2017-01-04 15:07:43 +01:00
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2017-01-05 13:08:30 +01:00
< meta property = "og:description" content = "2017-01-02 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 I tested on DSpace Test as well and it doesn’t work there either 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 2017-01-04 I tried to shard my local dev instance and it fails the same way: $ JAVA_OPTS="-Xms768m -Xmx768m -Dfile." / >
2017-01-04 15:07:43 +01:00
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2017-01-05 13:08:30 +01:00
< meta itemprop = "description" content = "2017-01-02 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 I tested on DSpace Test as well and it doesn’t work there either 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 2017-01-04 I tried to shard my local dev instance and it fails the same way: $ JAVA_OPTS="-Xms768m -Xmx768m -Dfile." >
2017-01-04 15:07:43 +01:00
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2017-01-04 15:07:43 +01:00
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2017-01-05 13:08:30 +01:00
< meta name = "twitter:description" content = "2017-01-02 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 I tested on DSpace Test as well and it doesn’t work there either 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 2017-01-04 I tried to shard my local dev instance and it fails the same way: $ JAVA_OPTS="-Xms768m -Xmx768m -Dfile." / >
2017-01-04 15:07:43 +01:00
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< h2 class = "blog-post-title" > < a href = "https://alanorth.github.io/cgspace-notes/2017-01/" > January, 2017< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2017-01-02T10:43:00+03:00" > Mon Jan 02, 2017< / time > by Alan Orth in
< i class = "fa fa-tag" aria-hidden = "true" > < / i > < a href = "/cgspace-notes/tags/notes" rel = "tag" > Notes< / a >
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< h2 id = "2017-01-02" > 2017-01-02< / h2 >
< ul >
< 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 >
< li > I tested on DSpace Test as well and it doesn’ t work there either< / li >
< 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 >
< / ul >
2017-01-05 13:08:30 +01:00
< h2 id = "2017-01-04" > 2017-01-04< / h2 >
< ul >
< li > I tried to shard my local dev instance and it fails the same way:< / li >
< / ul >
< pre > < code > $ JAVA_OPTS=" -Xms768m -Xmx768m -Dfile.encoding=UTF-8" ~/dspace/bin/dspace stats-util -s
Moving: 9318 into core statistics-2016
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2016
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2016
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
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.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2291)
at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
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:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
Caused by: org.apache.http.client.ClientProtocolException
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
... 10 more
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.
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:659)
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:487)
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
... 14 more
Caused by: java.net.SocketException: Broken pipe (Write failed)
at java.net.SocketOutputStream.socketWrite0(Native Method)
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
at java.net.SocketOutputStream.write(SocketOutputStream.java:153)
at org.apache.http.impl.io.AbstractSessionOutputBuffer.write(AbstractSessionOutputBuffer.java:181)
at org.apache.http.impl.io.ChunkedOutputStream.flushCacheWithAppend(ChunkedOutputStream.java:124)
at org.apache.http.impl.io.ChunkedOutputStream.write(ChunkedOutputStream.java:181)
at org.apache.http.entity.InputStreamEntity.writeTo(InputStreamEntity.java:132)
at org.apache.http.entity.HttpEntityWrapper.writeTo(HttpEntityWrapper.java:89)
at org.apache.http.impl.client.EntityEnclosingRequestWrapper$EntityWrapper.writeTo(EntityEnclosingRequestWrapper.java:108)
at org.apache.http.impl.entity.EntitySerializer.serialize(EntitySerializer.java:117)
at org.apache.http.impl.AbstractHttpClientConnection.sendRequestEntity(AbstractHttpClientConnection.java:265)
at org.apache.http.impl.conn.ManagedClientConnectionImpl.sendRequestEntity(ManagedClientConnectionImpl.java:203)
at org.apache.http.protocol.HttpRequestExecutor.doSendRequest(HttpRequestExecutor.java:236)
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:121)
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:685)
... 16 more
< / code > < / pre >
< ul >
< li > And the DSpace log shows:< / li >
< / ul >
< pre > < code > 2017-01-04 22:39:05,412 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2016
2017-01-04 22:39:05,412 INFO org.dspace.statistics.SolrLogger @ Moving: 9318 records into core statistics-2016
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)
2017-01-04 22:39:07,310 INFO org.apache.http.impl.client.SystemDefaultHttpClient @ Retrying request to {}-> http://localhost:8081
< / code > < / pre >
< ul >
< li > Despite failing instantly, a < code > statistics-2016< / code > directory was created, but it only has a data dir (no conf)< / li >
< li > The Tomcat access logs show more:< / li >
< / ul >
