<li>Add tests for the new <code>/items</code> POST handlers to the DSpace 6.x branch of my <ahref="https://github.com/ilri/dspace-statistics-api/tree/v6_x">dspace-statistics-api</a>
<ul>
<li>It took a bit of extra work because I had to learn how to mock the responses for when Solr is not available</li>
<li>Tag and release version 1.3.0 on GitHub: <ahref="https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0">https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0</a></li>
</ul>
</li>
<li>Trying to test the changes Atmire sent last week but I had to re-create my local database from a recent CGSpace dump
<ul>
<li>During the FlywayDB migration I got an error:</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>2020-10-06 21:36:04,138 ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ Batch entry 0 update public.bitstreamformatregistry set description='Electronic publishing', internal='FALSE', mimetype='application/epub+zip', short_description='EPUB', support_level=1 where bitstream_format_id=78 was aborted: ERROR: duplicate key value violates unique constraint "bitstreamformatregistry_short_description_key"
Detail: Key (short_description)=(EPUB) already exists. Call getNextException to see other errors in the batch.
2020-10-06 21:36:04,143 ERROR org.dspace.storage.rdbms.DatabaseRegistryUpdater @ Error attempting to update Bitstream Format and/or Metadata Registries
org.hibernate.exception.ConstraintViolationException: could not execute batch
at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:129)
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:124)
at org.hibernate.engine.jdbc.batch.internal.BatchingBatch.performExecution(BatchingBatch.java:122)
at org.hibernate.engine.jdbc.batch.internal.BatchingBatch.doExecuteBatch(BatchingBatch.java:101)
at org.hibernate.engine.jdbc.batch.internal.AbstractBatchImpl.execute(AbstractBatchImpl.java:161)
at org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.executeBatch(JdbcCoordinatorImpl.java:207)
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:390)
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:304)
at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:349)
at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:56)
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1195)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.hibernate.context.internal.ThreadLocalSessionContext$TransactionProtectionWrapper.invoke(ThreadLocalSessionContext.java:352)
at com.sun.proxy.$Proxy162.flush(Unknown Source)
at org.dspace.core.HibernateDBConnection.commit(HibernateDBConnection.java:83)
at org.dspace.core.Context.commit(Context.java:435)
at org.dspace.core.Context.complete(Context.java:380)
at org.dspace.administer.MetadataImporter.loadRegistry(MetadataImporter.java:164)
at org.dspace.storage.rdbms.DatabaseRegistryUpdater.updateRegistries(DatabaseRegistryUpdater.java:72)
at org.dspace.storage.rdbms.DatabaseRegistryUpdater.afterMigrate(DatabaseRegistryUpdater.java:121)
at org.flywaydb.core.internal.command.DbMigrate$3.doInTransaction(DbMigrate.java:250)
at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:246)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:959)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:917)
at org.flywaydb.core.Flyway.execute(Flyway.java:1373)
at org.flywaydb.core.Flyway.migrate(Flyway.java:917)
at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:663)
at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:575)
at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:551)
at org.dspace.core.Context.<clinit>(Context.java:103)
at org.dspace.app.util.AbstractDSpaceWebapp.register(AbstractDSpaceWebapp.java:74)
at org.dspace.app.util.DSpaceWebappListener.contextInitialized(DSpaceWebappListener.java:31)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5197)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5720)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1016)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:992)
</code></pre><ul>
<li>I checked the database migrations with <code>dspace database info</code> and they were all OK
<ul>
<li>Then I restarted the Tomcat again and it started up OK…</li>
</ul>
</li>
<li>There were two issues I had reported to Atmire last month:
<ul>
<li>Importing items from the command line throws a <code>NullPointerException</code> from <code>com.atmire.dspace.cua.CUASolrLoggerServiceImpl</code> for every item, but the item still gets imported</li>
<li>No results for author name in Listing and Reports, despite there being hits in Discovery search</li>
</ul>
</li>
<li>To test the first one I imported a very simple CSV file with one item with minimal data
<ul>
<li>There is a new error now (but the item does get imported):</li>
New item: aff5e78d-87c9-438d-94f8-1050b649961c (10568/108548)
+ New owning collection (10568/3): ILRI articles in journals
+ Added (dc.contributor.author): Orth, Alan
+ Added (dc.date.issued): 2020-09-01
+ Added (dc.title): Testing CUA import NPE
Tue Oct 06 22:06:14 CEST 2020 | Query:containerItem:aff5e78d-87c9-438d-94f8-1050b649961c
Error while updating
