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<?xml version="1.0" encoding="utf-8"?>
<feed xmlns="http://www.w3.org/2005/Atom"><title>Ibis Project Blog</title><link href="http://www.ibis-project.org/" rel="alternate"></link><link href="/atom.xml" rel="self"></link><id>http://www.ibis-project.org/</id><updated>2016-06-14T10:00:00-07:00</updated><entry><title>Announcing hs2client, a fast new C++ / Python Thrift client for Impala and Hive</title><link href="http://www.ibis-project.org/new-native-impala-hive-client/" rel="alternate"></link><updated>2016-06-14T10:00:00-07:00</updated><author><name>Wes McKinney</name></author><id>tag:www.ibis-project.org,2016-06-14:new-native-impala-hive-client/</id><summary type="html">
<p>This year, I collaborated with members of the <a href="http://impala.io/">Apache Impala (incubating)</a>
team at Cloudera to create a new C++ library to eventually become a faster,
more memory-efficient replacement for <a href="https://github.com/cloudera/impyla">impyla</a>, <a href="https://github.com/dropbox/PyHive">PyHive</a>, and other
(largely pure Python) client libraries for talking to Apache Hive and Impala.</p>
<p>We are excited to release this effort, dubbed <strong>hs2client</strong>, as a new
Apache-licensed <a href="https://github.com/cloudera/hs2client">open source project on GitHub</a>. As you may guess from the
name, this library implement the HiveServer2 Thrift API as a C++ library, with
careful handling of result sets to allow languages like Python to access data
at high performance.</p>
<p>The initial preview release contains:</p>
<ul>
<li>
<p>A C++ library, <code>libhs2client</code>, which provides a clean C++ API for the
HiveServer2 Thrift API. This can be built and dynamically or statically
linked in C/C++ applications with no direct exposure to Apache Thrift.</p>
</li>
<li>
<p>Python bindings, with optimized reads to <strong>pandas.DataFrame</strong></p>
</li>
</ul>
<p>To try out the library, you can install a dev build of the project right now
with conda:</p>
<div class="highlight"><pre><span></span>conda install hs2client -c cloudera/channel/dev
</pre></div>
<p>
<div class="text_cell_render border-box-sizing rendered_html">
<h2 id="optimizing-for-speed-and-memory-use">Optimizing for speed and memory use</h2>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<p>The Python bindings for <code>libhs2client</code> are careful about performance and memory in a few key ways:</p>
<ul>
<li>Converting row batches directly into pandas-compatible NumPy arrays</li>
<li>Care with categorical data: string data is deduplicated while it's being converted for pandas. In the future, it would be straightforward to add an option to return all string data as <code>pandas.Categorical</code> arrays</li>
</ul>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<h2 id="hs2client-demo-and-simple-benchmark">hs2client demo and simple benchmark</h2>
<p>The initial API is oriented at modeling the HiveServer2 protocol closely. Connecting to a cluster yields a <code>Service</code> instance:</p>
</div>
<div class="cell border-box-sizing code_cell vbox">
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<div class="prompt input_prompt">
In&nbsp;[1]:
</div>
<div class="input_area box-flex1">
<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="kn">import</span> <span class="nn">hs2client</span>
<span class="n">service</span> <span class="o">=</span> <span class="n">hs2client</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="s1">&#39;localhost&#39;</span><span class="p">,</span> <span class="mi">21050</span><span class="p">,</span> <span class="s1">&#39;wesm&#39;</span><span class="p">)</span>
</pre></div>
</div>
</div>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<p>To execute queries, you open a session then use its <code>execute</code> method.</p>
</div>
<div class="cell border-box-sizing code_cell vbox">
<div class="input hbox">
<div class="prompt input_prompt">
In&nbsp;[2]:
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">session</span> <span class="o">=</span> <span class="n">service</span><span class="o">.</span><span class="n">open_session</span><span class="p">()</span>
<span class="n">op</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;select 1&quot;</span><span class="p">)</span>
</pre></div>
</div>
</div>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<p>Queries are asynchronous by default.</p>
</div>
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In&nbsp;[3]:
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">op</span><span class="o">.</span><span class="n">is_finished</span>
</pre></div>
</div>
</div>
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<pre>
True
</pre>
</div>
</div>
</div>
</div>
</div>
<div class="cell border-box-sizing code_cell vbox">
<div class="input hbox">
<div class="prompt input_prompt">
In&nbsp;[4]:
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<div class="input_area box-flex1">
<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">op</span><span class="o">.</span><span class="n">get_state</span><span class="p">()</span>
</pre></div>
</div>
</div>
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<pre>
&apos;finished&apos;
</pre>
</div>
</div>
</div>
</div>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<p>Result sets can be fetch currently to <code>pandas.DataFrame</code> objects:</p>
