Add notes for 2023-06-28
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@ -166,4 +166,66 @@ ERROR DOMException: CSSStyleSheet.cssRules getter: Not allowed to access cross-o
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- Upload thumbnails for about 42 IITA Journal Articles after resolving their DOIs and making sure they were not CC ND
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- I fixed a few bugs in `get_scihub_pdfs.py` in the process
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## 2023-06-21
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- Stefano got back to me about the MODS OAI-PMH schema test on DSpace Test
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- 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
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- I updated DSpace Test with the new date format and said I'd work on the custom AGRIS set
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## 2023-06-25
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- Export CGSpace to check for missing Initiative collection mappings
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- 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
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- I decided to run all updates and reboot it since it's Sunday anyway
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## 2023-06-26
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- Since the new DSpace 7 will respect newlines in metadata fields I am curious to see how many of our abstracts have poor newlines
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- I exported CGSpace and used a custom text facet with this GREL expression in OpenRefine to count the number of newlines in each cell:
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```console
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value.split('\n').length()
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```
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- Also useful to check for general length of the text in the cell to make sure it's a reasonably long string
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- 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
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- I fixed a few dozen
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- Do a bit of work on thumbnails on CGSpace
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- I'm trying to troubleshoot the Discovery error I get on DSpace 7:
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```console
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java.lang.NullPointerException: Cannot invoke "org.dspace.discovery.configuration.DiscoverySearchFilterFacet.getIndexFieldName()" because the return value of "org.dspace.content.authority.DSpaceControlledVocabularyIndex.getFacetConfig()" is null
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```
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- I reverted to the default `submission-forms.xml` and the `getFacetConfig()` error goes away...
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- Kill some long-held locks on CGSpace PostgreSQL, as some users are complaining of slowness in archiving
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- I did some testing of the LDAP login issue related to groupmaps
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- 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)
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- 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
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## 2023-06-27
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- I debugged the NullPointerException and somehow it disappeared
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- It seems to be related to the external controlled vocabularies in the submission form
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- I removed them all, then added them all back, and now the issue is solved... hmmmm
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- Oh now, now they are gone again, sigh...
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## 2023-06-28
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- Spent a lot of time debugging the browse indexes
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- 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`
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- 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
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- Yes, if I remove them all from my submission form then this works: http://localhost:8080/server/api/discover/browses
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- I went through each of our vocabularies and tested them one by one:
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- dcterms-subject: OK
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- dc-contributor-author: NO
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- cg-creator-identifier: NO
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- cg-contributor-affiliation: OK (and with `facetType: "affiliation"` in API response?!)
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- cg-contributor-donor: OK (`facetType: "sponsorship"`)
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- cg-journal: NO
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- cg-coverage-subregion: NO
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- cg-species-breed: NO
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- Now I need to figure out what it is about those five that causes them to not work!
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- 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.
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<!-- vim: set sw=2 ts=2: -->
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@ -24,7 +24,7 @@ From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-06/" />
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<meta property="article:published_time" content="2023-06-02T10:29:36+03:00" />
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<meta property="article:modified_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="article:modified_time" content="2023-06-19T16:26:41+03:00" />
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@ -54,9 +54,9 @@ From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then
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"@type": "BlogPosting",
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"headline": "June, 2023",
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"url": "https://alanorth.github.io/cgspace-notes/2023-06/",
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"wordCount": "1179",
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"wordCount": "1766",
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"datePublished": "2023-06-02T10:29:36+03:00",
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"dateModified": "2023-06-17T23:14:32+03:00",
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"dateModified": "2023-06-19T16:26:41+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -321,6 +321,88 @@ From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-21">2023-06-21</h2>
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<ul>
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<li>Stefano got back to me about the MODS OAI-PMH schema test on DSpace Test
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<ul>
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<li>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: <a href="https://melspace.loc.codeobia.com/oai/agris?verb=ListRecords&metadataPrefix=mods">https://melspace.loc.codeobia.com/oai/agris?verb=ListRecords&metadataPrefix=mods</a></li>
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<li>I updated DSpace Test with the new date format and said I’d work on the custom AGRIS set</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-25">2023-06-25</h2>
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<ul>
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<li>Export CGSpace to check for missing Initiative collection mappings</li>
