2022-01-01 14:21:47 +01:00
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Start a full harvest on AReS
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< h1 class = "blog-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/" rel = "home" > CGSpace Notes< / a > < / h1 >
< 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 >
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< 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 >
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< h2 id = "2022-01-01" > 2022-01-01< / h2 >
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< 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 >
< 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" > $ cat 2022-01-06-add-orcids.csv
dc.contributor.author,cg.creator.identifier
" Jones, Chris" ," Chris Jones: 0000-0001-9096-9728"
" Jones, Christopher S." ," Chris Jones: 0000-0001-9096-9728"
$ ./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 >
2022-01-12 18:55:47 +01:00
< / code > < / pre > < / div > < h2 id = "2022-01-09" > 2022-01-09< / h2 >
< 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 >
< 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" > ...
> openrxv-backend@0.0.1 build
> nest build
< span style = "color:#960050;background-color:#1e0010" >
< / 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 style = "color:#960050;background-color:#1e0010" >
< / 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
~~~~~~~~~~~~~~~~~~~~~
node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias ' AggregationsSingleBucketAggregate' circularly references itself.
< span style = "color:#960050;background-color:#1e0010" >
< / span > < span style = "color:#960050;background-color:#1e0010" > < / span > 3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
< span style = "color:#960050;background-color:#1e0010" >
< / span > < span style = "color:#960050;background-color:#1e0010" > < / span > Found 2 error(s).
< / code > < / pre > < / div > < ul >
< 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 >
< 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" > $ 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
1
1 ------------------
1 (3506 rows)
1 application_name
9 psql
10
3487 dspaceWeb
< / code > < / pre > < / div > < ul >
< 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 >
< 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" > $ 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 >
12
< / code > < / pre > < / div > < ul >
< li > I set a system alert on DSpace and then restarted the server< / li >
< / ul >
2022-01-12 18:55:47 +01:00
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< h4 > Recent Posts< / h4 >
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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 >
< li > < a href = "/cgspace-notes/2021-11/" > November, 2021< / a > < / li >
< li > < a href = "/cgspace-notes/2021-10/" > October, 2021< / a > < / li >
< li > < a href = "/cgspace-notes/2021-09/" > September, 2021< / a > < / li >
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< h4 > Links< / h4 >
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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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