</div>
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<div class="prompt input_prompt">
In&nbsp;[5]:
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">df</span> <span class="o">=</span> <span class="n">op</span><span class="o">.</span><span class="n">fetchall_pandas</span><span class="p">()</span>
</pre></div>
</div>
</div>
</div>
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<div class="input hbox">
<div class="prompt input_prompt">
In&nbsp;[6]:
</div>
<div class="input_area box-flex1">
<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">df</span>
</pre></div>
</div>
</div>
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<div class="output vbox">
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Out[6]:</div>
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<div class="output_html rendered_html">
<div style="max-width:1500px;overflow:auto;">
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>1</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>1</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<p>Compared with comparable database clients, we've optimized the fetch path to have excellent performance (IO speeds) and memory use.</p>
</div>
<div class="cell border-box-sizing code_cell vbox">
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="kn">as</span> <span class="nn">pd</span>
<span class="n">N</span><span class="p">,</span> <span class="n">K</span> <span class="o">=</span> <span class="mi">1000000</span><span class="p">,</span> <span class="mi">10</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randn</span><span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">K</span><span class="p">),</span>
<span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;data{0}&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">K</span><span class="p">)])</span>
<span class="kn">import</span> <span class="nn">ibis</span>
<span class="n">con</span> <span class="o">=</span> <span class="n">ibis</span><span class="o">.</span><span class="n">impala</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="s1">&#39;localhost&#39;</span><span class="p">,</span>
<span class="n">hdfs_client</span><span class="o">=</span><span class="n">ibis</span><span class="o">.</span><span class="n">hdfs_connect</span><span class="p">(</span><span class="n">port</span><span class="o">=</span><span class="mi">5070</span><span class="p">))</span>
<span class="n">con</span><span class="o">.</span><span class="n">drop_database</span><span class="p">(</span><span class="s1">&#39;hs2_test&#39;</span><span class="p">,</span> <span class="n">force</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
<span class="n">con</span><span class="o">.</span><span class="n">create_database</span><span class="p">(</span><span class="s1">&#39;hs2_test&#39;</span><span class="p">)</span>
<span class="n">con</span><span class="o">.</span><span class="n">create_table</span><span class="p">(</span><span class="s1">&#39;test_data&#39;</span><span class="p">,</span> <span class="n">df</span><span class="p">,</span> <span class="n">database</span><span class="o">=</span><span class="s1">&#39;hs2_test&#39;</span><span class="p">)</span>
</pre></div>
</div>
</div>
</div>
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<div class="input hbox">
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In&nbsp;[16]:
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<div class="input_area box-flex1">
<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">op</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">execute_sync</span><span class="p">(</span><span class="s1">&#39;select * from hs2_test.test_data&#39;</span><span class="p">)</span>
<span class="o">%</span><span class="k">time</span> <span class="n">df</span> <span class="o">=</span> <span class="n">op</span><span class="o">.</span><span class="n">fetchall_pandas</span><span class="p">()</span>
</pre></div>
</div>
</div>
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<pre>
CPU times: user 200 ms, sys: 64 ms, total: 264 ms
Wall time: 682 ms
</pre>
</div>
</div>
</div>
</div>
</div>
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<div class="input_area box-flex1">
<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">speed</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">memory_usage</span><span class="p">()</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">/</span> <span class="mf">0.682</span> <span class="o">/</span> <span class="mi">2</span><span class="o">**</span><span class="mi">20</span>
<span class="k">print</span><span class="p">(</span><span class="s1">&#39;Speed: {0:.2f} MB/s&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">speed</span><span class="p">))</span>
</pre></div>
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<pre>
Speed: 111.87 MB/s
</pre>
</div>
</div>
</div>
</div>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<p>This benchmark is being run on <code>localhost</code>, but it shows we can move over 110 MB/s through the Thrift protocol <strong>and</strong> convert to a fully-formed pandas DataFrame.</p>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<h2 id="hs2client-compared-with-impyla">hs2client compared with impyla</h2>
