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I wrote a script to query Sherpa’s API for our ISSNs: sherpa-issn-lookup.py
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I’m curious to see how the results compare with the results from Crossref yesterday
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AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
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I simply took everything down with docker-compose and then back up, and then it was OK
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Perhaps one of the containers crashed, I should have looked closer but I was in a hurry
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|
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I wrote a script to query Sherpa’s API for our ISSNs: sherpa-issn-lookup.py
|
||
|
||
I’m curious to see how the results compare with the results from Crossref yesterday
|
||
|
||
|
||
AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
|
||
|
||
I simply took everything down with docker-compose and then back up, and then it was OK
|
||
Perhaps one of the containers crashed, I should have looked closer but I was in a hurry
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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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/2021-04/">April, 2021</a></h2>
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<time datetime="2021-04-01T09:50:54+03:00">Thu Apr 01, 2021</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2021-04-01">2021-04-01</h2>
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<ul>
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||
<li>I wrote a script to query Sherpa’s API for our ISSNs: <code>sherpa-issn-lookup.py</code>
|
||
<ul>
|
||
<li>I’m curious to see how the results compare with the results from Crossref yesterday</li>
|
||
</ul>
|
||
</li>
|
||
<li>AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
|
||
<ul>
|
||
<li>I simply took everything down with docker-compose and then back up, and then it was OK</li>
|
||
<li>Perhaps one of the containers crashed, I should have looked closer but I was in a hurry</li>
|
||
</ul>
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||
</li>
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||
</ul>
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<h2 id="2021-04-03">2021-04-03</h2>
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<ul>
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<li>Biruk from ICT contacted me to say that some CGSpace users still can’t log in
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<ul>
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<li>I guess the CGSpace LDAP bind account is really still locked after last week’s reset</li>
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<li>He fixed the account and then I was finally able to bind and query:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b "dc=cgiarad,dc=org" -D "cgspace-account" -W "(sAMAccountName=otheraccounttoquery)"
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</code></pre><h2 id="2021-04-04">2021-04-04</h2>
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<ul>
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<li>Check the index aliases on AReS Explorer to make sure they are sane before starting a new harvest:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
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</code></pre><ul>
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<li>Then set the <code>openrxv-items-final</code> index to read-only so we can make a backup:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
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{"acknowledged":true}%
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$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-backup
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{"acknowledged":true,"shards_acknowledged":true,"index":"openrxv-items-final-backup"}%
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$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
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</code></pre><ul>
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<li>Then start a harvesting on AReS Explorer</li>
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<li>Help Enrico get some 2020 statistics for the Roots, Tubers and Bananas (RTB) community on CGSpace
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<ul>
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<li>He was hitting <a href="https://github.com/ilri/OpenRXV/issues/66">a bug on AReS</a> and also he only needed stats for 2020, and AReS currently only gives all-time stats</li>
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</ul>
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</li>
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<li>I cleaned up about 230 ISSNs on CGSpace in OpenRefine
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<ul>
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<li>I had exported them last week, then filtered for anything not looking like an ISSN with this GREL: <code>isNotNull(value.match(/^\p{Alnum}{4}-\p{Alnum}{4}$/))</code></li>
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<li>Then I applied them on CGSpace with the <code>fix-metadata-values.py</code> script:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ ./ilri/fix-metadata-values.py -i /tmp/2021-04-01-ISSNs.csv -db dspace -u dspace -p 'fuuu' -f cg.issn -t 'correct' -m 253
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</code></pre><ul>
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<li>For now I only fixed obvious errors like “1234-5678.” and “e-ISSN: 1234-5678” etc, but there are still lots of invalid ones which need more manual work:
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<ul>
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<li>Too few characters</li>
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<li>Too many characters</li>
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<li>ISBNs</li>
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</ul>
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</li>
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<li>Create the CGSpace community and collection structure for the new Accelerating Impacts of CGIAR Climate Research for Africa (AICCRA) and assign all workflow steps</li>
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</ul>
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<h2 id="2021-04-05">2021-04-05</h2>
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<ul>
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<li>The AReS Explorer harvesting from yesterday finished, and the results look OK, but actually the Elasticsearch indexes are messed up again:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
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{
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"openrxv-items-final": {
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"aliases": {}
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},
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"openrxv-items-temp": {
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"aliases": {
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||
"openrxv-items": {}
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}
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},
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...
