Add notes for 2021-02-23

2024-11-22 06:35:03 +01:00 · 2021-02-24 09:21:07 +02:00 · 2021-02-24 09:21:07 +02:00 · 6b348cb3a2
commit 6b348cb3a2
parent 3be27df78e
23 changed files with 267 additions and 29 deletions
--- a/content/posts/2021-02.md
+++ b/content/posts/2021-02.md
@ -528,4 +528,129 @@ $ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
 # start indexing in AReS
 ```

+## 2021-02-22
+
+- Start looking at splitting the series name and number in `dcterms.isPartOf` now that we have migrated to CG Core v2
+  - The numbers will go to `cg.number`
+  - I notice there are about 100 series without a number, but they still have a semicolon, for example `Esporo 72;`
+  - I think I will replace those like this:
+
+```console
+localhost/dspace63= > UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, '^(.+?);$','\1', 'g') WHERE metadata_field_id=166 AND dspace_object_id IN (SELECT uuid FROM item) AND text_value ~ ';$';
+UPDATE 104
+```
+
+- As for splitting the other values, I think I can export the `dspace_object_id` and `text_value` and then upload it as a CSV rather than writing a Python script to create the new metadata values
+
+## 2021-02-22
+
+- Check the results of the AReS harvesting from last night:
+
+```console
+$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
+{
+  "count" : 101380,
+  "_shards" : {
+    "total" : 1,
+    "successful" : 1,
+    "skipped" : 0,
+    "failed" : 0
+  }
+}
+```
+
+- Set the current items index to read only and make a backup:
+
+```console
+$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d' {"settings": {"index.blocks.write":true}}'
+$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2021-02-22
+```
+
+- Delete the current items index and clone the temp one to it:
+
+```console
+$ curl -XDELETE 'http://localhost:9200/openrxv-items'
+$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
+$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items
+```
+
+- Then delete the temp and backup:
+
+```console
+$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
+{"acknowledged":true}%
+$ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-02-22'
+```
+
+## 2021-02-23
+
+- CodeObia sent a [pull request for clickable countries on AReS](https://github.com/ilri/OpenRXV/pull/75)
+  - I deployed it and it seems to work, so I asked Abenet and Peter to test it so we can get feedback
+- Remove semicolons from series names without numbers:
+
+```console
+dspace=# BEGIN;
+dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, '^(.+?);$','\1', 'g') WHERE metadata_field_id=166 AND dspace_object_id IN (SELECT uuid FROM item) AND text_value ~ ';$';
+UPDATE 104
+dspace=# COMMIT;
+```
+
+- Set all `text_lang` values on CGSpace to `en_US` to make the series replacements easier (this didn't work, read below):
+
+```console
+dspace=# BEGIN;
+dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE text_lang !='en_US' AND dspace_object_id IN (SELECT uuid FROM item);
+UPDATE 911
+cgspace=# COMMIT;
+```
+
+- Then export all series with their IDs to CSV:
+
+```console
+dspace=# \COPY (SELECT dspace_object_id, text_value as "dcterms.isPartOf[en_US]" FROM metadatavalue WHERE metadata_field_id=166 AND dspace_object_id IN (SELECT uuid FROM item)) TO /tmp/2021-02-23-series.csv WITH CSV HEADER;
+```
+
+- In OpenRefine I trimmed and consolidated whitespace, then made some quick cleanups to normalize the fields based on a sanity check
+  - For example many Spore items are like "Spore, Spore 23"
+  - Also, "Agritrade, August 2002"
+- Then I copied the column to a new one called `cg.number[en_US]` and split the values for each on the semicolon using `value.split(';')[0]` and `value.split(';')[1]`
+- I tried to upload some of the series data to DSpace Test but I'm having an issue where some fields change that shouldn't
+  - It seems not all fields get updated when I set the text_lang globally, but if I updated it manually like this it works:
+
+```console
+dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE metadata_value_id=5355845;
+UPDATE 1
+```
+
+- This also seems to work, using the id for just that one item:
+
+```console
+dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id='9840d19b-a6ae-4352-a087-6d74d2629322';
+UPDATE 37
+```
+
+- This seems to work better for some reason:
+
+```console
+dspacetest=# UPDATE metadatavalue SET text_lang='en_US' WHERE metadata_field_id=166 AND dspace_object_id IN (SELECT uuid FROM item);
+UPDATE 18659
+```
+
+- I split the CSV file in batches of 5,000 using xsv, then imported them one by one in CGSpace:
+
+```console
+$ dspace metadata-import -f /tmp/0.csv
+```
+
+- It took FOREVER to import each file... like several hours. MY GOD DSpace 6 is slow.