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Expected mime type application/octet-stream but got text/html. <!doctype html><html lang="en"><head><title>HTTP Status 404 – Not Found</title><style type="text/css">body {font-family:Tahoma,Arial,sans-serif;} h1, h2, h3, b {color:white;background-color:#525D76;} h1 {font-size:22px;} h2 {font-size:16px;} h3 {font-size:14px;} p {font-size:12px;} a {color:black;} .line {height:1px;background-color:#525D76;border:none;}</style></head><body><h1>HTTP Status 404 – Not Found</h1><hr class="line" /><p><b>Type</b> Status Report</p><p><b>Message</b> The requested resource [/solr/update] is not available</p><p><b>Description</b> The origin server did not find a current representation for the target resource or is not willing to disclose that one exists.</p><hr class="line" /><h3>Apache Tomcat/7.0.104</h3></body></html>
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:512)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.commit(SolrServer.java:168)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1131)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:212)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1104)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1093)
at org.dspace.statistics.StatisticsLoggingConsumer.consume(SourceFile:104)
at org.dspace.event.BasicDispatcher.consume(BasicDispatcher.java:177)
at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:123)
at org.dspace.core.Context.dispatchEvents(Context.java:455)
at org.dspace.core.Context.commit(Context.java:424)
at org.dspace.core.Context.complete(Context.java:380)
at org.dspace.app.bulkedit.MetadataImport.main(MetadataImport.java:1399)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><ul>
<li>Also, I tested Listings and Reports and there are still no hits for “Orth, Alan” as a contributor, despite there being dozens of items in the repository and the Solr query generated by Listings and Reports actually returning hits:</li>
<li>Then we post an item in JSON format to <code>/rest/collections/{uuid}/items</code>:</li>
</ul>
<pretabindex="0"><code>$ http POST https://dspacetest.cgiar.org/rest/collections/f10ad667-2746-4705-8b16-4439abe61d22/items Cookie:JSESSIONID=EABAC9EFF942028AA52DFDA16DBCAFDE < item-object.json
</code></pre><ul>
<li>Format of JSON is:</li>
</ul>
<pretabindex="0"><code>{ "metadata": [
{
"key": "dc.title",
"value": "Testing REST API post",
"language": "en_US"
},
{
"key": "dc.contributor.author",
"value": "Orth, Alan",
"language": "en_US"
},
{
"key": "dc.date.issued",
"value": "2020-09-01",
"language": "en_US"
}
],
"archived":"false",
"withdrawn":"false"
}
</code></pre><ul>
<li>What is unclear to me is the <code>archived</code> parameter, it seems to do nothing… perhaps it is only used for the <code>/items</code> endpoint when printing information about an item
<ul>
<li>If I submit to a collection that has a workflow, even as a super admin and with “archived=false” in the JSON, the item enters the workflow (“Awaiting editor’s attention”)</li>
<li>If I submit to a new collection without a workflow the item gets archived immediately</li>
<li>I created <ahref="https://gist.github.com/alanorth/40fc3092aefd78f978cca00e8abeeb7a">some notes</a> to share with Salem and Leroy for future reference when we start discussion POSTing items to the REST API</li>
</ul>
</li>
<li>I created an account for Salem on DSpace Test and added it to the submitters group of an ICARDA collection with no other workflow steps so we can see what happens
<ul>
<li>We are curious to see if he gets a UUID when posting from MEL</li>
</ul>
</li>
<li>I did some tests by adding his account to certain workflow steps and trying to POST the item</li>
<li>Member of collection “Submitters” step:
<ul>
<li>HTTP Status 401 – Unauthorized</li>
<li>The request has not been applied because it lacks valid authentication credentials for the target resource.</li>
</ul>
</li>
<li>Member of collection “Accept/Reject” step:
<ul>
<li>Same error…</li>
</ul>
</li>
<li>Member of collection “Accept/Reject/Edit Metadata” step:
<ul>
<li>Same error…</li>
</ul>
</li>
<li>Member of collection Administrators with no other workflow steps…:
<ul>
<li>Posts straight to archive</li>
</ul>
</li>
<li>Member of collection Administrators with empty “Accept/Reject/Edit Metadata” step:
<ul>
<li>Posts straight to archive</li>
</ul>
</li>
<li>Member of collection Administrators with populated “Accept/Reject/Edit Metadata” step:
<ul>
<li>Does <em>not</em> post straight to archive, goes to workflow</li>
</ul>
</li>
<li>Note that community administrators have no role in item submission other than being able to create/manage collection groups</li>
</ul>
<h2id="2020-10-08">2020-10-08</h2>
<ul>
<li>I did some testing of the DSpace 5 REST API because Salem and I were curious
<ul>
<li>The authentication is a little different (uses a serialized JSON object instead of a form and the token is an HTTP header instead of a cookie):</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>$ http POST http://localhost:8080/rest/login email=aorth@fuuu.com 'password=ddddd'
$ http POST http://localhost:8080/rest/collections/1549/items rest-dspace-token:d846f138-75d3-47ba-9180-b88789a28099 < item-object.json
</code></pre><ul>