<p>In Ibis and other Python projects, we have been using <a href="http://github.com/cloudera/impyla">impyla</a> to execute queries and access result sets. impyla either uses Apache Thrift's official Python implementation (on Python 2) or <a href="https://github.com/eleme/thriftpy">thriftpy</a> (on Python 3) for interacting with the Impala or Hive Thrift service. Because of this, the main difference is the performance in fetching large result sets.</p>
<p>Here, I will perform an equivalent fetch using impyla via ibis:</p>
</div>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="c1"># Connect to Impala via impyla (on Python 2)</span>
<span class="n">con</span> <span class="o">=</span> <span class="n">ibis</span><span class="o">.</span><span class="n">impala</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="s1">&#39;localhost&#39;</span><span class="p">,</span> <span class="n">port</span><span class="o">=</span><span class="mi">21050</span><span class="p">)</span>
<span class="n">expr</span> <span class="o">=</span> <span class="n">con</span><span class="o">.</span><span class="n">sql</span><span class="p">(</span><span class="s1">&#39;select * from hs2_test.test_data&#39;</span><span class="p">)</span>
<span class="o">%</span><span class="k">time</span> <span class="n">df</span> <span class="o">=</span> <span class="n">expr</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">limit</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span>
</pre></div>
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CPU times: user 1.15 s, sys: 52 ms, total: 1.2 s
Wall time: 1.66 s
</pre>
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</div>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">speed</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">memory_usage</span><span class="p">()</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">/</span> <span class="mf">1.66</span> <span class="o">/</span> <span class="mi">2</span><span class="o">**</span><span class="mi">20</span>
<span class="k">print</span><span class="p">(</span><span class="s1">&#39;Speed: {0:.2f} MB/s&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">speed</span><span class="p">))</span>
</pre></div>
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Speed: 45.96 MB/s
</pre>
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<div class="text_cell_render border-box-sizing rendered_html">
<p>In this particular use case with an all-numeric table (which is ideal for deserialization performance), the speed difference is only 2x or a bit more.</p>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<h2 id="hs2client-roadmap">hs2client roadmap</h2>
<p>The <a href="http://github.com/cloudera/hs2client">code is hosted on GitHub</a>.</p>
<p>The C++ library does not yet implement some important features that are needed to be a drop-in replacement for impyla or other Hive or Impala drivers:</p>
<ul>
<li>SSL transport (with certificate verification)</li>
<li>SASL Thrift transport for secure (i.e. Kerberos) clusters, or insecure clusters using SASL</li>
</ul>
<p>On the Python side, we must implement a DB API 2.0 compatibility layer, since currently data can only be fetched to pandas, not Python tuples as with most Python database drivers.</p>
<p>We of course welcome contributions from the community to build out some of these features.</p>
</div></p></summary></entry><entry><title>Ibis 0.8: Initial PostgreSQL support, bug fixes</title><link href="http://www.ibis-project.org/release-0.8/" rel="alternate"></link><updated>2016-05-19T08:00:00-07:00</updated><author><name>Wes McKinney</name></author><id>tag:www.ibis-project.org,2016-05-19:release-0.8/</id><summary type="html">
<p>Thanks to contributions from pandas core team member <a href="http://github.com/cpcloud">Philip Cloud</a>, Ibis
now has initial support for PostgreSQL. The 0.8 release also includes many bug
fixes from 0.7, and all Ibis users are recommended to upgrade.</p>
<p>Read more in the <a href="http://docs.ibis-project.org/release.html">release notes</a>.</p>
<h2>What is new with Ibis</h2>
<p>Ibis development has been slower in 2016 as I've been investing energies in
<a href="http://arrow.apache.org">Apache Arrow</a>, <a href="http://parquet.apache.org">Apache Parquet</a>, and other projects that are all part of
the broader goal of making Python work better with Hadoop and other distributed
data systems. Some of the this functionality, like the ability to read Parquet
files natively in Python, will start showing up in Ibis in the relatively near
future.</p>
<p>In the meantime, we've been stabilizing and improving the existing Ibis
functionality while working with the community to bring about new features.</p>
<h2>PostgreSQL support in Ibis</h2>
<p>The PostgreSQL database contains vast analytical functionality, far too much to
cover completely right away, but Ibis now has support for a meaningful and
useful subset of Postgres's built-in functions. It is also capable of
performing window functions as well as a many date, string, and mathematical
operations. If you find a Postgres function you'd like to see made available in
Ibis, please let us know on the GitHub issue tracker.</p>
<p>Here's an example of what connecting to a PostgreSQL database and executing an
expression looks like:</p>
