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Add notes for 2016-10

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Alan Orth 2016-10-03 18:28:33 +03:00
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5
content/post/2016-09.md
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@ -540,6 +540,11 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
- Add `cg.identifier.ciatproject` to metadata registry in preparation for CIAT project tag
- Merge changes for CIAT project tag ([#282](https://github.com/ilri/DSpace/pull/282))
- DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console
- People on DSpace mailing list gave me a query to get authors from certain collections:
```
dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
```
## 2016-09-30

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@ -0,0 +1,26 @@
+++
date = "2016-10-03T15:53:00+03:00"
author = "Alan Orth"
title = "October, 2016"
tags = ["Notes"]
+++
## 2016-10-03
- Testing adding [ORCIDs to a CSV](https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing) file for a single item to see if the author orders get messed up
- Need to test the following scenarios to see how author order is affected:
- ORCIDs only
- ORCIDs plus normal authors
- I exported a random item's metadata as CSV, deleted *all columns* except id and collection, and made a new coloum called `ORCID:dc.contributor.author` with the following random ORCIDs from the ORCID registry:
```
0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
```
- Hmm, with the `dc.contributor.author` column removed, DSpace doesn't detect any changes
- With a blank `dc.contributor.author` column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors
- I added the [disclaimer text](https://github.com/ilri/DSpace/issues/234) to the About page, then added a footer link to the disclaimer's ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: https://github.com/twbs/bootstrap/issues/1768
![Bootstrap issue with in-page anchors](2016/10/bootstrap-issue.png)
- Looks like we'll just have to add the text to the About page (without a link) or add a separate page

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@ -35,7 +35,7 @@
<meta property="twitter:title" content="November, 2015">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2015-11-22">2015-11-22</h2>
<h2 id="2015-11-22">2015-11-22</h2>
<ul>
<li>CGSpace went down</li>
@ -96,6 +94,8 @@
78
</code></pre>
<p></p>
<ul>
<li>For now I have increased the limit from 60 to 90, run updates, and rebooted the server</li>
</ul>
@ -229,7 +229,6 @@ db.statementpool = true
<li>This might help with REST API speed (which I mentioned above and still need to do real tests)</li>
</ul>
</article>
@ -246,6 +245,8 @@ db.statementpool = true
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -254,8 +255,6 @@ db.statementpool = true
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

13
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@ -35,7 +35,7 @@
<meta property="twitter:title" content="December, 2015">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2015-12-02">2015-12-02</h2>
<h2 id="2015-12-02">2015-12-02</h2>
<ul>
<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
@ -97,6 +95,8 @@
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
</code></pre>
<p></p>
<ul>
<li>I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper</li>
<li>Need to remember to go check if everything is ok in a few days and then change CGSpace</li>
@ -244,7 +244,6 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<li>Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot&rsquo;s crawl rate to the &ldquo;Let Google optimize&rdquo; setting</li>
</ul>
</article>
@ -261,6 +260,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -269,8 +270,6 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

13
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@ -35,7 +35,7 @@
<meta property="twitter:title" content="January, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-01-13">2016-01-13</h2>
<h2 id="2016-01-13">2016-01-13</h2>
<ul>
<li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li>
@ -92,6 +90,8 @@
<li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li>
</ul>
<p></p>
<h2 id="2016-01-14">2016-01-14</h2>
<ul>
@ -169,7 +169,6 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} \; | so
<p><img src="2016/01/xmlui-subjects-after.png" alt="XMLUI subjects after" /></p>
</article>
@ -186,6 +185,8 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} \; | so
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -194,8 +195,6 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} \; | so
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

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@ -35,7 +35,7 @@
<meta property="twitter:title" content="February, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-02-05">2016-02-05</h2>
<h2 id="2016-02-05">2016-02-05</h2>
<ul>
<li>Looking at some DAGRIS data for Abenet Yabowork</li>
@ -99,6 +97,8 @@
<li>Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;</li>
</ul>
<p></p>
<h2 id="2016-02-06">2016-02-06</h2>
<ul>
@ -408,7 +408,6 @@ Bitstream: tést señora alimentación.pdf
<li>Re-deploy CGSpace with the Google Scholar fix, but I&rsquo;m waiting on the Atmire fixes for now, as the branch history is ugly</li>
</ul>
</article>
@ -425,6 +424,8 @@ Bitstream: tést señora alimentación.pdf
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -433,8 +434,6 @@ Bitstream: tést señora alimentación.pdf
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

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public/2016-03/index.html
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@ -35,7 +35,7 @@
<meta property="twitter:title" content="March, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-03-02">2016-03-02</h2>
<h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
@ -92,6 +90,8 @@
<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
</ul>
<p></p>
<h2 id="2016-03-07">2016-03-07</h2>
<ul>
@ -322,7 +322,6 @@
<li>After all of this we need to start implementing controlled vocabularies for fields, either with the Javascript lookup or like existing ILRI subjects</li>
</ul>
</article>
@ -339,6 +338,8 @@
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -347,8 +348,6 @@
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

13
public/2016-04/index.html
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@ -35,7 +35,7 @@
<meta property="twitter:title" content="April, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-04-04">2016-04-04</h2>
<h2 id="2016-04-04">2016-04-04</h2>
<ul>
<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
@ -94,6 +92,8 @@
<li>Also, I noticed the <code>checker</code> log has some errors we should pay attention to:</li>
</ul>
<p></p>
<pre><code>Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
@ -535,7 +535,6 @@ dspace.log.2016-04-27:7271
<li>I will check the logs again in a few days to look for patterns, see who is accessing it, etc</li>
</ul>
</article>
@ -552,6 +551,8 @@ dspace.log.2016-04-27:7271
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -560,8 +561,6 @@ dspace.log.2016-04-27:7271
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

13
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@ -35,7 +35,7 @@
<meta property="twitter:title" content="May, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-05-01">2016-05-01</h2>
<h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
@ -96,6 +94,8 @@
3168
</code></pre>
<p></p>
<ul>
<li>The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29</li>
<li>100% of the requests coming from Ethiopia are like this and result in an HTTP 500:</li>
@ -381,7 +381,6 @@ sys 0m20.540s
<li>Clean up and import ~65 more CTA items into CGSpace</li>
</ul>
</article>
@ -398,6 +397,8 @@ sys 0m20.540s
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -406,8 +407,6 @@ sys 0m20.540s
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

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@ -35,7 +35,7 @@
<meta property="twitter:title" content="June, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-06-01">2016-06-01</h2>
<h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
@ -95,6 +93,8 @@
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
<p></p>
<pre><code>dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
@ -428,7 +428,6 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<pre><code># update metadatavalue set text_value = regexp_replace(text_value, '(Poole, J),', '\1') where metadata_field_id=3 and text_value = 'Poole, J,';
</code></pre>
</article>
@ -445,6 +444,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -453,8 +454,6 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

13
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@ -35,7 +35,7 @@
<meta property="twitter:title" content="July, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-07-01">2016-07-01</h2>
<h2 id="2016-07-01">2016-07-01</h2>
<ul>
<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
@ -103,6 +101,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>In this case the select query was showing 95 results before the update</li>
</ul>
<p></p>
<h2 id="2016-07-02">2016-07-02</h2>
<ul>
@ -330,7 +330,6 @@ discovery.index.authority.ignore-variants=true
<li>Also change &ldquo;Subjects&rdquo; to &ldquo;AGROVOC keywords&rdquo; in Discovery sidebar/search and Browse by (<a href="https://github.com/ilri/DSpace/issues/257">#257</a>)</li>
</ul>
</article>
@ -347,6 +346,8 @@ discovery.index.authority.ignore-variants=true
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -355,8 +356,6 @@ discovery.index.authority.ignore-variants=true
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

