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Add notes for 2021-09-13
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@ -34,7 +34,7 @@ It looks like we might be able to use OUs now, instead of DCs:
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$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
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"/>
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<meta name="generator" content="Hugo 0.87.0" />
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<meta name="generator" content="Hugo 0.88.1" />
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@ -127,11 +127,11 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=or
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<li>We had been using <code>DC=ILRI</code> to determine whether a user was ILRI or not</li>
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<li>It looks like we might be able to use OUs now, instead of DCs:</li>
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</ul>
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<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
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<pre tabindex="0"><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
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</code></pre><ul>
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<li>User who has been migrated to the root vs user still in the hierarchical structure:</li>
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</ul>
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<pre><code>distinguishedName: CN=Last\, First (ILRI),OU=ILRI Kenya Employees,OU=ILRI Kenya,OU=ILRIHUB,DC=CGIARAD,DC=ORG
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<pre tabindex="0"><code>distinguishedName: CN=Last\, First (ILRI),OU=ILRI Kenya Employees,OU=ILRI Kenya,OU=ILRIHUB,DC=CGIARAD,DC=ORG
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distinguishedName: CN=Last\, First (ILRI),OU=ILRI Ethiopia Employees,OU=ILRI Ethiopia,DC=ILRI,DC=CGIARAD,DC=ORG
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</code></pre><ul>
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<li>Changing the DSpace LDAP config to use <code>OU=ILRIHUB</code> seems to work:</li>
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@ -140,7 +140,7 @@ distinguishedName: CN=Last\, First (ILRI),OU=ILRI Ethiopia Employees,OU=ILRI Eth
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<ul>
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<li>Notes for local PostgreSQL database recreation from production snapshot:</li>
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</ul>
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<pre><code>$ dropdb dspacetest
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<pre tabindex="0"><code>$ dropdb dspacetest
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$ createdb -O dspacetest --encoding=UNICODE dspacetest
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$ psql dspacetest -c 'alter user dspacetest createuser;'
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$ pg_restore -O -U dspacetest -d dspacetest ~/Downloads/cgspace_2016-09-01.backup
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@ -150,7 +150,7 @@ $ vacuumdb dspacetest
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</code></pre><ul>
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<li>Some names that I thought I fixed in July seem not to be:</li>
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</ul>
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<pre><code>dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Poole, %';
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<pre tabindex="0"><code>dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Poole, %';
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text_value | authority | confidence
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-----------------------+--------------------------------------+------------
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Poole, Elizabeth Jane | b6efa27f-8829-4b92-80fe-bc63e03e3ccb | 600
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@ -163,12 +163,12 @@ $ vacuumdb dspacetest
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</code></pre><ul>
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<li>At least a few of these actually have the correct ORCID, but I will unify the authority to be c3a22456-8d6a-41f9-bba0-de51ef564d45</li>
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</ul>
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<pre><code>dspacetest=# update metadatavalue set authority='c3a22456-8d6a-41f9-bba0-de51ef564d45', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Poole, %';
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<pre tabindex="0"><code>dspacetest=# update metadatavalue set authority='c3a22456-8d6a-41f9-bba0-de51ef564d45', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Poole, %';
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UPDATE 69
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</code></pre><ul>
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<li>And for Peter Ballantyne:</li>
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</ul>
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<pre><code>dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Ballantyne, %';
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<pre tabindex="0"><code>dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Ballantyne, %';
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text_value | authority | confidence
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-------------------+--------------------------------------+------------
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Ballantyne, Peter | 2dcbcc7b-47b0-4fd7-bef9-39d554494081 | 600
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@ -180,12 +180,12 @@ UPDATE 69
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</code></pre><ul>
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<li>Again, a few have the correct ORCID, but there should only be one authority…</li>
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</ul>
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<pre><code>dspacetest=# update metadatavalue set authority='4f04ca06-9a76-4206-bd9c-917ca75d278e', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Ballantyne, %';
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<pre tabindex="0"><code>dspacetest=# update metadatavalue set authority='4f04ca06-9a76-4206-bd9c-917ca75d278e', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Ballantyne, %';
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UPDATE 58
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</code></pre><ul>
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<li>And for me:</li>
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</ul>
