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Add notes for 2020-04-07
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@ -20,4 +20,72 @@ categories: ["Notes"]
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- Altmetric responded about [one item](https://hdl.handle.net/10568/101286) that had no donut since at least 2019-12 and said they fixed some problems with their bot's user agent
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- I decided to [tweet the item](https://twitter.com/mralanorth/status/1245703049445851140), as I can't remember if I ever did it before
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## 2020-04-05
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- Update PostgreSQL JDBC driver to version 42.2.12
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## 2020-04-07
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- Yesterday Atmire sent me their [pull request for DSpace 6 modules](https://github.com/ilri/DSpace/pull/445)
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- Peter pointed out that some items have his ORCID identifier (`cg.creator.id`) twice
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- I think this is because my early `add-orcid-identifiers.py` script was adding identifiers to existing records without properly checking if there was already one present (at first it only checked if there was one with the exact `place` value)
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- As a test I dropped all his ORCID identifiers and added them back with the `add-orcid-identifiers.py` script:
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```
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$ psql -h localhost -U postgres dspace -c "DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value LIKE '%Ballantyne%';"
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DELETE 97
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$ ./add-orcid-identifiers-csv.py -i 2020-04-07-peter-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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```
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- I used this CSV with the script (all records with his name have the name standardized like this):
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```
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dc.contributor.author,cg.creator.id
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"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
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```
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- Then I tried another way, to identify all duplicate ORCID identifiers for a given resource ID and group them so I can see if count is greater than 1:
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```
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dspace=# \COPY (SELECT DISTINCT(resource_id, text_value) as distinct_orcid, COUNT(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 240 GROUP BY distinct_orcid ORDER BY count DESC) TO /tmp/2020-04-07-duplicate-orcids.csv WITH CSV HEADER;
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COPY 15209
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```
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- Of those, about nine authors had duplicate ORCID identifiers over about thirty records, so I created a CSV with all their name variations and ORCID identifiers:
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```
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dc.contributor.author,cg.creator.id
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"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
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"Ramirez-Villegas, Julian","Julian Ramirez-Villegas: 0000-0002-8044-583X"
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"Villegas-Ramirez, J","Julian Ramirez-Villegas: 0000-0002-8044-583X"
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"Ishitani, Manabu","Manabu Ishitani: 0000-0002-6950-4018"
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"Manabu, Ishitani","Manabu Ishitani: 0000-0002-6950-4018"
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"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
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"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
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"Buruchara, Robin A.","Robin Buruchara: 0000-0003-0934-1218"
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"Buruchara, Robin","Robin Buruchara: 0000-0003-0934-1218"
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"Jarvis, Andy","Andy Jarvis: 0000-0001-6543-0798"
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"Jarvis, Andrew","Andy Jarvis: 0000-0001-6543-0798"
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"Jarvis, A.","Andy Jarvis: 0000-0001-6543-0798"
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"Tohme, Joseph M.","Joe Tohme: 0000-0003-2765-7101"
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"Hansen, James","James Hansen: 0000-0002-8599-7895"
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"Hansen, James W.","James Hansen: 0000-0002-8599-7895"
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"Asseng, Senthold","Senthold Asseng: 0000-0002-7583-3811"
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```
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- Then I deleted *all* their existing ORCID identifier records:
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```
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dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value SIMILAR TO '%(0000-0001-6543-0798|0000-0001-9346-2893|0000-0002-6950-4018|0000-0002-7583-3811|0000-0002-8044-583X|0000-0002-8599-7895|0000-0003-0934-1218|0000-0003-2765-7101)%';
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DELETE 994
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```
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- And then I added them again using the `add-orcid-identifiers` records:
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```
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$ ./add-orcid-identifiers-csv.py -i 2020-04-07-fix-duplicate-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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```
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- I ran the fixes on DSpace Test and CGSpace as well
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<!-- vim: set sw=2 ts=2: -->
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@ -25,7 +25,7 @@ On the same note, the one item Abenet pointed out last week now has a donut with
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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/2020-04/" />
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<meta property="article:published_time" content="2020-04-02T10:53:24+03:00" />
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<meta property="article:modified_time" content="2020-04-02T12:33:41+03:00" />
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<meta property="article:modified_time" content="2020-04-02T16:30:44+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="April, 2020"/>
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@ -55,9 +55,9 @@ On the same note, the one item Abenet pointed out last week now has a donut with
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"@type": "BlogPosting",
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"headline": "April, 2020",
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"url": "https://alanorth.github.io/cgspace-notes/2020-04/",
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"wordCount": "178",
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"wordCount": "535",
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"datePublished": "2020-04-02T10:53:24+03:00",
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"dateModified": "2020-04-02T12:33:41+03:00",
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"dateModified": "2020-04-02T16:30:44+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -154,6 +154,65 @@ On the same note, the one item Abenet pointed out last week now has a donut with
