CGSpace Notes

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

April, 2016

by Alan Orth in  

2016-04-04

  • Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit
  • We are backing up all logs in the log folder, including useless stuff like solr, cocoon, handle-plugin, etc
  • After running DSpace for over five years I’ve never needed to look in any other log file than dspace.log, leave alone one from last year!
  • This will save us a few gigs of backup space we’re paying for on S3
  • Also, I noticed the checker log has some errors we should pay attention to:
Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:146)
        at edu.sdsc.grid.io.local.LocalFileInputStream.open(LocalFileInputStream.java:171)
        at edu.sdsc.grid.io.GeneralFileInputStream.<init>(GeneralFileInputStream.java:145)
        at edu.sdsc.grid.io.local.LocalFileInputStream.<init>(LocalFileInputStream.java:139)
        at edu.sdsc.grid.io.FileFactory.newFileInputStream(FileFactory.java:630)
        at org.dspace.storage.bitstore.BitstreamStorageManager.retrieve(BitstreamStorageManager.java:525)
        at org.dspace.checker.BitstreamDAO.getBitstream(BitstreamDAO.java:60)
        at org.dspace.checker.CheckerCommand.processBitstream(CheckerCommand.java:303)
        at org.dspace.checker.CheckerCommand.checkBitstream(CheckerCommand.java:171)
        at org.dspace.checker.CheckerCommand.process(CheckerCommand.java:120)
        at org.dspace.app.checker.ChecksumChecker.main(ChecksumChecker.java:236)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:225)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:77)
******************************************************
  • So this would be the tomcat7 Unix user, who seems to have a default limit of 1024 files in its shell
  • For what it’s worth, we have been setting the actual Tomcat 7 process’ limit to 16384 for a few years (in /etc/default/tomcat7)
  • Looks like cron will read limits from /etc/security/limits.* so we can do something for the tomcat7 user there
  • Submit pull request for Tomcat 7 limits in Ansible dspace role (#30)

2016-04-05

  • Reduce Amazon S3 storage used for logs from 46 GB to 6GB by deleting a bunch of logs we don’t need!

    # s3cmd ls s3://cgspace.cgiar.org/log/ > /tmp/s3-logs.txt
# grep checker.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep cocoon.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep handle-plugin.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep solr.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del

  • Also, adjust the cron jobs for backups so they only backup dspace.log and some stats files (.dat)

  • Try to do some metadata field migrations using the Atmire batch UI (dc.Species → cg.species) but it took several hours and even missed a few records

2016-04-06

  • A better way to move metadata on this scale is via SQL, for example dc.type.output → dc.type (their IDs in the metadatafieldregistry are 66 and 109, respectively):

    dspacetest=# update metadatavalue set metadata_field_id=109 where metadata_field_id=66;
UPDATE 40852

  • After that an index-discovery -bf is required

  • Start working on metadata migrations, add 25 or so new metadata fields to CGSpace

2016-04-07

  • Write shell script to do the migration of fields: https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b

  • Testing with a few fields it seems to work well:

    $ ./migrate-fields.sh
UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
UPDATE 40883
UPDATE metadatavalue SET metadata_field_id=202 WHERE metadata_field_id=72
UPDATE 21420
UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
UPDATE 51258

2016-04-08

  • Discuss metadata renaming with Abenet, we decided it’s better to start with the center-specific subjects like ILRI, CIFOR, CCAFS, IWMI, and CPWF
  • I’ve e-mailed CCAFS and CPWF people to ask them how much time it will take for them to update their systems to cope with this change

2016-04-10

  • Looking at the DOI issue reported by Leroy from CIAT a few weeks ago

  • It seems the dx.doi.org URLs are much more proper in our repository!

    dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and text_value like 'http://dx.doi.org%';
count
-------
5638
(1 row)

dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and text_value like 'http://doi.org%';
count
-------
 3

  • I will manually edit the dc.identifier.doi in 10568⁄72509 and tweet the link, then check back in a week to see if the donut gets updated

2016-04-11

  • The donut is already updated and shows the correct number now
  • CCAFS people say it will only take them an hour to update their code for the metadata renames, so I proposed we’d do it tentatively on Monday the 18th.

