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Add notes for 2018-04-18

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Alan Orth 2018-04-18 12:38:12 +03:00
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content/posts/2018-04.md
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@ -332,3 +332,37 @@ Total time: 4 minutes 12 seconds
## 2018-04-16
- Communicate with Bioversity about their project to migrate their e-Library (Typo3) and Sci-lit databases to CGSpace
## 2018-04-18
- IWMI people are asking about building a search query that outputs RSS for their reports
- They want the same results as this Discovery query: https://cgspace.cgiar.org/discover?filtertype_1=dateAccessioned&filter_relational_operator_1=contains&filter_1=2018&submit_apply_filter=&query=&scope=10568%2F16814&rpp=100&sort_by=dc.date.issued_dt&order=desc
- They will need to use OpenSearch, but I can't remember all the parameters
- Apparently search sort options for OpenSearch are in `dspace.cfg`:
```
webui.itemlist.sort-option.1 = title:dc.title:title
webui.itemlist.sort-option.2 = dateissued:dc.date.issued:date
webui.itemlist.sort-option.3 = dateaccessioned:dc.date.accessioned:date
webui.itemlist.sort-option.4 = type:dc.type:text
```
- They want items by issue date, so we need to use sort option 2
- According to the DSpace Manual there are only the following parameters to OpenSearch: format, scope, rpp, start, and sort_by
- The OpenSearch `query` parameter expects a Discovery search filter that is defined in `dspace/config/spring/api/discovery.xml`
- So for IWMI they should be able to use something like this: https://cgspace.cgiar.org/open-search/discover?query=dateIssued:2018&scope=10568/16814&sort_by=2&order=DESC&format=rss
- There are also `rpp` (results per page) and `start` parameters but in my testing now on DSpace 5.5 they behave very strangely
- For example, set `rpp=1` and then check the results for `start` values of 0, 1, and 2 and they are all the same!
- If I have time I will check if this behavior persists on DSpace 6.x on the official DSpace demo and file a bug
- Also, the DSpace Manual as of 5.x has very poor documentation for OpenSearch
- They don't tell you to use Discovery search filters in the `query` (with format `query=dateIssued:2018`)
- They don't tell you that the sort options are actually defined in `dspace.cfg` (ie, you need to use `2` instead of `dc.date.issued_dt`)
- They are missing the `order` parameter (ASC vs DESC)
- I notice that DSpace Test has crashed again, due to memory:
```
# grep -c 'java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
178
```
- I will increase the JVM heap size from 5120M to 6144M, though we don't have much room left to grow as DSpace Test (linode19) is using a smaller instance size than CGSpace

