Update notes for 2021-04-26

content/posts/2021-04.md

@@ -747,4 +747,154 @@ $ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisti
   - I'm not sure if that means that it worked? I sent feedback to Atmire
 - Meeting with Moayad to discuss OpenRXV development progress
 
+## 2021-04-25
+
+- The indexes on AReS are messed up again
+  - I made a backup of the indexes, then deleted the `openrxv-items-final` and `openrxv-items-temp` indexes, re-created the `openrxv-items` alias, and restored the data into `openrxv-items`:
+
+```console
+$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
+$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
+$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
+$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
+$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
+$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
+$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
+```
+
+- Then I started a fresh AReS harvest
+
+## 2021-04-26
+
+- The AReS harvest last night seems to have finished successfully and the number of items looks good:
+
+```console
+$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
+yellow open openrxv-items-temp       H-CGsyyLTaqAj6-nKXZ-7w 1 1      0 0    283b    283b
+yellow open openrxv-items-final      ul3SKsa7Q9Cd_K7qokBY_w 1 1 103951 0   254mb   254mb
+```
+
+- And the aliases seem correct for once:
+
+```console
+$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
+...
+    "openrxv-items-final": {
+        "aliases": {
+            "openrxv-items": {}
+        }
+    },
+    "openrxv-items-temp": {
+        "aliases": {}
+    },
+...
+```
+
+- That's 250 new items in the index since the last harvest!
+- Re-create my local Artifactory container because I'm getting errors starting it and it has been a few months since it was updated:
+
+```console
+$ podman rm artifactory
+$ podman pull docker.bintray.io/jfrog/artifactory-oss:latest
+$ podman create --ulimit nofile=32000:32000 --name artifactory -v artifactory_data:/var/opt/jfrog/artifactory -p 8081-8082:8081-8082 docker.bintray.io/jfrog/artifactory-oss
+$ podman start artifactory
+```
+
+- Start testing DSpace 7.0 Beta 5 so I can evaluate if it solves some of the problems we are having on DSpace 6, and if it's missing things like multiple handle resolvers, etc
+  - I see it needs Java JDK 11, Tomcat 9, Solr 8, and PostgreSQL 11
+  - Also, according to the [installation notes](https://wiki.lyrasis.org/display/DSDOC7x/Installing+DSpace) I see you can install the old DSpace 6 REST API, so that's potentially useful for us
+  - I see that all web applications on the backend are now rolled into just one "server" application
+  - The build process took 11 minutes the first time (due to downloading the world with Maven) and ~2 minutes the second time
+  - The `local.cfg` content and syntax is very similar DSpace 6
+- I got the basic `fresh_install` up and running
+  - Then I tried to import a DSpace 6 database from production
+- I tried to delete all the Atmire SQL migrations:
+
+```console
+localhost/dspace7b5= > DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';
+```
+
+- But I got an error when running `dspace database migrate`:
+
+```console
+$ ~/dspace7b5/bin/dspace database migrate
+
+Database URL: jdbc:postgresql://localhost:5432/dspace7b5
+Migrating database to latest version... (Check dspace logs for details)
+Migration exception:
+java.sql.SQLException: Flyway migration error occurred
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:738)
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:632)
+        at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:228)
+        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
+        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
+        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:273)
+        at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:129)
+        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:94)
+Caused by: org.flywaydb.core.api.FlywayException: Validate failed: 
+Detected applied migration not resolved locally: 5.0.2017.09.25
+Detected applied migration not resolved locally: 6.0.2017.01.30
+Detected applied migration not resolved locally: 6.0.2017.09.25
+
+        at org.flywaydb.core.Flyway.doValidate(Flyway.java:292)
+        at org.flywaydb.core.Flyway.access$100(Flyway.java:73)
+        at org.flywaydb.core.Flyway$1.execute(Flyway.java:166)
+        at org.flywaydb.core.Flyway$1.execute(Flyway.java:158)
+        at org.flywaydb.core.Flyway.execute(Flyway.java:527)
+        at org.flywaydb.core.Flyway.migrate(Flyway.java:158)
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:729)
+        ... 9 more
+```
+
+- I deleted those migrations:
+
+```console
+localhost/dspace7b5= > DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
+```
+
+- Then when I ran the migration again it failed for a new reason, related to the configurable workflow:
+
+```console
+Database URL: jdbc:postgresql://localhost:5432/dspace7b5
+Migrating database to latest version... (Check dspace logs for details)
+Migration exception:
+java.sql.SQLException: Flyway migration error occurred
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:738)
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:632)
+        at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:228)
+        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
+        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
+        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:273)
+        at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:129)
+        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:94)
+Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateException:
+Migration V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql failed
+--------------------------------------------------------------------
+SQL State  : 42P01
+Error Code : 0
+Message    : ERROR: relation "cwf_pooltask" does not exist
+  Position: 8
+Location   : org/dspace/storage/rdbms/sqlmigration/postgres/V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql (/home/aorth/src/apache-tomcat-9.0.45/file:/home/aorth/dspace7b5/lib/dspace-api-7.0-beta5.jar!/org/dspace/storage/rdbms/sqlmigration/postgres/V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql)
+Line       : 16
+Statement  : UPDATE cwf_pooltask SET workflow_id='defaultWorkflow' WHERE workflow_id='default'
+...
+```
+
+- The [DSpace 7 upgrade docs](https://wiki.lyrasis.org/display/DSDOC7x/Upgrading+DSpace) say I need to apply these previously optional migrations:
+
+```console
+$ ~/dspace7b5/bin/dspace database migrate ignored
+```
+
+- Now I see all migrations have completed and DSpace actually starts up fine!
+- I will try to do a full re-index to see how long it takes:
+
+```console
+$ time ~/dspace7b5/bin/dspace index-discovery -b
+```
+
 <!-- vim: set sw=2 ts=2: -->

