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<meta property="og:title" content="January, 2017" />
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<meta property="og:description" content="2017-01-02
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I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error
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I tested on DSpace Test as well and it doesn’t work there either
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I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years
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<meta property="og:updated_time" content="2017-01-02T10:43:00+03:00"/>
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<meta name="twitter:description" content="2017-01-02
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I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error
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I tested on DSpace Test as well and it doesn’t work there either
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I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00+03:00">Mon Jan 02, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-01-02">2017-01-02</h2>
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<ul>
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<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
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<li>I tested on DSpace Test as well and it doesn’t work there either</li>
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<li>I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years</li>
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</ul>
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<p></p>
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<h2 id="2017-01-04">2017-01-04</h2>
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<ul>
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<li>I tried to shard my local dev instance and it fails the same way:</li>
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</ul>
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<pre><code>$ JAVA_OPTS="-Xms768m -Xmx768m -Dfile.encoding=UTF-8" ~/dspace/bin/dspace stats-util -s
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Moving: 9318 into core statistics-2016
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Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2016
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org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2016
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at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
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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.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2291)
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at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
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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:226)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
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Caused by: org.apache.http.client.ClientProtocolException
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at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
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at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
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at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
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at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
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... 10 more
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Caused by: org.apache.http.client.NonRepeatableRequestException: Cannot retry request with a non-repeatable request entity. The cause lists the reason the original request failed.
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at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:659)
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at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:487)
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at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
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... 14 more
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Caused by: java.net.SocketException: Broken pipe (Write failed)
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at java.net.SocketOutputStream.socketWrite0(Native Method)
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at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
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at java.net.SocketOutputStream.write(SocketOutputStream.java:153)
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at org.apache.http.impl.io.AbstractSessionOutputBuffer.write(AbstractSessionOutputBuffer.java:181)
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at org.apache.http.impl.io.ChunkedOutputStream.flushCacheWithAppend(ChunkedOutputStream.java:124)
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at org.apache.http.impl.io.ChunkedOutputStream.write(ChunkedOutputStream.java:181)
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at org.apache.http.entity.InputStreamEntity.writeTo(InputStreamEntity.java:132)
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at org.apache.http.entity.HttpEntityWrapper.writeTo(HttpEntityWrapper.java:89)
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at org.apache.http.impl.client.EntityEnclosingRequestWrapper$EntityWrapper.writeTo(EntityEnclosingRequestWrapper.java:108)
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at org.apache.http.impl.entity.EntitySerializer.serialize(EntitySerializer.java:117)
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at org.apache.http.impl.AbstractHttpClientConnection.sendRequestEntity(AbstractHttpClientConnection.java:265)
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at org.apache.http.impl.conn.ManagedClientConnectionImpl.sendRequestEntity(ManagedClientConnectionImpl.java:203)
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at org.apache.http.protocol.HttpRequestExecutor.doSendRequest(HttpRequestExecutor.java:236)
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at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:121)
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at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:685)
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... 16 more