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}
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</code></pre><ul>
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<li><code>openrxv-items</code> should be an alias of <code>openrxv-items-final</code>, not <code>openrxv-temp</code>… I will have to fix that manually</li>
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<li>Enrico asked for more information on the RTB stats I gave him yesterday
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<ul>
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<li>I remembered (again) that we can’t filter Atmire’s CUA stats by date issued</li>
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<li>To show, for example, views/downloads in the year 2020 for RTB issued in 2020, we would need to use the DSpace statistics API and post a list of IDs and a custom date range</li>
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<li>I tried to do that here by exporting the RTB community and extracting the IDs for items issued in 2020:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ ~/dspace63/bin/dspace metadata-export -i 10568/80100 -f /tmp/rtb.csv
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$ csvcut -c 'id,dcterms.issued,dcterms.issued[],dcterms.issued[en_US]' /tmp/rtb.csv | \
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sed '1d' | \
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csvsql --no-header --no-inference --query 'SELECT a AS id,COALESCE(b, "")||COALESCE(c, "")||COALESCE(d, "") AS issued FROM stdin' | \
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csvgrep -c issued -m 2020 | \
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csvcut -c id | \
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sed '1d' | \
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sort | \
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uniq
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</code></pre><ul>
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<li>So I remember in the future, this basically does the following:
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||
<ul>
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<li>Use csvcut to extract the id and all date issued columns from the CSV</li>
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||
<li>Use sed to remove the header so we can refer to the columns using default a, b, c instead of their real names (which are tricky to match due to special characters)</li>
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||
<li>Use csvsql to concatenate the various date issued columns (coalescing where null)</li>
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||
<li>Use csvgrep to filter items by date issued in 2020</li>
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||
<li>Use csvcut to extract the id column</li>
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||
<li>Use sed to delete the header row</li>
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||
<li>Use sort and uniq to filter out any duplicate IDs (there were three)</li>
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||
</ul>
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||
</li>
|
||
<li>Then I have a list of 296 IDs for RTB items issued in 2020</li>
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||
<li>I constructed a JSON file to post to the DSpace Statistics API:</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-json" data-lang="json">{
|
||
<span style="color:#f92672">"limit"</span>: <span style="color:#ae81ff">100</span>,
|
||
<span style="color:#f92672">"page"</span>: <span style="color:#ae81ff">0</span>,
|
||
<span style="color:#f92672">"dateFrom"</span>: <span style="color:#e6db74">"2020-01-01T00:00:00Z"</span>,
|
||
<span style="color:#f92672">"dateTo"</span>: <span style="color:#e6db74">"2020-12-31T00:00:00Z"</span>,
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||
<span style="color:#f92672">"items"</span>: [
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||
<span style="color:#e6db74">"00358715-b70c-4fdd-aa55-730e05ba739e"</span>,
|
||
<span style="color:#e6db74">"004b54bb-f16f-4cec-9fbc-ab6c6345c43d"</span>,
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||
<span style="color:#e6db74">"02fb7630-d71a-449e-b65d-32b4ea7d6904"</span>,
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<span style="color:#960050;background-color:#1e0010">...</span>
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]
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}
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</code></pre></div><ul>
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<li>Then I submitted the file three times (changing the page parameter):</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page1.json
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$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page2.json
|
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$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page3.json
|
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</code></pre><ul>
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<li>Then I extracted the views and downloads in the most ridiculous way:</li>
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</ul>
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||
<pre><code class="language-console" data-lang="console">$ grep views /tmp/page*.json | grep -o -E '[0-9]+$' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
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30364
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||
$ grep downloads /tmp/page*.json | grep -o -E '[0-9]+,' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
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9100
|
||
</code></pre><ul>
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<li>For curiousity I did the same exercise for items issued in 2019 and got the following:
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<ul>
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<li>Views: 30721</li>
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<li>Downloads: 10205</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-04-06">2021-04-06</h2>
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<ul>
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<li>Margarita from CCAFS was having problems deleting an item from CGSpace again
|
||
<ul>
|
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<li>The error was “Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e …”</li>
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<li>This is the same issue as last month</li>
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</ul>
|
||
</li>
|
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<li>Create a new collection on CGSpace for a new CIP project at Mishel Portilla’s request</li>
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<li>I got a notice that CGSpace was down
|
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<ul>
|
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<li>I didn’t see anything strange at first, but there are an insane amount of database connections:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
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<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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12413
|
||
</code></pre><ul>
|
||
<li>The system journal shows thousands of these messages in the system journal, this is the first one:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">Apr 06 07:52:13 linode18 tomcat7[556]: Apr 06, 2021 7:52:13 AM org.apache.tomcat.jdbc.pool.ConnectionPool abandon
|
||
</code></pre><ul>
|
||
<li>Around that time in the dspace log I see nothing unusual, but maybe these?</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">2021-04-06 07:52:29,409 INFO com.atmire.dspace.cua.CUASolrLoggerServiceImpl @ Updating : 200/127 docs in http://localhost:8081/solr/statistics
|
||
</code></pre><ul>
|
||
<li>(BTW what is the deal with the “200/127”? I should send a comment to Atmire)
|
||
<ul>
|
||
<li>I file a ticket with Atmire: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-tickets">https://tracker.atmire.com/tickets-cgiar-ilri/view-tickets</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>I restarted the PostgreSQL and Tomcat services and now I see less connections, but still WAY high:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
3640
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
2968
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
13
|
||
</code></pre><ul>
|
||
<li>After ten minutes or so it went back down…</li>
|
||
<li>And now it’s back up in the thousands… I am seeing a lot of stuff in dspace log like this:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">2021-04-06 11:59:34,364 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717951
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717952
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717953
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717954
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717955
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717956
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717957
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717958
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717959
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717960
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717961
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717962
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717963
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717964
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717965
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717966
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717967
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717968
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717969
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717970
|
||
2021-04-06 11:59:34,365 INFO org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717971
|
||
</code></pre><ul>
|
||
<li>I sent some notes and a log to Atmire on our existing issue about the database stuff
|
||
<ul>
|
||
<li>Also I asked them about the possibility of doing a formal review of Hibernate</li>
|
||
</ul>
|
||
</li>
|
||
<li>Falcon 3.0.0 was released so I updated the 3.0.0 branch for dspace-statistics-api and merged it to <code>v6_x</code>
|
||
<ul>
|
||
<li>I also fixed one minor (unrelated) bug in the tests</li>
|
||
<li>Then I deployed the new version on DSpace Test</li>
|
||
</ul>
|
||
</li>
|
||
<li>I had a meeting with Peter and Abenet about CGSpace TODOs</li>
|
||
<li>CGSpace went down again and the PostgreSQL locks are through the roof:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
12154
|
||
</code></pre><ul>
|
||
<li>I don’t see any activity on REST API, but in the last four hours there have been 3,500 DSpace sessions:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console"># grep -a -E '2021-04-06 (13|14|15|16|17):' /home/cgspace.cgiar.org/log/dspace.log.2021-04-06 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
|
||
3547
|
||
</code></pre><ul>
|
||
<li>I looked at the same time of day for the past few weeks and it seems to be a normal number of sessions:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console"># for file in /home/cgspace.cgiar.org/log/dspace.log.2021-0{3,4}-*; do grep -a -E "2021-0(3|4)-[0-9]{2} (13|14|15|16|17):" "$file" | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l; done
|
||
...