<li>The item submission works exactly the same as in DSpace 6:</li>
</ul>
<ol>
<li>The submitting user must be a collection admin</li>
<li>If the collection has a workflow the item will enter it and the API returns an item ID</li>
<li>If the collection does not have a workflow then the item is committed to the archive and you get a Handle</li>
</ol>
<h2id="2020-10-09">2020-10-09</h2>
<ul>
<li>Skype with Peter about AReS and CGSpace
<ul>
<li>We discussed removing Atmire Listings and Reports from DSpace 6 because we can probably make the same reports in AReS and this module is the one that is currently holding us back from the upgrade</li>
<li>We discussed allowing partners to submit content via the REST API and perhaps making it an extra fee due to the burden it incurs with unfinished submissions, manual duplicate checking, developer support, etc</li>
<li>He was excited about the possibility of using my statistics API for more things on AReS as well as item view pages</li>
</ul>
</li>
<li>Also I fixed a bunch of the CRP mappings in the AReS value mapper and started a fresh re-indexing</li>
</ul>
<h2id="2020-10-12">2020-10-12</h2>
<ul>
<li>Looking at CGSpace’s Solr statistics for 2020-09 and I see:
<ul>
<li><code>RTB website BOT</code>: 212916</li>
<li><code>Java/1.8.0_66</code>: 3122</li>
<li><code>Mozilla/5.0 (compatible; um-LN/1.0; mailto: techinfo@ubermetrics-technologies.com; Windows NT 6.1; WOW64; rv:40.0) Gecko/20100101 Firefox/40.1</code>: 614</li>
<li>After a few minutes I saw these four hits in Solr… WTF
<ul>
<li>So is there some issue with DSpace’s parsing of the spider agent files?</li>
<li>I added <code>RTB website BOT</code> to the ilri pattern file, restarted Tomcat, and made four more requests to the bitstream</li>
<li>These four requests were recorded in Solr too, WTF!</li>
<li>It seems like the patterns aren’t working at all…</li>
<li>I decided to try something drastic and removed all pattern files, adding only one single pattern <code>bot</code> to make sure this is not because of a syntax or precedence issue</li>
<li>Now even those four requests were recorded in Solr, WTF!</li>
<li>I will try one last thing, to put a single entry with the exact pattern <code>RTB website BOT</code> in a single spider agents pattern file…</li>
<li>Nope! Still records the hits… WTF</li>
<li>As a last resort I tried to use the vanilla <ahref="https://github.com/DSpace/DSpace/blob/dspace-6_x/dspace/config/spiders/agents/example">DSpace 6 <code>example</code> file</a></li>
<li>And the hits still get recorded… WTF</li>
<li>So now I’m wondering if this is because of our custom Atmire shit?</li>
<li>I will have to test on a vanilla DSpace instance I guess before I can complain to the dspace-tech mailing list</li>
</ul>
</li>
<li>I re-factored the <code>check-spider-hits.sh</code> script to read patterns from a text file rather than sed’s stdout, and to properly search for spaces in patterns that use <code>\s</code> because Lucene’s search syntax doesn’t support it (and spaces work just fine)
<li>I added <code>[Ss]pider</code> to the Tomcat Crawler Session Manager Valve regex because this can catch a few more generic bots and force them to use the same Tomcat JSESSIONID</li>
<li>I added a few of the patterns from above to our local agents list and ran the <code>check-spider-hits.sh</code> on CGSpace:</li>
Purging 1702 hits from TrendsmapResolver in statistics-2018
Purging 1062 hits from Vizzit in statistics-2018
Purging 920 hits from Scoop\.it in statistics-2018
Total number of bot hits purged: 3684
</code></pre><h2id="2020-10-13">2020-10-13</h2>
<ul>
<li>Skype with Peter about AReS again
<ul>
<li>We decided to use Title Case for our countries on CGSpace to minimize the need for mapping on AReS</li>
<li>We did some work to add a dozen more mappings for strange and incorrect CRPs on AReS</li>
</ul>
</li>
<li>I can update the country metadata in PostgreSQL like this:</li>
</ul>
<pretabindex="0"><code>dspace=> BEGIN;
dspace=> UPDATE metadatavalue SET text_value=INITCAP(text_value) WHERE resource_type_id=2 AND metadata_field_id=228;
UPDATE 51756
dspace=> COMMIT;
</code></pre><ul>
<li>I will need to pay special attention to Côte d’Ivoire, Bosnia and Herzegovina, and a few others though… maybe better do search and replace using <code>fix-metadata-values.csv</code>
<ul>
<li>Export a list of distinct values from the database:</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>dspace=> \COPY (SELECT DISTINCT(text_value) as "cg.coverage.country" FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=228) TO /tmp/2020-10-13-countries.csv WITH CSV HEADER;
COPY 195
</code></pre><ul>
<li>Then use OpenRefine and make a new column for corrections, then use this GREL to convert to title case: <code>value.toTitlecase()</code>
<ul>
<li>I still had to double check everything to catch some corner cases (Andorra, Timor-leste, etc)</li>
</ul>
</li>
<li>For the input forms I found out how to do a complicated search and replace in vim:</li>
<li>It uses a <ahref="https://jbodah.github.io/blog/2016/11/01/positivenegative-lookaheadlookbehind-vim/">negative lookahead</a> (aka “lookaround” in PCRE?) to match words that are <em>not</em>“pair”, “displayed”, etc because we don’t want to edit the XML tags themselves…
