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446 lines
21 KiB
HTML
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta property="og:title" content="October, 2020" />
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<meta property="og:description" content="2020-10-06
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Add tests for the new /items POST handlers to the DSpace 6.x branch of my dspace-statistics-api
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It took a bit of extra work because I had to learn how to mock the responses for when Solr is not available
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Tag and release version 1.3.0 on GitHub: https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0
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Trying to test the changes Atmire sent last week but I had to re-create my local database from a recent CGSpace dump
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During the FlywayDB migration I got an error:
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-10/" />
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<meta property="article:published_time" content="2020-10-06T16:55:54+03:00" />
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<meta property="article:modified_time" content="2020-10-08T11:15:49+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="October, 2020"/>
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<meta name="twitter:description" content="2020-10-06
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Add tests for the new /items POST handlers to the DSpace 6.x branch of my dspace-statistics-api
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It took a bit of extra work because I had to learn how to mock the responses for when Solr is not available
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Tag and release version 1.3.0 on GitHub: https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0
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Trying to test the changes Atmire sent last week but I had to re-create my local database from a recent CGSpace dump
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During the FlywayDB migration I got an error:
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"/>
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<meta name="generator" content="Hugo 0.76.2" />
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<script type="application/ld+json">
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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"keywords": "Notes"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2020-10/">
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<title>October, 2020 | CGSpace Notes</title>
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<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f3d2a1f5980bab30ddd0d8cadbd496475309fc48e2b1d052c5c09e6facffcb0f.js" integrity="sha256-89Kh9ZgLqzDd0NjK29SWR1MJ/EjisdBSxcCeb6z/yw8=" crossorigin="anonymous"></script>
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<header class="blog-header">
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<div class="container">
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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</div>
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</header>
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<div class="container">
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<div class="row">
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<div class="col-sm-8 blog-main">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-10/">October, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-10-06T16:55:54+03:00">Tue Oct 06, 2020</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2020-10-06">2020-10-06</h2>
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<ul>
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<li>Add tests for the new <code>/items</code> POST handlers to the DSpace 6.x branch of my <a href="https://github.com/ilri/dspace-statistics-api/tree/v6_x">dspace-statistics-api</a>
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<ul>
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<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>
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<li>Tag and release version 1.3.0 on GitHub: <a href="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>
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</ul>
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</li>
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<li>Trying to test the changes Atmire sent last week but I had to re-create my local database from a recent CGSpace dump
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<ul>
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<li>During the FlywayDB migration I got an error:</li>
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</ul>
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</li>
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</ul>
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<pre><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"
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Detail: Key (short_description)=(EPUB) already exists. Call getNextException to see other errors in the batch.
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2020-10-06 21:36:04,138 WARN org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ SQL Error: 0, SQLState: 23505
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2020-10-06 21:36:04,138 ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ ERROR: duplicate key value violates unique constraint "bitstreamformatregistry_short_description_key"
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Detail: Key (short_description)=(EPUB) already exists.
