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Alan Orth 2024-03-19 09:01:13 +03:00
parent 83c053f7ee
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41 changed files with 141 additions and 48 deletions
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2
content/posts/2022-06.md
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@ -169,7 +169,7 @@ $ csvjoin --outer -c alpha2 ~/Downloads/clarisa-countries.csv ~/Downloads/UNSD\
- Then re-export the UN M.49 countries to a clean list because the one I did yesterday somehow has errors: - Then re-export the UN M.49 countries to a clean list because the one I did yesterday somehow has errors:
```console ```console
csvcut -d ';' -c 'ISO-alpha2 Code,Country or Area' ~/Downloads/UNSD\ —\ Methodology.csv | sed -e '1s/ISO-alpha2 Code/alpha2/' -e '1s/Country or Area/UN M.49 Name/' > ~/Downloads/un-countries.csv $ csvcut -d ';' -c 'ISO-alpha2 Code,Country or Area' ~/Downloads/UNSD\ —\ Methodology.csv | sed -e '1s/ISO-alpha2 Code/alpha2/' -e '1s/Country or Area/UN M.49 Name/' > ~/Downloads/un-countries.csv
``` ```
- Check the number of lines in each file: - Check the number of lines in each file:

44
content/posts/2024-03.md
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@ -113,4 +113,48 @@ $ csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],cg.link.permalink[en_US
SELECT ds6_item2itemhandle(dspace_object_id) AS handle FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item WHERE NOT discoverable) AND metadata_field_id=28 AND text_value LIKE 'Submitted by Alliance TIP Submit%'; SELECT ds6_item2itemhandle(dspace_object_id) AS handle FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item WHERE NOT discoverable) AND metadata_field_id=28 AND text_value LIKE 'Submitted by Alliance TIP Submit%';
``` ```
## 2024-03-14
- Looking in to reports of rate limiting of Altmetric's bot on CGSpace
- I don't see any HTTP 429 responses for their user agents in any of our logs...
- I tried myself on an item page and never hit a limit...
```console
$ for num in {1..60}; do echo -n "Request ${num}: "; curl -s -o /dev/null -w "%{http_code}" https://dspace7test.ilri.org/items/c9b8999d-3001-42ba-a267-14f4bfa90b53 && echo; done
Request 1: 200
Request 2: 200
Request 3: 200
Request 4: 200
...
Request 60: 200
```
- All responses were HTTP 200...
- In any case, I whitelisted their production IPs and told them to try again
- I imported 468 of IFPRI's 2023 records that were confirmed to not be duplicates to CGSpace
- I also spent some time merging metadata from 415 of the remaining 432 duplicates with the metadata for the existing items on CGSpace
- This was a bit of dirty work using csvkit, xsv, and OpenRefine
## 2024-03-17
- There are 17 records from IFPRI's 2023 batch that are remaining from the 432 that I identified as already being on CGSpace
- These are different in that they are duplicates on CGSpace as well, so the csvjoin failed and the metadata got messed up in my migration
- I looked closer and whittled this down to 14 actual records, and spent some time working on them
- I isolated 12 of these items that existed on CGSpace and added publication ranks, project identifiers, and provenance links
- Now there only remain two confusing records about the Inkomati catchment
## 2024-03-18
- Checking to see how many IFPRI records we have migrated so far:
```console
$ csvgrep -c 'dc.description.provenance[en_US]' -m 'Original URL from IFPRI CONTENTdm' cgspace.csv \
| csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],dc.description.provenance[en_US],dcterms.type[en_US]' \
| tee /tmp/ifpri-records.csv \
| csvstat --count
898
```
- I finalized the remaining two on Inkomati catchment and now we are at 900!