<ul>
<li>I had to fix a few manually after doing this, as above with PostgreSQL</li>
</ul>
</li>
</ul>
<h2id="2020-10-14">2020-10-14</h2>
<ul>
<li>I discussed the title casing of countries with Abenet and she suggested we also apply title casing to regions
<ul>
<li>I exported the list of regions from the database:</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>dspace=> \COPY (SELECT DISTINCT(text_value) as "cg.coverage.region" FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=227) TO /tmp/2020-10-14-regions.csv WITH CSV HEADER;
COPY 34
</code></pre><ul>
<li>I did the same as the countries in OpenRefine for the database values and in vim for the input forms</li>
<li>After testing the replacements locally I ran them on CGSpace:</li>
<li>I added a dozen or so more mappings to fix some country outliers on AReS
<ul>
<li>I will start a fresh harvest there once the Discovery update is done on CGSpace</li>
</ul>
</li>
<li>I also adjusted my <code>fix-metadata-values.py</code> and <code>delete-metadata-values.py</code> scripts to work on DSpace 6 where there is no more <code>resource_type_id</code> field
<ul>
<li>I will need to do it on a few more scripts as well, but I’ll do that after we migrate to DSpace 6 because those scripts are less important</li>
</ul>
</li>
<li>I found a new setting in DSpace 6’s <code>usage-statistics.cfg</code> about case insensitive matching of bots that defaults to false, so I enabled it in our DSpace 6 branch
<ul>
<li>I am curious to see if that resolves the strange issues I noticed yesterday about bot matching of patterns in the spider agents file completely not working</li>
</ul>
</li>
</ul>
<h2id="2020-10-15">2020-10-15</h2>
<ul>
<li>Re-deploy latest code on both CGSpace and DSpace Test to get the input forms changes
<ul>
<li>Run system updates and reboot each server (linode18 and linode26)</li>
<li>I had to restart Tomcat seven times on CGSpace before all Solr stats cores came up OK</li>
</ul>
</li>
<li>Skype with Peter and Abenet about AReS and CGSpace
<ul>
<li>We agreed to lower case the AGROVOC subjects on CGSpace to make it harmonized with MELSpace and WorldFish</li>
<li>We agreed to separate the AGROVOC from the other center- and CRP-specific subjects so that the search and tag clouds are cleaner and more useful</li>
<li>We added a filter for journal title</li>
</ul>
</li>
<li>I enabled anonymous access to the “Export search metadata” option on DSpace Test
<ul>
<li>If I search for author containing “Orth, Alan” or “Orth Alan” the export search metadata returns HTTP 400</li>
<li>If I search for author containing “Orth” it exports a CSV properly…</li>
</ul>
</li>
<li>I created issues on the OpenRXV repository:
<ul>
<li><ahref="https://github.com/ilri/OpenRXV/issues/42">Can’t download templates that have spaces in their file name</a></li>
<li><ahref="https://github.com/ilri/OpenRXV/issues/43">Can’t search for text values with a space in “Mapping Values” interface</a></li>
</ul>
</li>
<li>Atmire responded about the Listings and Reports and Content and Usage Statistics issues with DSpace 6 that I reported last week
<ul>
<li>They said that the CUA issue was a mistake and should be fixed in a minor version bump</li>
<li>They asked me to confirm if the L&R version bump from last week did not solve the issue there (which I had tested locally, but not on DSpace Test)</li>
<li>I will test them both again on DSpace Test and report back</li>
</ul>
</li>
<li>I posted a message on Yammer to inform all our users about the changes to countries, regions, and AGROVOC subjects</li>
<li>I modified all AGROVOC subjects to be lower case in PostgreSQL and then exported a list of the top 1500 to update the controlled vocabulary in our submission form:</li>
</ul>
<pretabindex="0"><code>dspace=> BEGIN;
dspace=> UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE resource_type_id=2 AND metadata_field_id=57;
UPDATE 335063
dspace=> COMMIT;
dspace=> \COPY (SELECT DISTINCT text_value as "dc.subject", count(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=57 GROUP BY "dc.subject" ORDER BY count DESC LIMIT 1500) TO /tmp/2020-10-15-top-1500-agrovoc-subject.csv WITH CSV HEADER;
COPY 1500
</code></pre><ul>
<li>Use my <code>agrovoc-lookup.py</code> script to validate subject terms against the AGROVOC REST API, extract matches with <code>csvgrep</code>, and then update and format the controlled vocabulary:</li>
<li>They are using the user agent “CCAFS Website Publications importer BOT” so they are getting rate limited by nginx</li>
<li>Ideally they would use the REST <code>find-by-metadata-field</code> endpoint, but it is <em>really</em> slow for large result sets (like twenty minutes!):</li>
<li>Interesting! I added a find/replace manually in AReS and now I see the one I POSTed…</li>
<li>I fixed a few bugs in the Simple and Extended PDF reports on AReS
<ul>
<li>Add missing ISI Journal and Type to Simple PDF report</li>
<li>Fix DOIs in Simple PDF report</li>
<li>Add missing “<ahref="https://hdl.handle.net">https://hdl.handle.net</a>” to Handles in Extented PDF report</li>
</ul>
</li>
<li>Testing Atmire CUA and L&R based on their feedback from a few days ago