< 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
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
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
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
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
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
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
127.0.0.1 - - [04/Jan/2017:22:44:00 +0200] " POST /solr/datatables/update?wt=javabin& version=2 HTTP/1.1" 200 41
127.0.0.1 - - [04/Jan/2017:22:44:00 +0200] " POST /solr/datatables/update HTTP/1.1" 200 40
< / code > < / pre >
< ul >
< li > Very interesting… it creates the core and then fails somehow< / li >
< / ul >
2017-01-08 15:55:49 +01:00
< h2 id = "2017-01-08" > 2017-01-08< / h2 >
< ul >
< 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 >
< / ul >
2017-01-09 15:20:52 +01:00
< h2 id = "2017-01-09" > 2017-01-09< / h2 >
< ul >
< 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 >
< li > She said she only mapped it once, but it appears to be mapped 184 times< / li >
< / ul >
< p > < img src = "/cgspace-notes/2017/01/mapping-crazy-duplicate.png" alt = "Crazy item mapping" / > < / p >
2017-01-10 14:25:11 +01:00
< h2 id = "2017-01-10" > 2017-01-10< / h2 >
< ul >
< 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 >
< li > I’ ve asked on the dspace-tech mailing list to see if anyone can help< / li >
2017-01-10 15:21:47 +01:00
< li > I found an old post on the mailing list discussing a similar issue, and listing some SQL commands that might help< / li >
< li > For example, this shows 186 mappings for the item, the first three of which are real:< / li >
< / ul >
< pre > < code > dspace=# select * from collection2item where item_id = '80596';
< / code > < / pre >
< ul >
< li > Then I deleted the others:< / li >
< / ul >
< pre > < code > dspace=# delete from collection2item where item_id = '80596' and id not in (90792, 90806, 90807);
< / code > < / pre >
< ul >
< li > And in the item view it now shows the correct mappings< / li >
< li > I will have to ask the DSpace people if this is a valid approach< / li >
< li > Finish looking at the Journal Title corrections of the top 500 Journal Titles so we can make a controlled vocabulary from it< / li >
2017-01-10 14:25:11 +01:00
< / ul >
2017-01-11 10:45:50 +01:00
< h2 id = "2017-01-11" > 2017-01-11< / h2 >
< ul >
< 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 >
2017-01-11 17:19:57 +01:00
< li > Error in < code > fix-metadata-values.py< / code > when it tries to print the value for Entwicklung & Ländlicher Raum:< / li >
< / ul >
< pre > < code > Traceback (most recent call last):
File " ./fix-metadata-values.py" , line 80, in < module>
print(" Fixing {} occurences of: {}" .format(records_to_fix, record[0]))
UnicodeEncodeError: 'ascii' codec can't encode character u'\xe4' in position 15: ordinal not in range(128)
< / code > < / pre >
< ul >
< li > Seems we need to encode as UTF-8 before printing to screen, ie:< / li >
< / ul >
< pre > < code > print(" Fixing {} occurences of: {}" .format(records_to_fix, record[0].encode('utf-8')))
< / code > < / pre >
< ul >
< li > See: < a href = "http://stackoverflow.com/a/36427358/487333" > http://stackoverflow.com/a/36427358/487333< / a > < / li >
< 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 >
< li > Now back to cleaning up some journal titles so we can make the controlled vocabulary:< / li >
< / ul >
< 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'
< / code > < / pre >
< ul >
< li > Now get the top 500 journal titles:< / li >
< / ul >
< 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
nt desc limit 500) to /tmp/journal-titles.csv with csv;
< / code > < / pre >
< ul >
< li > The values are a bit dirty and outdated, since the file I had given to Abenet and Peter was from November< / li >
< li > I will have to go through these and fix some more before making the controlled vocabulary< / li >
2017-01-11 17:42:55 +01:00
< 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 >
2017-01-11 10:45:50 +01:00
< / ul >
2017-01-13 10:14:29 +01:00
< h2 id = "2017-01-13" > 2017-01-13< / h2 >
< ul >
< 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 >
< / ul >
2017-01-16 10:42:52 +01:00
< h2 id = "2017-01-16" > 2017-01-16< / h2 >
< ul >
< li > Fix the two items Maria found with duplicate mappings with this script:< / li >
< / ul >
< pre > < code > /* 184 in correct mappings: https://cgspace.cgiar.org/handle/10568/78596 */
delete from collection2item where item_id = '80596' and id not in (90792, 90806, 90807);
/* 1 incorrect mapping: https://cgspace.cgiar.org/handle/10568/78658 */
delete from collection2item where id = '91082';
< / code > < / pre >
2017-01-04 15:07:43 +01:00
2017-01-08 16:08:08 +01:00
2017-01-04 15:07:43 +01:00
2017-01-08 16:08:08 +01:00
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2017-01-09 15:20:52 +01:00
2017-01-04 15:07:43 +01:00
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< 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 >
< / ol >
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2017-01-09 15:20:52 +01:00
2017-01-04 15:07:43 +01:00
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< 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 >
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2017-01-05 14:44:45 +01:00
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