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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <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> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <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="/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> <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"><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> <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"><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> <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> <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"><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> <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"><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> <li>I set a system alert on DSpace and then restarted the server</li> </ul> <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> <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> <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> <li>Most of the PDFs have only YYYY, so this is annoying…</li> </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> <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> <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> <pre tabindex="0"><code>cells['dcterms.bibliographicCitation[en_US]'].value.split("doi: ")[1] </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> <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> <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 1–200 and sent the resulting CSV to Gaia</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> <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+(-|–)\d+/) </span></span></code></pre></div><ul> <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> <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+)(-|–)(\d+).*/)[0] + </span></span><span style="display:flex;"><span>'-' + </span></span><span style="display:flex;"><span>cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*:\s?(\d+)(-|–)(\d+).*/)[2] </span></span></code></pre></div><ul> <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> </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"><span style="display:flex;"><span>cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*( |;)(\d+)\((\d+)\).*/)[1] </span></span></code></pre></div><ul> <li>This was 3,000 items so I imported the changes on CGSpace 1,000 at a time…</li> </ul> <!-- raw HTML omitted --> </article> </div> <!-- /.blog-main --> <aside class="col-sm-3 ml-auto blog-sidebar"> <section class="sidebar-module"> <h4>Recent Posts</h4> <ol class="list-unstyled"> <li><a href="/cgspace-notes/2022-08/">August, 2022</a></li> <li><a href="/cgspace-notes/2022-07/">July, 2022</a></li> <li><a href="/cgspace-notes/2022-06/">June, 2022</a></li> <li><a href="/cgspace-notes/2022-05/">May, 2022</a></li> <li><a href="/cgspace-notes/2022-04/">April, 2022</a></li> </ol> </section> <section class="sidebar-module"> <h4>Links</h4> <ol class="list-unstyled"> <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> </ol> </section> </aside> </div> <!-- /.row --> </div> <!-- /.container --> <footer class="blog-footer"> <p dir="auto"> Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>. </p> <p> <a href="#">Back to top</a> </p> </footer> </body> </html>