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Add notes for 2022-03-04
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@ -18,7 +18,7 @@
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="May, 2017"/>
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<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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<meta name="generator" content="Hugo 0.92.2" />
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<meta name="generator" content="Hugo 0.93.1" />
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@ -159,7 +159,7 @@
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<li>This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using <code>dspace cleanup -v</code>, or else you’ll run out of disk space</li>
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<li>In the end I realized it’s better to use submission mode (<code>-s</code>) to ingest the community object as a single AIP without its children, followed by each of the collections:</li>
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</ul>
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<pre tabindex="0"><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit"
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<pre tabindex="0"><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit"
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$ [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10568/87775 /home/aorth/10947-1/10947-1.zip
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$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
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$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done
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@ -184,13 +184,13 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<li>The CGIAR Library metadata has some blank metadata values, which leads to <code>|||</code> in the Discovery facets</li>
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<li>Clean these up in the database using:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
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<pre tabindex="0"><code>dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
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</code></pre><ul>
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<li>I ended up running into issues during data cleaning and decided to wipe out the entire community and re-sync DSpace Test assetstore and database from CGSpace rather than waiting for the cleanup task to clean up</li>
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<li>Hours into the re-ingestion I ran into more errors, and had to erase everything and start over <em>again</em>!</li>
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<li>Now, no matter what I do I keep getting foreign key errors…</li>
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</ul>
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<pre tabindex="0"><code>Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "handle_pkey"
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<pre tabindex="0"><code>Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "handle_pkey"
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Detail: Key (handle_id)=(80928) already exists.
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</code></pre><ul>
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<li>I think those errors actually come from me running the <code>update-sequences.sql</code> script while Tomcat/DSpace are running</li>
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@ -202,7 +202,7 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<li>I clarified that the scope of the implementation should be that ORCIDs are stored in the database and exposed via REST / API like other fields</li>
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<li>Finally finished importing all the CGIAR Library content, final method was:</li>
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</ul>
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<pre tabindex="0"><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit"
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<pre tabindex="0"><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit"
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$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2517/10947-2517.zip
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$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2515/10947-2515.zip
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$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2516/10947-2516.zip
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@ -215,7 +215,7 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<li>The <code>-XX:-UseGCOverheadLimit</code> JVM option helps with some issues in large imports</li>
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<li>After this I ran the <code>update-sequences.sql</code> script (with Tomcat shut down), and cleaned up the 200+ blank metadata records:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
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<pre tabindex="0"><code>dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
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</code></pre><h2 id="2017-05-13">2017-05-13</h2>
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<ul>
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<li>After quite a bit of troubleshooting with importing cleaned up data as CSV, it seems that there are actually <a href="https://en.wikipedia.org/wiki/Null_character">NUL</a> characters in the <code>dc.description.abstract</code> field (at least) on the lines where CSV importing was failing</li>
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@ -230,7 +230,7 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<li>Merge changes to CCAFS project identifiers and flagships: <a href="https://github.com/ilri/DSpace/pull/320">#320</a></li>
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<li>Run updates for CCAFS flagships on CGSpace:</li>
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</ul>
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<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/ccafs-flagships-may7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p 'fuuu'
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<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/ccafs-flagships-may7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p 'fuuu'
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</code></pre><ul>
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<li>
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<p>These include:</p>
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@ -258,7 +258,7 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<ul>
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<li>Looking into the error I get when trying to create a new collection on DSpace Test:</li>
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</ul>
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<pre tabindex="0"><code>ERROR: duplicate key value violates unique constraint "handle_pkey" Detail: Key (handle_id)=(84834) already exists.
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<pre tabindex="0"><code>ERROR: duplicate key value violates unique constraint "handle_pkey" Detail: Key (handle_id)=(84834) already exists.
