+++ date = "2016-05-01T23:06:00+03:00" author = "Alan Orth" title = "May, 2016" tags = ["Notes"] +++ ## 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](https://github.com/ilri/DSpace/pull/223)) ![Item type in Discovery results](2016/05/discovery-types.png) ## 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](https://wiki.duraspace.org/display/DSDOC5x/Metadata+and+Bitstream+Format+Registries#MetadataandBitstreamFormatRegistries-DublinCoreTermsRegistry(DCTERMS)) 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](https://github.com/ilri/DSpace/pull/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](https://github.com/ilri/DSpace/pull/226), [#225](https://github.com/ilri/DSpace/pull/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