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2020-10-06 21:36:04,142 ERROR org.hibernate.engine.jdbc.batch.internal.BatchingBatch @ HHH000315: Exception executing batch [could not execute batch]
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2020-10-06 21:36:04,143 ERROR org.dspace.storage.rdbms.DatabaseRegistryUpdater @ Error attempting to update Bitstream Format and/or Metadata Registries
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org.hibernate.exception.ConstraintViolationException: could not execute batch
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at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:129)
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at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
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at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:124)
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at org.hibernate.engine.jdbc.batch.internal.BatchingBatch.performExecution(BatchingBatch.java:122)
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at org.hibernate.engine.jdbc.batch.internal.BatchingBatch.doExecuteBatch(BatchingBatch.java:101)
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at org.hibernate.engine.jdbc.batch.internal.AbstractBatchImpl.execute(AbstractBatchImpl.java:161)
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at org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.executeBatch(JdbcCoordinatorImpl.java:207)
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at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:390)
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at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:304)
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at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:349)
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at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:56)
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at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1195)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.hibernate.context.internal.ThreadLocalSessionContext$TransactionProtectionWrapper.invoke(ThreadLocalSessionContext.java:352)
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at com.sun.proxy.$Proxy162.flush(Unknown Source)
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at org.dspace.core.HibernateDBConnection.commit(HibernateDBConnection.java:83)
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at org.dspace.core.Context.commit(Context.java:435)
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at org.dspace.core.Context.complete(Context.java:380)
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at org.dspace.administer.MetadataImporter.loadRegistry(MetadataImporter.java:164)
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at org.dspace.storage.rdbms.DatabaseRegistryUpdater.updateRegistries(DatabaseRegistryUpdater.java:72)
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at org.dspace.storage.rdbms.DatabaseRegistryUpdater.afterMigrate(DatabaseRegistryUpdater.java:121)
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at org.flywaydb.core.internal.command.DbMigrate$3.doInTransaction(DbMigrate.java:250)
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at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
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at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:246)
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at org.flywaydb.core.Flyway$1.execute(Flyway.java:959)
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at org.flywaydb.core.Flyway$1.execute(Flyway.java:917)
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at org.flywaydb.core.Flyway.execute(Flyway.java:1373)
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at org.flywaydb.core.Flyway.migrate(Flyway.java:917)
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at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:663)
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at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:575)
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at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:551)
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at org.dspace.core.Context.<clinit>(Context.java:103)
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at org.dspace.app.util.AbstractDSpaceWebapp.register(AbstractDSpaceWebapp.java:74)
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at org.dspace.app.util.DSpaceWebappListener.contextInitialized(DSpaceWebappListener.java:31)
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at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5197)
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at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5720)
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at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
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at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1016)
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at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:992)
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</code></pre><ul>
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<li>I checked the database migrations with <code>dspace database info</code> and they were all OK
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<ul>
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<li>Then I restarted the Tomcat again and it started up OK…</li>
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</ul>
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</li>
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<li>There were two issues I had reported to Atmire last month:
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<ul>
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<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>
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<li>No results for author name in Listing and Reports, despite there being hits in Discovery search</li>
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</ul>
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</li>
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<li>To test the first one I imported a very simple CSV file with one item with minimal data
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<ul>
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<li>There is a new error now (but the item does get imported):</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ dspace metadata-import -f /tmp/2020-10-06-import-test.csv -e aorth@mjanja.ch
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Loading @mire database changes for module MQM
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Changes have been processed
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-----------------------------------------------------------
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New item:
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+ New owning collection (10568/3): ILRI articles in journals
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+ Add (dc.contributor.author): Orth, Alan
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+ Add (dc.date.issued): 2020-09-01
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+ Add (dc.title): Testing CUA import NPE
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1 item(s) will be changed
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Do you want to make these changes? [y/n] y
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-----------------------------------------------------------
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New item: aff5e78d-87c9-438d-94f8-1050b649961c (10568/108548)
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+ New owning collection (10568/3): ILRI articles in journals
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+ Added (dc.contributor.author): Orth, Alan
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+ Added (dc.date.issued): 2020-09-01
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+ Added (dc.title): Testing CUA import NPE
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Tue Oct 06 22:06:14 CEST 2020 | Query:containerItem:aff5e78d-87c9-438d-94f8-1050b649961c
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Error while updating
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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>
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at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:512)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
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at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
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at org.apache.solr.client.solrj.SolrServer.commit(SolrServer.java:168)
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at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1131)
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at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:212)
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at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1104)
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at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1093)
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at org.dspace.statistics.StatisticsLoggingConsumer.consume(SourceFile:104)
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at org.dspace.event.BasicDispatcher.consume(BasicDispatcher.java:177)