13
public/2016-08/index.html
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@ -35,7 +35,7 @@
<meta property="twitter:title" content="August, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-08-01">2016-08-01</h2>
<h2 id="2016-08-01">2016-08-01</h2>
<ul>
<li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li>
@ -100,6 +98,8 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre>
<p></p>
<ul>
<li>Lots of conflicts that don&rsquo;t make sense (ie, shouldn&rsquo;t conflict!)</li>
<li>This file in particular conflicts almost 10 times: <code>dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss</code></li>
@ -409,7 +409,6 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
<li>Run all system updates and reboot the server</li>
</ul>
</article>
@ -426,6 +425,8 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -434,8 +435,6 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

17
public/2016-09/index.html
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@ -35,7 +35,7 @@
<meta property="twitter:title" content="September, 2016">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -82,9 +82,7 @@
</p>
</header>
<h2 id="2016-09-01">2016-09-01</h2>
<h2 id="2016-09-01">2016-09-01</h2>
<ul>
<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
@ -96,6 +94,8 @@
<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;
</code></pre>
<p></p>
<ul>
<li>User who has been migrated to the root vs user still in the hierarchical structure:</li>
</ul>
@ -704,8 +704,12 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<li>Add <code>cg.identifier.ciatproject</code> to metadata registry in preparation for CIAT project tag</li>
<li>Merge changes for CIAT project tag (<a href="https://github.com/ilri/DSpace/pull/282">#282</a>)</li>
<li>DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console</li>
<li>People on DSpace mailing list gave me a query to get authors from certain collections:</li>
</ul>
<pre><code>dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
</code></pre>
<h2 id="2016-09-30">2016-09-30</h2>
<ul>
@ -713,7 +717,6 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<li>There is a patch but it is only for 5.5 and doesn&rsquo;t apply cleanly to 5.1</li>
</ul>
</article>
@ -730,6 +733,8 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -738,8 +743,6 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

174
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-10/" title="October, 2016">October, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-10-03T15:53:00&#43;03:00">Mon Oct 03, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-10-03">2016-10-03</h2>
<ul>
<li>Testing adding <a href="https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing">ORCIDs to a CSV</a> file for a single item to see if the author orders get messed up</li>
<li>Need to test the following scenarios to see how author order is affected:
<ul>
<li>ORCIDs only</li>
<li>ORCIDs plus normal authors</li>
</ul></li>
<li>I exported a random item&rsquo;s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
</ul>
<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
</code></pre>
<ul>
<li>Hmm, with the <code>dc.contributor.author</code> column removed, DSpace doesn&rsquo;t detect any changes</li>
<li>With a blank <code>dc.contributor.author</code> column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors</li>
<li>I added the <a href="https://github.com/ilri/DSpace/issues/234">disclaimer text</a> to the About page, then added a footer link to the disclaimer&rsquo;s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: <a href="https://github.com/twbs/bootstrap/issues/1768">https://github.com/twbs/bootstrap/issues/1768</a></li>
</ul>
<p><img src="2016/10/bootstrap-issue.png" alt="Bootstrap issue with in-page anchors" /></p>
<ul>
<li>Looks like we&rsquo;ll just have to add the text to the About page (without a link) or add a separate page</li>
</ul>
</article>
</div> <!-- /.blog-main -->
<aside class="col-sm-3 offset-sm-1 blog-sidebar">
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
<li><a href="/cgspace-notes/2016-07/">July, 2016</a></li>
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
</ol>
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<section class="sidebar-module">
<h4>Links</h4>
<ol class="list-unstyled">
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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@ -32,7 +32,7 @@
<meta property="twitter:title" content="CGSpace Notes">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -74,6 +74,20 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-10/" title="October, 2016">October, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-10-03T15:53:00&#43;03:00">Mon Oct 03, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
2016-10-03 Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up Need to test the following scenarios to see how author order is affected: ORCIDs only ORCIDs plus normal authors I exported a random item&rsquo;s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry: 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X Hmm, with the dc.
<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-09/" title="September, 2016">September, 2016</a></h2>
@ -95,6 +109,7 @@
<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;
</code></pre>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-09/'>Read more →</a>
</article>
@ -124,6 +139,7 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-08/'>Read more →</a>
</article>
@ -156,6 +172,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>In this case the select query was showing 95 results before the update</li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-07/'>Read more →</a>
</article>
@ -180,35 +197,11 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-05/" title="May, 2016">May, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-05-01T23:06:00&#43;03:00">Sun May 01, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
<li>I have blocked access to the API now</li>
<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
</ul>
<pre><code># awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
3168
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2016-05/'>Read more →</a>
</article>
@ -224,6 +217,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -232,8 +227,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

