2022-01-01 14:21:47 +01:00
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Start a full harvest on AReS
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< p class = "lead blog-description" dir = "auto" > Documenting day-to-day work on the < a href = "https://cgspace.cgiar.org" > CGSpace< / a > repository.< / p >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2022-01/" > January, 2022< / a > < / h2 >
< p class = "blog-post-meta" >
< time datetime = "2022-01-01T15:20:54+02:00" > Sat Jan 01, 2022< / time >
in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2022-01-01" > 2022-01-01< / h2 >
< ul >
< li > Start a full harvest on AReS< / li >
< / ul >
2022-01-06 14:48:27 +01:00
< h2 id = "2022-01-06" > 2022-01-06< / h2 >
< ul >
< li > Add ORCID identifier for Chris Jones to CGSpace
< ul >
< li > Also tag eighty-eight of his items in CGSpace:< / li >
< / ul >
< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > $ cat 2022-01-06-add-orcids.csv
< / span > < / span > < span style = "display:flex;" > < span > dc.contributor.author,cg.creator.identifier
< / span > < / span > < span style = "display:flex;" > < span > " Jones, Chris" ," Chris Jones: 0000-0001-9096-9728"
< / span > < / span > < span style = "display:flex;" > < span > " Jones, Christopher S." ," Chris Jones: 0000-0001-9096-9728"
< / span > < / span > < span style = "display:flex;" > < span > $ ./ilri/add-orcid-identifiers-csv.py -i 2022-01-06-add-orcids.csv -db dspace63 -u dspacetest -p < span style = "color:#e6db74" > ' dom@in34sniper' < / span >
< / span > < / span > < / code > < / pre > < / div > < h2 id = "2022-01-09" > 2022-01-09< / h2 >
2022-01-12 18:55:47 +01:00
< ul >
< li > Validate and register CGSpace on < a href = "https://www.openarchives.org/Register/ValidateSite?log=Z2V7WCT7" > OpenArchives< / a >
< ul >
< li > Last month IWMI colleagues were asking me to look into this, and after checking the OpenArchives mailing list it seems there was a problem on the server side< / li >
< li > Now it has worked and the message is “ Successfully updated OAI registration database to status COMPLIANT.” < / li >
< li > I received an email (as the Admin contact on our OAI) that says:< / li >
< / ul >
< / li >
< / ul >
< blockquote >
< p > Your repository has been registered in the OAI database of conforming repositories.< / p >
< / blockquote >
< ul >
< li > Now I’ m taking a screenshot of the validation page for posterity, because the logs seem to go away after some time< / li >
< / ul >
< p > < img src = "/cgspace-notes/2022/01/openarchives-registration.png" alt = "OpenArchives.org registration" > < / p >
< ul >
< li > I tried to re-build the Docker image for OpenRXV and got an error in the backend:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > ...
< / span > < / span > < span style = "display:flex;" > < span > > openrxv-backend@0.0.1 build
< / span > < / span > < span style = "display:flex;" > < span > > nest build
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" >
< / span > < / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" > < / span > node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias ' AggregationsAggregate' circularly references itself.
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" >
< / span > < / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" > < / span > 2454 export type AggregationsAggregate = AggregationsSingleBucketAggregate | AggregationsAutoDateHistogramAggregate | AggregationsFiltersAggregate | AggregationsSignificantTermsAggregate< any> | AggregationsTermsAggregate< any> | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate< AggregationsBucket> | AggregationsMatrixStatsAggregate | AggregationsKeyedValueAggregate | AggregationsMetricAggregate
< / span > < / span > < span style = "display:flex;" > < span > ~~~~~~~~~~~~~~~~~~~~~
< / span > < / span > < span style = "display:flex;" > < span > node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias ' AggregationsSingleBucketAggregate' circularly references itself.
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" >
< / span > < / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" > < / span > 3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
< / span > < / span > < span style = "display:flex;" > < span > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" >
< / span > < / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" > < / span > Found 2 error(s).