<div class="highlight"><pre><span></span><span class="n">In</span> <span class="p">[</span><span class="mi">7</span><span class="p">]:</span> <span class="n">client</span> <span class="o">=</span> <span class="n">ibis</span><span class="o">.</span><span class="n">postgres</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">host</span><span class="o">=</span><span class="s1">&#39;localhost&#39;</span><span class="p">,</span> <span class="n">user</span><span class="o">=</span><span class="s1">&#39;ibis_test&#39;</span><span class="p">,</span>
<span class="n">password</span><span class="o">=</span><span class="s1">&#39;ibis_test&#39;</span><span class="p">,</span>
<span class="n">database</span><span class="o">=</span><span class="s1">&#39;ibis_testing&#39;</span><span class="p">)</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">8</span><span class="p">]:</span> <span class="n">client</span><span class="o">.</span><span class="n">list_tables</span><span class="p">()</span>
<span class="n">Out</span><span class="p">[</span><span class="mi">8</span><span class="p">]:</span> <span class="p">[</span><span class="s1">u&#39;functional_alltypes&#39;</span><span class="p">]</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">9</span><span class="p">]:</span> <span class="n">t</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">table</span><span class="p">(</span><span class="s1">&#39;functional_alltypes&#39;</span><span class="p">)</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">10</span><span class="p">]:</span> <span class="n">t</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s1">&#39;string_col&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">size</span><span class="p">()</span><span class="o">.</span><span class="n">execute</span><span class="p">()</span>
<span class="n">Out</span><span class="p">[</span><span class="mi">10</span><span class="p">]:</span>
<span class="n">string_col</span> <span class="n">count</span>
<span class="mi">0</span> <span class="mi">8</span> <span class="mi">730</span>
<span class="mi">1</span> <span class="mi">9</span> <span class="mi">730</span>
<span class="mi">2</span> <span class="mi">2</span> <span class="mi">730</span>
<span class="mi">3</span> <span class="mi">5</span> <span class="mi">730</span>
<span class="mi">4</span> <span class="mi">3</span> <span class="mi">730</span>
<span class="mi">5</span> <span class="mi">1</span> <span class="mi">730</span>
<span class="mi">6</span> <span class="mi">7</span> <span class="mi">730</span>
<span class="mi">7</span> <span class="mi">0</span> <span class="mi">730</span>
<span class="mi">8</span> <span class="mi">4</span> <span class="mi">730</span>
<span class="mi">9</span> <span class="mi">6</span> <span class="mi">730</span>
</pre></div></summary></entry><entry><title>Ibis 0.7: Kudu-Impala integration, SQL compiler improvements</title><link href="http://www.ibis-project.org/release-0.7/" rel="alternate"></link><updated>2016-03-16T05:00:00-07:00</updated><author><name>Wes McKinney</name></author><id>tag:www.ibis-project.org,2016-03-16:release-0.7/</id><summary type="html">
<p>Ibis 0.7.0 has been released! The biggest new feature in the release is
<a href="http://blog.ibis-project.org/kudu-impala-ibis/">Impala-Kudu integration</a>. This is great timing, because <a href="https://github.com/apache/incubator-kudu/tree/master/python">Kudu's Python client</a> went beta officially in its recent 0.7.0 release.</p>
<p>In addition to many bug fixes, Ibis includes a much smarter SQL compiler for
more complex pandas-like expressions. For example, consider the following
operation:</p>
<div class="highlight"><pre><span></span><span class="n">table</span> <span class="o">=</span> <span class="n">ibis</span><span class="o">.</span><span class="n">table</span><span class="p">([(</span><span class="s1">&#39;flag&#39;</span><span class="p">,</span> <span class="s1">&#39;string&#39;</span><span class="p">),</span>
<span class="p">(</span><span class="s1">&#39;value&#39;</span><span class="p">,</span> <span class="s1">&#39;double&#39;</span><span class="p">)],</span>
<span class="s1">&#39;tbl&#39;</span><span class="p">)</span>
<span class="n">flagged</span> <span class="o">=</span> <span class="n">table</span><span class="p">[</span><span class="n">table</span><span class="o">.</span><span class="n">flag</span> <span class="o">==</span> <span class="s1">&#39;1&#39;</span><span class="p">]</span>
<span class="n">unflagged</span> <span class="o">=</span> <span class="n">table</span><span class="p">[</span><span class="n">table</span><span class="o">.</span><span class="n">flag</span> <span class="o">==</span> <span class="s1">&#39;0&#39;</span><span class="p">]</span>
<span class="n">fv</span> <span class="o">=</span> <span class="n">flagged</span><span class="o">.</span><span class="n">value</span>
<span class="n">uv</span> <span class="o">=</span> <span class="n">unflagged</span><span class="o">.</span><span class="n">value</span>
<span class="n">expr</span> <span class="o">=</span> <span class="p">(</span><span class="n">fv</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span> <span class="o">/</span> <span class="n">fv</span><span class="o">.</span><span class="n">sum</span><span class="p">())</span> <span class="o">-</span> <span class="p">(</span><span class="n">uv</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span> <span class="o">/</span> <span class="n">uv</span><span class="o">.</span><span class="n">sum</span><span class="p">())</span>
</pre></div>
<p>Now in Ibis 0.7.0, this expression can be transformed to the correct effective
