Update notes

content/posts/2023-03.md

@@ -9,7 +9,55 @@ categories: ["Notes"]
 
 - Remove `cg.subject.wle` and `cg.identifier.wletheme` from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)
 - [iso-codes 4.13.0 was released](https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28), which incorporates my changes to the common names for Iran, Laos, and Syria
+- I finally got through with porting the input form from DSpace 6 to DSpace 7
 
 <!--more-->
 
+- I can't put my finger on it, but the input form has to be formatted very particularly, for example if your rows have more than two fields in them with out a sufficient Bootstrap grid style, or if you use a `twobox`, etc, the entire form step appears blank
+
+## 2023-03-02
+
+- I did some experiments with the new [Pandas 2.0.0rc0 Apache Arrow support](https://datapythonista.me/blog/pandas-20-and-the-arrow-revolution-part-i)
+  - There is a change to the way nulls are handled and it causes my tests for `pd.isna(field)` to fail
+  - I think we need consider blanks as null, but I'm not sure
+- I made some adjustments to the Discovery sidebar facets on DSpace 6 while I was looking at the DSpace 7 configuration
+  - I downgraded CIFOR subject, Humidtropics subject, Drylands subject, ICARDA subject, and Language from DiscoverySearchFilterFacet to DiscoverySearchFilter in `discovery.xml` since we are no longer using them in sidebar facets
+
+## 2023-03-03
+
+- Atmire merged one of my old pull requests into COUNTER-Robots:
+  - [COUNTER_Robots_list.json: Add new bots](https://github.com/atmire/COUNTER-Robots/pull/54)
+- I will update the local ILRI overrides in our DSpace spider agents file
+
+## 2023-03-04
+
+- Submit a [pull request on pycountry to use iso-codes 4.13.0](https://github.com/flyingcircusio/pycountry/pull/156)
+
+## 2023-03-05
+
+- Start a harvest on AReS
+
+## 2023-03-06
+
+- Export CGSpace to do Initiative collection mappings
+  - There were thirty-three that needed updating
+- Send Abenet and Sam a list of twenty-one CAS publications that had been marked as "multiple documents" that we uploaded as metadata-only items
+  - Goshu will download the PDFs for each and upload them to the items on CGSpace manually
+- I spent some time trying to get csv-metadata-quality working with the new Arrow backend for Pandas 2.0.0rc0
+  - It seems there is a problem recognizing empty strings as na with `pd.isna()`
+  - If I do `pd.isna(field) or field == ""` then it works as expected, but that feels hacky
+  - I'm going to test again on the next release...
+  - Note that I had been setting both of these global options:
+
+```
+pd.options.mode.dtype_backend = 'pyarrow'
+pd.options.mode.nullable_dtypes = True
+```
+
+- Then reading the CSV like this:
+
+```
+df = pd.read_csv(args.input_file, engine='pyarrow', dtype='string[pyarrow]'
+```
+
 <!-- vim: set sw=2 ts=2: -->

docs/2023-02/index.html

@@ -18,7 +18,7 @@ I want to try to expand my use of their data to journals, publishers, volumes, i
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-02/" />
 <meta property="article:published_time" content="2023-02-01T10:57:36+03:00" />
-<meta property="article:modified_time" content="2023-02-26T19:59:12+03:00" />
+<meta property="article:modified_time" content="2023-03-01T08:30:25+03:00" />
 
 
 
@@ -44,7 +44,7 @@ I want to try to expand my use of their data to journals, publishers, volumes, i
   "url": "https://alanorth.github.io/cgspace-notes/2023-02/",
   "wordCount": "3087",
   "datePublished": "2023-02-01T10:57:36+03:00",
-  "dateModified": "2023-02-26T19:59:12+03:00",
+  "dateModified": "2023-03-01T08:30:25+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"

docs/2023-03/index.html

@@ -11,11 +11,12 @@
 
 Remove cg.subject.wle and cg.identifier.wletheme from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)
 iso-codes 4.13.0 was released, which incorporates my changes to the common names for Iran, Laos, and Syria
+I finally got through with porting the input form from DSpace 6 to DSpace 7
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-03/" />
 <meta property="article:published_time" content="2023-03-01T07:58:36+03:00" />
-<meta property="article:modified_time" content="2023-03-01T07:58:36+03:00" />
+<meta property="article:modified_time" content="2023-03-01T08:30:25+03:00" />
 
 
 
@@ -25,6 +26,7 @@ iso-codes 4.13.0 was released, which incorporates my changes to the common names
 
 Remove cg.subject.wle and cg.identifier.wletheme from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)
 iso-codes 4.13.0 was released, which incorporates my changes to the common names for Iran, Laos, and Syria
+I finally got through with porting the input form from DSpace 6 to DSpace 7
 "/>
 <meta name="generator" content="Hugo 0.110.0">
 
