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Alan Orth
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The theme used to have a <base> tag, which tells the browser which base to use for relative URLs, but this was actually a buggy and incorrect theme behavior, so we need to update our links. $ sed -i 's/(\(201[567]\)/(\/cgspace-notes\/\1/' content/post/*.md
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date = "2016-05-01T23:06:00+03:00"
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author = "Alan Orth"
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title = "May, 2016"
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tags = ["Notes"]
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+++
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## 2016-05-01
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- Since yesterday there have been 10,000 REST errors and the site has been unstable again
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- I have blocked access to the API now
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- There are 3,000 IPs accessing the REST API in a 24-hour period!
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```
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# awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
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3168
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```
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<!--more-->
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- The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29
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- 100% of the requests coming from Ethiopia are like this and result in an HTTP 500:
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```
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GET /rest/handle/10568/NaN?expand=parentCommunityList,metadata HTTP/1.1
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```
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- For now I'll block just the Ethiopian IP
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- The owner of that application has said that the `NaN` (not a number) is an error in his code and he'll fix it
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## 2016-05-03
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- Update nginx to 1.10.x branch on CGSpace
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- 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))
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## 2016-05-06
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- DSpace Test is down, `catalina.out` has lots of messages about heap space from some time yesterday (!)
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- It looks like Sisay was doing some batch imports
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- Hmm, also disk space is full
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- 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
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- I will re-generate the Discovery indexes after re-deploying
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- Testing `renew-letsencrypt.sh` script for nginx
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```
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#!/usr/bin/env bash
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readonly SERVICE_BIN=/usr/sbin/service
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readonly LETSENCRYPT_BIN=/opt/letsencrypt/letsencrypt-auto
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# stop nginx so LE can listen on port 443
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$SERVICE_BIN nginx stop
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$LETSENCRYPT_BIN renew -nvv --standalone --standalone-supported-challenges tls-sni-01 > /var/log/letsencrypt/renew.log 2>&1
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LE_RESULT=$?
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$SERVICE_BIN nginx start
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if [[ "$LE_RESULT" != 0 ]]; then
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echo 'Automated renewal failed:'
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cat /var/log/letsencrypt/renew.log
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exit 1
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fi
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```
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- Seems to work well
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## 2016-05-10
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- Start looking at more metadata migrations
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- There are lots of fields in `dcterms` namespace that look interesting, like:
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- dcterms.type
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- dcterms.spatial
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- Not sure what `dcterms` is...
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- 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
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- CGSpace's `dc` registry has 96 items, and the default DSpace one has 73.
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## 2016-05-11
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- Identify and propose the next phase of CGSpace fields to migrate:
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- dc.title.jtitle → cg.title.journal
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- dc.identifier.status → cg.identifier.status
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- dc.river.basin → cg.river.basin
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- dc.Species → cg.species
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- dc.targetaudience → cg.targetaudience
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- dc.fulltextstatus → cg.fulltextstatus
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- dc.editon → cg.edition
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- dc.isijournal → cg.isijournal
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- Start a test rebase of the `5_x-prod` branch on top of the `dspace-5.5` tag
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- There were a handful of conflicts that I didn't understand
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- 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:
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```
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[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]
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```
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- I've sent them a question about it
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- A user mentioned having problems with uploading a 33 MB PDF
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- I told her I would increase the limit temporarily tomorrow morning
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- Turns out she was able to decrease the size of the PDF so we didn't have to do anything
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## 2016-05-12
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- 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
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- 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:
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- dc.rplace.region → cg.coverage.region
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- dc.cplace.country → cg.coverage.country
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- Questions for CG people:
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- Our `dc.place` and `dc.srplace.subregion` could both map to `cg.coverage.admin-unit`?
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- Should we use `dc.contributor.crp` or `cg.contributor.crp` for the CRP (ours is `dc.crsubject.crpsubject`)?