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<li>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
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<ul>
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<li>I decided to run all updates and reboot it since it’s Sunday anyway</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-26">2023-06-26</h2>
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<ul>
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<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
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<ul>
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<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>
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</ul>
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</li>
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</ul>
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<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('\n').length()
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</span></span></code></pre></div><ul>
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<li>Also useful to check for general length of the text in the cell to make sure it’s a reasonably long string
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<ul>
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<li>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</li>
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<li>I fixed a few dozen</li>
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</ul>
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</li>
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<li>Do a bit of work on thumbnails on CGSpace</li>
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<li>I’m trying to troubleshoot the Discovery error I get on DSpace 7:</li>
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</ul>
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<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 "org.dspace.discovery.configuration.DiscoverySearchFilterFacet.getIndexFieldName()" because the return value of "org.dspace.content.authority.DSpaceControlledVocabularyIndex.getFacetConfig()" is null
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</span></span></code></pre></div><ul>
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<li>I reverted to the default <code>submission-forms.xml</code> and the <code>getFacetConfig()</code> error goes away…</li>
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<li>Kill some long-held locks on CGSpace PostgreSQL, as some users are complaining of slowness in archiving</li>
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<li>I did some testing of the LDAP login issue related to groupmaps
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<ul>
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<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>
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</ul>
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</li>
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<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>
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</ul>
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<h2 id="2023-06-27">2023-06-27</h2>
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<ul>
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<li>I debugged the NullPointerException and somehow it disappeared
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<ul>
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<li>It seems to be related to the external controlled vocabularies in the submission form</li>
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<li>I removed them all, then added them all back, and now the issue is solved… hmmmm</li>
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<li>Oh now, now they are gone again, sigh…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-28">2023-06-28</h2>
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<ul>
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<li>Spent a lot of time debugging the browse indexes
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<ul>
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<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><vocabulary>srsc</vocabulary></code> in the <code>submission-forms.xml</code></li>
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<li>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</li>
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<li>Yes, if I remove them all from my submission form then this works: http://localhost:8080/server/api/discover/browses</li>
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<li>I went through each of our vocabularies and tested them one by one:
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<ul>
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<li>dcterms-subject: OK</li>
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<li>dc-contributor-author: NO</li>
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<li>cg-creator-identifier: NO</li>
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<li>cg-contributor-affiliation: OK (and with <code>facetType: "affiliation"</code> in API response?!)</li>
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<li>cg-contributor-donor: OK (<code>facetType: "sponsorship"</code>)</li>
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<li>cg-journal: NO</li>
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<li>cg-coverage-subregion: NO</li>
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<li>cg-species-breed: NO</li>
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</ul>
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</li>
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<li>Now I need to figure out what it is about those five that causes them to not work!</li>
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<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>
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</ul>
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</li>
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</ul>
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
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<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
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@ -10,7 +10,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
|
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<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
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<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
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@ -10,7 +10,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
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@ -10,7 +10,7 @@
|
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
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|
||||
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|
|||
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@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2023-06-17T23:14:32+03:00" />
|
||||
<meta property="og:updated_time" content="2023-06-19T16:26:41+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -3,19 +3,19 @@
|
|||
xmlns:xhtml="http://www.w3.org/1999/xhtml">
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
|
||||
<lastmod>2023-06-17T23:14:32+03:00</lastmod>
|
||||
<lastmod>2023-06-19T16:26:41+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2023-06-17T23:14:32+03:00</lastmod>
|
||||
<lastmod>2023-06-19T16:26:41+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2023-06/</loc>
|
||||
<lastmod>2023-06-17T23:14:32+03:00</lastmod>
|
||||
<lastmod>2023-06-19T16:26:41+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||
<lastmod>2023-06-17T23:14:32+03:00</lastmod>
|
||||
<lastmod>2023-06-19T16:26:41+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||
<lastmod>2023-06-17T23:14:32+03:00</lastmod>
|
||||
<lastmod>2023-06-19T16:26:41+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2023-05/</loc>
|
||||
<lastmod>2023-05-30T20:19:17+03:00</lastmod>
|
||||
|
|
|
|||
Loading…
Reference in New Issue