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Add notes for 2021-09-17

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Alan Orth 2021-09-17 15:03:28 +03:00
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content/posts/2021-09.md
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@ -100,5 +100,60 @@ $ ./ilri/add-orcid-identifiers-csv.py -i 2021-09-15-add-orcids.csv -db dspace -u
- Found a bug with the DSpace 6.3 REST API, it returns HTTP 500 for `dc.title` even though it exists in the registry: https://demo.dspace.org/rest/registries/schema/dc/metadata-fields/title - Found a bug with the DSpace 6.3 REST API, it returns HTTP 500 for `dc.title` even though it exists in the registry: https://demo.dspace.org/rest/registries/schema/dc/metadata-fields/title
- Seems to be with any field that does not have a qualifier - Seems to be with any field that does not have a qualifier
- I filed an issue: https://github.com/DSpace/DSpace/issues/7946 - I filed an issue: https://github.com/DSpace/DSpace/issues/7946
- I decided to update all the metadata field descriptions in our registry so I can use that instead of the "hint" for each field in the input form
- I will include examples as well so that it becomes a better resource
## 2021-09-17
- I filed [an issue about using SPDX License Identifiers in CG Core v2](https://github.com/AgriculturalSemantics/cg-core/issues/41)
- Peter Ballantyne emailed me to say that CGSpace was very slow
- The front page was returning a blank white page
- I looked at the database and the connections look low:
```console
$ psql -c 'SELECT * FROM pg_stat_activity' | wc -l
63
```
- Load on the server is under 1.0, and there are only about 1,000 XMLUI sessions, which seems to be normal for this time of day according to Munin
- But the DSpace log file shows tons of database issues:
```console
$ grep -c "Timeout waiting for idle object" dspace.log.2021-09-17
14779
```
- The earliest one I see is around midnight (now is 2PM):
```console
2021-09-17 00:01:49,572 WARN org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ SQL Error: 0, SQLState: null
2021-09-17 00:01:49,572 ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ Cannot get a connection, pool error Timeout waiting for idle object
```
- But I was definitely logged into the site this morning so there were no issues then...
- It seems that a few errors are normal, but there's obviously something wrong today:
```console
$ grep -c "Timeout waiting for idle object" dspace.log.2021-09-*
dspace.log.2021-09-01:116
dspace.log.2021-09-02:163
dspace.log.2021-09-03:77
dspace.log.2021-09-04:13
dspace.log.2021-09-05:310
dspace.log.2021-09-06:0
dspace.log.2021-09-07:29
dspace.log.2021-09-08:86
dspace.log.2021-09-09:24
dspace.log.2021-09-10:26
dspace.log.2021-09-11:12
dspace.log.2021-09-12:5
dspace.log.2021-09-13:10
dspace.log.2021-09-14:102
dspace.log.2021-09-15:542
dspace.log.2021-09-16:368
dspace.log.2021-09-17:15235
```
- I restarted the server and DSpace came up fine... so it must have been some kind of fluke
<!-- vim: set sw=2 ts=2: --> <!-- vim: set sw=2 ts=2: -->

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@ -26,7 +26,7 @@ The syntax Moayad showed me last month doesn&rsquo;t seem to honor the search qu
<meta property="og:type" content="article" /> <meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-09/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-09/" />
<meta property="article:published_time" content="2021-09-01T09:14:07+03:00" /> <meta property="article:published_time" content="2021-09-01T09:14:07+03:00" />
<meta property="article:modified_time" content="2021-09-16T06:49:05+03:00" /> <meta property="article:modified_time" content="2021-09-16T16:35:00+03:00" />
@ -58,9 +58,9 @@ The syntax Moayad showed me last month doesn&rsquo;t seem to honor the search qu
"@type": "BlogPosting", "@type": "BlogPosting",
"headline": "September, 2021", "headline": "September, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-09/", "url": "https://alanorth.github.io/cgspace-notes/2021-09/",
"wordCount": "842", "wordCount": "1097",
"datePublished": "2021-09-01T09:14:07+03:00", "datePublished": "2021-09-01T09:14:07+03:00",
"dateModified": "2021-09-16T06:49:05+03:00", "dateModified": "2021-09-16T16:35:00+03:00",
"author": { "author": {
"@type": "Person", "@type": "Person",
"name": "Alan Orth" "name": "Alan Orth"
@ -257,6 +257,59 @@ $ ./ilri/add-orcid-identifiers-csv.py -i 2021-09-15-add-orcids.csv -db dspace -u
<li>I filed an issue: <a href="https://github.com/DSpace/DSpace/issues/7946">https://github.com/DSpace/DSpace/issues/7946</a></li> <li>I filed an issue: <a href="https://github.com/DSpace/DSpace/issues/7946">https://github.com/DSpace/DSpace/issues/7946</a></li>
</ul> </ul>
</li> </li>
<li>I decided to update all the metadata field descriptions in our registry so I can use that instead of the &ldquo;hint&rdquo; for each field in the input form
<ul>
<li>I will include examples as well so that it becomes a better resource</li>
</ul>
</li>
</ul>
<h2 id="2021-09-17">2021-09-17</h2>
<ul>
<li>I filed <a href="https://github.com/AgriculturalSemantics/cg-core/issues/41">an issue about using SPDX License Identifiers in CG Core v2</a></li>
<li>Peter Ballantyne emailed me to say that CGSpace was very slow
<ul>
<li>The front page was returning a blank white page</li>
<li>I looked at the database and the connections look low:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_stat_activity' | wc -l
63
</code></pre><ul>
<li>Load on the server is under 1.0, and there are only about 1,000 XMLUI sessions, which seems to be normal for this time of day according to Munin</li>
<li>But the DSpace log file shows tons of database issues:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ grep -c &quot;Timeout waiting for idle object&quot; dspace.log.2021-09-17
14779
</code></pre><ul>
<li>The earliest one I see is around midnight (now is 2PM):</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">2021-09-17 00:01:49,572 WARN org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ SQL Error: 0, SQLState: null
2021-09-17 00:01:49,572 ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ Cannot get a connection, pool error Timeout waiting for idle object
</code></pre><ul>
<li>But I was definitely logged into the site this morning so there were no issues then&hellip;</li>
<li>It seems that a few errors are normal, but there&rsquo;s obviously something wrong today:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ grep -c &quot;Timeout waiting for idle object&quot; dspace.log.2021-09-*
dspace.log.2021-09-01:116
dspace.log.2021-09-02:163
dspace.log.2021-09-03:77
dspace.log.2021-09-04:13
dspace.log.2021-09-05:310
dspace.log.2021-09-06:0
dspace.log.2021-09-07:29
dspace.log.2021-09-08:86
dspace.log.2021-09-09:24
dspace.log.2021-09-10:26
dspace.log.2021-09-11:12
dspace.log.2021-09-12:5
dspace.log.2021-09-13:10
dspace.log.2021-09-14:102
dspace.log.2021-09-15:542
dspace.log.2021-09-16:368
dspace.log.2021-09-17:15235
</code></pre><ul>
<li>I restarted the server and DSpace came up fine&hellip; so it must have been some kind of fluke</li>
</ul> </ul>
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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2021-09-16T06:49:05+03:00" /> <meta property="og:updated_time" content="2021-09-16T16:35:00+03:00" />

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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-09-16T06:49:05+03:00" /> <meta property="og:updated_time" content="2021-09-16T16:35:00+03:00" />

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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-09-16T06:49:05+03:00" /> <meta property="og:updated_time" content="2021-09-16T16:35:00+03:00" />

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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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