<metaproperty="og:description"content="2016-11-01 Add dc.type to the output options for Atmire’s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com."/>
<metaitemprop="description"content="2016-11-01 Add dc.type to the output options for Atmire’s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com.">
<metaname="twitter:description"content="2016-11-01 Add dc.type to the output options for Atmire’s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com."/>
<li>Add <code>dc.type</code> to the output options for Atmire’s Listings and Reports module (<ahref="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
<li>Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (<ahref="https://github.com/ilri/DSpace/issues/63">#63</a>)</li>
<li>After re-deploying and re-indexing I didn’t see the same issue, and the indexing completed in 85 minutes, which is about how long it is supposed to take</li>
<li>I noticed some weird CRPs in the database, and they don’t show up in Discovery for some reason, perhaps the <code>:</code></li>
<li>I’ll export these and fix them in batch:</li>
</ul>
<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=230 group by text_value order by count desc) to /tmp/crp.csv with csv;
<li>Add <code>AMR</code> to ILRI subjects and remove one duplicate instance of IITA in author affiliations controlled vocabulary (<ahref="https://github.com/ilri/DSpace/pull/288">#288</a>)</li>
<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=3 group by text_value order by count desc limit 210) to /tmp/210-authors.csv with csv;
<li>CGSpace crashed so I quickly ran system updates, applied one or two of the waiting changes from the <code>5_x-prod</code> branch, and rebooted the server</li>
<li>The error was <code>Timeout waiting for idle object</code> but I haven’t looked into the Tomcat logs to see what happened</li>
<li>Also, I ran the corrections for CRPs from earlier this week</li>
<li>But the results are deceiving because metadata fields can have text languages and your query must match exactly!</li>
</ul>
<pre><code>dspace=# select distinct text_value, text_lang from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS';
text_value | text_lang
------------+-----------
SEEDS |
SEEDS |
SEEDS | en_US
(3 rows)
</code></pre>
<ul>
<li>So basically, the text language here could be null, blank, or en_US</li>
<li>To query metadata with these properties, you can do:</li>
<li>The results (55+34=89) don’t seem to match those from the database:</li>
</ul>
<pre><code>dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang is null;
count
-------
15
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang='';
count
-------
4
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang='en_US';
count
-------
66
</code></pre>
<ul>
<li>So, querying from the API I get 55 + 34 = 89 results, but the database actually only has 85…</li>
<li>And the <code>find-by-metadata-field</code> endpoint doesn’t seem to have a way to get all items with the field, or a wildcard value</li>
<li>I’ll ask a question on the dspace-tech mailing list</li>
<li>And speaking of <code>text_lang</code>, this is interesting:</li>
</ul>
<pre><code>dspacetest=# select distinct text_lang from metadatavalue where resource_type_id=2;
<pre><code>dspace=# \copy (select distinct text_lang, count(*) from metadatavalue where resource_type_id=2 group by text_lang order by count desc) to /tmp/text-langs.csv with csv;
COPY 14
</code></pre>
<ul>
<li>Perhaps we need to fix them all in batch, or experiment with fixing only certain metadatavalues:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_lang='en_US' where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS';
<li>The <code>fix-metadata.py</code> script I have is meant for specific metadata values, so if I want to update some <code>text_lang</code> values I should just do it directly in the database</li>
<li>For example, on a limited set:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_lang=NULL where resource_type_id=2 and metadata_field_id=203 and text_value='LIVESTOCK' and text_lang='';
UPDATE 420
</code></pre>
<ul>
<li>And assuming I want to do it for all fields:</li>
</ul>
<pre><code>dspacetest=# update metadatavalue set text_lang=NULL where resource_type_id=2 and text_lang='';
UPDATE 183726
</code></pre>
<ul>
<li>After that restarted Tomcat and PostgreSQL (because I’m superstitious about caches) and now I see the following in REST API query:</li>
<li>I applied Atmire’s suggestions to fix Listings and Reports for DSpace 5.5 and now it works</li>
<li>There were some issues with the <code>dspace/modules/jspui/pom.xml</code>, which is annoying because all I did was rebase our working 5.1 code on top of 5.5, meaning Atmire’s installation procedure must have changed</li>
<li>So there is apparently this Tomcat native way to limit web crawlers to one session: <ahref="https://tomcat.apache.org/tomcat-7.0-doc/config/valve.html#Crawler_Session_Manager_Valve">Crawler Session Manager</a></li>
<li>After adding that to <code>server.xml</code> bots matching the pattern in the configuration will all use ONE session, just like normal users:</li>
</ul>
<pre><code>$ http --print h https://dspacetest.cgiar.org 'User-Agent:Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html)'
