mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-24 23:50:17 +01:00
Update notes for 2018-05-15
This commit is contained in:
parent
837d07d3a7
commit
8cb0ad095b
GPG Key ID:
0FB860CC9C45B1B9
@ -175,6 +175,7 @@ $ lein run /tmp/crps.csv id
|
||||
## 2018-05-14
|
||||
|
||||
- Send a message to the OpenRefine mailing list about the bug with reconciling multi-value cells
|
||||
- Help Silvia Alonso get a list of all her publications since 2013 from Listings and Reports
|
||||
|
||||
## 2018-05-15
|
||||
|
||||
@ -200,3 +201,52 @@ return "blank"
|
||||
- More information and good examples here: https://programminghistorian.org/lessons/fetch-and-parse-data-with-openrefine
|
||||
- Finish looking at the 2,640 CIFOR records on DSpace Test ([10568/92904](https://dspacetest.cgiar.org/handle/10568/92904)), cleaning up authors and adding collection mappings
|
||||
- They can now be moved to CGSpace as far as I'm concerned, but I don't know if Sisay will do it or me
|
||||
- I was checking the CIFOR data for duplicates using Atmire's Metadata Quality Module (and found some duplicates actually), but then DSpace died...
|
||||
- I didn't see anything in the Tomcat, DSpace, or Solr logs, but I saw this in `dmest -T`:
|
||||
|
||||
```
|
||||
[Tue May 15 12:10:01 2018] Out of memory: Kill process 3763 (java) score 706 or sacrifice child
|
||||
[Tue May 15 12:10:01 2018] Killed process 3763 (java) total-vm:14667688kB, anon-rss:5705268kB, file-rss:0kB, shmem-rss:0kB
|
||||
[Tue May 15 12:10:01 2018] oom_reaper: reaped process 3763 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
|
||||
```
|
||||
|
||||
- So the Linux kernel killed Java...
|
||||
- Maria from Bioversity mailed to say she got an error while submitting an item on CGSpace:
|
||||
|
||||
```
|
||||
Unable to load Submission Information, since WorkspaceID (ID:S96060) is not a valid in-process submission
|
||||
```
|
||||
|
||||
- Looking in the DSpace log I see something related:
|
||||
|
||||
```
|
||||
2018-05-15 12:35:30,858 INFO org.dspace.submit.step.CompleteStep @ m.garruccio@cgiar.org:session_id=8AC4499945F38B45EF7A1226E3042DAE:submission_complete:Completed submission with id=96060
|
||||
```
|
||||
|
||||
- So I'm not sure...
|
||||
- I finally figured out how to get OpenRefine to reconcile values from Solr via [conciliator](https://github.com/codeforkjeff/conciliator):
|
||||
- The trick was to use a more appropriate Solr fieldType `text_en` instead of `text_general` so that more terms match, for example uppercase and lower case:
|
||||
|
||||
```
|
||||
$ ./bin/solr start
|
||||
$ ./bin/solr create_core -c countries
|
||||
$ ./bin/post -c countries ~/src/git/DSpace/2018-05-10-countries.csv
|
||||
$ curl -X POST -H 'Content-type:application/json' --data-binary '{"add-field": {"name":"country", "type":"text_en", "multiValued":false, "stored":true}}' http://localhost:8983/solr/countries/schema
|
||||
```
|
||||
|
||||
- It still doesn't catch simple mistakes like "ALBANI" or "AL BANIA" for "ALBANIA", and it doesn't return scores, so I have to select matches manually:
|
||||
|
||||
|
||||
|
||||
- I should probably make a general copy field and set it to be the default search field, like DSpace's search core does (see schema.xml):
|
||||
|
||||
```
|
||||
<defaultSearchField>search_text</defaultSearchField>
|
||||
...
|
||||
<copyField source="*" dest="search_text"/>
|
||||
```
|
||||
|
||||
- Actually, I wonder how much of their schema I could just copy...