|
||
3572
|
||
4085
|
||
3476
|
||
3128
|
||
2949
|
||
2016
|
||
1839
|
||
4513
|
||
3463
|
||
4425
|
||
3328
|
||
2783
|
||
3898
|
||
3848
|
||
7799
|
||
255
|
||
534
|
||
2755
|
||
599
|
||
4463
|
||
3547
|
||
</code></pre><ul>
|
||
<li>What about total number of sessions per day?</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console"># for file in /home/cgspace.cgiar.org/log/dspace.log.2021-0{3,4}-*; do echo "$file:"; grep -a -o -E 'session_id=[A-Z0-9]{32}' "$file" | sort | uniq | wc -l; done
|
||
...
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-03-28:
|
||
11784
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-03-29:
|
||
15104
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-03-30:
|
||
19396
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-03-31:
|
||
32612
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-04-01:
|
||
26037
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-04-02:
|
||
14315
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-04-03:
|
||
12530
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-04-04:
|
||
13138
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-04-05:
|
||
16756
|
||
/home/cgspace.cgiar.org/log/dspace.log.2021-04-06:
|
||
12343
|
||
</code></pre><ul>
|
||
<li>So it’s not the number of sessions… it’s something with the workload…</li>
|
||
<li>I had to step away for an hour or so and when I came back the site was still down and there were still 12,000 locks
|
||
<ul>
|
||
<li>I restarted postgresql and tomcat7…</li>
|
||
</ul>
|
||
</li>
|
||
<li>The locks in PostgreSQL shot up again…</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
3447
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
3527
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
4582
|
||
</code></pre><ul>
|
||
<li>I don’t know what the hell is going on, but the PostgreSQL connections and locks are way higher than ever before:</li>
|
||
</ul>
|
||
<p><img src="/cgspace-notes/2021/04/postgres_connections_cgspace-week.png" alt="PostgreSQL connections week">
|
||
<img src="/cgspace-notes/2021/04/postgres_locks_cgspace-week.png" alt="PostgreSQL locks week">
|
||
<img src="/cgspace-notes/2021/04/jmx_tomcat_dbpools-week.png" alt="Tomcat database pool"></p>
|
||
<ul>
|
||
<li>Otherwise, the number of DSpace sessions is completely normal:</li>
|
||
</ul>
|
||
<p><img src="/cgspace-notes/2021/04/jmx_dspace_sessions-week.png" alt="DSpace sessions"></p>
|
||
<ul>
|
||
<li>While looking at the nginx logs I see that MEL is trying to log into CGSpace’s REST API and delete items:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">34.209.213.122 - - [06/Apr/2021:03:50:46 +0200] "POST /rest/login HTTP/1.1" 401 727 "-" "MEL"
|
||
34.209.213.122 - - [06/Apr/2021:03:50:48 +0200] "DELETE /rest/items/95f52bf1-f082-4e10-ad57-268a76ca18ec/metadata HTTP/1.1" 401 704 "-" "-"
|
||
</code></pre><ul>
|
||
<li>I see a few of these per day going back several months
|
||
<ul>
|
||
<li>I sent a message to Salem and Enrico to ask if they know</li>
|
||
</ul>
|
||
</li>
|
||
<li>Also annoying, I see tons of what look like penetration testing requests from Qualys:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">2021-04-04 06:35:17,889 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:no DN found for user "'><qss a=X158062356Y1_2Z>
|
||
2021-04-04 06:35:17,889 INFO org.dspace.authenticate.PasswordAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:authenticate:attempting password auth of user="'><qss a=X158062356Y1_2Z>
|
||
2021-04-04 06:35:17,890 INFO org.dspace.app.xmlui.utils.AuthenticationUtil @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:email="'><qss a=X158062356Y1_2Z>, realm=null, result=2
|
||
2021-04-04 06:35:18,145 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:auth:attempting trivial auth of user=was@qualys.com
|
||
2021-04-04 06:35:18,519 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:no DN found for user was@qualys.com
|
||
2021-04-04 06:35:18,520 INFO org.dspace.authenticate.PasswordAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:authenticate:attempting password auth of user=was@qualys.com
|
||
</code></pre><ul>
|
||
<li>I deleted the ilri/AReS repository on GitHub since we haven’t updated it in two years
|
||
<ul>
|
||
<li>All development is happening in <a href="https://github.com/ilri/openRXV">https://github.com/ilri/openRXV</a> now</li>
|
||
</ul>
|
||
</li>
|
||
<li>10PM and the server is down again, with locks through the roof:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
12198
|
||
</code></pre><ul>
|
||
<li>I see that there are tons of PostgreSQL connections getting abandoned today, compared to very few in the past few weeks:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ journalctl -u tomcat7 --since=today | grep -c 'ConnectionPool abandon'
|
||
1838
|
||
$ journalctl -u tomcat7 --since=2021-03-20 --until=2021-04-05 | grep -c 'ConnectionPool abandon'
|
||
3
|
||
</code></pre><ul>
|
||
<li>I even restarted the server and connections were low for a few minutes until they shot back up:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
13
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
8651
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