SQL:</p>
<div class="highlight"><pre><span></span><span class="k">SELECT</span> <span class="n">t0</span><span class="p">.</span><span class="o">`</span><span class="n">tmp</span><span class="o">`</span> <span class="o">-</span> <span class="n">t1</span><span class="p">.</span><span class="o">`</span><span class="n">tmp</span><span class="o">`</span> <span class="k">AS</span> <span class="o">`</span><span class="n">tmp</span><span class="o">`</span>
<span class="k">FROM</span> <span class="p">(</span>
<span class="k">SELECT</span> <span class="k">avg</span><span class="p">(</span><span class="o">`</span><span class="n">value</span><span class="o">`</span><span class="p">)</span> <span class="o">/</span> <span class="k">sum</span><span class="p">(</span><span class="o">`</span><span class="n">value</span><span class="o">`</span><span class="p">)</span> <span class="k">AS</span> <span class="o">`</span><span class="n">tmp</span><span class="o">`</span>
<span class="k">FROM</span> <span class="n">tbl</span>
<span class="k">WHERE</span> <span class="o">`</span><span class="n">flag</span><span class="o">`</span> <span class="o">=</span> <span class="s1">&#39;1&#39;</span>
<span class="p">)</span> <span class="n">t0</span>
<span class="k">CROSS</span> <span class="k">JOIN</span> <span class="p">(</span>
<span class="k">SELECT</span> <span class="k">avg</span><span class="p">(</span><span class="o">`</span><span class="n">value</span><span class="o">`</span><span class="p">)</span> <span class="o">/</span> <span class="k">sum</span><span class="p">(</span><span class="o">`</span><span class="n">value</span><span class="o">`</span><span class="p">)</span> <span class="k">AS</span> <span class="o">`</span><span class="n">tmp</span><span class="o">`</span>
<span class="k">FROM</span> <span class="n">tbl</span>
<span class="k">WHERE</span> <span class="o">`</span><span class="n">flag</span><span class="o">`</span> <span class="o">=</span> <span class="s1">&#39;0&#39;</span>
<span class="p">)</span> <span class="n">t1</span>
</pre></div>
<p>Thanks to all who contributed patches:</p>
<div class="highlight"><pre><span></span>$ git log v0.6.0..v0.7.0 --pretty<span class="o">=</span>format:%aN <span class="p">|</span> sort <span class="p">|</span> uniq -c <span class="p">|</span> sort -rn
<span class="m">21</span> Wes McKinney
<span class="m">1</span> Uri Laserson
<span class="m">1</span> Kristopher Overholt
</pre></div></summary></entry><entry><title>Interactive Analytics on Dynamic Big Data in Python using Kudu, Impala, and Ibis</title><link href="http://www.ibis-project.org/kudu-impala-ibis/" rel="alternate"></link><updated>2015-12-15T08:00:00-08:00</updated><author><name>Wes McKinney</name></author><id>tag:www.ibis-project.org,2015-12-15:kudu-impala-ibis/</id><summary type="html">
<p>The new <a href="http://getkudu.io">Apache Kudu (incubating)</a> columnar storage engine together with
<a href="http://impala.io">Apache Impala (incubating)</a> interactive SQL engine enable a new fully open
source big data architecture for data that is arriving and changing very
quickly. By integrating Kudu and Impala with Ibis, this functionality is now
available to Python programmers with an easy-to-use pandas-like API.</p>
<p>I spent this last week expanding the Kudu Python client (a Cython wrapper for
the C++ client API) and adding initial integration with Ibis. While my <a href="http://gerrit.cloudera.org:8080/#/c/1593/">Kudu patch</a> is still in code review, I will give you a preview here of how it all
works.</p>
<p>Since Kudu, a native C++ storage engine, now builds on OS X, I'm writing this
blog using the Kudu client on OS X, so now is a great time for developers on
both OS X and Linux to get involved with developing Python tools for Kudu.</p>
<p>Using Impala on OS X is in the works, see the <a href="https://issues.cloudera.org/browse/IMPALA-2761">issue tracker</a> for more. As
soon as we can, we'll provide a combined Kudu/Impala DMG installer for
installing the environment locally on Mac computers.</p>
<!--
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<p>Read on for more about Kudu and a full stack demo.</p>
<p>
<div class="text_cell_render border-box-sizing rendered_html">
<h2 id="kudu-overview">Kudu overview</h2>
<p>Kudu was designed for the Hadoop ecosystem in part to simplify architectures involving very fast-arriving and fast-changing data that needs to be immediately available for analytical queries. In the past, complex architectures were devised using the fast <a href="https://parquet.apache.org/">Parquet</a> columnar format stored in HDFS in conjunction with <a href="https://hbase.apache.org/">HBase</a> (for new data, but very slow for analytics), but there were numerous drawbacks that made a purpose-built column-oriented storage engine desirable. For example, while Parquet is extremely fast for analytics, data can only be appended to a dataset and not deleted or updated.</p>
<p>You can read much more about Kudu in Todd Lipcon's <a href="http://www.slideshare.net/cloudera/kudu-new-hadoop-storage-for-fast-analytics-on-fast-data">recent slide deck</a> and in an <a href="http://getkudu.io/overview.html">website overview</a>.</p>
<p>ZoomData put together a <a href="https://www.youtube.com/watch?v=ck_kRb6qLKE">cool demo</a> showing a real time analytics dashboard powered by Impala and Kudu.</p>