< / span > < / span > < / code > < / pre > < / div > < ul >
2022-01-12 18:55:47 +01:00
< li > Ah, it seems the code on the server was slightly out of date
< ul >
< li > I checked out the latest master branch and it built< / li >
< / ul >
< / li >
< / ul >
< h2 id = "2022-01-12" > 2022-01-12< / h2 >
< ul >
< li > Fix some citation formatting issues in Gaia’ s < a href = "https://dspacetest.cgiar.org/handle/10568/115230" > eighteen CAS Green Cover publications on DSpace Test< / a > < / li >
< / ul >
2022-01-19 16:14:26 +01:00
< h2 id = "2022-01-19" > 2022-01-19< / h2 >
< ul >
< li > Francesca was having issues with a submission on CGSpace this week
< ul >
< li > I checked and see a lot of locks in PostgreSQL:< / li >
< / ul >
< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > $ psql -c < span style = "color:#e6db74" > " SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" < / span > | sort | uniq -c | sort -n
< / span > < / span > < span style = "display:flex;" > < span > 1
< / span > < / span > < span style = "display:flex;" > < span > 1 ------------------
< / span > < / span > < span style = "display:flex;" > < span > 1 (3506 rows)
< / span > < / span > < span style = "display:flex;" > < span > 1 application_name
< / span > < / span > < span style = "display:flex;" > < span > 9 psql
< / span > < / span > < span style = "display:flex;" > < span > 10
< / span > < / span > < span style = "display:flex;" > < span > 3487 dspaceWeb
< / span > < / span > < / code > < / pre > < / div > < ul >
2022-01-19 16:14:26 +01:00
< li > As before, I see messages from PostgreSQL about processes waiting for locks since I enabled the < code > log_lock_waits< / code > setting last month:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > $ grep -E < span style = "color:#e6db74" > ' ^2022-01*' < / span > /var/log/postgresql/postgresql-10-main.log | grep -c < span style = "color:#e6db74" > ' still waiting for' < / span >
< / span > < / span > < span style = "display:flex;" > < span > 12
< / span > < / span > < / code > < / pre > < / div > < ul >
2022-01-19 16:14:26 +01:00
< li > I set a system alert on DSpace and then restarted the server< / li >
< / ul >
2022-01-27 14:58:05 +01:00
< h2 id = "2022-01-20" > 2022-01-20< / h2 >
< ul >
< li > Abenet gave me a thumbs up for Gaia’ s eighteen CAS Green Cover items from last month
< ul >
< li > I created a SimpleArchiveFormat bundle with SAFBuilder and then imported them on CGSpace:< / li >
< / ul >
< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > $ JAVA_OPTS< span style = "color:#f92672" > =< / span > < span style = "color:#e6db74" > " -Xmx1024m -Dfile.encoding=UTF-8" < / span > dspace import --add --eperson< span style = "color:#f92672" > =< / span > aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile< span style = "color:#f92672" > =< / span > ./2022-01-20-green-covers.map
< / span > < / span > < / code > < / pre > < / div > < h2 id = "2022-01-21" > 2022-01-21< / h2 >
2022-01-27 14:58:05 +01:00
< ul >
< li > Start working on the rest of the ~980 CGIAR TAC and ICW documents from Gaia
< ul >
< li > I did some cleanups and standardization of author names< / li >
< li > I also noticed that a few dozen items had no dates at all, so I checked the PDFs and found dates for them in the text< / li >
< li > Otherwise all items have only a year, which is not great… < / li >
< / ul >
< / li >
< li > Proof of concept upgrade of OpenRXV from Angular 9 to Angular 10
< ul >
< li > I did some basic tests and created a < a href = "https://github.com/ilri/OpenRXV/pull/128" > pull request< / a > < / li >
< / ul >
< / li >
< / ul >
< h2 id = "2022-01-22" > 2022-01-22< / h2 >
< ul >
< li > Spend some time adding months to the CGIAR TAC and IWC records from Gaia
< ul >
2022-02-10 18:35:40 +01:00
< li > Most of the PDFs have only YYYY, so this is annoying… < / li >
2022-01-27 14:58:05 +01:00
< / ul >
< / li >
< / ul >
< h2 id = "2022-01-23" > 2022-01-23< / h2 >
< ul >
< li > Finalize cleaning up the dates on the CGIAR TAC and IWC records from Gaia< / li >
< li > Rebuild AReS and start a fresh harvest< / li >
< / ul >
< h2 id = "2022-01-25" > 2022-01-25< / h2 >
< ul >
< li > Help Udana from IWMI answer some questions about licenses on their journal articles
< ul >
< li > I was surprised to see they have 921 total, but only about 200 have a < code > dcterms.license< / code > field< / li >