145
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@ -2,22 +2,58 @@
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>CGSpace Notes</title>
<link>https://alanorth.github.io/cgspace-notes/</link>
<link>https://alanorth.github.io/cgspace-notes/index.xml</link>
<description>Recent content on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Thu, 01 Sep 2016 15:53:00 +0300</lastBuildDate>
<lastBuildDate>Mon, 03 Oct 2016 15:53:00 +0300</lastBuildDate>
<atom:link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>October, 2016</title>
<link>https://alanorth.github.io/cgspace-notes/2016-10/</link>
<pubDate>Mon, 03 Oct 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-10/</guid>
<description>
&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Testing adding &lt;a href=&#34;https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing&#34;&gt;ORCIDs to a CSV&lt;/a&gt; file for a single item to see if the author orders get messed up&lt;/li&gt;
&lt;li&gt;Need to test the following scenarios to see how author order is affected:
&lt;ul&gt;
&lt;li&gt;ORCIDs only&lt;/li&gt;
&lt;li&gt;ORCIDs plus normal authors&lt;/li&gt;
&lt;/ul&gt;&lt;/li&gt;
&lt;li&gt;I exported a random item&amp;rsquo;s metadata as CSV, deleted &lt;em&gt;all columns&lt;/em&gt; except id and collection, and made a new coloum called &lt;code&gt;ORCID:dc.contributor.author&lt;/code&gt; with the following random ORCIDs from the ORCID registry:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;Hmm, with the &lt;code&gt;dc.contributor.author&lt;/code&gt; column removed, DSpace doesn&amp;rsquo;t detect any changes&lt;/li&gt;
&lt;li&gt;With a blank &lt;code&gt;dc.contributor.author&lt;/code&gt; column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors&lt;/li&gt;
&lt;li&gt;I added the &lt;a href=&#34;https://github.com/ilri/DSpace/issues/234&#34;&gt;disclaimer text&lt;/a&gt; to the About page, then added a footer link to the disclaimer&amp;rsquo;s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: &lt;a href=&#34;https://github.com/twbs/bootstrap/issues/1768&#34;&gt;https://github.com/twbs/bootstrap/issues/1768&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;img src=&#34;2016/10/bootstrap-issue.png&#34; alt=&#34;Bootstrap issue with in-page anchors&#34; /&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Looks like we&amp;rsquo;ll just have to add the text to the About page (without a link) or add a separate page&lt;/li&gt;
&lt;/ul&gt;
</description>
</item>
<item>
<title>September, 2016</title>
<link>https://alanorth.github.io/cgspace-notes/2016-09/</link>
<pubDate>Thu, 01 Sep 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-09/</guid>
<description>
&lt;h2 id=&#34;2016-09-01&#34;&gt;2016-09-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-09-01&#34;&gt;2016-09-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors&lt;/li&gt;
@ -29,6 +65,8 @@
&lt;pre&gt;&lt;code&gt;$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &amp;quot;dc=cgiarad,dc=org&amp;quot; -D &amp;quot;admigration1@cgiarad.org&amp;quot; -W &amp;quot;(sAMAccountName=admigration1)&amp;quot;
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;User who has been migrated to the root vs user still in the hierarchical structure:&lt;/li&gt;
&lt;/ul&gt;
@ -637,15 +675,18 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
&lt;li&gt;Add &lt;code&gt;cg.identifier.ciatproject&lt;/code&gt; to metadata registry in preparation for CIAT project tag&lt;/li&gt;
&lt;li&gt;Merge changes for CIAT project tag (&lt;a href=&#34;https://github.com/ilri/DSpace/pull/282&#34;&gt;#282&lt;/a&gt;)&lt;/li&gt;
&lt;li&gt;DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console&lt;/li&gt;
&lt;li&gt;People on DSpace mailing list gave me a query to get authors from certain collections:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in (&#39;10568/5472&#39;, &#39;10568/5473&#39;)));
&lt;/code&gt;&lt;/pre&gt;
&lt;h2 id=&#34;2016-09-30&#34;&gt;2016-09-30&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Deny access to REST API&amp;rsquo;s &lt;code&gt;find-by-metadata-field&lt;/code&gt; endpoint to protect against an upstream security issue (DS-3250)&lt;/li&gt;
&lt;li&gt;There is a patch but it is only for 5.5 and doesn&amp;rsquo;t apply cleanly to 5.1&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -654,9 +695,7 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<pubDate>Mon, 01 Aug 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-08/</guid>
<description>
&lt;h2 id=&#34;2016-08-01&#34;&gt;2016-08-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-08-01&#34;&gt;2016-08-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add updated distribution license from Sisay (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/259&#34;&gt;#259&lt;/a&gt;)&lt;/li&gt;
@ -672,6 +711,8 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Lots of conflicts that don&amp;rsquo;t make sense (ie, shouldn&amp;rsquo;t conflict!)&lt;/li&gt;
&lt;li&gt;This file in particular conflicts almost 10 times: &lt;code&gt;dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss&lt;/code&gt;&lt;/li&gt;
@ -979,8 +1020,7 @@ $ JAVA_OPTS=&amp;quot;-Dfile.encoding=UTF-8 -Xmx512m&amp;quot; /home/cgspace.cgi
&lt;ul&gt;
&lt;li&gt;Run corrections for Delia Grace and &lt;code&gt;CONGO, DR&lt;/code&gt;, and deploy August changes to CGSpace&lt;/li&gt;
&lt;li&gt;Run all system updates and reboot the server&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -989,9 +1029,7 @@ $ JAVA_OPTS=&amp;quot;-Dfile.encoding=UTF-8 -Xmx512m&amp;quot; /home/cgspace.cgi
<pubDate>Fri, 01 Jul 2016 10:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-07/</guid>
<description>
&lt;h2 id=&#34;2016-07-01&#34;&gt;2016-07-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-07-01&#34;&gt;2016-07-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add &lt;code&gt;dc.description.sponsorship&lt;/code&gt; to Discovery sidebar facets and make investors clickable in item view (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/232&#34;&gt;#232&lt;/a&gt;)&lt;/li&gt;
@ -1010,6 +1048,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
&lt;li&gt;In this case the select query was showing 95 results before the update&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-07-02&#34;&gt;2016-07-02&lt;/h2&gt;
&lt;ul&gt;
@ -1235,8 +1275,7 @@ discovery.index.authority.ignore-variants=true
&lt;ul&gt;
&lt;li&gt;Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by&lt;/li&gt;
&lt;li&gt;Also change &amp;ldquo;Subjects&amp;rdquo; to &amp;ldquo;AGROVOC keywords&amp;rdquo; in Discovery sidebar/search and Browse by (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/257&#34;&gt;#257&lt;/a&gt;)&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1245,9 +1284,7 @@ discovery.index.authority.ignore-variants=true
<pubDate>Wed, 01 Jun 2016 10:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-06/</guid>
<description>
&lt;h2 id=&#34;2016-06-01&#34;&gt;2016-06-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-06-01&#34;&gt;2016-06-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Experimenting with IFPRI OAI (we want to harvest their publications)&lt;/li&gt;
@ -1258,6 +1295,8 @@ discovery.index.authority.ignore-variants=true
&lt;li&gt;Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in &lt;code&gt;dc.identifier.fund&lt;/code&gt; to &lt;code&gt;cg.identifier.cpwfproject&lt;/code&gt; and then the rest to &lt;code&gt;dc.description.sponsorship&lt;/code&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like &#39;PN%&#39; or text_value like &#39;PHASE%&#39; or text_value = &#39;CBA&#39; or text_value = &#39;IA&#39;);
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
@ -1589,8 +1628,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;# update metadatavalue set text_value = regexp_replace(text_value, &#39;(Poole, J),&#39;, &#39;\1&#39;) where metadata_field_id=3 and text_value = &#39;Poole, J,&#39;;
&lt;/code&gt;&lt;/pre&gt;
</description>
&lt;/code&gt;&lt;/pre&gt;</description>
</item>
<item>
@ -1599,9 +1637,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<pubDate>Sun, 01 May 2016 23:06:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-05/</guid>
<description>
&lt;h2 id=&#34;2016-05-01&#34;&gt;2016-05-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-05-01&#34;&gt;2016-05-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Since yesterday there have been 10,000 REST errors and the site has been unstable again&lt;/li&gt;
@ -1613,6 +1649,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
3168
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29&lt;/li&gt;
&lt;li&gt;100% of the requests coming from Ethiopia are like this and result in an HTTP 500:&lt;/li&gt;
@ -1896,8 +1934,7 @@ sys 0m20.540s
&lt;li&gt;Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.&lt;/li&gt;
&lt;li&gt;Re-sync DSpace Test data with CGSpace&lt;/li&gt;
&lt;li&gt;Clean up and import ~65 more CTA items into CGSpace&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1906,9 +1943,7 @@ sys 0m20.540s
<pubDate>Mon, 04 Apr 2016 11:06:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-04/</guid>
<description>
&lt;h2 id=&#34;2016-04-04&#34;&gt;2016-04-04&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-04-04&#34;&gt;2016-04-04&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit&lt;/li&gt;
@ -1918,6 +1953,8 @@ sys 0m20.540s
&lt;li&gt;Also, I noticed the &lt;code&gt;checker&lt;/code&gt; log has some errors we should pay attention to:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
@ -2357,8 +2394,7 @@ dspace.log.2016-04-27:7271
&lt;ul&gt;
&lt;li&gt;I will check the logs again in a few days to look for patterns, see who is accessing it, etc&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2367,9 +2403,7 @@ dspace.log.2016-04-27:7271
<pubDate>Wed, 02 Mar 2016 16:50:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-03/</guid>
<description>
&lt;h2 id=&#34;2016-03-02&#34;&gt;2016-03-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-03-02&#34;&gt;2016-03-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at issues with author authorities on CGSpace&lt;/li&gt;
@ -2377,6 +2411,8 @@ dspace.log.2016-04-27:7271
&lt;li&gt;Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-03-07&#34;&gt;2016-03-07&lt;/h2&gt;
&lt;ul&gt;
@ -2605,8 +2641,7 @@ dspace.log.2016-04-27:7271
&lt;li&gt;We decided to proceed with some deletes first, then identify CGSpace-specific fields to clean/move to &lt;code&gt;cg.*&lt;/code&gt;, and then worry about broader changes to DC&lt;/li&gt;
&lt;li&gt;Before we move or rename and fields we need to circulate a list of fields we intend to change to CCAFS, CWPF, etc who might be harvesting the fields&lt;/li&gt;
&lt;li&gt;After all of this we need to start implementing controlled vocabularies for fields, either with the Javascript lookup or like existing ILRI subjects&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2615,9 +2650,7 @@ dspace.log.2016-04-27:7271
<pubDate>Fri, 05 Feb 2016 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-02/</guid>
<description>
&lt;h2 id=&#34;2016-02-05&#34;&gt;2016-02-05&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-02-05&#34;&gt;2016-02-05&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at some DAGRIS data for Abenet Yabowork&lt;/li&gt;
@ -2632,6 +2665,8 @@ dspace.log.2016-04-27:7271
&lt;li&gt;Also, lots of things like &amp;ldquo;COTE D`LVOIRE&amp;rdquo; and &amp;ldquo;COTE D IVOIRE&amp;rdquo;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-02-06&#34;&gt;2016-02-06&lt;/h2&gt;
&lt;ul&gt;
@ -2939,8 +2974,7 @@ Bitstream: tést señora alimentación.pdf
&lt;ul&gt;
&lt;li&gt;Finally import the 1127 CIAT items into CGSpace: &lt;a href=&#34;https://cgspace.cgiar.org/handle/10568/35710&#34;&gt;https://cgspace.cgiar.org/handle/10568/35710&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;Re-deploy CGSpace with the Google Scholar fix, but I&amp;rsquo;m waiting on the Atmire fixes for now, as the branch history is ugly&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2949,9 +2983,7 @@ Bitstream: tést señora alimentación.pdf
<pubDate>Wed, 13 Jan 2016 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-01/</guid>
<description>
&lt;h2 id=&#34;2016-01-13&#34;&gt;2016-01-13&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-01-13&#34;&gt;2016-01-13&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Move ILRI collection &lt;code&gt;10568/12503&lt;/code&gt; from &lt;code&gt;10568/27869&lt;/code&gt; to &lt;code&gt;10568/27629&lt;/code&gt; using the &lt;a href=&#34;https://gist.github.com/alanorth/392c4660e8b022d99dfa&#34;&gt;move_collections.sh&lt;/a&gt; script I wrote last year.&lt;/li&gt;
@ -2959,6 +2991,8 @@ Bitstream: tést señora alimentación.pdf
&lt;li&gt;Update GitHub wiki for documentation of &lt;a href=&#34;https://github.com/ilri/DSpace/wiki/Maintenance-Tasks&#34;&gt;maintenance tasks&lt;/a&gt;.&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-01-14&#34;&gt;2016-01-14&lt;/h2&gt;
&lt;ul&gt;
@ -3034,8 +3068,7 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
&lt;li&gt;After:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;img src=&#34;2016/01/xmlui-subjects-after.png&#34; alt=&#34;XMLUI subjects after&#34; /&gt;&lt;/p&gt;
</description>
&lt;p&gt;&lt;img src=&#34;2016/01/xmlui-subjects-after.png&#34; alt=&#34;XMLUI subjects after&#34; /&gt;&lt;/p&gt;</description>
</item>
<item>
@ -3044,9 +3077,7 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
<pubDate>Wed, 02 Dec 2015 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2015-12/</guid>
<description>
&lt;h2 id=&#34;2015-12-02&#34;&gt;2015-12-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2015-12-02&#34;&gt;2015-12-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Replace &lt;code&gt;lzop&lt;/code&gt; with &lt;code&gt;xz&lt;/code&gt; in log compression cron jobs on DSpace Test—it uses less space:&lt;/li&gt;
@ -3059,6 +3090,8 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper&lt;/li&gt;
&lt;li&gt;Need to remember to go check if everything is ok in a few days and then change CGSpace&lt;/li&gt;
@ -3204,8 +3237,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
&lt;ul&gt;
&lt;li&gt;Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn&amp;rsquo;t as good, but it&amp;rsquo;s much faster and causes less IO/CPU load&lt;/li&gt;
&lt;li&gt;Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot&amp;rsquo;s crawl rate to the &amp;ldquo;Let Google optimize&amp;rdquo; setting&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -3214,9 +3246,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<pubDate>Mon, 23 Nov 2015 17:00:57 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2015-11/</guid>
<description>
&lt;h2 id=&#34;2015-11-22&#34;&gt;2015-11-22&lt;/h2&gt;
<description>&lt;h2 id=&#34;2015-11-22&#34;&gt;2015-11-22&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;CGSpace went down&lt;/li&gt;
@ -3228,6 +3258,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
78
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;For now I have increased the limit from 60 to 90, run updates, and rebooted the server&lt;/li&gt;
&lt;/ul&gt;
@ -3359,8 +3391,7 @@ db.statementpool = true
&lt;li&gt;Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace&amp;rsquo;s thirst can ever be quenched&lt;/li&gt;
&lt;li&gt;On another note, SUNScholar&amp;rsquo;s notes suggest adjusting some other postgres variables: &lt;a href=&#34;http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database&#34;&gt;http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;This might help with REST API speed (which I mentioned above and still need to do real tests)&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
</channel>