<!-- vim: set sw=2 ts=2: --> <!-- vim: set sw=2 ts=2: -->

4
docs/2022-06/index.html
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@ -58,7 +58,7 @@ There seem to be many more of these:
"@type": "BlogPosting", "@type": "BlogPosting",
"headline": "June, 2022", "headline": "June, 2022",
"url": "https://alanorth.github.io/cgspace-notes/2022-06/", "url": "https://alanorth.github.io/cgspace-notes/2022-06/",
"wordCount": "1788", "wordCount": "1789",
"datePublished": "2022-06-06T09:01:36+03:00", "datePublished": "2022-06-06T09:01:36+03:00",
"dateModified": "2023-04-27T13:10:13-07:00", "dateModified": "2023-04-27T13:10:13-07:00",
"author": { "author": {
@ -321,7 +321,7 @@ There seem to be many more of these:
<li>Spent some more time working on my <code>countries-to-csv.py</code> script to fix some logic errors</li> <li>Spent some more time working on my <code>countries-to-csv.py</code> script to fix some logic errors</li>
<li>Then re-export the UN M.49 countries to a clean list because the one I did yesterday somehow has errors:</li> <li>Then re-export the UN M.49 countries to a clean list because the one I did yesterday somehow has errors:</li>
</ul> </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>csvcut -d &#39;;&#39; -c &#39;ISO-alpha2 Code,Country or Area&#39; ~/Downloads/UNSD\ —\ Methodology.csv | sed -e &#39;1s/ISO-alpha2 Code/alpha2/&#39; -e &#39;1s/Country or Area/UN M.49 Name/&#39; &gt; ~/Downloads/un-countries.csv <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>$ csvcut -d <span style="color:#e6db74">&#39;;&#39;</span> -c <span style="color:#e6db74">&#39;ISO-alpha2 Code,Country or Area&#39;</span> ~/Downloads/UNSD<span style="color:#ae81ff">\ </span>—<span style="color:#ae81ff">\ </span>Methodology.csv | sed -e <span style="color:#e6db74">&#39;1s/ISO-alpha2 Code/alpha2/&#39;</span> -e <span style="color:#e6db74">&#39;1s/Country or Area/UN M.49 Name/&#39;</span> &gt; ~/Downloads/un-countries.csv
</span></span></code></pre></div><ul> </span></span></code></pre></div><ul>
<li>Check the number of lines in each file:</li> <li>Check the number of lines in each file:</li>
</ul> </ul>

57
docs/2024-03/index.html
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@ -19,7 +19,7 @@ It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808
<meta property="og:type" content="article" /> <meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2024-03/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2024-03/" />
<meta property="article:published_time" content="2024-03-01T09:55:00+03:00" /> <meta property="article:published_time" content="2024-03-01T09:55:00+03:00" />
<meta property="article:modified_time" content="2024-03-11T21:58:15+03:00" /> <meta property="article:modified_time" content="2024-03-14T09:29:05+03:00" />
@ -44,9 +44,9 @@ It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808
"@type": "BlogPosting", "@type": "BlogPosting",
"headline": "March, 2024", "headline": "March, 2024",
"url": "https://alanorth.github.io/cgspace-notes/2024-03/", "url": "https://alanorth.github.io/cgspace-notes/2024-03/",
"wordCount": "627", "wordCount": "923",
"datePublished": "2024-03-01T09:55:00+03:00", "datePublished": "2024-03-01T09:55:00+03:00",
"dateModified": "2024-03-11T21:58:15+03:00", "dateModified": "2024-03-14T09:29:05+03:00",
"author": { "author": {
"@type": "Person", "@type": "Person",
"name": "Alan Orth" "name": "Alan Orth"
@ -236,7 +236,56 @@ It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808
</li> </li>
</ul> </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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">SELECT</span> ds6_item2itemhandle(dspace_object_id) <span style="color:#66d9ef">AS</span> handle <span style="color:#66d9ef">FROM</span> metadatavalue <span style="color:#66d9ef">WHERE</span> dspace_object_id <span style="color:#66d9ef">IN</span> (<span style="color:#66d9ef">SELECT</span> uuid <span style="color:#66d9ef">FROM</span> item <span style="color:#66d9ef">WHERE</span> <span style="color:#66d9ef">NOT</span> discoverable) <span style="color:#66d9ef">AND</span> metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">28</span> <span style="color:#66d9ef">AND</span> text_value <span style="color:#66d9ef">LIKE</span> <span style="color:#e6db74">&#39;Submitted by Alliance TIP Submit%&#39;</span>; <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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">SELECT</span> ds6_item2itemhandle(dspace_object_id) <span style="color:#66d9ef">AS</span> handle <span style="color:#66d9ef">FROM</span> metadatavalue <span style="color:#66d9ef">WHERE</span> dspace_object_id <span style="color:#66d9ef">IN</span> (<span style="color:#66d9ef">SELECT</span> uuid <span style="color:#66d9ef">FROM</span> item <span style="color:#66d9ef">WHERE</span> <span style="color:#66d9ef">NOT</span> discoverable) <span style="color:#66d9ef">AND</span> metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">28</span> <span style="color:#66d9ef">AND</span> text_value <span style="color:#66d9ef">LIKE</span> <span style="color:#e6db74">&#39;Submitted by Alliance TIP Submit%&#39;</span>;
</span></span></code></pre></div><!-- raw HTML omitted --> </span></span></code></pre></div><h2 id="2024-03-14">2024-03-14</h2>
<ul>
<li>Looking in to reports of rate limiting of Altmetric&rsquo;s bot on CGSpace
<ul>
<li>I don&rsquo;t see any HTTP 429 responses for their user agents in any of our logs&hellip;</li>
<li>I tried myself on an item page and never hit a limit&hellip;</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>$ <span style="color:#66d9ef">for</span> num in <span style="color:#f92672">{</span>1..60<span style="color:#f92672">}</span>; <span style="color:#66d9ef">do</span> echo -n <span style="color:#e6db74">&#34;Request </span><span style="color:#e6db74">${</span>num<span style="color:#e6db74">}</span><span style="color:#e6db74">: &#34;</span>; curl -s -o /dev/null -w <span style="color:#e6db74">&#34;%{http_code}&#34;</span> https://dspace7test.ilri.org/items/c9b8999d-3001-42ba-a267-14f4bfa90b53 <span style="color:#f92672">&amp;&amp;</span> echo; <span style="color:#66d9ef">done</span>
</span></span><span style="display:flex;"><span>Request 1: 200
</span></span><span style="display:flex;"><span>Request 2: 200
</span></span><span style="display:flex;"><span>Request 3: 200
</span></span><span style="display:flex;"><span>Request 4: 200
</span></span><span style="display:flex;"><span>...