<ul>
<li>I no longer get the NullPointerException from CUA when importing metadata on the command line (!)</li>
<li>Listings and Reports now shows results for simple queries that I tested (!), though it seems that there are some new JavaScript libraries I need to allow in nginx</li>
</ul>
</li>
<li>I sent a mail to the dspace-tech mailing list asking about the error with DSpace 6’s “Export Search Metadata” function
<ul>
<li>If I search for an author like “Orth, Alan” it gives an HTTP 400, but if I search for “Orth” alone it exports a CSV</li>
<li>I replicated the same issue on demo.dspace.org</li>
</ul>
</li>
</ul>
<h2id="2020-10-19">2020-10-19</h2>
<ul>
<li>Last night I learned how to POST mappings to Elasticsearch for AReS:</li>
<li>Adjust the report templates on AReS based on some of Peter’s feedback</li>
<li>I wrote a quick Python script to filter and convert the old AReS mappings to <ahref="https://www.elastic.co/guide/en/elasticsearch/reference/current/docs-bulk.html">Elasticsearch’s Bulk API</a> format:</li>
</span></span><spanstyle="display:flex;"><span><spanstyle="color:#75715e"># Iterate over old mapping file, which is in format "find": "replace", ie:</span>
</span></span><spanstyle="display:flex;"><span><spanstyle="color:#75715e"># And convert to proper dictionaries for import into Elasticsearch's Bulk API:</span>
</span></span><spanstyle="display:flex;"><span><spanstyle="color:#75715e"># Skip all upper and all lower case strings because they are indicative of</span>
</span></span><spanstyle="display:flex;"><span><spanstyle="color:#75715e"># some AGROVOC or other mappings we no longer want to do</span>
<li>It filters all upper and lower case strings as well as any replacements that end in an acronym like “- ILRI”, reducing the number of mappings from around 4,000 to about 900</li>
<li>I deleted the existing <code>openrxv-values</code> Elasticsearch core and then POSTed it:</li>
<li>Then in AReS I didn’t see the mappings in the dashboard until I added a new one manually, after which they all appeared
<ul>
<li>I started a new harvesting</li>
</ul>
</li>
<li>I checked the CIMMYT DSpace repository and I see they have <ahref="https://repository.cimmyt.org/rest">the REST API enabled</a>
<ul>
<li>The data doesn’t look too bad actually: they have countries in title case, AGROVOC in upper case, CRPs, etc</li>
<li>According to <ahref="https://repository.cimmyt.org/oai/request?verb=ListRecords&metadataPrefix=oai_dc">their OAI</a> they have 6,500 items in the repository</li>
<li>I would be interested to explore the possibility to harvest them…</li>
</ul>
</li>
<li>Bosede said they were having problems with the “Access” step during item submission
<ul>
<li>I looked at the Munin graphs for PostgreSQL and both connections and locks look normal so I’m not sure what it could be</li>
<li>I restarted the PostgreSQL service just to see if that would help</li>
<li>She said she was still experiencing the issue…</li>
</ul>
</li>
<li>I ran the <code>dspace cleanup -v</code> process on CGSpace and got an error:</li>
</ul>
<pretabindex="0"><code>Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
Detail: Key (bitstream_id)=(192921) is still referenced from table "bundle".
</code></pre><ul>
<li>The solution is, as always:</li>
</ul>
<pretabindex="0"><code>$ psql -d dspace -U dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (192921);'
UPDATE 1
</code></pre><ul>
<li>After looking at the CGSpace Solr stats for 2020-10 I found some hits to purge:</li>
<li>And I saw three hits in Solr with <code>isBot: true</code>!!!
<ul>
<li>I made a few more requests with user agent “fumanchu” and it logs them with <code>isBot: false</code>…</li>
<li>I made a request with user agent “Delphi 2009” which is in the ilri pattern file, and it was logged with <code>isBot: true</code></li>
<li>I made a few more requests and confirmed that if a pattern is in the list it gets logged with <code>isBot: true</code> despite the fact that <code>usage-statistics.logBots</code> is false…</li>
<li>So WTF this means that it <em>knows</em> they are from a bot, but it logs them anyways</li>
<li>Is this an issue with Atmire’s modules?</li>
<li>I sent them feedback on the ticket</li>
</ul>
</li>
</ul>
<h2id="2020-10-21">2020-10-21</h2>
<ul>
<li>Peter needs to do some reporting on gender across the entirety of CGSpace so he asked me to tag a bunch of items with the AGROVOC “gender” subject (in CGIAR Gender Platform community, all ILRI items with subject “gender” or “women”, all CCAFS with “gender and social inclusion” etc)
<ul>
<li>First I exported the Gender Platform community and tagged all the items there with “gender” in OpenRefine</li>
<li>Then I exported all of CGSpace and extracted just the ILRI and other center-specific tags with <code>csvcut</code>:</li>
<li>Then I went through all center subjects looking for “WOMEN” or “GENDER” and checking if they were missing the associated AGROVOC subject
<ul>
<li>To reduce the size of the CSV file I removed all center subject columns after filtering them, and I flagged all rows that I changed so I could upload a CSV with only the items that were modified</li>