49
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View File

@ -32,7 +32,7 @@
<meta property="twitter:title" content="Posts">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -74,6 +74,20 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-10/" title="October, 2016">October, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-10-03T15:53:00&#43;03:00">Mon Oct 03, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
2016-10-03 Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up Need to test the following scenarios to see how author order is affected: ORCIDs only ORCIDs plus normal authors I exported a random item&rsquo;s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry: 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X Hmm, with the dc.
<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-09/" title="September, 2016">September, 2016</a></h2>
@ -95,6 +109,7 @@
<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;
</code></pre>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-09/'>Read more →</a>
</article>
@ -124,6 +139,7 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-08/'>Read more →</a>
</article>
@ -156,6 +172,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>In this case the select query was showing 95 results before the update</li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-07/'>Read more →</a>
</article>
@ -180,35 +197,11 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-05/" title="May, 2016">May, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-05-01T23:06:00&#43;03:00">Sun May 01, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
<li>I have blocked access to the API now</li>
<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
</ul>
<pre><code># awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
3168
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2016-05/'>Read more →</a>
</article>
@ -224,6 +217,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -232,8 +227,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

149
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@ -1,23 +1,59 @@
<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>Posts on CGSpace Notes</title>
<link>https://alanorth.github.io/cgspace-notes/post/</link>
<description>Recent content in Posts on CGSpace Notes</description>
<title>Post-rsses on CGSpace Notes</title>
<link>https://alanorth.github.io/cgspace-notes/post/index.xml</link>
<description>Recent content in Post-rsses on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Thu, 01 Sep 2016 15:53:00 +0300</lastBuildDate>
<lastBuildDate>Mon, 03 Oct 2016 15:53:00 +0300</lastBuildDate>
<atom:link href="https://alanorth.github.io/cgspace-notes/post/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>October, 2016</title>
<link>https://alanorth.github.io/cgspace-notes/2016-10/</link>
<pubDate>Mon, 03 Oct 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-10/</guid>
<description>
&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Testing adding &lt;a href=&#34;https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing&#34;&gt;ORCIDs to a CSV&lt;/a&gt; file for a single item to see if the author orders get messed up&lt;/li&gt;
&lt;li&gt;Need to test the following scenarios to see how author order is affected:
&lt;ul&gt;
&lt;li&gt;ORCIDs only&lt;/li&gt;
&lt;li&gt;ORCIDs plus normal authors&lt;/li&gt;
&lt;/ul&gt;&lt;/li&gt;
&lt;li&gt;I exported a random item&amp;rsquo;s metadata as CSV, deleted &lt;em&gt;all columns&lt;/em&gt; except id and collection, and made a new coloum called &lt;code&gt;ORCID:dc.contributor.author&lt;/code&gt; with the following random ORCIDs from the ORCID registry:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;Hmm, with the &lt;code&gt;dc.contributor.author&lt;/code&gt; column removed, DSpace doesn&amp;rsquo;t detect any changes&lt;/li&gt;
&lt;li&gt;With a blank &lt;code&gt;dc.contributor.author&lt;/code&gt; column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors&lt;/li&gt;
&lt;li&gt;I added the &lt;a href=&#34;https://github.com/ilri/DSpace/issues/234&#34;&gt;disclaimer text&lt;/a&gt; to the About page, then added a footer link to the disclaimer&amp;rsquo;s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: &lt;a href=&#34;https://github.com/twbs/bootstrap/issues/1768&#34;&gt;https://github.com/twbs/bootstrap/issues/1768&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;img src=&#34;2016/10/bootstrap-issue.png&#34; alt=&#34;Bootstrap issue with in-page anchors&#34; /&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Looks like we&amp;rsquo;ll just have to add the text to the About page (without a link) or add a separate page&lt;/li&gt;
&lt;/ul&gt;
</description>
</item>
<item>
<title>September, 2016</title>
<link>https://alanorth.github.io/cgspace-notes/2016-09/</link>
<pubDate>Thu, 01 Sep 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-09/</guid>
<description>
&lt;h2 id=&#34;2016-09-01&#34;&gt;2016-09-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-09-01&#34;&gt;2016-09-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors&lt;/li&gt;
@ -29,6 +65,8 @@
&lt;pre&gt;&lt;code&gt;$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &amp;quot;dc=cgiarad,dc=org&amp;quot; -D &amp;quot;admigration1@cgiarad.org&amp;quot; -W &amp;quot;(sAMAccountName=admigration1)&amp;quot;
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;User who has been migrated to the root vs user still in the hierarchical structure:&lt;/li&gt;
&lt;/ul&gt;
@ -637,15 +675,18 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
&lt;li&gt;Add &lt;code&gt;cg.identifier.ciatproject&lt;/code&gt; to metadata registry in preparation for CIAT project tag&lt;/li&gt;
&lt;li&gt;Merge changes for CIAT project tag (&lt;a href=&#34;https://github.com/ilri/DSpace/pull/282&#34;&gt;#282&lt;/a&gt;)&lt;/li&gt;
&lt;li&gt;DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console&lt;/li&gt;
&lt;li&gt;People on DSpace mailing list gave me a query to get authors from certain collections:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in (&#39;10568/5472&#39;, &#39;10568/5473&#39;)));
&lt;/code&gt;&lt;/pre&gt;
&lt;h2 id=&#34;2016-09-30&#34;&gt;2016-09-30&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Deny access to REST API&amp;rsquo;s &lt;code&gt;find-by-metadata-field&lt;/code&gt; endpoint to protect against an upstream security issue (DS-3250)&lt;/li&gt;
&lt;li&gt;There is a patch but it is only for 5.5 and doesn&amp;rsquo;t apply cleanly to 5.1&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -654,9 +695,7 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<pubDate>Mon, 01 Aug 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-08/</guid>
<description>
&lt;h2 id=&#34;2016-08-01&#34;&gt;2016-08-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-08-01&#34;&gt;2016-08-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add updated distribution license from Sisay (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/259&#34;&gt;#259&lt;/a&gt;)&lt;/li&gt;
@ -672,6 +711,8 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Lots of conflicts that don&amp;rsquo;t make sense (ie, shouldn&amp;rsquo;t conflict!)&lt;/li&gt;
&lt;li&gt;This file in particular conflicts almost 10 times: &lt;code&gt;dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss&lt;/code&gt;&lt;/li&gt;
@ -979,8 +1020,7 @@ $ JAVA_OPTS=&amp;quot;-Dfile.encoding=UTF-8 -Xmx512m&amp;quot; /home/cgspace.cgi
&lt;ul&gt;
&lt;li&gt;Run corrections for Delia Grace and &lt;code&gt;CONGO, DR&lt;/code&gt;, and deploy August changes to CGSpace&lt;/li&gt;
&lt;li&gt;Run all system updates and reboot the server&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -989,9 +1029,7 @@ $ JAVA_OPTS=&amp;quot;-Dfile.encoding=UTF-8 -Xmx512m&amp;quot; /home/cgspace.cgi
<pubDate>Fri, 01 Jul 2016 10:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-07/</guid>
<description>
&lt;h2 id=&#34;2016-07-01&#34;&gt;2016-07-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-07-01&#34;&gt;2016-07-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add &lt;code&gt;dc.description.sponsorship&lt;/code&gt; to Discovery sidebar facets and make investors clickable in item view (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/232&#34;&gt;#232&lt;/a&gt;)&lt;/li&gt;
@ -1010,6 +1048,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
&lt;li&gt;In this case the select query was showing 95 results before the update&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-07-02&#34;&gt;2016-07-02&lt;/h2&gt;
&lt;ul&gt;
@ -1235,8 +1275,7 @@ discovery.index.authority.ignore-variants=true
&lt;ul&gt;
&lt;li&gt;Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by&lt;/li&gt;
&lt;li&gt;Also change &amp;ldquo;Subjects&amp;rdquo; to &amp;ldquo;AGROVOC keywords&amp;rdquo; in Discovery sidebar/search and Browse by (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/257&#34;&gt;#257&lt;/a&gt;)&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1245,9 +1284,7 @@ discovery.index.authority.ignore-variants=true