</span></span><span style="display:flex;"><span>Request 60: 200
</span></span></code></pre></div><ul>
<li>All responses were HTTP 200&hellip;</li>
<li>In any case, I whitelisted their production IPs and told them to try again</li>
<li>I imported 468 of IFPRI&rsquo;s 2023 records that were confirmed to not be duplicates to CGSpace
<ul>
<li>I also spent some time merging metadata from 415 of the remaining 432 duplicates with the metadata for the existing items on CGSpace</li>
<li>This was a bit of dirty work using csvkit, xsv, and OpenRefine</li>
</ul>
</li>
</ul>
<h2 id="2024-03-17">2024-03-17</h2>
<ul>
<li>There are 17 records from IFPRI&rsquo;s 2023 batch that are remaining from the 432 that I identified as already being on CGSpace
<ul>
<li>These are different in that they are duplicates on CGSpace as well, so the csvjoin failed and the metadata got messed up in my migration</li>
<li>I looked closer and whittled this down to 14 actual records, and spent some time working on them</li>
<li>I isolated 12 of these items that existed on CGSpace and added publication ranks, project identifiers, and provenance links</li>
<li>Now there only remain two confusing records about the Inkomati catchment</li>
</ul>
</li>
</ul>
<h2 id="2024-03-18">2024-03-18</h2>
<ul>
<li>Checking to see how many IFPRI records we have migrated so far:</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>$ csvgrep -c <span style="color:#e6db74">&#39;dc.description.provenance[en_US]&#39;</span> -m <span style="color:#e6db74">&#39;Original URL from IFPRI CONTENTdm&#39;</span> cgspace.csv <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c &#39;id,dc.title[en_US],dc.identifier.uri[en_US],dc.description.provenance[en_US],dcterms.type[en_US]&#39; \
</span></span><span style="display:flex;"><span> | tee /tmp/ifpri-records.csv \
</span></span><span style="display:flex;"><span> | csvstat --count
</span></span><span style="display:flex;"><span>898
</span></span></code></pre></div><ul>
<li>I finalized the remaining two on Inkomati catchment and now we are at 900!</li>
</ul>
<!-- raw HTML omitted -->

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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: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/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+03:00" />

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@ -6,7 +6,7 @@
<description>Recent content in Categories on CGSpace Notes</description> <description>Recent content in Categories on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator> <generator>Hugo -- gohugo.io</generator>
<language>en-us</language> <language>en-us</language>
<lastBuildDate>Mon, 11 Mar 2024 21:58:15 +0300</lastBuildDate> <lastBuildDate>Thu, 14 Mar 2024 09:29:05 +0300</lastBuildDate>
<atom:link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="self" type="application/rss+xml" /> <atom:link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="self" type="application/rss+xml" />
<item> <item>
<title>Notes</title> <title>Notes</title>

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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: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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+03:00" />

2
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@ -6,7 +6,7 @@
<description>Recent content in Notes on CGSpace Notes</description> <description>Recent content in Notes on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator> <generator>Hugo -- gohugo.io</generator>
<language>en-us</language> <language>en-us</language>
<lastBuildDate>Mon, 11 Mar 2024 21:58:15 +0300</lastBuildDate> <lastBuildDate>Thu, 14 Mar 2024 09:29:05 +0300</lastBuildDate>
<atom:link href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" rel="self" type="application/rss+xml" /> <atom:link href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" rel="self" type="application/rss+xml" />
<item> <item>
<title>March, 2024</title> <title>March, 2024</title>

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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: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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+03:00" />

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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: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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+03:00" />

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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: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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+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="2024-03-11T21:58:15+03:00" /> <meta property="og:updated_time" content="2024-03-14T09:29:05+03:00" />

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@ -10,7 +10,7 @@
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