Update notes for 2020-12-14

2024-06-25 23:53:46 +02:00 · 2020-12-14 19:49:25 +02:00 · 2020-12-14 19:49:25 +02:00 · 403fa49d46
commit 403fa49d46
parent 20f00d1279
23 changed files with 264 additions and 28 deletions
--- a/content/posts/2020-12.md
+++ b/content/posts/2020-12.md
@ -241,4 +241,114 @@ $ curl -XDELETE http://localhost:9200/openrxv-items-final
 $ curl -XDELETE http://localhost:9200/openrxv-items-temp
 ```

+- Peter asked me for a list of all submitters and approvers that were active recently on CGSpace
+  - I can probably extract that from the `dc.description.provenance` field, for example any that contains a 2020 date:
+
+```console
+localhost/dspace63= > SELECT * FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-[0-9]{2}-*';
+```
+
+## 2020-12-14
+
+- The re-harvesting finished last night on AReS but there are no records in the `openrxv-items-final` index
+  - Strangely, there are 99,000 items in the temp index:
+
+```console
+$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*' | json_pp
+{
+   "count" : 99992,
+   "_shards" : {
+      "skipped" : 0,
+      "total" : 1,
+      "failed" : 0,
+      "successful" : 1
+   }
+}
+```
+
+- I'm going to try to [clone](https://www.elastic.co/guide/en/elasticsearch/reference/master/indices-clone-index.html) the temp index to the final one...
+  - First, set the `openrxv-items-temp` index to block writes (read only) and then clone it to `openrxv-items-final`:
+
+```console
+$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
+$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
+{"acknowledged":true,"shards_acknowledged":true,"index":"openrxv-items-final"}
+$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
+```
+
+- Now I see that the `openrxv-items-final` index has items, but there are still none in AReS Explorer UI!
+
+```console
+$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
+{
+  "count" : 99992,
+  "_shards" : {
+    "total" : 1,
+    "successful" : 1,
+    "skipped" : 0,
+    "failed" : 0
+  }
+}
+```
+
+- The api logs show this from last night after the harvesting:
+
+```console
+[Nest] 92   - 12/13/2020, 1:58:52 PM   [HarvesterService] Starting Harvest
+[Nest] 92   - 12/13/2020, 10:50:20 PM   [FetchConsumer] OnGlobalQueueDrained
+[Nest] 92   - 12/13/2020, 11:00:20 PM   [PluginsConsumer] OnGlobalQueueDrained
+[Nest] 92   - 12/13/2020, 11:00:20 PM   [HarvesterService] reindex function is called
+(node:92) UnhandledPromiseRejectionWarning: ResponseError: index_not_found_exception
+    at IncomingMessage.<anonymous> (/backend/node_modules/@elastic/elasticsearch/lib/Transport.js:232:25)
+    at IncomingMessage.emit (events.js:326:22)
+    at endReadableNT (_stream_readable.js:1223:12)
+    at processTicksAndRejections (internal/process/task_queues.js:84:21)
+```
+
+- But I'm not sure why the frontend doesn't show any data despite there being documents in the index...
+- I talked to Moayad and he reminded me that OpenRXV uses an alias to point to temp and final indexes, but the UI actually uses the `openrxv-items` index
+- I cloned the `openrxv-items-final` index to `openrxv-items` index and now I see items in the explorer UI
+- The PDF report was broken and I looked in the API logs and saw this:
+
+```console
+(node:94) UnhandledPromiseRejectionWarning: Error: Error: Could not find soffice binary
+    at ExportService.downloadFile (/backend/dist/export/services/export/export.service.js:51:19)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)
+```
+
+- I installed `unoconv` in the backend api container and now it works... but I wonder why this changed...
