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<li class="chapter" data-level="1.4" data-path="imagej-module.html"><a href="imagej-module.html"><i class="fa fa-check"></i><b>1.4</b> ImageJ Module</a><ul>
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<li class="chapter" data-level="2.3" data-path="python-script-wrapper.html"><a href="python-script-wrapper.html"><i class="fa fa-check"></i><b>2.3</b> Python Script Wrapper</a><ul>
<li><a href="python-script-wrapper.html#example.-python-script-wrapper"><em>Example.</em> Python Script Wrapper</a></li>
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<li class="chapter" data-level="2.4" data-path="source-code.html"><a href="source-code.html"><i class="fa fa-check"></i><b>2.4</b> Source Code</a><ul>
<li><a href="source-code.html#example.-composite-strength-module"><em>Example.</em> Composite Strength Module</a></li>
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<li class="chapter" data-level="2.5" data-path="runtime-module-configuration.html"><a href="runtime-module-configuration.html"><i class="fa fa-check"></i><b>2.5</b> Runtime Module Configuration</a></li>
<li class="chapter" data-level="2.6" data-path="python-setup.html"><a href="python-setup.html"><i class="fa fa-check"></i><b>2.6</b> Python Setup</a></li>
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<li class="chapter" data-level="3" data-path="bqapi.html"><a href="bqapi.html"><i class="fa fa-check"></i><b>3</b> BQAPI</a></li>
<li class="chapter" data-level="4" data-path="bisque-development.html"><a href="bisque-development.html"><i class="fa fa-check"></i><b>4</b> BisQue Development</a><ul>
<li class="chapter" data-level="4.1" data-path="source-code-installation.html"><a href="source-code-installation.html"><i class="fa fa-check"></i><b>4.1</b> Source Code Installation</a><ul>
<li class="chapter" data-level="" data-path="source-code-installation.html"><a href="source-code-installation.html#clone-the-repository-and-prepare-virtual-environment"><i class="fa fa-check"></i>Clone the repository and Prepare Virtual Environment</a></li>
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<li class="chapter" data-level="4.2" data-path="planteome-deep-segment.html"><a href="planteome-deep-segment.html"><i class="fa fa-check"></i><b>4.2</b> Planteome Deep Segment</a></li>
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<li class="chapter" data-level="4.3.1" data-path="rancher-2-0-setup-wkubernetes-engine.html"><a href="rancher-2-0-setup-wkubernetes-engine.html#pre-requisite"><i class="fa fa-check"></i><b>4.3.1</b> Pre-requisite</a></li>
<li class="chapter" data-level="4.3.2" data-path="rancher-2-0-setup-wkubernetes-engine.html"><a href="rancher-2-0-setup-wkubernetes-engine.html#setup-workload-on-the-bq-cluster"><i class="fa fa-check"></i><b>4.3.2</b> Setup Workload on the bq-cluster</a></li>
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<li class="chapter" data-level="4.4" data-path="connoisseurgpu-workload-provisioning.html"><a href="connoisseurgpu-workload-provisioning.html"><i class="fa fa-check"></i><b>4.4</b> Connoisseur/GPU Workload provisioning</a></li>
<li class="chapter" data-level="4.5" data-path="rancher-condor.html"><a href="rancher-condor.html"><i class="fa fa-check"></i><b>4.5</b> Rancher Condor</a><ul>
<li class="chapter" data-level="4.5.1" data-path="rancher-condor.html"><a href="rancher-condor.html#topology"><i class="fa fa-check"></i><b>4.5.1</b> Topology</a></li>
<li class="chapter" data-level="4.5.2" data-path="rancher-condor.html"><a href="rancher-condor.html#masterworker-condor-config"><i class="fa fa-check"></i><b>4.5.2</b> Master/Worker Condor Config</a></li>
<li class="chapter" data-level="4.5.3" data-path="rancher-condor.html"><a href="rancher-condor.html#bisquesvc-submit-node-condor-config"><i class="fa fa-check"></i><b>4.5.3</b> BisqueSvc Submit Node Condor Config</a></li>
<li class="chapter" data-level="4.5.4" data-path="rancher-condor.html"><a href="rancher-condor.html#state-logs"><i class="fa fa-check"></i><b>4.5.4</b> State & logs</a></li>
<li class="chapter" data-level="4.5.5" data-path="rancher-condor.html"><a href="rancher-condor.html#test-condor"><i class="fa fa-check"></i><b>4.5.5</b> Test Condor</a></li>
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<h2><span class="header-section-number">4.1</span> Source Code Installation</h2>
<hr />
<blockquote>
<p><strong>NOTE</strong>: The source code installation has only been tested on <code>Ubuntu 16.04</code>.</p>
</blockquote>
<p><strong>Pre-requisites</strong></p>
<div class="sourceCode" id="cb1"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" title="1"><span class="fu">sudo</span> apt-get install -y python python-dev python-virtualenv python-numpy python-scipy </a>
<a class="sourceLine" id="cb1-2" title="2"><span class="fu">sudo</span> apt-get install -y libxml2-dev libxslt1-dev libhdf5-dev</a>
<a class="sourceLine" id="cb1-3" title="3"><span class="fu">sudo</span> apt-get install -y libmysqlclient-dev libpq-dev mercurial git cmake</a>
<a class="sourceLine" id="cb1-4" title="4"><span class="fu">sudo</span> apt-get install -y postgresql postgresql-client libsqlite3-dev</a>
<a class="sourceLine" id="cb1-5" title="5"><span class="fu">sudo</span> apt-get install -y python-paver python-setuptools</a>
<a class="sourceLine" id="cb1-6" title="6"><span class="fu">sudo</span> apt-get install -y graphviz libgraphviz-dev pkg-config</a>
<a class="sourceLine" id="cb1-7" title="7"><span class="fu">sudo</span> apt-get install -y openslide-tools python-openslide</a>
<a class="sourceLine" id="cb1-8" title="8"><span class="fu">sudo</span> apt-get install -y libfftw3-dev libbz2-dev libz-dev</a>
<a class="sourceLine" id="cb1-9" title="9"><span class="fu">sudo</span> apt-get install -y liblcms2-dev libtiff-dev libpng-dev</a>
<a class="sourceLine" id="cb1-10" title="10"><span class="fu">sudo</span> apt-get install -y libgdcm2.6 libopenslide-dev libopenslide0</a></code></pre></div>
<p><strong>Install Openjpeg</strong></p>
<div class="sourceCode" id="cb2"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb2-1" title="1"><span class="fu">git</span> clone https://github.com/uclouvain/openjpeg</a>
<a class="sourceLine" id="cb2-2" title="2"><span class="bu">cd</span> openjpeg <span class="kw">&&</span> <span class="fu">mkdir</span> build <span class="kw">&&</span> <span class="bu">cd</span> build</a>
<a class="sourceLine" id="cb2-3" title="3"><span class="fu">cmake</span> .. -DCMAKE_BUILD_TYPE=Release</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="fu">sudo</span> make -j4 install</a>
<a class="sourceLine" id="cb2-5" title="5"><span class="fu">sudo</span> ldconfig</a></code></pre></div>
<p><strong>Install BioImageConvert</strong></p>
<ul>
<li><a href="https://biodev.ece.ucsb.edu/projects/imgcnv">BioImageConvert Source Repository</a></li>
<li><a href="https://bitbucket.org/dimin/bioimageconvert/downloads/">Prebuilt Binaries Repository</a></li>
<li>Setup for pre-built binaries (below)</li>
</ul>
<div class="sourceCode" id="cb3"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb3-1" title="1"><span class="co"># Ubuntu 18 version</span></a>
<a class="sourceLine" id="cb3-2" title="2"><span class="fu">wget</span> https://bitbucket.org/dimin/bioimageconvert/downloads/imgcnv_ubuntu18_2.5.0.tar.gz</a>
<a class="sourceLine" id="cb3-3" title="3"></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># Ubuntu 16 version</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="fu">wget</span> https://bitbucket.org/dimin/bioimageconvert/downloads/imgcnv_ubuntu16_2.4.3.tar.gz</a>
<a class="sourceLine" id="cb3-6" title="6"><span class="fu">tar</span> -xvzf imgcnv_ubuntu16_2.4.3.tar.gz</a>
<a class="sourceLine" id="cb3-7" title="7"></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="fu">sudo</span> cp imgcnv_ubuntu16_2.4.3/imgcnv /usr/local/bin/</a>
<a class="sourceLine" id="cb3-9" title="9"><span class="fu">sudo</span> cp imgcnv_ubuntu16_2.4.3/libimgcnv.so.2.4.3 /usr/local/lib/</a>
<a class="sourceLine" id="cb3-10" title="10"><span class="fu">sudo</span> ln -s /usr/local/lib/libimgcnv.so.2.4.3 /usr/local/lib/libimgcnv.so.2.4</a>
<a class="sourceLine" id="cb3-11" title="11"><span class="fu">sudo</span> ln -s /usr/local/lib/libimgcnv.so.2.4 /usr/local/lib/libimgcnv.so.2</a>
<a class="sourceLine" id="cb3-12" title="12"><span class="fu">sudo</span> ln -s /usr/local/lib/libimgcnv.so.2 /usr/local/lib/libimgcnv.so</a>
<a class="sourceLine" id="cb3-13" title="13"><span class="fu">sudo</span> ldconfig</a></code></pre></div>
<p>Alternately, Compile by source and Install (You are on your own here)</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb4-1" title="1"><span class="ex">hg</span> clone --insecure http://biodev.ece.ucsb.edu/hg/imgcnv</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="bu">cd</span> imgcnv <span class="kw">&&</span> <span class="fu">make</span> -j6 </a>
<a class="sourceLine" id="cb4-3" title="3"><span class="fu">sudo</span> make install</a></code></pre></div>
<hr />
<div id="clone-the-repository-and-prepare-virtual-environment" class="section level3 unnumbered">
<h3>Clone the repository and Prepare Virtual Environment</h3>
<p>We will clone the stable repository and work inside a python virtual environment for setup requirements.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb5-1" title="1"><span class="fu">git</span> clone https://github.com/UCSB-VRL/bisque.git bisque-stable</a></code></pre></div>
<ul>
<li>Its always a good practive to use a virtualenv to develop projects</li>
</ul>
<div class="sourceCode" id="cb6"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb6-1" title="1"><span class="fu">sudo</span> pip install virtualenvwrapper</a></code></pre></div>
<ul>
<li>Edit ~/.bashrc and export the following variables
<ul>
<li>In case of issues around virtualenvwrapper make sure the paths in the variables below exist</li>
</ul></li>
</ul>
<div class="sourceCode" id="cb7"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb7-1" title="1"><span class="co"># virtualenv and virtualenvwrapper</span></a>
<a class="sourceLine" id="cb7-2" title="2"><span class="bu">export</span> <span class="va">PATH=</span>/usr/local/bin:<span class="va">$PATH</span></a>
<a class="sourceLine" id="cb7-3" title="3"><span class="bu">export</span> <span class="va">VIRTUALENVWRAPPER_PYTHON=</span>/usr/bin/python</a>
<a class="sourceLine" id="cb7-4" title="4"><span class="bu">export</span> <span class="va">VIRTUALENVWRAPPER_VIRTUALENV=</span>/usr/local/bin/virtualenv</a>
<a class="sourceLine" id="cb7-5" title="5"><span class="bu">source</span> /usr/local/bin/virtualenvwrapper.sh</a></code></pre></div>
<ul>
<li>Now load this using “source ~/.bashrc”</li>
<li>Create a virtual envrionment “mkvirtualenv -p /usr/bin/python2 bqdev”</li>
<li>Change environment “workon bqdev”</li>
</ul>
<p>__Deprecated Bootstrap Installer (Do Not Use this Script)_ _</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb8-1" title="1">$ <span class="fu">mkdir</span> bisque <span class="kw">&&</span> <span class="bu">cd</span> bisque</a>
<a class="sourceLine" id="cb8-2" title="2">$ <span class="fu">wget</span> http://biodev.ece.ucsb.edu/projects/bisquik/export/tip/bisque-stable/contrib/bootstrap/bisque-bootstrap.py</a>
<a class="sourceLine" id="cb8-3" title="3">$ <span class="ex">python</span> bisque-bootstrap.py bqenv</a>
<a class="sourceLine" id="cb8-4" title="4"></a>
<a class="sourceLine" id="cb8-5" title="5"><span class="co"># Activate Virtualenv</span></a>
<a class="sourceLine" id="cb8-6" title="6"><span class="ex">bisque</span>$ source bqenv/bin/activate</a></code></pre></div>
<ul>
<li>Now Install requirements</li>
</ul>
<div class="sourceCode" id="cb9"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb9-1" title="1"><span class="ex">pip</span> install -i https://biodev.ece.ucsb.edu/py/bisque/xenial/+simple/ -r requirements.txt</a>
<a class="sourceLine" id="cb9-2" title="2"></a>
<a class="sourceLine" id="cb9-3" title="3"><span class="ex">Alternate</span> Index Url for Development: https://biodev.ece.ucsb.edu/py/bisque/dev/+simple</a>
<a class="sourceLine" id="cb9-4" title="4"><span class="ex">Index</span> Url Debian Stretch: https://biodev.ece.ucsb.edu/py/bisque/stretch/+simple/</a>
<a class="sourceLine" id="cb9-5" title="5"><span class="ex">Index</span> Url Ubuntu xenial: https://biodev.ece.ucsb.edu/py/bisque/xenial/+simple/</a></code></pre></div>
<ul>
<li>Fix the requirements.txt (Only if the installation fails)</li>
</ul>
<div class="sourceCode" id="cb10"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb10-1" title="1"><span class="co">#Fix the requirements.txt file using sed -i 's/.*psycopg2==2.6.1.*/psycopg2==2.7.1./' requirements.txt</span></a>
<a class="sourceLine" id="cb10-2" title="2"><span class="va">psycopg2=</span>=<span class="ex">2.7.1</span></a>
<a class="sourceLine" id="cb10-3" title="3"><span class="va">Minimatic=</span>=<span class="ex">1.0</span></a>
<a class="sourceLine" id="cb10-4" title="4"><span class="va">Paste=</span>=<span class="ex">1.7.5.1</span></a>
<a class="sourceLine" id="cb10-5" title="5"><span class="va">httplib2=</span>=<span class="ex">0.7.3</span></a>
