<metaproperty="og:description"content="2022-04-01 I did G1GC tests on DSpace Test (linode26) to compliment the CMS tests I did yesterday The Discovery indexing took this long: real 334m33.625s user 227m51.331s sys 3m43.037s 2022-04-04 Start a full harvest on AReS Help Marianne with submit/approve access on a new collection on CGSpace Go back in Gaia’s batch reports to find records that she indicated for replacing on CGSpace (ie, those with better new copies, new versions, etc) Looking at the Solr statistics for 2022-03 on CGSpace I see 54."/>
Send Gaia the last batch of potential duplicates for items 701 to 980:
<metaname="twitter:description"content="2022-04-01 I did G1GC tests on DSpace Test (linode26) to compliment the CMS tests I did yesterday The Discovery indexing took this long: real 334m33.625s user 227m51.331s sys 3m43.037s 2022-04-04 Start a full harvest on AReS Help Marianne with submit/approve access on a new collection on CGSpace Go back in Gaia’s batch reports to find records that she indicated for replacing on CGSpace (ie, those with better new copies, new versions, etc) Looking at the Solr statistics for 2022-03 on CGSpace I see 54."/>
Send Gaia the last batch of potential duplicates for items 701 to 980:
</span></span></span><spanstyle="display:flex;"><span><spanstyle="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 12914
</span></span></code></pre></div><ul>
<li>I added a few from that list to the local overrides in our DSpace while I wait for feedback from the COUNTER-Robots project</li>
</ul>
<h2id="2022-03-05">2022-03-05</h2>
<ul>
<li>Start AReS harvest</li>
</ul>
<h2id="2022-03-10">2022-03-10</h2>
<ul>
<li>A few days ago Gaia sent me her notes on the fourth batch of TAC/ICW documents (items 701–980 in the spreadsheet)
<ul>
<li>I created a filter in LibreOffice and selected the IDs for items with the action “delete”, then I created a custom text facet in OpenRefine with this GREL:</li>
<li>Help Marianne with submit/approve access on a new collection on CGSpace</li>
<h2id="2022-03-16">2022-03-16</h2>
<li>Go back in Gaia’s batch reports to find records that she indicated for replacing on CGSpace (ie, those with better new copies, new versions, etc)</li>
<li>Looking at the Solr statistics for 2022-03 on CGSpace
<ul>
<ul>
<li>Meeting with KM/KS group to start talking about the way forward for repositories and web publishing
<li>I see 54.229.218.204 on Amazon AWS made 49,000 requests, some of which with this user agent: <code>Apache-HttpClient/4.5.9 (Java/1.8.0_322)</code>, and many others with a normal browser agent, so that’s fishy!</li>
<ul>
<li>The DSpace agent pattern <code>http.?agent</code> seems to have caught the first ones, but I’ll purge the IP ones</li>
<li>We agreed to form a sub-group of the transition task team to put forward a recommendation for repository and web publishing</li>
<li>I see 40.77.167.80 is Bing or MSN Bot, but using a normal browser user agent, and if I search Solr for <code>dns:*msnbot* AND dns:*.msn.com.</code> I see over 100,000, which is a problem I noticed a few months ago too…</li>
<li>I extracted the MSN Bot IPs from Solr using an IP facet, then used the <code>check-spider-ip-hits.sh</code> script to purge them</li>
</ul>
</ul>
</li>
</li>
</ul>
</ul>
<h2id="2022-03-20">2022-03-20</h2>
<h2id="2022-04-10">2022-04-10</h2>
<ul>
<ul>
<li>Start a full harvest on AReS</li>
<li>Start a full harvest on AReS</li>
</ul>
</ul>
<h2id="2022-03-21">2022-03-21</h2>
<h2id="2022-04-13">2022-04-13</h2>
<ul>
<ul>
<li>Review a few submissions for Open Repositories 2022</li>
<li>UptimeRobot mailed to say that CGSpace was down
<li>Test one tentative DSpace 6.4 patch and give feedback on a few more that Hrafn missed</li>
</ul>
<h2id="2022-03-22">2022-03-22</h2>
<ul>
<ul>
<li>I accidentally dropped the PostgreSQL database on DSpace Test, forgetting that I had all the CGIAR CAS items there
<li>I looked and found the load at 44…</li>
<ul>
<li>I had been meaning to update my local database…</li>
</ul>
</li>
<li>I re-imported the CGIAR CAS documents to <ahref="https://dspacetest.cgiar.org/handle/10568/118432">DSpace Test</a> and generated the PDF thumbnails:</li>
<li>137.184.159.211 is on DigitalOcean using this user agent: <code>GuzzleHttp/6.3.3 curl/7.81.0 PHP/7.4.28</code>
<li>185.192.69.15 is in the UK</li>
<ul>
<li>I added a block for that IP in nginx and the load went down…</li>
<li>I blocked this IP in nginx and the load went down immediately</li>
</ul>
</ul>
</li>
<h2id="2022-04-16">2022-04-16</h2>
