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Add notes for 2020-08-09

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Alan Orth 2020-08-10 09:27:50 +03:00
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141
content/posts/2020-08.md
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@ -209,4 +209,145 @@ on_id=[A-Z0-9]{32}' | sort | uniq | wc -l
- I ran it on CGSpace and it cleaned up 3,769 thumbnails!
- Afterwards I ran `dspace cleanup -v` to remove the deleted thumbnails
## 2020-08-08
- The Atmire stats processing for the statistics-2018 Solr core keeps stopping with this error:
```
Exception: 50 consecutive records couldn't be saved. There's most likely an issue with the connection to the solr server. Shutting down.
java.lang.RuntimeException: 50 consecutive records couldn't be saved. There's most likely an issue with the connection to the solr server. Shutting down.
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.storeOnServer(SourceFile:317)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.processRecords(SourceFile:177)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.performRun(SourceFile:161)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.update(SourceFile:128)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI.main(SourceFile:78)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
```
- It lists a few of the records that it is having issues with and they all have integer IDs
- When I checked Solr I see 8,000 of them, some of which have type 0 and some with no type...
- I purged them and then the process continues:
```
$ curl -s "http://localhost:8081/solr/statistics-2018/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:/[0-9]+/</query></delete>'
```
## 2020-08-09
- The Atmire script did something to the server and created 132GB of log files so the root partition ran out of space...
- I removed the log file and tried to re-run the process but it seems to be looping over 11,000 records and failing, creating millions of lines in the logs again:
```
# grep -oE "Record uid: ([a-f0-9\\-]*){1} couldn't be processed" /home/dspacetest.cgiar.org/log/dspace.log.2020-08-09 > /tmp/not-processed-errors.txt
# wc -l /tmp/not-processed-errors.txt
2202973 /tmp/not-processed-errors.txt
# sort /tmp/not-processed-errors.txt | uniq -c | tail -n 10
220 Record uid: ffe52878-ba23-44fb-8df7-a261bb358abc couldn't be processed
220 Record uid: ffecb2b0-944d-4629-afdf-5ad995facaf9 couldn't be processed
220 Record uid: ffedde6b-0782-4d9f-93ff-d1ba1a737585 couldn't be processed
220 Record uid: ffedfb13-e929-4909-b600-a18295520a97 couldn't be processed
220 Record uid: fff116fb-a1a0-40d0-b0fb-b71e9bb898e5 couldn't be processed
221 Record uid: fff1349d-79d5-4ceb-89a1-ce78107d982d couldn't be processed
220 Record uid: fff13ddb-b2a2-410a-9baa-97e333118c74 couldn't be processed
220 Record uid: fff232a6-a008-47d0-ad83-6e209bb6cdf9 couldn't be processed
221 Record uid: fff75243-c3be-48a0-98f8-a656f925cb68 couldn't be processed