<a class="sourceLine" id="cb10-6" title="6"><span class="co">#tgext.registration==0.1dev</span></a>
<a class="sourceLine" id="cb10-7" title="7"></a>
<a class="sourceLine" id="cb10-8" title="8"><span class="co"># Install separately since packages may be deprecated in PyPi</span></a>
<a class="sourceLine" id="cb10-9" title="9"><span class="ex">easy_install</span> http://biodev.ece.ucsb.edu/binaries/depot/tgext.registration2/tgext.registration2-0.5.2.tar.gz</a></code></pre></div>
<hr />
</div>
<div id="configure-bisque-environment" class="section level3 unnumbered">
<h3>Configure Bisque Environment</h3>
<ul>
<li>Run the Paver setup</li>
</ul>
<div class="sourceCode" id="cb11"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb11-1" title="1">$ <span class="ex">paver</span> setup</a></code></pre></div>
<ul>
<li>Expected paver log tail</li>
</ul>
<div class="sourceCode" id="cb12"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb12-1" title="1"><span class="ex">Installing</span> collected packages: bqengine</a>
<a class="sourceLine" id="cb12-2" title="2"> <span class="ex">Running</span> setup.py develop for bqengine</a>
<a class="sourceLine" id="cb12-3" title="3"><span class="ex">Successfully</span> installed bqengine</a>
<a class="sourceLine" id="cb12-4" title="4"></a>
<a class="sourceLine" id="cb12-5" title="5"><span class="ex">Now</span> run:</a>
<a class="sourceLine" id="cb12-6" title="6"><span class="ex">bq-admin</span> setup </a></code></pre></div>
<ul>
<li>Run the bq-admin standalone setup</li>
</ul>
<div class="sourceCode" id="cb13"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb13-1" title="1">$ <span class="ex">bq-admin</span> setup</a></code></pre></div>
<ul>
<li>Expected bq-admin setup log tail (also observe the various inputs in the log for this setup)</li>
</ul>
<div class="sourceCode" id="cb14"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb14-1" title="1"> <span class="kw">(</span><span class="ex">bqdev</span><span class="kw">)</span> <span class="ex">rahul@loup</span>:~/repository/github/bisque$ bq-admin setup </a>
<a class="sourceLine" id="cb14-2" title="2"> <span class="ex">INFO</span>:root:Generating grammar tables from /usr/lib/python2.7/lib2to3/Grammar.txt</a>
<a class="sourceLine" id="cb14-3" title="3"> <span class="ex">INFO</span>:root:Generating grammar tables from /usr/lib/python2.7/lib2to3/PatternGrammar.txt</a>
<a class="sourceLine" id="cb14-4" title="4"> <span class="ex">Developer</span> installation</a>
<a class="sourceLine" id="cb14-5" title="5"> <span class="ex">DIRS</span>: {<span class="st">'bin'</span>: <span class="st">'/home/rahul/.virtualenvs/bqdev/bin'</span>, <span class="st">'run'</span>: <span class="st">'.'</span>, <span class="st">'share'</span>: <span class="st">'.'</span>, <span class="st">'plugins'</span>: <span class="st">'./plugins'</span>, <span class="st">'packages'</span>: <span class="st">'/home/rahul/.virtualenvs/bqdev/lib/python2.7/site-packages'</span>, <span class="st">'data'</span>: <span class="st">'./data'</span>, <span class="st">'virtualenv'</span>: <span class="st">'/home/rahul/.virtualenvs/bqdev'</span>, <span class="st">'default'</span>: <span class="st">'./config-defaults'</span>, <span class="st">'jslocation'</span>: <span class="st">'bqcore'</span>, <span class="st">'modules'</span>: <span class="st">'./modules'</span>, <span class="st">'depot'</span>: <span class="st">'./external'</span>, <span class="st">'config'</span>: <span class="st">'./config'</span>, <span class="st">'public'</span>: <span class="st">'./public'</span>}</a>
<a class="sourceLine" id="cb14-6" title="6"> <span class="ex">INFO</span>:root:Generating grammar tables from /usr/lib/python2.7/lib2to3/Grammar.txt</a>
<a class="sourceLine" id="cb14-7" title="7"> <span class="ex">INFO</span>:root:Generating grammar tables from /usr/lib/python2.7/lib2to3/PatternGrammar.txt</a>
<a class="sourceLine" id="cb14-8" title="8"> <span class="ex">Developer</span> installation</a>
<a class="sourceLine" id="cb14-9" title="9"> <span class="ex">DIRS</span>: {<span class="st">'bin'</span>: <span class="st">'/home/rahul/.virtualenvs/bqdev/bin'</span>, <span class="st">'run'</span>: <span class="st">'.'</span>, <span class="st">'share'</span>: <span class="st">'.'</span>, <span class="st">'plugins'</span>: <span class="st">'./plugins'</span>, <span class="st">'packages'</span>: <span class="st">'/home/rahul/.virtualenvs/bqdev/lib/python2.7/site-packages'</span>, <span class="st">'data'</span>: <span class="st">'./data'</span>, <span class="st">'virtualenv'</span>: <span class="st">'/home/rahul/.virtualenvs/bqdev'</span>, <span class="st">'default'</span>: <span class="st">'./config-defaults'</span>, <span class="st">'jslocation'</span>: <span class="st">'bqcore'</span>, <span class="st">'modules'</span>: <span class="st">'./modules'</span>, <span class="st">'depot'</span>: <span class="st">'./external'</span>, <span class="st">'config'</span>: <span class="st">'./config'</span>, <span class="st">'public'</span>: <span class="st">'./public'</span>}</a>
<a class="sourceLine" id="cb14-10" title="10"> <span class="ex">This</span> is the main installer for Bisque</a>
<a class="sourceLine" id="cb14-11" title="11"></a>
<a class="sourceLine" id="cb14-12" title="12"> <span class="ex">The</span> system will initialize and be ready for use after a succesfull</a>
<a class="sourceLine" id="cb14-13" title="13"> <span class="ex">setup</span> has completed.</a>
<a class="sourceLine" id="cb14-14" title="14"></a>
<a class="sourceLine" id="cb14-15" title="15"> <span class="ex">Several</span> questions must be answered to complete the install. Each</a>
<a class="sourceLine" id="cb14-16" title="16"> <span class="ex">question</span> is presented with default in brackets []. Pressing</a>
<a class="sourceLine" id="cb14-17" title="17"> <span class="op"><</span><span class="ex">enter</span><span class="op">></span> means that you are accepting the default value. You may</a>
<a class="sourceLine" id="cb14-18" title="18"> <span class="ex">request</span> more information by responding with single <span class="st">'?'</span> and then <span class="op"><</span>enter<span class="op">></span>.</a>
<a class="sourceLine" id="cb14-19" title="19"></a>
<a class="sourceLine" id="cb14-20" title="20"> <span class="ex">For</span> example:</a>
<a class="sourceLine" id="cb14-21" title="21"> <span class="ex">What</span> is postal abbreviation of Alaska [AK]?</a>
<a class="sourceLine" id="cb14-22" title="22"></a>
<a class="sourceLine" id="cb14-23" title="23"> <span class="ex">The</span> default answer is AK and is chosen by simply entering <span class="op"><</span>enter<span class="op">></span></a>