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@ -45,7 +45,7 @@ Update GitHub wiki for documentation of maintenance tasks.
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@ -59,7 +59,7 @@ Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&r
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@ -45,7 +45,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
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@ -49,7 +49,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
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@ -53,7 +53,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
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@ -67,7 +67,7 @@ In this case the select query was showing 95 results before the update
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@ -61,7 +61,7 @@ $ git rebase -i dspace-5.5
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@ -53,7 +53,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=or
"/>
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@ -61,7 +61,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
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@ -45,7 +45,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
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@ -69,7 +69,7 @@ Another worrying error from dspace.log is:
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@ -45,7 +45,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
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@ -73,7 +73,7 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
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@ -77,7 +77,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
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@ -63,7 +63,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Th
"/>
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@ -29,7 +29,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2017"/>
<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="June, 2017"/>
<meta name="twitter:description" content="2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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@ -77,7 +77,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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@ -53,7 +53,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account
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@ -57,7 +57,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
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@ -77,7 +77,7 @@ COPY 54701
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@ -185,7 +185,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
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@ -47,7 +47,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-pl
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@ -41,7 +41,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
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@ -21,7 +21,7 @@ Catalina logs at least show some memory errors yesterday:
<meta property="article:published_time" content="2018-04-01T16:13:54&#43;02:00"/>
<meta property="article:modified_time" content="2018-04-15T11:18:17&#43;03:00"/>
<meta property="article:modified_time" content="2018-04-16T12:10:44&#43;03:00"/>
@ -43,7 +43,7 @@ Catalina logs at least show some memory errors yesterday:
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@ -53,9 +53,9 @@ Catalina logs at least show some memory errors yesterday:
"@type": "BlogPosting",
"headline": "April, 2018",
"url": "https://alanorth.github.io/cgspace-notes/2018-04/",
"wordCount": "1613",
"wordCount": "1912",
"datePublished": "2018-04-01T16:13:54&#43;02:00",
"dateModified": "2018-04-15T11:18:17&#43;03:00",
"dateModified": "2018-04-16T12:10:44&#43;03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -494,6 +494,44 @@ Total time: 4 minutes 12 seconds
<li>Communicate with Bioversity about their project to migrate their e-Library (Typo3) and Sci-lit databases to CGSpace</li>
</ul>
<h2 id="2018-04-18">2018-04-18</h2>
<ul>
<li>IWMI people are asking about building a search query that outputs RSS for their reports</li>
<li>They want the same results as this Discovery query: <a href="https://cgspace.cgiar.org/discover?filtertype_1=dateAccessioned&amp;filter_relational_operator_1=contains&amp;filter_1=2018&amp;submit_apply_filter=&amp;query=&amp;scope=10568%2F16814&amp;rpp=100&amp;sort_by=dc.date.issued_dt&amp;order=desc">https://cgspace.cgiar.org/discover?filtertype_1=dateAccessioned&amp;filter_relational_operator_1=contains&amp;filter_1=2018&amp;submit_apply_filter=&amp;query=&amp;scope=10568%2F16814&amp;rpp=100&amp;sort_by=dc.date.issued_dt&amp;order=desc</a></li>
<li>They will need to use OpenSearch, but I can&rsquo;t remember all the parameters</li>
<li>Apparently search sort options for OpenSearch are in <code>dspace.cfg</code>:</li>
</ul>
<pre><code>webui.itemlist.sort-option.1 = title:dc.title:title
webui.itemlist.sort-option.2 = dateissued:dc.date.issued:date
webui.itemlist.sort-option.3 = dateaccessioned:dc.date.accessioned:date
webui.itemlist.sort-option.4 = type:dc.type:text
</code></pre>
<ul>
<li>They want items by issue date, so we need to use sort option 2</li>
<li>According to the DSpace Manual there are only the following parameters to OpenSearch: format, scope, rpp, start, and sort_by</li>
<li>The OpenSearch <code>query</code> parameter expects a Discovery search filter that is defined in <code>dspace/config/spring/api/discovery.xml</code></li>
<li>So for IWMI they should be able to use something like this: <a href="https://cgspace.cgiar.org/open-search/discover?query=dateIssued:2018&amp;scope=10568/16814&amp;sort_by=2&amp;order=DESC&amp;format=rss">https://cgspace.cgiar.org/open-search/discover?query=dateIssued:2018&amp;scope=10568/16814&amp;sort_by=2&amp;order=DESC&amp;format=rss</a></li>
<li>There are also <code>rpp</code> (results per page) and <code>start</code> parameters but in my testing now on DSpace 5.5 they behave very strangely</li>
<li>For example, set <code>rpp=1</code> and then check the results for <code>start</code> values of 0, 1, and 2 and they are all the same!</li>
<li>If I have time I will check if this behavior persists on DSpace 6.x on the official DSpace demo and file a bug</li>
<li>Also, the DSpace Manual as of 5.x has very poor documentation for OpenSearch</li>
<li>They don&rsquo;t tell you to use Discovery search filters in the <code>query</code> (with format <code>query=dateIssued:2018</code>)</li>
<li>They don&rsquo;t tell you that the sort options are actually defined in <code>dspace.cfg</code> (ie, you need to use <code>2</code> instead of <code>dc.date.issued_dt</code>)</li>
<li>They are missing the <code>order</code> parameter (ASC vs DESC)</li>
<li>I notice that DSpace Test has crashed again, due to memory:</li>
</ul>
<pre><code># grep -c 'java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
178
</code></pre>
<ul>
<li>I will increase the JVM heap size from 5120M to 6144M, though we don&rsquo;t have much room left to grow as DSpace Test (linode19) is using a smaller instance size than CGSpace</li>
</ul>

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@ -4,7 +4,7 @@
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<lastmod>2018-04-16T12:10:44+03:00</lastmod>
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@ -159,7 +159,7 @@
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<lastmod>2018-04-15T11:18:17+03:00</lastmod>
<lastmod>2018-04-16T12:10:44+03:00</lastmod>
<priority>0</priority>
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@ -170,7 +170,7 @@
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