docs/2021-04/index.html

@@ -24,7 +24,7 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-04/" />
 <meta property="article:published_time" content="2021-04-01T09:50:54+03:00" />
-<meta property="article:modified_time" content="2021-04-19T20:11:44+03:00" />
+<meta property="article:modified_time" content="2021-04-21T22:53:24+03:00" />
 
 
 
@@ -54,9 +54,9 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
   "@type": "BlogPosting",
   "headline": "April, 2021",
   "url": "https://alanorth.github.io/cgspace-notes/2021-04/",
-  "wordCount": "3896",
+  "wordCount": "4547",
   "datePublished": "2021-04-01T09:50:54+03:00",
-  "dateModified": "2021-04-19T20:11:44+03:00",
+  "dateModified": "2021-04-21T22:53:24+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -861,7 +861,145 @@ $ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisti
 </li>
 <li>Meeting with Moayad to discuss OpenRXV development progress</li>
 </ul>
-<!-- raw HTML omitted -->
+<h2 id="2021-04-25">2021-04-25</h2>
+<ul>
+<li>The indexes on AReS are messed up again
+<ul>
+<li>I made a backup of the indexes, then deleted the <code>openrxv-items-final</code> and <code>openrxv-items-temp</code> indexes, re-created the <code>openrxv-items</code> alias, and restored the data into <code>openrxv-items</code>:</li>
+</ul>
+</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
+$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
+$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
+$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
+$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
+$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{&quot;actions&quot; : [{&quot;add&quot; : { &quot;index&quot; : &quot;openrxv-items-final&quot;, &quot;alias&quot; : &quot;openrxv-items&quot;}}]}'
+$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
+</code></pre><ul>
+<li>Then I started a fresh AReS harvest</li>
+</ul>
+<h2 id="2021-04-26">2021-04-26</h2>
+<ul>
+<li>The AReS harvest last night seems to have finished successfully and the number of items looks good:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
+yellow open openrxv-items-temp       H-CGsyyLTaqAj6-nKXZ-7w 1 1      0 0    283b    283b
+yellow open openrxv-items-final      ul3SKsa7Q9Cd_K7qokBY_w 1 1 103951 0   254mb   254mb
+</code></pre><ul>
+<li>And the aliases seem correct for once:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
+...
+    &quot;openrxv-items-final&quot;: {
+        &quot;aliases&quot;: {
+            &quot;openrxv-items&quot;: {}
+        }
+    },
+    &quot;openrxv-items-temp&quot;: {
+        &quot;aliases&quot;: {}
+    },
+...
+</code></pre><ul>
+<li>That&rsquo;s 250 new items in the index since the last harvest!</li>
+<li>Re-create my local Artifactory container because I&rsquo;m getting errors starting it and it has been a few months since it was updated:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ podman rm artifactory
+$ podman pull docker.bintray.io/jfrog/artifactory-oss:latest
+$ podman create --ulimit nofile=32000:32000 --name artifactory -v artifactory_data:/var/opt/jfrog/artifactory -p 8081-8082:8081-8082 docker.bintray.io/jfrog/artifactory-oss
+$ podman start artifactory
+</code></pre><ul>
+<li>Start testing DSpace 7.0 Beta 5 so I can evaluate if it solves some of the problems we are having on DSpace 6, and if it&rsquo;s missing things like multiple handle resolvers, etc
+<ul>
+<li>I see it needs Java JDK 11, Tomcat 9, Solr 8, and PostgreSQL 11</li>
+<li>Also, according to the <a href="https://wiki.lyrasis.org/display/DSDOC7x/Installing+DSpace">installation notes</a> I see you can install the old DSpace 6 REST API, so that&rsquo;s potentially useful for us</li>
+<li>I see that all web applications on the backend are now rolled into just one &ldquo;server&rdquo; application</li>
+<li>The build process took 11 minutes the first time (due to downloading the world with Maven) and ~2 minutes the second time</li>
+<li>The <code>local.cfg</code> content and syntax is very similar DSpace 6</li>
+</ul>
+</li>
+<li>I got the basic <code>fresh_install</code> up and running
+<ul>
+<li>Then I tried to import a DSpace 6 database from production</li>
+</ul>
+</li>
+<li>I tried to delete all the Atmire SQL migrations:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">localhost/dspace7b5= &gt; DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';
+</code></pre><ul>
+<li>But I got an error when running <code>dspace database migrate</code>:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ ~/dspace7b5/bin/dspace database migrate
+
+Database URL: jdbc:postgresql://localhost:5432/dspace7b5
+Migrating database to latest version... (Check dspace logs for details)
+Migration exception:
+java.sql.SQLException: Flyway migration error occurred
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:738)
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:632)