< li > I updated about thirty manually, but really Udana should do more… < / li >
< / ul >
< / li >
< li > Normalize the metadata < code > text_lang< / code > attributes on CGSpace database:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > 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;
< / span > < / span > < span style = "display:flex;" > < span > text_lang | count
< / span > < / span > < span style = "display:flex;" > < span > -----------+---------
< / span > < / span > < span style = "display:flex;" > < span > en_US | 2803350
< / span > < / span > < span style = "display:flex;" > < span > en | 6232
< / span > < / span > < span style = "display:flex;" > < span > | 3200
< / span > < / span > < span style = "display:flex;" > < span > fr | 2
< / span > < / span > < span style = "display:flex;" > < span > vn | 2
< / span > < / span > < span style = "display:flex;" > < span > 92 | 1
< / span > < / span > < span style = "display:flex;" > < span > sp | 1
< / span > < / span > < span style = "display:flex;" > < span > | 0
< / span > < / span > < span style = "display:flex;" > < span > (8 rows)
< / span > < / span > < span style = "display:flex;" > < span > dspace=# UPDATE metadatavalue SET text_lang=' en_US' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN (' en' , ' 92' , ' ' );
< / span > < / span > < span style = "display:flex;" > < span > UPDATE 9433
< / span > < / span > < / code > < / pre > < / div > < ul >
2022-01-27 14:58:05 +01:00
< li > Then export the WLE Journal Articles collection again so there are fewer columns to mess with< / li >
< / ul >
< h2 id = "2022-01-26" > 2022-01-26< / h2 >
< ul >
< li > Send Gaia an example of the duplicate report for the first 200 TAC items to see what she thinks< / li >
< / ul >
< h2 id = "2022-01-27" > 2022-01-27< / h2 >
< ul >
< li > Work on WLE’ s Journal Articles a bit more
< ul >
< li > I realized that ~130 items have DOIs in their citation, but no < code > cg.identifier.doi< / code > field< / li >
< li > I used this OpenRefine GREL to copy them:< / li >
< / ul >
< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > cells[' dcterms.bibliographicCitation[en_US]' ].value.split(" doi: " )[1]
2022-01-27 14:58:05 +01:00
< / code > < / pre > < ul >
< li > I also spent a bit of time cleaning up ILRI Journal Articles, but I notice that we don’ t put DOIs in the citation so it’ s not possible to fix items that are missing DOIs that way
< ul >
< li > And I cleaned up and normalized some licenses< / li >
< / ul >
< / li >
< li > Francesca from Bioversity was having issues with a submission on CGSpace again
< ul >
< li > I looked at PostgreSQL and see an increasing number of locks:< / li >
< / ul >
< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > $ psql -c < span style = "color:#e6db74" > " SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" < / span > | sort | uniq -c | sort -n
< / span > < / span > < span style = "display:flex;" > < span > 1
< / span > < / span > < span style = "display:flex;" > < span > 1 ------------------
< / span > < / span > < span style = "display:flex;" > < span > 1 (537 rows)
< / span > < / span > < span style = "display:flex;" > < span > 1 application_name
< / span > < / span > < span style = "display:flex;" > < span > 9 psql
< / span > < / span > < span style = "display:flex;" > < span > 51 dspaceApi
< / span > < / span > < span style = "display:flex;" > < span > 477 dspaceWeb
< / span > < / span > < span style = "display:flex;" > < span > $ grep -E < span style = "color:#e6db74" > ' ^2022-01*' < / span > /var/log/postgresql/postgresql-10-main.log | grep -c < span style = "color:#e6db74" > ' still waiting for' < / span >
< / span > < / span > < span style = "display:flex;" > < span > 3
< / span > < / span > < / code > < / pre > < / div > < ul >
2022-01-31 07:00:59 +01:00
< li > I set a system alert on CGSpace and then restarted Tomcat and PostgreSQL
< ul >
< li > The issue in Francesca’ s case was actually that someone had taken the task, not that PostgreSQL transactions were locked!< / li >
< / ul >
< / li >
< / ul >
< h2 id = "2022-01-28" > 2022-01-28< / h2 >
< ul >
< li > Finalize the last ~100 WLE Journal Article items without licensese and DOIs
< ul >
