Purging 9446 hits from 45.134.26.171 in statistics
Purging 6490 hits from 3.225.28.105 in statistics
Purging 11949 hits from 217.182.21.193 in statistics
Total number of bot hits purged: 54702
```
- Export donors and affiliations from CGSpace database:
```console
localhost/dspace63= ☘ \COPY (SELECT DISTINCT text_value as "cg.contributor.donor", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 248 GROUP BY text_value ORDER BY count DESC) to /tmp/2022-02-02-donors.csv WITH CSV HEADER;
COPY 1036
localhost/dspace63= ☘ \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2022-02-02-affiliations.csv WITH CSV HEADER;
COPY 7901
```
- Then check matches against the latest ROR dump:
```console
$ csvcut -c cg.contributor.donor /tmp/2022-02-02-donors.csv | sed '1d' > /tmp/2022-02-02-donors.txt
- I see we have 258/1036 (24.9%) of our donors matching ROR (as of the 2021-09-23 ROR dump)
- I see we have 1986/7901 (25.1%) of our affiliations matching ROR (as of the 2021-09-23 ROR dump)
- Update the PostgreSQL JDBC driver to 42.3.2 in the Ansible Infrastructure playbooks and deploy on DSpace Test
- Mishell from CIP sent me a copy of a security scan their ICT had done on CGSpace using QualysGuard
- The report was very long and generic, highlighting low-severity things like being able to post crap to search forms and have it appear on the results page
- Also they say we're using old jQuery and bootstrap, etc (fair enough) but there are no exploits per se
- At least now I know why all those Qualys IPs are scanning us all the time!!!
- Mishell also said she's having issues logging into CGSpace
- According to the logs her account is failing on LDAP authentication
- I checked CGSpace's LDAP credentials using ldapsearch and was able to connect so it's gotta be something with her account
- I synchronized DSpace Test with a fresh snapshot of CGSpace
- I noticed a bunch of thumbnails missing for items submitted in the last week on CGSpace so I ran the `dspace filter-media` script manually and eventually it crashed:
Full Filter Name: org.dspace.app.mediafilter.PoiWordFilter
org.dspace.app.mediafilter.PoiWordFilter
File: Agreement_on_the_Estab_of_ILRI.doc.txt
FILTERED: bitstream 31db7d05-5369-4309-adeb-3b888c80b73d (item: 10568/67391) and created 'Agreement_on_the_Estab_of_ILRI.doc.txt'
```
- Meeting with the repositories working group to discuss issues moving forward in the One CGIAR
## 2022-02-07
- Gaia sent me her feedback on the duplicates for the TAC and ICW items for CGSpace a few days ago
- I used the IDs marked "delete" in her spreadsheet to create a custom text facet with this GREL in OpenRefine:
```console
or(
isNotNull(value.match('1')),
isNotNull(value.match('4')),
isNotNull(value.match('5')),
isNotNull(value.match('6')),
isNotNull(value.match('8')),
...
sNotNull(value.match('178')),
isNotNull(value.match('186')),
isNotNull(value.match('188')),
isNotNull(value.match('189')),
isNotNull(value.match('197'))
)
```
- Then I flagged all of these (seventy-five items)...
- I decided to flag the deletes instead of star the keeps because there are some items in the original file that we not marked as duplicates so we have to keep those too
- I generated the next batch of 200 items, from IDs 201 to 400, checked them for duplicates, and then added the PDF file names to the CSV for reference:
- Create a SAF archive for the first 200 items (IDs 1 to 200) that were *not* flagged as duplicates and upload them to a [new collection on DSpace Test](https://dspacetest.cgiar.org/handle/10568/117921):
- Last week Gaia sent me her notes on the second batch of TAC/ICW documents (items 201–400 in the spreadsheet)
- I created a filter in LibreOffice and selected the IDs for items with the action "delete", then I created a custom text facet in OpenRefine with this GREL:
```
or(
isNotNull(value.match('201')),
isNotNull(value.match('203')),
isNotNull(value.match('209')),
isNotNull(value.match('209')),
isNotNull(value.match('215')),
isNotNull(value.match('220')),
isNotNull(value.match('225')),
isNotNull(value.match('226')),
isNotNull(value.match('227')),
...