+        at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:228)
+        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
+        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
+        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:273)
+        at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:129)
+        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:94)
+Caused by: org.flywaydb.core.api.FlywayException: Validate failed: 
+Detected applied migration not resolved locally: 5.0.2017.09.25
+Detected applied migration not resolved locally: 6.0.2017.01.30
+Detected applied migration not resolved locally: 6.0.2017.09.25
+
+        at org.flywaydb.core.Flyway.doValidate(Flyway.java:292)
+        at org.flywaydb.core.Flyway.access$100(Flyway.java:73)
+        at org.flywaydb.core.Flyway$1.execute(Flyway.java:166)
+        at org.flywaydb.core.Flyway$1.execute(Flyway.java:158)
+        at org.flywaydb.core.Flyway.execute(Flyway.java:527)
+        at org.flywaydb.core.Flyway.migrate(Flyway.java:158)
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:729)
+        ... 9 more
+</code></pre><ul>
+<li>I deleted those migrations:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">localhost/dspace7b5= &gt; DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
+</code></pre><ul>
+<li>Then when I ran the migration again it failed for a new reason, related to the configurable workflow:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">Database URL: jdbc:postgresql://localhost:5432/dspace7b5
+Migrating database to latest version... (Check dspace logs for details)
+Migration exception:
+java.sql.SQLException: Flyway migration error occurred
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:738)
+        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:632)
+        at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:228)
+        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
+        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
+        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:273)
+        at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:129)
+        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:94)
+Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateException:
+Migration V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql failed
+--------------------------------------------------------------------
+SQL State  : 42P01
+Error Code : 0
+Message    : ERROR: relation &quot;cwf_pooltask&quot; does not exist
+  Position: 8
+Location   : org/dspace/storage/rdbms/sqlmigration/postgres/V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql (/home/aorth/src/apache-tomcat-9.0.45/file:/home/aorth/dspace7b5/lib/dspace-api-7.0-beta5.jar!/org/dspace/storage/rdbms/sqlmigration/postgres/V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql)
+Line       : 16
+Statement  : UPDATE cwf_pooltask SET workflow_id='defaultWorkflow' WHERE workflow_id='default'
+...
+</code></pre><ul>
+<li>The <a href="https://wiki.lyrasis.org/display/DSDOC7x/Upgrading+DSpace">DSpace 7 upgrade docs</a> say I need to apply these previously optional migrations:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ ~/dspace7b5/bin/dspace database migrate ignored
+</code></pre><ul>
+<li>Now I see all migrations have completed and DSpace actually starts up fine!</li>
+<li>I will try to do a full re-index to see how long it takes:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ time ~/dspace7b5/bin/dspace index-discovery -b
+</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="2021-04-19T20:11:44+03:00" />
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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/notes/" />
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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/notes/" />
-<meta property="og:updated_time" content="2021-04-19T20:11:44+03:00" />
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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/notes/" />
-<meta property="og:updated_time" content="2021-04-19T20:11:44+03:00" />
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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/notes/" />
-<meta property="og:updated_time" content="2021-04-19T20:11:44+03:00" />
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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/notes/" />
-<meta property="og:updated_time" content="2021-04-19T20:11:44+03:00" />
+<meta property="og:updated_time" content="2021-04-21T22:53:24+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="2021-04-19T20:11:44+03:00" />
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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/" />
-<meta property="og:updated_time" content="2021-04-19T20:11:44+03:00" />
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