2016-04-12

  • Looking at quality of WLE data (cg.subject.iwmi) in SQL:

    dspacetest=# select text_value, count(*) from metadatavalue where metadata_field_id=217 group by text_value order by count(*) desc;

  • Listings and Reports is still not returning reliable data for dc.type

  • I think we need to ask Atmire, as their documentation isn’t too clear on the format of the filter configs

  • Alternatively, I want to see if I move all the data from dc.type.output to dc.type and then re-index, if it behaves better

  • Looking at our input-forms.xml I see we have two sets of ILRI subjects, but one has a few extra subjects

  • Remove one set of ILRI subjects and remove duplicate VALUE CHAINS from existing list (#216)

  • I decided to keep the set of subjects that had FMD and RANGELANDS added, as it appears to have been requested to have been added, and might be the newer list

  • I found 226 blank metadatavalues:

    dspacetest# select * from metadatavalue where resource_type_id=2 and text_value='';

  • I think we should delete them and do a full re-index:

    dspacetest=# delete from metadatavalue where resource_type_id=2 and text_value='';
DELETE 226

  • I deleted them on CGSpace but I’ll wait to do the re-index as we’re going to be doing one in a few days for the metadata changes anyways

  • In other news, moving the dc.type.output to dc.type and re-indexing seems to have fixed the Listings and Reports issue from above

  • Unfortunately this isn’t a very good solution, because Listings and Reports config should allow us to filter on dc.type.* but the documentation isn’t very clear and I couldn’t reach Atmire today

  • We want to do the dc.type.output move on CGSpace anyways, but we should wait as it might affect other external people!

2016-04-14

  • Communicate with Macaroni Bros again about dc.type
  • Help Sisay with some rsync and Linux stuff
  • Notify CIAT people of metadata changes (I had forgotten them last week)

2016-04-15

  • DSpace Test had crashed, so I ran all system updates, rebooted, and re-deployed DSpace code

2016-04-18

  • Talk to CIAT people about their portal again
  • Start looking more at the fields we want to delete
  • The following metadata fields have 0 items using them, so we can just remove them from the registry and any references in XMLUI, input forms, etc:
    • dc.description.abstractother
    • dc.whatwasknown
    • dc.whatisnew
    • dc.description.nationalpartners
    • dc.peerreviewprocess
    • cg.species.animal
  • Deleted!
  • The following fields have some items using them and I have to decide what to do with them (delete or move):
    • dc.icsubject.icrafsubject: 6 items, mostly in CPWF collections
    • dc.type.journal: 11 items, mostly in ILRI collections
    • dc.publicationcategory: 1 item, in CPWF
    • dc.GRP: 2 items, CPWF
    • dc.Species.animal: 6 items, in ILRI and AnGR
    • cg.livestock.agegroup: 9 items, in ILRI collections
    • cg.livestock.function: 20 items, mostly in EADD

  • Test metadata migration on local instance again:

    $ ./migrate-fields.sh
UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
UPDATE 40885
UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
UPDATE 51330
UPDATE metadatavalue SET metadata_field_id=208 WHERE metadata_field_id=82
UPDATE 5986
UPDATE metadatavalue SET metadata_field_id=210 WHERE metadata_field_id=88
UPDATE 2456
UPDATE metadatavalue SET metadata_field_id=215 WHERE metadata_field_id=106
UPDATE 3872
UPDATE metadatavalue SET metadata_field_id=217 WHERE metadata_field_id=108
UPDATE 46075
$ JAVA_OPTS="-Xms512m -Xmx512m -Dfile.encoding=UTF-8" ~/dspace/bin/dspace index-discovery -bf

  • CGSpace was down but I’m not sure why, this was in catalina.out:

    Apr 18, 2016 7:32:26 PM com.sun.jersey.spi.container.ContainerResponse logException
SEVERE: Mapped exception to response: 500 (Internal Server Error)
javax.ws.rs.WebApplicationException
    at org.dspace.rest.Resource.processFinally(Resource.java:163)
    at org.dspace.rest.HandleResource.getObject(HandleResource.java:81)
    at sun.reflect.GeneratedMethodAccessor198.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
    at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185)
    at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
    at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
    at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
    at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
    at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
    at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
    at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1511)
    at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1442)
    at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1391)
    at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1381)
    at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
...

  • Everything else in the system looked normal (50GB disk space available, nothing weird in dmesg, etc)

  • After restarting Tomcat a few more of these errors were logged but the application was up

2016-04-19

  • Get handles for items that are using a given metadata field, ie dc.Species.animal (105):

    # select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=105);
handle
-------------
10568/10298
10568/16413
10568/16774
10568/34487

  • Delete metadata values for dc.GRP and dc.icsubject.icrafsubject:

    # delete from metadatavalue where resource_type_id=2 and metadata_field_id=96;
# delete from metadatavalue where resource_type_id=2 and metadata_field_id=83;

  • They are old ICRAF fields and we haven’t used them since 2011 or so

  • Also delete them from the metadata registry

  • CGSpace went down again, dspace.log had this:

    2016-04-19 15:02:17,025 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object

  • I restarted Tomcat and PostgreSQL and now it’s back up

  • I bet this is the same crash as yesterday, but I only saw the errors in catalina.out

  • Looks to be related to this, from dspace.log:

    2016-04-19 15:16:34,670 ERROR org.dspace.rest.Resource @ Something get wrong. Aborting context in finally statement.