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</code></pre><ul>
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<li>I tried updating the sequences a few times, with Tomcat running and stopped, but it hasn’t helped</li>
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<li>It appears item with <code>handle_id</code> 84834 is one of the imported CGIAR Library items:</li>
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@ -279,7 +279,7 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<li>I’ve posted on the dspace-test mailing list to see if I can just manually set the <code>handle_seq</code> to that value</li>
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<li>Actually, it seems I can manually set the handle sequence using:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# select setval('handle_seq',86873);
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<pre tabindex="0"><code>dspace=# select setval('handle_seq',86873);
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</code></pre><ul>
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<li>After that I can create collections just fine, though I’m not sure if it has other side effects</li>
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</ul>
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@ -294,31 +294,31 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<li>Do some cleanups of community and collection names in CGIAR System Management Office community on DSpace Test, as well as move some items as Peter requested</li>
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<li>Peter wanted a list of authors in here, so I generated a list of collections using the “View Source” on each community and this hacky awk:</li>
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</ul>
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<pre tabindex="0"><code>$ grep 10947/ /tmp/collections | grep -v cocoon | awk -F/ '{print $3"/"$4}' | awk -F\" '{print $1}' | vim -
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<pre tabindex="0"><code>$ grep 10947/ /tmp/collections | grep -v cocoon | awk -F/ '{print $3"/"$4}' | awk -F\" '{print $1}' | vim -
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</code></pre><ul>
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<li>Then I joined them together and ran this old SQL query from the dspace-tech mailing list which gives you authors for items in those collections:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# select distinct text_value
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from metadatavalue
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where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author')
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where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author')
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AND resource_type_id = 2
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AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10947/2', '10947/3', '10947/1
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0', '10947/4', '10947/5', '10947/6', '10947/7', '10947/8', '10947/9', '10947/11', '10947/25', '10947/12', '10947/26', '10947/27', '10947/28', '10947/29', '109
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47/30', '10947/13', '10947/14', '10947/15', '10947/16', '10947/31', '10947/32', '10947/33', '10947/34', '10947/35', '10947/36', '10947/37', '10947/17', '10947
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/18', '10947/38', '10947/19', '10947/39', '10947/40', '10947/41', '10947/42', '10947/43', '10947/2512', '10947/44', '10947/20', '10947/21', '10947/45', '10947
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/46', '10947/47', '10947/48', '10947/49', '10947/22', '10947/23', '10947/24', '10947/50', '10947/51', '10947/2518', '10947/2776', '10947/2790', '10947/2521',
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'10947/2522', '10947/2782', '10947/2525', '10947/2836', '10947/2524', '10947/2878', '10947/2520', '10947/2523', '10947/2786', '10947/2631', '10947/2589', '109
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47/2519', '10947/2708', '10947/2526', '10947/2871', '10947/2527', '10947/4467', '10947/3457', '10947/2528', '10947/2529', '10947/2533', '10947/2530', '10947/2
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531', '10947/2532', '10947/2538', '10947/2534', '10947/2540', '10947/2900', '10947/2539', '10947/2784', '10947/2536', '10947/2805', '10947/2541', '10947/2535'
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, '10947/2537', '10568/93761')));
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AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10947/2', '10947/3', '10947/1
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0', '10947/4', '10947/5', '10947/6', '10947/7', '10947/8', '10947/9', '10947/11', '10947/25', '10947/12', '10947/26', '10947/27', '10947/28', '10947/29', '109
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47/30', '10947/13', '10947/14', '10947/15', '10947/16', '10947/31', '10947/32', '10947/33', '10947/34', '10947/35', '10947/36', '10947/37', '10947/17', '10947
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/18', '10947/38', '10947/19', '10947/39', '10947/40', '10947/41', '10947/42', '10947/43', '10947/2512', '10947/44', '10947/20', '10947/21', '10947/45', '10947
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/46', '10947/47', '10947/48', '10947/49', '10947/22', '10947/23', '10947/24', '10947/50', '10947/51', '10947/2518', '10947/2776', '10947/2790', '10947/2521',
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'10947/2522', '10947/2782', '10947/2525', '10947/2836', '10947/2524', '10947/2878', '10947/2520', '10947/2523', '10947/2786', '10947/2631', '10947/2589', '109
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47/2519', '10947/2708', '10947/2526', '10947/2871', '10947/2527', '10947/4467', '10947/3457', '10947/2528', '10947/2529', '10947/2533', '10947/2530', '10947/2
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531', '10947/2532', '10947/2538', '10947/2534', '10947/2540', '10947/2900', '10947/2539', '10947/2784', '10947/2536', '10947/2805', '10947/2541', '10947/2535'
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, '10947/2537', '10568/93761')));
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</code></pre><ul>
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<li>To get a CSV (with counts) from that:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*)
