I’ll update the DSpace role in our Ansible infrastructure playbooks and run the updated playbooks on CGSpace and DSpace Test
Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month
I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:
I’ll update the DSpace role in our Ansible infrastructure playbooks and run the updated playbooks on CGSpace and DSpace Test
Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month
I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:
<li>I’ll update the DSpace role in our <ahref="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li>
<li>Also, I’ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month</li>
<li>I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:</li>
<pre><code>02-Sep-2018 11:18:52.678 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener]
java.lang.RuntimeException: Failure during filter init: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/dspacetest.cgiar.org/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#4c5d5a2' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#4c5d5a2': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)}
at org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener.contextInitialized(DSpaceKernelServletContextListener.java:92)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4776)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5240)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:629)
at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1838)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/dspacetest.cgiar.org/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#4c5d5a2' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#4c5d5a2': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations:
<li>I’m looking over the latest round of IITA records from Sisay: <ahref="https://dspacetest.cgiar.org/handle/10568/104230">Mercy1806_August_29</a>
<li>Several metadata fields had values with newlines in them (even in some titles!), which I fixed by trimming the consecutive whitespaces in Open Refine</li>
<li>I got all items that were from 2011 and onwards using a custom facet with this GREL on the <code>dc.date.issued</code> column: <code>isNotNull(value.match(/201[1-8].*/))</code> and then blanking their CRPs</li>
<li>Some inconsistencies in <code>cg.subject.iita</code> like COWPEA and COWPEAS, and YAM and YAMS, etc, as well as some spelling mistakes like IMPACT ASSESSMENTN</li>
<li>Some values in the <code>dc.identifier.isbn</code> are actually ISSNs so I moved them to the <code>dc.identifier.issn</code> column</li>
<li>I found one invalid ISSN using a custom text facet with the regex from the <ahref="https://en.wikipedia.org/wiki/International_Standard_Serial_Number#Code_format">ISSN page on Wikipedia</a>: <code>isNotBlank(value.match(/^\d{4}-\d{3}[\dxX]$/))</code></li>
<li>One invalid value for <code>dc.type</code></li>
<li>Abenet says she hasn’t received any more subscription emails from the CUA module since she unsubscribed yesterday, so I think we don’t need create an issue on Atmire’s bug tracker anymore</li>
<li>Move some top-level CRP communities to be below the new <ahref="https://cgspace.cgiar.org/handle/10568/97114">CGIAR Research Programs and Platforms</a> community:</li>
<li>Start working on adding metadata for access and usage rights that we started earlier in 2018 (and also in 2017)</li>
<li>The current <code>cg.identifier.status</code> field will become “Access rights” and <code>dc.rights</code> will become “Usage rights”</li>
<li>I have some work in progress on the <ahref="https://github.com/alanorth/DSpace/tree/5_x-rights"><code>5_x-rights</code> branch</a></li>
<li>Linode said that CGSpace (linode18) had a high CPU load earlier today</li>
<li>I added <code>.*crawl.*</code> to the Tomcat Session Crawler Manager Valve, so I’m not sure why the bot is creating so many sessions…</li>
<li>Peter was communicating with Altmetric about the OAI mapping issue for item <ahref="https://cgspace.cgiar.org/oai/request?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:cgspace.cgiar.org:10568/82810">10568/82810</a> again</li>
<li>Altmetric said it was somehow related to the OAI <code>dateStamp</code> not getting updated when the mappings changed, but I said that back in <ahref="/cgspace-notes/2018-07/">2018-07</a> when this happened it was because the OAI was actually just not reflecting all the item’s mappings</li>
<li>The <code>dateStamp</code> is most probably only updated when the item’s metadata changes, not its mappings, so if Altmetric is relying on that we’re in a tricky spot</li>
<li>We need to make sure that our OAI isn’t publicizing stale data… I was going to post something on the dspace-tech mailing list, but never did</li>