+- Help Dominique Perera debug some issues with the WordPress DSpace importer plugin from Macaroni Bros
+  - She is not seeing the community list for CGSpace, and I see weird requests like this in the logs:
+
+```console
+104.198.97.97 - - [23/Feb/2021:11:41:17 +0100] "GET /rest/communities?limit=1000 HTTP/1.1" 200 188779 "https://cgspace.cgiar.org/rest /communities?limit=1000" "RTB website BOT"
+104.198.97.97 - - [23/Feb/2021:11:41:18 +0100] "GET /rest/communities//communities HTTP/1.1" 404 714 "https://cgspace.cgiar.org/rest/communities//communities" "RTB website BOT"
+```
+
+- The first request is OK, but the second one is malformed for sure
+
 <!-- vim: set sw=2 ts=2: -->
--- a/docs/2021-02/index.html
+++ b/docs/2021-02/index.html
@ -32,7 +32,7 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-02/" />
 <meta property="article:published_time" content="2021-02-01T10:13:54+02:00" />
-<meta property="article:modified_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="article:modified_time" content="2021-02-21T20:37:27+02:00" />



@ -70,9 +70,9 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
  "@type": "BlogPosting",
  "headline": "February, 2021",
  "url": "https://alanorth.github.io/cgspace-notes/2021-02/",
-  "wordCount": "3111",
+  "wordCount": "3754",
  "datePublished": "2021-02-01T10:13:54+02:00",
-  "dateModified": "2021-02-21T18:20:37+02:00",
+  "dateModified": "2021-02-21T20:37:27+02:00",
  "author": {
    "@type": "Person",
    "name": "Alan Orth"
@ -678,7 +678,120 @@ $ dspace metadata-import -e aorth@mjanja.ch -f /tmp/cifor.csv
 </ul>
 <pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
 # start indexing in AReS
-</code></pre><!-- raw HTML omitted -->
+</code></pre><h2 id="2021-02-22">2021-02-22</h2>
+<ul>
+<li>Start looking at splitting the series name and number in <code>dcterms.isPartOf</code> now that we have migrated to CG Core v2
+<ul>
+<li>The numbers will go to <code>cg.number</code></li>
+<li>I notice there are about 100 series without a number, but they still have a semicolon, for example <code>Esporo 72;</code></li>
+<li>I think I will replace those like this:</li>
+</ul>
+</li>
+</ul>
+<pre><code class="language-console" data-lang="console">localhost/dspace63= &gt; UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, '^(.+?);$','\1', 'g') WHERE metadata_field_id=166 AND dspace_object_id IN (SELECT uuid FROM item) AND text_value ~ ';$';
+UPDATE 104
+</code></pre><ul>
+<li>As for splitting the other values, I think I can export the <code>dspace_object_id</code> and <code>text_value</code> and then upload it as a CSV rather than writing a Python script to create the new metadata values</li>
+</ul>
+<h2 id="2021-02-22-1">2021-02-22</h2>
+<ul>
+<li>Check the results of the AReS harvesting from last night:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty'
+{
+  &quot;count&quot; : 101380,
+  &quot;_shards&quot; : {
+    &quot;total&quot; : 1,
+    &quot;successful&quot; : 1,
+    &quot;skipped&quot; : 0,
+    &quot;failed&quot; : 0
+  }
+}
+</code></pre><ul>
+<li>Set the current items index to read only and make a backup:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Type: application/json' -d' {&quot;settings&quot;: {&quot;index.blocks.write&quot;:true}}'
+$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2021-02-22
+</code></pre><ul>
+<li>Delete the current items index and clone the temp one to it:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items'
+$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
+$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items
+</code></pre><ul>
+<li>Then delete the temp and backup:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
+{&quot;acknowledged&quot;:true}%
+$ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-02-22'
+</code></pre><h2 id="2021-02-23">2021-02-23</h2>
+<ul>
+<li>CodeObia sent a <a href="https://github.com/ilri/OpenRXV/pull/75">pull request for clickable countries on AReS</a>
+<ul>
+<li>I deployed it and it seems to work, so I asked Abenet and Peter to test it so we can get feedback</li>
+</ul>
+</li>
+<li>Remove semicolons from series names without numbers:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">dspace=# BEGIN;
+dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, '^(.+?);$','\1', 'g') WHERE metadata_field_id=166 AND dspace_object_id IN (SELECT uuid FROM item) AND text_value ~ ';$';
+UPDATE 104
+dspace=# COMMIT;
+</code></pre><ul>
+<li>Set all <code>text_lang</code> values on CGSpace to <code>en_US</code> to make the series replacements easier (this didn&rsquo;t work, read below):</li>
+</ul>
+<pre><code class="language-console" data-lang="console">dspace=# BEGIN;
+dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE text_lang !='en_US' AND dspace_object_id IN (SELECT uuid FROM item);
+UPDATE 911
+cgspace=# COMMIT;
