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
$ ./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
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