<li>I said no, but that we might be able to piggyback on the Atmire statlet REST API</li>
<li>For example, when you expand the “statlet” at the bottom of an item like <ahref="https://cgspace.cgiar.org/handle/10568/97103">10568/97103</a> you can see the following request in the browser console:</li>
<li>I had a quick look at the DSpace 5.x manual and it doesn’t not seem that this is possible (you can only add metadata)</li>
<li>Testing the new LDAP server the CGNET says will be replacing the old one, it doesn’t seem that they are using the global catalog on port 3269 anymore, now only 636 is open</li>
<li>I did a clean deploy of DSpace 5.8 on Ubuntu 18.04 with some stripped down Tomcat 8 configuration and actually managed to get it up and running without the autowire errors that I had previously experienced</li>
<li>I realized that it always works on my local machine with Tomcat 8.5.x, but not when I do the deployment from Ansible in Ubuntu 18.04</li>
<li>So there must be something in my Tomcat 8 <code>server.xml</code> template</li>
<li>Add the DSpace build.properties as a template into my <ahref="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> for configuring DSpace machines</li>
<li>One stupid thing there is that I add all the variables in a private vars file, which is apparently higher precedence than host vars, meaning that I can’t override them (like SMTP server) on a per-host basis</li>
<li>Discuss access and usage rights with Peter</li>
<li>I suggested that we leave access rights (<code>cg.identifier.access</code>) as it is now, with “Open Access” or “Limited Access”, and then simply re-brand that as “Access rights” in the UIs and relevant drop downs</li>
<li>Then we continue as planned to add <code>dc.rights</code> as “Usage rights”</li>
<li>Need to double check the new <ahref="https://cgspace.cgiar.org/handle/10568/97114">CRP community</a> to see why the collection counts aren’t updated after we moved the communities there last week
<li>I want to explore creating a thin API to make the item view and download stats available from Solr so CodeObia can use them in the AReS explorer</li>
<li>The id in the Solr query is the item’s database id (get it from the REST API or something)</li>
<li>Next, I adopted a query to get the downloads and it shows 889, which is similar to the number Atmire’s statlet shows, though the query logic here is confusing:</li>
<li>According to the <ahref="https://wiki.apache.org/solr/SolrQuerySyntax">SolrQuerySyntax</a> page on the Apache wiki, the <code>[* TO *]</code> syntax just selects a range (in this case all values for a field)</li>
<li><code>type:0</code> is for bitstreams according to the DSpace Solr documentation</li>
<li><code>-(bundleName:[*+TO+*]-bundleName:ORIGINAL)</code> seems to be a <ahref="https://wiki.apache.org/solr/NegativeQueryProblems">negative query starting with all documents</a>, subtracting those with <code>bundleName:ORIGINAL</code>, and then negating the whole thing… meaning only documents from <code>bundleName:ORIGINAL</code>?</li>
<li>Also, Solr’s <code>fq</code> is similar to the regular <code>q</code> query parameter, but it is considered for the Solr query cache so it should be faster for multiple queries</li>
<li>I managed to create a simple proof of concept REST API to expose item view and download statistics: <ahref="https://github.com/alanorth/cgspace-statistics-api">cgspace-statistics-api</a></li>
<li>It uses the Python-based <ahref="https://falcon.readthedocs.io">Falcon</a> web framework and talks to Solr directly using the <ahref="https://github.com/moonlitesolutions/SolrClient">SolrClient</a> library (which seems to have issues in Python 3.7 currently)</li>
<li>The numbers are different than those that come from Atmire’s statlets for some reason, but as I’m querying Solr directly, I have no idea where their numbers come from!</li>
<li>I emailed Jane Poole to ask if there is some money we can use from the Big Data Platform (BDP) to fund the purchase of some Atmire credits for CGSpace</li>
<li>I learned that there is an efficient way to do <ahref="http://yonik.com/solr/paging-and-deep-paging/">“deep paging” in large Solr results sets by using <code>cursorMark</code></a>, but it doesn’t work with faceting</li>
<li>Contact Atmire to ask how we can buy more credits for future development (<ahref="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=644">#644</a>)</li>
<li>I researched the Solr <code>filterCache</code> size and I found out that the formula for calculating the potential memory use of <strong>each entry</strong> in the cache is:</li>
<li>So I think we can forget about tuning this for now!</li>
<li><ahref="http://lucene.472066.n3.nabble.com/Calculating-filterCache-size-td4142526.html">Discussion on the mailing list about <code>filterCache</code> size</a></li>