isNotNull(value.match('396'))
```
- Then I flagged all matching records and exported a CSV to use with SAFBuilder
- Upgrade PostgreSQL on DSpace Test from version 10 to 12
- First, I installed the new version of PostgreSQL via the Ansible playbook scripts
- Then I stopped Tomcat and all PostgreSQL clusters and used `pg_upgrade` to upgrade the old version:
```console
# systemctl stop tomcat7
# pg_ctlcluster 10 main stop
# tar -cvzpf var-lib-postgresql-10.tar.gz /var/lib/postgresql/10
# tar -cvzpf etc-postgresql-10.tar.gz /etc/postgresql/10
# pg_ctlcluster 12 main stop
# pg_dropcluster 12 main
# pg_upgradecluster 10 main
# pg_ctlcluster 12 main start
```
- After that I [re-indexed the database indexes using a query](https://adamj.eu/tech/2021/04/13/reindexing-all-tables-after-upgrading-to-postgresql-13/):
- I updated my `migrate-fields.sh` script to use field names instead of IDs
- The script now looks up the appropriate `metadata_field_id` values for each field in the metadata registry
## 2022-02-18
- Normalize the `text_lang` attributes of metadata on CGSpace:
```console
dspace=# SELECT DISTINCT text_lang, count(text_lang) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) GROUP BY text_lang ORDER BY count DESC;
text_lang | count
-----------+---------
en_US | 2838588
en | 1082
| 801
fr | 2
vn | 2
en_US. | 1
sp | 1
| 0
(8 rows)
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN ('en', 'en_US.', '');
UPDATE 1884
dspace=# UPDATE metadatavalue SET text_lang='vi' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN ('vn');
UPDATE 2
dspace=# UPDATE metadatavalue SET text_lang='es' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN ('sp');
UPDATE 1
```
- I then exported the entire repository and did some cleanup on DOIs
- I found ~1,200 items with no `cg.identifier.doi`, but which had a DOI in their citation
- I cleaned up and normalized a few hundred others to use https://doi.org format
- I'm debating using the Crossref API to search for our DOIs and improve our metadata
- For example: https://api.crossref.org/works/10.1016/j.ecolecon.2008.03.011
- There is good data on publishers, issue dates, volume/issue, and sometimes even licenses
- I cleaned up ~1,200 URLs that were using HTTP instead of HTTPS, fixed a bunch of handles, removed some handles from DOI field, etc
## 2022-02-20
- Yesterday I wrote a script to check our DOIs against Crossref's API and the did some investigation on dates, volumes, issues, pages, and types
- While investigating issue dates in OpenRefine I created a new column using this GREL to show the number of days between Crossref's date and ours:
dspace=# UPDATE metadatavalue SET text_value='Academics' WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=144 AND text_value = 'Academicians';
UPDATE 354
dspace=# UPDATE metadatavalue SET text_value='Scientists' WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=144 AND text_value = 'SCIENTISTS';
- A few days ago Gaia sent me her notes on the third batch of TAC/ICW documents (items 401–700 in the spreadsheet)
- I created a filter in LibreOffice and selected the IDs for items with the action "delete", then I created a custom text facet in OpenRefine with this GREL:
```
or(
isNotNull(value.match('405')),
isNotNull(value.match('410')),
isNotNull(value.match('412')),
isNotNull(value.match('414')),
isNotNull(value.match('419')),
isNotNull(value.match('436')),
isNotNull(value.match('448')),
isNotNull(value.match('449')),
isNotNull(value.match('450')),
...
isNotNull(value.match('699'))
)
```
- Then I flagged all matching records, exported a CSV to use with SAFBuilder, and imported them on DSpace Test:
