbnails, especially to see if they handle CMYK files properly
<ul>
<li>The quality is JPEG 75 and I don’t see a way to set the thumbnail dimensions, but the resulting image is indeed sRGB:</li>
<li>ILRI ICT reset the password for the CGSpace mail account, but I still can’t get it to send mail from DSpace’s <code>test-email</code> utility</li>
<li>I even added extra mail properties to <code>dspace.cfg</code> as suggested by someone on the dspace-tech mailing list:</li>
- Error: com.sun.mail.smtp.SMTPSendFailedException: 530 5.7.57 SMTP; Client was not authenticated to send anonymous mail during MAIL FROM [AM6PR06CA0001.eurprd06.prod.outlook.com]
</code></pre>
<ul>
<li>I tried to log into the Outlook 365 web mail and it doesn’t work so I’ve emailed ILRI ICT again</li>
<li>After reading the <ahref="https://javaee.github.io/javamail/FAQ#commonmistakes">common mistakes in the JavaMail FAQ</a> I reconfigured the extra properties in DSpace’s mail configuration to be simply:</li>
<li>… and then I was able to send a mail using my personal account where I know the credentials work</li>
<li>The CGSpace account still gets this error message:</li>
</ul>
<pre><code>Error sending email:
- Error: javax.mail.AuthenticationFailedException
</code></pre>
<ul>
<li>I updated the <ahref="https://github.com/ilri/DSpace/pull/410">DSpace SMTP settings in <code>dspace.cfg</code></a> as well as the <ahref="https://github.com/ilri/rmg-ansible-public/commit/ab5fe4d10e16413cd04ffb1bc3179dc970d6d47c">variables in the DSpace role of the Ansible infrastructure scripts</a></li>
<li>Thierry from CTA is having issues with his account on DSpace Test, and there is no admin password reset function on DSpace (only via email, which is disabled on DSpace Test), so I have to delete and re-create his account:</li>
</ul>
<pre><code>$ dspace user --delete --email blah@cta.int
<li>On this note, I saw a thread on the dspace-tech mailing list that says this functionality exists if you enable <code>webui.user.assumelogin = true</code></li>
<li>I will enable this on CGSpace (<ahref="https://github.com/ilri/DSpace/pull/411">#411</a>)</li>
<li>Test re-creating my local PostgreSQL and Artifactory containers with podman instead of Docker (using the volumes from my old Docker containers though):</li>
<li>Which totally works, but Podman’s rootless support doesn’t work with port mappings yet…</li>
<li>Deploy the Tomcat-7-from-tarball branch on CGSpace (linode18), but first stop the Ubuntu Tomcat 7 and do some basic prep before running the Ansible playbook:</li>
</ul>
<pre><code># systemctl stop tomcat7
# apt remove tomcat7 tomcat7-admin
# useradd -m -r -s /bin/bash dspace
# mv /usr/share/tomcat7/.m2 /home/dspace
# mv /usr/share/tomcat7/src /home/dspace
# chown -R dspace:dspace /home/dspace
# chown -R dspace:dspace /home/cgspace.cgiar.org
# dpkg -P tomcat7-admin tomcat7-common
</code></pre>
<ul>
<li>After running the playbook CGSpace came back up, but I had an issue with some Solr cores not being loaded (similar to last month) and this was in the Solr log:</li>
<li>After restarting Tomcat the usage statistics are back</li>
<li>Interestingly, many of the locks were from last month, last year, and even 2015! I’m pretty sure that’s not supposed to be how locks work…</li>
<li>Help Sarah Kasyoka finish an item submission that she was having issues with due to the file size</li>