<pubDate>Wed, 01 Jun 2016 10:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-06/</guid>
<description>
&lt;h2 id=&#34;2016-06-01&#34;&gt;2016-06-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-06-01&#34;&gt;2016-06-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Experimenting with IFPRI OAI (we want to harvest their publications)&lt;/li&gt;
@ -1258,6 +1295,8 @@ discovery.index.authority.ignore-variants=true
&lt;li&gt;Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in &lt;code&gt;dc.identifier.fund&lt;/code&gt; to &lt;code&gt;cg.identifier.cpwfproject&lt;/code&gt; and then the rest to &lt;code&gt;dc.description.sponsorship&lt;/code&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like &#39;PN%&#39; or text_value like &#39;PHASE%&#39; or text_value = &#39;CBA&#39; or text_value = &#39;IA&#39;);
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
@ -1589,8 +1628,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;# update metadatavalue set text_value = regexp_replace(text_value, &#39;(Poole, J),&#39;, &#39;\1&#39;) where metadata_field_id=3 and text_value = &#39;Poole, J,&#39;;
&lt;/code&gt;&lt;/pre&gt;
</description>
&lt;/code&gt;&lt;/pre&gt;</description>
</item>
<item>
@ -1599,9 +1637,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<pubDate>Sun, 01 May 2016 23:06:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-05/</guid>
<description>
&lt;h2 id=&#34;2016-05-01&#34;&gt;2016-05-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-05-01&#34;&gt;2016-05-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Since yesterday there have been 10,000 REST errors and the site has been unstable again&lt;/li&gt;
@ -1613,6 +1649,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
3168
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29&lt;/li&gt;
&lt;li&gt;100% of the requests coming from Ethiopia are like this and result in an HTTP 500:&lt;/li&gt;
@ -1896,8 +1934,7 @@ sys 0m20.540s
&lt;li&gt;Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.&lt;/li&gt;
&lt;li&gt;Re-sync DSpace Test data with CGSpace&lt;/li&gt;
&lt;li&gt;Clean up and import ~65 more CTA items into CGSpace&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1906,9 +1943,7 @@ sys 0m20.540s
<pubDate>Mon, 04 Apr 2016 11:06:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-04/</guid>
<description>
&lt;h2 id=&#34;2016-04-04&#34;&gt;2016-04-04&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-04-04&#34;&gt;2016-04-04&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit&lt;/li&gt;
@ -1918,6 +1953,8 @@ sys 0m20.540s
&lt;li&gt;Also, I noticed the &lt;code&gt;checker&lt;/code&gt; log has some errors we should pay attention to:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
@ -2357,8 +2394,7 @@ dspace.log.2016-04-27:7271
&lt;ul&gt;
&lt;li&gt;I will check the logs again in a few days to look for patterns, see who is accessing it, etc&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2367,9 +2403,7 @@ dspace.log.2016-04-27:7271
<pubDate>Wed, 02 Mar 2016 16:50:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-03/</guid>
<description>
&lt;h2 id=&#34;2016-03-02&#34;&gt;2016-03-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-03-02&#34;&gt;2016-03-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at issues with author authorities on CGSpace&lt;/li&gt;
@ -2377,6 +2411,8 @@ dspace.log.2016-04-27:7271
&lt;li&gt;Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-03-07&#34;&gt;2016-03-07&lt;/h2&gt;
&lt;ul&gt;
@ -2605,8 +2641,7 @@ dspace.log.2016-04-27:7271
&lt;li&gt;We decided to proceed with some deletes first, then identify CGSpace-specific fields to clean/move to &lt;code&gt;cg.*&lt;/code&gt;, and then worry about broader changes to DC&lt;/li&gt;
&lt;li&gt;Before we move or rename and fields we need to circulate a list of fields we intend to change to CCAFS, CWPF, etc who might be harvesting the fields&lt;/li&gt;
&lt;li&gt;After all of this we need to start implementing controlled vocabularies for fields, either with the Javascript lookup or like existing ILRI subjects&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2615,9 +2650,7 @@ dspace.log.2016-04-27:7271
<pubDate>Fri, 05 Feb 2016 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-02/</guid>
<description>
&lt;h2 id=&#34;2016-02-05&#34;&gt;2016-02-05&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-02-05&#34;&gt;2016-02-05&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at some DAGRIS data for Abenet Yabowork&lt;/li&gt;
@ -2632,6 +2665,8 @@ dspace.log.2016-04-27:7271
&lt;li&gt;Also, lots of things like &amp;ldquo;COTE D`LVOIRE&amp;rdquo; and &amp;ldquo;COTE D IVOIRE&amp;rdquo;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-02-06&#34;&gt;2016-02-06&lt;/h2&gt;
&lt;ul&gt;
@ -2939,8 +2974,7 @@ Bitstream: tést señora alimentación.pdf
&lt;ul&gt;
&lt;li&gt;Finally import the 1127 CIAT items into CGSpace: &lt;a href=&#34;https://cgspace.cgiar.org/handle/10568/35710&#34;&gt;https://cgspace.cgiar.org/handle/10568/35710&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;Re-deploy CGSpace with the Google Scholar fix, but I&amp;rsquo;m waiting on the Atmire fixes for now, as the branch history is ugly&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2949,9 +2983,7 @@ Bitstream: tést señora alimentación.pdf
<pubDate>Wed, 13 Jan 2016 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-01/</guid>
<description>
&lt;h2 id=&#34;2016-01-13&#34;&gt;2016-01-13&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-01-13&#34;&gt;2016-01-13&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Move ILRI collection &lt;code&gt;10568/12503&lt;/code&gt; from &lt;code&gt;10568/27869&lt;/code&gt; to &lt;code&gt;10568/27629&lt;/code&gt; using the &lt;a href=&#34;https://gist.github.com/alanorth/392c4660e8b022d99dfa&#34;&gt;move_collections.sh&lt;/a&gt; script I wrote last year.&lt;/li&gt;
@ -2959,6 +2991,8 @@ Bitstream: tést señora alimentación.pdf
&lt;li&gt;Update GitHub wiki for documentation of &lt;a href=&#34;https://github.com/ilri/DSpace/wiki/Maintenance-Tasks&#34;&gt;maintenance tasks&lt;/a&gt;.&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-01-14&#34;&gt;2016-01-14&lt;/h2&gt;
&lt;ul&gt;
@ -3034,8 +3068,7 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
&lt;li&gt;After:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;img src=&#34;2016/01/xmlui-subjects-after.png&#34; alt=&#34;XMLUI subjects after&#34; /&gt;&lt;/p&gt;
</description>
&lt;p&gt;&lt;img src=&#34;2016/01/xmlui-subjects-after.png&#34; alt=&#34;XMLUI subjects after&#34; /&gt;&lt;/p&gt;</description>
</item>
<item>
@ -3044,9 +3077,7 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
<pubDate>Wed, 02 Dec 2015 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2015-12/</guid>
<description>
&lt;h2 id=&#34;2015-12-02&#34;&gt;2015-12-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2015-12-02&#34;&gt;2015-12-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Replace &lt;code&gt;lzop&lt;/code&gt; with &lt;code&gt;xz&lt;/code&gt; in log compression cron jobs on DSpace Test—it uses less space:&lt;/li&gt;
@ -3059,6 +3090,8 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper&lt;/li&gt;
&lt;li&gt;Need to remember to go check if everything is ok in a few days and then change CGSpace&lt;/li&gt;
@ -3204,8 +3237,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
&lt;ul&gt;
&lt;li&gt;Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn&amp;rsquo;t as good, but it&amp;rsquo;s much faster and causes less IO/CPU load&lt;/li&gt;
&lt;li&gt;Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot&amp;rsquo;s crawl rate to the &amp;ldquo;Let Google optimize&amp;rdquo; setting&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -3214,9 +3246,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<pubDate>Mon, 23 Nov 2015 17:00:57 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2015-11/</guid>
<description>
&lt;h2 id=&#34;2015-11-22&#34;&gt;2015-11-22&lt;/h2&gt;
<description>&lt;h2 id=&#34;2015-11-22&#34;&gt;2015-11-22&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;CGSpace went down&lt;/li&gt;
@ -3228,6 +3258,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
78
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;For now I have increased the limit from 60 to 90, run updates, and rebooted the server&lt;/li&gt;
&lt;/ul&gt;
@ -3359,8 +3391,7 @@ db.statementpool = true
&lt;li&gt;Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace&amp;rsquo;s thirst can ever be quenched&lt;/li&gt;
&lt;li&gt;On another note, SUNScholar&amp;rsquo;s notes suggest adjusting some other postgres variables: &lt;a href=&#34;http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database&#34;&gt;http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;This might help with REST API speed (which I mentioned above and still need to do real tests)&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
</channel>

