Add notes for 2023-02-21

content/posts/2023-02.md

@@ -202,4 +202,130 @@ Done.
 
 - I think that particular error is because I applied the [indexes in this unmerged DSpace 6 patch](https://github.com/DSpace/DSpace/pull/1792), so I don't need to report this as an error in DSpace 7
 
+## 2023-02-16
+
+- I found a suspicious number of PostgreSQL locks on CGSpace and decided to investigate:
+
+```console
+$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
+     44 dspaceApi
+    372 dspaceCli
+    446 dspaceWeb
+```
+
+- This started happening yesterday and I killed a few locks that were several hours old after inspecting the `locks-age.sql` output
+- I also checked the `locks.sql` output, which helpfully lists the blocked PID and the blocking PID, to find one blocking PID that was idle in transaction
+  - I killed that process and then all other locks were instantly processed
+- I filed [a GitHub issue](https://github.com/DSpace/dspace-angular/issues/2103) on dspace-angular requesting the item view to use the bitstream description instead of the file name if present
+- Weekly CG Core types meeting
+  - I need to go through the actions and remove those items that are only for CGSpace internal use, ie:
+    - CD-ROM
+    - Manuscript-unpublished
+    - Photo Report
+    - Questionnaire
+    - Wiki
+- Weekly CGIAR Repository Working Group meeting
+- I did some experiments with Crossref dates for about 20,000 DOIs in CGSpace using my `crossref-doi-lookup.py` script
+- Some things I noted from reading the [Crossref API docs](https://github.com/CrossRef/rest-api-doc/blob/master/api_format.md) and inspecting the records for a few dozen DOIs manually:
+  - `["created"]["date-parts"]` → Date on which the DOI was first registered (not useful for us)
+  - `["published-print"]["date-parts"]` → Date on which the work was published in print
+  - `["journal-issue"]["published-print"]["date-parts"]` → When present, is 99% the same as the above
+  - `["published-online"]["date-parts"]` → Date on which the work was published online
+  - `["journal-issue"]["published-online"]["date-parts"]` → Much more rare, and only 50% the same as the above, so unreliable
+  - `["issued"]["date-parts"]` → Earliest of published-print and published-online (not useful to us)
+- After checking the DOIs manully I decided that when the `published-print` date exists, it is usually more accurate than our issued dates
+  - I set 12,300 issue dates to those from Crossref
+- I also decided that, when `published-online` exists, it is usually accurate when I check the publisher page (we don't have many online dates to compare)
+  - I set the available date for ~7,000 items to the published-online date as long as:
+    - There was no `dcterms.available` date already
+    - It was different than the issued date, because for now I only want online dates that are different, in case this is an online only journal in which case that can be the issue date... maybe I'll re-visit that later
+
+## 2023-02-17
+
+- It seems some (all?) of the changes I applied to dates last night didn't get saved...
+  - I don't know what happened, so I will run them again after some investigation
+  - I submitted the first batch of ~7,600 changes and it took twelve hours!
+  - I almost cancelled it because after applying the changes there was a lock blocking everything for two hours, and it seemed to be stuck, but I kept checking it and saw that the `query_start` and `state_change` were being updated despite it being state "idle in transaction":
+
+```console
+$ psql -c 'SELECT * FROM pg_stat_activity WHERE pid=1025176' | less -S
+```
+
+- I will apply the other changes in smaller batches...