221 Record uid: fff88af8-88d4-4f79-ba1a-79853973c872 couldn't be processed
```
- I looked at some of those records and saw strange objects in their `containerCommunity`, `containerCollection`, etc...
```
{
"responseHeader": {
"status": 0,
"QTime": 0,
"params": {
"q": "uid:fff1349d-79d5-4ceb-89a1-ce78107d982d",
"indent": "true",
"wt": "json",
"_": "1596957629970"
}
},
"response": {
"numFound": 1,
"start": 0,
"docs": [
{
"containerCommunity": [
"155",
"155",
"{set=null}"
],
"uid": "fff1349d-79d5-4ceb-89a1-ce78107d982d",
"containerCollection": [
"1099",
"830",
"{set=830}"
],
"owningComm": [
"155",
"155",
"{set=null}"
],
"isInternal": false,
"isBot": false,
"statistics_type": "view",
"time": "2018-05-08T23:17:00.157Z",
"owningColl": [
"1099",
"830",
"{set=830}"
],
"_version_": 1621500445042147300
}
]
}
}
```
- I deleted those 11,724 records with the strange "set" object in the collections and communities, as well as 360,000 records with `id: -1`
```
$ curl -s "http://localhost:8081/solr/statistics-2018/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>owningColl:/.*set.*/</query></delete>'
$ curl -s "http://localhost:8081/solr/statistics-2018/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:\-1</query></delete>'
```
- I was going to compare the CUA stats for 2018 and 2019 on CGSpace and DSpace Test, but after Linode rebooted CGSpace (linode18) for maintenance yesterday the solr cores didn't all come back up OK
- I had to restart Tomcat five times before they all came up!
- After that I generated a report for 2018 and 2019 on each server and found that the difference is about 10,000–20,000 per month, which is much less than I was expecting
- I noticed some authors that should have ORCID identifiers, but didn't (perhaps older items before we were tagging ORCID metadata)
- With the simple list below I added 1,341 identifiers!
```
$ cat 2020-08-09-add-ILRI-orcids.csv
dc.contributor.author,cg.creator.id
"Grace, Delia","Delia Grace: 0000-0002-0195-9489"
"Delia Grace","Delia Grace: 0000-0002-0195-9489"
"Baker, Derek","Derek Baker: 0000-0001-6020-6973"
"Ngan Tran Thi","Tran Thi Ngan: 0000-0002-7184-3086"
"Dang Xuan Sinh","Sinh Dang-Xuan: 0000-0002-0522-7808"
"Hung Nguyen-Viet","Hung Nguyen-Viet: 0000-0001-9877-0596"
"Pham Van Hung","Pham Anh Hung: 0000-0001-9366-0259"
"Lindahl, Johanna F.","Johanna Lindahl: 0000-0002-1175-0398"
"Teufel, Nils","Nils Teufel: 0000-0001-5305-6620"
"Duncan, Alan J.",Alan Duncan: 0000-0002-3954-3067"
"Moodley, Arshnee","Arshnee Moodley: 0000-0002-6469-3948"
```
- That got me curious, so I generated a list of all the unique ORCID identifiers we have in the database:
```
dspace=# \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240) TO /tmp/2020-08-09-orcid-identifiers.csv;
COPY 2095
dspace=# \q
$ grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' /tmp/2020-08-09-orcid-identifiers.csv | sort | uniq > /tmp/2020-08-09-orcid-identifiers-uniq.csv
$ wc -l /tmp/2020-08-09-orcid-identifiers-uniq.csv
1949 /tmp/2020-08-09-orcid-identifiers-uniq.csv
```
<!-- vim: set sw=2 ts=2: -->