< li > I did as many as I could, also updating http links to https for many journal links< / li >
< / ul >
< / li >
< li > Federica Bottamedi contacted us from the system office to say that she took over for Vini (Abhilasha Vaid)
< ul >
< li > She created an account on CGSpace and now we need to see which workflows she should belong to< / li >
< / ul >
< / li >
< li > Start a fresh harvesting on AReS< / li >
< li > I adjusted the < code > check-duplicates.py< / code > script to write the output to a CSV file including the id, both titles, both dates, and the handle link
< ul >
< li > I included the id because I will need a unique field to join the resulting list of non-duplicates with the original CSV where the rest of the metadata and filenames are< / li >
< li > Since these items are not in DSpace yet, I generated simple numeric IDs in OpenRefine using this GREL transform: < code > row.index + 1< / code > < / li >
< li > Then I ran < code > check-duplicates.py< / code > on items 1– < / li >
< / ul >
< / li >
< li > Delete one duplicate item I saw in IITA’ s Journal Articles that was uploaded earlier in WLE
< ul >
< li > Also do some general cleanup on IITA’ s Journal Articles collection in OpenRefine< / li >
< / ul >
< / li >
< li > Delete one duplicate item I saw in ILRI’ s Journal Articles collection
< ul >
< li > Also do some general cleanup on ILRI’ s Journal Articles collection in OpenRefine and csv-metadata-quality< / li >
< / ul >
< / li >
< / ul >
< h2 id = "2022-01-29" > 2022-01-29< / h2 >
< ul >
< li > I did some more cleanup on the ILRI Journal Articles
< ul >
< li > I added missing journal titles for items that had ISSNs< / li >
< li > Then I added pages for items that had them in the citation< / li >
< li > First, I faceted the citation field based on whether or not the item had something like “ : 232-234” present:< / li >
< / ul >
< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > value.contains(/:\s?\d+(-|–
< / span > < / span > < / code > < / pre > < / div > < ul >
2022-01-31 07:00:59 +01:00
< li > Then I faceted by blank on < code > dcterms.extent< / code > and did a transform to extract the page information for over 1,000 items!< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > ' p. ' +
< / span > < / span > < span style = "display:flex;" > < span > cells[' dcterms.bibliographicCitation[en_US]' ].value.match(/.*:\s?(\d+)(-|–
< / span > < / span > < span style = "display:flex;" > < span > ' -' +
< / span > < / span > < span style = "display:flex;" > < span > cells[' dcterms.bibliographicCitation[en_US]' ].value.match(/.*:\s?(\d+)(-|–
< / span > < / span > < / code > < / pre > < / div > < ul >
2022-01-31 07:00:59 +01:00
< li > Then I did similar for < code > cg.volume< / code > and < code > cg.issue< / code > , also based on the citation, for example to extract the “ 16” from “ Journal of Blah 16(1)” , where “ 16” is the second capture group in a zero-based match:< / li >
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< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > cells[' dcterms.bibliographicCitation[en_US]' ].value.match(/.*( |;)(\d+)\((\d+)\).*/)[1]
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2022-01-31 07:00:59 +01:00
< li > This was 3,000 items so I imported the changes on CGSpace 1,000 at a time… < / li >
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< h4 > Recent Posts< / h4 >
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< li > < a href = "/cgspace-notes/2022-04/" > April, 2022< / a > < / li >
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< li > < a href = "/cgspace-notes/2022-03/" > March, 2022< / a > < / li >
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2022-02-10 18:35:40 +01:00
< li > < a href = "/cgspace-notes/2022-02/" > February, 2022< / a > < / li >
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< li > < a href = "/cgspace-notes/2022-01/" > January, 2022< / a > < / li >
< li > < a href = "/cgspace-notes/2021-12/" > December, 2021< / a > < / li >
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< li > < a href = "https://cgspace.cgiar.org" > CGSpace< / a > < / li >
< li > < a href = "https://dspacetest.cgiar.org" > DSpace Test< / a > < / li >
< li > < a href = "https://github.com/ilri/DSpace" > CGSpace @ GitHub< / a > < / li >
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