<pre><code>dspacetest=# select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=78 and (text_value='' OR text_value IS NULL);
<li>Working on cleaning up Abenet’s DAGRIS data with OpenRefine</li>
<li>I discovered two really nice functions in OpenRefine: <code>value.trim()</code> and <code>value.escape("javascript")</code> which shows whitespace characters like <code>\r\n</code>!</li>
<li>For some reason when you import an Excel file into OpenRefine it exports dates like 1949 to 1949.0 in the CSV</li>
<li>I re-import the resulting CSV and run a GREL on the date issued column: <code>value.replace("\.0", "")</code></li>
<li>I need to start running DSpace in Mac OS X instead of a Linux VM</li>
<li><p>Add CATALINA_OPTS in <code>/opt/brew/Cellar/tomcat/8.0.30/libexec/bin/setenv.sh</code>, as this script is sourced by the <code>catalina</code> startup script</p></li>
<li>Finish cleaning up and importing ~400 DAGRIS items into CGSpace</li>
<li>Whip up some quick CSS to make the button in the submission workflow use the XMLUI theme’s brand colors (<ahref="https://github.com/ilri/DSpace/issues/154">#154</a>)</li>
<li><p>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <ahref="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></p></li>
<li><p>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs…</p></li>
<li><p>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")</code></p></li>
<li><p>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</p></li>
<li><p>Logs don’t always show anything right when it fails, but eventually one of these appears:</p>
<li><p>Then I wrote a tool called <ahref="https://gist.github.com/alanorth/2206f24483fe5f0454fc"><code>generate-thumbnails.py</code></a> to download the PDFs and generate thumbnails for them, for example:</p>
<li>Looking at CIAT’s records again, there are some problems with a dozen or so files (out of 1200)</li>
<li>A few items are using the same exact PDF</li>
<li>A few items are using HTM or DOC files</li>
<li>A few items link to PDFs on IFPRI’s e-Library or Research Gate</li>
<li>A few items have no item</li>
<li>Also, I’m not sure if we import these items, will be remove the <code>dc.identifier.url</code> field from the records?</li>
</ul>
<h2id="2016-02-12-1">2016-02-12</h2>
<ul>
<li>Looking at CIAT’s records again, there are some files linking to PDFs on Slide Share, Embrapa, UEA UK, and Condesan, so I’m not sure if we can use those</li>
<li><p>I suggest that we import ~850 or so of the clean ones first, then do the rest after I can find a clean/reliable way to decode the filenames</p></li>
<li><p>This python2 snippet seems to work in the CLI, but not so well in OpenRefine:</p>
<li><p>Merge pull requests for submission form theming (<ahref="https://github.com/ilri/DSpace/pull/178">#178</a>) and missing center subjects in XMLUI item views (<ahref="https://github.com/ilri/DSpace/pull/176">#176</a>)</p></li>
<li><p>They will be deployed on CGSpace the next time I re-deploy</p></li>
<li><p>This turns the URLs into human-readable versions that we can use as proper filenames</p></li>
<li><p>Run web server and system updates on DSpace Test and reboot</p></li>
<li><p>To merge <code>dc.identifier.url</code> and <code>dc.identifier.url[]</code>, rename the second column so it doesn’t have the brackets, like <code>dc.identifier.url2</code></p></li>
<li><p>Then you create a facet for blank values on each column, show the rows that have values for one and not the other, then transform each independently to have the contents of the other, with “||” in between</p></li>
<li><p>Work on Python script for parsing and downloading PDF records from <code>dc.identifier.url</code></p></li>
<li><p>To get filenames from <code>dc.identifier.url</code>, create a new column based on this transform: <code>forEach(value.split('||'), v, v.split('/')[-1]).join('||')</code></p></li>
<li><p>This also works for records that have multiple URLs (separated by “||”)</p></li>
<li>Re-deploy CGSpace, run all system updates, and reboot</li>
<li>More work on CIAT data, cleaning and doing a last metadata-only import into DSpace Test</li>
<li>SAFBuilder has a bug preventing it from processing filenames containing more than one underscore</li>
<li>Need to re-process the filename column to replace multiple underscores with one: <code>value.replace(/_{2,}/, "_")</code></li>
</ul>
<h2id="2016-02-20">2016-02-20</h2>
<ul>
<li>Turns out the “bug” in SAFBuilder isn’t a bug, it’s a feature that allows you to encode extra information like the destintion bundle in the filename</li>
<pre><code>java.io.FileNotFoundException: /usr/share/tomcat7/SimpleArchiveFormat/item_1021/CIAT_COLOMBIA_000075_Medición_de_palatabilidad_en_forrajes.pdf (No such file or directory)
<li><p>Seems it could be something with the HFS+ filesystem actually, as it’s not UTF-8 (<ahref="http://www.cio.com/article/2868393/linus-torvalds-apples-hfs-is-probably-the-worst-file-system-ever.html">it’s something like UCS-2</a>)</p></li>
<li><p>HFS+ stores filenames as a string, and filenames with accents get stored as <ahref="https://blog.vrypan.net/2012/11/13/hfsplus-unicode-and-accented-chars/">character+accent</a> whereas Linux’s ext4 stores them as an array of bytes</p></li>
<li><p>Running the SAFBuilder on Mac OS X works if you’re going to import the resulting bundle on Mac OS X, but if your DSpace is running on Linux you need to run the SAFBuilder there where the filesystem’s encoding matches</p></li>
<li>Got notified by some CIFOR colleagues that the Google Scholar team had contacted them about CGSpace’s incorrect ordering of authors in Google Scholar metadata</li>
<li>Turns out there is a patch, and it was merged in DSpace 5.4: <ahref="https://jira.duraspace.org/browse/DS-2679">https://jira.duraspace.org/browse/DS-2679</a></li>
<li>I’ve merged it into our <code>5_x-prod</code> branch that is currently based on DSpace 5.1</li>
<li>We found a bug when a user searches from the homepage, sorts the results, and then tries to click “View More” in a sidebar facet</li>
<li>I am not sure what causes it yet, but I opened an issue for it: <ahref="https://github.com/ilri/DSpace/issues/179">https://github.com/ilri/DSpace/issues/179</a></li>
<li>Have more problems with SAFBuilder on Mac OS X</li>
<li>Now it doesn’t recognize description hints in the filename column, like: <code>test.pdf__description:Blah</code></li>
<li>But on Linux it works fine</li>
<li>Trying to test Atmire’s series of stats and CUA fixes from January and February, but their branch history is really messy and it’s hard to see what’s going on</li>
<li>Rebasing their branch on top of our production branch results in a broken Tomcat, so I’m going to tell them to fix their history and make a proper pull request</li>
<li>Looking at the filenames for the CIAT Reports, some have some really ugly characters, like: <code>'</code> or <code>,</code> or <code>=</code> or <code>[</code> or <code>]</code> or <code>(</code> or <code>)</code> or <code>_.pdf</code> or <code>._</code> etc</li>
<li><p>It’s tricky to parse those things in some programming languages so I’d rather just get rid of the weird stuff now in OpenRefine:</p>
<li><p>Finally import the 1127 CIAT items into CGSpace: <ahref="https://cgspace.cgiar.org/handle/10568/35710">https://cgspace.cgiar.org/handle/10568/35710</a></p></li>
<li><p>Re-deploy CGSpace with the Google Scholar fix, but I’m waiting on the Atmire fixes for now, as the branch history is ugly</p></li>
