Posts on CGSpace Notes

June, 2018

Mon, 04 Jun 2018 19:49:54 -0700

2018-06-04

Test the DSpace 5.8 module upgrades from Atmire (#378)
- There seems to be a problem with the CUA and L&R versions in pom.xml because they are using SNAPSHOT and it doesn’t build
I added the new CCAFS Phase II Project Tag PII-FP1_PACCA2 and merged it into the 5_x-prod branch (#379)
I proofed and tested the ILRI author corrections that Peter sent back to me this week:

$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n

I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in March, 2018

May, 2018

Tue, 01 May 2018 16:43:54 +0300

2018-05-01

I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
- http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E
- http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
Then I reduced the JVM heap size from 6144 back to 5120m
Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use

April, 2018

Sun, 01 Apr 2018 16:13:54 +0200

2018-04-01

I tried to test something on DSpace Test but noticed that it’s down since god knows when
Catalina logs at least show some memory errors yesterday:

March, 2018

Fri, 02 Mar 2018 16:07:54 +0200

2018-03-02

Export a CSV of the IITA community metadata for Martin Mueller

February, 2018

Thu, 01 Feb 2018 16:28:54 +0200

2018-02-01

Peter gave feedback on the dc.rights proof of concept that I had sent him last week
We don’t need to distinguish between internal and external works, so that makes it just a simple list
Yesterday I figured out how to monitor DSpace sessions using JMX
I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01

January, 2018

Tue, 02 Jan 2018 08:35:54 -0800

2018-01-02

Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time
I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary
The nginx logs show HTTP 200s until 02/Jan/2018:11:27:17 +0000 when Uptime Robot got an HTTP 500
In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”
And just before that I see this:

Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].

Ah hah! So the pool was actually empty!
I need to increase that, let’s try to bump it up from 50 to 75
After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw
I notice this error quite a few times in dspace.log:

2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.

And there are many of these errors every day for the past month:

$ grep -c "Error while searching for sidebar facets" dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34

Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains

December, 2017

Fri, 01 Dec 2017 13:53:54 +0300

2017-12-01

Uptime Robot noticed that CGSpace went down
The logs say “Timeout waiting for idle object”
PostgreSQL activity says there are 115 connections currently
The list of connections to XMLUI and REST API for today:

November, 2017

Thu, 02 Nov 2017 09:37:54 +0200

2017-11-01

The CORE developers responded to say they are looking into their bot not respecting our robots.txt

2017-11-02

Today there have been no hits by CORE and no alerts from Linode (coincidence?)

# grep -c "CORE" /var/log/nginx/access.log
0

Generate list of authors on CGSpace for Peter to go through and correct:

dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701

October, 2017

Sun, 01 Oct 2017 08:07:54 +0300

2017-10-01

Peter emailed to point out that many items in the ILRI archive collection have multiple handles:

http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336

There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine
Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections

CGIAR Library Migration

Mon, 18 Sep 2017 16:38:35 +0300

Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called CGIAR System Organization.

September, 2017

Thu, 07 Sep 2017 16:54:52 +0700

2017-09-06

Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two hours

2017-09-07

Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group

August, 2017

Tue, 01 Aug 2017 11:51:52 +0300

2017-08-01

Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours
I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)
The good thing is that, according to dspace.log.2017-08-01, they are all using the same Tomcat session
This means our Tomcat Crawler Session Valve is working
But many of the bots are browsing dynamic URLs like:
- /handle/10568/3353/discover
- /handle/10568/16510/browse
The robots.txt only blocks the top-level /discover and /browse URLs… we will need to find a way to forbid them from accessing these!
Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): https://jira.duraspace.org/browse/DS-2962
It turns out that we’re already adding the X-Robots-Tag "none" HTTP header, but this only forbids the search engine from indexing the page, not crawling it!
Also, the bot has to successfully browse the page first so it can receive the HTTP header…
We might actually have to block these requests with HTTP 403 depending on the user agent
Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415
This was due to newline characters in the dc.description.abstract column, which caused OpenRefine to choke when exporting the CSV
I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet

July, 2017

Sat, 01 Jul 2017 18:03:52 +0300

2017-07-01

Run system updates and reboot DSpace Test

2017-07-04

Merge changes for WLE Phase II theme rename (#329)
Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:

June, 2017

Thu, 01 Jun 2017 10:14:52 +0300

2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we’ll create a new sub-community for Phase II and create collections for the research themes there The current “Research Themes” community will be renamed to “WLE Phase I Research Themes” Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg.

May, 2017

Mon, 01 May 2017 16:21:52 +0200

2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace.