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<pre><code>dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Orth, A%';
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<pre tabindex="0"><code>dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Orth, A%';
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text_value | authority | confidence
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------------+--------------------------------------+------------
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Orth, Alan | 4884def0-4d7e-4256-9dd4-018cd60a5871 | 600
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@ -197,7 +197,7 @@ UPDATE 11
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</code></pre><ul>
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<li>And for CCAFS author Bruce Campbell that I had discussed with CCAFS earlier this week:</li>
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</ul>
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<pre><code>dspacetest=# update metadatavalue set authority='0e414b4c-4671-4a23-b570-6077aca647d8', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Campbell, B%';
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<pre tabindex="0"><code>dspacetest=# update metadatavalue set authority='0e414b4c-4671-4a23-b570-6077aca647d8', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Campbell, B%';
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UPDATE 166
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dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Campbell, B%';
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text_value | authority | confidence
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@ -215,7 +215,7 @@ dspacetest=# select distinct text_value, authority, confidence from metadatavalu
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<ul>
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<li>After one week of logging TLS connections on CGSpace:</li>
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</ul>
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<pre><code># zgrep "DES-CBC3" /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | wc -l
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<pre tabindex="0"><code># zgrep "DES-CBC3" /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | wc -l
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217
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# zcat -f -- /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | wc -l
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1164376
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@ -226,7 +226,7 @@ TLSv1/EDH-RSA-DES-CBC3-SHA
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<li>So this represents <code>0.02%</code> of 1.16M connections over a one-week period</li>
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<li>Transforming some filenames in OpenRefine so they can have a useful description for SAFBuilder:</li>
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</ul>
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<pre><code>value + "__description:" + cells["dc.type"].value
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<pre tabindex="0"><code>value + "__description:" + cells["dc.type"].value
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</code></pre><ul>
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<li>This gives you, for example: <code>Mainstreaming gender in agricultural R&D.pdf__description:Brief</code></li>
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</ul>
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@ -251,7 +251,7 @@ TLSv1/EDH-RSA-DES-CBC3-SHA
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<li>If I unzip the original zip from CIAT on Windows, re-zip it with 7zip on Windows, and then unzip it on Linux directly, the file names seem to be proper UTF-8</li>
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<li>We should definitely clean filenames so they don’t use characters that are tricky to process in CSV and shell scripts, like: <code>,</code>, <code>'</code>, and <code>"</code></li>
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</ul>
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<pre><code>value.replace("'","").replace(",","").replace('"','')
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<pre tabindex="0"><code>value.replace("'","").replace(",","").replace('"','')
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</code></pre><ul>
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<li>I need to write a Python script to match that for renaming files in the file system</li>
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<li>When importing SAF bundles it seems you can specify the target collection on the command line using <code>-c 10568/4003</code> or in the <code>collections</code> file inside each item in the bundle</li>
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@ -263,7 +263,7 @@ TLSv1/EDH-RSA-DES-CBC3-SHA
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</li>
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<li>Import CIAT Gender Network records to CGSpace, first creating the SAF bundles as my user, then importing as the <code>tomcat7</code> user, and deleting the bundle, for each collection’s items:</li>
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</ul>
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<pre><code>$ ./safbuilder.sh -c /home/aorth/ciat-gender-2016-09-06/66601.csv
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<pre tabindex="0"><code>$ ./safbuilder.sh -c /home/aorth/ciat-gender-2016-09-06/66601.csv
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$ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgiar.org/bin/dspace import -a -e aorth@mjanja.ch -c 10568/66601 -s /home/aorth/ciat-gender-2016-09-06/SimpleArchiveFormat -m 66601.map
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$ rm -rf ~/ciat-gender-2016-09-06/SimpleArchiveFormat/
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</code></pre><h2 id="2016-09-07">2016-09-07</h2>
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@ -274,7 +274,7 @@ $ rm -rf ~/ciat-gender-2016-09-06/SimpleArchiveFormat/
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<li>See: <a href="https://www.postgresql.org/docs/9.3/static/routine-vacuuming.html">https://www.postgresql.org/docs/9.3/static/routine-vacuuming.html</a></li>
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<li>CGSpace went down and the error seems to be the same as always (lately):</li>
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</ul>
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<pre><code>2016-09-07 11:39:23,162 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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<pre tabindex="0"><code>2016-09-07 11:39:23,162 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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...
