Add notes for 2023-06-28

content/posts/2023-06.md

@@ -166,4 +166,66 @@ ERROR DOMException: CSSStyleSheet.cssRules getter: Not allowed to access cross-o
 - Upload thumbnails for about 42 IITA Journal Articles after resolving their DOIs and making sure they were not CC ND
   - I fixed a few bugs in `get_scihub_pdfs.py` in the process
 
+## 2023-06-21
+
+- Stefano got back to me about the MODS OAI-PMH schema test on DSpace Test
+  - He said that it's fine if we use iso8601 encoding for dates instead of w3cdtf and asked if we can create a custom end point for AGRIS that only includes types like Journal Articles similar to how Salem did it: https://melspace.loc.codeobia.com/oai/agris?verb=ListRecords&metadataPrefix=mods
+  - I updated DSpace Test with the new date format and said I'd work on the custom AGRIS set
+
+## 2023-06-25
+
+- Export CGSpace to check for missing Initiative collection mappings
+- I wanted to start a harvest on AReS but I've seen the load on the server high for a few days and I'm not sure what it is
+  - I decided to run all updates and reboot it since it's Sunday anyway
+
+## 2023-06-26
+
+- Since the new DSpace 7 will respect newlines in metadata fields I am curious to see how many of our abstracts have poor newlines
+  - I exported CGSpace and used a custom text facet with this GREL expression in OpenRefine to count the number of newlines in each cell:
+
+```console
+value.split('\n').length()
+```
+
+- Also useful to check for general length of the text in the cell to make sure it's a reasonably long string
+  - I spent some time trying to find a pattern that I could use to identify "easy" targets, but there are so many exceptions that it will have to be done manually
+  - I fixed a few dozen
+- Do a bit of work on thumbnails on CGSpace
+- I'm trying to troubleshoot the Discovery error I get on DSpace 7:
+
+```console
+java.lang.NullPointerException: Cannot invoke "org.dspace.discovery.configuration.DiscoverySearchFilterFacet.getIndexFieldName()" because the return value of "org.dspace.content.authority.DSpaceControlledVocabularyIndex.getFacetConfig()" is null
+```
+
+- I reverted to the default `submission-forms.xml` and the `getFacetConfig()` error goes away...
+- Kill some long-held locks on CGSpace PostgreSQL, as some users are complaining of slowness in archiving
+- I did some testing of the LDAP login issue related to groupmaps
+  - It does seem to be a regression from the [LDAP auth patch](https://github.com/DSpace/DSpace/pull/8814) from last month, so I [filed an issue](https://github.com/DSpace/DSpace/issues/8920)
+- I spent some time on working on Angular and I figured out how to add a custom Angular component to show the UN SDG Goal icons on DSpace 7
+
+## 2023-06-27
+
+- I debugged the NullPointerException and somehow it disappeared
+  - It seems to be related to the external controlled vocabularies in the submission form
+  - I removed them all, then added them all back, and now the issue is solved... hmmmm
+  - Oh now, now they are gone again, sigh...
+
+## 2023-06-28
+
+- Spent a lot of time debugging the browse indexes
+  - Looking at the [DSpace 7 demo API](https://api7.dspace.org/server/api/discover/browses) I see the four default browse indexes from `dspace.cfg` and the one default `srsc` one that gets automatically enabled from the `<vocabulary>srsc</vocabulary>` in the `submission-forms.xml`
+  - The same API call on my test DSpace 7 configuration results in the HTTP 500 I've been seeing for some time, and I am pretty sure it's due to the automagic configuration of hierarchical browses based on the submission form
+  - Yes, if I remove them all from my submission form then this works: http://localhost:8080/server/api/discover/browses
+  - I went through each of our vocabularies and tested them one by one:
+    - dcterms-subject: OK
+    - dc-contributor-author: NO
+    - cg-creator-identifier: NO
+    - cg-contributor-affiliation: OK (and with `facetType: "affiliation"` in API response?!)
+    - cg-contributor-donor: OK (`facetType:	"sponsorship"`)
+    - cg-journal: NO
+    - cg-coverage-subregion: NO
+    - cg-species-breed: NO
+  - Now I need to figure out what it is about those five that causes them to not work!
+  - Ah, after debugging with someone on the DSpace Slack, I realized that DSpace expects these vocabularies to have corresponding indexes configured in `discovery.xml`, and they must be added as search filters AND sidebar facets.
+
 <!-- vim: set sw=2 ts=2: -->

docs/2023-06/index.html

@@ -24,7 +24,7 @@ From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-06/" />
 <meta property="article:published_time" content="2023-06-02T10:29:36+03:00" />
-<meta property="article:modified_time" content="2023-06-17T23:14:32+03:00" />
+<meta property="article:modified_time" content="2023-06-19T16:26:41+03:00" />
 
 
 
