CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

January, 2017

by Alan Orth in  

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.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

  • And the DSpace log shows:

    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

  • Despite failing instantly, a statistics-2016 directory was created, but it only has a data dir (no conf)

  • The Tomcat access logs show more:

    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

  • Very interesting… it creates the core and then fails somehow

2017-01-08

  • Put Sisay’s item-view.xsl code to show mapped collections on CGSpace (#295)

2017-01-09

  • A user wrote to tell me that the new display of an item’s mappings had a crazy bug for at least one item: https://cgspace.cgiar.org/handle/10568/78596
  • She said she only mapped it once, but it appears to be mapped 184 times

Crazy item mapping

2017-01-10

  • 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”
  • I’ve asked on the dspace-tech mailing list to see if anyone can help
  • I found an old post on the mailing list discussing a similar issue, and listing some SQL commands that might help

  • For example, this shows 186 mappings for the item, the first three of which are real:

    dspace=#  select * from collection2item where item_id = '80596';

  • Then I deleted the others:

    dspace=# delete from collection2item where item_id = '80596' and id not in (90792, 90806, 90807);

  • And in the item view it now shows the correct mappings

  • I will have to ask the DSpace people if this is a valid approach

  • Finish looking at the Journal Title corrections of the top 500 Journal Titles so we can make a controlled vocabulary from it

2017-01-11

  • Maria found another item with duplicate mappings: https://cgspace.cgiar.org/handle/10568/78658

  • Error in fix-metadata-values.py when it tries to print the value for Entwicklung & Ländlicher Raum:

    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)

  • Seems we need to encode as UTF-8 before printing to screen, ie:

    print("Fixing {} occurences of: {}".format(records_to_fix, record[0].encode('utf-8')))

  • See: http://stackoverflow.com/a/36427358/487333

  • 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

  • Now back to cleaning up some journal titles so we can make the controlled vocabulary:

    $ ./fix-metadata-values.py -i /tmp/fix-27-journal-titles.csv -f dc.source -t correct -m 55 -d dspace -u dspace -p 'fuuu'

  • Now get the top 500 journal titles:

    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 count desc limit 500) to /tmp/journal-titles.csv with csv;

  • The values are a bit dirty and outdated, since the file I had given to Abenet and Peter was from November

  • I will have to go through these and fix some more before making the controlled vocabulary

  • Added 30 more corrections or so, now there are 49 total and I’ll have to get the top 500 after applying them

2017-01-13

2017-01-16

  • Fix the two items Maria found with duplicate mappings with this script:

    /* 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';

2017-01-17

  • Helping clean up some file names in the 232 CIAT records that Sisay worked on last week
  • There are about 30 files with %20 (space) and Spanish accents in the file name
  • At first I thought we should fix these, but actually it is prescribed by the W3 working group to convert these to UTF8 and URL encode them!
  • 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

  • Seems like the only ones I should replace are the ' apostrophe characters, as %27:

    value.replace("'",'%27')

  • Add the item’s Type to the filename column as a hint to SAF Builder so it can set a more useful description field:

    value + "__description:" + cells["dc.type"].value

  • Test importing of the new CIAT records (actually there are 232, not 234):

    $ 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

  • Many of the PDFs are 20, 30, 40, 50+ MB, which makes a total of 4GB

  • 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:

    $ 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

  • Somewhere on the Internet suggested using a DPI of 144

2017-01-19

  • 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

  • Import 232 CIAT records into CGSpace:

    $ 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

2017-01-22

  • 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)
  • 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

2017-01-23

  • I merged Atmire’s pull request into the development branch so they can deploy it on DSpace Test

  • Move some old ILRI Program communities to a new subcommunity for former programs (10568⁄79164):

    $ for community in 10568/171 10568/27868 10568/231 10568/27869 10568/150 10568/230 10568/32724 10568/172; do /home/cgspace.cgiar.org/bin/dspace community-filiator --remove --parent=10568/27866 --child="$community" && /home/cgspace.cgiar.org/bin/dspace community-filiator --set --parent=10568/79164 --child="$community"; done

  • Move some collections with move-collections.sh using the following config:

    10568/42161 10568/171 10568/79341
10568/41914 10568/171 10568/79340

2017-01-24

  • Run all updates on DSpace Test and reboot the server

  • Run fixes for Journal titles on CGSpace:

    $ ./fix-metadata-values.py -i /tmp/fix-49-journal-titles.csv -f dc.source -t correct -m 55 -d dspace -u dspace -p 'password'

  • Create a new list of the top 500 journal titles from the database:

    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 count desc limit 500) to /tmp/journal-titles.csv with csv;

  • Then sort them in OpenRefine and create a controlled vocabulary by manually adding the XML markup, pull request (#298)

  • This would be the last issue remaining to close the meta issue about switching to controlled vocabularies (#69)

2017-01-25

  • Atmire says the com.atmire.statistics.util.UpdateSolrStorageReports and com.atmire.utils.ReportSender are no longer necessary because they are using a Spring scheduler for these tasks now
  • Pull request to remove them from the Ansible templates: https://github.com/ilri/rmg-ansible-public/pull/80
  • Still testing the Atmire modules on DSpace Test, and it looks like a few issues we had reported are now fixed:
    • XLS Export from Content statistics
    • Most popular items
    • Show statistics on collection pages
  • But now we have a new issue with the “Types” in Content statistics not being respected—we only get the defaults, despite having custom settings in dspace/config/modules/atmire-cua.cfg

2017-01-27

  • Magdalena pointed out that somehow the Anonymous group had been added to the Administrators group on CGSpace (!)
  • Discuss plans to update CCAFS metadata and communities for their new flagships and phase II project identifiers
  • The flagships are in cg.subject.ccafs, and we need to probably make a new field for the phase II project identifiers

2017-01-28

  • Merge controlled vocabulary for journal titles (dc.source) into CGSpace (#298)
  • Merge new CIAT subject into CGSpace (#296)

2017-01-29

  • Run all system updates on DSpace Test, redeploy DSpace code, and reboot the server
  • Run all system updates on CGSpace, redeploy DSpace code, and reboot the server