--- title: "August, 2022" date: 2022-08-01T10:22:36+03:00 author: "Alan Orth" categories: ["Notes"] --- ## 2022-08-01 - Our request to add [CC-BY-3.0-IGO to SPDX](https://github.com/spdx/license-list-XML/issues/1525) was approved a few weeks ago ## 2022-08-02 - Resume working on the MARLO Innovations - Last week Jose had sent me an updated CSV with UTF-8 formatting, which was missing the filename column - I joined it with the older file (stripped down to just the `cg.number` and `filename` columns and then did the same cleanups I had done last week - I noticed there are six PDFs unused, so I asked Jose - Spent some time trying to understand the REST API submission issues that Rafael from CIAT is having with tip-approve and tip-submit - First, according to my notes in 2020-10, a user must be a *collection admin* in order to submit via the REST API - Second, a collection must have a "Accept/Reject/Edit Metadata" step defined in the workflow - Also, I referenced my notes from this gist I had made for exactly this purpose! https://gist.github.com/alanorth/40fc3092aefd78f978cca00e8abeeb7a ## 2022-08-03 - I came up with an interesting idea to add missing countries and AGROVOC terms to the MARLO Innovation metadata - I copied the abstract column to two new fields: `countrytest` and `agrovoctest` and then used this Jython code as a transform to drop terms that don't match (using CGSpace's country list and list of 1,400 AGROVOC terms): ```python with open(r"/tmp/cgspace-countries.txt",'r') as f : countries = [name.rstrip().lower() for name in f] return "||".join([x for x in value.split(' ') if x.lower() in countries]) ``` - Then I joined them with the other country and AGROVOC columns - I had originally tried to use csv-metadata-quality to look up and drop invalid AGROVOC terms but it was timing out ever dozen or so requests - Then I briefly tried to use lightrdf to export a text file of labels from AGROVOC's RDF, but I couldn't figure it out - I just realized this will not match countries with spaces in our cell value, ugh... and Jython has weird syntax and errors and I can't get normal Python code to work here, I'm missing something - Then I extracted the titles, dates, and types and added IDs, then ran them through `check-duplicates.py` to find the existing items on CGSpace so I can add them as `dcterm.relation` links ```console $ csvcut -l -c dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-08-03-Innovations-Cleaned.csv | sed '1s/line_number/id/' > /tmp/innovations-temp.csv $ ./ilri/check-duplicates.py -i /tmp/innovations-temp.csv -u dspacetest -db dspacetest -p 'dom@in34sniper' -o /tmp/ccafs-duplicates.csv ``` - There were about 115 with existing items on CGSpace - Then I did some minor processing and checking of the duplicates file (for example, some titles appear more than once in both files), and joined with the other file (left join): ```console $ csvjoin --left -c dc.title ~/Downloads/2022-08-03-Innovations-Cleaned.csv ~/Downloads/2022-08-03-Innovations-relations.csv > /tmp/innovations-with-relations.csv ``` - Then I used SAFBuilder to create a SimpleItemArchive and import to DSpace Test: ```console $ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m" $ dspace import --add --eperson=aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile=./2022-08-03-innovations.map ``` - Meeting with Mohammed Salem about harmonizing MEL and CGSpace metadata fields - I still need to share our results and recommendations with Peter, Enrico, Sara, Svetlana, et al - I made some minor fixes to csv-metadata-quality while working on the MARLO CRP Innovations ## 2022-08-05 - I discussed issues with the DSpace 7 submission forms on Slack and Mark Wood found that the migration tool creates a non-working submission form - After updating the class name of the collection step and removing the "complete" and "sample" steps the submission form was working - Now the issue is that the controlled vocabularies show up like this: ![Controlled vocabulary bug in DSpace 7](/cgspace-notes/2022/08/dspace7-submission.png) - I think we need to add IDs, I will have to check what the implications of that are - Emilio contacted me last week to say they have re-worked their harvester on Hetzner to use a new user agent: `AICCRA website harvester` - I verified that I see it in the REST API logs, but I don't see any new stats hits for it - I do see 11,000 hits from that IP last month when I had the incorrect nginx configuration that was sending a literal `$http_user_agent` so I purged those - It is lucky that we have `harvest` in the DSpace spider agent example file so Solr doesn't log these hits, nothing needed to be done in nginx ## 2022-08-13 - I noticed there was high load on CGSpace, around 9 or 10 - Looking at the Munin graphs it seems to just be the last two hours or so, with a slight increase in PostgreSQL connections, firewall traffic, and a more noticeable increase in CPU - DSpace sessions are normal - The number of unique hosts making requests to nginx is pretty low, though it's only 6AM in the server's time - I see one IP in Sweden making a lot of requests with a normal user agent: 80.248.237.167 - This host is on Internet Vikings (INTERNETBOLAGET), and I see 140,000 requests from them in Solr - I see reports of excessive scraping on AbuseIPDB.com - I'm gonna add their 80.248.224.0/20 to the bot-networks.conf in nginx - I will also purge all the hits from this IP in Solr statistics - I also see the core.ac.uk bot making tens of thousands of requests today, but we are already tagging that as a bot in Tomcat's Crawler Session Manager valve, so they should be sharing a Tomcat session with other bots and not creating too many sessions ## 2022-08-15 - Start indexing on AReS - Add CONSERVATION to ILRI subjects on CGSpace - I see that AGROVOC has `conservation agriculture` and I suggested that we use that instead ## 2022-08-17 - Peter and Jose sent more feedback about the CRP Innovation records from MARLO - We expanded the CRP names in the citation and removed the `cg.identifier.url` URLs because they are ugly and will stop working eventually - The mappings of MARLO links will be done internally with the `cg.number` IDs like "IN-1119" and the Handle URIs ## 2022-08-18 - I talked to Jose about the CCAFS MARLO records - He still hasn't finished re-processing the PDFs to update the internal MARLO links - I started looking at the other records (MELIAs, OICRs, Policies) and found some minor issues in the MELIAs so I sent feedback to Jose - On second thought, I opened the MELIAs file in OpenRefine and it looks OK, so this must have been a parsing issue in LibreOffice when I was checking the file (or perhaps I didn't use the correct quoting when importing) - Import the original MELIA v2 CSV file into OpenRefine to fix encoding before processing with csvcut/csvjoin - Then extract the IDs and filenames from the original V2 file and join with the UTF-8 file: ```console $ csvcut -c 'cg.number (series/report No.)',File ~/Downloads/MELIA-Metadata-v2-csv.csv > MELIA-v2-IDs-Files.csv $ csvjoin -c 'cg.number (series/report No.)' MELIAs\ metadata\ utf8\ 20220816_JM.csv MELIA-v2-IDs-Files.csv > MELIAs-UTF-8-with-files.csv ``` - Then I imported them into OpenRefine to start metadata cleaning and enrichment - Make some minor changes to [cgspace-submission-guidelines](https://github.com/ilri/cgspace-submission-guidelines) - Upgrade to Bootstrap v5.2.0 - Dedupe value pairs and controlled vocabularies before writing them - Sort the controlled vocabularies before writing them (we don't do this for value pairs because some are added in specific order, like CRPs)