April, 2017

Sun, 02 Apr 2017 17:08:52 +0200

2017-04-02

Merge one change to CCAFS flagships that I had forgotten to remove last month (“MANAGING CLIMATE RISK”): https://github.com/ilri/DSpace/pull/317
Quick proof-of-concept hack to add dc.rights to the input form, including some inline instructions/hints:

Remove redundant/duplicate text in the DSpace submission license
Testing the CMYK patch on a collection with 650 items:

$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt

March, 2017

Wed, 01 Mar 2017 17:08:52 +0200

2017-03-01

Run the 279 CIAT author corrections on CGSpace

2017-03-02

Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace
CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles
They might come in at the top level in one “CGIAR System” community, or with several communities
I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?
Need to send Peter and Michael some notes about this in a few days
Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI
Filed an issue on DSpace issue tracker for the filter-media bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: DS-3516
Discovered that the ImageMagic filter-media plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK
Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see ¹⁰⁵⁶⁸⁄₅₁₉₉₉):

$ identify ~/Desktop/alc_contrastes_desafios.jpg
/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000

February, 2017

Tue, 07 Feb 2017 07:04:52 -0800

2017-02-07

An item was mapped twice erroneously again, so I had to remove one of the mappings manually:

dspace=# select * from collection2item where item_id = '80278';
  id   | collection_id | item_id
-------+---------------+---------
 92551 |           313 |   80278
 92550 |           313 |   80278
 90774 |          1051 |   80278
(3 rows)
dspace=# delete from collection2item where id = 92551 and item_id = 80278;
DELETE 1

Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301)
Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name

January, 2017

Mon, 02 Jan 2017 10:43:00 +0300

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

December, 2016

Fri, 02 Dec 2016 10:43:00 +0300

2016-12-02

CGSpace was down for five hours in the morning while I was sleeping
While looking in the logs for errors, I see tons of warnings about Atmire MQM:

2016-12-02 03:00:32,352 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail="dc.title", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail="THUMBNAIL", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail="-1", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")

I see thousands of them in the logs for the last few months, so it’s not related to the DSpace 5.5 upgrade
I’ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is:

November, 2016

Tue, 01 Nov 2016 09:21:00 +0300

2016-11-01

Add dc.type to the output options for Atmire’s Listings and Reports module (#286)

October, 2016

Mon, 03 Oct 2016 15:53:00 +0300

2016-10-03

Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up
Need to test the following scenarios to see how author order is affected:
- ORCIDs only
- ORCIDs plus normal authors
I exported a random item’s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry:

0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X

September, 2016

Thu, 01 Sep 2016 15:53:00 +0300

2016-09-01

Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors
Discuss how the migration of CGIAR’s Active Directory to a flat structure will break our LDAP groups in DSpace
We had been using DC=ILRI to determine whether a user was ILRI or not
It looks like we might be able to use OUs now, instead of DCs:

$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"

August, 2016

Mon, 01 Aug 2016 15:53:00 +0300

2016-08-01

Add updated distribution license from Sisay (#259)
Play with upgrading Mirage 2 dependencies in bower.json because most are several versions of out date
Bootstrap is at 3.3.0 but upstream is at 3.3.7, and upgrading to anything beyond 3.3.1 breaks glyphicons and probably more
bower stuff is a dead end, waste of time, too many issues
Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of fonts)
Start working on DSpace 5.1 → 5.5 port:

$ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5

July, 2016

Fri, 01 Jul 2016 10:53:00 +0300

2016-07-01

Add dc.description.sponsorship to Discovery sidebar facets and make investors clickable in item view (#232)
I think this query should find and replace all authors that have “,” at the end of their names:

dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
UPDATE 95
dspacetest=# select text_value from  metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
 text_value
------------
(0 rows)

In this case the select query was showing 95 results before the update

June, 2016

Wed, 01 Jun 2016 10:53:00 +0300

2016-06-01

Experimenting with IFPRI OAI (we want to harvest their publications)
After reading the ContentDM documentation I found IFPRI’s OAI endpoint: http://ebrary.ifpri.org/oai/oai.php
After reading the OAI documentation and testing with an OAI validator I found out how to get their publications
This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&from=2016-01-01&set=p15738coll2&metadataPrefix=oai_dc
You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship

May, 2016

Sun, 01 May 2016 23:06:00 +0300

2016-05-01

Since yesterday there have been 10,000 REST errors and the site has been unstable again
I have blocked access to the API now
There are 3,000 IPs accessing the REST API in a 24-hour period!

# awk '{print $1}' /var/log/nginx/rest.log  | uniq | wc -l
3168

April, 2016

Mon, 04 Apr 2016 11:06:00 +0300

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:

March, 2016

Wed, 02 Mar 2016 16:50:00 +0300

2016-03-02

Looking at issues with author authorities on CGSpace
For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module
Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server

February, 2016

Fri, 05 Feb 2016 13:18:00 +0300

2016-02-05

Looking at some DAGRIS data for Abenet Yabowork
Lots of issues with spaces, newlines, etc causing the import to fail
I noticed we have a very interesting list of countries on CGSpace:

Not only are there 49,000 countries, we have some blanks (25)…
Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”

January, 2016

Wed, 13 Jan 2016 13:18:00 +0300

2016-01-13

Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_collections.sh script I wrote last year.
I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.
Update GitHub wiki for documentation of maintenance tasks.

December, 2015

Wed, 02 Dec 2015 13:18:00 +0300

2015-12-02

Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less space:

# cd /home/dspacetest.cgiar.org/log
# ls -lh dspace.log.2015-11-18*
-rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz

November, 2015

Mon, 23 Nov 2015 17:00:57 +0300

2015-11-22

CGSpace went down
Looks like DSpace exhausted its PostgreSQL connection pool
Last week I had increased the limit from 30 to 60, which seemed to help, but now there are many more idle connections:

$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
78