1
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@ -1,6 +1,7 @@
User-agent: *
Disallow: /cgspace-notes/2016-10/
Disallow: /cgspace-notes/2016-09/
Disallow: /cgspace-notes/2016-08/
Disallow: /cgspace-notes/2016-07/

7
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@ -3,7 +3,12 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2016-09-01T15:53:00+03:00</lastmod>
<lastmod>2016-10-03T15:53:00+03:00</lastmod>
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<url>
<loc>https://alanorth.github.io/cgspace-notes/2016-10/</loc>
<lastmod>2016-10-03T15:53:00+03:00</lastmod>
</url>
<url>

49
public/tags/notes/index.html
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@ -32,7 +32,7 @@
<meta property="twitter:title" content="Notes">
<meta property="twitter:description" content="">
<meta name="generator" content="Hugo 0.16" />
<meta name="generator" content="Hugo 0.17-DEV" />
<base href="https://alanorth.github.io/cgspace-notes/">
@ -74,6 +74,20 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-10/" title="October, 2016">October, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-10-03T15:53:00&#43;03:00">Mon Oct 03, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
2016-10-03 Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up Need to test the following scenarios to see how author order is affected: ORCIDs only ORCIDs plus normal authors I exported a random item&rsquo;s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry: 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X Hmm, with the dc.
<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-09/" title="September, 2016">September, 2016</a></h2>
@ -95,6 +109,7 @@
<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;
</code></pre>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-09/'>Read more →</a>
</article>
@ -124,6 +139,7 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-08/'>Read more →</a>
</article>
@ -156,6 +172,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>In this case the select query was showing 95 results before the update</li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-07/'>Read more →</a>
</article>
@ -180,35 +197,11 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-05/" title="May, 2016">May, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-05-01T23:06:00&#43;03:00">Sun May 01, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
<li>I have blocked access to the API now</li>
<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
</ul>
<pre><code># awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
3168
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2016-05/'>Read more →</a>
</article>
@ -224,6 +217,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
@ -232,8 +227,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
</ol>
</section>