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</code></pre><ul>
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@ -284,7 +284,7 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
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<ul>
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<li>CGSpace crashed twice today, errors from <code>catalina.out</code>:</li>
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</ul>
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<pre><code>org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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<pre tabindex="0"><code>org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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at org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:114)
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</code></pre><ul>
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<li>I enabled logging of requests to <code>/rest</code> again</li>
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@ -293,29 +293,29 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
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<ul>
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<li>CGSpace crashed again, errors from <code>catalina.out</code>:</li>
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</ul>
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<pre><code>org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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<pre tabindex="0"><code>org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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at org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:114)
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</code></pre><ul>
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<li>I restarted Tomcat and it was ok again</li>
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<li>CGSpace crashed a few hours later, errors from <code>catalina.out</code>:</li>
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</ul>
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<pre><code>Exception in thread "http-bio-127.0.0.1-8081-exec-25" java.lang.OutOfMemoryError: Java heap space
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<pre tabindex="0"><code>Exception in thread "http-bio-127.0.0.1-8081-exec-25" java.lang.OutOfMemoryError: Java heap space
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at java.lang.StringCoding.decode(StringCoding.java:215)
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</code></pre><ul>
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<li>We haven’t seen that in quite a while…</li>
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<li>Indeed, in a month of logs it only occurs 15 times:</li>
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</ul>
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<pre><code># grep -rsI "OutOfMemoryError" /var/log/tomcat7/catalina.* | wc -l
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<pre tabindex="0"><code># grep -rsI "OutOfMemoryError" /var/log/tomcat7/catalina.* | wc -l
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15
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</code></pre><ul>
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<li>I also see a bunch of errors from dspace.log:</li>
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</ul>
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<pre><code>2016-09-14 12:23:07,981 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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<pre tabindex="0"><code>2016-09-14 12:23:07,981 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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</code></pre><ul>
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<li>Looking at REST requests, it seems there is one IP hitting us nonstop:</li>
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||||
</ul>
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<pre><code># awk '{print $1}' /var/log/nginx/rest.log | sort -n | uniq -c | sort -h | tail -n 3
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<pre tabindex="0"><code># awk '{print $1}' /var/log/nginx/rest.log | sort -n | uniq -c | sort -h | tail -n 3
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820 50.87.54.15
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12872 70.32.99.142
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25744 70.32.83.92
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@ -328,19 +328,19 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
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<li>I think the stability issues are definitely from REST</li>