+- Lately I've noticed a lot of activity from the country code tagger curation task
+  - Looking in the logs I see items being tagged that are very old and should have already been tagged years ago
+  - Also, I see a ton of these errors whenever the task is updating an item:
+
+```console
+2023-02-17 08:01:00,252 INFO  org.dspace.curate.Curator @ Curation task: countrycodetagger performed on: 10568/89020 with status: 0. Result: '10568/89020: added 1 alpha2 country code(s)'
+2023-02-17 08:01:00,467 ERROR com.atmire.versioning.ModificationLogger @ Error while writing item to versioning index: a0fe9d9a-6ac1-4b6a-8fcb-dae07a6bbf58 message:missing required field: epersonID
+org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: missing required field: epersonID
+        at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
+        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
+        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
+        at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
+        at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:116)
+        at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:102)
+        at com.atmire.versioning.ModificationLogger.indexItem(ModificationLogger.java:263)
+        at com.atmire.versioning.ModificationConsumer.end(ModificationConsumer.java:134)
+        at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:157)
+        at org.dspace.core.Context.dispatchEvents(Context.java:455)
+        at org.dspace.curate.Curator.visit(Curator.java:541)
+        at org.dspace.curate.Curator$TaskRunner.run(Curator.java:568)
+        at org.dspace.curate.Curator.doCollection(Curator.java:515)
+        at org.dspace.curate.Curator.doCommunity(Curator.java:487)
+        at org.dspace.curate.Curator.doSite(Curator.java:451)
+        at org.dspace.curate.Curator.curate(Curator.java:269)
+        at org.dspace.curate.Curator.curate(Curator.java:203)
+        at org.dspace.curate.CurationCli.main(CurationCli.java:220)
+        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
+        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+        at java.lang.reflect.Method.invoke(Method.java:498)
+        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
+        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
+```
+
+- This must be related...
+
+## 2023-02-18
+
+- I realized why the country-code-tagger was tagging everything: I had overridden the `force` parameter last week!
+- Start a harvest on AReS
+
+## 2023-02-20
+
+- IWMI is concerned that some of their items with top Altmetric attention scores don't show up in the AReS Explorer
+  - I looked into it for one and found that AReS is using the Handle, but Altmetric hasn't associated the Handle with the DOI
+- Looking into country and region issues for the PRMS team
+  - Last week they had some questions about some invalid countries that ended up being typos
+  - I realized my cgspace-java-helpers country-code-tagger curation task is not using the latest version, so it was missing Türkiye
+  - I compiled the new version and ran it manually, but I have to upload a new version to Maven Central and then update the dependency in `dspace/modules/additions/pom.xml` ughhhhhh
+  - I tagged version 6.2 with the change for Türkiye and uploaded to to Maven Central with `mvn clean deploy`
+- I'm having second thoughts about switching to UN M.49 for countries because there are just too many tradeoffs
+  - I want to find a way to keep our existing list, and codify some rules for it
+  - There are several discussions related to the shortcomings of ISO themselves and the iso-codes project, for example:
+    - [Inconsistency with articles in ISO-3166-1 English short names](https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/33) (this one was filed by me two years ago!)
+    - [ISO 3166-1: What's the policy for `common_name`?](https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/44)
+  - I almost want to say fuck it, let's just use iso-codes and tell everyone to deal with it, but make sure we handle ISO 3166-1 Alpha2 or probably Alpha3 in the future
+  - Something like:
+    - Prefer `common_name` if it exists
+    - Prefer the shorter of `name` and `official name`
+
+## 2023-02-21
+
+- Continue working on my `parse-iso-codes.py` script to parse the iso-codes JSON for ISO 3166-1
+  - I also started a spreadsheet to track current CGSpace country names, proposed new names using the compromise above, and UN M.49 names
+  - I proposed this to Peter but he wasn't happy because there are still some stupidly long and political names there