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- 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
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- `dc.title.jtitle` could either map to `dc.publisher` or `dc.source` depending on how you read things
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- Found ~200 messed up CIAT values in `dc.publisher`:
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```
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# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to "% %";
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```
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## 2016-05-13
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- More theorizing about CGcore
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- Add two new fields:
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- dc.srplace.subregion → cg.coverage.admin-unit
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- dc.place → cg.place
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- `dc.place` is our own field, so it's easy to move
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- 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)
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## 2016-05-18
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- Work on 707 CCAFS records
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- They have thumbnails on Flickr and elsewhere
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- In OpenRefine I created a new `filename` column based on the `thumbnail` column with the following GREL:
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```
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if(cells['thumbnails'].value.contains('hqdefault'), cells['thumbnails'].value.split('/')[-2] + '.jpg', cells['thumbnails'].value.split('/')[-1])
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```
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- Because ~400 records had the same filename on Flickr (hqdefault.jpg) but different UUIDs in the URL
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- So for the `hqdefault.jpg` ones I just take the UUID (-2) and use it as the filename
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- Before importing with SAFBuilder I tested adding "__bundle:THUMBNAIL" to the `filename` column and it works fine
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## 2016-05-19
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- More quality control on `filename` field of CCAFS records to make processing in shell and SAFBuilder more reliable:
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```
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value.replace('_','').replace('-','')
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```
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- 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`
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- And `dc.identifier.fund` is MOSTLY used for CPWF project identifier but has some other sponsorship things
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- We should move PN*, SG*, CBA, IA, and PHASE* values to `cg.identifier.cpwfproject`
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- The rest, like BMGF and USAID etc, might have to go to either `dc.description.sponsorship` or `cg.identifier.fund` (not sure yet)
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- There are also some mistakes in CPWF's things, like "PN 47"
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- This ought to catch all the CPWF values (there don't appear to be and SG* values):
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```
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# 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');
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```
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## 2016-05-20
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- More work on CCAFS Video and Images records
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- For SAFBuilder we need to modify filename column to have the thumbnail bundle:
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```
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value + "__bundle:THUMBNAIL"
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```
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- Also, I fixed some weird characters using OpenRefine's transform with the following GREL:
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```
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value.replace(/\u0081/,'')
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```
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- Write shell script to resize thumbnails with height larger than 400: https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256
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- Upload 707 CCAFS records to DSpace Test
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- A few miscellaneous fixes for XMLUI display niggles (spaces in item lists and link target `_black`): [#224](https://github.com/ilri/DSpace/pull/224)
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- Work on configuration changes for Phase 2 metadata migrations
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## 2016-05-23
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- Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine
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- LibreOffice excludes empty cells when it exports and all the fields shift over to the left and cause URLs to go to Subjects, etc.
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- Google Docs does this better, but somehow reorders the rows and when I paste the thumbnail/filename row in they don't match!
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- I will have to try later
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## 2016-05-30
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- Export CCAFS video and image records from DSpace Test using the migrate option (`-m`):
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```
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$ mkdir ~/ccafs-images
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$ /home/dspacetest.cgiar.org/bin/dspace export -t COLLECTION -i 10568/79355 -d ~/ccafs-images -n 0 -m
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```
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- And then import to CGSpace:
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```
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$ 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
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```
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- But now we have double authors for "CGIAR Research Program on Climate Change, Agriculture and Food Security" in the authority
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- I'm trying to do a Discovery index before messing with the authority index
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- Looks like we are missing the `index-authority` cron job, so who knows what's up with our authority index
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- Run system updates on DSpace Test, re-deploy code, and reboot the server
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- Clean up and import ~200 CTA records to CGSpace via CSV like:
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```
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$ export JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8"
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$ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA-May30/CTA-42229.csv &> ~/CTA-May30/CTA-42229.log
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```
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- Discovery indexing took a few hours for some reason, and after that I started the `index-authority` script
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```
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$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace index-authority
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```
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## 2016-05-31
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- The `index-authority` script ran over night and was finished in the morning
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- Hopefully this was because we haven't been running it regularly and it will speed up next time
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- I am running it again with a timer to see:
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```
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$ time /home/cgspace.cgiar.org/bin/dspace index-authority
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Retrieving all data
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Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
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Cleaning the old index
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Writing new data
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All done !
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real 37m26.538s
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user 2m24.627s
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sys 0m20.540s
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```
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- Update `tomcat7` crontab on CGSpace and DSpace Test to have the `index-authority` script that we were missing
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- 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))
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- 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.
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- Re-sync DSpace Test data with CGSpace
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- Clean up and import ~65 more CTA items into CGSpace
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