<li>In total it was about 1,100 items that I tagged across the Gender Platform community and elsewhere</li>
<li>Also, I ran the CSVs through my <code>csv-metadata-quality</code> checker to do basic sanity checks, which ended up removing a few dozen duplicated subjects</li>
</ul>
</li>
</ul>
<h2id="2020-10-22">2020-10-22</h2>
<ul>
<li>Bosede was getting this error on CGSpace yesterday:</li>
</ul>
<pretabindex="0"><code>Authorization denied for action WORKFLOW_STEP_1 on COLLECTION:1072 by user 1759
</code></pre><ul>
<li>Collection 1072 appears to be <ahref="https://cgspace.cgiar.org/handle/10568/69542">IITA Miscellaneous</a>
<ul>
<li>The submit step is defined, but has no users or groups</li>
<li>I added the IITA submitters there and told Bosede to try again</li>
</ul>
</li>
<li>Add two new blocks to list the top communities and collections on AReS</li>
<li>I want to extract all CRPs and affiliations from AReS to do some text processing and create some mappings…
<ul>
<li>First extract 10,000 affiliations from Elasticsearch by only including the <code>affiliation</code> source:</li>
<li>Then I decided to try a different approach and I adjusted my <code>convert-mapping.py</code> script to re-consider some replacement patterns with acronyms from the original AReS <code>mapping.json</code> file to hopefully address some MEL to CGSpace mappings
<ul>
<li>For example, to changes this:
<ul>
<li>find: International Livestock Research Institute</li>
<li>replace: International Livestock Research Institute - ILRI</li>
</ul>
</li>
<li>… into this:
<ul>
<li>find: International Livestock Research Institute - ILRI</li>
<li>replace: International Livestock Research Institute</li>
</ul>
</li>
</ul>
</li>
<li>I re-uploaded the mappings to Elasticsearch like I did yesterday and restarted the harvesting</li>
</ul>
<h2id="2020-10-24">2020-10-24</h2>
<ul>
<li>Atmire sent a small version bump to CUA (6.x-4.1.10-ilri-RC5) to fix the logging of bot requests when <code>usage-statistics.logBots</code> is false
<ul>
<li>I tested it by making several requests to DSpace Test with the <code>RTB website BOT</code> and <code>Delphi 2009</code> user agents and can verify that they are no longer logged</li>
</ul>
</li>
<li>I spent a few hours working on mappings on AReS
<ul>
<li>I decided to do a full re-harvest on AReS with <em>no mappings</em> so I could extract the CRPs and affiliations to see how much work they needed</li>
<li>I worked on my Python script to process some cleanups of the values to create find/replace mappings for common scenarios:
<ul>
<li>Removing acronyms from the end of strings</li>
<li>Removing “CRP on " from strings</li>
</ul>
</li>
<li>The problem is that the mappings are applied to all fields, and we want to keep “CGIAR Research Program on …” in the authors, but not in the CRPs field</li>
<li>Really the best solution is to have each repository use the same controlled vocabularies</li>
</ul>
</li>
</ul>
<h2id="2020-10-25">2020-10-25</h2>
<ul>
<li>I re-installed DSpace Test with a fresh snapshot of CGSpace’s to test the DSpace 6 upgrade (the last time was in 2020-05, and we’ve fixed a lot of issues since then):</li>
<li>After the fifth or so run I got this error:</li>
</ul>
<pretabindex="0"><code>Exception: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><ul>
<li>So basically, as I saw at this same step in 2020-05, there are some documents that have IDs that have <em>not</em> been converted to UUID, and have <em>not</em> been labeled as “unmigrated” either…
<ul>
<li>I see there are about 217,000 of them, 99% of which are of <code>type: 5</code> which is “site”</li>
<li>I purged them:</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>$ curl -s "http://localhost:8083/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</query></delete>"
</code></pre><ul>
<li>Then I restarted the <code>solr-upgrade-statistics-6x</code> process, which apparently had no records left to process</li>
<li>I started processing the statistics-2019 core…
<ul>
<li>I managed to process 7.5 million records in 7 hours without any errors!</li>
</ul>
</li>
</ul>
<h2id="2020-10-26">2020-10-26</h2>
<ul>
<li>The statistics processing on the statistics-2018 core errored after 1.8 million records:</li>
</ul>
<pretabindex="0"><code>Exception: Java heap space
java.lang.OutOfMemoryError: Java heap space
</code></pre><ul>
<li>I had the same problem when I processed the statistics-2018 core in 2020-07 and 2020-08
<ul>
<li>I will try to purge some unmigrated records (around 460,000), most of which are of <code>type: 5</code> (site) <del>so not relevant to our views and downloads anyways</del>:</li>
<li>I restarted the process and it crashed again a few minutes later
<ul>
<li>I increased the memory to 4096m and tried again</li>
<li>It eventually completed, after which time I purge all remaining 350,000 unmigrated records (99% of which were <code>type: 5</code>):</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>$ curl -s "http://localhost:8083/solr/statistics-2018/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</query></delete>"
</code></pre><ul>
<li>Then I started processing the statistics-2017 core…
<ul>