8940
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
10504
|
||
</code></pre><ul>
|
||
<li>I had to go to bed and I bet it will crash and be down for hours until I wake up…</li>
|
||
<li>What the hell is this user agent?</li>
|
||
</ul>
|
||
<pre><code>54.197.119.143 - - [06/Apr/2021:19:18:11 +0200] "GET /handle/10568/16499 HTTP/1.1" 499 0 "-" "GetUrl/1.0 wdestiny@umich.edu (Linux)"
|
||
</code></pre><h2 id="2021-04-07">2021-04-07</h2>
|
||
<ul>
|
||
<li>CGSpace was still down from last night of course, with tons of database locks:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
12168
|
||
</code></pre><ul>
|
||
<li>I restarted the server again and the locks came back</li>
|
||
<li>Atmire responded to the message from yesterday
|
||
<ul>
|
||
<li>The noticed something in the logs about emails failing to be sent</li>
|
||
<li>There appears to be an issue sending mails on workflow tasks when a user in that group has an invalid email address:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">2021-04-01 12:45:11,414 WARN org.dspace.workflowbasic.BasicWorkflowServiceImpl @ a.akwarandu@cgiar.org:session_id=2F20F20D4A8C36DB53D42DE45DFA3CCE:notifyGroupofTask:cannot email user group_id=aecf811b-b7e9-4b6f-8776-3d372e6a048b workflow_item_id=33085\colon; Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException\colon; 501 5.1.3 Invalid address
|
||
</code></pre><ul>
|
||
<li>The issue is not the named user above, but a member of the group…</li>
|
||
<li>And the group does have users with invalid email addresses (probably accounts created automatically after authenticating with LDAP):</li>
|
||
</ul>
|
||
<p><img src="/cgspace-notes/2021/04/group-invalid-email.png" alt="DSpace group"></p>
|
||
<ul>
|
||
<li>I extracted all the group IDs from recent logs that had users with invalid email addresses:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ grep -a -E 'email user group_id=\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' /home/cgspace.cgiar.org/log/dspace.log.* | grep -o -E '\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' | sort | uniq
|
||
0a30d6ae-74a6-4eee-a8f5-ee5d15192ee6
|
||
1769137c-36d4-42b2-8fec-60585e110db7
|
||
203c8614-8a97-4ac8-9686-d9d62cb52acc
|
||
294603de-3d09-464e-a5b0-09e452c6b5ab
|
||
35878555-9623-4679-beb8-bb3395fdf26e
|
||
3d8a5efa-5509-4bf9-9374-2bc714aceb99
|
||
4238208a-f848-47cb-9dd2-43f9f954a4af
|
||
44939b84-1894-41e7-b3e6-8c8d1781057b
|
||
49ba087e-75a3-45ce-805c-69eeda0f786b
|
||
4a6606ce-0284-421d-bf80-4dafddba2d42
|
||
527de6aa-9cd0-4988-bf5f-c9c92ba2ac10
|
||
54cd1b16-65bf-4041-9d84-fb2ea3301d6d
|
||
58982847-5f7c-4b8b-a7b0-4d4de702136e
|
||
5f0b85be-bd23-47de-927d-bca368fa1fbc
|
||
646ada17-e4ef-49f6-9378-af7e58596ce1
|
||
7e2f4bf8-fbc9-4b2f-97a4-75e5427bef90
|
||
8029fd53-f9f5-4107-bfc3-8815507265cf
|
||
81faa934-c602-4608-bf45-de91845dfea7
|
||
8611a462-210c-4be1-a5bb-f87a065e6113
|
||
8855c903-ef86-433c-b0be-c12300eb0f84
|
||
8c7ece98-3598-4de7-a885-d61fd033bea8
|
||
8c9a0d01-2d12-4a99-84f9-cdc25ac072f9
|
||
8f9f888a-b501-41f3-a462-4da16150eebf
|
||
94168f0e-9f45-4112-ac8d-3ba9be917842
|
||
96998038-f381-47dc-8488-ff7252703627
|
||
9768f4a8-3018-44e9-bf58-beba4296327c
|
||
9a99e8d2-558e-4fc1-8011-e4411f658414
|
||
a34e6400-78ed-45c0-a751-abc039eed2e6
|
||
a9da5af3-4ec7-4a9b-becb-6e3d028d594d
|
||
abf5201c-8be5-4dee-b461-132203dd51cb
|
||
adb5658c-cef3-402f-87b6-b498f580351c
|
||
aecf811b-b7e9-4b6f-8776-3d372e6a048b
|
||
ba5aae61-ea34-4ac1-9490-4645acf2382f
|
||
bf7f3638-c7c6-4a8f-893d-891a6d3dafff
|
||
c617ada0-09d1-40ed-b479-1c4860a4f724
|
||
cff91d44-a855-458c-89e5-bd48c17d1a54
|
||
e65171ae-a2bf-4043-8f54-f8457bc9174b
|
||
e7098b40-4701-4ca2-b9a9-3a1282f67044
|
||
e904f122-71dc-439b-b877-313ef62486d7
|
||
ede59734-adac-4c01-8691-b45f19088d37
|
||
f88bd6bb-f93f-41cb-872f-ff26f6237068
|
||
f985f5fb-be5c-430b-a8f1-cf86ae4fc49a
|
||
fe800006-aaec-4f9e-9ab4-f9475b4cbdc3
|
||
</code></pre><h2 id="2021-04-08">2021-04-08</h2>
|
||
<ul>
|
||
<li>I can’t believe it but the server has been down for twelve hours or so
|
||
<ul>
|
||
<li>The locks have not changed since I went to bed last night:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
12070
|
||
</code></pre><ul>
|
||
<li>I restarted PostgreSQL and Tomcat and the locks go straight back up!</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
13
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
986
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
1194
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
1212
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
1489
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
2124
|
||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||
5934
|
||
</code></pre><h2 id="2021-04-09">2021-04-09</h2>
|
||
<ul>
|
||
<li>Atmire managed to get CGSpace back up by killing all the PostgreSQL connections yesterday
|
||
<ul>
|
||
<li>I don’t know how they did it…</li>
|
||
<li>They also think it’s weird that restarting PostgreSQL didn’t kill the connections</li>
|
||
<li>They asked some more questions, like for example if there were also issues on DSpace Test</li>
|
||