+- I bumped the version of cgspace-java-helpers to 6.2-SNAPSHOT and pushed it to Maven Central because I can't figure out how to get non-snapshot releases to go there
+- Ouch, grunt 1.6.0 was released a few weeks ago, which relies on Node.js v16, thus breaking the Mirage 2 build in DSpace 6
+  - I filed [an issue in DSpace](https://github.com/DSpace/DSpace/issues/8676)
+- Help Moises from CIP troubleshoot harvesting issues on their WordPress site
+  - I see 2,000 requests with the user agent "RTB website BOT" today and they are all HTTP 200
+
+```console
+# grep 'RTB website BOT' /var/log/nginx/rest.log | awk '{print $9}' | sort | uniq -c | sort -h
+   2023 200
+```
+
 <!-- 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="2023-02-14T23:13:35+03:00" />
+<meta property="article:modified_time" content="2023-02-15T19:47:13+03:00" />
 
 
 
@@ -42,9 +42,9 @@ I want to try to expand my use of their data to journals, publishers, volumes, i
   "@type": "BlogPosting",
   "headline": "February, 2023",
   "url": "https://alanorth.github.io/cgspace-notes/2023-02/",
-  "wordCount": "1245",
+  "wordCount": "2333",
   "datePublished": "2023-02-01T10:57:36+03:00",
-  "dateModified": "2023-02-14T23:13:35+03:00",
+  "dateModified": "2023-02-15T19:47:13+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -340,7 +340,175 @@ I want to try to expand my use of their data to journals, publishers, volumes, i
 </span></span></code></pre></div><ul>
 <li>I think that particular error is because I applied the <a href="https://github.com/DSpace/DSpace/pull/1792">indexes in this unmerged DSpace 6 patch</a>, so I don&rsquo;t need to report this as an error in DSpace 7</li>
 </ul>
-<!-- raw HTML omitted -->
+<h2 id="2023-02-16">2023-02-16</h2>
+<ul>
+<li>I found a suspicious number of PostgreSQL locks on CGSpace and decided to investigate:</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"><span style="display:flex;"><span>$ psql -c <span style="color:#e6db74">&#39;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;&#39;</span> | grep -o -E <span style="color:#e6db74">&#39;(dspaceWeb|dspaceApi|dspaceCli)&#39;</span> | sort | uniq -c
+</span></span><span style="display:flex;"><span>     44 dspaceApi
+</span></span><span style="display:flex;"><span>    372 dspaceCli
+</span></span><span style="display:flex;"><span>    446 dspaceWeb
+</span></span></code></pre></div><ul>
+<li>This started happening yesterday and I killed a few locks that were several hours old after inspecting the <code>locks-age.sql</code> output</li>
+<li>I also checked the <code>locks.sql</code> output, which helpfully lists the blocked PID and the blocking PID, to find one blocking PID that was idle in transaction
+<ul>
+<li>I killed that process and then all other locks were instantly processed</li>
+</ul>
+</li>
+<li>I filed <a href="https://github.com/DSpace/dspace-angular/issues/2103">a GitHub issue</a> on dspace-angular requesting the item view to use the bitstream description instead of the file name if present</li>
+<li>Weekly CG Core types meeting
+<ul>
+<li>I need to go through the actions and remove those items that are only for CGSpace internal use, ie:
+<ul>
+<li>CD-ROM</li>
+<li>Manuscript-unpublished</li>
+<li>Photo Report</li>
+<li>Questionnaire</li>
+<li>Wiki</li>
+</ul>
+</li>
+</ul>
+</li>
+<li>Weekly CGIAR Repository Working Group meeting</li>
+<li>I did some experiments with Crossref dates for about 20,000 DOIs in CGSpace using my <code>crossref-doi-lookup.py</code> script</li>
+<li>Some things I noted from reading the <a href="https://github.com/CrossRef/rest-api-doc/blob/master/api_format.md">Crossref API docs</a> and inspecting the records for a few dozen DOIs manually:
+<ul>
+<li><code>[&quot;created&quot;][&quot;date-parts&quot;]</code> → Date on which the DOI was first registered (not useful for us)</li>
+<li><code>[&quot;published-print&quot;][&quot;date-parts&quot;]</code> → Date on which the work was published in print</li>
+<li><code>[&quot;journal-issue&quot;][&quot;published-print&quot;][&quot;date-parts&quot;]</code> → When present, is 99% the same as the above</li>
+<li><code>[&quot;published-online&quot;][&quot;date-parts&quot;]</code> → Date on which the work was published online</li>
+<li><code>[&quot;journal-issue&quot;][&quot;published-online&quot;][&quot;date-parts&quot;]</code> → Much more rare, and only 50% the same as the above, so unreliable</li>
+<li><code>[&quot;issued&quot;][&quot;date-parts&quot;]</code> → Earliest of published-print and published-online (not useful to us)</li>
+</ul>
+</li>
+<li>After checking the DOIs manully I decided that when the <code>published-print</code> date exists, it is usually more accurate than our issued dates