@@ -36,9 +38,9 @@ iso-codes 4.13.0 was released, which incorporates my changes to the common names
   "@type": "BlogPosting",
   "headline": "March, 2023",
   "url": "https://alanorth.github.io/cgspace-notes/2023-03/",
-  "wordCount": "41",
+  "wordCount": "380",
   "datePublished": "2023-03-01T07:58:36+03:00",
-  "dateModified": "2023-03-01T07:58:36+03:00",
+  "dateModified": "2023-03-01T08:30:25+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -116,8 +118,70 @@ iso-codes 4.13.0 was released, which incorporates my changes to the common names
 <ul>
 <li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
 <li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
+<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
 </ul>
-<!-- raw HTML omitted -->
+<ul>
+<li>I can&rsquo;t put my finger on it, but the input form has to be formatted very particularly, for example if your rows have more than two fields in them with out a sufficient Bootstrap grid style, or if you use a <code>twobox</code>, etc, the entire form step appears blank</li>
+</ul>
+<h2 id="2023-03-02">2023-03-02</h2>
+<ul>
+<li>I did some experiments with the new <a href="https://datapythonista.me/blog/pandas-20-and-the-arrow-revolution-part-i">Pandas 2.0.0rc0 Apache Arrow support</a>
+<ul>
+<li>There is a change to the way nulls are handled and it causes my tests for <code>pd.isna(field)</code> to fail</li>
+<li>I think we need consider blanks as null, but I&rsquo;m not sure</li>
+</ul>
+</li>
+<li>I made some adjustments to the Discovery sidebar facets on DSpace 6 while I was looking at the DSpace 7 configuration
+<ul>
+<li>I downgraded CIFOR subject, Humidtropics subject, Drylands subject, ICARDA subject, and Language from DiscoverySearchFilterFacet to DiscoverySearchFilter in <code>discovery.xml</code> since we are no longer using them in sidebar facets</li>
+</ul>
+</li>
+</ul>
+<h2 id="2023-03-03">2023-03-03</h2>
+<ul>
+<li>Atmire merged one of my old pull requests into COUNTER-Robots:
+<ul>
+<li><a href="https://github.com/atmire/COUNTER-Robots/pull/54">COUNTER_Robots_list.json: Add new bots</a></li>
+</ul>
+</li>
+<li>I will update the local ILRI overrides in our DSpace spider agents file</li>
+</ul>
+<h2 id="2023-03-04">2023-03-04</h2>
+<ul>
+<li>Submit a <a href="https://github.com/flyingcircusio/pycountry/pull/156">pull request on pycountry to use iso-codes 4.13.0</a></li>
+</ul>
+<h2 id="2023-03-05">2023-03-05</h2>
+<ul>
+<li>Start a harvest on AReS</li>
+</ul>
+<h2 id="2023-03-06">2023-03-06</h2>
+<ul>
+<li>Export CGSpace to do Initiative collection mappings
+<ul>
+<li>There were thirty-three that needed updating</li>
+</ul>
+</li>
+<li>Send Abenet and Sam a list of twenty-one CAS publications that had been marked as &ldquo;multiple documents&rdquo; that we uploaded as metadata-only items
+<ul>
+<li>Goshu will download the PDFs for each and upload them to the items on CGSpace manually</li>
+</ul>
+</li>
+<li>I spent some time trying to get csv-metadata-quality working with the new Arrow backend for Pandas 2.0.0rc0
+<ul>
+<li>It seems there is a problem recognizing empty strings as na with <code>pd.isna()</code></li>
+<li>If I do <code>pd.isna(field) or field == &quot;&quot;</code> then it works as expected, but that feels hacky</li>
+<li>I&rsquo;m going to test again on the next release&hellip;</li>
+<li>Note that I had been setting both of these global options:</li>
+</ul>
+</li>
+</ul>
+<pre tabindex="0"><code>pd.options.mode.dtype_backend = &#39;pyarrow&#39;
+pd.options.mode.nullable_dtypes = True
+</code></pre><ul>
+<li>Then reading the CSV like this:</li>
+</ul>
+<pre tabindex="0"><code>df = pd.read_csv(args.input_file, engine=&#39;pyarrow&#39;, dtype=&#39;string[pyarrow]&#39;
+</code></pre><!-- raw HTML omitted -->
 
   
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 
@@ -94,6 +94,7 @@
 <ul>
 <li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
 <li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
+<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
 </ul>
   <a href='https://alanorth.github.io/cgspace-notes/2023-03/'>Read more →</a>
 </article> 

docs/categories/notes/index.xml

@@ -17,6 +17,7 @@
 <ul>
 <li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
 <li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
+<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
 &lt;/ul&gt;</description>
     </item>
     

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

docs/categories/notes/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/categories/notes/" />
-<meta property="og:updated_time" content="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

docs/categories/notes/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/categories/notes/" />
-<meta property="og:updated_time" content="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 
@@ -109,6 +109,7 @@
 <ul>
 <li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
 <li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
+<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
 </ul>
   <a href='https://alanorth.github.io/cgspace-notes/2023-03/'>Read more →</a>
 </article> 

docs/index.xml

@@ -17,6 +17,7 @@
 <ul>
 <li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
 <li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
+<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
 &lt;/ul&gt;</description>
     </item>
     

docs/page/10/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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

docs/page/8/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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

docs/page/9/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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 
@@ -109,6 +109,7 @@
 <ul>
 <li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
 <li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
+<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
 </ul>
   <a href='https://alanorth.github.io/cgspace-notes/2023-03/'>Read more →</a>
 </article> 

docs/posts/index.xml

@@ -17,6 +17,7 @@
 <ul>
 <li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
 <li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
+<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
 &lt;/ul&gt;</description>
     </item>
     

docs/posts/page/10/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="2023-03-01T07:58:36+03:00" />
+<meta property="og:updated_time" content="2023-03-01T08:30:25+03:00" />
 
 
 

docs/posts/page/2/index.html

@@ -10,7 +10,7 @@
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