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Update notes for 2019-09-20
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@ -236,6 +236,7 @@ $ tidy -xml -utf8 -m -iq -w 0 dspace/config/controlled-vocabularies/dc-contribut
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## 2019-09-20
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- Deploy a fresh snapshot of CGSpace's PostgreSQL database on DSpace Test so we can get more accurate duplicate checking with the upcoming Bioversity and IITA migrations
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- Skype with Carol and Francesca to discuss the Bioveristy migration to CGSpace
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- They want to do some enrichment of the metadata to add countries and regions
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- Also, they noticed that some items have a blank ISSN in the citation like "ISSN:"
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@ -248,4 +249,46 @@ $ tidy -xml -utf8 -m -iq -w 0 dspace/config/controlled-vocabularies/dc-contribut
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$ perl-rename -n 's/_{2,3}/_/g' *.pdf
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```
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- I was going preparing to run SAFBuilder for the Bioversity migration and decided to check the list of PDFs on my local machine versus on DSpace Test (where I had downloaded them last month)
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- There are a *few dozen* that have completely fucked up names due to some encoding error
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- To make matters worse, when I tried to download them, some of the links in the "URL" column that Francesco included are wrong, so I had to go to the permalink and get a link that worked
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- After downloading everything I had to use Ubuntu's version of rename to get rid of all the double and triple underscores:
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```
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$ rename -v 's/___/_/g' *.pdf
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$ rename -v 's/__/_/g' *.pdf
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```
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- I'm still waiting to hear what Carol and Francesca want to do with the `1195.pdf.LCK` file (for now I've removed it from the CSV, but for future reference it has the number 630 in its permalink)
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- I wrote two fairly long GREL expressions to clean up the institutional author names in the `dc.contributor.author` and `dc.identifier.citation` fields using OpenRefine
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- The first targets acronyms in parentheses like "International Livestock Research Institute (ILRI)":
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```
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value.replace(/,? ?\((ANDES|APAFRI|APFORGEN|Canada|CFC|CGRFA|China|CacaoNet|CATAS|CDU|CIAT|CIRF|CIP|CIRNMA|COSUDE|Colombia|COA|COGENT|CTDT|Denmark|DfLP|DSE|ECPGR|ECOWAS|ECP\/GR|England|EUFORGEN|FAO|France|Francia|FFTC|Germany|GEF|GFU|GGCO|GRPI|italy|Italy|Italia|India|ICCO|ICAR|ICGR|ICRISAT|IDRC|INFOODS|IPGRI|IBPGR|ICARDA|ILRI|INIBAP|INBAR|IPK|ISG|IT|Japan|JIRCAS|Kenya|LI\-BIRD|Malaysia|NARC|NBPGR|Nepal|OOAS|RDA|RISBAP|Rome|ROPPA|SEARICE|Senegal|SGRP|Sweden|Syrian Arab Republic|The Netherlands|UNDP|UK|UNEP|UoB|UoM|United Kingdom|WAHO)\)/,"")
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```
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- The second targets cities and countries after names like "International Livestock Research Intstitute, Kenya":
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```
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replace(/,? ?(ali|Aleppo|Amsterdam|Beijing|Bonn|Burkina Faso|CN|Dakar|Gatersleben|London|Montpellier|Nairobi|New Delhi|Kaski|Kepong|Malaysia|Khumaltar|Lima|Ltpur|Ottawa|Patancheru|Peru|Pokhara|Rome|Uppsala|University of Mauritius|Tsukuba)/,"")
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```
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- I imported the 1,427 Bioversity records with bitstreams to a new collection called [2019-09-20 Bioversity Migration Test](https://dspacetest.cgiar.org/handle/10568/103688) on DSpace Test (after splitting them in two batches of about 700 each):
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```
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$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx768m'
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$ dspace import -a me@cgiar.org -m 2019-09-20-bioversity1.map -s /home/aorth/Bioversity/bioversity1
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$ dspace import -a me@cgiar.org -m 2019-09-20-bioversity2.map -s /home/aorth/Bioversity/bioversity2
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```
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- After that I exported the collection again and started doing some quality checks and cleanups:
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- Change all DOIs to use https://doi.org format
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- Change all bioversityinternational.org links to use https://
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- Fix ten authors with invalid names like "Orth,." by checking the correct name in the citation
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- Fix several invalid ISBNs, but there are several more that contain incorrect ISBNs in their PDFs!
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- Fix some citations that were using "ISSN" instead of ISBN
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- The next steps are:
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- Check for duplicates
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- Continue with institutional author normalization
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- Ask which collection to map items with type Brochure, Journal Item, and Thesis?