<a class="sourceLine" id="cb14-24" title="24"></a>
<a class="sourceLine" id="cb14-25" title="25"> </a>
<a class="sourceLine" id="cb14-26" title="26"> <span class="ex">Beginning</span> install of [<span class="st">'bisque'</span>, <span class="st">'engine'</span>] with [<span class="st">'server'</span>] </a>
<a class="sourceLine" id="cb14-27" title="27"> <span class="ex">CALLING</span> <span class="op"><</span>function install_external_binaries at 0x7f9533ffac08<span class="op">></span></a>
<a class="sourceLine" id="cb14-28" title="28"> <span class="ex">Fetch</span> external binary files from Bisque development server [Y]? Y</a>
<a class="sourceLine" id="cb14-29" title="29"> <span class="ex">Matched</span> section Linux-64bit-*</a>
<a class="sourceLine" id="cb14-30" title="30"> <span class="ex">extjs.zip</span> found locally</a>
<a class="sourceLine" id="cb14-31" title="31"> <span class="ex">bioformats-pack.zip</span> found locally</a>
<a class="sourceLine" id="cb14-32" title="32"> <span class="ex">libmbgl-linux-64-large.a</span> found locally</a>
<a class="sourceLine" id="cb14-33" title="33"> <span class="ex">feature_extractors.zip</span> found locally</a>
<a class="sourceLine" id="cb14-34" title="34"> <span class="ex">ImarisConvert.tar.gz</span> found locally</a>
<a class="sourceLine" id="cb14-35" title="35"> <span class="ex">opencv-2.4.6.zip</span> found locally</a>
<a class="sourceLine" id="cb14-36" title="36"> <span class="ex">CALLING</span> <span class="op"><</span>function install_dependencies at 0x7f9533ffad70<span class="op">></span></a>
<a class="sourceLine" id="cb14-37" title="37"> <span class="ex">2.4.3</span></a>
<a class="sourceLine" id="cb14-38" title="38"></a>
<a class="sourceLine" id="cb14-39" title="39"> <span class="ex">Found</span> imgcnv version 2.4.3</a>
<a class="sourceLine" id="cb14-40" title="40"></a>
<a class="sourceLine" id="cb14-41" title="41"></a>
<a class="sourceLine" id="cb14-42" title="42"> <span class="ex">Imgcnv</span> is installed and no-precompiled version exists. Using installed version</a>
<a class="sourceLine" id="cb14-43" title="43"> <span class="ex">ImarisConvert</span> is up to date</a>
<a class="sourceLine" id="cb14-44" title="44"> <span class="ex">No</span> pre-compiled version of openslide exists for your system</a>
<a class="sourceLine" id="cb14-45" title="45"> <span class="ex">Please</span> visit our mailing list https://groups.google.com/forum/#!forum/bisque-bioimage for help</a>
<a class="sourceLine" id="cb14-46" title="46"> <span class="ex">Bioformats</span> is up to date</a>
<a class="sourceLine" id="cb14-47" title="47"> <span class="ex">CALLING</span> <span class="op"><</span>function install_features at 0x7f9533ffb050<span class="op">></span></a>
<a class="sourceLine" id="cb14-48" title="48"> <span class="ex">Install</span> feature extractors (Feature Server) [<span class="ex">Y</span>]? </a>
<a class="sourceLine" id="cb14-49" title="49"> <span class="ex">Unpacking</span> ./external/feature_extractors.zip into ./bqfeature/bq</a>
<a class="sourceLine" id="cb14-50" title="50"> <span class="ex">Install</span> source code for feature extractors [N]? </a>
<a class="sourceLine" id="cb14-51" title="51"> <span class="ex">To</span> enable the feature service to read OME-bigtiff for feature extraction install</a>
<a class="sourceLine" id="cb14-52" title="52"> <span class="ex">libtiff4</span></a>
<a class="sourceLine" id="cb14-53" title="53"> <span class="ex">For</span> Debian use the command apt-get install libtiff5-dev</a>
<a class="sourceLine" id="cb14-54" title="54"> </a>
<a class="sourceLine" id="cb14-55" title="55"> <span class="ex">Install</span> OpenCV-2.4.6 [Y]? </a>
<a class="sourceLine" id="cb14-56" title="56"> <span class="ex">Extracted</span> opencv-2.4.6/python2.7/cv.py -<span class="op">></span> /home/rahul/.virtualenvs/bqdev/lib/python2.7/site-packages/cv.py</a>
<a class="sourceLine" id="cb14-57" title="57"> <span class="ex">Extracted</span> opencv-2.4.6/python2.7/cv2.so -<span class="op">></span> /home/rahul/.virtualenvs/bqdev/lib/python2.7/site-packages/cv2.so</a>
<a class="sourceLine" id="cb14-58" title="58"> <span class="ex">CALLING</span> <span class="op"><</span>function install_plugins at 0x7f9533ff9b18<span class="op">></span></a>
<a class="sourceLine" id="cb14-59" title="59"> <span class="ex">Try</span> to install plugins [Y]? </a>
<a class="sourceLine" id="cb14-60" title="60"> <span class="ex">INFO</span> <span class="st">'svn'</span>not found: cannot fetch source repositories with svn </a>
<a class="sourceLine" id="cb14-61" title="61"> <span class="ex">INSTALL</span> PLGINS [<span class="st">'./plugins'</span>]</a>
<a class="sourceLine" id="cb14-62" title="62"> <span class="ex">Checking</span> ./plugins for modules</a>
<a class="sourceLine" id="cb14-63" title="63"> <span class="ex">CALLING</span> <span class="op"><</span>function install_public_static at 0x7f9533ffa848<span class="op">></span></a>
<a class="sourceLine" id="cb14-64" title="64"> <span class="ex">Deploy</span> all static resources to public directory [Y]? </a>
<a class="sourceLine" id="cb14-65" title="65"> <span class="ex">Creating</span> ./public</a>
<a class="sourceLine" id="cb14-66" title="66"> <span class="ex">INFO</span>:bq.image_service.server:Available converters: openslide (1.1.1), <span class="ex">imgcnv</span> (2.4.3), <span class="ex">ImarisConvert</span> (8.0.2), <span class="ex">bioformats</span> (5.1.1)</a>
<a class="sourceLine" id="cb14-67" title="67"> <span class="ex">Problem</span> loading registration = bq.registration.controllers.registration_service: <span class="st">'User'</span></a>
<a class="sourceLine" id="cb14-68" title="68"></a>
<a class="sourceLine" id="cb14-69" title="69"> <span class="ex">Generating</span> packaged JS and CSS files</a>
<a class="sourceLine" id="cb14-70" title="70"></a>
<a class="sourceLine" id="cb14-71" title="71"> <span class="ex">INFO</span>:minimatic:Combined -<span class="op">></span> ./public/core/css/all_css.css:</a>
<a class="sourceLine" id="cb14-72" title="72"> <span class="ex">INFO</span>:minimatic:Combined -<span class="op">></span> ./public/core/js/all_js.js:</a>
<a class="sourceLine" id="cb14-73" title="73"> <span class="ex">CALLING</span> <span class="op"><</span>function install_server_defaults at 0x7f9533ffa410<span class="op">></span></a>
<a class="sourceLine" id="cb14-74" title="74"> <span class="ex">Server</span> config</a>
<a class="sourceLine" id="cb14-75" title="75"> <span class="ex">Top</span> level site variables are:</a>