<li>I increased the nginx upload limit, but she said she was having problems and couldn’t really tell me why</li>
<li>I logged in as her and completed the submission with no problems…</li>
<li>Tomcat was killed around 3AM by the kernel’s OOM killer according to <code>dmesg</code>:</li>
</ul>
<pre><code>[Fri Feb 15 03:10:42 2019] Out of memory: Kill process 12027 (java) score 670 or sacrifice child
[Fri Feb 15 03:10:42 2019] Killed process 12027 (java) total-vm:14108048kB, anon-rss:5450284kB, file-rss:0kB, shmem-rss:0kB
[Fri Feb 15 03:10:43 2019] oom_reaper: reaped process 12027 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
</code></pre>
<ul>
<li>The <code>tomcat7</code> service shows:</li>
</ul>
<pre><code>Feb 15 03:10:44 linode19 systemd[1]: tomcat7.service: Main process exited, code=killed, status=9/KILL
</code></pre>
<ul>
<li>I suspect it was related to the media-filter cron job that runs at 3AM but I don’t see anything particular in the log files</li>
<li>I want to try to normalize the <code>text_lang</code> values to make working with metadata easier</li>
<li>We currently have a bunch of weird values that DSpace uses like <code>NULL</code>, <code>en_US</code>, and <code>en</code> and others that have been entered manually by editors:</li>
</ul>
<pre><code>dspace=# SELECT DISTINCT text_lang, count(*) FROM metadatavalue WHERE resource_type_id=2 GROUP BY text_lang ORDER BY count DESC;
text_lang | count
-----------+---------
| 1069539
en_US | 577110
| 334768
en | 133501
es | 12
* | 11
es_ES | 2
fr | 2
spa | 2
E. | 1
ethnob | 1
</code></pre>
<ul>
<li>The majority are <code>NULL</code>, <code>en_US</code>, the blank string, and <code>en</code>—the rest are not enough to be significant</li>
<li>Theoretically this field could help if you wanted to search for Spanish-language fields in the API or something, but even for the English fields there are two different values (and those are from DSpace itself)!</li>
<li>I’m going to normalized these to <code>NULL</code> at least on DSpace Test for now:</li>
</ul>
<pre><code>dspace=# UPDATE metadatavalue SET text_lang = NULL WHERE resource_type_id=2 AND text_lang IS NOT NULL;
UPDATE 1045410
</code></pre>
<ul>
<li>I started proofing IITA’s 2019-01 records that Sisay uploaded this week
<ul>
<li>There were 259 records in IITA’s original spreadsheet, but there are 276 in Sisay’s collection</li>
<li>Also, I found that there are at least twenty duplicates in these records that we will need to address</li>
</ul></li>
<li>ILRI ICT fixed the password for the CGSpace support email account and I tested it on Outlook 365 web and DSpace and it works</li>
<li>Re-create my local PostgreSQL container to for new PostgreSQL version and to use podman’s volumes:</li>
<li>Then re-create my Artifactory container as well, taking into account ulimit open file requirements by Artifactory as well as the user limitations caused by rootless subuid mappings:</li>
<li>More on the <ahref="https://podman.io/blogs/2018/10/03/podman-remove-content-homedir.html">subuid permissions issue with rootless containers here</a></li>
<li>I ran DSpace’s cleanup task on CGSpace (linode18) and there were errors:</li>
</ul>
<pre><code>$ dspace cleanup -v
Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
Detail: Key (bitstream_id)=(162844) is still referenced from table "bundle".