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</code></pre>
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<ul>
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<li>And the DSpace log shows:</li>
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</ul>
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<pre><code>2017-01-04 22:39:05,412 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2016
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2017-01-04 22:39:05,412 INFO org.dspace.statistics.SolrLogger @ Moving: 9318 records into core statistics-2016
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2017-01-04 22:39:07,310 INFO org.apache.http.impl.client.SystemDefaultHttpClient @ I/O exception (java.net.SocketException) caught when processing request to {}->http://localhost:8081: Broken pipe (Write failed)
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2017-01-04 22:39:07,310 INFO org.apache.http.impl.client.SystemDefaultHttpClient @ Retrying request to {}->http://localhost:8081
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</code></pre>
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<ul>
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<li>Despite failing instantly, a <code>statistics-2016</code> directory was created, but it only has a data dir (no conf)</li>
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<li>The Tomcat access logs show more:</li>
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</ul>
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<pre><code>127.0.0.1 - - [04/Jan/2017:22:39:05 +0200] "GET /solr/statistics/select?q=type%3A2+AND+id%3A1&wt=javabin&version=2 HTTP/1.1" 200 107
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127.0.0.1 - - [04/Jan/2017:22:39:05 +0200] "GET /solr/statistics/select?q=*%3A*&rows=0&facet=true&facet.range=time&facet.range.start=NOW%2FYEAR-17YEARS&facet.range.end=NOW%2FYEAR%2B0YEARS&facet.range.gap=%2B1YEAR&facet.mincount=1&wt=javabin&version=2 HTTP/1.1" 200 423
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127.0.0.1 - - [04/Jan/2017:22:39:05 +0200] "GET /solr/admin/cores?action=STATUS&core=statistics-2016&indexInfo=true&wt=javabin&version=2 HTTP/1.1" 200 77
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127.0.0.1 - - [04/Jan/2017:22:39:05 +0200] "GET /solr/admin/cores?action=CREATE&name=statistics-2016&instanceDir=statistics&dataDir=%2FUsers%2Faorth%2Fdspace%2Fsolr%2Fstatistics-2016%2Fdata&wt=javabin&version=2 HTTP/1.1" 200 63
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127.0.0.1 - - [04/Jan/2017:22:39:07 +0200] "GET /solr/statistics/select?csv.mv.separator=%7C&q=*%3A*&fq=time%3A%28%5B2016%5C-01%5C-01T00%5C%3A00%5C%3A00Z+TO+2017%5C-01%5C-01T00%5C%3A00%5C%3A00Z%5D+NOT+2017%5C-01%5C-01T00%5C%3A00%5C%3A00Z%29&rows=10000&wt=csv HTTP/1.1" 200 4359517
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127.0.0.1 - - [04/Jan/2017:22:39:07 +0200] "GET /solr/statistics/admin/luke?show=schema&wt=javabin&version=2 HTTP/1.1" 200 16248
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127.0.0.1 - - [04/Jan/2017:22:39:07 +0200] "POST /solr//statistics-2016/update/csv?commit=true&softCommit=false&waitSearcher=true&f.previousWorkflowStep.split=true&f.previousWorkflowStep.separator=%7C&f.previousWorkflowStep.encapsulator=%22&f.actingGroupId.split=true&f.actingGroupId.separator=%7C&f.actingGroupId.encapsulator=%22&f.containerCommunity.split=true&f.containerCommunity.separator=%7C&f.containerCommunity.encapsulator=%22&f.range.split=true&f.range.separator=%7C&f.range.encapsulator=%22&f.containerItem.split=true&f.containerItem.separator=%7C&f.containerItem.encapsulator=%22&f.p_communities_map.split=true&f.p_communities_map.separator=%7C&f.p_communities_map.encapsulator=%22&f.ngram_query_search.split=true&f.ngram_query_search.separator=%7C&f.ngram_query_search.encapsulator=%22&f.containerBitstream.split=true&f.containerBitstream.separator=%7C&f.containerBitstream.encapsulator=%22&f.owningItem.split=true&f.owningItem.separator=%7C&f.owningItem.encapsulator=%22&f.actingGroupParentId.split=true&f.actingGroupParentId.separator=%7C&f.actingGroupParentId.encapsulator=%22&f.text.split=true&f.text.separator=%7C&f.text.encapsulator=%22&f.simple_query_search.split=true&f.simple_query_search.separator=%7C&f.simple_query_search.encapsulator=%22&f.owningComm.split=true&f.owningComm.separator=%7C&f.owningComm.encapsulator=%22&f.owner.split=true&f.owner.separator=%7C&f.owner.encapsulator=%22&f.filterquery.split=true&f.filterquery.separator=%7C&f.filterquery.encapsulator=%22&f.p_group_map.split=true&f.p_group_map.separator=%7C&f.p_group_map.encapsulator=%22&f.actorMemberGroupId.split=true&f.actorMemberGroupId.separator=%7C&f.actorMemberGroupId.encapsulator=%22&f.bitstreamId.split=true&f.bitstreamId.separator=%7C&f.bitstreamId.encapsulator=%22&f.group_name.split=true&f.group_name.separator=%7C&f.group_name.encapsulator=%22&f.p_communities_name.split=true&f.p_communities_name.separator=%7C&f.p_communities_name.encapsulator=%22&f.query.split=true&f.query.separator=%7C&f.query.encapsulator=%22&f.workflowStep.split=true&f.workflowStep.separator=%7C&f.workflowStep.encapsulator=%22&f.containerCollection.split=true&f.containerCollection.separator=%7C&f.containerCollection.encapsulator=%22&f.complete_query_search.split=true&f.complete_query_search.separator=%7C&f.complete_query_search.encapsulator=%22&f.p_communities_id.split=true&f.p_communities_id.separator=%7C&f.p_communities_id.encapsulator=%22&f.rangeDescription.split=true&f.rangeDescription.separator=%7C&f.rangeDescription.encapsulator=%22&f.group_id.split=true&f.group_id.separator=%7C&f.group_id.encapsulator=%22&f.bundleName.split=true&f.bundleName.separator=%7C&f.bundleName.encapsulator=%22&f.ngram_simplequery_search.split=true&f.ngram_simplequery_search.separator=%7C&f.ngram_simplequery_search.encapsulator=%22&f.group_map.split=true&f.group_map.separator=%7C&f.group_map.encapsulator=%22&f.owningColl.split=true&f.owningColl.separator=%7C&f.owningColl.encapsulator=%22&f.p_group_id.split=true&f.p_group_id.separator=%7C&f.p_group_id.encapsulator=%22&f.p_group_name.split=true&f.p_group_name.separator=%7C&f.p_group_name.encapsulator=%22&wt=javabin&version=2 HTTP/1.1" 409 156
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127.0.0.1 - - [04/Jan/2017:22:44:00 +0200] "POST /solr/datatables/update?wt=javabin&version=2 HTTP/1.1" 200 41
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127.0.0.1 - - [04/Jan/2017:22:44:00 +0200] "POST /solr/datatables/update HTTP/1.1" 200 40