148
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@ -1,23 +1,58 @@
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<title>Notes on CGSpace Notes</title>
<link>https://alanorth.github.io/cgspace-notes/tags/notes/</link>
<description>Recent content in Notes on CGSpace Notes</description>
<title>CGSpace Notes</title>
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<description>Recent content on CGSpace Notes</description>
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<title>October, 2016</title>
<link>https://alanorth.github.io/cgspace-notes/2016-10/</link>
<pubDate>Mon, 03 Oct 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-10/</guid>
<description>
&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Testing adding &lt;a href=&#34;https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing&#34;&gt;ORCIDs to a CSV&lt;/a&gt; file for a single item to see if the author orders get messed up&lt;/li&gt;
&lt;li&gt;Need to test the following scenarios to see how author order is affected:
&lt;ul&gt;
&lt;li&gt;ORCIDs only&lt;/li&gt;
&lt;li&gt;ORCIDs plus normal authors&lt;/li&gt;
&lt;/ul&gt;&lt;/li&gt;
&lt;li&gt;I exported a random item&amp;rsquo;s metadata as CSV, deleted &lt;em&gt;all columns&lt;/em&gt; except id and collection, and made a new coloum called &lt;code&gt;ORCID:dc.contributor.author&lt;/code&gt; with the following random ORCIDs from the ORCID registry:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;Hmm, with the &lt;code&gt;dc.contributor.author&lt;/code&gt; column removed, DSpace doesn&amp;rsquo;t detect any changes&lt;/li&gt;
&lt;li&gt;With a blank &lt;code&gt;dc.contributor.author&lt;/code&gt; column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors&lt;/li&gt;
&lt;li&gt;I added the &lt;a href=&#34;https://github.com/ilri/DSpace/issues/234&#34;&gt;disclaimer text&lt;/a&gt; to the About page, then added a footer link to the disclaimer&amp;rsquo;s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: &lt;a href=&#34;https://github.com/twbs/bootstrap/issues/1768&#34;&gt;https://github.com/twbs/bootstrap/issues/1768&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;img src=&#34;2016/10/bootstrap-issue.png&#34; alt=&#34;Bootstrap issue with in-page anchors&#34; /&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Looks like we&amp;rsquo;ll just have to add the text to the About page (without a link) or add a separate page&lt;/li&gt;
&lt;/ul&gt;
</description>
</item>
<item>
<title>September, 2016</title>
<link>https://alanorth.github.io/cgspace-notes/2016-09/</link>
<pubDate>Thu, 01 Sep 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-09/</guid>
<description>
&lt;h2 id=&#34;2016-09-01&#34;&gt;2016-09-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-09-01&#34;&gt;2016-09-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors&lt;/li&gt;
@ -29,6 +64,8 @@
&lt;pre&gt;&lt;code&gt;$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &amp;quot;dc=cgiarad,dc=org&amp;quot; -D &amp;quot;admigration1@cgiarad.org&amp;quot; -W &amp;quot;(sAMAccountName=admigration1)&amp;quot;
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;User who has been migrated to the root vs user still in the hierarchical structure:&lt;/li&gt;
&lt;/ul&gt;
@ -637,15 +674,18 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
&lt;li&gt;Add &lt;code&gt;cg.identifier.ciatproject&lt;/code&gt; to metadata registry in preparation for CIAT project tag&lt;/li&gt;
&lt;li&gt;Merge changes for CIAT project tag (&lt;a href=&#34;https://github.com/ilri/DSpace/pull/282&#34;&gt;#282&lt;/a&gt;)&lt;/li&gt;
&lt;li&gt;DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console&lt;/li&gt;
&lt;li&gt;People on DSpace mailing list gave me a query to get authors from certain collections:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in (&#39;10568/5472&#39;, &#39;10568/5473&#39;)));
&lt;/code&gt;&lt;/pre&gt;
&lt;h2 id=&#34;2016-09-30&#34;&gt;2016-09-30&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Deny access to REST API&amp;rsquo;s &lt;code&gt;find-by-metadata-field&lt;/code&gt; endpoint to protect against an upstream security issue (DS-3250)&lt;/li&gt;
&lt;li&gt;There is a patch but it is only for 5.5 and doesn&amp;rsquo;t apply cleanly to 5.1&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -654,9 +694,7 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<pubDate>Mon, 01 Aug 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-08/</guid>
<description>
&lt;h2 id=&#34;2016-08-01&#34;&gt;2016-08-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-08-01&#34;&gt;2016-08-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add updated distribution license from Sisay (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/259&#34;&gt;#259&lt;/a&gt;)&lt;/li&gt;
@ -672,6 +710,8 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Lots of conflicts that don&amp;rsquo;t make sense (ie, shouldn&amp;rsquo;t conflict!)&lt;/li&gt;
&lt;li&gt;This file in particular conflicts almost 10 times: &lt;code&gt;dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss&lt;/code&gt;&lt;/li&gt;
@ -979,8 +1019,7 @@ $ JAVA_OPTS=&amp;quot;-Dfile.encoding=UTF-8 -Xmx512m&amp;quot; /home/cgspace.cgi
&lt;ul&gt;
&lt;li&gt;Run corrections for Delia Grace and &lt;code&gt;CONGO, DR&lt;/code&gt;, and deploy August changes to CGSpace&lt;/li&gt;
&lt;li&gt;Run all system updates and reboot the server&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -989,9 +1028,7 @@ $ JAVA_OPTS=&amp;quot;-Dfile.encoding=UTF-8 -Xmx512m&amp;quot; /home/cgspace.cgi
<pubDate>Fri, 01 Jul 2016 10:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-07/</guid>
<description>
&lt;h2 id=&#34;2016-07-01&#34;&gt;2016-07-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-07-01&#34;&gt;2016-07-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add &lt;code&gt;dc.description.sponsorship&lt;/code&gt; to Discovery sidebar facets and make investors clickable in item view (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/232&#34;&gt;#232&lt;/a&gt;)&lt;/li&gt;
@ -1010,6 +1047,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
&lt;li&gt;In this case the select query was showing 95 results before the update&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-07-02&#34;&gt;2016-07-02&lt;/h2&gt;
&lt;ul&gt;
@ -1235,8 +1274,7 @@ discovery.index.authority.ignore-variants=true
&lt;ul&gt;
&lt;li&gt;Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by&lt;/li&gt;
&lt;li&gt;Also change &amp;ldquo;Subjects&amp;rdquo; to &amp;ldquo;AGROVOC keywords&amp;rdquo; in Discovery sidebar/search and Browse by (&lt;a href=&#34;https://github.com/ilri/DSpace/issues/257&#34;&gt;#257&lt;/a&gt;)&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1245,9 +1283,7 @@ discovery.index.authority.ignore-variants=true
<pubDate>Wed, 01 Jun 2016 10:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-06/</guid>
<description>
&lt;h2 id=&#34;2016-06-01&#34;&gt;2016-06-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-06-01&#34;&gt;2016-06-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Experimenting with IFPRI OAI (we want to harvest their publications)&lt;/li&gt;
@ -1258,6 +1294,8 @@ discovery.index.authority.ignore-variants=true
&lt;li&gt;Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in &lt;code&gt;dc.identifier.fund&lt;/code&gt; to &lt;code&gt;cg.identifier.cpwfproject&lt;/code&gt; and then the rest to &lt;code&gt;dc.description.sponsorship&lt;/code&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like &#39;PN%&#39; or text_value like &#39;PHASE%&#39; or text_value = &#39;CBA&#39; or text_value = &#39;IA&#39;);
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
@ -1589,8 +1627,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;# update metadatavalue set text_value = regexp_replace(text_value, &#39;(Poole, J),&#39;, &#39;\1&#39;) where metadata_field_id=3 and text_value = &#39;Poole, J,&#39;;
&lt;/code&gt;&lt;/pre&gt;