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<li>Crashed AGAIN, errors from dspace.log:</li>
|
||||
</ul>
|
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<pre><code>2016-09-14 14:31:43,069 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
|
||||
<pre tabindex="0"><code>2016-09-14 14:31:43,069 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
|
||||
org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
|
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</code></pre><ul>
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<li>And more heap space errors:</li>
|
||||
</ul>
|
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<pre><code># grep -rsI "OutOfMemoryError" /var/log/tomcat7/catalina.* | wc -l
|
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<pre tabindex="0"><code># grep -rsI "OutOfMemoryError" /var/log/tomcat7/catalina.* | wc -l
|
||||
19
|
||||
</code></pre><ul>
|
||||
<li>There are no more rest requests since the last crash, so maybe there are other things causing this.</li>
|
||||
<li>Hmm, I noticed a shitload of IPs from 180.76.0.0/16 are connecting to both CGSpace and DSpace Test (58 unique IPs concurrently!)</li>
|
||||
<li>They seem to be coming from Baidu, and so far during today alone account for 1/6 of every connection:</li>
|
||||
</ul>
|
||||
<pre><code># grep -c ip_addr= /home/cgspace.cgiar.org/log/dspace.log.2016-09-14
|
||||
<pre tabindex="0"><code># grep -c ip_addr= /home/cgspace.cgiar.org/log/dspace.log.2016-09-14
|
||||
29084
|
||||
# grep -c ip_addr=180.76.15 /home/cgspace.cgiar.org/log/dspace.log.2016-09-14
|
||||
5192
|
||||
@ -349,16 +349,16 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
|
||||
<li>From the activity control panel I can see 58 unique IPs hitting the site <em>concurrently</em>, which has GOT to hurt our stability</li>
|
||||
<li>A list of all 2000 unique IPs from CGSpace logs today:</li>
|
||||
</ul>
|
||||
<pre><code># grep ip_addr= /home/cgspace.cgiar.org/log/dspace.log.2016-09-11 | awk -F: '{print $5}' | sort -n | uniq -c | sort -h | tail -n 100
|
||||
<pre tabindex="0"><code># grep ip_addr= /home/cgspace.cgiar.org/log/dspace.log.2016-09-11 | awk -F: '{print $5}' | sort -n | uniq -c | sort -h | tail -n 100
|
||||
</code></pre><ul>
|
||||
<li>Looking at the top 20 IPs or so, most are Yahoo, MSN, Google, Baidu, TurnitIn (iParadigm), etc… do we have any real users?</li>
|
||||
<li>Generate a list of all author affiliations for Peter Ballantyne to go through, make corrections, and create a lookup list from:</li>
|
||||
</ul>
|
||||
<pre><code>dspacetest=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=211 group by text_value order by count desc) to /tmp/affiliations.csv with csv;
|
||||
<pre tabindex="0"><code>dspacetest=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=211 group by text_value order by count desc) to /tmp/affiliations.csv with csv;
|
||||
</code></pre><ul>
|
||||
<li>Looking into the Catalina logs again around the time of the first crash, I see:</li>
|
||||
</ul>
|
||||
<pre><code>Wed Sep 14 09:47:27 UTC 2016 | Query:id: 78581 AND type:2
|
||||
<pre tabindex="0"><code>Wed Sep 14 09:47:27 UTC 2016 | Query:id: 78581 AND type:2
|
||||
Wed Sep 14 09:47:28 UTC 2016 | Updating : 6/6 docs.
|
||||
Commit
|
||||
Commit done
|
||||
@ -368,7 +368,7 @@ Exception in thread "http-bio-127.0.0.1-8081-exec-193" java.lang.OutOf
|
||||
<li>And after that I see a bunch of “pool error Timeout waiting for idle object”</li>
|
||||
<li>Later, near the time of the next crash I see:</li>
|
||||
</ul>
|
||||
<pre><code>dn:CN=Haman\, Magdalena (CIAT-CCAFS),OU=Standard,OU=Users,OU=HQ,OU=CIATHUB,dc=cgiarad,dc=org
|
||||
<pre tabindex="0"><code>dn:CN=Haman\, Magdalena (CIAT-CCAFS),OU=Standard,OU=Users,OU=HQ,OU=CIATHUB,dc=cgiarad,dc=org
|
||||
Wed Sep 14 11:29:55 UTC 2016 | Query:id: 79078 AND type:2
|
||||
Wed Sep 14 11:30:20 UTC 2016 | Updating : 6/6 docs.
|
||||
Commit
|
||||
@ -389,7 +389,7 @@ java.util.Map does not have a no-arg default constructor.
|
||||
</code></pre><ul>
|
||||
<li>Then 20 minutes later another outOfMemoryError:</li>
|
||||
</ul>
|
||||
<pre><code>Exception in thread "http-bio-127.0.0.1-8081-exec-25" java.lang.OutOfMemoryError: Java heap space
|
||||
<pre tabindex="0"><code>Exception in thread "http-bio-127.0.0.1-8081-exec-25" java.lang.OutOfMemoryError: Java heap space
|
||||
at java.lang.StringCoding.decode(StringCoding.java:215)
|
||||
</code></pre><ul>
|
||||
<li>Perhaps these particular issues <em>are</em> memory issues, the munin graphs definitely show some weird purging/allocating behavior starting this week</li>
|
||||
@ -402,7 +402,7 @@ java.util.Map does not have a no-arg default constructor.