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</code></pre>
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<ul>
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<li>Very interesting… it creates the core and then fails somehow</li>
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</ul>
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<h2 id="2017-01-08">2017-01-08</h2>
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<ul>
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<li>Put Sisay’s <code>item-view.xsl</code> code to show mapped collections on CGSpace (<a href="https://github.com/ilri/DSpace/pull/295">#295</a>)</li>
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</ul>
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<h2 id="2017-01-09">2017-01-09</h2>
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<ul>
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<li>A user wrote to tell me that the new display of an item’s mappings had a crazy bug for at least one item: <a href="https://cgspace.cgiar.org/handle/10568/78596">https://cgspace.cgiar.org/handle/10568/78596</a></li>
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<li>She said she only mapped it once, but it appears to be mapped 184 times</li>
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</ul>
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<p><img src="/cgspace-notes/2017/01/mapping-crazy-duplicate.png" alt="Crazy item mapping" /></p>
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<h2 id="2017-01-10">2017-01-10</h2>
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<ul>
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<li>I tried to clean up the duplicate mappings by exporting the item’s metadata to CSV, editing, and re-importing, but DSpace said “no changes were detected”</li>
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<li>I’ve asked on the dspace-tech mailing list to see if anyone can help</li>
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<li>I found an old post on the mailing list discussing a similar issue, and listing some SQL commands that might help</li>
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<li>For example, this shows 186 mappings for the item, the first three of which are real:</li>
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</ul>
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<pre><code>dspace=# select * from collection2item where item_id = '80596';
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</code></pre>
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<ul>
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<li>Then I deleted the others:</li>
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</ul>
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<pre><code>dspace=# delete from collection2item where item_id = '80596' and id not in (90792, 90806, 90807);
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</code></pre>
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<ul>
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<li>And in the item view it now shows the correct mappings</li>
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<li>I will have to ask the DSpace people if this is a valid approach</li>
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<li>Finish looking at the Journal Title corrections of the top 500 Journal Titles so we can make a controlled vocabulary from it</li>
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</ul>
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<h2 id="2017-01-11">2017-01-11</h2>
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<ul>
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<li>Maria found another item with duplicate mappings: <a href="https://cgspace.cgiar.org/handle/10568/78658">https://cgspace.cgiar.org/handle/10568/78658</a></li>
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<li>Error in <code>fix-metadata-values.py</code> when it tries to print the value for Entwicklung & Ländlicher Raum:</li>
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</ul>
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<pre><code>Traceback (most recent call last):
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File "./fix-metadata-values.py", line 80, in <module>
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print("Fixing {} occurences of: {}".format(records_to_fix, record[0]))
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UnicodeEncodeError: 'ascii' codec can't encode character u'\xe4' in position 15: ordinal not in range(128)
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</code></pre>
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<ul>
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<li>Seems we need to encode as UTF-8 before printing to screen, ie:</li>
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</ul>
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<pre><code>print("Fixing {} occurences of: {}".format(records_to_fix, record[0].encode('utf-8')))
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</code></pre>
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<ul>
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<li>See: <a href="http://stackoverflow.com/a/36427358/487333">http://stackoverflow.com/a/36427358/487333</a></li>
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<li>I’m actually not sure if we need to encode() the strings to UTF-8 before writing them to the database… I’ve never had this issue before</li>
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<li>Now back to cleaning up some journal titles so we can make the controlled vocabulary:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/fix-27-journal-titles.csv -f dc.source -t correct -m 55 -d dspace-u dspace-p 'fuuu'
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</code></pre>
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<ul>
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<li>Now get the top 500 journal titles:</li>
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</ul>
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<pre><code>dspace-# \copy (select distinct text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=55 group by text_value order by cou
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nt desc limit 500) to /tmp/journal-titles.csv with csv;
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</code></pre>
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<ul>