+<ul>
+<li>I set 12,300 issue dates to those from Crossref</li>
+</ul>
+</li>
+<li>I also decided that, when <code>published-online</code> exists, it is usually accurate when I check the publisher page (we don&rsquo;t have many online dates to compare)
+<ul>
+<li>I set the available date for ~7,000 items to the published-online date as long as:
+<ul>
+<li>There was no <code>dcterms.available</code> date already</li>
+<li>It was different than the issued date, because for now I only want online dates that are different, in case this is an online only journal in which case that can be the issue date&hellip; maybe I&rsquo;ll re-visit that later</li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+<h2 id="2023-02-17">2023-02-17</h2>
+<ul>
+<li>It seems some (all?) of the changes I applied to dates last night didn&rsquo;t get saved&hellip;
+<ul>
+<li>I don&rsquo;t know what happened, so I will run them again after some investigation</li>
+<li>I submitted the first batch of ~7,600 changes and it took twelve hours!</li>
+<li>I almost cancelled it because after applying the changes there was a lock blocking everything for two hours, and it seemed to be stuck, but I kept checking it and saw that the <code>query_start</code> and <code>state_change</code> were being updated despite it being state &ldquo;idle in transaction&rdquo;:</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"><span style="display:flex;"><span>$ psql -c <span style="color:#e6db74">&#39;SELECT * FROM pg_stat_activity WHERE pid=1025176&#39;</span> | less -S
+</span></span></code></pre></div><ul>
+<li>I will apply the other changes in smaller batches&hellip;</li>
+<li>Lately I&rsquo;ve noticed a lot of activity from the country code tagger curation task
+<ul>
+<li>Looking in the logs I see items being tagged that are very old and should have already been tagged years ago</li>
+<li>Also, I see a ton of these errors whenever the task is updating an item:</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"><span style="display:flex;"><span>2023-02-17 08:01:00,252 INFO  org.dspace.curate.Curator @ Curation task: countrycodetagger performed on: 10568/89020 with status: 0. Result: &#39;10568/89020: added 1 alpha2 country code(s)&#39;
+</span></span><span style="display:flex;"><span>2023-02-17 08:01:00,467 ERROR com.atmire.versioning.ModificationLogger @ Error while writing item to versioning index: a0fe9d9a-6ac1-4b6a-8fcb-dae07a6bbf58 message:missing required field: epersonID
+</span></span><span style="display:flex;"><span>org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: missing required field: epersonID
+</span></span><span style="display:flex;"><span>        at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
+</span></span><span style="display:flex;"><span>        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
+</span></span><span style="display:flex;"><span>        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
+</span></span><span style="display:flex;"><span>        at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
+</span></span><span style="display:flex;"><span>        at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:116)
+</span></span><span style="display:flex;"><span>        at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:102)
+</span></span><span style="display:flex;"><span>        at com.atmire.versioning.ModificationLogger.indexItem(ModificationLogger.java:263)
+</span></span><span style="display:flex;"><span>        at com.atmire.versioning.ModificationConsumer.end(ModificationConsumer.java:134)
+</span></span><span style="display:flex;"><span>        at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:157)
+</span></span><span style="display:flex;"><span>        at org.dspace.core.Context.dispatchEvents(Context.java:455)
+</span></span><span style="display:flex;"><span>        at org.dspace.curate.Curator.visit(Curator.java:541)
+</span></span><span style="display:flex;"><span>        at org.dspace.curate.Curator$TaskRunner.run(Curator.java:568)
+</span></span><span style="display:flex;"><span>        at org.dspace.curate.Curator.doCollection(Curator.java:515)
+</span></span><span style="display:flex;"><span>        at org.dspace.curate.Curator.doCommunity(Curator.java:487)
+</span></span><span style="display:flex;"><span>        at org.dspace.curate.Curator.doSite(Curator.java:451)
+</span></span><span style="display:flex;"><span>        at org.dspace.curate.Curator.curate(Curator.java:269)
+</span></span><span style="display:flex;"><span>        at org.dspace.curate.Curator.curate(Curator.java:203)