</code></pre>
<ul>
<li><p>The solution is, as always:</p>
<pre><code>$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (162844);'
UPDATE 1
</code></pre></li>
<li><p>I merged the Atmire Metadata Quality Module (MQM) changes to the <code>5_x-prod</code> branch and deployed it on CGSpace (<ahref="https://github.com/ilri/DSpace/pull/407">#407</a>)</p></li>
<li><p>Then I ran all system updates on CGSpace server and rebooted it</p></li>
<li><p>The following IPs were all hitting the server hard simultaneously and are located on Amazon and use the user agent “Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0”:</p>
<ul>
<li>52.54.252.47</li>
<li>34.230.15.139</li>
<li>100.24.48.177</li>
<li>3.84.172.18</li>
<li>3.80.196.188</li>
<li>3.83.14.11</li>
<li>54.164.83.99</li>
<li>18.212.208.240</li>
</ul></li>
<li><p>Actually, even up to the top 30 IPs are almost all on Amazon and use the same user agent!</p></li>
<li><p>For reference most of these IPs hitting the XMLUI this afternoon are on Amazon:</p></li>
<li>I will add this user agent to the <ahref="https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/nginx/default.conf.j2">“badbots” rate limiting in our nginx configuration</a></li>
<li>I realized that I had effectively only been applying the “badbots” rate limiting to requests at the root, so I added it to the other blocks that match Discovery, Browse, etc as well</li>
<li>I merged the changes to the <code>5_x-prod</code> branch and they will go live the next time we re-deploy CGSpace (<ahref="https://github.com/ilri/DSpace/pull/412">#412</a>)</li>
<li>143.233.242.130 is in Greece and using the user agent “Indy Library”, like the top IP yesterday (94.71.244.172)</li>
<li>That user agent is in our Tomcat list of crawlers so at least its resource usage is controlled by forcing it to use a single Tomcat session, but I don’t know if DSpace recognizes if this is a bot or not, so the logs are probably skewed because of this</li>
<li>The user is requesting only things like <code>/handle/10568/56199?show=full</code> so it’s nothing malicious, only annoying</li>
<li>Otherwise there are still shit loads of IPs from Amazon still hammering the server, though I see HTTP 503 errors now after yesterday’s nginx rate limiting updates
<ul>
<li>I should really try to script something around <ahref="https://ipapi.co/api/">ipapi.co</a> to get these quickly and easily</li>
</ul></li>
<li>The top requests in the API logs today are:</li>
<li><code>2a01:7e00::f03c:91ff:fe0a:d645</code> is on Linode, and I can see from the XMLUI access logs that it is Drupal, so I assume it is part of the new ILRI website harvester…</li>
<li>Jesus, Linode just sent another alert as we speak that the load on CGSpace (linode18) has been at 450% the last two hours! I’m so fucking sick of this</li>
<li>Our usage stats have exploded the last few months:</li>
<li>I need to follow up with the DSpace developers and Atmire to see how they classify which requests are bots so we can try to estimate the impact caused by these users and perhaps try to update the list to make the stats more accurate</li>
<li>I found one IP address in Nigeria that has an Android user agent and has requested a bitstream from <ahref="https://hdl.handle.net/10568/96140"><sup>10568</sup>⁄<sub>96140</sub></a> almost 200 times:</li>
<li>That is so weird, they are all using this Android user agent:</li>
</ul>
<pre><code>Mozilla/5.0 (Linux; Android 7.0; TECNO Camon CX Build/NRD90M) AppleWebKit/537.36 (KHTML, like Gecko) Version/4.0 Chrome/33.0.0.0 Mobile Safari/537.36
</code></pre>
<ul>
<li>I wrote a quick and dirty Python script called <code>resolve-addresses.py</code> to resolve IP addresses to their owning organization’s name, ASN, and country using the <ahref="https://ipapi.co">IPAPI.co API</a></li>
<li>This returns six items for me, which is the <ahref="https://cgspace.cgiar.org/discover?filtertype_1=orcid&filter_relational_operator_1=contains&filter_1=Alan+S.+Orth%3A+0000-0002-1735-7458&submit_apply_filter=&query=">same I see in a Discovery search</a></li>
<li>Hector Tobon from CIAT asked if it was possible to get item statistics from CGSpace so I told him to use my <ahref="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a></li>