<li>The processing finished with no errors and afterwards I purged 800,000 unmigrated records (all with <code>type: 5</code>):</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>$ curl -s "http://localhost:8083/solr/statistics-2017/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</query></delete>"
</code></pre><ul>
<li>Also I purged 2.7 million unmigrated records from the statistics-2019 core</li>
<li>I filed an issue with Atmire about the duplicate values in the <code>owningComm</code> and <code>containerCommunity</code> fields in Solr: <ahref="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839</a></li>
<li>Add new ORCID identifier for <ahref="https://orcid.org/0000-0003-3871-6277">Perle LATRE DE LATE</a> to controlled vocabulary</li>
<li>Use <code>move-collections.sh</code> to move a few AgriFood Tools collections on CGSpace into a new <ahref="https://hdl.handle.net/10568/109982">sub community</a></li>
</ul>
<h2id="2020-10-27">2020-10-27</h2>
<ul>
<li>I purged 849,408 unmigrated records from the statistics-2016 core after it finished processing…</li>
<li>I purged 285,000 unmigrated records from the statistics-2015 core after it finished processing…</li>
<li>I purged 196,000 unmigrated records from the statistics-2014 core after it finished processing…</li>
<li>I finally finished processing all the statistics cores with the <code>solr-upgrade-statistics-6x</code> utility on DSpace Test
<li>Peter asked me to add the new preferred AGROVOC subject “covid-19” to all items we had previously added “coronavirus disease”, and to make sure all items with ILRI subject “ZOONOTIC DISEASES” have the AGROVOC subject “zoonoses”
<ul>
<li>I exported all the records on CGSpace from the CLI and extracted the columns I needed to process them in OpenRefine:</li>
<li>I sanity checked the CSV in <code>csv-metadata-quality</code> after exporting from OpenRefine, then applied the changes to 453 items on CGSpace</li>
<li>Skype with Peter and Abenet about CGSpace Explorer (AReS)
<ul>
<li>They want to do a big push in ILRI and our partners to use it in mid November (around 16th) so we need to clean up the metadata and try to fix the views/downloads issue by then</li>
<li>I filed <ahref="https://github.com/ilri/OpenRXV/issues/45">an issue</a> on OpenRXV for the views/downloads</li>
<li>We also talked about harvesting CIMMYT’s repository into AReS, perhaps with only a subset of their data, though they seem to have some issues with their data:
<ul>
<li>dc.contributor.author and dcterms.creator</li>
<li>dc.title and dcterms.title</li>
<li>dc.region.focus</li>
<li>dc.coverage.countryfocus</li>
<li>dc.rights.accesslevel (access status)</li>
<li>dc.source.journal (source)</li>
<li>dcterms.type and dc.type</li>
<li>dc.subject.agrovoc</li>
</ul>
</li>
</ul>
</li>
<li>I did some work on my previous <code>create-mappings.py</code> script to process journal titles and sponsors/investors as well as CRPs and affiliations
<ul>
<li>I converted it to use the Elasticsearch scroll API directly rather than consuming a JSON file</li>
<li>The result is about 1200 mappings, mostly to remove acronyms at the end of metadata values</li>
<li>I added a few custom mappings using <code>convert-mapping.py</code> and then uploaded them to AReS:</li>
<li>After that I had to manually create and delete a fake mapping in the AReS UI so that the mappings would show up</li>
<li>I fixed a few strings in the OpenRXV admin dashboard and then re-built the frontent container:</li>
</ul>
<pretabindex="0"><code>$ docker-compose up --build -d angular_nginx
</code></pre><h2id="2020-10-28">2020-10-28</h2>
<ul>
<li>Fix a handful more of grammar and spelling issues in OpenRXV and then re-build the containers:</li>
</ul>
<pretabindex="0"><code>$ docker-compose up --build -d --force-recreate angular_nginx
</code></pre><ul>
<li>Also, I realized that the mysterious issue with countries getting changed to inconsistent lower case like “Burkina faso” is due to the country formatter (see: <code>backend/src/harvester/consumers/fetch.consumer.ts</code>)
<ul>
<li>I don’t understand Typescript syntax so for now I will just disable that formatter in each repository configuration and I’m sure it will be better, as we’re all using title case like “Kenya” and “Burkina Faso” now anyways</li>
</ul>
</li>
<li>Also, I fixed a few mappings with WorldFish data</li>
<li>Peter really wants us to move forward with the alignment of our regions to UN M.49, and the CKM web team hasn’t responded to any of the mails we’ve sent recently so I will just do it
<ul>
<li>These are the changes that will happen in the input forms:
<ul>
<li>East Africa → Eastern Africa</li>
<li>West Africa → Western Africa</li>
<li>Southeast Asia → South-eastern Asia</li>
<li>South Asia → Southern Asia</li>
<li>Africa South of Sahara → Sub-Saharan Africa</li>
<li>North Africa → Northern Africa</li>
<li>West Asia → Western Asia</li>
</ul>
</li>
<li>There are some regions we use that are not present, for example Sahel, ACP, Middle East, and West and Central Africa. I will advocate for closer alignment later</li>
<li>I ran my <code>fix-metadata-values.py</code> script to update the values in the database:</li>
<li>I realized I had been using an incorrect Solr query to purge unmigrated items after processing with <code>solr-upgrade-statistics-6x</code>…