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<li>The values are a bit dirty and outdated, since the file I had given to Abenet and Peter was from November</li>
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<li>I will have to go through these and fix some more before making the controlled vocabulary</li>
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<li>Added 30 more corrections or so, now there are 49 total and I’ll have to get the top 500 after applying them</li>
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</ul>
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<h2 id="2017-01-13">2017-01-13</h2>
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<ul>
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<li>Add <code>FOOD SYSTEMS</code> to CIAT subjects, waiting to merge: <a href="https://github.com/ilri/DSpace/pull/296">https://github.com/ilri/DSpace/pull/296</a></li>
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</ul>
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<h2 id="2017-01-16">2017-01-16</h2>
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<ul>
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<li>Fix the two items Maria found with duplicate mappings with this script:</li>
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</ul>
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<pre><code>/* 184 in correct mappings: https://cgspace.cgiar.org/handle/10568/78596 */
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delete from collection2item where item_id = '80596' and id not in (90792, 90806, 90807);
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/* 1 incorrect mapping: https://cgspace.cgiar.org/handle/10568/78658 */
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delete from collection2item where id = '91082';
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</code></pre>
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|
<h2 id="2017-01-17">2017-01-17</h2>
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|
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<ul>
|
|
<li>Helping clean up some file names in the 232 CIAT records that Sisay worked on last week</li>
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<li>There are about 30 files with <code>%20</code> (space) and Spanish accents in the file name</li>
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|
<li>At first I thought we should fix these, but actually it is <a href="https://www.w3.org/TR/html4/appendix/notes.html#h-B.2.1">prescribed by the W3 working group to convert these to UTF8 and URL encode them</a>!</li>
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<li>And the file names don’t really matter either, as long as the SAF Builder tool can read them—after that DSpace renames them with a hash in the assetstore</li>
|
|
<li>Seems like the only ones I should replace are the <code>'</code> apostrophe characters, as <code>%27</code>:</li>
|
|
</ul>
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|
|
|
<pre><code>value.replace("'",'%27')
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Add the item’s Type to the filename column as a hint to SAF Builder so it can set a more useful description field:</li>
|
|
</ul>
|
|
|
|
<pre><code>value + "__description:" + cells["dc.type"].value
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Test importing of the new CIAT records (actually there are 232, not 234):</li>
|
|
</ul>
|
|
|
|
<pre><code>$ JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" /home/dspacetest.cgiar.org/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568
|
|
/79042 --source /home/aorth/CIAT_234/SimpleArchiveFormat/ --mapfile=/tmp/ciat.map &> /tmp/ciat.log
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Many of the PDFs are 20, 30, 40, 50+ MB, which makes a total of 4GB</li>
|
|
<li>These are scanned from paper and likely have no compression, so we should try to test if these compression techniques help without comprimising the quality too much:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ convert -compress Zip -density 150x150 input.pdf output.pdf
|
|
$ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -dQUIET -dBATCH -sOutputFile=output.pdf input.pdf
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Somewhere on the Internet suggested using a DPI of 144</li>
|
|
</ul>
|
|
|
|
<h2 id="2017-01-19">2017-01-19</h2>
|
|
|
|
<ul>
|
|
<li>In testing a random sample of CIAT’s PDFs for compressability, it looks like all of these methods generally increase the file size so we will just import them as they are</li>
|
|
<li>Import 232 CIAT records into CGSpace:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/68704 --source /home/aorth/CIAT_232/SimpleArchiveFormat/ --mapfile=/tmp/ciat.map &> /tmp/ciat.log
|
|
</code></pre>
|
|
|
|
<h2 id="2017-01-22">2017-01-22</h2>
|
|
|
|
<ul>
|
|
<li>Looking at some records that Sisay is having problems importing into DSpace Test (seems to be because of copious whitespace return characters from Excel’s CSV exporter)</li>
|
|
<li>There were also some issues with an invalid dc.date.issued field, and I trimmed leading / trailing whitespace and cleaned up some URLs with unneeded parameters like ?show=full</li>
|
|
</ul>
|
|
|
|
<h2 id="2017-01-23">2017-01-23</h2>
|
|
|
|
<ul>
|
|
<li>I merged Atmire’s pull request into the development branch so they can deploy it on DSpace Test</li>
|
|
</ul>
|
|
|
|
|
|
|
|
|
|
|
|
</article>
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|
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|
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|
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 offset-sm-1 blog-sidebar">
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<section class="sidebar-module">
|
|
<h4>Recent Posts</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
<li><a href="/cgspace-notes/2017-01/">January, 2017</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2016-12/">December, 2016</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2016-11/">November, 2016</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
|
|
|
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</ol>
|
|
</section>
|
|
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|
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<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>
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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p>
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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