<li>I was playing with <ahref="http://yasgui.org/">YasGUI</a> to query AGROVOC’s SPARQL endpoint, but they must have a cached version or something because I get an HTTP 404 if I try to go to the endpoint manually</li>
<li>I think I want to stick to the regular <ahref="http://aims.fao.org/agrovoc/webservices">web services</a> to validate AGROVOC terms</li>
<li>There seems to be a REST API for AGROVOC here: <ahref="http://agrovoc.uniroma2.it/agrovoc/rest/v1/search?query=FISH&lang=en">http://agrovoc.uniroma2.it/agrovoc/rest/v1/search?query=FISH&lang=en</a></li>
<li>See this <ahref="https://jira.duraspace.org/browse/VIVO-1655">issue on the VIVO tracker</a> for more information about this endpoint</li>
<li>The old-school AGROVOC SOAP WSDL works with the <ahref="https://python-zeep.readthedocs.io/en/master/">Zeep Python library</a>, but in my tests the results are way too broad despite trying to use a “exact match” searching</li>
<li>I wrote a script <ahref="https://github.com/ilri/DSpace/blob/5_x-prod/agrovoc-lookup.py">agrovoc-lookup.py</a> to resolve subject terms against the public AGROVOC REST API</li>
<li>It allows specifying the language the term should be queried in as well as output files to save the matched and unmatched terms to</li>
<li>I ran our top 1500 subjects through English, Spanish, and French and saved the matched and unmatched terms to separate files:</li>
</ul>
<pre><code>$ ./agrovoc-lookup.py -l en -i /tmp/top-1500-subjects.txt -om /tmp/matched-subjects-en.txt -or /tmp/rejected-subjects-en.txt
$ ./agrovoc-lookup.py -l es -i /tmp/top-1500-subjects.txt -om /tmp/matched-subjects-es.txt -or /tmp/rejected-subjects-es.txt
<li>And then a list of all the unique <em>unmatched</em> terms using some utility I’ve never heard of before called <code>comm</code> or with <code>diff</code>:</li>
<li>Generate a list of countries and regions from CGSpace for Sisay to look through:</li>
</ul>
<pre><code>dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 228 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC) to /tmp/2019-02-21-countries.csv WITH CSV HEADER;
COPY 202
dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 227 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC) to /tmp/2019-02-21-regions.csv WITH CSV HEADER;
<li>I did a bit more work on the IITA research theme (adding it to Discovery search filters) and it’s almost ready so I created a pull request (<ahref="https://github.com/ilri/DSpace/pull/413">#413</a>)</li>
<li>I still need to test the batch tagging of IITA items with themes based on their IITA subjects:
<ul>
<li>NATURAL RESOURCE MANAGEMENT research theme to items with NATURAL RESOURCE MANAGEMENT subject</li>
<li>BIOTECH & PLANT BREEDING research theme to items with PLANT BREEDING subject</li>
<li>SOCIAL SCIENCE & AGRIBUSINESS research theme to items with AGRIBUSINESS subject</li>
<li>PLANT PRODUCTION & HEALTH research theme to items with PLANT PRODUCTION subject</li>
<li>PLANT PRODUCTION & HEALTH research theme to items with PLANT HEALTH subject</li>
<li>NUTRITION & HUMAN HEALTH research theme to items with NUTRITION subject</li>
<li>Help Udana from WLE with some issues related to CGSpace items on their <ahref="https://www.wle.cgiar.org/publications">Publications website</a>
<ul>
<li>He wanted some IWMI items to show up in their publications website</li>
<li>The items were mapped into WLE collections, but still weren’t showing up on the publications website</li>
<li>I told him that he needs to add the <code>cg.identifier.wletheme</code> to the items so that the website indexer finds them</li>
<li>A few days ago he added the metadata to <ahref="https://cgspace.cgiar.org/handle/10568/93011"><sup>10568</sup>⁄<sub>93011</sub></a> and now I see that the item is present on the <ahref="https://www.wle.cgiar.org/resource-recovery-waste-business-models-energy-nutrient-and-water-reuse-low-and-middle-income">WLE publications website</a></li>
</ul></li>
<li><p>Start looking at IITA’s latest round of batch uploads called <ahref="https://dspacetest.cgiar.org/handle/10568/108684">“IITA_Feb_14” on DSpace Test</a></p>