<li>205.186.128.185 is on Media Temple, but it’s OK because it’s the CCAFS publications importer bot</li>
<li>54.195.118.125 is on Amazon, but is also a CCAFS publications importer bot apparently (perhaps a test server)</li>
<li>70.32.90.172 is on Media Temple and has no user agent</li>
<li>What is surprising to me is that we already have an nginx rule to return HTTP 403 for requests without a user agent
<ul>
<ul>
<li>I verified it works as expected with an empty user agent:</li>
<li>Start harvest on AReS</li>
</ul>
<h2id="2022-04-18">2022-04-18</h2>
<ul>
<li>I woke up to several notices from UptimeRobot that CGSpace had gone down and up in the night (of course I’m on holiday out of the country for Easter)
<ul>
<li>I see there are many locks in use from the XMLUI:</li>
<divclass="highlight"><pretabindex="0"style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><codeclass="language-console"data-lang="console"><spanstyle="display:flex;"><span>$ psql -c <spanstyle="color:#e6db74">'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;'</span> | grep -o -E <spanstyle="color:#e6db74">'(dspaceWeb|dspaceApi)'</span> | sort | uniq -c
</span></span><spanstyle="display:flex;"><span>Due to abuse we no longer permit requests without a user agent. Please specify a descriptive user agent, for example containing the word 'bot', if you are accessing the site programmatically. For more information see here: https://dspacetest.cgiar.org/page/about.
<li>I note that the nginx log shows ‘-’ for a request with an empty user agent, which would be indistinguishable from a request with a ‘-’, for example these were successful:</li>
<li>Looking at the top IPs making requests it seems they are Yandex, bingbot, and Googlebot:</li>
<li>Maria from ABC asked about a reporting discrepancy on AReS
<ul>
<li>I think it’s because the last harvest was over the weekend, and she was expecting to see items submitted this week</li>
</ul>
</li>
<li>Paola from ABC said they are decomissioning the server where many of their library PDFs are hosted
<ul>
<li>She asked if we can download them and upload them directly to CGSpace</li>
</ul>
</li>
<li>I re-created my local Artifactory container</li>
<li>I am doing a walkthrough of DSpace 7.3-SNAPSHOT to see how things are lately
<ul>
<li>One thing I realized is that OAI is no longer a standalone web application, it is part of the <code>server</code> app now: http://localhost:8080/server/oai/request?verb=Identify</li>
</ul>
</li>
<li>Deploy PostgreSQL 12 on CGSpace (linode18) but don’t switch over yet, because I see some users active
<ul>
<li>I did this on DSpace Test in 2022-02 so I just followed the same procedure</li>
<li>After that I ran all system updates and rebooted the server</li>
</ul>
</li>
</ul>
<h2id="2022-03-25">2022-03-25</h2>
<ul>
<li>Looking at the PostgreSQL database size on CGSpace after the update yesterday:</li>
<li>The space saving in indexes of recent PostgreSQL releases is awesome!</li>
<li>Import a DSpace 6.x database dump from production into my local DSpace 7 database
<ul>
<li>I see I still the same errors <ahref="/cgspace-notes/2021-04/">I saw in 2021-04</a> when testing DSpace 7.0 beta 5</li>
<li>I had to delete some old migrations, as well as all Atmire ones first:</li>
</ul>
</li>
</ul>
<divclass="highlight"><pretabindex="0"style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><codeclass="language-console"data-lang="console"><spanstyle="display:flex;"><span>localhost/dspace7= ☘ DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
</span></span><spanstyle="display:flex;"><span>localhost/dspace7= ☘ DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%'
</span></span></code></pre></div><ul>
</span></span></code></pre></div><ul>
<li>Then I was able to migrate to DSpace 7 with <code>dspace database migrate ignored</code> as the <ahref="https://wiki.lyrasis.org/display/DSDOC7x/Upgrading+DSpace">DSpace upgrade notes say</a>
<li>Overall, it seems we had 17,000 unique IPs connecting in the last nine hours (currently 9:14AM and log file rolled over at 00:00):</li>
<li>That’s a lot of unique IPs, and I see some patterns of IPs in China making ten to twenty requests each
<ul>
<ul>
<li>I see that the <ahref="https://github.com/DSpace/dspace-angular/issues/1357">flash of unstyled content bug</a> still exists on dspace-angluar… ouch!</li>
<li>The ISPs I’ve seen so far are ChinaNet and China Unicom</li>
</ul>
</ul>
</li>
</li>
<li>I extracted all the IPs from today and resolved them:</li>