+</span></span><span style="display:flex;"><span>        at org.dspace.curate.CurationCli.main(CurationCli.java:220)
+</span></span><span style="display:flex;"><span>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+</span></span><span style="display:flex;"><span>        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
+</span></span><span style="display:flex;"><span>        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+</span></span><span style="display:flex;"><span>        at java.lang.reflect.Method.invoke(Method.java:498)
+</span></span><span style="display:flex;"><span>        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
+</span></span><span style="display:flex;"><span>        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
+</span></span></code></pre></div><ul>
+<li>This must be related&hellip;</li>
+</ul>
+<h2 id="2023-02-18">2023-02-18</h2>
+<ul>
+<li>I realized why the country-code-tagger was tagging everything: I had overridden the <code>force</code> parameter last week!</li>
+<li>Start a harvest on AReS</li>
+</ul>
+<h2 id="2023-02-20">2023-02-20</h2>
+<ul>
+<li>IWMI is concerned that some of their items with top Altmetric attention scores don&rsquo;t show up in the AReS Explorer
+<ul>
+<li>I looked into it for one and found that AReS is using the Handle, but Altmetric hasn&rsquo;t associated the Handle with the DOI</li>
+</ul>
+</li>
+<li>Looking into country and region issues for the PRMS team
+<ul>
+<li>Last week they had some questions about some invalid countries that ended up being typos</li>
+<li>I realized my cgspace-java-helpers country-code-tagger curation task is not using the latest version, so it was missing Türkiye</li>
+<li>I compiled the new version and ran it manually, but I have to upload a new version to Maven Central and then update the dependency in <code>dspace/modules/additions/pom.xml</code> ughhhhhh</li>
+<li>I tagged version 6.2 with the change for Türkiye and uploaded to to Maven Central with <code>mvn clean deploy</code></li>
+</ul>
+</li>
+<li>I&rsquo;m having second thoughts about switching to UN M.49 for countries because there are just too many tradeoffs
+<ul>
+<li>I want to find a way to keep our existing list, and codify some rules for it</li>
+<li>There are several discussions related to the shortcomings of ISO themselves and the iso-codes project, for example:
+<ul>
+<li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/33">Inconsistency with articles in ISO-3166-1 English short names</a> (this one was filed by me two years ago!)</li>
+<li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/44">ISO 3166-1: What&rsquo;s the policy for <code>common_name</code>?</a></li>
+</ul>
+</li>
+<li>I almost want to say fuck it, let&rsquo;s just use iso-codes and tell everyone to deal with it, but make sure we handle ISO 3166-1 Alpha2 or probably Alpha3 in the future</li>
+<li>Something like:
+<ul>
+<li>Prefer <code>common_name</code> if it exists</li>
+<li>Prefer the shorter of <code>name</code> and <code>official name</code></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+<h2 id="2023-02-21">2023-02-21</h2>
+<ul>
+<li>Continue working on my <code>parse-iso-codes.py</code> script to parse the iso-codes JSON for ISO 3166-1
+<ul>
+<li>I also started a spreadsheet to track current CGSpace country names, proposed new names using the compromise above, and UN M.49 names</li>
+<li>I proposed this to Peter but he wasn&rsquo;t happy because there are still some stupidly long and political names there</li>
+</ul>
+</li>
+<li>I bumped the version of cgspace-java-helpers to 6.2-SNAPSHOT and pushed it to Maven Central because I can&rsquo;t figure out how to get non-snapshot releases to go there</li>
+<li>Ouch, grunt 1.6.0 was released a few weeks ago, which relies on Node.js v16, thus breaking the Mirage 2 build in DSpace 6
+<ul>
+<li>I filed <a href="https://github.com/DSpace/DSpace/issues/8676">an issue in DSpace</a></li>
+</ul>
+</li>
+<li>Help Moises from CIP troubleshoot harvesting issues on their WordPress site
+<ul>
+<li>I see 2,000 requests with the user agent &ldquo;RTB website BOT&rdquo; today and they are all HTTP 200</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"><span style="display:flex;"><span># grep <span style="color:#e6db74">&#39;RTB website BOT&#39;</span> /var/log/nginx/rest.log | awk <span style="color:#e6db74">&#39;{print $9}&#39;</span> | sort | uniq -c | sort -h
+</span></span><span style="display:flex;"><span>   2023 200
+</span></span></code></pre></div><!-- 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" />
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