<p>For Python users, here are the key details:</p>
<ul>
<li>Kudu has a SQL-like tabular data model; table columns are typed, and columns can be added and remove from tables. A Kudu cluster can store any number of tables.</li>
<li>Tables must have one or more <em>primary keys</em>. Like SQL databases, these will impact the performance of retrieving individual records.</li>
<li>Data is stored column-oriented, and individual table columns can be read (or <em>scanned</em>) very fast.</li>
<li>You can mutate a table by adding, deleting, or updating rows.</li>
<li>Data can be selected by indicating a number of conditions or <em>predicates</em> that must hold true</li>
<li>Kudu does not perform analytics: its job is to manage tabular data and serve it to compute engines as fast as possible.</li>
</ul>
<p>Kudu is not coupled to any particular compute engine. Any system that can use its C++ or Java clients can use it. There are a few compute system integrations built or in progress:</p>
<ul>
<li><a href="http://getkudu.io/docs/kudu_impala_integration.html"><strong>Apache Impala (incubating)</strong></a></li>
<li><a href="https://issues.cloudera.org/browse/KUDU-1214"><strong>Apache Spark</strong></a>: Still in active development</li>
<li><a href="https://github.com/dremio/drill-storage-kudu"><strong>Apache Drill</strong></a>: Built during the recent Drill-Kudu hackathon</li>
</ul>
<h2 id="basic-kudu-use-in-python">Basic Kudu use in Python</h2>
<p>Let's take our first steps in Python. I've booted up the Kudu Quickstart VM (for VirtualBox) that you can download from the Kudu website. I've installed the Kudu Python client and now import it and connect to the Kudu master in the VM:</p>
</div>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="kn">import</span> <span class="nn">kudu</span>
<span class="n">client</span> <span class="o">=</span> <span class="n">kudu</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="s1">&#39;quickstart.cloudera&#39;</span><span class="p">,</span> <span class="mi">7051</span><span class="p">)</span>
</pre></div>
</div>
</div>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<p>Since this is a brand new cluster, there are no tables created yet:</p>
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<div class="prompt input_prompt">
In&nbsp;[2]:
</div>
<div class="input_area box-flex1">
<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">client</span><span class="o">.</span><span class="n">list_tables</span><span class="p">()</span>
</pre></div>
</div>
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[]
</pre>
</div>
</div>
</div>
</div>
</div>
<div class="text_cell_render border-box-sizing rendered_html">
<p>To create one, we first create a schema and then create the table:</p>
</div>
<div class="cell border-box-sizing code_cell vbox">
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<div class="prompt input_prompt">
In&nbsp;[3]:
</div>
<div class="input_area box-flex1">
<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">builder</span> <span class="o">=</span> <span class="n">kudu</span><span class="o">.</span><span class="n">schema_builder</span><span class="p">()</span>
<span class="n">builder</span><span class="o">.</span><span class="n">add_column</span><span class="p">(</span><span class="s1">&#39;id&#39;</span><span class="p">,</span> <span class="n">kudu</span><span class="o">.</span><span class="n">int64</span><span class="p">,</span> <span class="n">nullable</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
<span class="n">builder</span><span class="o">.</span><span class="n">add_column</span><span class="p">(</span><span class="s1">&#39;item&#39;</span><span class="p">,</span> <span class="n">kudu</span><span class="o">.</span><span class="n">string</span><span class="p">)</span>
<span class="n">builder</span><span class="o">.</span><span class="n">add_column</span><span class="p">(</span><span class="s1">&#39;price&#39;</span><span class="p">,</span> <span class="n">kudu</span><span class="o">.</span><span class="n">double</span><span class="p">)</span>
<span class="n">builder</span><span class="o">.</span><span class="n">set_primary_keys</span><span class="p">([</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
<span class="n">schema</span> <span class="o">=</span> <span class="n">builder</span><span class="o">.</span><span class="n">build</span><span class="p">()</span>
<span class="n">schema</span>
</pre></div>
</div>
</div>
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<pre>
kudu.Schema {
id int64(nullable=False) PRIMARY KEY
item string(nullable=True)
price double(nullable=True)
}
</pre>
</div>
</div>
</div>
</div>
</div>
<div class="cell border-box-sizing code_cell vbox">
<div class="input hbox">
<div class="prompt input_prompt">
In&nbsp;[4]:
</div>
<div class="input_area box-flex1">
<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="k">if</span> <span class="n">client</span><span class="o">.</span><span class="n">table_exists</span><span class="p">(</span><span class="s1">&#39;purchases&#39;</span><span class="p">):</span>
<span class="n">client</span><span class="o">.</span><span class="n">delete_table</span><span class="p">(</span><span class="s1">&#39;purchases&#39;</span><span class="p">)</span>
<span class="n">client</span><span class="o">.</span><span class="n">create_table</span><span class="p">(</span><span class="s1">&#39;purchases&#39;</span><span class="p">,</span> <span class="n">schema</span><span class="p">)</span>