<a class="sourceLine" id="cb14-76" title="76"> <span class="ex">bisque.admin_email</span>=YourEmail@YourOrganization</a>
<a class="sourceLine" id="cb14-77" title="77"> <span class="ex">bisque.admin_id</span>=admin</a>
<a class="sourceLine" id="cb14-78" title="78"> <span class="ex">bisque.organization</span>=Your Organization</a>
<a class="sourceLine" id="cb14-79" title="79"> <span class="ex">bisque.paths.root</span>=.</a>
<a class="sourceLine" id="cb14-80" title="80"> <span class="ex">bisque.server</span>=http://0.0.0.0:8088</a>
<a class="sourceLine" id="cb14-81" title="81"> <span class="ex">bisque.title</span>=Image Repository</a>
<a class="sourceLine" id="cb14-82" title="82"> <span class="ex">Change</span> a site variable [N]? Y</a>
<a class="sourceLine" id="cb14-83" title="83"> <span class="ex">Enter</span> the root URL of the server [http://0.0.0.0:8088]? http://loup.ece.ucsb.edu:8080</a>
<a class="sourceLine" id="cb14-84" title="84"> <span class="ex">Your</span> real name administrator account []? </a>
<a class="sourceLine" id="cb14-85" title="85"> <span class="ex">A</span> login ID for the administrator account [admin]? </a>
<a class="sourceLine" id="cb14-86" title="86"> <span class="ex">An</span> email for the administrator [YourEmail@YourOrganization]? </a>
<a class="sourceLine" id="cb14-87" title="87"> <span class="ex">A</span> small organization title for the main page [Your Organization]? </a>
<a class="sourceLine" id="cb14-88" title="88"> <span class="ex">The</span> main title for the web page header [Image Repository]? </a>
<a class="sourceLine" id="cb14-89" title="89"> <span class="ex">Installation</span> Directory [.]? </a>
<a class="sourceLine" id="cb14-90" title="90"> <span class="ex">Do</span> you want to create new server configuations [Y]? </a>
<a class="sourceLine" id="cb14-91" title="91"> {<span class="st">'backend'</span>: <span class="st">'paster'</span>,</a>
<a class="sourceLine" id="cb14-92" title="92"> <span class="st">'e1.bisque.has_database'</span>: <span class="st">'false'</span>,</a>
<a class="sourceLine" id="cb14-93" title="93"> <span class="st">'e1.bisque.static_files'</span>: <span class="st">'false'</span>,</a>
<a class="sourceLine" id="cb14-94" title="94"> <span class="st">'e1.services_enabled'</span>: <span class="st">'engine_service'</span>,</a>
<a class="sourceLine" id="cb14-95" title="95"> <span class="st">'e1.url'</span>: <span class="st">'http://0.0.0.0:27000'</span>,</a>
<a class="sourceLine" id="cb14-96" title="96"> <span class="st">'h1.bisque.static_files'</span>: <span class="st">'true'</span>,</a>
<a class="sourceLine" id="cb14-97" title="97"> <span class="st">'h1.services_disabled'</span>: <span class="st">''</span>,</a>
<a class="sourceLine" id="cb14-98" title="98"> <span class="st">'h1.services_enabled'</span>: <span class="st">''</span>,</a>
<a class="sourceLine" id="cb14-99" title="99"> <span class="st">'h1.url'</span>: <span class="st">'http://0.0.0.0:8088'</span>,</a>
<a class="sourceLine" id="cb14-100" title="100"> <span class="st">'servers'</span>: <span class="st">'h1'</span>}</a>
<a class="sourceLine" id="cb14-101" title="101"> <span class="ex">The</span> server agent for bisque [paster]? </a>
<a class="sourceLine" id="cb14-102" title="102"> <span class="ex">list</span> of server entries to be configured [h1]? </a>
<a class="sourceLine" id="cb14-103" title="103"> <span class="ex">Install</span> (update) <span class="ex">paster</span> configs (application server and configs) [<span class="ex">Y</span>]? </a>
<a class="sourceLine" id="cb14-104" title="104"> <span class="ex">PARAMS</span> {<span class="st">'h1.bisque.static_files'</span>: <span class="st">'true'</span>, <span class="st">'h1.services_enabled'</span>: <span class="st">''</span>, <span class="st">'e1.bisque.has_database'</span>: <span class="st">'false'</span>, <span class="st">'h1.url'</span>: <span class="st">'http://0.0.0.0:8088'</span>, <span class="st">'servers'</span>: <span class="st">'h1'</span>, <span class="st">'h1.services_disabled'</span>: <span class="st">''</span>, <span class="st">'e1.url'</span>: <span class="st">'http://0.0.0.0:27000'</span>, <span class="st">'e1.bisque.static_files'</span>: <span class="st">'false'</span>, <span class="st">'e1.services_enabled'</span>: <span class="st">'engine_service'</span>, <span class="st">'backend'</span>: <span class="st">'paster'</span>}</a>
<a class="sourceLine" id="cb14-105" title="105"> <span class="ex">h1</span>: the url of the server [http://0.0.0.0:8088]? http://loup.ece.ucsb.edu:8080</a>
<a class="sourceLine" id="cb14-106" title="106"> <span class="ex">h1</span>: Services enabled []? </a>
<a class="sourceLine" id="cb14-107" title="107"> <span class="ex">h1</span>: Services disabled []? </a>
<a class="sourceLine" id="cb14-108" title="108"> <span class="ex">Created</span> paster config: ./config/h1_paster.cfg</a>
<a class="sourceLine" id="cb14-109" title="109"> <span class="ex">CALLING</span> <span class="op"><</span>function install_mail at 0x7f9533ffa758<span class="op">></span></a>
<a class="sourceLine" id="cb14-110" title="110"> <span class="ex">Enable</span> mail delivery [Y]? N</a>
<a class="sourceLine" id="cb14-111" title="111"> <span class="ex">CALLING</span> <span class="op"><</span>function install_secrets at 0x7f9533ffa8c0<span class="op">></span></a>
<a class="sourceLine" id="cb14-112" title="112"> <span class="ex">Encrypt</span> cookies with secret phrase [CEMWOJ65]? </a>
<a class="sourceLine" id="cb14-113" title="113"> <span class="ex">CALLING</span> <span class="op"><</span>function install_database at 0x7f9533ff9578<span class="op">></span></a>
<a class="sourceLine" id="cb14-114" title="114"> <span class="ex">A</span> database URI [sqlite:///data/bisque.db]? </a>
<a class="sourceLine" id="cb14-115" title="115"> <span class="ex">Trying</span> to import driver sqlite3...</a>
<a class="sourceLine" id="cb14-116" title="116"> <span class="ex">Driver</span> successfully imported.</a>
<a class="sourceLine" id="cb14-117" title="117"> <span class="ex">Create</span> and initialize database [Y]? </a>
<a class="sourceLine" id="cb14-118" title="118"> <span class="ex">A</span> database URI [sqlite:///data/bisque.db]? </a>
<a class="sourceLine" id="cb14-119" title="119"> <span class="ex">Checking</span> whether database <span class="st">"data/bisque.db"</span> already exists...</a>
<a class="sourceLine" id="cb14-120" title="120"> <span class="ex">Yes</span>, it exists.</a>
<a class="sourceLine" id="cb14-121" title="121"> <span class="ex">Upgrading</span> database version (alembic)</a>
<a class="sourceLine" id="cb14-122" title="122"> <span class="ex">INFO</span> [alembic.migration] Context impl SQLiteImpl.</a>
