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Update notes for 2019-02-15
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0FB860CC9C45B1B9
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@ -660,4 +660,70 @@ $ podman run --name dspacedb -v /home/aorth/.local/lib/containers/volumes/dspace
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- I increased the nginx upload limit, but she said she was having problems and couldn't really tell me why
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- I logged in as her and completed the submission with no problems...
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## 2019-02-15
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- Tomcat was killed around 3AM by the kernel's OOM killer according to `dmesg`:
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```
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[Fri Feb 15 03:10:42 2019] Out of memory: Kill process 12027 (java) score 670 or sacrifice child
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[Fri Feb 15 03:10:42 2019] Killed process 12027 (java) total-vm:14108048kB, anon-rss:5450284kB, file-rss:0kB, shmem-rss:0kB
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[Fri Feb 15 03:10:43 2019] oom_reaper: reaped process 12027 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
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```
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- The `tomcat7` service shows:
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```
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Feb 15 03:10:44 linode19 systemd[1]: tomcat7.service: Main process exited, code=killed, status=9/KILL
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```
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- I suspect it was related to the media-filter cron job that runs at 3AM but I don't see anything particular in the log files
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- I want to try to normalize the `text_lang` values to make working with metadata easier
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- We currently have a bunch of weird values that DSpace uses like `NULL`, `en_US`, and `en` and others that have been entered manually by editors:
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```
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dspace=# SELECT DISTINCT text_lang, count(*) FROM metadatavalue WHERE resource_type_id=2 GROUP BY text_lang ORDER BY count DESC;
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text_lang | count
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-----------+---------
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| 1069539
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en_US | 577110
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| 334768
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en | 133501
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es | 12
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* | 11
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es_ES | 2
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fr | 2
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spa | 2
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E. | 1
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ethnob | 1
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```
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- The majority are `NULL`, `en_US`, the blank string, and `en`—the rest are not enough to be significant
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- Theoretically this field could help if you wanted to search for Spanish-language fields in the API or something, but even for the English fields there are two different values (and those are from DSpace itself)!
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- I'm going to normalized these to `NULL` at least on DSpace Test for now:
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```
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dspace=# UPDATE metadatavalue SET text_lang = NULL WHERE resource_type_id=2 AND text_lang IS NOT NULL;
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UPDATE 1045410
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```
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- I started proofing IITA's 2019-01 records that Sisay uploaded this week
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- There were 259 records in IITA's original spreadsheet, but there are 276 in Sisay's collection
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- Also, I found that there are at least twenty duplicates in these records that we will need to address
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- ILRI ICT fixed the password for the CGSpace support email account and I tested it on Outlook 365 web and DSpace and it works
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- Re-create my local PostgreSQL container to for new PostgreSQL version and to use podman's volumes:
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```
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$ podman pull postgres:9.6-alpine
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$ podman volume create dspacedb_data
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$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
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$ createuser -h localhost -U postgres --pwprompt dspacetest
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$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspacetest
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
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$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost dspace_2019-02-11.backup
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$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'
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```
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- And it's all running without root!
