- Remove `cg.subject.wle` and `cg.identifier.wletheme` from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)
- [iso-codes 4.13.0 was released](https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28), which incorporates my changes to the common names for Iran, Laos, and Syria
- I can't put my finger on it, but the input form has to be formatted very particularly, for example if your rows have more than two fields in them with out a sufficient Bootstrap grid style, or if you use a `twobox`, etc, the entire form step appears blank
## 2023-03-02
- I did some experiments with the new [Pandas 2.0.0rc0 Apache Arrow support](https://datapythonista.me/blog/pandas-20-and-the-arrow-revolution-part-i)
- There is a change to the way nulls are handled and it causes my tests for `pd.isna(field)` to fail
- I think we need consider blanks as null, but I'm not sure
- I made some adjustments to the Discovery sidebar facets on DSpace 6 while I was looking at the DSpace 7 configuration
- I downgraded CIFOR subject, Humidtropics subject, Drylands subject, ICARDA subject, and Language from DiscoverySearchFilterFacet to DiscoverySearchFilter in `discovery.xml` since we are no longer using them in sidebar facets
## 2023-03-03
- Atmire merged one of my old pull requests into COUNTER-Robots:
- [COUNTER_Robots_list.json: Add new bots](https://github.com/atmire/COUNTER-Robots/pull/54)
- I will update the local ILRI overrides in our DSpace spider agents file
## 2023-03-04
- Submit a [pull request on pycountry to use iso-codes 4.13.0](https://github.com/flyingcircusio/pycountry/pull/156)
## 2023-03-05
- Start a harvest on AReS
## 2023-03-06
- Export CGSpace to do Initiative collection mappings
- There were thirty-three that needed updating
- Send Abenet and Sam a list of twenty-one CAS publications that had been marked as "multiple documents" that we uploaded as metadata-only items
- Goshu will download the PDFs for each and upload them to the items on CGSpace manually
- I spent some time trying to get csv-metadata-quality working with the new Arrow backend for Pandas 2.0.0rc0
- It seems there is a problem recognizing empty strings as na with `pd.isna()`
- If I do `pd.isna(field) or field == ""` then it works as expected, but that feels hacky
- I'm going to test again on the next release...
- Note that I had been setting both of these global options:
- Peter sent me a list of items that had ILRI affiation on Altmetric, but that didn't have Handles
- I ran a duplicate check on them to find if they exist or if we can import them
- There were about ninety matches, but a few dozen of those were pre-prints!
- After excluding those there were about sixty-one items we already have on CGSpace so I will add their DOIs to the existing items
- After joining these with the records from CGSpace and inspecting the DOIs I found that only forty-four were new DOIs
- Surprisingly some of the DOIs on Altmetric were not working, though we also had some that were not working (specifically the Journal of Agricultural Economics seems to have reassigned DOIs)
- For the rest of the ~359 items I extracted their DOIs and looked up the metadata on Crossref using my `crossref-doi-lookup.py` script
- After spending some time cleaning the data in OpenRefine I realized we don't get access status from Crossref
- We can imply it if the item is Creative Commons, but otherwise I might be able to use [Unpaywall's API](https://unpaywall.org/products/api)
- I found some false positives in Unpaywall, so I might only use their data when it says the DOI is not OA...
- During this process I updated my `crossref-doi-lookup.py` script to get more information from Crossref like ISSNs, ISBNs, full journal title, and subjects
- Then I created a GiST [index on the `metadatavalue` table to try to speed up the trgm similarity operations](https://alexklibisz.com/2022/02/18/optimizing-postgres-trigram-search):
```console
localhost/dspacetest= ☘ CREATE INDEX metadatavalue_text_value_trgm_gist_idx ON metadatavalue USING gist(text_value gist_trgm_ops(siglen=64)); # \di+ shows index size is 795MB
```
- That took a few minutes to build... then the duplicate checker ran in 12 minutes: `0.07s user 0.02s system 0% cpu 12:43.08 total`
- On a hunch, I tried with a GIN index:
```console
localhost/dspacetest= ☘ CREATE INDEX metadatavalue_text_value_trgm_gin_idx ON metadatavalue USING gin(text_value gin_trgm_ops); # \di+ shows index size is 274MB
```
- This ran in 19 minutes: `0.08s user 0.01s system 0% cpu 19:49.73 total`
- So clearly the GiST index is better for this task
- I am curious if I increase the signature length in the GiST index from 64 to 256 (which will for sure increase the size taken):
```console
localhost/dspacetest= ☘ CREATE INDEX metadatavalue_text_value_trgm_gist_idx ON metadatavalue USING gist(text_value gist_trgm_ops(siglen=256)); # \di+ shows index size is 716MB, which is less than the previous GiST index...
```
- This one finished in ten minutes: `0.07s user 0.02s system 0% cpu 10:04.04 total`
- I might also want to [increase my `work_mem`](https://stackoverflow.com/questions/43008382/postgresql-gin-index-slower-than-gist-for-pg-trgm) (default 4MB):
```console
localhost/dspacetest= ☘ SELECT setting, unit FROM pg_settings WHERE name = 'work_mem';
setting │ unit
─────────┼──────
4096 │ kB
(1 row)
```
- After updating my Crossref lookup script and checking the remaining ~359 items I found a eight more duplicates already existing on CGSpace
- Wow, I found a [really cool way to fetch URLs in OpenRefine](https://programminghistorian.org/en/lessons/fetch-and-parse-data-with-openrefine#example-1-fetching-and-parsing-html)
- I used this to fetch the open access status for each DOI from Unpaywall
- First, create a new column called "url" based on the DOI that builds the request URL. I used a Jython expression:
request_url = unpaywall_baseurl + doi + '?email=' + email
return request_url
```
- Then create a new column based on fetching the values in that column. I called it "unpaywall_status"
- Then you get a JSON blob in each and you can extract the Open Access status with a GREL like `value.parseJson()['is_oa']`
- I checked a handful of results manually and found that the limited access status was more trustworthy from Unpaywall than the open access, so I will just tag the limited access ones
- I merged the funders and affiliations from Altmetric into my file, then used the same technique to get Crossref data for open access items directly into OpenRefine and parsed the abstracts
- The syntax was hairy because it's marked up with tags like `<jats:p>`, but this got me most of the way there:
- I uploaded the 350 items to DSpace Test so Peter and Abenet can explore them
- Meeting with FAO AGRIS team about how to detect duplicates
- They are currently using a sha256 hash on titles, which will work, but will only return exact matches
- I told them to try to normalize the string, drop stop words, etc to increase the possibility that the hash matches
- Meeting with Abenet to discuss CGSpace issues
- She reminded me about needing a metadata field for first author when the affiliation is ILRI
- I said I prefer to write a small script for her that will check the first author and first affiliation... I could do it easily in Python, but would need to put a web frontend on it for her