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at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:123)
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at org.dspace.core.Context.dispatchEvents(Context.java:455)
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at org.dspace.core.Context.commit(Context.java:424)
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at org.dspace.core.Context.complete(Context.java:380)
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at org.dspace.app.bulkedit.MetadataImport.main(MetadataImport.java:1399)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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</code></pre><ul>
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<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>
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</ul>
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<pre><code>2020-10-06 22:23:44,116 INFO org.apache.solr.core.SolrCore @ [search] webapp=/solr path=/select params={q=*:*&fl=handle,search.resourcetype,search.resourceid,search.uniqueid&start=0&fq=NOT(withdrawn:true)&fq=NOT(discoverable:false)&fq=search.resourcetype:2&fq=author_keyword:Orth,\+A.+OR+author_keyword:Orth,\+Alan&fq=dateIssued.year:[2013+TO+2021]&rows=500&wt=javabin&version=2} hits=18 status=0 QTime=10
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</code></pre><ul>
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<li>Solr returns <code>hits=18</code> for the L&R query, but there are no result shown in the L&R UI</li>
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<li>I sent all this feedback to Atmire…</li>
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</ul>
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<h2 id="2020-10-07">2020-10-07</h2>
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<ul>
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<li>Udana from IWMI had asked about stats discrepencies from reports they had generated in previous months or years
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<ul>
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<li>I told him that we very often purge bots and the number of stats can change drastically</li>
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<li>Also, I told him that it is not possible to compare stats from previous exports and that the stats should be taking with a grain of salt</li>
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</ul>
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</li>
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<li>Testing POSTing items to the DSpace 6 REST API
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<ul>
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<li>We need to authenticate to get a JSESSIONID cookie first:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ http -f POST https://dspacetest.cgiar.org/rest/login email=aorth@fuuu.com 'password=fuuuu'
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$ http https://dspacetest.cgiar.org/rest/status Cookie:JSESSIONID=EABAC9EFF942028AA52DFDA16DBCAFDE
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</code></pre><ul>
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<li>Then we post an item in JSON format to <code>/rest/collections/{uuid}/items</code>:</li>
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</ul>
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<pre><code>$ http POST https://dspacetest.cgiar.org/rest/collections/f10ad667-2746-4705-8b16-4439abe61d22/items Cookie:JSESSIONID=EABAC9EFF942028AA52DFDA16DBCAFDE < item-object.json
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</code></pre><ul>
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<li>Format of JSON is:</li>
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</ul>
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<pre><code>{ "metadata": [
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{
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"key": "dc.title",
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"value": "Testing REST API post",
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"language": "en_US"
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},
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{
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"key": "dc.contributor.author",
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"value": "Orth, Alan",
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"language": "en_US"
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},
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{
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"key": "dc.date.issued",
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"value": "2020-09-01",
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"language": "en_US"
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}
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],
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"archived":"false",
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"withdrawn":"false"
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}
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</code></pre><ul>
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<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
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<ul>
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<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>
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<li>If I submit to a new collection without a workflow the item gets archived immediately</li>
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<li>I created <a href="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>
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</ul>
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</li>
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<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
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<ul>
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<li>We are curious to see if he gets a UUID when posting from MEL</li>
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</ul>
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</li>
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<li>I did some tests by adding his account to certain workflow steps and trying to POST the item</li>
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<li>Member of collection “Submitters” step:
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<ul>
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<li>HTTP Status 401 – Unauthorized</li>
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<li>The request has not been applied because it lacks valid authentication credentials for the target resource.</li>
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</ul>
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</li>
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<li>Member of collection “Accept/Reject” step:
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<ul>
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<li>Same error…</li>
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</ul>
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</li>
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<li>Member of collection “Accept/Reject/Edit Metadata” step:
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<ul>
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<li>Same error…</li>
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</ul>
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</li>
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<li>Member of collection Administrators with no other workflow steps…:
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<ul>
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<li>Posts straight to archive</li>
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</ul>
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</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>
|
||
<h2 id="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>
|
||
<pre><code>$ http POST http://localhost:8080/rest/login email=aorth@fuuu.com 'password=ddddd'
|
||
$ http http://localhost:8080/rest/status rest-dspace-token:d846f138-75d3-47ba-9180-b88789a28099
|
||
$ 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>
|
||
<!-- raw HTML omitted -->
|
||
|
||
|
||
|
||
|
||
|
||
</article>
|
||
|
||
|
||
|
||
</div> <!-- /.blog-main -->
|
||
|
||
<aside class="col-sm-3 ml-auto blog-sidebar">
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Recent Posts</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2020-10/">October, 2020</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2020-07/">July, 2020</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2020-06/">June, 2020</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Links</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
||
|
||
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
||
|
||
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
</aside>
|
||
|
||
|
||
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|
||
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|
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|
||
<footer class="blog-footer">
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<p dir="auto">
|
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|
||
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|
||
<p>
|
||
<a href="#">Back to top</a>
|
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