+- Skype with Abenet and Peter to discuss AReS that will be shown to ILRI scientists this week
+  - Peter noticed that [this item](https://hdl.handle.net/10568/110133) from the [ILRI policy and research briefs](https://cgspace.cgiar.org/handle/10568/24450) collection is missing in AReS, despite it being added one month ago in CGSpace and me harvesting on AReS last night
+    - The item appears fine in the REST API when I check the items in that collection
+  - Peter also noticed that [this item](https://hdl.handle.net/10568/110447) appears twice in AReS
+    - The item is _not_ duplicated on CGSpace or in the REST API
+  - We noticed that there are 136 items in the ILRI policy and research briefs collection according to AReS, yet on CGSpace there are only 132
+    - This is confirmed in the REST API (using [query-json](https://github.com/davesnx/query-json)):
+
+```
+$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&limit=100&offset=0' | json_pp > /tmp/policy1.json
+$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&limit=100&offset=100' | json_pp > /tmp/policy2.json
+$ query-json '.items | length' /tmp/policy1.json
+100
+$ query-json '.items | length' /tmp/policy2.json
+32
+```
+
+- I realized that the issue of missing/duplicate items in AReS might be because of this [REST API bug that causes /items to return items in non-deterministic order](https://jira.lyrasis.org/browse/DS-3849)
+- I decided to cherry-pick the following two patches from DSpace 6.4 into our `6_x-prod` (6.3) branch:
+  - High CPU usage when calling the collection_id/items REST endpoint
+    - Jira: https://jira.lyrasis.org/browse/DS-4342
+    - c2e6719fa763e291b81b2d61da2f8c758fe38ff3
+  - REST API items resource returns items in non-deterministic order
+    - Jira: https://jira.lyrasis.org/browse/DS-3849
+    - 2a2ea0cb5d03e6da9355a2eff12aad667e465433
+- After deploying the REST API fixes I decided to harvest from AReS again to see if the missing and duplicate items get fixed
+  - I made a backup of the current `openrxv-items-temp` index just in case:
+
+```console
+$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
+$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-2020-12-14
+$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
+```
+
 <!-- vim: set sw=2 ts=2: -->
--- a/docs/2020-12/index.html
+++ b/docs/2020-12/index.html
@ -20,7 +20,7 @@ I started processing those (about 411,000 records):
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-12/" />
 <meta property="article:published_time" content="2020-12-01T11:32:54+02:00" />
-<meta property="article:modified_time" content="2020-12-10T23:43:09+02:00" />
+<meta property="article:modified_time" content="2020-12-13T16:16:10+02:00" />



@ -46,9 +46,9 @@ I started processing those (about 411,000 records):
  "@type": "BlogPosting",
  "headline": "December, 2020",
  "url": "https://alanorth.github.io/cgspace-notes/2020-12/",
-  "wordCount": "1378",
+  "wordCount": "2037",
  "datePublished": "2020-12-01T11:32:54+02:00",
-  "dateModified": "2020-12-10T23:43:09+02:00",
+  "dateModified": "2020-12-13T16:16:10+02:00",
  "author": {
    "@type": "Person",
    "name": "Alan Orth"
@ -364,6 +364,132 @@ Caused by: org.apache.http.TruncatedChunkException: Truncated chunk ( expected s
 </ul>
 <pre><code>$ curl -XDELETE http://localhost:9200/openrxv-items-final
 $ curl -XDELETE http://localhost:9200/openrxv-items-temp
+</code></pre><ul>
+<li>Peter asked me for a list of all submitters and approvers that were active recently on CGSpace
+<ul>
+<li>I can probably extract that from the <code>dc.description.provenance</code> field, for example any that contains a 2020 date:</li>
+</ul>
+</li>
+</ul>
+<pre><code class="language-console" data-lang="console">localhost/dspace63= &gt; SELECT * FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-[0-9]{2}-*';
+</code></pre><h2 id="2020-12-14">2020-12-14</h2>
+<ul>
+<li>The re-harvesting finished last night on AReS but there are no records in the <code>openrxv-items-final</code> index
+<ul>
+<li>Strangely, there are 99,000 items in the temp index:</li>
+</ul>
+</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*' | json_pp
+{
+   &quot;count&quot; : 99992,
+   &quot;_shards&quot; : {
+      &quot;skipped&quot; : 0,
+      &quot;total&quot; : 1,
+      &quot;failed&quot; : 0,
+      &quot;successful&quot; : 1
+   }
+}
+</code></pre><ul>
+<li>I&rsquo;m going to try to <a href="https://www.elastic.co/guide/en/elasticsearch/reference/master/indices-clone-index.html">clone</a> the temp index to the final one&hellip;
+<ul>
+<li>First, set the <code>openrxv-items-temp</code> index to block writes (read only) and then clone it to <code>openrxv-items-final</code>:</li>
+</ul>
+</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings?pretty&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-final
+{&quot;acknowledged&quot;:true,&quot;shards_acknowledged&quot;:true,&quot;index&quot;:&quot;openrxv-items-final&quot;}
+$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings?pretty&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
+</code></pre><ul>
+<li>Now I see that the <code>openrxv-items-final</code> index has items, but there are still none in AReS Explorer UI!</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&amp;pretty'
+{
+  &quot;count&quot; : 99992,
+  &quot;_shards&quot; : {
+    &quot;total&quot; : 1,
+    &quot;successful&quot; : 1,
+    &quot;skipped&quot; : 0,
+    &quot;failed&quot; : 0
+  }
+}
+</code></pre><ul>
+<li>The api logs show this from last night after the harvesting:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">[Nest] 92   - 12/13/2020, 1:58:52 PM   [HarvesterService] Starting Harvest
+[Nest] 92   - 12/13/2020, 10:50:20 PM   [FetchConsumer] OnGlobalQueueDrained
+[Nest] 92   - 12/13/2020, 11:00:20 PM   [PluginsConsumer] OnGlobalQueueDrained
+[Nest] 92   - 12/13/2020, 11:00:20 PM   [HarvesterService] reindex function is called
+(node:92) UnhandledPromiseRejectionWarning: ResponseError: index_not_found_exception
+    at IncomingMessage.&lt;anonymous&gt; (/backend/node_modules/@elastic/elasticsearch/lib/Transport.js:232:25)