<li>Strangely enough, I checked DSpace Test and notice a clear spike in PostgreSQL locks on the morning of April 6th as well!</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<p><img src="/cgspace-notes/2021/04/postgres_locks_ALL-week-PROD.png" alt="PostgreSQL locks week CGSpace">
|
||
<img src="/cgspace-notes/2021/04/postgres_locks_ALL-week-TEST.png" alt="PostgreSQL locks week DSpace Test"></p>
|
||
<ul>
|
||
<li>I definitely need to look into that!</li>
|
||
</ul>
|
||
<h2 id="2021-04-11">2021-04-11</h2>
|
||
<ul>
|
||
<li>I am trying to resolve the AReS Elasticsearch index issues that happened last week
|
||
<ul>
|
||
<li>I decided to back up the <code>openrxv-items</code> index to <code>openrxv-items-backup</code> and then delete all the others:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
||
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-backup
|
||
$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
|
||
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
|
||
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
|
||
</code></pre><ul>
|
||
<li>Then I updated all Docker containers and rebooted the server (linode20) so that the correct indexes would be created again:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
|
||
</code></pre><ul>
|
||
<li>Then I realized I have to clone the backup index directly to <code>openrxv-items-final</code>, and re-create the <code>openrxv-items</code> alias:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
|
||
$ curl -X PUT "localhost:9200/openrxv-items-backup/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
||
$ curl -s -X POST http://localhost:9200/openrxv-items-backup/_clone/openrxv-items-final
|
||
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
|
||
</code></pre><ul>
|
||
<li>Now I see both <code>openrxv-items-final</code> and <code>openrxv-items</code> have the current number of items:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'
|
||
{
|
||
"count" : 103373,
|
||
"_shards" : {
|
||
"total" : 1,
|
||
"successful" : 1,
|
||
"skipped" : 0,
|
||
"failed" : 0
|
||
}
|
||
}
|
||
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
|
||
{
|
||
"count" : 103373,
|
||
"_shards" : {
|
||
"total" : 1,
|
||
"successful" : 1,
|
||
"skipped" : 0,
|
||
"failed" : 0
|
||
}
|
||
}
|
||
</code></pre><ul>
|
||
<li>Then I started a fresh harvesting in the AReS Explorer admin dashboard</li>
|
||
</ul>
|
||
<h2 id="2021-04-12">2021-04-12</h2>
|
||
<ul>
|
||
<li>The harvesting on AReS finished last night, but the indexes got messed up again
|
||
<ul>
|
||
<li>I will have to fix them manually next time…</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2021-04-13">2021-04-13</h2>
|
||
<ul>
|
||
<li>Looking into the logs on 2021-04-06 on CGSpace and DSpace Test to see if there is anything specific that stands out about the activty on those days that would cause the PostgreSQL issues
|
||
<ul>
|
||
<li>Digging into the Munin graphs for the last week I found a few other things happening on that morning:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<p><img src="/cgspace-notes/2021/04/sda-week.png" alt="/dev/sda disk latency week">
|
||
<img src="/cgspace-notes/2021/04/classes_unloaded-week.png" alt="JVM classes unloaded week">
|
||
<img src="/cgspace-notes/2021/04/nginx_status-week.png" alt="Nginx status week"></p>
|
||
<ul>
|
||
<li>13,000 requests in the last two months from a user with user agent <code>SomeRandomText</code>, for example:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">84.33.2.97 - - [06/Apr/2021:06:25:13 +0200] "GET /bitstream/handle/10568/77776/CROP%20SCIENCE.jpg.jpg HTTP/1.1" 404 10890 "-" "SomeRandomText"
|
||
</code></pre><ul>
|
||
<li>I purged them:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ ./ilri/check-spider-hits.sh -f /tmp/agents.txt -p
|
||
Purging 13159 hits from SomeRandomText in statistics
|
||
|
||
Total number of bot hits purged: 13159
|
||
</code></pre><ul>
|
||
<li>I noticed there were 78 items submitted in the hour before CGSpace crashed:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console"># grep -a -E '2021-04-06 0(6|7):' /home/cgspace.cgiar.org/log/dspace.log.2021-04-06 | grep -c -a add_item
|
||
78
|
||
</code></pre><ul>
|
||
<li>Of those 78, 77 of them were from Udana</li>
|
||
<li>Compared to other mornings (0 to 9 AM) this month that seems to be pretty high:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console"># for num in {01..13}; do grep -a -E "2021-04-$num 0" /home/cgspace.cgiar.org/log/dspace.log.2021-04-$num | grep -c -a
|
||
add_item; done
|
||
32
|
||
0
|
||
0
|
||
2
|
||
8
|
||
108
|
||
4
|
||
0
|
||
29
|
||
0
|
||
1
|
||
1
|
||
2
|
||
</code></pre><h2 id="2021-04-15">2021-04-15</h2>
|
||
<ul>
|
||
<li>Release v1.4.2 of the DSpace Statistics API on GitHub: <a href="https://github.com/ilri/dspace-statistics-api/releases/tag/v1.4.2">https://github.com/ilri/dspace-statistics-api/releases/tag/v1.4.2</a>
|
||
<ul>
|
||
<li>This has been running on DSpace Test for the last week or so, and mostly contains the Falcon 3.0.0 changes</li>
|
||
</ul>
|
||
</li>
|
||
<li>Re-sync DSpace Test with data from CGSpace
|
||
<ul>
|
||
<li>Run system updates on DSpace Test (linode26) and reboot the server</li>
|
||
</ul>
|
||
</li>
|
||
<li>Update the PostgreSQL JDBC driver on DSpace Test (linode26) to 42.2.19