<span class="n">client</span><span class="o">.</span><span class="n">list_tables</span><span class="p">()</span>
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[&apos;purchases&apos;]
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<p>Now, we can get a handle for this new table and see its schema:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">purchases</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">table</span><span class="p">(</span><span class="s1">&#39;purchases&#39;</span><span class="p">)</span>
<span class="n">purchases</span>
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&lt;kudu.client.Table at 0x1037fc8f0&gt;
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">purchases</span><span class="o">.</span><span class="n">schema</span>
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kudu.Schema {
id int64(nullable=False) PRIMARY KEY
item string(nullable=True)
price double(nullable=True)
}
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<p>Now, let's insert some data:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">data</span> <span class="o">=</span> <span class="p">[</span>
<span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;spam&#39;</span><span class="p">,</span> <span class="mf">2.49</span><span class="p">),</span>
<span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="s1">&#39;eggs&#39;</span><span class="p">,</span> <span class="mf">1.25</span><span class="p">),</span>
<span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s1">&#39;coffee&#39;</span><span class="p">,</span> <span class="mf">2.35</span><span class="p">),</span>
<span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="s1">&#39;spam&#39;</span><span class="p">,</span> <span class="mf">2.00</span><span class="p">),</span>
<span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="s1">&#39;eggs&#39;</span><span class="p">,</span> <span class="mf">2.49</span><span class="p">),</span>
<span class="p">(</span><span class="mi">6</span><span class="p">,</span> <span class="s1">&#39;coffee&#39;</span><span class="p">,</span> <span class="mf">2.75</span><span class="p">),</span>
<span class="p">(</span><span class="mi">7</span><span class="p">,</span> <span class="s1">&#39;eggs&#39;</span><span class="p">,</span> <span class="mf">2.75</span><span class="p">),</span>
<span class="p">(</span><span class="mi">8</span><span class="p">,</span> <span class="s1">&#39;coffee&#39;</span><span class="p">,</span> <span class="mf">1.95</span><span class="p">),</span>
<span class="p">(</span><span class="mi">9</span><span class="p">,</span> <span class="s1">&#39;spam&#39;</span><span class="p">,</span> <span class="mf">3.00</span><span class="p">),</span>
<span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="s1">&#39;eggs&#39;</span><span class="p">,</span> <span class="mf">2.25</span><span class="p">),</span>
<span class="p">(</span><span class="mi">11</span><span class="p">,</span> <span class="s1">&#39;eggs&#39;</span><span class="p">,</span> <span class="mf">2.00</span><span class="p">),</span>
<span class="p">(</span><span class="mi">12</span><span class="p">,</span> <span class="s1">&#39;coffee&#39;</span><span class="p">,</span> <span class="mf">2.35</span><span class="p">)</span>
<span class="p">]</span>
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<p>To add, change, or remove data from a table, you must create a <em>session</em> to group the operations:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">session</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">new_session</span><span class="p">()</span>
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<p>Now, you create insert operations and add them to the session and call its <code>flush</code> method:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="k">for</span> <span class="n">_id</span><span class="p">,</span> <span class="n">_item</span><span class="p">,</span> <span class="n">_price</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
<span class="n">op</span> <span class="o">=</span> <span class="n">purchases</span><span class="o">.</span><span class="n">new_insert</span><span class="p">()</span>
<span class="n">op</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">_id</span>
<span class="n">op</span><span class="p">[</span><span class="s1">&#39;item&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">_item</span>
<span class="n">op</span><span class="p">[</span><span class="s1">&#39;price&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">_price</span>
<span class="n">session</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="n">op</span><span class="p">)</span>
<span class="n">session</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
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<p>Now, suppose we wanted to select some data from the table. To do this, we create a <em>scanner</em> for the table in question:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">scanner</span> <span class="o">=</span> <span class="n">purchases</span><span class="o">.</span><span class="n">scanner</span><span class="p">()</span>
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<p>To read all of the data out, you <em>open</em> the scanner and call one of its read methods:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">scanner</span><span class="o">.</span><span class="n">open</span><span class="p">()</span>