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<!-- vim: set sw=2 ts=2: -->
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@ -42,7 +42,7 @@ sys 0m1.979s
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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/2019-02/" />
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<meta property="article:published_time" content="2019-02-01T21:37:30+02:00"/>
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<meta property="article:modified_time" content="2019-02-14T19:44:18+02:00"/>
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<meta property="article:modified_time" content="2019-02-14T21:30:51+02:00"/>
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="February, 2019"/>
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@ -89,9 +89,9 @@ sys 0m1.979s
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"@type": "BlogPosting",
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"headline": "February, 2019",
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"url": "https://alanorth.github.io/cgspace-notes/2019-02/",
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"wordCount": "3685",
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"wordCount": "4131",
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"datePublished": "2019-02-01T21:37:30+02:00",
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"dateModified": "2019-02-14T19:44:18+02:00",
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"dateModified": "2019-02-14T21:30:51+02:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -907,6 +907,82 @@ $ podman run --name dspacedb -v /home/aorth/.local/lib/containers/volumes/dspace
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<li>I logged in as her and completed the submission with no problems…</li>
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</ul>
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<h2 id="2019-02-15">2019-02-15</h2>
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<ul>
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<li>Tomcat was killed around 3AM by the kernel’s OOM killer according to <code>dmesg</code>:</li>
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</ul>
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<pre><code>[Fri Feb 15 03:10:42 2019] Out of memory: Kill process 12027 (java) score 670 or sacrifice child
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[Fri Feb 15 03:10:42 2019] Killed process 12027 (java) total-vm:14108048kB, anon-rss:5450284kB, file-rss:0kB, shmem-rss:0kB
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[Fri Feb 15 03:10:43 2019] oom_reaper: reaped process 12027 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
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</code></pre>
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<ul>
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<li>The <code>tomcat7</code> service shows:</li>
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</ul>
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<pre><code>Feb 15 03:10:44 linode19 systemd[1]: tomcat7.service: Main process exited, code=killed, status=9/KILL
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</code></pre>
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<ul>
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<li>I suspect it was related to the media-filter cron job that runs at 3AM but I don’t see anything particular in the log files</li>
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<li>I want to try to normalize the <code>text_lang</code> values to make working with metadata easier</li>
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<li>We currently have a bunch of weird values that DSpace uses like <code>NULL</code>, <code>en_US</code>, and <code>en</code> and others that have been entered manually by editors:</li>
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</ul>
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<pre><code>dspace=# SELECT DISTINCT text_lang, count(*) FROM metadatavalue WHERE resource_type_id=2 GROUP BY text_lang ORDER BY count DESC;
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text_lang | count
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-----------+---------
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| 1069539
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en_US | 577110
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| 334768
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en | 133501
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es | 12
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* | 11
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es_ES | 2
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fr | 2
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spa | 2
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E. | 1
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ethnob | 1
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</code></pre>
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<ul>
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<li>The majority are <code>NULL</code>, <code>en_US</code>, the blank string, and <code>en</code>—the rest are not enough to be significant</li>
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<li>Theoretically this field could help if you wanted to search for Spanish-language fields in the API or something, but even for the English fields there are two different values (and those are from DSpace itself)!</li>
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<li>I’m going to normalized these to <code>NULL</code> at least on DSpace Test for now:</li>
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</ul>
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<pre><code>dspace=# UPDATE metadatavalue SET text_lang = NULL WHERE resource_type_id=2 AND text_lang IS NOT NULL;
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UPDATE 1045410
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</code></pre>
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<ul>
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<li>I started proofing IITA’s 2019-01 records that Sisay uploaded this week
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<ul>
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<li>There were 259 records in IITA’s original spreadsheet, but there are 276 in Sisay’s collection</li>
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<li>Also, I found that there are at least twenty duplicates in these records that we will need to address</li>
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</ul></li>
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<li>ILRI ICT fixed the password for the CGSpace support email account and I tested it on Outlook 365 web and DSpace and it works</li>
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<li>Re-create my local PostgreSQL container to for new PostgreSQL version and to use podman’s volumes:</li>
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</ul>
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<pre><code>$ podman pull postgres:9.6-alpine
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$ podman volume create dspacedb_data
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$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
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$ createuser -h localhost -U postgres --pwprompt dspacetest
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$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspacetest
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
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$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost dspace_2019-02-11.backup
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$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'
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</code></pre>
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<ul>
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<li>And it’s all running without root!</li>
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</ul>
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<!-- vim: set sw=2 ts=2: -->
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@ -4,7 +4,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2019-02/</loc>
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<lastmod>2019-02-14T19:44:18+02:00</lastmod>
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<lastmod>2019-02-14T21:30:51+02:00</lastmod>
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</url>
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<url>
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@ -209,7 +209,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2019-02-14T19:44:18+02:00</lastmod>
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<lastmod>2019-02-14T21:30:51+02:00</lastmod>
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<priority>0</priority>
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</url>
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@ -220,7 +220,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2019-02-14T19:44:18+02:00</lastmod>
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<lastmod>2019-02-14T21:30:51+02:00</lastmod>
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<priority>0</priority>
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</url>
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@ -232,13 +232,13 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
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<lastmod>2019-02-14T19:44:18+02:00</lastmod>
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<lastmod>2019-02-14T21:30:51+02:00</lastmod>
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<priority>0</priority>
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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>2019-02-14T19:44:18+02:00</lastmod>
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<lastmod>2019-02-14T21:30:51+02:00</lastmod>
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<priority>0</priority>
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</url>
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