+    at IncomingMessage.emit (events.js:326:22)
+    at endReadableNT (_stream_readable.js:1223:12)
+    at processTicksAndRejections (internal/process/task_queues.js:84:21)
+</code></pre><ul>
+<li>But I&rsquo;m not sure why the frontend doesn&rsquo;t show any data despite there being documents in the index&hellip;</li>
+<li>I talked to Moayad and he reminded me that OpenRXV uses an alias to point to temp and final indexes, but the UI actually uses the <code>openrxv-items</code> index</li>
+<li>I cloned the <code>openrxv-items-final</code> index to <code>openrxv-items</code> index and now I see items in the explorer UI</li>
+<li>The PDF report was broken and I looked in the API logs and saw this:</li>
+</ul>
+<pre><code class="language-console" data-lang="console">(node:94) UnhandledPromiseRejectionWarning: Error: Error: Could not find soffice binary
+    at ExportService.downloadFile (/backend/dist/export/services/export/export.service.js:51:19)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)
+</code></pre><ul>
+<li>I installed <code>unoconv</code> in the backend api container and now it works&hellip; but I wonder why this changed&hellip;</li>
+<li>Skype with Abenet and Peter to discuss AReS that will be shown to ILRI scientists this week
+<ul>
+<li>Peter noticed that <a href="https://hdl.handle.net/10568/110133">this item</a> from the <a href="https://cgspace.cgiar.org/handle/10568/24450">ILRI policy and research briefs</a> collection is missing in AReS, despite it being added one month ago in CGSpace and me harvesting on AReS last night
+<ul>
+<li>The item appears fine in the REST API when I check the items in that collection</li>
+</ul>
+</li>
+<li>Peter also noticed that <a href="https://hdl.handle.net/10568/110447">this item</a> appears twice in AReS
+<ul>
+<li>The item is <em>not</em> duplicated on CGSpace or in the REST API</li>
+</ul>
+</li>
+<li>We noticed that there are 136 items in the ILRI policy and research briefs collection according to AReS, yet on CGSpace there are only 132
+<ul>
+<li>This is confirmed in the REST API (using <a href="https://github.com/davesnx/query-json">query-json</a>):</li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+<pre><code>$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&amp;limit=100&amp;offset=0' | json_pp &gt; /tmp/policy1.json
+$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&amp;limit=100&amp;offset=100' | json_pp &gt; /tmp/policy2.json
+$ query-json '.items | length' /tmp/policy1.json
+100
+$ query-json '.items | length' /tmp/policy2.json
+32
+</code></pre><ul>
+<li>I realized that the issue of missing/duplicate items in AReS might be because of this <a href="https://jira.lyrasis.org/browse/DS-3849">REST API bug that causes /items to return items in non-deterministic order</a></li>
+<li>I decided to cherry-pick the following two patches from DSpace 6.4 into our <code>6_x-prod</code> (6.3) branch:
+<ul>
+<li>High CPU usage when calling the collection_id/items REST endpoint
+<ul>
+<li>Jira: <a href="https://jira.lyrasis.org/browse/DS-4342">https://jira.lyrasis.org/browse/DS-4342</a></li>
+<li>c2e6719fa763e291b81b2d61da2f8c758fe38ff3</li>
+</ul>
+</li>
+<li>REST API items resource returns items in non-deterministic order
+<ul>
+<li>Jira: <a href="https://jira.lyrasis.org/browse/DS-3849">https://jira.lyrasis.org/browse/DS-3849</a></li>
+<li>2a2ea0cb5d03e6da9355a2eff12aad667e465433</li>
+</ul>
+</li>
+</ul>
+</li>
+<li>After deploying the REST API fixes I decided to harvest from AReS again to see if the missing and duplicate items get fixed
+<ul>
+<li>I made a backup of the current <code>openrxv-items-temp</code> index just in case:</li>
+</ul>
+</li>
+</ul>
+<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings?pretty&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-2020-12-14
+$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings?pretty&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
 </code></pre><!-- 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="2020-12-10T23:43:09+02:00" />
+<meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />



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+++ 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="2020-12-10T23:43:09+02:00" />
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@ -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="2020-12-10T23:43:09+02:00" />
+<meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />



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+++ 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="2020-12-10T23:43:09+02:00" />
+<meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />



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+++ 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/" />
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+++ 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="2020-12-10T23:43:09+02:00" />
+<meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />



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+++ 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="2020-12-10T23:43:09+02:00" />
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@ -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="2020-12-10T23:43:09+02:00" />
+<meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />



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@ -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="2020-12-10T23:43:09+02:00" />
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@ -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="2020-12-10T23:43:09+02:00" />
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--- a/docs/page/5/index.html
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@ -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="2020-12-10T23:43:09+02:00" />
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+++ 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="2020-12-10T23:43:09+02:00" />
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@ -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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