<ul>
<li>One mispelled authorship type</li>
<li>A few dozen incorrect inconsistent affiliations (I dumped a list of the top 1500 affiliations and reconciled against it, but it was still a lot of work)</li>
<li>One issue with smart quotes in countries</li>
<li>A few IITA subjects with syntax errors</li>
<li>Some whitespace and consistency issues in sponsorships</li>
<li>Eight items with invalid ISBN: 0-471-98560-3</li>
<li>Two incorrectly formatted ISSNs</li>
<li>Lots of incorrect values in subjects, but that’s a difficult problem to do in an automated way</li>
</ul></li>
<li><p>I figured out how to query AGROVOC from OpenRefine using Jython by creating a custom text facet:</p></li>
<li>You have to make sure to URL encode the value with <code>quote_plus()</code> and it totally works, but it seems to refresh the facets (and therefore re-query everything) when you select a facet so that makes it basically unusable</li>
<li>There is a <ahref="https://programminghistorian.org/en/lessons/fetch-and-parse-data-with-openrefine#example-2-url-queries-and-parsing-json">good resource discussing OpenRefine, Jython, and web scraping</a></li>
</ul>
<h2id="2019-02-24">2019-02-24</h2>
<ul>
<li>I decided to try to validate the AGROVOC subjects in IITA’s recent batch upload by dumping all their terms, checking them in en/es/fr with <code>agrovoc-lookup.py</code>, then reconciling against the final list using reconcile-csv with OpenRefine</li>
<li>I’m not sure how to deal with terms like “CORN” that are alternative labels (<code>altLabel</code>) in AGROVOC where the preferred label (<code>prefLabel</code>) would be “MAIZE”</li>
<li>For example, <ahref="http://agrovoc.uniroma2.it/agrovoc/rest/v1/search?query=CORN*&lang=en">a query</a> for <code>CORN*</code> returns:</li>
<li>There are dozens of other entries like “corn (soft wheat)”, “corn (zea)”, “corn bran”, “Cornales”, etc that could potentially match and to determine if they are related programatically is difficult</li>
<li>Shit, and then there are terms like “GENETIC DIVERSITY” that should <ahref="http://agrovoc.uniroma2.it/agrovoc/agrovoc/en/page/c_33952">technically be</a>“genetic diversity (as resource)”</li>
<li>I applied all changes to the IITA Feb 14 batch data except the affiliations and sponsorships because I think I made some mistakes with the copying of reconciled values so I will try to look at those again separately</li>
<li>I went back and re-did the affiliations and sponsorships and then applied them on the IITA Feb 14 collection on DSpace Test</li>
<li>I did a duplicate check of the IITA Feb 14 records on DSpace Test and there were about fifteen or twenty items reported
<ul>
<li>A few of them are actually in previous IITA batch updates, which means they have been uploaded to CGSpace yet, so I worry that there would be many more</li>
<li>I want to re-synchronize CGSpace to DSpace Test to make sure that the duplicate checking is accurate, but I’m not sure I can because the Earlham guys are still testing COPO actively on DSpace Test</li>
<li>There seems to be something going on with Solr on CGSpace (linode18) because statistics on communities and collections are blank for January and February this year</li>
<li>I see some errors started recently in Solr (yesterday):</li>
<li>But I don’t see anything interesting in yesterday’s Solr log…</li>
<li>I see this in the Tomcat 7 logs yesterday:</li>
</ul>
<pre><code>Feb 25 21:09:29 linode18 tomcat7[1015]: Error while updating
Feb 25 21:09:29 linode18 tomcat7[1015]: java.lang.UnsupportedOperationException: Multiple update components target the same field:solr_update_time_stamp
Feb 25 21:09:29 linode18 tomcat7[1015]: at org.dspace.statistics.SolrLogger$9.visit(SourceFile:1241)
Feb 25 21:09:29 linode18 tomcat7[1015]: at org.dspace.statistics.SolrLogger.visitEachStatisticShard(SourceFile:268)
Feb 25 21:09:29 linode18 tomcat7[1015]: at org.dspace.statistics.SolrLogger.update(SourceFile:1225)
Feb 25 21:09:29 linode18 tomcat7[1015]: at org.dspace.statistics.SolrLogger.update(SourceFile:1220)
Feb 25 21:09:29 linode18 tomcat7[1015]: at org.dspace.statistics.StatisticsLoggingConsumer.consume(SourceFile:103)
...