|
||
<ul>
|
||
<li>It has been a few months since we updated this, and there have been a few releases since 42.2.14 that we are currently using</li>
|
||
</ul>
|
||
</li>
|
||
<li>Create a test account for Rafael from Bioversity-CIAT to submit some items to DSpace Test:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p 'fuuuuuuuu'
|
||
</code></pre><ul>
|
||
<li>I added the account to the Alliance Admins account, which is should allow him to submit to any Alliance collection
|
||
<ul>
|
||
<li>According to my notes from <a href="/cgspace-notes/2020-10/">2020-10</a> the account must be in the admin group in order to submit via the REST API</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2021-04-18">2021-04-18</h2>
|
||
<ul>
|
||
<li>Update all containers on AReS (linode20):</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
|
||
</code></pre><ul>
|
||
<li>Then run all system updates and reboot the server</li>
|
||
<li>I learned a new command for Elasticsearch:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl http://localhost:9200/_cat/indices
|
||
yellow open openrxv-values ChyhGwMDQpevJtlNWO1vcw 1 1 1579 0 537.6kb 537.6kb
|
||
yellow open openrxv-items-temp PhV5ieuxQsyftByvCxzSIw 1 1 103585 104372 482.7mb 482.7mb
|
||
yellow open openrxv-shared J_8cxIz6QL6XTRZct7UBBQ 1 1 127 0 115.7kb 115.7kb
|
||
yellow open openrxv-values-00001 jAoXTLR0R9mzivlDVbQaqA 1 1 3903 0 696.2kb 696.2kb
|
||
green open .kibana_task_manager_1 O1zgJ0YlQhKCFAwJZaNSIA 1 0 2 2 20.6kb 20.6kb
|
||
yellow open openrxv-users 1hWGXh9kS_S6YPxAaBN8ew 1 1 5 0 28.6kb 28.6kb
|
||
green open .apm-agent-configuration f3RAkSEBRGaxJZs3ePVxsA 1 0 0 0 283b 283b
|
||
yellow open openrxv-items-final sgk-s8O-RZKdcLRoWt3G8A 1 1 970 0 2.3mb 2.3mb
|
||
green open .kibana_1 HHPN7RD_T7qe0zDj4rauQw 1 0 25 7 36.8kb 36.8kb
|
||
yellow open users M0t2LaZhSm2NrF5xb64dnw 1 1 2 0 11.6kb 11.6kb
|
||
</code></pre><ul>
|
||
<li>Somehow the <code>openrxv-items-final</code> index only has a few items and the majority are in <code>openrxv-items-temp</code>, via the <code>openrxv-items</code> alias (which is in the temp index):</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'
|
||
{
|
||
"count" : 103585,
|
||
"_shards" : {
|
||
"total" : 1,
|
||
"successful" : 1,
|
||
"skipped" : 0,
|
||
"failed" : 0
|
||
}
|
||
}
|
||
</code></pre><ul>
|
||
<li>I found a cool tool to help with exporting and restoring Elasticsearch indexes:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
|
||
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
|
||
...
|
||
Sun, 18 Apr 2021 06:27:07 GMT | Total Writes: 103585
|
||
Sun, 18 Apr 2021 06:27:07 GMT | dump complete
|
||
</code></pre><ul>
|
||
<li>It took only two or three minutes to export everything…</li>
|
||
<li>I did a test to restore the index:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-test --type=mapping
|
||
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-test --limit 1000 --type=data
|
||
</code></pre><ul>
|
||
<li>So that’s pretty cool!</li>
|
||
<li>I deleted the <code>openrxv-items-final</code> index and <code>openrxv-items-temp</code> indexes and then restored the mappings to <code>openrxv-items-final</code>, added the <code>openrxv-items</code> alias, and started restoring the data to <code>openrxv-items</code> with elasticdump:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
|
||
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
|
||
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
|
||
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
|
||
</code></pre><ul>
|
||
<li>AReS seems to be working fine аfter that, so I created the <code>openrxv-items-temp</code> index and then started a fresh harvest on AReS Explorer:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items-temp"
|
||
</code></pre><ul>
|
||
<li>Run system updates on CGSpace (linode18) and run the latest Ansible infrastructure playbook to update the DSpace Statistics API, PostgreSQL JDBC driver, etc, and then reboot the system</li>
|
||
<li>I wasted a bit of time trying to get TSLint and then ESLint running for OpenRXV on GitHub Actions</li>
|
||
</ul>
|
||
<h2 id="2021-04-19">2021-04-19</h2>
|
||
<ul>
|
||
<li>The AReS harvesting last night seems to have completed successfully, but the number of results is strange:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
|
||
yellow open openrxv-items-temp kNUlupUyS_i7vlBGiuVxwg 1 1 103741 105553 483.6mb 483.6mb
|
||
yellow open openrxv-items-final HFc3uytTRq2GPpn13vkbmg 1 1 970 0 2.3mb 2.3mb
|
||
</code></pre><ul>
|
||
<li>The indices endpoint doesn’t include the <code>openrxv-items</code> alias, but it is currently in the <code>openrxv-items-temp</code> index so the number of items is the same:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'
|
||
{
|
||
"count" : 103741,
|
||
"_shards" : {
|
||
"total" : 1,
|
||
"successful" : 1,
|
||
"skipped" : 0,
|
||
"failed" : 0
|
||
}
|
||
}
|
||
</code></pre><ul>
|
||
<li>A user was having problems resetting their password on CGSpace, with some message about SMTP etc
|
||
<ul>
|
||
<li>I checked and we are indeed locked out of our mailbox:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ dspace test-email
|
||
...
