Add notes for 2022-02-14

content/posts/2022-02.md

@@ -341,4 +341,75 @@ Total number of bot hits purged: 14696
 - Peter asked me to add a new item type on CGSpace: Opinion Piece
 - Map an item on CGSpace for Maria since she couldn't find it in the item mapper
 
+## 2022-02-11
+
+- CGSpace is slow and the load has been over 400% for a few hours
+  - The number of DSpace sessions seems normal, even lower than a few days ago
+  - The number of PostgreSQL connections is low, but I see there are lots of "AccessShare" locks (green on Munin, not blue like usual)
+  - I will run all system updates, copy the latest config changes, and restart the server
+
+## 2022-02-12
+
+- Install PostgreSQL 12 on my local dev environment to starting DSpace 6.x workflows with it:
+
+```console
+$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:12-alpine
+$ createuser -h localhost -p 5432 -U postgres --pwprompt dspacetest
+$ createdb -h localhost -p 5432 -U postgres -O dspacetest --encoding=UNICODE dspacetest
+$ psql -h localhost -U postgres -c 'ALTER USER dspacetest SUPERUSER;'
+$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost ~/Downloads/dspace-2022-02-12.backup
+$ psql -h localhost -U postgres -c 'ALTER USER dspacetest NOSUPERUSER;'
+```
+
+- Eventually I will updated DSpace Test, then CGSpace (time to start paying off some technical debt!)
+- Start a full Discovery re-index on CGSpace:
+
+```console
+$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
+
+real    292m49.263s
+user    201m26.097s
+sys     3m2.459s
+```
+
+- Start a full harvest on AReS
+
+## 2022-02-14
+
+- Last week Gaia sent me her notes on the second batch of TAC/ICW documents (items 201–400 in the spreadsheet)
+  - I created a filter in LibreOffice and selected the IDs for items with the action "delete", then I created a custom text facet in OpenRefine with this GREL:
+
+```
+or(
+isNotNull(value.match('201')),
+isNotNull(value.match('203')),
+isNotNull(value.match('209')),
+isNotNull(value.match('209')),
+isNotNull(value.match('215')),
+isNotNull(value.match('220')),
+isNotNull(value.match('225')),
+isNotNull(value.match('226')),
+isNotNull(value.match('227')),
+...
+isNotNull(value.match('396'))
+```
+
+- Then I flagged all matching records and exported a CSV to use with SAFBuilder
+  - Then I imported the SAF bundle on DSpace Test:
+
+```console
+$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=fuuu@umm.com --source /tmp/SimpleArchiveFormat --mapfile=./2022-02-14-tac-batch2-201to400.map
+```
+
+- Export the next batch from OpenRefine (items with ID 401 to 700), check duplicates, and then join with the file names:
+
+```console
+$ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-01-21-CGSpace-TAC-ICW-batch3-401to700.csv > /tmp/tac3.csv
+$ ./ilri/check-duplicates.py -i /tmp/tac3.csv -db dspacetest -u dspacetest -p 'dom@in34sniper' -o /tmp/2022-02-14-tac-batch3-401-700.csv
+$ csvcut -c id,filename ~/Downloads/2022-01-21-CGSpace-TAC-ICW-batch3-401to700.csv > /tmp/tac3-filenames.csv
+$ csvjoin -c id /tmp/2022-02-14-tac-batch3-401-700.csv /tmp/tac3-filenames.csv > /tmp/2022-02-14-tac-batch3-401-700-filenames.csv
+```
+
+- I sent these 300 items to Gaia...
+
 <!-- vim: set sw=2 ts=2: -->

docs/2022-02/index.html

@@ -21,7 +21,7 @@ We agreed to try to do more alignment of affiliations/funders with ROR
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-02/" />
 <meta property="article:published_time" content="2022-02-01T14:06:54+02:00" />
-<meta property="article:modified_time" content="2022-02-10T20:35:40+03:00" />
+<meta property="article:modified_time" content="2022-02-14T09:40:59+03:00" />
 
 
 