<li><ahref="https://docs.google.com/document/d/1vl-nmlprSULvNZKQNrqp65eLnLhG9s_ydXQtg9iML10/edit">Article discussing testing methodology for different <code>filterCache</code> sizes</a></li>
<li>Discuss Handle links on Twitter with IWMI</li>
<li>I see that there was a nice optimization to the ImageMagick PDF CMYK detection in the upstream <code>dspace-5_x</code> branch: <ahref="https://github.com/DSpace/DSpace/pull/2204">DS-3664</a></li>
<li>The fix will go into DSpace 5.10, and we are currently on DSpace 5.8 but I think I’ll cherry-pick that fix into our <code>5_x-prod</code> branch:
<li>I think it would also be nice to cherry-pick the fixes for <ahref="https://github.com/DSpace/DSpace/pull/2020">DS-3883</a>, which is related to optimizing the XMLUI item display of items with many bitstreams
<li>I did more work on my <ahref="https://github.com/alanorth/cgspace-statistics-api">cgspace-statistics-api</a>, fixing some item view counts and adding indexing via SQLite (I’m trying to avoid having to set up <em>yet another</em> database, user, password, etc) during deployment</li>
<li>It appears SQLite doesn’t support <code>FULL OUTER JOIN</code> so some people on StackOverflow have emulated it with <code>LEFT JOIN</code> and <code>UNION</code>:</li>
<li>Note the special <code>excluded.views</code> form! See <ahref="https://www.sqlite.org/lang_UPSERT.html">SQLite’s lang_UPSERT documentation</a></li>
<li>Oh nice, I finally finished the Falcon API route to page through all the results using SQLite’s amazing <code>LIMIT</code> and <code>OFFSET</code> support</li>
<li>But when I deployed it on my Ubuntu 16.04 environment I realized Ubuntu’s SQLite is old and doesn’t support <code>UPSERT</code>, so my indexing doesn’t work…</li>
<li>Apparently <code>UPSERT</code> came in SQLite 3.24.0 (2018-06-04), and Ubuntu 16.04 has 3.11.0</li>
<li>Ok this is hilarious, I manually downloaded the <ahref="https://packages.ubuntu.com/cosmic/libsqlite3-0">libsqlite3 3.24.0 deb from Ubuntu 18.10 “cosmic”</a> and installed it in Ubnutu 16.04 and now the Python <code>indexer.py</code> works</li>
<li>This is definitely a dirty hack, but the list of packages we use that depend on <code>libsqlite3-0</code> in Ubuntu 16.04 are actually pretty few:</li>
<li>Or maybe I should just bite the bullet and migrate this to PostgreSQL, as it <ahref="https://wiki.postgresql.org/wiki/UPSERT">supports <code>UPSERT</code> since version 9.5</a> and also seems to have my new favorite <code>LIMIT</code> and <code>OFFSET</code></li>
<li>I changed the syntax of the SQLite stuff and PostgreSQL is working flawlessly with psycopg2… hmmm.</li>
<li>For reference, creating a PostgreSQL database for testing this locally (though <code>indexer.py</code> will create the table):</li>
<li>I need to inspect the <code>id</code> values that are returned for views and cross check them with the <code>owningItem</code> values for bitstream downloads…</li>
<li>Also, I could try to check all IDs against the items table to see if they are actually items (perhaps the Solr <code>id</code> field doesn’t correspond with <em>actual</em> DSpace items?)</li>
<li>I want to purge the bot hits from the Solr statistics core, as I am now realizing that I don’t give a shit about tens of millions of hits by Google and Bing indexing my shit every day (at least not in Solr!)</li>
<li>CGSpace’s Solr core has 150,000,000 documents in it… and it’s still pretty fast to query, but it’s really a maintenance and backup burden</li>
<li>DSpace Test currently has about 2,000,000 documents with <code>isBot:true</code> in its Solr statistics core, and the size on disk is 2GB (it’s not much, but I have to test this somewhere!)</li>
<li>According to the <ahref="https://wiki.duraspace.org/display/DSDOC5x/SOLR+Statistics+Maintenance">DSpace 5.x Solr documentation</a> I can use <code>dspace stats-util -f</code>, so let’s try it:</li>
<li>I was just writing a message to the dspace-tech mailing list and then I decided to check the number of bot view events on DSpace Test again, and now it’s 201 instead of 2,000,000, and statistics core is only 30MB now!</li>
<li>I will set the <code>logBots = false</code> property in <code>dspace/config/modules/usage-statistics.cfg</code> on DSpace Test and check if the number of <code>isBot:true</code> events goes up any more…</li>
<li>I restarted the server with <code>logBots = false</code> and after it came back up I see 266 events with <code>isBots:true</code> (maybe they were buffered)… I will check again tomorrow</li>
<li>After a few hours I see there are still only 266 view events with <code>isBot:true</code> on DSpace Test’s Solr statistics core, so I’m definitely going to deploy this on CGSpace soon</li>