|
||
Error sending email:
|
||
- Error: javax.mail.SendFailedException: Send failure (javax.mail.AuthenticationFailedException: 550 5.2.1 Mailbox cannot be accessed [PR0P264CA0280.FRAP264.PROD.OUTLOOK.COM]
|
||
)
|
||
</code></pre><ul>
|
||
<li>I have to write to ICT…</li>
|
||
<li>I decided to switch back to the G1GC garbage collector on DSpace Test
|
||
<ul>
|
||
<li>Reading Shawn Heisy’s discussion again: <a href="https://cwiki.apache.org/confluence/display/SOLR/ShawnHeisey">https://cwiki.apache.org/confluence/display/SOLR/ShawnHeisey</a></li>
|
||
<li>I am curious to check the JVM stats in a few days to see if there is a marked change</li>
|
||
</ul>
|
||
</li>
|
||
<li>Work on minor changes to get DSpace working on Ubuntu 20.04 for our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a></li>
|
||
</ul>
|
||
<h2 id="2021-04-21">2021-04-21</h2>
|
||
<ul>
|
||
<li>Send Abdullah feedback on the <a href="https://github.com/ilri/OpenRXV/pull/91">filter on click pull request</a> for OpenRXV
|
||
<ul>
|
||
<li>I see it adds a new “allow filter on click” checkbox in the layout settings, but it doesn’t modify the filters</li>
|
||
<li>Also, it seems to have broken the existing clicking of the countries on the map</li>
|
||
</ul>
|
||
</li>
|
||
<li>Atmire recently sent feedback about the CUA duplicates processor
|
||
<ul>
|
||
<li>Last month when I ran it it got stuck on the storage reports, apparently, so I will try again (with a fresh Solr statistics core from production) and skip the storage reports (<code>-g</code>):</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
|
||
$ cp atmire-cua-update.xml-20210124-132112.old /home/dspacetest.cgiar.org/config/spring/api/atmire-cua-update.xml
|
||
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -r 100 -c statistics -t 12 -g
|
||
</code></pre><ul>
|
||
<li>The first run processed 1,439 docs, the second run processed 0 docs
|
||
<ul>
|
||
<li>I’m not sure if that means that it worked? I sent feedback to Atmire</li>
|
||
</ul>
|
||
</li>
|
||
<li>Meeting with Moayad to discuss OpenRXV development progress</li>
|
||
</ul>
|
||
<h2 id="2021-04-25">2021-04-25</h2>
|
||
<ul>
|
||
<li>The indexes on AReS are messed up again
|
||
<ul>
|
||
<li>I made a backup of the indexes, then deleted the <code>openrxv-items-final</code> and <code>openrxv-items-temp</code> indexes, re-created the <code>openrxv-items</code> alias, and restored the data into <code>openrxv-items</code>:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
|
||
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
|
||
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
|
||
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
|
||
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
|
||
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
|
||
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
|
||
</code></pre><ul>
|
||
<li>Then I started a fresh AReS harvest</li>
|
||
</ul>
|
||
<h2 id="2021-04-26">2021-04-26</h2>
|
||
<ul>
|
||
<li>The AReS harvest last night seems to have finished successfully and the number of items looks good:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
|
||
yellow open openrxv-items-temp H-CGsyyLTaqAj6-nKXZ-7w 1 1 0 0 283b 283b
|
||
yellow open openrxv-items-final ul3SKsa7Q9Cd_K7qokBY_w 1 1 103951 0 254mb 254mb
|
||
</code></pre><ul>
|
||
<li>And the aliases seem correct for once:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
|
||
...
|
||
"openrxv-items-final": {
|
||
"aliases": {
|
||
"openrxv-items": {}
|
||
}
|
||
},
|
||
"openrxv-items-temp": {
|
||
"aliases": {}
|
||
},
|
||
...