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from metadatavalue
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where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author')
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where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author')
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AND resource_type_id = 2
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AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10947/2', '10947/3', '10947/10', '10947/4', '10947/5', '10947/6', '10947/7', '10947/8', '10947/9', '10947/11', '10947/25', '10947/12', '10947/26', '10947/27', '10947/28', '10947/29', '10947/30', '10947/13', '10947/14', '10947/15', '10947/16', '10947/31', '10947/32', '10947/33', '10947/34', '10947/35', '10947/36', '10947/37', '10947/17', '10947/18', '10947/38', '10947/19', '10947/39', '10947/40', '10947/41', '10947/42', '10947/43', '10947/2512', '10947/44', '10947/20', '10947/21', '10947/45', '10947/46', '10947/47', '10947/48', '10947/49', '10947/22', '10947/23', '10947/24', '10947/50', '10947/51', '10947/2518', '10947/2776', '10947/2790', '10947/2521', '10947/2522', '10947/2782', '10947/2525', '10947/2836', '10947/2524', '10947/2878', '10947/2520', '10947/2523', '10947/2786', '10947/2631', '10947/2589', '10947/2519', '10947/2708', '10947/2526', '10947/2871', '10947/2527', '10947/4467', '10947/3457', '10947/2528', '10947/2529', '10947/2533', '10947/2530', '10947/2531', '10947/2532', '10947/2538', '10947/2534', '10947/2540', '10947/2900', '10947/2539', '10947/2784', '10947/2536', '10947/2805', '10947/2541', '10947/2535', '10947/2537', '10568/93761'))) group by text_value order by count desc) to /tmp/cgiar-librar-authors.csv with csv;
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AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10947/2', '10947/3', '10947/10', '10947/4', '10947/5', '10947/6', '10947/7', '10947/8', '10947/9', '10947/11', '10947/25', '10947/12', '10947/26', '10947/27', '10947/28', '10947/29', '10947/30', '10947/13', '10947/14', '10947/15', '10947/16', '10947/31', '10947/32', '10947/33', '10947/34', '10947/35', '10947/36', '10947/37', '10947/17', '10947/18', '10947/38', '10947/19', '10947/39', '10947/40', '10947/41', '10947/42', '10947/43', '10947/2512', '10947/44', '10947/20', '10947/21', '10947/45', '10947/46', '10947/47', '10947/48', '10947/49', '10947/22', '10947/23', '10947/24', '10947/50', '10947/51', '10947/2518', '10947/2776', '10947/2790', '10947/2521', '10947/2522', '10947/2782', '10947/2525', '10947/2836', '10947/2524', '10947/2878', '10947/2520', '10947/2523', '10947/2786', '10947/2631', '10947/2589', '10947/2519', '10947/2708', '10947/2526', '10947/2871', '10947/2527', '10947/4467', '10947/3457', '10947/2528', '10947/2529', '10947/2533', '10947/2530', '10947/2531', '10947/2532', '10947/2538', '10947/2534', '10947/2540', '10947/2900', '10947/2539', '10947/2784', '10947/2536', '10947/2805', '10947/2541', '10947/2535', '10947/2537', '10568/93761'))) group by text_value order by count desc) to /tmp/cgiar-librar-authors.csv with csv;
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</code></pre><h2 id="2017-05-23">2017-05-23</h2>
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<ul>
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<li>Add Affiliation to filters on Listing and Reports module (<a href="https://github.com/ilri/DSpace/pull/325">#325</a>)</li>
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@ -343,21 +343,21 @@ COPY 111
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<li>Communicate with MARLO people about progress on exposing ORCIDs via the REST API, as it is set to be discussed in the <a href="https://wiki.lyrasis.org/display/cmtygp/DCAT+Meeting+June+2017">June, 2017 DCAT meeting</a></li>
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<li>Find all of Amos Omore’s author name variations so I can link them to his authority entry that has an ORCID:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like 'Omore, A%';
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<pre tabindex="0"><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like 'Omore, A%';
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</code></pre><ul>
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<li>Set the authority for all variations to one containing an ORCID:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# update metadatavalue set authority='4428ee88-90ef-4107-b837-3c0ec988520b', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Omore, A%';
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<pre tabindex="0"><code>dspace=# update metadatavalue set authority='4428ee88-90ef-4107-b837-3c0ec988520b', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Omore, A%';
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UPDATE 187
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</code></pre><ul>
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<li>Next I need to do Edgar Twine:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like 'Twine, E%';
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<pre tabindex="0"><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like 'Twine, E%';
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</code></pre><ul>
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<li>But it doesn’t look like any of his existing entries are linked to an authority which has an ORCID, so I edited the metadata via “Edit this Item” and looked up his ORCID and linked it there</li>
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<li>Now I should be able to set his name variations to the new authority:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# update metadatavalue set authority='f70d0a01-d562-45b8-bca3-9cf7f249bc8b', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Twine, E%';
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<pre tabindex="0"><code>dspace=# update metadatavalue set authority='f70d0a01-d562-45b8-bca3-9cf7f249bc8b', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Twine, E%';
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</code></pre><ul>
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<li>Run the corrections on CGSpace and then update discovery / authority</li>
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<li>I notice that there are a handful of <code>java.lang.OutOfMemoryError: Java heap space</code> errors in the Catalina logs on CGSpace, I should go look into that…</li>
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