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</ul>
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</li>
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</ul>
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<h2 id="2020-04-05">2020-04-05</h2>
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<ul>
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<li>Update PostgreSQL JDBC driver to version 42.2.12</li>
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</ul>
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<h2 id="2020-04-07">2020-04-07</h2>
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<ul>
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<li>Yesterday Atmire sent me their <a href="https://github.com/ilri/DSpace/pull/445">pull request for DSpace 6 modules</a></li>
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<li>Peter pointed out that some items have his ORCID identifier (<code>cg.creator.id</code>) twice
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<ul>
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<li>I think this is because my early <code>add-orcid-identifiers.py</code> script was adding identifiers to existing records without properly checking if there was already one present (at first it only checked if there was one with the exact <code>place</code> value)</li>
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<li>As a test I dropped all his ORCID identifiers and added them back with the <code>add-orcid-identifiers.py</code> script:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ psql -h localhost -U postgres dspace -c "DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value LIKE '%Ballantyne%';"
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DELETE 97
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$ ./add-orcid-identifiers-csv.py -i 2020-04-07-peter-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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</code></pre><ul>
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<li>I used this CSV with the script (all records with his name have the name standardized like this):</li>
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</ul>
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<pre><code>dc.contributor.author,cg.creator.id
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"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
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</code></pre><ul>
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<li>Then I tried another way, to identify all duplicate ORCID identifiers for a given resource ID and group them so I can see if count is greater than 1:</li>
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</ul>
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<pre><code>dspace=# \COPY (SELECT DISTINCT(resource_id, text_value) as distinct_orcid, COUNT(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 240 GROUP BY distinct_orcid ORDER BY count DESC) TO /tmp/2020-04-07-duplicate-orcids.csv WITH CSV HEADER;
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COPY 15209
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</code></pre><ul>
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<li>Of those, about nine authors had duplicate ORCID identifiers over about thirty records, so I created a CSV with all their name variations and ORCID identifiers:</li>
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</ul>
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<pre><code>dc.contributor.author,cg.creator.id
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"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
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"Ramirez-Villegas, Julian","Julian Ramirez-Villegas: 0000-0002-8044-583X"
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"Villegas-Ramirez, J","Julian Ramirez-Villegas: 0000-0002-8044-583X"
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"Ishitani, Manabu","Manabu Ishitani: 0000-0002-6950-4018"
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"Manabu, Ishitani","Manabu Ishitani: 0000-0002-6950-4018"
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"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
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"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
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"Buruchara, Robin A.","Robin Buruchara: 0000-0003-0934-1218"
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"Buruchara, Robin","Robin Buruchara: 0000-0003-0934-1218"
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"Jarvis, Andy","Andy Jarvis: 0000-0001-6543-0798"
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"Jarvis, Andrew","Andy Jarvis: 0000-0001-6543-0798"
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"Jarvis, A.","Andy Jarvis: 0000-0001-6543-0798"
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"Tohme, Joseph M.","Joe Tohme: 0000-0003-2765-7101"
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"Hansen, James","James Hansen: 0000-0002-8599-7895"
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"Hansen, James W.","James Hansen: 0000-0002-8599-7895"
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"Asseng, Senthold","Senthold Asseng: 0000-0002-7583-3811"
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</code></pre><ul>
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<li>Then I deleted <em>all</em> their existing ORCID identifier records:</li>
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</ul>
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<pre><code>dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value SIMILAR TO '%(0000-0001-6543-0798|0000-0001-9346-2893|0000-0002-6950-4018|0000-0002-7583-3811|0000-0002-8044-583X|0000-0002-8599-7895|0000-0003-0934-1218|0000-0003-2765-7101)%';
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DELETE 994
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</code></pre><ul>
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<li>And then I added them again using the <code>add-orcid-identifiers</code> records:</li>
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</ul>
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<pre><code>$ ./add-orcid-identifiers-csv.py -i 2020-04-07-fix-duplicate-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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</code></pre><ul>
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<li>I ran the fixes on DSpace Test and CGSpace as well</li>
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</ul>
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<!-- raw HTML omitted -->
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@ -4,27 +4,27 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2020-04/</loc>
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<lastmod>2020-04-02T12:33:41+03:00</lastmod>
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<lastmod>2020-04-02T16:30:44+03:00</lastmod>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
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<lastmod>2020-04-02T12:33:41+03:00</lastmod>
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<lastmod>2020-04-02T16:30:44+03:00</lastmod>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2020-04-02T12:33:41+03:00</lastmod>
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<lastmod>2020-04-02T16:30:44+03:00</lastmod>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
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<lastmod>2020-04-02T12:33:41+03:00</lastmod>
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<lastmod>2020-04-02T16:30:44+03:00</lastmod>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
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<lastmod>2020-04-02T12:33:41+03:00</lastmod>
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<lastmod>2020-04-02T16:30:44+03:00</lastmod>
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</url>
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<url>
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