@@ -48,9 +48,9 @@ We agreed to try to do more alignment of affiliations/funders with ROR
   "@type": "BlogPosting",
   "headline": "February, 2022",
   "url": "https://alanorth.github.io/cgspace-notes/2022-02/",
-  "wordCount": "1838",
+  "wordCount": "2194",
   "datePublished": "2022-02-01T14:06:54+02:00",
-  "dateModified": "2022-02-10T20:35:40+03:00",
+  "dateModified": "2022-02-14T09:40:59+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -462,6 +462,76 @@ Purging 217 hits from 1science in statistics
 <li>Peter asked me to add a new item type on CGSpace: Opinion Piece</li>
 <li>Map an item on CGSpace for Maria since she couldn&rsquo;t find it in the item mapper</li>
 </ul>
+<h2 id="2022-02-11">2022-02-11</h2>
+<ul>
+<li>CGSpace is slow and the load has been over 400% for a few hours
+<ul>
+<li>The number of DSpace sessions seems normal, even lower than a few days ago</li>
+<li>The number of PostgreSQL connections is low, but I see there are lots of &ldquo;AccessShare&rdquo; locks (green on Munin, not blue like usual)</li>
+<li>I will run all system updates, copy the latest config changes, and restart the server</li>
+</ul>
+</li>
+</ul>
+<h2 id="2022-02-12">2022-02-12</h2>
+<ul>
+<li>Install PostgreSQL 12 on my local dev environment to starting DSpace 6.x workflows with it:</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">$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD<span style="color:#f92672">=</span>postgres -p 5432:5432 -d postgres:12-alpine
+$ createuser -h localhost -p <span style="color:#ae81ff">5432</span> -U postgres --pwprompt dspacetest
+$ createdb -h localhost -p <span style="color:#ae81ff">5432</span> -U postgres -O dspacetest --encoding<span style="color:#f92672">=</span>UNICODE dspacetest
+$ psql -h localhost -U postgres -c <span style="color:#e6db74">&#39;ALTER USER dspacetest SUPERUSER;&#39;</span>
+$ pg_restore -h localhost -U postgres -d dspacetest -O --role<span style="color:#f92672">=</span>dspacetest -h localhost ~/Downloads/dspace-2022-02-12.backup
+$ psql -h localhost -U postgres -c <span style="color:#e6db74">&#39;ALTER USER dspacetest NOSUPERUSER;&#39;</span>
+</code></pre></div><ul>
+<li>Eventually I will updated DSpace Test, then CGSpace (time to start paying off some technical debt!)</li>
+<li>Start a full Discovery re-index on CGSpace:</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">$ time chrt -b <span style="color:#ae81ff">0</span> ionice -c2 -n7 nice -n19 dspace index-discovery -b
+<span style="color:#960050;background-color:#1e0010">
+</span><span style="color:#960050;background-color:#1e0010"></span>real    292m49.263s
+user    201m26.097s
+sys     3m2.459s
+</code></pre></div><ul>
+<li>Start a full harvest on AReS</li>
+</ul>
+<h2 id="2022-02-14">2022-02-14</h2>
+<ul>
+<li>Last week Gaia sent me her notes on the second batch of TAC/ICW documents (items 201–400 in the spreadsheet)
+<ul>
+<li>I created a filter in LibreOffice and selected the IDs for items with the action &ldquo;delete&rdquo;, then I created a custom text facet in OpenRefine with this GREL:</li>
+</ul>
+</li>
+</ul>
+<pre tabindex="0"><code>or(
+isNotNull(value.match('201')),
+isNotNull(value.match('203')),
+isNotNull(value.match('209')),
+isNotNull(value.match('209')),
+isNotNull(value.match('215')),
+isNotNull(value.match('220')),
+isNotNull(value.match('225')),
+isNotNull(value.match('226')),
+isNotNull(value.match('227')),
+...
+isNotNull(value.match('396'))
+</code></pre><ul>
+<li>Then I flagged all matching records and exported a CSV to use with SAFBuilder
+<ul>
+<li>Then I imported the SAF bundle on DSpace Test:</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">$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</span> dspace import --add --eperson<span style="color:#f92672">=</span>fuuu@umm.com --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2022-02-14-tac-batch2-201to400.map
+</code></pre></div><ul>
+<li>Export the next batch from OpenRefine (items with ID 401 to 700), check duplicates, and then join with the file names:</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">$ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-01-21-CGSpace-TAC-ICW-batch3-401to700.csv &gt; /tmp/tac3.csv
+$ ./ilri/check-duplicates.py -i /tmp/tac3.csv -db dspacetest -u dspacetest -p <span style="color:#e6db74">&#39;dom@in34sniper&#39;</span> -o /tmp/2022-02-14-tac-batch3-401-700.csv
+$ csvcut -c id,filename ~/Downloads/2022-01-21-CGSpace-TAC-ICW-batch3-401to700.csv &gt; /tmp/tac3-filenames.csv
+$ csvjoin -c id /tmp/2022-02-14-tac-batch3-401-700.csv /tmp/tac3-filenames.csv &gt; /tmp/2022-02-14-tac-batch3-401-700-filenames.csv
+</code></pre></div><ul>
+<li>I sent these 300 items to Gaia&hellip;</li>
+</ul>
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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/" />
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 <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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+    <lastmod>2022-02-14T09:40:59+03:00</lastmod>
   </url><url>
     <loc>https://alanorth.github.io/cgspace-notes/2022-01/</loc>
     <lastmod>2022-02-07T09:49:34+03:00</lastmod>