<li>A handful of spider user agents that I identified were merged into COUNTER-Robots so I updated the ILRI override in our DSpace and regenerated the <code>example</code> file that contains most patterns
<ul>
<li>I updated CGSpace, then ran all system updates and rebooted the host</li>
<li>I also ran <code>dspace cleanup -v</code> to prune the database</li>
</ul>
</li>
</ul>
<h2id="2022-04-24">2022-04-24</h2>
<ul>
<li>Start a harvest on AReS</li>
<li>Start a harvest on AReS</li>
</ul>
</ul>
<h2id="2022-03-26">2022-03-26</h2>
<ul>
<li>Update dspace-statistics-api to Falcon 3.1.0 and <ahref="https://github.com/ilri/dspace-statistics-api/releases/tag/v1.4.3">release v1.4.3</a></li>
</ul>
<h2id="2022-03-28">2022-03-28</h2>
<ul>
<li>Create another test account for Rafael from Bioversity-CIAT to submit some items to DSpace Test:</li>
</ul>
<divclass="highlight"><pretabindex="0"style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><codeclass="language-console"data-lang="console"><spanstyle="display:flex;"><span>$ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p <spanstyle="color:#e6db74">'fuuuuuuuu'</span>
</span></span></code></pre></div><ul>
<li>I added the account to the Alliance Admins account, which is should allow him to submit to any Alliance collection
<ul>
<li>According to my notes from <ahref="/cgspace-notes/2020-10/">2020-10</a> the account must be in the admin group in order to submit via the REST API</li>
</ul>
</li>
<li>Abenet and I noticed 1,735 items in CTA’s community that have the title “delete”
<ul>
<li>We asked Peter and he said we should delete them</li>
<li>I exported the CTA community metadata and used OpenRefine to filter all items with the “delete” title, then used the “expunge” bulkedit action to remove them</li>
</ul>
</li>
<li>I realized I forgot to clean up the old Let’s Encrypt certbot stuff after upgrading CGSpace (linode18) to Ubuntu 20.04 a few weeks ago
<ul>
<li>I also removed the pre-Ubuntu 20.04 Let’s Encrypt stuff from the Ansble infrastructure playbooks</li>
</ul>
</li>
</ul>
<h2id="2022-03-29">2022-03-29</h2>
<ul>
<li>Gaia sent me her notes on the final review of duplicates of all TAC/ICW documents
<ul>
<li>I created a filter in LibreOffice and selected the IDs for items with the action “delete”, then I created a custom text facet in OpenRefine with this GREL:</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>or(
isNotNull(value.match('33')),
isNotNull(value.match('179')),
isNotNull(value.match('452')),
isNotNull(value.match('489')),
isNotNull(value.match('541')),
isNotNull(value.match('568')),
isNotNull(value.match('646')),
isNotNull(value.match('889'))
)
</code></pre><ul>
<li>Then I flagged all matching records, exported a CSV to use with SAFBuilder, and imported the 692 items on CGSpace, and generated the thumbnails:</li>
<li>After that I did some normalization on the <code>cg.subject.system</code> metadata and extracted a few dozen countries to the country field</li>
<li>Start a harvest on AReS</li>
</ul>
<h2id="2022-03-30">2022-03-30</h2>
<ul>
<li>Yesterday Rafael from CIAT asked me to re-create his approver account on DSpace Test as well</li>
</ul>
<divclass="highlight"><pretabindex="0"style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><codeclass="language-console"data-lang="console"><spanstyle="display:flex;"><span>$ dspace user -a -m tip-approve@cgiar.org -g Rafael -s Rodriguez -p <spanstyle="color:#e6db74">'fuuuu'</span>
</span></span></code></pre></div><ul>
<li>I started looking into the request regarding the CIAT Library PDFs
<ul>
<li>There are over 4,000 links to PDFs hosted on that server in CGSpace metadata</li>
<li>The links seem to be down though! I emailed Paola to ask</li>
</ul>
</li>
</ul>
<h2id="2022-03-31">2022-03-31</h2>
<ul>
<li>Switch DSpace Test (linode26) back to CMS GC so I can do some monitoring and evaluation of GC before switching to G1GC</li>
<li>I will do the following for CMS and G1GC on DSpace Test:
<li>Leroy from CIAT said that the CIAT Library server has security issues so was limited to internal traffic
<ul>
<li>I extracted a list of URLs from CGSpace to send him:</li>
</ul>
</li>
</ul>
<divclass="highlight"><pretabindex="0"style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><codeclass="language-console"data-lang="console"><spanstyle="display:flex;"><span>localhost/dspacetest= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE metadata_field_id=219 AND text_value ~ 'https?://ciat-library') to /tmp/2022-03-31-ciat-library-urls.csv WITH CSV HEADER;
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