@@ -54,9 +54,9 @@ From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then
   "@type": "BlogPosting",
   "headline": "June, 2023",
   "url": "https://alanorth.github.io/cgspace-notes/2023-06/",
-  "wordCount": "1179",
+  "wordCount": "1766",
   "datePublished": "2023-06-02T10:29:36+03:00",
-  "dateModified": "2023-06-17T23:14:32+03:00",
+  "dateModified": "2023-06-19T16:26:41+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -321,6 +321,88 @@ From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then
 </ul>
 </li>
 </ul>
+<h2 id="2023-06-21">2023-06-21</h2>
+<ul>
+<li>Stefano got back to me about the MODS OAI-PMH schema test on DSpace Test
+<ul>
+<li>He said that it&rsquo;s fine if we use iso8601 encoding for dates instead of w3cdtf and asked if we can create a custom end point for AGRIS that only includes types like Journal Articles similar to how Salem did it: <a href="https://melspace.loc.codeobia.com/oai/agris?verb=ListRecords&amp;metadataPrefix=mods">https://melspace.loc.codeobia.com/oai/agris?verb=ListRecords&amp;metadataPrefix=mods</a></li>
+<li>I updated DSpace Test with the new date format and said I&rsquo;d work on the custom AGRIS set</li>
+</ul>
+</li>
+</ul>
+<h2 id="2023-06-25">2023-06-25</h2>
+<ul>
+<li>Export CGSpace to check for missing Initiative collection mappings</li>
+<li>I wanted to start a harvest on AReS but I&rsquo;ve seen the load on the server high for a few days and I&rsquo;m not sure what it is
+<ul>
+<li>I decided to run all updates and reboot it since it&rsquo;s Sunday anyway</li>
+</ul>
+</li>
+</ul>
+<h2 id="2023-06-26">2023-06-26</h2>
+<ul>
+<li>Since the new DSpace 7 will respect newlines in metadata fields I am curious to see how many of our abstracts have poor newlines
+<ul>
+<li>I exported CGSpace and used a custom text facet with this GREL expression in OpenRefine to count the number of newlines in each cell:</li>
+</ul>
+</li>
+</ul>
+<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>value.split(&#39;\n&#39;).length()
+</span></span></code></pre></div><ul>
+<li>Also useful to check for general length of the text in the cell to make sure it&rsquo;s a reasonably long string
+<ul>
+<li>I spent some time trying to find a pattern that I could use to identify &ldquo;easy&rdquo; targets, but there are so many exceptions that it will have to be done manually</li>
+<li>I fixed a few dozen</li>
+</ul>
+</li>
+<li>Do a bit of work on thumbnails on CGSpace</li>
+<li>I&rsquo;m trying to troubleshoot the Discovery error I get on DSpace 7:</li>
+</ul>
+<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>java.lang.NullPointerException: Cannot invoke &#34;org.dspace.discovery.configuration.DiscoverySearchFilterFacet.getIndexFieldName()&#34; because the return value of &#34;org.dspace.content.authority.DSpaceControlledVocabularyIndex.getFacetConfig()&#34; is null
+</span></span></code></pre></div><ul>
+<li>I reverted to the default <code>submission-forms.xml</code> and the <code>getFacetConfig()</code> error goes away&hellip;</li>
+<li>Kill some long-held locks on CGSpace PostgreSQL, as some users are complaining of slowness in archiving</li>
+<li>I did some testing of the LDAP login issue related to groupmaps
+<ul>
+<li>It does seem to be a regression from the <a href="https://github.com/DSpace/DSpace/pull/8814">LDAP auth patch</a> from last month, so I <a href="https://github.com/DSpace/DSpace/issues/8920">filed an issue</a></li>
+</ul>
+</li>
+<li>I spent some time on working on Angular and I figured out how to add a custom Angular component to show the UN SDG Goal icons on DSpace 7</li>
+</ul>
+<h2 id="2023-06-27">2023-06-27</h2>
+<ul>
+<li>I debugged the NullPointerException and somehow it disappeared
+<ul>
+<li>It seems to be related to the external controlled vocabularies in the submission form</li>
+<li>I removed them all, then added them all back, and now the issue is solved&hellip; hmmmm</li>
+<li>Oh now, now they are gone again, sigh&hellip;</li>
+</ul>
+</li>
+</ul>
+<h2 id="2023-06-28">2023-06-28</h2>
+<ul>
+<li>Spent a lot of time debugging the browse indexes
+<ul>
+<li>Looking at the <a href="https://api7.dspace.org/server/api/discover/browses">DSpace 7 demo API</a> I see the four default browse indexes from <code>dspace.cfg</code> and the one default <code>srsc</code> one that gets automatically enabled from the <code>&lt;vocabulary&gt;srsc&lt;/vocabulary&gt;</code> in the <code>submission-forms.xml</code></li>
+<li>The same API call on my test DSpace 7 configuration results in the HTTP 500 I&rsquo;ve been seeing for some time, and I am pretty sure it&rsquo;s due to the automagic configuration of hierarchical browses based on the submission form</li>
+<li>Yes, if I remove them all from my submission form then this works: http://localhost:8080/server/api/discover/browses</li>
+<li>I went through each of our vocabularies and tested them one by one:
+<ul>
+<li>dcterms-subject: OK</li>
+<li>dc-contributor-author: NO</li>
+<li>cg-creator-identifier: NO</li>
+<li>cg-contributor-affiliation: OK (and with <code>facetType: &quot;affiliation&quot;</code> in API response?!)</li>
+<li>cg-contributor-donor: OK (<code>facetType:	&quot;sponsorship&quot;</code>)</li>
+<li>cg-journal: NO</li>
+<li>cg-coverage-subregion: NO</li>
+<li>cg-species-breed: NO</li>
+</ul>
+</li>
+<li>Now I need to figure out what it is about those five that causes them to not work!</li>
+<li>Ah, after debugging with someone on the DSpace Slack, I realized that DSpace expects these vocabularies to have corresponding indexes configured in <code>discovery.xml</code>, and they must be added as search filters AND sidebar facets.</li>
+</ul>
+</li>
+</ul>
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docs/posts/page/7/index.html

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docs/posts/page/8/index.html

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docs/posts/page/9/index.html

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