142
docs/2020-08/index.html
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@ -19,7 +19,7 @@ It is class based so I can easily add support for other vocabularies, and the te
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-08/" />
<meta property="article:published_time" content="2020-08-02T15:35:54+03:00" />
<meta property="article:modified_time" content="2020-08-06T16:24:01+03:00" />
<meta property="article:modified_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="August, 2020"/>
@ -43,9 +43,9 @@ It is class based so I can easily add support for other vocabularies, and the te
"@type": "BlogPosting",
"headline": "August, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-08/",
"wordCount": "1421",
"wordCount": "2049",
"datePublished": "2020-08-02T15:35:54+03:00",
"dateModified": "2020-08-06T16:24:01+03:00",
"dateModified": "2020-08-07T19:55:21+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -370,7 +370,141 @@ on_id=[A-Z0-9]{32}' | sort | uniq | wc -l
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
<h2 id="2020-08-08">2020-08-08</h2>
<ul>
<li>The Atmire stats processing for the statistics-2018 Solr core keeps stopping with this error:</li>
</ul>
<pre><code>Exception: 50 consecutive records couldn't be saved. There's most likely an issue with the connection to the solr server. Shutting down.
java.lang.RuntimeException: 50 consecutive records couldn't be saved. There's most likely an issue with the connection to the solr server. Shutting down.
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.storeOnServer(SourceFile:317)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.processRecords(SourceFile:177)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.performRun(SourceFile:161)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.update(SourceFile:128)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI.main(SourceFile:78)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><ul>
<li>It lists a few of the records that it is having issues with and they all have integer IDs
<ul>
<li>When I checked Solr I see 8,000 of them, some of which have type 0 and some with no type&hellip;</li>
<li>I purged them and then the process continues:</li>
</ul>
</li>
</ul>
<pre><code>$ curl -s &quot;http://localhost:8081/solr/statistics-2018/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary '&lt;delete&gt;&lt;query&gt;id:/[0-9]+/&lt;/query&gt;&lt;/delete&gt;'
</code></pre><h2 id="2020-08-09">2020-08-09</h2>
<ul>
<li>The Atmire script did something to the server and created 132GB of log files so the root partition ran out of space&hellip;</li>
<li>I removed the log file and tried to re-run the process but it seems to be looping over 11,000 records and failing, creating millions of lines in the logs again:</li>
</ul>
<pre><code># grep -oE &quot;Record uid: ([a-f0-9\\-]*){1} couldn't be processed&quot; /home/dspacetest.cgiar.org/log/dspace.log.2020-08-09 &gt; /tmp/not-processed-errors.txt
# wc -l /tmp/not-processed-errors.txt
2202973 /tmp/not-processed-errors.txt
# sort /tmp/not-processed-errors.txt | uniq -c | tail -n 10
220 Record uid: ffe52878-ba23-44fb-8df7-a261bb358abc couldn't be processed
220 Record uid: ffecb2b0-944d-4629-afdf-5ad995facaf9 couldn't be processed
220 Record uid: ffedde6b-0782-4d9f-93ff-d1ba1a737585 couldn't be processed
220 Record uid: ffedfb13-e929-4909-b600-a18295520a97 couldn't be processed
220 Record uid: fff116fb-a1a0-40d0-b0fb-b71e9bb898e5 couldn't be processed
221 Record uid: fff1349d-79d5-4ceb-89a1-ce78107d982d couldn't be processed
220 Record uid: fff13ddb-b2a2-410a-9baa-97e333118c74 couldn't be processed
220 Record uid: fff232a6-a008-47d0-ad83-6e209bb6cdf9 couldn't be processed
221 Record uid: fff75243-c3be-48a0-98f8-a656f925cb68 couldn't be processed
221 Record uid: fff88af8-88d4-4f79-ba1a-79853973c872 couldn't be processed
</code></pre><ul>
<li>I looked at some of those records and saw strange objects in their <code>containerCommunity</code>, <code>containerCollection</code>, etc&hellip;</li>
</ul>
<pre><code>{
&quot;responseHeader&quot;: {
&quot;status&quot;: 0,
&quot;QTime&quot;: 0,
&quot;params&quot;: {
&quot;q&quot;: &quot;uid:fff1349d-79d5-4ceb-89a1-ce78107d982d&quot;,
&quot;indent&quot;: &quot;true&quot;,
&quot;wt&quot;: &quot;json&quot;,
&quot;_&quot;: &quot;1596957629970&quot;
}
},
&quot;response&quot;: {
&quot;numFound&quot;: 1,
&quot;start&quot;: 0,
&quot;docs&quot;: [
{
&quot;containerCommunity&quot;: [
&quot;155&quot;,
&quot;155&quot;,
&quot;{set=null}&quot;
],
&quot;uid&quot;: &quot;fff1349d-79d5-4ceb-89a1-ce78107d982d&quot;,
&quot;containerCollection&quot;: [