<a class="sourceLine" id="cb14-123" title="123"> <span class="ex">INFO</span> [alembic.migration] Will assume non-transactional DDL.</a>
<a class="sourceLine" id="cb14-124" title="124"> <span class="ex">CALLING</span> <span class="op"><</span>function install_preferences at 0x7f9533ffa7d0<span class="op">></span></a>
<a class="sourceLine" id="cb14-125" title="125"> <span class="ex">Initialize</span> Preferences [Y]? </a>
<a class="sourceLine" id="cb14-126" title="126"> <span class="ex">Force</span> initialization [N]? </a>
<a class="sourceLine" id="cb14-127" title="127"> <span class="ex">INFO</span>:bq.config:DATABASE sqlite:///data/bisque.db</a>
<a class="sourceLine" id="cb14-128" title="128"> <span class="ex">INFO</span>:bq.config:SQLLite special handling NullPool timoout</a>
<a class="sourceLine" id="cb14-129" title="129"> <span class="ex">INFO</span>:bq.image_service.server:Available converters: openslide (1.1.1), <span class="ex">imgcnv</span> (2.4.3), <span class="ex">ImarisConvert</span> (8.0.2), <span class="ex">bioformats</span> (5.1.1)</a>
<a class="sourceLine" id="cb14-130" title="130"> <span class="ex">INFO</span>:bq.blobs.mounts:Loaded drivers OrderedDict([(<span class="st">'local'</span>, {<span class="st">'top'</span>: <span class="st">'file://$datadir/imagedir/'</span>, <span class="st">'mounturl'</span>: <span class="st">'file://$datadir/imagedir/$user/'</span>})])</a>
<a class="sourceLine" id="cb14-131" title="131"> <span class="ex">WARNING</span>:bq.blobs.mounts:SQLITE does not support subtransactions: some mount service operations will fail</a>
<a class="sourceLine" id="cb14-132" title="132"> <span class="ex">INFO</span>:bq.blobs.plugins:Resource plugins: [<span class="st">'(bisque_pipeline, bq)'</span>, <span class="st">'(cellprofiler_pipeline, cppipe)'</span>, <span class="st">'(cellprofiler_pipeline, cp)'</span>, <span class="st">'(dream3d_pipeline, json)'</span>, <span class="st">'(imagej_pipeline, ijm)'</span>, <span class="st">'(text, asc)'</span>, <span class="st">'(text, ascii)'</span>, <span class="st">'(text, zw)'</span>, <span class="st">'(text, hz)'</span>, <span class="st">'(text, txt)'</span>, <span class="st">'(text, utxt)'</span>, <span class="st">'(text, utf8)'</span>, <span class="st">'(table, csv)'</span>, <span class="st">'(table, hdf)'</span>, <span class="st">'(table, hdf5)'</span>, <span class="st">'(table, h5)'</span>, <span class="st">'(table, he5)'</span>, <span class="st">'(table, h5ebsd)'</span>, <span class="st">'(table, dream3d)'</span>, <span class="st">'(table, csv)'</span>, <span class="st">'(table, xls)'</span>, <span class="st">'(table, xlsx)'</span>]</a>
<a class="sourceLine" id="cb14-133" title="133"> <span class="ex">WARNING</span>:bq.service:Following service were not found: set([<span class="st">'mnt'</span>])</a>
<a class="sourceLine" id="cb14-134" title="134"> <span class="ex">/home/rahul/.virtualenvs/bqdev/local/lib/python2.7/site-packages/sqlalchemy/sql</span>/sqltypes.py:<span class="ex">226</span>: SAWarning: Unicode type received non-unicode bind param value <span class="st">'system'</span>. (this warning may be suppressed after 10 occurrences)</a>
<a class="sourceLine" id="cb14-135" title="135"> <span class="kw">(</span><span class="ex">util.ellipses_string</span>(value<span class="kw">)</span>,))</a>
<a class="sourceLine" id="cb14-136" title="136"> <span class="ex">NO</span> ACTION: System object initialized at <span class="op"><</span>system created=<span class="st">"2019-02-04T10:51:57.823907"</span> name=<span class="st">"system"</span> owner=<span class="st">"http://localhost/data_service/00-2jimYQLLjB3yy3HuTwQM5c"</span> permission=<span class="st">"published"</span> resource_uniq=<span class="st">"00-UAZfWJYjDKp4yhabV3PP7S"</span> ts=<span class="st">"2019-02-04T10:51:57.823907"</span> uri=<span class="st">"http://localhost/data_service/00-UAZfWJYjDKp4yhabV3PP7S"</span>/<span class="op">></span> </a>
<a class="sourceLine" id="cb14-137" title="137"> <span class="ex">Problem</span> initializing preferences.. please use bq-admin preferences</a>
<a class="sourceLine" id="cb14-138" title="138"></a>
<a class="sourceLine" id="cb14-139" title="139"> <span class="ex">Initialize</span> your database with:</a>
<a class="sourceLine" id="cb14-140" title="140"> $ <span class="ex">bq-admin</span> setup createdb</a>
<a class="sourceLine" id="cb14-141" title="141"></a>
<a class="sourceLine" id="cb14-142" title="142"> <span class="ex">You</span> can start bisque with:</a>
<a class="sourceLine" id="cb14-143" title="143"> $ <span class="ex">bq-admin</span> server start</a>
<a class="sourceLine" id="cb14-144" title="144"> <span class="kw">then</span> <span class="ex">point</span> your browser to:</a>
<a class="sourceLine" id="cb14-145" title="145"> <span class="ex">http</span>://loup.ece.ucsb.edu:8080</a>
<a class="sourceLine" id="cb14-146" title="146"> <span class="ex">If</span> you need to shutdown the servers, then use:</a>
<a class="sourceLine" id="cb14-147" title="147"> $ <span class="ex">bq-admin</span> server stop</a>
<a class="sourceLine" id="cb14-148" title="148"> <span class="ex">You</span> can login as admin and change the default password.</a>
<a class="sourceLine" id="cb14-149" title="149"></a>
<a class="sourceLine" id="cb14-150" title="150"> <span class="ex">Send</span> Installation/Registration report [Y]? N</a>
<a class="sourceLine" id="cb14-151" title="151"> <span class="kw">(</span><span class="ex">bqdev</span><span class="kw">)</span> <span class="ex">rahul@loup</span>:~/repository/github/bisque$ </a>
<a class="sourceLine" id="cb14-152" title="152"></a></code></pre></div>
<ul>
<li>Add “config/runtime-bisque.cfg” for module configuration and docker image registry
<ul>
<li>Edit and add run config from config-defaults/runtime-bisque.defaults to config/runtime-bisque.cfg</li>
<li>Here are some local changes but requires docker to be setup</li>
</ul></li>
</ul>
<pre><code>runtime.platforms = command
runtime.staging_base = staging/
[docker]
docker.enabled = true
# A hub where to push containers to
docker.hub = biodev.ece.ucsb.edu:5000</code></pre>
<hr />
</div>
<div id="run-bisque-server" class="section level3 unnumbered">
<h3>Run Bisque Server</h3>
<ul>
<li><p>Start/Stop the server</p>
<pre><code>$ bq-admin server start
$ bq-admin server stop</code></pre></li>
<li><p>Overview of Installation (Just for review)</p>
<pre><code>workon bqdev
paver setup [server|engine]
bq-admin setup [server|engine]
bq-admin deploy public</code></pre></li>
</ul>
<p>Open in browser