<ul>
<li>Instead of this: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
<li>I should have used this: <code>id:/.+-unmigrated/</code></li>
<li>Or perhaps this (with a check first!): <code>*:* NOT id:/.{36}/</code></li>
<li>We need to make sure to explicitly purge the unmigrated records, then purge any that are not matching the UUID pattern (after inspecting manually!)</li>
<li>There are still 3.7 million records in our ten years of Solr statistics that are unmigrated (I only noticed because the DSpace Statistics API indexer kept failing)</li>
<li>I don’t think this is serious enough to re-start the simulation of the DSpace 6 migration over again, but I definitely want to make sure I use the correct query when I do CGSpace</li>
</ul>
</li>
<li>The AReS indexing finished after I removed the country formatting from all the repository configurations and now I see values like “SA”, “CA”, etc…
<ul>
<li>So really we need this to fix MELSpace countries, so I will re-enable the country formatting for their repository</li>
</ul>
</li>
<li>Send Peter a list of affiliations, authors, journals, publishers, investors, and series for correction:</li>
</ul>
<pretabindex="0"><code>dspace=> \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-10-28-affiliations.csv WITH CSV HEADER;
COPY 6357
dspace=> \COPY (SELECT DISTINCT text_value as "dc.description.sponsorship", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 29 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-10-28-sponsors.csv WITH CSV HEADER;
COPY 730
dspace=> \COPY (SELECT DISTINCT text_value as "dc.contributor.author", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 3 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-10-28-authors.csv WITH CSV HEADER;
COPY 71748
dspace=> \COPY (SELECT DISTINCT text_value as "dc.publisher", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 39 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-10-28-publishers.csv WITH CSV HEADER;
COPY 3882
dspace=> \COPY (SELECT DISTINCT text_value as "dc.source", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 55 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-10-28-journal-titles.csv WITH CSV HEADER;
COPY 3684
dspace=> \COPY (SELECT DISTINCT text_value as "dc.relation.ispartofseries", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 43 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-10-28-series.csv WITH CSV HEADER;
COPY 5598
</code></pre><ul>
<li>I noticed there are still some mapping for acronyms and other fixes that haven’t been applied, so I ran my <code>create-mappings.py</code> script against Elasticsearch again
<ul>
<li>Now I’m comparing yesterday’s mappings with today’s and I don’t see any duplicates…</li>
<li>The latest indexing (second for today!) finally finshed on AReS and the countries and affiliations/crps/journals all look MUCH better
<ul>
<li>There are still a few acronyms present, some of which are in the value mappings and some which aren’t</li>
</ul>
</li>
<li>Lower case some straggling AGROVOC subjects on CGSpace:</li>
</ul>
<pretabindex="0"><code>dspace=# BEGIN;
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE resource_type_id=2 AND metadata_field_id=57 AND text_value ~ '[[:upper:]]';
UPDATE 123
dspace=# COMMIT;
</code></pre><ul>
<li>Move some top-level communities to the CGIAR System community for Peter:</li>
<li>The <code>AtomicStatisticsUpdateCLI</code> process finished on the current DSpace Test statistics core after about 32 hours
<ul>
<li>I started it on the statistics-2019 core</li>
</ul>
</li>
<li>Atmire responded about the duplicate values in Solr that I had asked about a few days ago
<ul>
<li>They said it could be due to the schema and asked if I see it only on old records or even on new ones created in the new CUA with DSpace 6</li>
<li>I did a test and found that I got duplicate data after browsing for a minute on DSpace Test (version 6) and sent them a screenshot</li>
</ul>
</li>
<li>Looking over Peter’s corrections to journal titles (dc.source) and publishers (dc.publisher)
<ul>
<li>I had to check the corrections for strange Unicode errors and replacements with “|” and “;” in OpenRefine using this GREL:</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>or(
isNotNull(value.match(/.*\uFFFD.*/)),
isNotNull(value.match(/.*\u00A0.*/)),
isNotNull(value.match(/.*\u200A.*/)),
isNotNull(value.match(/.*\u2019.*/)),
isNotNull(value.match(/.*\u00b4.*/)),
isNotNull(value.match(/.*\u007e.*/))
).toString()
</code></pre><ul>
<li>Then I did a test to apply the corrections and deletions on my local DSpace:</li>
<li>I will wait to apply them on CGSpace when I have all the other corrections from Peter processed</li>
</ul>
<h2id="2020-10-31">2020-10-31</h2>
<ul>
<li>I had the idea to use the country formatter for CGSpace on the AReS Explorer because we have the <code>cg.coverage.iso3166-alpha2</code> field…
<ul>
<li>This will be better than using the raw text values because AReS will match directly from the ISO 3166-1 list when using the country formatter</li>
</ul>
</li>
<li>Quickly process the sponsor corrections Peter sent me a few days ago and test them locally:</li>