</description>
&lt;/code&gt;&lt;/pre&gt;</description>
</item>
<item>
@ -1599,9 +1636,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<pubDate>Sun, 01 May 2016 23:06:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-05/</guid>
<description>
&lt;h2 id=&#34;2016-05-01&#34;&gt;2016-05-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-05-01&#34;&gt;2016-05-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Since yesterday there have been 10,000 REST errors and the site has been unstable again&lt;/li&gt;
@ -1613,6 +1648,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
3168
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29&lt;/li&gt;
&lt;li&gt;100% of the requests coming from Ethiopia are like this and result in an HTTP 500:&lt;/li&gt;
@ -1896,8 +1933,7 @@ sys 0m20.540s
&lt;li&gt;Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.&lt;/li&gt;
&lt;li&gt;Re-sync DSpace Test data with CGSpace&lt;/li&gt;
&lt;li&gt;Clean up and import ~65 more CTA items into CGSpace&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1906,9 +1942,7 @@ sys 0m20.540s
<pubDate>Mon, 04 Apr 2016 11:06:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-04/</guid>
<description>
&lt;h2 id=&#34;2016-04-04&#34;&gt;2016-04-04&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-04-04&#34;&gt;2016-04-04&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit&lt;/li&gt;
@ -1918,6 +1952,8 @@ sys 0m20.540s
&lt;li&gt;Also, I noticed the &lt;code&gt;checker&lt;/code&gt; log has some errors we should pay attention to:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
@ -2357,8 +2393,7 @@ dspace.log.2016-04-27:7271
&lt;ul&gt;
&lt;li&gt;I will check the logs again in a few days to look for patterns, see who is accessing it, etc&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2367,9 +2402,7 @@ dspace.log.2016-04-27:7271
<pubDate>Wed, 02 Mar 2016 16:50:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-03/</guid>
<description>
&lt;h2 id=&#34;2016-03-02&#34;&gt;2016-03-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-03-02&#34;&gt;2016-03-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at issues with author authorities on CGSpace&lt;/li&gt;
@ -2377,6 +2410,8 @@ dspace.log.2016-04-27:7271
&lt;li&gt;Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-03-07&#34;&gt;2016-03-07&lt;/h2&gt;
&lt;ul&gt;
@ -2605,8 +2640,7 @@ dspace.log.2016-04-27:7271
&lt;li&gt;We decided to proceed with some deletes first, then identify CGSpace-specific fields to clean/move to &lt;code&gt;cg.*&lt;/code&gt;, and then worry about broader changes to DC&lt;/li&gt;
&lt;li&gt;Before we move or rename and fields we need to circulate a list of fields we intend to change to CCAFS, CWPF, etc who might be harvesting the fields&lt;/li&gt;
&lt;li&gt;After all of this we need to start implementing controlled vocabularies for fields, either with the Javascript lookup or like existing ILRI subjects&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2615,9 +2649,7 @@ dspace.log.2016-04-27:7271
<pubDate>Fri, 05 Feb 2016 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-02/</guid>
<description>
&lt;h2 id=&#34;2016-02-05&#34;&gt;2016-02-05&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-02-05&#34;&gt;2016-02-05&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Looking at some DAGRIS data for Abenet Yabowork&lt;/li&gt;
@ -2632,6 +2664,8 @@ dspace.log.2016-04-27:7271
&lt;li&gt;Also, lots of things like &amp;ldquo;COTE D`LVOIRE&amp;rdquo; and &amp;ldquo;COTE D IVOIRE&amp;rdquo;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-02-06&#34;&gt;2016-02-06&lt;/h2&gt;
&lt;ul&gt;
@ -2939,8 +2973,7 @@ Bitstream: tést señora alimentación.pdf
&lt;ul&gt;
&lt;li&gt;Finally import the 1127 CIAT items into CGSpace: &lt;a href=&#34;https://cgspace.cgiar.org/handle/10568/35710&#34;&gt;https://cgspace.cgiar.org/handle/10568/35710&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;Re-deploy CGSpace with the Google Scholar fix, but I&amp;rsquo;m waiting on the Atmire fixes for now, as the branch history is ugly&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -2949,9 +2982,7 @@ Bitstream: tést señora alimentación.pdf
<pubDate>Wed, 13 Jan 2016 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-01/</guid>
<description>
&lt;h2 id=&#34;2016-01-13&#34;&gt;2016-01-13&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-01-13&#34;&gt;2016-01-13&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Move ILRI collection &lt;code&gt;10568/12503&lt;/code&gt; from &lt;code&gt;10568/27869&lt;/code&gt; to &lt;code&gt;10568/27629&lt;/code&gt; using the &lt;a href=&#34;https://gist.github.com/alanorth/392c4660e8b022d99dfa&#34;&gt;move_collections.sh&lt;/a&gt; script I wrote last year.&lt;/li&gt;
@ -2959,6 +2990,8 @@ Bitstream: tést señora alimentación.pdf
&lt;li&gt;Update GitHub wiki for documentation of &lt;a href=&#34;https://github.com/ilri/DSpace/wiki/Maintenance-Tasks&#34;&gt;maintenance tasks&lt;/a&gt;.&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-01-14&#34;&gt;2016-01-14&lt;/h2&gt;
&lt;ul&gt;
@ -3034,8 +3067,7 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
&lt;li&gt;After:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;img src=&#34;2016/01/xmlui-subjects-after.png&#34; alt=&#34;XMLUI subjects after&#34; /&gt;&lt;/p&gt;
</description>
&lt;p&gt;&lt;img src=&#34;2016/01/xmlui-subjects-after.png&#34; alt=&#34;XMLUI subjects after&#34; /&gt;&lt;/p&gt;</description>
</item>
<item>
@ -3044,9 +3076,7 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
<pubDate>Wed, 02 Dec 2015 13:18:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2015-12/</guid>
<description>
&lt;h2 id=&#34;2015-12-02&#34;&gt;2015-12-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2015-12-02&#34;&gt;2015-12-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Replace &lt;code&gt;lzop&lt;/code&gt; with &lt;code&gt;xz&lt;/code&gt; in log compression cron jobs on DSpace Test—it uses less space:&lt;/li&gt;
@ -3059,6 +3089,8 @@ $ find SimpleArchiveForBio/ -iname &amp;ldquo;*.pdf&amp;rdquo; -exec basename {}
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper&lt;/li&gt;
&lt;li&gt;Need to remember to go check if everything is ok in a few days and then change CGSpace&lt;/li&gt;
@ -3204,8 +3236,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
&lt;ul&gt;
&lt;li&gt;Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn&amp;rsquo;t as good, but it&amp;rsquo;s much faster and causes less IO/CPU load&lt;/li&gt;
&lt;li&gt;Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot&amp;rsquo;s crawl rate to the &amp;ldquo;Let Google optimize&amp;rdquo; setting&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -3214,9 +3245,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<pubDate>Mon, 23 Nov 2015 17:00:57 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2015-11/</guid>
<description>
&lt;h2 id=&#34;2015-11-22&#34;&gt;2015-11-22&lt;/h2&gt;
<description>&lt;h2 id=&#34;2015-11-22&#34;&gt;2015-11-22&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;CGSpace went down&lt;/li&gt;
@ -3228,6 +3257,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
78
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;For now I have increased the limit from 60 to 90, run updates, and rebooted the server&lt;/li&gt;
&lt;/ul&gt;
@ -3359,8 +3390,7 @@ db.statementpool = true
&lt;li&gt;Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace&amp;rsquo;s thirst can ever be quenched&lt;/li&gt;
&lt;li&gt;On another note, SUNScholar&amp;rsquo;s notes suggest adjusting some other postgres variables: &lt;a href=&#34;http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database&#34;&gt;http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;This might help with REST API speed (which I mentioned above and still need to do real tests)&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
</channel>

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