<img src="img/BisqueClientScreen.png" alt="Browser Client" /></p>
</div>
<div id="upload-dataset" class="section level3 unnumbered">
<h3>Upload Dataset</h3>
<ul>
<li><p>Upload an <a href="img/cells.ome.tif">image file</a> from your local directory to Bisque
<img src="img/UploadImageData.png" alt="Upload Image file" /></p></li>
<li>Browse uploaded dataset in the file explorer
<ul>
<li>Select Browse menu item in the navigation bar and click on dataset</li>
<li>Thereafter click on the files tab and click through the local database folder in the left document tree section.</li>
</ul>
<div class="figure">
<img src="img/DatasetBrowse.png" alt="Upload Image file" />
<p class="caption">Upload Image file</p>
</div></li>
<li>Select the uploaded file to view
<ul>
<li>This visualization is by default 2D in nature.</li>
<li>The various slices can be stepped through or played using the scroll bar on righ bottom of the image view area</li>
</ul>
<div class="figure">
<img src="img/ViewCell2DImage.png" alt="View 2D Image file" />
<p class="caption">View 2D Image file</p>
</div>
<ul>
<li>A 3D visualization can be explored by clicking the cube icon towards the right of share and delete icons on the tool bar right below the navigation bar.</li>
</ul>
<div class="figure">
<img src="img/ViewCell3DImage.png" alt="View 3D Image file" />
<p class="caption">View 3D Image file</p>
</div></li>
</ul>
<hr />
</div>
<div id="module" class="section level3 unnumbered">
<h3>Module</h3>
<p><strong>Load/Install Module packages and dependencies</strong></p>
<p>Lets take module/MetaData code as an example.</p>
<ul>
<li>Ensure ~/bisque/config/runtime-bisque.cfg has the configuration as below</li>
</ul>
<div class="sourceCode" id="cb18"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb18-1" title="1"><span class="ex">runtime.staging_base</span> = staging/</a>
<a class="sourceLine" id="cb18-2" title="2"><span class="ex">docker.hub</span> = biodev.ece.ucsb.edu:5000</a></code></pre></div>
<ul>
<li>Make sure the runtime-module.cfg is as per below</li>
</ul>
<div class="sourceCode" id="cb19"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb19-1" title="1"><span class="ex">module_enabled</span> = True</a>
<a class="sourceLine" id="cb19-2" title="2"><span class="ex">runtime.platforms</span>=command</a>
<a class="sourceLine" id="cb19-3" title="3">[<span class="ex">command</span>]</a>
<a class="sourceLine" id="cb19-4" title="4"><span class="ex">environments</span> = Staged</a>
<a class="sourceLine" id="cb19-5" title="5"><span class="ex">executable</span> = python MetaData.py</a>
<a class="sourceLine" id="cb19-6" title="6"><span class="ex">files</span> = MetaData.py</a></code></pre></div>
<ul>
<li>Now build/compile this module</li>
</ul>
<div class="sourceCode" id="cb20"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb20-1" title="1"> <span class="bu">cd</span> ~/bisque/modules/MetaData</a>
<a class="sourceLine" id="cb20-2" title="2"> <span class="ex">python</span> setup.py</a></code></pre></div>
<p>Open up the Bisque web interface at <a href="http://loup.ece.ucsb.edu:8088" class="uri">http://loup.ece.ucsb.edu:8088</a></p>
<ul>
<li>Login using admin:admin</li>
<li>Update the email address in the users context menu item (This is important)</li>
<li>Open Module Manager from the admin user context menu</li>
<li>Paste the following URL in the Module->Engine Module</li>
</ul>
<pre><code>http://loup.ece.ucsb.edu:8088/engine_service/</code></pre>
<ul>
<li>List of engine modules could be seen</li>
<li><p>Drag-n-Drop say MetaData module from the list to the left window and close the window</p>
<p><img src="img/module_metadata/DragRegModule.png" alt="Bisque Module" />
<img src="img/module_metadata/RegisterModuleMetaData.png" alt="Bisque Module" /></p></li>
</ul>
</div>
<div id="debug-module" class="section level3 unnumbered">
<h3>Debug Module</h3>
<ul>
<li>Every module run will generate a model execution identifier to track this execution. You can observe this after clicking the run command and you have a result. It could be success or fail in the Results section</li>
</ul>
<pre><code>http://loup.ece.ucsb.edu:8088/module_service/MetaData/?wpublic=1#mex=http://loup.ece.ucsb.edu:8088/module_service/mex/00-ZmuAoE43wTxByycmaCnvBF</code></pre>
<ul>
<li>The mex identifier (==MEX_ID=00-ZmuAoE43wTxByycmaCnvBF==) observed from URL can be used to locate this execution code & resulting logs in the staging folders</li>
<li>change directory to this staging folder and observe the files there</li>
</ul>
<div class="sourceCode" id="cb23"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb23-1" title="1"><span class="bu">cd</span> ~/bisque/staging/00-ZmuAoE43wTxByycmaCnvBF</a>
<a class="sourceLine" id="cb23-2" title="2"><span class="ex">rahul@loup</span>:~/bisque/staging/00-ZmuAoE43wTxByycmaCnvBF$ tree </a>
<a class="sourceLine" id="cb23-3" title="3"><span class="ex">.</span></a>
<a class="sourceLine" id="cb23-4" title="4">├── <span class="ex">MetaData.log</span></a>
<a class="sourceLine" id="cb23-5" title="5">├── <span class="ex">MetaData.py</span></a>
<a class="sourceLine" id="cb23-6" title="6">├── <span class="ex">python.log</span></a>
<a class="sourceLine" id="cb23-7" title="7">└── <span class="ex">state00-ZmuAoE43wTxByycmaCnvBF.bq</span></a>
<a class="sourceLine" id="cb23-8" title="8"><span class="ex">0</span> directories, 4 files</a></code></pre></div>
<ul>
<li>Here we can see that the MetaData.log and python.log files are generated</li>
<li>In case of issues these are the log files that we need to look into for detailed error reporting</li>
<li>main log file is the bisque_8088.log file at the ~/bisque home directory</li>
</ul>
<div class="sourceCode" id="cb24"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb24-1" title="1"><span class="ex">13</span>:45:11,996 INFO [bq.root] [admin] POST http://loup.ece.ucsb.edu:8088/module_service/mex/00-ZmuAoE43wTxByycmaCnvBF?view=short</a>
<a class="sourceLine" id="cb24-2" title="2"><span class="ex">13</span>:45:12,001 INFO [bq.module_server] MEX APPEND http://loup.ece.ucsb.edu:8088/module_service/mex/00-ZmuAoE43wTxByycmaCnvBF?view=short</a>
<a class="sourceLine" id="cb24-3" title="3"><span class="ex">13</span>:45:12,205 INFO [bq.engine_service.command_run] SUCCESS Command python MetaData.py http://loup.ece.ucsb.edu:8088/data_service/00-6dpWgEAue2iz8YZcKPHejh http://loup.ece.ucsb.edu:8088/module_service/mex/00-ZmuAoE43wTxByycmaCnvBF admin:00-ZmuAoE43wTxByycmaCnvBF with 0</a>
<a class="sourceLine" id="cb24-4" title="4"><span class="ex">13</span>:45:12,206 INFO [bq.engine_service.command_run] All processes have returned [<span class="st">'finished'</span>]</a>
