+++ date = "2017-05-01T16:21:52+02:00" author = "Alan Orth" title = "May, 2017" tags = ["Notes"] +++ ## 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.cgiar.org/handle/10568/80731 ## 2017-05-05 - Discovered that CGSpace has ~700 items that are missing the `cg.identifier.status` field - Need to perhaps try using the "required metadata" curation task to find fields missing these items: ``` $ [dspace]/bin/dspace curate -t requiredmetadata -i 10568/1 -r - > /tmp/curation.out ``` - It seems the curation task dies when it finds an item which has missing metadata ## 2017-05-06 - Add "Blog Post" to `dc.type` - Create ticket on Atmire tracker to ask about commissioning them to develop the feature to expose ORCID via REST/OAI: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=510 - According to the [DSpace curation docs](https://wiki.duraspace.org/display/DSDOC5x/Curation+System) the fact that the `requiredmetadata` curation task stops when it finds a missing metadata field is by design ## 2017-05-07 - Testing one replacement for CCAFS Flagships (`cg.subject.ccafs`), first changed in the submission forms, and then in the database: ``` $ ./fix-metadata-values.py -i ccafs-flagships-may7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu ``` - Also, CCAFS wants to re-order their flagships to prioritize the Phase II ones - Waiting for feedback from CCAFS, then I can merge [#320](https://github.com/ilri/DSpace/pull/320) ## 2017-05-08 - Start working on CGIAR Library migration - We decided to use AIP export to preserve the hierarchies and handles of communities and collections - When ingesting some collections I was getting `java.lang.OutOfMemoryError: GC overhead limit exceeded`, which can be solved by disabling the GC timeout with `-XX:-UseGCOverheadLimit` - Other times I was getting an error about heap space, so I kept bumping the RAM allocation by 512MB each time (up to 4096m!) it crashed - This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using `dspace cleanup -v`, or else you'll run out of disk space - In the end I realized it's better to use submission mode (`-s`) to ingest the community object as a single AIP without its children, followed by each of the collections: ``` $ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit" $ [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10568/87775 /home/aorth/10947-1/10947-1.zip $ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done ``` - Note that in submission mode DSpace ignores the handle specified in `mets.xml` in the zip file, so you need to turn that off with `-o ignoreHandle=false` - The `-u` option supresses prompts, to allow the process to run without user input - Give feedback to CIFOR about their data quality: - Suggestion: uppercase dc.subject, cg.coverage.region, and cg.coverage.subregion in your crosswalk so they match CGSpace and therefore can be faceted / reported on easier - Suggestion: use CGSpace's CRP names (cg.contributor.crp), see: dspace/config/input-forms.xml - Suggestion: clean up duplicates and errors in funders, perhaps use a controlled vocabulary like ours, see: dspace/config/controlled-vocabularies/dc-description-sponsorship.xml - Suggestion: use dc.type "Blog Post" instead of "Blog" for your blog post items (we are also adding a "Blog Post" type to CGSpace soon) - Question: many of your items use dc.document.uri AND cg.identifier.url with the same text value? - Help Marianne from WLE with an Open Search query to show the latest WLE CRP outputs: https://cgspace.cgiar.org/open-search/discover?query=crpsubject:WATER%2C+LAND+AND+ECOSYSTEMS&sort_by=2&order=DESC - This uses the webui's item list sort options, see `webui.itemlist.sort-option` in `dspace.cfg` - The equivalent Discovery search would be: https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&filter_relational_operator_1=equals&filter_1=WATER%2C+LAND+AND+ECOSYSTEMS&submit_apply_filter=&query=&rpp=10&sort_by=dc.date.issued_dt&order=desc ## 2017-05-09 - The CGIAR Library metadata has some blank metadata values, which leads to `|||` in the Discovery facets - Clean these up in the database using: ``` dspace=# delete from metadatavalue where resource_type_id=2 and text_value='' ``` - I ended up running into issues during data cleaning and decided to wipe out the entire community and re-sync DSpace Test assetstore and database from CGSpace rather than waiting for the cleanup task to clean up - Hours into the re-ingestion I ran into more errors, and had to erase everything and start over _again_! - Now, no matter what I do I keep getting foreign key errors... ``` Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "handle_pkey" Detail: Key (handle_id)=(80928) already exists. ``` - I think those errors actually come from me running the `update-sequences.sql` script while Tomcat/DSpace are running - Apparently you need to stop Tomcat! ## 2017-05-10 - Atmire says they are willing to extend the ORCID implementation, and I've asked them to provide a quote - I clarified that the scope of the implementation should be that ORCIDs are stored in the database and exposed via REST / API like other fields - Finally finished importing all the CGIAR Library content, final method was: ``` $ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit" $ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2517/10947-2517.zip $ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2515/10947-2515.zip $ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2516/10947-2516.zip $ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip $ [dspace]/bin/dspace packager -s -t AIP -o ignoreHandle=false -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip $ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done ``` - Basically, import the smaller communities using recursive AIP import (with `skipIfParentMissing`) - Then, for the larger collection, create the community, collections, and items separately, ingesting the items one by one - The `-XX:-UseGCOverheadLimit` JVM option helps with some issues in large imports - After this I ran the `update-sequences.sql` script (with Tomcat shut down), and cleaned up the 200+ blank metadata records: ``` dspace=# delete from metadatavalue where resource_type_id=2 and text_value=''; ``` ## 2017-05-13 - After quite a bit of troubleshooting with importing cleaned up data as CSV, it seems that there are actually [NUL](https://en.wikipedia.org/wiki/Null_character) characters in the `dc.description.abstract` field (at least) on the lines where CSV importing was failing - I tried to find a way to remove the characters in vim or Open Refine, but decided it was quicker to just remove the column temporarily and import it - The import was successful and detected 2022 changes, which should likely be the rest that were failing to import before ## 2017-05-15 - To delete the blank lines that cause isses during import we need to use a regex in vim `g/^$/d` - After that I started looking in the `dc.subject` field to try to pull countries and regions out, but there are too many values in there