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| title | date | author | tags | |
|---|---|---|---|---|
| June, 2019 | 2019-06-02T10:57:51+03:00 | Alan Orth |
|
2019-06-02
- Merge the Solr filterCache and XMLUI ISI journal changes to the
5_x-prodbranch and deploy on CGSpace - Run system updates on CGSpace (linode18) and reboot it
2019-06-03
- Skype with Marie-Angélique and Abenet about CG Core v2
- Here is a list of proposed metadata migrations for CGSpace
- dc.language.iso→DCTERMS.language (and switch to ISO 639-2 Alpha 3)
- dc.description.abstract→DCTERMS.abstract
- dc.identifier.citation→DCTERMS.bibliographicCitation
- dc.contributor.author→DCTERMS.creator (for people)
- dc.description.sponsorship→cg.contributor.donor (values from CrossRef or Grid.ac if possible)
- dc.rights→DCTERMS.license
- cg.identifier.status→DCTERMS.accessRights (values "open" or "restricted")
- cg.creator.id→cg.creator.identifier?
- dc.relation.ispartofseries→DCTERMS.isPartOf
- cg.link.relation→DCTERMS.relation
- Marie agreed that we need to adopt some controlled lists for our values, and pointed out that the MARLO team maintains a list of CRPs and Centers at CLARISA
- There is an API there but it needs a password for access...
2019-06-04
- The MARLO team responded and said they will give us access to the CLARISA API
- Marie-Angélique proposed to integrate
dcterms.isPartOf,dcterms.abstract, anddcterms.bibliographicCitationinto the CG Core v2 schema- I told her I would attempt to integrate those and the others above into DSpace Test soon and report back
- We also need to discuss with the ILRI Data Portal, MEL/MELSpace, and users who consume the CGSpace API
- Add Arabic language to input-forms.xml (#427), as Bioversity is adding some Arabic items and noticed it missing
2019-06-05
- Send mail to CGSpace and MELSpace people to let them know about the proposed metadata field migrations after the discussion with Marie-Angélique
2019-06-07
- Thierry noticed that the CUA statistics were missing previous years again, and I see that the Solr admin UI has the following message:
statistics-2018: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
- I had to restart Tomcat a few times for all the stats cores to get loaded with no issue
2019-06-10
- Rename the AReS repository on GitHub to OpenRXV: https://github.com/ilri/OpenRXV
- Create a new AReS repository: https://github.com/ilri/AReS
- Start looking at the 203 IITA records on DSpace Test from last month (IITA_May_16 aka "20194th.xls") using OpenRefine
- Trim leading, trailing, and consecutive whitespace on all columns, but I didn't notice very many issues
- Validate affiliations against latest list of top 1500 terms using reconcile-csv, correcting and standardizing about twenty-seven
- Validate countries against latest list of countries using reconcile-csv, correcting three
- Convert all DOIs to "https://dx.doi.org" format
- Normalize all
cg.identifier.urlGoogle book fields to "books.google.com" - Correct some inconsistencies in IITA subjects
- Correct two incorrect "Peer Review" in
dc.description.version - About fifteen items have incorrect ISBNs (looks like an Excel error because the values look like scientific numbers)
- Delete one blank item
- I managed to get to subjects, so I'll continue from there when I start working next
- Generate a new list of countries from the database for use with reconcile-csv
- After dumping, use csvcut to add line numbers, then change the csv header to match those you use in reconcile-csv, for example
idandname:
- After dumping, use csvcut to add line numbers, then change the csv header to match those you use in reconcile-csv, for example
dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 228 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC) to /tmp/countries.csv WITH CSV HEADER
COPY 192
$ csvcut -l -c 0 /tmp/countries.csv > 2019-06-10-countries.csv
- Get a list of all the unique AGROVOC subject terms in IITA's data and export it to a text file so I can validate them with my
agrovoc-lookup.pyscript:
$ csvcut -c dc.subject ~/Downloads/2019-06-10-IITA-20194th-Round-2.csv| sed 's/||/\n/g' | grep -v dc.subject | sort -u > iita-agrovoc.txt
$ ./agrovoc-lookup.py -i iita-agrovoc.txt -om iita-agrovoc-matches.txt -or iita-agrovoc-rejects.txt
$ wc -l iita-agrovoc*
402 iita-agrovoc-matches.txt
29 iita-agrovoc-rejects.txt
431 iita-agrovoc.txt
- Combine these IITA matches with the subjects I matched a few months ago:
$ csvcut -c name 2019-03-18-subjects-matched.csv | grep -v name | cat - iita-agrovoc-matches.txt | sort -u > 2019-06-10-subjects-matched.txt
- Then make a new list to use with reconcile-csv by adding line numbers with csvcut and changing the line number header to
id:
$ csvcut -c name -l 2019-06-10-subjects-matched.txt | sed 's/line_number/id/' > 2019-06-10-subjects-matched.csv
2019-06-20
- Share some feedback about AReS v2 with the colleagues and encourage them to do the same
2019-06-23
- Continue work on reviewing CG Core v2 standard and its implications to CGSpace an DSpace platforms in general
- Update my list of fields to migrate
- Submit an issue with my feedback to the CG Core project
- Update my local PostgreSQL container:
$ podman pull docker.io/library/postgres:9.6-alpine
$ podman rm dspacedb
$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
2019-06-25
- Normalize
text_langvalues for metadata on DSpace Test and CGSpace:
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('ethnob', 'en', '*', 'E.', '');
UPDATE 1551
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IS NULL;
UPDATE 2070
dspace=# UPDATE metadatavalue SET text_lang='es_ES' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('es', 'spa');
UPDATE 2
- Upload 202 IITA records from earlier this month (20194th.xls) to CGSpace
- Communicate with Bioversity contractor in charge of their migration from Typo3 to CGSpace
2019-06-28
- Start looking at the fifty-seven AfricaRice records sent by Ibnou earlier this month
- First, I see there are several items with type "Book" and "Book Chapter" should go in an "AfricaRice books and book chapters" collection, but none exists in the AfricaRice community
- Trim and collapse consecutive whitespace on author, affiliation, authorship types, title, subjects, doi, issn, source, citation, country, sponsors
- Standardize and correct affiliations like "Africa Rice Cente" and "Africa Rice Centre", including syntax errors with multi-value separators
- Lots of variation in affiliations, for example:
- Université Abomey-Calavi
- Université d'Abomey
- Université d'Abomey Calavi
- Université d'Abomey-Calavi
- University of Abomey-Calavi
- Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:
$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id- I always forget how to copy the reconciled values in OpenRefine, but you need to make a new colume and populate it using this GREL:
if(cell.recon.matched, cell.recon.match.name, value)
- Replace smart quotes with standard ASCII ones
- Fix typos in authoriship types
- Validate and normalize subjects against our 2019-06 list using reconcile-csv and OpenRefine:
$ lein run ~/src/git/DSpace/2019-06-10-subjects-matched.csv name id- Also add about 30 new AGROVOC subjects to our list that I verified manually
- There is one duplicate, both have the same DOI: https://doi.org/10.1016/j.agwat.2018.06.018
- Fix four ISBNs that were in the ISSN field