<a class="sourceLine" id="cb24-5" title="5"><span class="ex">13</span>:45:12,206 INFO [bq.engine_service.command_run] finishing 1 mexes -<span class="op">></span> [{<span class="st">'files'</span>: [<span class="st">'MetaData.py'</span>], <span class="st">'status'</span>: <span class="st">'finished'</span>, <span class="st">'executable'</span>: [<span class="st">'python'</span>, <span class="st">'MetaData.py'</span>, <span class="st">'http://loup.ece.ucsb.edu:8088/data_service/00-6dpWgEAue2iz8YZcKPHejh'</span>, <span class="st">'http://loup.ece.ucsb.edu:8088/module_service/mex/00-ZmuAoE43wTxByycmaCnvBF'</span>, <span class="st">'admin:00-ZmuAoE43wTxByycmaCnvBF'</span>], <span class="st">'initial_dir'</span>: <span class="st">'/home/rahul/repository/github/bisque-dev'</span>, <span class="st">'module_enabled'</span>: <span class="st">'True'</span>, <span class="st">'named_args'</span>: {<span class="st">'bisque_token'</span>: <span class="st">'admin:00-ZmuAoE43wTxByycmaCnvBF'</span>, <span class="st">'image_url'</span>: <span class="st">'http://loup.ece.ucsb.edu:8088/data_service/00-6dpWgEAue2iz8YZcKPHejh'</span>, <span class="st">'mex_url'</span>: <span class="st">'http://loup.ece.ucsb.edu:8088/module_service/mex/00-ZmuAoE43wTxByycmaCnvBF'</span>}, <span class="st">'bisque_token'</span>: <span class="ex">u</span><span class="st">'admin:00-ZmuAoE43wTxByycmaCnvBF'</span>, <span class="st">'environments'</span>: <span class="st">'Staged'</span>, <span class="st">'runtime.staging_base'</span>: <span class="st">'staging/'</span>, <span class="st">'mex_id'</span>: <span class="st">'00-ZmuAoE43wTxByycmaCnvBF'</span>, <span class="st">'runtime.matlab_launcher'</span>: <span class="st">'config-defaults/templates/matlab_launcher_SYS.tmpl'</span>, <span class="st">'arguments'</span>: [], <span class="st">'module_dir'</span>: <span class="st">'/home/rahul/repository/github/bisque-dev'</span>, <span class="st">'staging_path'</span>: <span class="st">'/home/rahul/repository/github/bisque-dev/staging/00-ZmuAoE43wTxByycmaCnvBF'</span>, <span class="st">'iterables'</span>: False, <span class="st">'log_name'</span>: <span class="st">'/home/rahul/repository/github/bisque-dev/staging/00-ZmuAoE43wTxByycmaCnvBF/python.log'</span>, <span class="st">'runtime.matlab_home'</span>: <span class="st">''</span>, <span class="st">'mex_url'</span>: <span class="st">'http://loup.ece.ucsb.edu:8088/module_service/mex/00-ZmuAoE43wTxByycmaCnvBF'</span>, <span class="st">'rundir'</span>: <span class="st">'/home/rahul/repository/github/bisque-dev/staging/00-ZmuAoE43wTxByycmaCnvBF'</span>, <span class="st">'runtime.platforms'</span>: <span class="st">'command'</span>}]</a></code></pre></div>
<ul>
<li>This will show us the COMMAND that was run to execute this module with MEX_URL</li>
</ul>
<div class="sourceCode" id="cb25"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb25-1" title="1"><span class="ex">python</span> MetaData.py \</a>
<a class="sourceLine" id="cb25-2" title="2">http://loup.ece.ucsb.edu:8088/data_service/00-6dpWgEAue2iz8YZcKPHejh <span class="dt">\ </span></a>
<a class="sourceLine" id="cb25-3" title="3"><span class="ex">http</span>://loup.ece.ucsb.edu:8088/module_service/mex/00-ZmuAoE43wTxByycmaCnvBF \</a>
<a class="sourceLine" id="cb25-4" title="4">admin:00-ZmuAoE43wTxByycmaCnvBF</a></code></pre></div>
<ul>
<li>This is the command that we can use to debug and rerun/replay this MEX in order to update the execution result. This is different from running the module again from the web interface since that will produce a new MEX_ID and create another staging folder corresponding to that.</li>
</ul>
</div>
<div id="g.-module-mexui" class="section level3 unnumbered">
<h3>G. Module MEX/UI</h3>
<ul>
<li><p>Click on Browse->mex to go to the Model execution page</p>
<div class="figure">
<img src="img/module_metadata/NavBrowseMex.png" alt="Mex Module" />
<p class="caption">Mex Module</p>
</div>
<div class="figure">
<img src="img/module_metadata/ModuleMexView.png" alt="Mex Browse" />
<p class="caption">Mex Browse</p>
</div></li>
<li>Here we will be able to see the various MEX sessions that were run for all modules under execution</li>
<li><p>We will be able to obtain the MEX_ID and view its state from here by selecting one of the executions of interest.</p>
<div class="figure">
<img src="img/module_metadata/ModuleRunMexView.png" alt="Mex Success Module" />
<p class="caption">Mex Success Module</p>
</div></li>
<li><p>In case we select a module that has errors in it then it would turn out to show the status with messages in red</p>
<div class="figure">
<img src="img/module_metadata/ModuleMexFailure.png" alt="Mex Success Module" />
<p class="caption">Mex Success Module</p>
</div></li>
<li>Now let us go to Browse->dataset and select the file that we ran the module for. Here we will be able to view the Annotation that was added by the Metadata module to this image.
<ul>
<li>Annotation can be visualized using the “Annotations” tab on the right</li>
</ul>
<div class="figure">
<img src="img/module_metadata/DatasetFileMetadataAnnotated.png" alt="Data Annot Module" />
<p class="caption">Data Annot Module</p>
</div>
<ul>
<li>The Model execution runs can be seen in the “Analysis” tab on the right</li>
</ul>
<div class="figure">
<img src="img/module_metadata/DatasetFileMetadataMex.png" alt="Data Mex Module" />
<p class="caption">Data Mex Module</p>
</div></li>
</ul>
<hr />
<div id="further" class="section level4 unnumbered">
<h4>Further</h4>
</div>
<div id="docker-condor-based-modules-require-additional-setup" class="section level4 unnumbered">
<h4>Docker & Condor based modules require additional setup</h4>
<ul>
<li>Install Docker (<a href="https://docs.docker.com/install/linux/docker-ce/ubuntu/" class="uri">https://docs.docker.com/install/linux/docker-ce/ubuntu/</a>)
<ul>
<li>Also go through the post-installation steps</li>
<li>Also install the <a href="https://github.com/nvidia/nvidia-docker/">Nvidia-docker</a> in case you are planning to use GPU based modules or connoisseur services.</li>
</ul></li>
<li>Install Condor (<a href="https://research.cs.wisc.edu/htcondor/ubuntu/" class="uri">https://research.cs.wisc.edu/htcondor/ubuntu/</a>)
<ul>
<li>Understand the configurations as well for master & slave setup</li>
<li><a href="../rancher2_condor">Bisque Condor Setup Instructions</a></li>
</ul>
<pre><code>rahul@bqdev:~$ /etc/init.d/condor restart
[ ok ] Restarting condor (via systemctl): condor.service.
rahul@bqdev:~$ ps -ef | grep condor</code></pre></li>
</ul>
</div>
</div>
</div>
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