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<!-- vim: set sw=2 ts=2: -->
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@ -40,7 +40,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
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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/2019-09/" />
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<meta property="article:published_time" content="2019-09-01T10:17:51+03:00" />
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<meta property="article:modified_time" content="2019-09-20T12:55:11+03:00" />
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<meta property="article:modified_time" content="2019-09-20T13:25:59+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="September, 2019"/>
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@ -85,9 +85,9 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
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"@type": "BlogPosting",
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"headline": "September, 2019",
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"url": "https:\/\/alanorth.github.io\/cgspace-notes\/2019-09\/",
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"wordCount": "1778",
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"wordCount": "2166",
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"datePublished": "2019-09-01T10:17:51\x2b03:00",
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"dateModified": "2019-09-20T12:55:11\x2b03:00",
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"dateModified": "2019-09-20T13:25:59\x2b03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -438,6 +438,8 @@ $ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-s
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<h2 id="2019-09-20">2019-09-20</h2>
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<ul>
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<li>Deploy a fresh snapshot of CGSpace’s PostgreSQL database on DSpace Test so we can get more accurate duplicate checking with the upcoming Bioversity and IITA migrations</li>
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<li><p>Skype with Carol and Francesca to discuss the Bioveristy migration to CGSpace</p>
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<ul>
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@ -452,6 +454,60 @@ $ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-s
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<pre><code>$ perl-rename -n 's/_{2,3}/_/g' *.pdf
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</code></pre></li>
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</ul></li>
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<li><p>I was going preparing to run SAFBuilder for the Bioversity migration and decided to check the list of PDFs on my local machine versus on DSpace Test (where I had downloaded them last month)</p>
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<ul>
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<li>There are a <em>few dozen</em> that have completely fucked up names due to some encoding error</li>
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<li>To make matters worse, when I tried to download them, some of the links in the “URL” column that Francesco included are wrong, so I had to go to the permalink and get a link that worked</li>
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<li><p>After downloading everything I had to use Ubuntu’s version of rename to get rid of all the double and triple underscores:</p>
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<pre><code>$ rename -v 's/___/_/g' *.pdf
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$ rename -v 's/__/_/g' *.pdf
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</code></pre></li>
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</ul></li>
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<li><p>I’m still waiting to hear what Carol and Francesca want to do with the <code>1195.pdf.LCK</code> file (for now I’ve removed it from the CSV, but for future reference it has the number 630 in its permalink)</p></li>
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<li><p>I wrote two fairly long GREL expressions to clean up the institutional author names in the <code>dc.contributor.author</code> and <code>dc.identifier.citation</code> fields using OpenRefine</p>
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<ul>
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<li><p>The first targets acronyms in parentheses like “International Livestock Research Institute (ILRI)”:</p>
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<pre><code>value.replace(/,? ?\((ANDES|APAFRI|APFORGEN|Canada|CFC|CGRFA|China|CacaoNet|CATAS|CDU|CIAT|CIRF|CIP|CIRNMA|COSUDE|Colombia|COA|COGENT|CTDT|Denmark|DfLP|DSE|ECPGR|ECOWAS|ECP\/GR|England|EUFORGEN|FAO|France|Francia|FFTC|Germany|GEF|GFU|GGCO|GRPI|italy|Italy|Italia|India|ICCO|ICAR|ICGR|ICRISAT|IDRC|INFOODS|IPGRI|IBPGR|ICARDA|ILRI|INIBAP|INBAR|IPK|ISG|IT|Japan|JIRCAS|Kenya|LI\-BIRD|Malaysia|NARC|NBPGR|Nepal|OOAS|RDA|RISBAP|Rome|ROPPA|SEARICE|Senegal|SGRP|Sweden|Syrian Arab Republic|The Netherlands|UNDP|UK|UNEP|UoB|UoM|United Kingdom|WAHO)\)/,"")
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</code></pre></li>
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<li><p>The second targets cities and countries after names like “International Livestock Research Intstitute, Kenya”:</p>
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<pre><code>replace(/,? ?(ali|Aleppo|Amsterdam|Beijing|Bonn|Burkina Faso|CN|Dakar|Gatersleben|London|Montpellier|Nairobi|New Delhi|Kaski|Kepong|Malaysia|Khumaltar|Lima|Ltpur|Ottawa|Patancheru|Peru|Pokhara|Rome|Uppsala|University of Mauritius|Tsukuba)/,"")
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</code></pre></li>
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</ul></li>
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<li><p>I imported the 1,427 Bioversity records with bitstreams to a new collection called <a href="https://dspacetest.cgiar.org/handle/10568/103688">2019-09-20 Bioversity Migration Test</a> on DSpace Test (after splitting them in two batches of about 700 each):</p>
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<pre><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx768m'
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$ dspace import -a me@cgiar.org -m 2019-09-20-bioversity1.map -s /home/aorth/Bioversity/bioversity1
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$ dspace import -a me@cgiar.org -m 2019-09-20-bioversity2.map -s /home/aorth/Bioversity/bioversity2
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</code></pre></li>
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<li><p>After that I exported the collection again and started doing some quality checks and cleanups:</p>
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<ul>
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<li>Change all DOIs to use <a href="https://doi.org">https://doi.org</a> format</li>
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<li>Change all bioversityinternational.org links to use https://</li>
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<li>Fix ten authors with invalid names like “Orth,.” by checking the correct name in the citation</li>
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<li>Fix several invalid ISBNs, but there are several more that contain incorrect ISBNs in their PDFs!</li>
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<li>Fix some citations that were using “ISSN” instead of ISBN</li>
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</ul></li>
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<li><p>The next steps are:</p>
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<ul>
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<li>Check for duplicates</li>
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<li>Continue with institutional author normalization</li>
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<li>Ask which collection to map items with type Brochure, Journal Item, and Thesis?</li>
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</ul></li>
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</ul>
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<!-- vim: set sw=2 ts=2: -->
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@ -4,27 +4,27 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2019-09-20T12:55:11+03:00</lastmod>
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<lastmod>2019-09-20T13:25:59+03:00</lastmod>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2019-09-20T12:55:11+03:00</lastmod>
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<lastmod>2019-09-20T13:25:59+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>2019-09-20T12:55:11+03:00</lastmod>
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<lastmod>2019-09-20T13:25:59+03:00</lastmod>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2019-09/</loc>
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<lastmod>2019-09-20T12:55:11+03:00</lastmod>
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<lastmod>2019-09-20T13:25:59+03:00</lastmod>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
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<lastmod>2019-09-20T12:55:11+03:00</lastmod>
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<lastmod>2019-09-20T13:25:59+03:00</lastmod>
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</url>
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<url>
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