|
||||
- Apparently the default search field is the `df` parameter and you could technically just add it to the query string, so no need to bother with that in the schema now
|
||||
- I copied over the DSpace `search_text` field type from the DSpace Solr config (had to remove some properties so Solr would start) but it doesn't seem to be any better at matching than the `text_en` type
|
||||
- I think I need to focus on trying to return scores with conciliator
|
||||
|
||||
@ -27,7 +27,7 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked
|
||||
|
||||
<meta property="article:published_time" content="2018-05-01T16:43:54+03:00"/>
|
||||
|
||||
<meta property="article:modified_time" content="2018-05-13T18:30:25+03:00"/>
|
||||
<meta property="article:modified_time" content="2018-05-15T13:25:03+03:00"/>
|
||||
|
||||
|
||||
|
||||
@ -65,9 +65,9 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked
|
||||
"@type": "BlogPosting",
|
||||
"headline": "May, 2018",
|
||||
"url": "https://alanorth.github.io/cgspace-notes/2018-05/",
|
||||
"wordCount": "1441",
|
||||
"wordCount": "1811",
|
||||
"datePublished": "2018-05-01T16:43:54+03:00",
|
||||
"dateModified": "2018-05-13T18:30:25+03:00",
|
||||
"dateModified": "2018-05-15T13:25:03+03:00",
|
||||
"author": {
|
||||
"@type": "Person",
|
||||
"name": "Alan Orth"
|
||||
@ -340,6 +340,7 @@ Livestock and Fish
|
||||
|
||||
<ul>
|
||||
<li>Send a message to the OpenRefine mailing list about the bug with reconciling multi-value cells</li>
|
||||
<li>Help Silvia Alonso get a list of all her publications since 2013 from Listings and Reports</li>
|
||||
</ul>
|
||||
|
||||
<h2 id="2018-05-15">2018-05-15</h2>
|
||||
@ -368,6 +369,62 @@ return "blank"
|
||||
<li>More information and good examples here: <a href="https://programminghistorian.org/lessons/fetch-and-parse-data-with-openrefine">https://programminghistorian.org/lessons/fetch-and-parse-data-with-openrefine</a></li>
|
||||
<li>Finish looking at the 2,640 CIFOR records on DSpace Test (<a href="https://dspacetest.cgiar.org/handle/10568/92904"><sup>10568</sup>⁄<sub>92904</sub></a>), cleaning up authors and adding collection mappings</li>
|
||||
<li>They can now be moved to CGSpace as far as I’m concerned, but I don’t know if Sisay will do it or me</li>
|
||||
<li>I was checking the CIFOR data for duplicates using Atmire’s Metadata Quality Module (and found some duplicates actually), but then DSpace died…</li>
|
||||
<li>I didn’t see anything in the Tomcat, DSpace, or Solr logs, but I saw this in <code>dmest -T</code>:</li>
|
||||
</ul>
|
||||
|
||||
<pre><code>[Tue May 15 12:10:01 2018] Out of memory: Kill process 3763 (java) score 706 or sacrifice child
|
||||
[Tue May 15 12:10:01 2018] Killed process 3763 (java) total-vm:14667688kB, anon-rss:5705268kB, file-rss:0kB, shmem-rss:0kB
|
||||
[Tue May 15 12:10:01 2018] oom_reaper: reaped process 3763 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
|
||||
</code></pre>
|
||||
|
||||
<ul>
|
||||
<li>So the Linux kernel killed Java…</li>
|
||||
<li>Maria from Bioversity mailed to say she got an error while submitting an item on CGSpace:</li>
|
||||
</ul>
|
||||
|
||||
<pre><code>Unable to load Submission Information, since WorkspaceID (ID:S96060) is not a valid in-process submission
|
||||
</code></pre>
|
||||
|
||||
<ul>
|
||||
<li>Looking in the DSpace log I see something related:</li>
|
||||
</ul>
|
||||
|
||||
<pre><code>2018-05-15 12:35:30,858 INFO org.dspace.submit.step.CompleteStep @ m.garruccio@cgiar.org:session_id=8AC4499945F38B45EF7A1226E3042DAE:submission_complete:Completed submission with id=96060
|
||||
</code></pre>
|