|
||
</code></pre><ul>
|
||
<li>That’s 250 new items in the index since the last harvest!</li>
|
||
<li>Re-create my local Artifactory container because I’m getting errors starting it and it has been a few months since it was updated:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ podman rm artifactory
|
||
$ podman pull docker.bintray.io/jfrog/artifactory-oss:latest
|
||
$ podman create --ulimit nofile=32000:32000 --name artifactory -v artifactory_data:/var/opt/jfrog/artifactory -p 8081-8082:8081-8082 docker.bintray.io/jfrog/artifactory-oss
|
||
$ podman start artifactory
|
||
</code></pre><ul>
|
||
<li>Start testing DSpace 7.0 Beta 5 so I can evaluate if it solves some of the problems we are having on DSpace 6, and if it’s missing things like multiple handle resolvers, etc
|
||
<ul>
|
||
<li>I see it needs Java JDK 11, Tomcat 9, Solr 8, and PostgreSQL 11</li>
|
||
<li>Also, according to the <a href="https://wiki.lyrasis.org/display/DSDOC7x/Installing+DSpace">installation notes</a> I see you can install the old DSpace 6 REST API, so that’s potentially useful for us</li>
|
||
<li>I see that all web applications on the backend are now rolled into just one “server” application</li>
|
||
<li>The build process took 11 minutes the first time (due to downloading the world with Maven) and ~2 minutes the second time</li>
|
||
<li>The <code>local.cfg</code> content and syntax is very similar DSpace 6</li>
|
||
</ul>
|
||
</li>
|
||
<li>I got the basic <code>fresh_install</code> up and running
|
||
<ul>
|
||
<li>Then I tried to import a DSpace 6 database from production</li>
|
||
</ul>
|
||
</li>
|
||
<li>I tried to delete all the Atmire SQL migrations:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">localhost/dspace7b5= > DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';
|
||
</code></pre><ul>
|
||
<li>But I got an error when running <code>dspace database migrate</code>:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ ~/dspace7b5/bin/dspace database migrate
|
||
|
||
Database URL: jdbc:postgresql://localhost:5432/dspace7b5
|
||
Migrating database to latest version... (Check dspace logs for details)
|
||
Migration exception:
|
||
java.sql.SQLException: Flyway migration error occurred
|
||
at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:738)
|
||
at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:632)
|
||
at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:228)
|
||
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
|
||
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
|
||
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:273)
|
||
at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:129)
|
||
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:94)
|
||
Caused by: org.flywaydb.core.api.FlywayException: Validate failed:
|
||
Detected applied migration not resolved locally: 5.0.2017.09.25
|
||
Detected applied migration not resolved locally: 6.0.2017.01.30
|
||
Detected applied migration not resolved locally: 6.0.2017.09.25
|
||
|
||
at org.flywaydb.core.Flyway.doValidate(Flyway.java:292)
|
||
at org.flywaydb.core.Flyway.access$100(Flyway.java:73)
|
||
at org.flywaydb.core.Flyway$1.execute(Flyway.java:166)
|
||
at org.flywaydb.core.Flyway$1.execute(Flyway.java:158)
|
||
at org.flywaydb.core.Flyway.execute(Flyway.java:527)
|
||
at org.flywaydb.core.Flyway.migrate(Flyway.java:158)
|
||
at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:729)
|
||
... 9 more
|
||
</code></pre><ul>
|
||
<li>I deleted those migrations:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">localhost/dspace7b5= > DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
|
||
</code></pre><ul>
|
||
<li>Then when I ran the migration again it failed for a new reason, related to the configurable workflow:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">Database URL: jdbc:postgresql://localhost:5432/dspace7b5
|
||
Migrating database to latest version... (Check dspace logs for details)
|
||
Migration exception:
|
||
java.sql.SQLException: Flyway migration error occurred
|
||
at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:738)
|
||
at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:632)
|
||
at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:228)
|
||
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
|
||
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
|
||
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:273)
|
||
at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:129)
|
||
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:94)
|
||
Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateException:
|
||
Migration V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql failed
|
||
--------------------------------------------------------------------
|
||
SQL State : 42P01
|
||
Error Code : 0
|
||
Message : ERROR: relation "cwf_pooltask" does not exist
|
||
Position: 8
|
||
Location : org/dspace/storage/rdbms/sqlmigration/postgres/V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql (/home/aorth/src/apache-tomcat-9.0.45/file:/home/aorth/dspace7b5/lib/dspace-api-7.0-beta5.jar!/org/dspace/storage/rdbms/sqlmigration/postgres/V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql)
|
||
Line : 16
|
||
Statement : UPDATE cwf_pooltask SET workflow_id='defaultWorkflow' WHERE workflow_id='default'
|
||
...
|
||
</code></pre><ul>
|
||
<li>The <a href="https://wiki.lyrasis.org/display/DSDOC7x/Upgrading+DSpace">DSpace 7 upgrade docs</a> say I need to apply these previously optional migrations:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ ~/dspace7b5/bin/dspace database migrate ignored
|
||
</code></pre><ul>
|
||
<li>Now I see all migrations have completed and DSpace actually starts up fine!</li>
|
||
<li>I will try to do a full re-index to see how long it takes:</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ time ~/dspace7b5/bin/dspace index-discovery -b
|
||
...
|
||
~/dspace7b5/bin/dspace index-discovery -b 25156.71s user 64.22s system 97% cpu 7:11:09.94 total
|
||
</code></pre><ul>
|
||
<li>Not good, that shit took almost seven hours!</li>
|
||
</ul>
|
||
<h2 id="2021-04-27">2021-04-27</h2>
|
||
<ul>
|
||
<li>Peter sent me a list of 500+ DOIs from CGSpace with no Altmetric score
|
||
<ul>
|
||
<li>I used csvgrep (with Windows encoding!) to extract those without our handle and save the DOIs to a text file, then got their handles with my <code>doi-to-handle.py</code> script:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre><code class="language-console" data-lang="console">$ csvgrep -e 'windows-1252' -c 'Handle.net IDs' -i -m '10568/' ~/Downloads/Altmetric\ -\ Research\ Outputs\ -\ CGSpace\ -\ 2021-04-26.csv | csvcut -c DOI | sed '1d' > /tmp/dois.txt
|
||
$ ./ilri/doi-to-handle.py -i /tmp/dois.txt -o /tmp/handles.csv -db dspace63 -u dspace -p 'fuuu' -d
|
||
</code></pre><ul>
|
||
<li>He will Tweet them…</li>
|
||
</ul>
|
||
<h2 id="2021-04-28">2021-04-28</h2>
|
||
<ul>
|
||
<li>Grant some IWMI colleagues access to the Atmire Content and Usage stats on CGSpace</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/2021-08/">August, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-07/">July, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-06/">June, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-05/">May, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-04/">April, 2021</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>
|
||
|
||
|
||
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|
||
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|
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|
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<footer class="blog-footer">
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<p dir="auto">
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||
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|
||
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|
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<a href="#">Back to top</a>
|
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