|
||||
<li>Oh great, the configuration on the actual server is different than in configuration management!</li>
|
||||
<li>Seems we added a bunch of settings to the <code>/etc/default/tomcat7</code> in December, 2015 and never updated our ansible repository:</li>
|
||||
</ul>
|
||||
<pre><code>JAVA_OPTS="-Djava.awt.headless=true -Xms3584m -Xmx3584m -XX:MaxPermSize=256m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8 -XX:-UseGCOverheadLimit -XX:MaxGCPauseMillis=250 -XX:GCTimeRatio=9 -XX:+PerfDisableSharedMem -XX:+ParallelRefProcEnabled -XX:G1HeapRegionSize=8m -XX:InitiatingHeapOccupancyPercent=75 -XX:+UseLargePages -XX:+AggressiveOpts"
|
||||
<pre tabindex="0"><code>JAVA_OPTS="-Djava.awt.headless=true -Xms3584m -Xmx3584m -XX:MaxPermSize=256m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8 -XX:-UseGCOverheadLimit -XX:MaxGCPauseMillis=250 -XX:GCTimeRatio=9 -XX:+PerfDisableSharedMem -XX:+ParallelRefProcEnabled -XX:G1HeapRegionSize=8m -XX:InitiatingHeapOccupancyPercent=75 -XX:+UseLargePages -XX:+AggressiveOpts"
|
||||
</code></pre><ul>
|
||||
<li>So I’m going to bump the heap +512m and remove all the other experimental shit (and update ansible!)</li>
|
||||
<li>Increased JVM heap to 4096m on CGSpace (linode01)</li>
|
||||
@ -416,7 +416,7 @@ java.util.Map does not have a no-arg default constructor.
|
||||
<ul>
|
||||
<li>CGSpace crashed again, and there are TONS of heap space errors but the datestamps aren’t on those lines so I’m not sure if they were yesterday:</li>
|
||||
</ul>
|
||||
<pre><code>dn:CN=Orentlicher\, Natalie (CIAT),OU=Standard,OU=Users,OU=HQ,OU=CIATHUB,dc=cgiarad,dc=org
|
||||
<pre tabindex="0"><code>dn:CN=Orentlicher\, Natalie (CIAT),OU=Standard,OU=Users,OU=HQ,OU=CIATHUB,dc=cgiarad,dc=org
|
||||
Thu Sep 15 18:45:25 UTC 2016 | Query:id: 55785 AND type:2
|
||||
Thu Sep 15 18:45:26 UTC 2016 | Updating : 100/218 docs.
|
||||
Thu Sep 15 18:45:26 UTC 2016 | Updating : 200/218 docs.
|
||||
@ -443,7 +443,7 @@ Exception in thread "Thread-54216" org.apache.solr.client.solrj.impl.H
|
||||
<li>I bumped the heap space from 4096m to 5120m to see if this is <em>really</em> about heap speace or not.</li>
|
||||
<li>Looking into some of these errors that I’ve seen this week but haven’t noticed before:</li>
|
||||
</ul>
|
||||
<pre><code># zcat -f -- /var/log/tomcat7/catalina.* | grep -c 'Failed to generate the schema for the JAX-B elements'
|
||||
<pre tabindex="0"><code># zcat -f -- /var/log/tomcat7/catalina.* | grep -c 'Failed to generate the schema for the JAX-B elements'
|
||||
113
|
||||
</code></pre><ul>
|
||||
<li>I’ve sent a message to Atmire about the Solr error to see if it’s related to their batch update module</li>
|
||||
@ -452,7 +452,7 @@ Exception in thread "Thread-54216" org.apache.solr.client.solrj.impl.H
|
||||
<ul>
|
||||
<li>Work on cleanups for author affiliations after Peter sent me his list of corrections/deletions:</li>
|
||||
</ul>
|
||||
<pre><code>$ ./fix-metadata-values.py -i affiliations_pb-322-corrections.csv -f cg.contributor.affiliation -t correct -m 211 -d dspace -u dspace -p fuuu
|
||||
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i affiliations_pb-322-corrections.csv -f cg.contributor.affiliation -t correct -m 211 -d dspace -u dspace -p fuuu
|
||||
$ ./delete-metadata-values.py -f cg.contributor.affiliation -i affiliations_pb-2-deletions.csv -m 211 -u dspace -d dspace -p fuuu
|
||||
</code></pre><ul>
|
||||
<li>After that we need to take the top ~300 and make a controlled vocabulary for it</li>
|
||||
@ -474,7 +474,7 @@ $ ./delete-metadata-values.py -f cg.contributor.affiliation -i affiliations_pb-2
|
||||