+</code></pre><ul>
+<li>Then export all series with their IDs to CSV:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">dspace=# \COPY (SELECT dspace_object_id, text_value as &quot;dcterms.isPartOf[en_US]&quot; FROM metadatavalue WHERE metadata_field_id=166 AND dspace_object_id IN (SELECT uuid FROM item)) TO /tmp/2021-02-23-series.csv WITH CSV HEADER;
+</code></pre><ul>
+<li>In OpenRefine I trimmed and consolidated whitespace, then made some quick cleanups to normalize the fields based on a sanity check
+<ul>
+<li>For example many Spore items are like &ldquo;Spore, Spore 23&rdquo;</li>
+<li>Also, &ldquo;Agritrade, August 2002&rdquo;</li>
+</ul>
+</li>
+<li>Then I copied the column to a new one called <code>cg.number[en_US]</code> and split the values for each on the semicolon using <code>value.split(';')[0]</code> and <code>value.split(';')[1]</code></li>
+<li>I tried to upload some of the series data to DSpace Test but I&rsquo;m having an issue where some fields change that shouldn&rsquo;t
+<ul>
+<li>It seems not all fields get updated when I set the text_lang globally, but if I updated it manually like this it works:</li>
+</ul>
+</li>
+</ul>
+<pre><code class="language-console" data-lang="console">dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE metadata_value_id=5355845;
+UPDATE 1
+</code></pre><ul>
+<li>This also seems to work, using the id for just that one item:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id='9840d19b-a6ae-4352-a087-6d74d2629322';
+UPDATE 37
+</code></pre><ul>
+<li>This seems to work better for some reason:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">dspacetest=# UPDATE metadatavalue SET text_lang='en_US' WHERE metadata_field_id=166 AND dspace_object_id IN (SELECT uuid FROM item);
+UPDATE 18659
+</code></pre><ul>
+<li>I split the CSV file in batches of 5,000 using xsv, then imported them one by one in CGSpace:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ dspace metadata-import -f /tmp/0.csv
+</code></pre><ul>
+<li>It took FOREVER to import each file&hellip; like several hours. MY GOD DSpace 6 is slow.</li>
+<li>Help Dominique Perera debug some issues with the WordPress DSpace importer plugin from Macaroni Bros
+<ul>
+<li>She is not seeing the community list for CGSpace, and I see weird requests like this in the logs:</li>
+</ul>
+</li>
+</ul>
+<pre><code class="language-console" data-lang="console">104.198.97.97 - - [23/Feb/2021:11:41:17 +0100] &quot;GET /rest/communities?limit=1000 HTTP/1.1&quot; 200 188779 &quot;https://cgspace.cgiar.org/rest /communities?limit=1000&quot; &quot;RTB website BOT&quot;
+104.198.97.97 - - [23/Feb/2021:11:41:18 +0100] &quot;GET /rest/communities//communities HTTP/1.1&quot; 404 714 &quot;https://cgspace.cgiar.org/rest/communities//communities&quot; &quot;RTB website BOT&quot;
+</code></pre><ul>
+<li>The first request is OK, but the second one is malformed for sure</li>
+</ul>
+<!-- raw HTML omitted -->

  

--- a/docs/categories/index.html
+++ b/docs/categories/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/categories/notes/index.html
+++ b/docs/categories/notes/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/categories/notes/page/2/index.html
+++ b/docs/categories/notes/page/2/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/categories/notes/page/3/index.html
+++ b/docs/categories/notes/page/3/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/categories/notes/page/4/index.html
+++ b/docs/categories/notes/page/4/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/categories/notes/page/5/index.html
+++ b/docs/categories/notes/page/5/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/index.html
+++ b/docs/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/page/2/index.html
+++ b/docs/page/2/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/page/3/index.html
+++ b/docs/page/3/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/page/4/index.html
+++ b/docs/page/4/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/page/5/index.html
+++ b/docs/page/5/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/page/6/index.html
+++ b/docs/page/6/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/page/7/index.html
+++ b/docs/page/7/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/posts/index.html
+++ b/docs/posts/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/posts/page/2/index.html
+++ b/docs/posts/page/2/index.html
@ -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:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
-<meta property="og:updated_time" content="2021-02-21T18:20:37+02:00" />
+<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />



--- a/docs/posts/page/3/index.html
+++ b/docs/posts/page/3/index.html
@ -10,7 +10,7 @@
 <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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