<span class="n">scanner</span><span class="o">.</span><span class="n">read_all_tuples</span><span class="p">()</span>
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[(1, &apos;spam&apos;, 2.49),
(2, &apos;eggs&apos;, 1.25),
(3, &apos;coffee&apos;, 2.35),
(4, &apos;spam&apos;, 2.0),
(5, &apos;eggs&apos;, 2.49),
(6, &apos;coffee&apos;, 2.75),
(7, &apos;eggs&apos;, 2.75),
(8, &apos;coffee&apos;, 1.95),
(9, &apos;spam&apos;, 3.0),
(10, &apos;eggs&apos;, 2.25),
(11, &apos;eggs&apos;, 2.0),
(12, &apos;coffee&apos;, 2.35)]
</pre>
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<p>To only read a particular subset of data, you add <em>predicates</em> to the scanner:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">scanner</span> <span class="o">=</span> <span class="n">purchases</span><span class="o">.</span><span class="n">scanner</span><span class="p">()</span>
<span class="n">scanner</span><span class="o">.</span><span class="n">add_predicate</span><span class="p">(</span><span class="n">purchases</span><span class="p">[</span><span class="s1">&#39;item&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;spam&#39;</span><span class="p">)</span>
<span class="n">scanner</span><span class="o">.</span><span class="n">open</span><span class="p">()</span>
<span class="n">scanner</span><span class="o">.</span><span class="n">read_all_tuples</span><span class="p">()</span>
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[(1, &apos;spam&apos;, 2.49), (4, &apos;spam&apos;, 2.0), (9, &apos;spam&apos;, 3.0)]
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">scanner</span> <span class="o">=</span> <span class="n">purchases</span><span class="o">.</span><span class="n">scanner</span><span class="p">()</span>
<span class="n">id_col</span> <span class="o">=</span> <span class="n">purchases</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span>
<span class="n">scanner</span><span class="o">.</span><span class="n">add_predicates</span><span class="p">([</span><span class="n">id_col</span> <span class="o">&gt;=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">id_col</span> <span class="o">&lt;=</span> <span class="mi">10</span><span class="p">])</span>
<span class="n">scanner</span><span class="o">.</span><span class="n">open</span><span class="p">()</span>
<span class="n">scanner</span><span class="o">.</span><span class="n">read_all_tuples</span><span class="p">()</span>
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[(5, &apos;eggs&apos;, 2.49),
(6, &apos;coffee&apos;, 2.75),
(7, &apos;eggs&apos;, 2.75),
(8, &apos;coffee&apos;, 1.95),
(9, &apos;spam&apos;, 3.0),
(10, &apos;eggs&apos;, 2.25)]
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<p>That's all we need to know for now. There's lots more to know about Kudu and things that can be added to the Python interface, such as:</p>
<ul>
<li>Native pandas DataFrame read/write capability</li>
<li>Hash and range partition configuration</li>
</ul>
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<h2 id="querying-existing-kudu-tables-with-ibis-and-impala">Querying existing Kudu tables with Ibis and Impala</h2>
<p>In the latest development version of Ibis, you can add Kudu to the mix when working with Impala. Let's take a look:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="kn">import</span> <span class="nn">ibis</span>
<span class="n">ibis</span><span class="o">.</span><span class="n">options</span><span class="o">.</span><span class="n">interactive</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">host</span> <span class="o">=</span> <span class="s1">&#39;quickstart.cloudera&#39;</span>
<span class="n">hdfs</span> <span class="o">=</span> <span class="n">ibis</span><span class="o">.</span><span class="n">hdfs_connect</span><span class="p">(</span><span class="n">host</span><span class="p">,</span> <span class="n">port</span><span class="o">=</span><span class="mi">50070</span><span class="p">)</span>
<span class="n">ic</span> <span class="o">=</span> <span class="n">ibis</span><span class="o">.</span><span class="n">impala</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">host</span><span class="p">,</span> <span class="n">port</span><span class="o">=</span><span class="mi">21050</span><span class="p">,</span> <span class="n">hdfs_client</span><span class="o">=</span><span class="n">hdfs</span><span class="p">)</span>
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<p>This Impala cluster is built with Kudu support, so I can connect my Ibis client to the Kudu master like so:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">ic</span><span class="o">.</span><span class="n">kudu</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">host</span><span class="p">,</span> <span class="mi">7051</span><span class="p">)</span>
</pre></div>
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<p>Now, let's see about that data we just wrote:</p>
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<div class="highlight-ipynb"><pre class="ipynb"><span></span><span class="n">ic</span><span class="o">.</span><span class="n">kudu</span><span class="o">.</span><span class="n">list_tables</span><span class="p">()</span>
</pre></div>
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