</code></pre>
<ul>
<li>In the Solr admin GUI I see we have the following error: “statistics-2011: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher”</li>
<li>I restarted Tomcat and upon startup I see lots of errors in the systemd journal, like:</li>
</ul>
<pre><code>Feb 25 21:37:49 linode18 tomcat7[28363]: SEVERE: IOException while loading persisted sessions: java.io.StreamCorruptedException: invalid type code: 00
Feb 25 21:37:49 linode18 tomcat7[28363]: java.io.StreamCorruptedException: invalid type code: 00
Feb 25 21:37:49 linode18 tomcat7[28363]: at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1601)
Feb 25 21:37:49 linode18 tomcat7[28363]: at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2287)
Feb 25 21:37:49 linode18 tomcat7[28363]: at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:561)
Feb 25 21:37:49 linode18 tomcat7[28363]: at java.lang.Throwable.readObject(Throwable.java:914)
Feb 25 21:37:49 linode18 tomcat7[28363]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
Feb 25 21:37:49 linode18 tomcat7[28363]: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
<li>Also, now the Solr admin UI says “statistics-2015: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher”</li>
<li>I can see that there are still hits being recorded for items (in the Solr admin UI as well as my statistics API), so the main stats core is working at least!</li>
<li>On a hunch I tried adding <code>ulimit -v unlimited</code> to the Tomcat <code>catalina.sh</code> and now Solr starts up with no core errors and I actually have statistics for January and February on <ahref="https://cgspace.cgiar.org/handle/10568/16814">some communities</a>, but not <ahref="https://cgspace.cgiar.org/handle/10568/1">others</a></li>
<li>I wonder if the address space limits that I added via <code>LimitAS=infinity</code> in the systemd service are somehow not working?</li>
<li>I did some tests with calling a shell script from systemd on DSpace Test (linode19) and the <code>LimitAS</code> setting does work, and the <code>infinity</code> setting in systemd does get translated to “unlimited” on the service</li>
<li>I thought it might be open file limit, but it seems we’re nowhere near the current limit of 16384:</li>
</ul>
<pre><code># lsof -u dspace | wc -l
3016
</code></pre>
<ul>
<li>For what it’s worth I see the same errors about <code>solr_update_time_stamp</code> on DSpace Test (linode19)</li>
<li>Update DSpace Test to <ahref="https://tomcat.apache.org/tomcat-7.0-doc/changelog.html#Tomcat_7.0.93_(violetagg)">Tomcat 7.0.93</a></li>
<li>Something seems to have happened (some Atmire scheduled task, perhaps the CUA one at 7AM?) on CGSpace because I checked a few communities and collections on CGSpace and there are now statistics for January and February</li>
</ul>
<p><imgsrc="/cgspace-notes/2019/02/statlets-working.png"alt="CGSpace statlets working again"/></p>
<ul>
<li>I still have not figured out what the <em>real</em> cause for the Solr cores to not load was, though</li>
<li>I sent a mail to the dspace-tech mailing list about the “solr_update_time_stamp” error</li>
<li>A CCAFS user sent a message saying they got this error when submitting to CGSpace:</li>
</ul>
<pre><code>Authorization denied for action WORKFLOW_STEP_1 on COLLECTION:1021 by user 3049
</code></pre>
<ul>
<li>According to the <ahref="https://cgspace.cgiar.org/rest/collections/1021">REST API</a> collection 1021 appears to be <ahref="https://cgspace.cgiar.org/handle/10568/66581">CCAFS Tools, Maps, Datasets and Models</a></li>
<li>I looked at the <code>WORKFLOW_STEP_1</code> (Accept/Reject) and the group is of course empty</li>
<li>As we’ve seen several times recently, we are not using this step so it should simply be deleted</li>
<li>He asked me to upload the files for him via the command line, but the file he referenced (<code>Thumbnails_feb_2019.zip</code>) doesn’t exist</li>
<li>I noticed that the command line batch import functionality is a bit weird when using zip files because you have to specify the directory where the zip file is location as well as the zip file’s name:</li>
