cgspace-notes/content/2016-05.md

+++ date = "2016-05-01T23:06:00+03:00" author = "Alan Orth" title = "May, 2016" tags = ["notes"] image = "../images/bg.jpg"

+++

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

• The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29
• 100% of the requests coming from Ethiopia are like this and result in an HTTP 500:

GET /rest/handle/10568/NaN?expand=parentCommunityList,metadata HTTP/1.1

• For now I'll block just the Ethiopian IP
• The owner of that application has said that the NaN (not a number) is an error in his code and he'll fix it

2016-05-03

• Update nginx to 1.10.x branch on CGSpace
• Fix a reference to dc.type.output in Discovery that I had missed when we migrated to dc.type last month (#223)

2016-05-06

• DSpace Test is down, catalina.out has lots of messages about heap space from some time yesterday (!)
• It looks like Sisay was doing some batch imports
• Hmm, also disk space is full
• I decided to blow away the solr indexes, since they are 50GB and we don't really need all the Atmire stuff there right now
• I will re-generate the Discovery indexes after re-deploying
• Testing renew-letsencrypt.sh script for nginx

#!/usr/bin/env bash

readonly SERVICE_BIN=/usr/sbin/service
readonly LETSENCRYPT_BIN=/opt/letsencrypt/letsencrypt-auto

# stop nginx so LE can listen on port 443
$SERVICE_BIN nginx stop

$LETSENCRYPT_BIN renew -nvv --standalone --standalone-supported-challenges tls-sni-01 > /var/log/letsencrypt/renew.log 2>&1

LE_RESULT=$?

$SERVICE_BIN nginx start

if [[ "$LE_RESULT" != 0 ]]; then
    echo 'Automated renewal failed:'

    cat /var/log/letsencrypt/renew.log

    exit 1
fi

• Seems to work well

2016-05-10

• Start looking at more metadata migrations
• There are lots of fields in dcterms namespace that look interesting, like:
  • dcterms.type
  • dcterms.spatial
• Not sure what dcterms is...
• Looks like these were added in DSpace 4 to allow for future work to make DSpace more flexible
• CGSpace's dc registry has 96 items, and the default DSpace one has 73.

2016-05-11

• Identify and propose the next phase of CGSpace fields to migrate:

  • dc.title.jtitle → cg.title.journal
  • dc.identifier.status → cg.identifier.status
  • dc.river.basin → cg.river.basin
  • dc.Species → cg.species
  • dc.targetaudience → cg.targetaudience
  • dc.fulltextstatus → cg.fulltextstatus
  • dc.editon → cg.edition
  • dc.isijournal → cg.isijournal

• Start a test rebase of the 5_x-prod branch on top of the dspace-5.5 tag

• There were a handful of conflicts that I didn't understand

• After completing the rebase I tried to build with the module versions Atmire had indicated as being 5.5 ready but I got this error:

[ERROR] Failed to execute goal on project additions: Could not resolve dependencies for project org.dspace.modules:additions:jar:5.5: Could not find artifact com.atmire:atmire-metadata-quality-api:jar:5.5-2.10.1-0 in sonatype-releases (https://oss.sonatype.org/content/repositories/releases/) -> [Help 1]

• I've sent them a question about it
• A user mentioned having problems with uploading a 33 MB PDF
• I told her I would increase the limit temporarily tomorrow morning
• Turns out she was able to decrease the size of the PDF so we didn't have to do anything

2016-05-12

• Looks like the issue that Abenet was having a few days ago with "Connection Reset" in Firefox might be due to a Firefox 46 issue: https://bugzilla.mozilla.org/show_bug.cgi?id=1268775
• I finally found a copy of the latest CG Core metadata guidelines and it looks like we can add a few more fields to our next migration:
  • dc.rplace.region → cg.coverage.region
  • dc.cplace.country → cg.coverage.country
• Questions for CG people:
  • Our dc.place and dc.srplace.subregion could both map to cg.coverage.admin-unit?
  • Should we use dc.contributor.crp or cg.contributor.crp for the CRP (ours is dc.crsubject.crpsubject)?
  • Our dc.contributor.affiliation and dc.contributor.corporate could both map to dc.contributor and possibly dc.contributor.center depending on if it's a CG center or not
  • dc.title.jtitle could either map to dc.publisher or dc.source depending on how you read things
• Found ~200 messed up CIAT values in dc.publisher:

# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to "%  %";

2016-05-13

• More theorizing about CGcore
• Add two new fields:
  • dc.srplace.subregion → cg.coverage.admin-unit
  • dc.place → cg.place
• dc.place is our own field, so it's easy to move
• I've removed dc.title.jtitle from the list for now because there's no use moving it out of DC until we know where it will go (see discussion yesterday)

2016-05-18

• Work on 707 CCAFS records
• They have thumbnails on Flickr and elsewhere
• In OpenRefine I created a new filename column based on the thumbnail column with the following GREL:

if(cells['thumbnails'].value.contains('hqdefault'), cells['thumbnails'].value.split('/')[-2] + '.jpg', cells['thumbnails'].value.split('/')[-1])

• Because ~400 records had the same filename on Flickr (hqdefault.jpg) but different UUIDs in the URL
• So for the hqdefault.jpg ones I just take the UUID (-2) and use it as the filename
• Before importing with SAFBuilder I tested adding "__bundle:THUMBNAIL" to the filename column and it works fine

2016-05-19

• More quality control on filename field of CCAFS records to make processing in shell and SAFBuilder more reliable:

value.replace('_','').replace('-','')

• We need to hold off on moving dc.Species to cg.species because it is only used for plants, and might be better to move it to something like cg.species.plant
• And dc.identifier.fund is MOSTLY used for CPWF project identifier but has some other sponsorship things
  • We should move PN*, SG*, CBA, IA, and PHASE* values to cg.identifier.cpwfproject
  • The rest, like BMGF and USAID etc, might have to go to either dc.description.sponsorship or cg.identifier.fund (not sure yet)
  • There are also some mistakes in CPWF's things, like "PN 47"
  • This ought to catch all the CPWF values (there don't appear to be and SG* values):

# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');

2016-05-20

• More work on CCAFS Video and Images records
• For SAFBuilder we need to modify filename column to have the thumbnail bundle:

value + "__bundle:THUMBNAIL"

• Also, I fixed some weird characters using OpenRefine's transform with the following GREL:

value.replace(/\u0081/,'')

• Write shell script to resize thumbnails with height larger than 400: https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256
• Upload 707 CCAFS records to DSpace Test
• A few miscellaneous fixes for XMLUI display niggles (spaces in item lists and link target _black): #224
• Work on configuration changes for Phase 2 metadata migrations

2016-05-23

• Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine
• LibreOffice excludes empty cells when it exports and all the fields shift over to the left and cause URLs to go to Subjects, etc.
• Google Docs does this better, but somehow reorders the rows and when I paste the thumbnail/filename row in they don't match!
• I will have to try later

2016-05-30

• Export CCAFS video and image records from DSpace Test using the migrate option (-m):

$ mkdir ~/ccafs-images
$ /home/dspacetest.cgiar.org/bin/dspace export -t COLLECTION -i 10568/79355 -d ~/ccafs-images -n 0 -m

• And then import to CGSpace:

$ JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/70974 --source /tmp/ccafs-images --mapfile=/tmp/ccafs-images-may30.map &> /tmp/ccafs-images-may30.log

• But now we have double authors for "CGIAR Research Program on Climate Change, Agriculture and Food Security" in the authority
• I'm trying to do a Discovery index before messing with the authority index
• Looks like we are missing the index-authority cron job, so who knows what's up with our authority index
• Run system updates on DSpace Test, re-deploy code, and reboot the server
• Clean up and import ~200 CTA records to CGSpace via CSV like:

$ export JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8"
$ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA-May30/CTA-42229.csv &> ~/CTA-May30/CTA-42229.log

• Discovery indexing took a few hours for some reason, and after that I started the index-authority script

$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace index-authority

2016-05-31

• The index-authority script ran over night and was finished in the morning
• Hopefully this was because we haven't been running it regularly and it will speed up next time
• I am running it again with a timer to see:

$ time /home/cgspace.cgiar.org/bin/dspace index-authority
Retrieving all data
Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
Cleaning the old index
Writing new data
All done !

real    37m26.538s
user    2m24.627s
sys     0m20.540s

• Update tomcat7 crontab on CGSpace and DSpace Test to have the index-authority script that we were missing
• Add new ILRI subject and CCAFS project tags to input-forms.xml (#226, #225)
• Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.
• Re-sync DSpace Test data with CGSpace
• Clean up and import ~65 more CTA items into CGSpace