||||
|
||||
<ul>
|
||||
<li>So I’m not sure…</li>
|
||||
<li>I finally figured out how to get OpenRefine to reconcile values from Solr via <a href="https://github.com/codeforkjeff/conciliator">conciliator</a>:</li>
|
||||
<li>The trick was to use a more appropriate Solr fieldType <code>text_en</code> instead of <code>text_general</code> so that more terms match, for example uppercase and lower case:</li>
|
||||
</ul>
|
||||
|
||||
<pre><code>$ ./bin/solr start
|
||||
$ ./bin/solr create_core -c countries
|
||||
$ ./bin/post -c countries ~/src/git/DSpace/2018-05-10-countries.csv
|
||||
$ curl -X POST -H 'Content-type:application/json' --data-binary '{"add-field": {"name":"country", "type":"text_en", "multiValued":false, "stored":true}}' http://localhost:8983/solr/countries/schema
|
||||
</code></pre>
|
||||
|
||||
<ul>
|
||||
<li>It still doesn’t catch simple mistakes like “ALBANI” or “AL BANIA” for “ALBANIA”, and it doesn’t return scores, so I have to select matches manually:</li>
|
||||
</ul>
|
||||
|
||||
<p><img src="/cgspace-notes/2018/05/openrefine-solr-conciliator.png" alt="OpenRefine reconciling countries from local Solr" /></p>
|
||||
|
||||
<ul>
|
||||
<li>I should probably make a general copy field and set it to be the default search field, like DSpace’s search core does (see schema.xml):</li>
|
||||
</ul>
|
||||
|
||||
<pre><code><defaultSearchField>search_text</defaultSearchField>
|
||||
...
|
||||
<copyField source="*" dest="search_text"/>
|
||||
</code></pre>
|
||||
|
||||
<ul>
|
||||
<li>Actually, I wonder how much of their schema I could just copy…</li>
|
||||
<li>Apparently the default search field is the <code>df</code> parameter and you could technically just add it to the query string, so no need to bother with that in the schema now</li>
|
||||
<li>I copied over the DSpace <code>search_text</code> field type from the DSpace Solr config (had to remove some properties so Solr would start) but it doesn’t seem to be any better at matching than the <code>text_en</code> type</li>
|
||||
<li>I think I need to focus on trying to return scores with conciliator</li>
|
||||
</ul>
|
||||
|
||||
|
||||
|
||||
BIN
docs/2018/05/openrefine-solr-conciliator.png
Normal file
BIN
docs/2018/05/openrefine-solr-conciliator.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 128 KiB |
@ -4,7 +4,7 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2018-05/</loc>
|
||||
<lastmod>2018-05-13T18:30:25+03:00</lastmod>
|
||||
<lastmod>2018-05-15T13:25:03+03:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
@ -164,7 +164,7 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2018-05-13T18:30:25+03:00</lastmod>
|
||||
<lastmod>2018-05-15T13:25:03+03:00</lastmod>
|
||||
<priority>0</priority>
|
||||
</url>
|
||||
|
||||
@ -175,7 +175,7 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
|
||||
<lastmod>2018-05-13T18:30:25+03:00</lastmod>
|
||||
<lastmod>2018-05-15T13:25:03+03:00</lastmod>
|
||||
<priority>0</priority>
|
||||
</url>
|
||||
|
||||
@ -187,13 +187,13 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||
<lastmod>2018-05-13T18:30:25+03:00</lastmod>
|
||||
<lastmod>2018-05-15T13:25:03+03:00</lastmod>
|
||||
<priority>0</priority>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
|
||||
<lastmod>2018-05-13T18:30:25+03:00</lastmod>
|
||||
<lastmod>2018-05-15T13:25:03+03:00</lastmod>
|
||||
<priority>0</priority>
|
||||
</url>
|
||||
|
||||
|
||||
BIN
static/2018/05/openrefine-solr-conciliator.png
Normal file
BIN
static/2018/05/openrefine-solr-conciliator.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 128 KiB |
Loading…
Reference in New Issue
Block a user