&quot;1099&quot;,
&quot;830&quot;,
&quot;{set=830}&quot;
],
&quot;owningComm&quot;: [
&quot;155&quot;,
&quot;155&quot;,
&quot;{set=null}&quot;
],
&quot;isInternal&quot;: false,
&quot;isBot&quot;: false,
&quot;statistics_type&quot;: &quot;view&quot;,
&quot;time&quot;: &quot;2018-05-08T23:17:00.157Z&quot;,
&quot;owningColl&quot;: [
&quot;1099&quot;,
&quot;830&quot;,
&quot;{set=830}&quot;
],
&quot;_version_&quot;: 1621500445042147300
}
]
}
}
</code></pre><ul>
<li>I deleted those 11,724 records with the strange &ldquo;set&rdquo; object in the collections and communities, as well as 360,000 records with <code>id: -1</code></li>
</ul>
<pre><code>$ curl -s &quot;http://localhost:8081/solr/statistics-2018/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary '&lt;delete&gt;&lt;query&gt;owningColl:/.*set.*/&lt;/query&gt;&lt;/delete&gt;'
$ curl -s &quot;http://localhost:8081/solr/statistics-2018/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary '&lt;delete&gt;&lt;query&gt;id:\-1&lt;/query&gt;&lt;/delete&gt;'
</code></pre><ul>
<li>I was going to compare the CUA stats for 2018 and 2019 on CGSpace and DSpace Test, but after Linode rebooted CGSpace (linode18) for maintenance yesterday the solr cores didn&rsquo;t all come back up OK
<ul>
<li>I had to restart Tomcat five times before they all came up!</li>
<li>After that I generated a report for 2018 and 2019 on each server and found that the difference is about 10,000–20,000 per month, which is much less than I was expecting</li>
</ul>
</li>
<li>I noticed some authors that should have ORCID identifiers, but didn&rsquo;t (perhaps older items before we were tagging ORCID metadata)
<ul>
<li>With the simple list below I added 1,341 identifiers!</li>
</ul>
</li>
</ul>
<pre><code>$ cat 2020-08-09-add-ILRI-orcids.csv
dc.contributor.author,cg.creator.id
&quot;Grace, Delia&quot;,&quot;Delia Grace: 0000-0002-0195-9489&quot;
&quot;Delia Grace&quot;,&quot;Delia Grace: 0000-0002-0195-9489&quot;
&quot;Baker, Derek&quot;,&quot;Derek Baker: 0000-0001-6020-6973&quot;
&quot;Ngan Tran Thi&quot;,&quot;Tran Thi Ngan: 0000-0002-7184-3086&quot;
&quot;Dang Xuan Sinh&quot;,&quot;Sinh Dang-Xuan: 0000-0002-0522-7808&quot;
&quot;Hung Nguyen-Viet&quot;,&quot;Hung Nguyen-Viet: 0000-0001-9877-0596&quot;
&quot;Pham Van Hung&quot;,&quot;Pham Anh Hung: 0000-0001-9366-0259&quot;
&quot;Lindahl, Johanna F.&quot;,&quot;Johanna Lindahl: 0000-0002-1175-0398&quot;
&quot;Teufel, Nils&quot;,&quot;Nils Teufel: 0000-0001-5305-6620&quot;
&quot;Duncan, Alan J.&quot;,Alan Duncan: 0000-0002-3954-3067&quot;
&quot;Moodley, Arshnee&quot;,&quot;Arshnee Moodley: 0000-0002-6469-3948&quot;
</code></pre><ul>
<li>That got me curious, so I generated a list of all the unique ORCID identifiers we have in the database:</li>
</ul>
<pre><code>dspace=# \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240) TO /tmp/2020-08-09-orcid-identifiers.csv;
COPY 2095
dspace=# \q
$ grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' /tmp/2020-08-09-orcid-identifiers.csv | sort | uniq &gt; /tmp/2020-08-09-orcid-identifiers-uniq.csv
$ wc -l /tmp/2020-08-09-orcid-identifiers-uniq.csv
1949 /tmp/2020-08-09-orcid-identifiers-uniq.csv
</code></pre><!-- raw HTML omitted -->

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@ -9,7 +9,7 @@
<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/categories/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>

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@ -9,7 +9,7 @@
<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/categories/notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>

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@ -9,7 +9,7 @@
<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/categories/notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>

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@ -9,7 +9,7 @@
<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/categories/notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace 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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace 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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace 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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace 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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-08-06T16:24:01+03:00" />
<meta property="og:updated_time" content="2020-08-07T19:55:21+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>

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