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170 lines
6.9 KiB
Markdown
170 lines
6.9 KiB
Markdown
---
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title: "April, 2024"
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date: 2024-04-04T10:23:00+03:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 2024-04-04
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- Work on CGSpace duplicate DOIs more
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<!--more-->
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## 2024-04-08
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- Start working on IFPRI's 2022 batch import
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- I ran the duplicate checker against CGSpace and started downloading all linked PDFs
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## 2024-04-09
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- Continue working on IFPRI's 2022 batch import
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- I started validating the potential duplicates in OpenRefine
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## 2024-04-12
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- Finish working on the 650 IFPRI 2022 records that were not already on CGSpace, then uploaded them
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- I need to merge the metadata for the remaining 212 that are already on CGSpace
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- Spend some time looking at duplicate DOIs again...
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## 2024-04-13
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- Spend some time looking at duplicate DOIs again...
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## 2024-04-14
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- Spend some time looking at duplicate DOIs again...
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## 2024-04-15
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- Spend some time looking at duplicate DOIs again...
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- Delete ~260 duplicate metadata values using the elaborate SQL and sort method I documented here: https://github.com/DSpace/DSpace/issues/8253#issuecomment-1331756418
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- Tony noticed that the DSpace 7 REST API is very slow with the embeds so I profiled a bit:
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```
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$ time curl -s -o /dev/null 'https://cgspace.cgiar.org/server/api/discover/search/objects?query=cg.identifier.project%3AIFPRI*&scope=8f1e9650-fe87-4e6e-889a-1cacfb747408&page=0&size=100&embed=thumbnail,bundles/bitstreams&sort=dcterms.issued,desc'
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curl -s -o /dev/null 0.01s user 0.01s system 0% cpu 47.515 total
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$ time curl -s -o /dev/null 'https://cgspace.cgiar.org/server/api/discover/search/objects?query=cg.identifier.project%3AIFPRI*&scope=8f1e9650-fe87-4e6e-889a-1cacfb747408&page=0&size=100&sort=dcterms.issued,desc'
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curl -s -o /dev/null 0.01s user 0.01s system 0% cpu 4.764 total
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```
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- Finalize processing the remaining 206 items from the IFPRI 2022 batch set that already existed on CGSpace
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- I merged metadata with the existing items
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- There are still six remaining items that I identified as being duplicates (3x2) in the IFPRI set itself
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## 2024-04-16
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- Spend some time looking at duplicate DOIs again...
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- Assist Deborah with an advanced query on CGSpace for biodiversity and health:
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```
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dcterms.issued:[2010 TO 2024] AND dcterms.type:"Journal Article" AND (dc.title:"biodiversity" OR dcterms.subject:"biodiversity" OR dc.title:"health" OR dcterms.subject:"health")
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```
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- Remove CIMMYT URLs and citations from 277 journal articles on CGSpace since it is a bit tacky
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- I used this Jython expression in OpenRefine with [Crossref's content negotiation](https://citation.crosscite.org/docs.html) to get citations for all DOIs:
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```python
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import urllib2
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doi = cells['cg.identifier.doi[en_US]'].value
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url = "https://api.crossref.org/works/" + doi + "/transform/text/x-bibliography"
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useragent = "Python (mailto:a.o@cgiar.org)"
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request = urllib2.Request(url.encode("utf-8"), headers={"User-Agent" : useragent})
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get = urllib2.urlopen(request)
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return get.read().decode('utf-8')
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```
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- It took ten or so minutes for it to finish (and note this is Python 2 inside OpenRefine so I had to be careful with Unicode), but worked well!
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## 2024-04-18
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- Write a SQL query to build the IFPRI CONTENTdm redirects to Handles:
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```sql
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SELECT m.text_value, h.handle FROM metadatavalue m JOIN handle h on m.dspace_object_id = h.resource_id WHERE m.metadata_field_id=28 AND m.text_value LIKE 'Original URL%' AND h.resource_type_id=2;
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```
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- Similarly, I need a SQL query to get the redirects for duplicate Handles, querying for `dcterms.replaces`:
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```sql
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SELECT m.text_value AS handle_from, h.handle AS handle_to FROM metadatavalue m JOIN handle h on m.dspace_object_id = h.resource_id WHERE m.metadata_field_id=181 AND h.resource_type_id=2;
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```
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- Then I can work that list into an nginx map with redirect, for example:
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```console
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server {
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...
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if ($new_uri) {
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return 301 $new_uri;
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}
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}
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map $request_uri $new_uri {
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/handle/10568/112821 /handle/10568/97605;
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}
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```
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## 2024-04-19
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- Spend some time looking at duplicate DOIs again...
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- Refresh ORCID identifiers from ORCID API and update CGSpace metadata and controlled vocabulary
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## 2024-04-20
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- I read an [interesting thread about DOI casing](https://github.com/greenelab/scihub/issues/9)
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- Apparently the DOI specification says ASCII characters in DOIs are case insensitive
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- Indeed, [Crossref recommends lower case](https://www.crossref.org/documentation/member-setup/constructing-your-dois/) for all DOIs
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- I was curious about the DOIs in our database so I checked before and after lower casing:
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```console
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localhost/dspace7= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=220 AND text_value IS NOT NULL AND text_value !='') TO /tmp/dois-sql-before.txt;
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COPY 25675
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localhost/dspace7= ☘ \COPY (SELECT DISTINCT(lower(text_value)) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=220 AND text_value IS NOT NULL AND text_value !='') TO /tmp/dois-sql-after.txt;
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COPY 25666
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```
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- I need to investigate options for lower casing these in the repository, for example in a curation task, and in all workflows around DSpace metadata...
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## 2024-04-23
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- Spent some time writing a Java curation task to normalize DOIs in items when they enter the workflow edit step
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- The workflow curation tasks are not documented very well but I got a basic configuration working
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- I found a bug in DSpace curation tasks and discussed on Slack
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- I finalized the `NormalizeDOIs` curation task and released v7.6.1.1 of the [cgspace-java-helpers](https://github.com/ilri/cgspace-java-helpers) project
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## 2024-04-24
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- A bit more testing of the curation tasks
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- I tested a patch by Mark Wood
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- I added support for normalizing DOIs to this same format to my [csv-metadata-quality](https://github.com/ilri/csv-metadata-quality) project
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## 2024-04-25
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- I lowercased the remaining 3,900 DOIs on CGSpace that had uppercase ASCII characters
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- Spend some time looking at duplicate DOIs again...
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## 2024-04-26
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- Spend some time looking at duplicate DOIs again...
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## 2024-04-29
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- Start working on the IFPRI 2020–2021 batch migration
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- I modified my `check_duplicates.py` script to check for DOIs instead of titles, and use a similarity of 1.0 to make sure the match is exact
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- I noticed something in the Tomcat log:
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```console
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tomcat9[690]: WARNING: The HTTP response header [Content-Disposition] with value [attachment; filename="Literature review on Women’s Empowerment and their Resilience2.pdf"] has been removed from the response because it is invalid
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tomcat9[690]: java.lang.IllegalArgumentException: The Unicode character [’] at code point [8,217] cannot be encoded as it is outside the permitted range of 0 to 255
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```
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- I found the bitstream's ID and then used the `ds6_bitstream2itemhandle` [SQL helper function](https://wiki.lyrasis.org/display/DSPACE/Helper+SQL+functions+for+DSpace+6) to find the item's handle
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- Then I replaced the curly quote with a regular quote in all bistreams
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<!-- vim: set sw=2 ts=2: -->
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