<li>Turns out the Solr search logic switched from OR to AND in DSpace 6.0 and the change is easy to backport: <a href="https://jira.duraspace.org/browse/DS-2809">https://jira.duraspace.org/browse/DS-2809</a></li>
|
||||
<li>We just need to set this in <code>dspace/solr/search/conf/schema.xml</code>:</li>
|
||||
</ul>
|
||||
<pre><code><solrQueryParser defaultOperator="AND"/>
|
||||
<pre tabindex="0"><code><solrQueryParser defaultOperator="AND"/>
|
||||
</code></pre><ul>
|
||||
<li>It actually works really well, and search results return much less hits now (before, after):</li>
|
||||
</ul>
|
||||
@ -483,7 +483,7 @@ $ ./delete-metadata-values.py -f cg.contributor.affiliation -i affiliations_pb-2
|
||||
<ul>
|
||||
<li>Found a way to improve the configuration of Atmire’s Content and Usage Analysis (CUA) module for date fields</li>
|
||||
</ul>
|
||||
<pre><code>-content.analysis.dataset.option.8=metadata:dateAccessioned:discovery
|
||||
<pre tabindex="0"><code>-content.analysis.dataset.option.8=metadata:dateAccessioned:discovery
|
||||
+content.analysis.dataset.option.8=metadata:dc.date.accessioned:date(month)
|
||||
</code></pre><ul>
|
||||
<li>This allows the module to treat the field as a date rather than a text string, so we can interrogate it more intelligently</li>
|
||||
@ -492,7 +492,7 @@ $ ./delete-metadata-values.py -f cg.contributor.affiliation -i affiliations_pb-2
|
||||
<li>45 minutes of downtime!</li>
|
||||
<li>Start processing the fixes to <code>dc.description.sponsorship</code> from Peter Ballantyne:</li>
|
||||
</ul>
|
||||
<pre><code>$ ./fix-metadata-values.py -i sponsors-fix-23.csv -f dc.description.sponsorship -t correct -m 29 -d dspace -u dspace -p fuuu
|
||||
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i sponsors-fix-23.csv -f dc.description.sponsorship -t correct -m 29 -d dspace -u dspace -p fuuu
|
||||
$ ./delete-metadata-values.py -i sponsors-delete-8.csv -f dc.description.sponsorship -m 29 -d dspace -u dspace -p fuuu
|
||||
</code></pre><ul>
|
||||
<li>I need to run these and the others from a few days ago on CGSpace the next time we run updates</li>
|
||||
@ -511,14 +511,14 @@ $ ./delete-metadata-values.py -i sponsors-delete-8.csv -f dc.description.sponsor
|
||||
<li>Not sure if it’s something like we already have too many filters there (30), or the filter name is reserved, etc…</li>
|
||||
<li>Generate a list of ILRI subjects for Peter and Abenet to look through/fix:</li>
|
||||
</ul>
|
||||
<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where resource_type_id=2 and metadata_field_id=203 group by text_value order by count desc) to /tmp/ilrisubjects.csv with csv;
|
||||
<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where resource_type_id=2 and metadata_field_id=203 group by text_value order by count desc) to /tmp/ilrisubjects.csv with csv;
|
||||
</code></pre><ul>
|
||||
<li>Regenerate Discovery indexes a few times after playing with <code>discovery.xml</code> index definitions (syntax, parameters, etc).</li>
|
||||
<li>Merge changes to boolean logic in Solr search (<a href="https://github.com/ilri/DSpace/pull/274">#274</a>)</li>
|
||||
<li>Run all sponsorship and affiliation fixes on CGSpace, deploy latest <code>5_x-prod</code> branch, and re-index Discovery on CGSpace</li>
|
||||
<li>Tested OCSP stapling on DSpace Test’s nginx and it works:</li>
|
||||
</ul>
|
||||
<pre><code>$ openssl s_client -connect dspacetest.cgiar.org:443 -servername dspacetest.cgiar.org -tls1_2 -tlsextdebug -status
|
||||
<pre tabindex="0"><code>$ openssl s_client -connect dspacetest.cgiar.org:443 -servername dspacetest.cgiar.org -tls1_2 -tlsextdebug -status
|
||||
...