  • We have 18,000 of these errors right now…

  • Delete a few more old metadata values: dc.Species.animal, dc.type.journal, and dc.publicationcategory:

    # delete from metadatavalue where resource_type_id=2 and metadata_field_id=105;
# delete from metadatavalue where resource_type_id=2 and metadata_field_id=85;
# delete from metadatavalue where resource_type_id=2 and metadata_field_id=95;

  • And then remove them from the metadata registry

2016-04-20

  • Re-deploy DSpace Test with the new subject and type fields, run all system updates, and reboot the server
  • Migrate fields and re-deploy CGSpace with the new subject and type fields, run all system updates, and reboot the server

  • Field migration went well:

    $ ./migrate-fields.sh
UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
UPDATE 40909
UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
UPDATE 51419
UPDATE metadatavalue SET metadata_field_id=208 WHERE metadata_field_id=82
UPDATE 5986
UPDATE metadatavalue SET metadata_field_id=210 WHERE metadata_field_id=88
UPDATE 2458
UPDATE metadatavalue SET metadata_field_id=215 WHERE metadata_field_id=106
UPDATE 3872
UPDATE metadatavalue SET metadata_field_id=217 WHERE metadata_field_id=108
UPDATE 46075

  • Also, I migrated CGSpace to using the PGDG PostgreSQL repo as the infrastructure playbooks had been using it for a while and it seemed to be working well

  • Basically, this gives us the ability to use the latest upstream stable 9.3.x release (currently 9.3.12)

  • Looking into the REST API errors again, it looks like these started appearing a few days ago in the tens of thousands:

    $ grep -c "Aborting context in finally statement" dspace.log.2016-04-20
21252

  • I found a recent discussion on the DSpace mailing list and I’ve asked for advice there

  • Looks like this issue was noted and fixed in DSpace 5.5 (we’re on 5.1): https://jira.duraspace.org/browse/DS-2936

  • I’ve sent a message to Atmire asking about compatibility with DSpace 5.5

2016-04-21

  • Fix a bunch of metadata consistency issues with IITA Journal Articles (Peer review, Formally published, messed up DOIs, etc)
  • Atmire responded with DSpace 5.5 compatible versions for their modules, so I’ll start testing those in a few weeks

2016-04-22

2016-04-26

2016-04-27

  • I woke up to ten or fifteen “up” and “down” emails from the monitoring website
  • Looks like the last one was “down” from about four hours ago

  • I think there must be something with this REST stuff:

    # grep -c "Aborting context in finally statement" dspace.log.2016-04-*
dspace.log.2016-04-01:0
dspace.log.2016-04-02:0
dspace.log.2016-04-03:0
dspace.log.2016-04-04:0
dspace.log.2016-04-05:0
dspace.log.2016-04-06:0
dspace.log.2016-04-07:0
dspace.log.2016-04-08:0
dspace.log.2016-04-09:0
dspace.log.2016-04-10:0
dspace.log.2016-04-11:0
dspace.log.2016-04-12:235
dspace.log.2016-04-13:44
dspace.log.2016-04-14:0
dspace.log.2016-04-15:35
dspace.log.2016-04-16:0
dspace.log.2016-04-17:0
dspace.log.2016-04-18:11942
dspace.log.2016-04-19:28496
dspace.log.2016-04-20:28474
dspace.log.2016-04-21:28654
dspace.log.2016-04-22:28763
dspace.log.2016-04-23:28773
dspace.log.2016-04-24:28775
dspace.log.2016-04-25:28626
dspace.log.2016-04-26:28655
dspace.log.2016-04-27:7271

  • I restarted tomcat and it is back up

  • Add Spanish XMLUI strings so those users see “CGSpace” instead of “DSpace” in the user interface (#222)

  • Submit patch to upstream DSpace for the misleading help text in the embargo step of the item submission: https://jira.duraspace.org/browse/DS-3172

  • Update infrastructure playbooks for nginx 1.10.x (stable) release: https://github.com/ilri/rmg-ansible-public/issues/32

  • Currently running on DSpace Test, we’ll give it a few days before we adjust CGSpace

  • CGSpace down, restarted tomcat and it’s back up

2016-04-28

  • Problems with stability again. I’ve blocked access to /rest for now to see if the number of errors in the log files drop
  • Later we could maybe start logging access to /rest and perhaps whitelist some IPs…

2016-04-30

  • Logs for today and yesterday have zero references to this REST error, so I’m going to open back up the REST API but log all requests

    location /rest {
	access_log /var/log/nginx/rest.log;
	proxy_pass http://127.0.0.1:8443;
}

  • I will check the logs again in a few days to look for patterns, see who is accessing it, etc