<li>Also, CGSpace currently has 60,089,394 view events with <code>isBot:true</code> in it’s Solr statistics core and it is 124GB!</li>
<li>Amazing! After running <code>dspace stats-util -f</code> on CGSpace the Solr statistics core went from 124GB to 60GB, and now there are only 700 events with <code>isBot:true</code> so I should really disable logging of bot events!</li>
<li>I made (and merged) a pull request to disable bot logging on the <code>5_x-prod</code> branch (<ahref="https://github.com/ilri/DSpace/pull/387">#387</a>)</li>
<li>The first thing I learned is that shit tons of IPs in Russia, Ukraine, Ireland, Brazil, Portugal, the US, Canada, etc are pretending to be “Googlebot”…</li>
<li>According to the <ahref="https://support.google.com/webmasters/answer/80553">Googlebot FAQ</a> the domain name in the reverse DNS lookup should contain either <code>googlebot.com</code> or <code>google.com</code></li>
<li>In Solr this appears to be an appropriate query that I can maybe use later (returns 81,000 documents):</li>
<li>Basically, it turns out that using <code>facet.mincount=1</code> is really beneficial for me because it reduces the size of the Solr result set, reduces the amount of data we need to ingest into PostgreSQL, and the API returns HTTP 404 Not Found for items without views or downloads anyways</li>
<li>I deployed the new version on CGSpace and now it looks pretty good!</li>
<li>I did a batch replacement of the access rights with my <ahref="https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897">fix-metadata-values.py</a> script on DSpace Test:</li>
<li>This changes “Open Access” to “Unrestricted Access” and “Limited Access” to “Restricted Access”</li>
<li>After that I did a full Discovery reindex:</li>
<li>I told Peter it’s better to do the access rights before the usage rights because the git branches are conflicting with each other and it’s actually a pain in the ass to keep changing the values as we discuss, rebase, merge, fix conflicts…</li>
<li>It’s pretty confusing, because until recently they were entering issue dates as only YYYY (like 2018) and their feeds were all showing items in the wrong order</li>
<li>I’m not exactly sure what their problem now is, though (confusing)</li>
<li>I updated the dspace-statistiscs-api to use psycopg2’s <code>execute_values()</code> to insert batches of 100 values into PostgreSQL instead of doing every insert individually</li>
<li>On CGSpace this reduces the total run time of <code>indexer.py</code> from 432 seconds to 400 seconds (most of the time is actually spent in getting the data from Solr though)</li>
<li>I will add their IPs to the list of bad bots in nginx so we can add a “bot” user agent to them and let Tomcat’s Crawler Session Manager Valve handle them</li>
<li>I merged some changes to author affiliations from Sisay as well as some corrections to organizational names using smart quotes like <code>Université d’Abomey Calavi</code> (<ahref="https://github.com/ilri/DSpace/pull/388">#388</a>)</li>
<li>Peter sent me a list of 43 author names to fix, but it had some encoding errors like <code>Belalcázar, John</code> like usual (I will tell him to stop trying to export as UTF-8 because it never seems to work)</li>
<li>I did batch replaces for both on CGSpace with my <ahref="https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897">fix-metadata-values.py</a> script:</li>
<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/2018-09-30-languages.csv with csv;
<pre><code>dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='Other';
DELETE 6
dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='other';
<pre><code>dspace=# SELECT resource_id FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
dspace=# SELECT handle,item_id FROM item, handle WHERE handle.resource_type_id=2 AND handle.resource_id = item.item_id AND handle.resource_id in (94530, 94529);
<pre><code>dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
<pre><code>dspace=# SELECT resource_id FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jn';
dspace=# SELECT handle,item_id FROM item, handle WHERE handle.resource_type_id=2 AND handle.resource_id = item.item_id AND handle.resource_id in (94001, 94003);
<pre><code>DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
UPDATE metadatavalue SET text_value='fr' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='fn';
UPDATE metadatavalue SET text_value='hi' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='in';
UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='Ja';
UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jn';
UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jp';
<li>Then there are 12 items with <code>en|hi</code>, but they were all in one collection so I just exported it as a CSV and then re-imported the corrected metadata</li>