|
||||
OCSP response:
|
||||
======================================
|
||||
@ -533,12 +533,12 @@ OCSP Response Data:
|
||||
<li>Discuss fixing some ORCIDs for CCAFS author Sonja Vermeulen with Magdalena Haman</li>
|
||||
<li>This author has a few variations:</li>
|
||||
</ul>
|
||||
<pre><code>dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeu
|
||||
<pre tabindex="0"><code>dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeu
|
||||
len, S%';
|
||||
</code></pre><ul>
|
||||
<li>And it looks like <code>fe4b719f-6cc4-4d65-8504-7a83130b9f83</code> is the authority with the correct ORCID linked</li>
|
||||
</ul>
|
||||
<pre><code>dspacetest=# update metadatavalue set authority='fe4b719f-6cc4-4d65-8504-7a83130b9f83w', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeulen, S%';
|
||||
<pre tabindex="0"><code>dspacetest=# update metadatavalue set authority='fe4b719f-6cc4-4d65-8504-7a83130b9f83w', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeulen, S%';
|
||||
UPDATE 101
|
||||
</code></pre><ul>
|
||||
<li>Hmm, now her name is missing from the authors facet and only shows the authority ID</li>
|
||||
@ -547,7 +547,7 @@ UPDATE 101
|
||||
<li>On a clean snapshot of the database I see the correct authority should be <code>f01f7b7b-be3f-4df7-a61d-b73c067de88d</code>, not <code>fe4b719f-6cc4-4d65-8504-7a83130b9f83</code></li>
|
||||
<li>Updating her authorities again and reindexing:</li>
|
||||
</ul>
|
||||
<pre><code>dspacetest=# update metadatavalue set authority='f01f7b7b-be3f-4df7-a61d-b73c067de88d', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeulen, S%';
|
||||
<pre tabindex="0"><code>dspacetest=# update metadatavalue set authority='f01f7b7b-be3f-4df7-a61d-b73c067de88d', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeulen, S%';
|
||||
UPDATE 101
|
||||
</code></pre><ul>
|
||||
<li>Use GitHub icon from Font Awesome instead of a PNG to save one extra network request</li>
|
||||
@ -564,14 +564,14 @@ UPDATE 101
|
||||
<li>Minor fix to a string in Atmire’s CUA module (<a href="https://github.com/ilri/DSpace/pull/280">#280</a>)</li>
|
||||
<li>This seems to be what I’ll need to do for Sonja Vermeulen (but with <code>2b4166b7-6e4d-4f66-9d8b-ddfbec9a6ae0</code> instead on the live site):</li>
|
||||
</ul>
|
||||
<pre><code>dspacetest=# update metadatavalue set authority='09e4da69-33a3-45ca-b110-7d3f82d2d6d2', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeulen, S%';
|
||||
<pre tabindex="0"><code>dspacetest=# update metadatavalue set authority='09e4da69-33a3-45ca-b110-7d3f82d2d6d2', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeulen, S%';
|
||||
dspacetest=# update metadatavalue set authority='09e4da69-33a3-45ca-b110-7d3f82d2d6d2', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Vermeulen SJ%';
|
||||
</code></pre><ul>
|
||||
<li>And then update Discovery and Authority indexes</li>
|
||||
<li>Minor fix for “Subject” string in Discovery search and Atmire modules (<a href="https://github.com/ilri/DSpace/pull/281">#281</a>)</li>
|
||||
<li>Start testing batch fixes for ILRI subject from Peter:</li>
|
||||
</ul>
|
||||
<pre><code>$ ./fix-metadata-values.py -i ilrisubjects-fix-32.csv -f cg.subject.ilri -t correct -m 203 -d dspace -u dspace -p fuuuu
|
||||
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i ilrisubjects-fix-32.csv -f cg.subject.ilri -t correct -m 203 -d dspace -u dspace -p fuuuu
|
||||
$ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -m 203 -d dspace -u dspace -p fuuu
|
||||
</code></pre><h2 id="2016-09-29">2016-09-29</h2>
|
||||
<ul>
|
||||
@ -580,7 +580,7 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
|
||||
<li>DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console</li>
|
||||
<li>People on DSpace mailing list gave me a query to get authors from certain collections:</li>
|
||||
</ul>
|
||||
<pre><code>dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
|
||||
<pre tabindex="0"><code>dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
|
||||
</code></pre><h2 id="2016-09-30">2016-09-30</h2>
|
||||
<ul>
|
||||
<li>Deny access to REST API’s <code>find-by-metadata-field</code> endpoint to protect against an upstream security issue (DS-3250)</li>
|
||||
|
||||
Reference in New Issue
Block a user