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<div id="python-script-wrapper" class="section level2">
<h2><span class="header-section-number">2.3</span> Python Script Wrapper</h2>
<blockquote>
<p><strong>FILENAME: </strong> <code>PythonScriptWrapper.py</code></p>
</blockquote>
<div id="example.-python-script-wrapper" class="section level3 unnumbered">
<h3><em>Example.</em> Python Script Wrapper</h3>
<div id="imports" class="section level4 unnumbered">
<h4>Imports</h4>
<p>The main imports for the <code>PythonScriptWrapper</code> are mostly for logging and communicating with BisQue. In this code snippet, the line <code>from NAME_OF_MODULE import predict_function</code> is importing a prediction function from a single <code>Python</code> file. If multiple functions need to be imported from a source folder, make sure there is an <code>__init__.py</code> or there will be import errors.</p>
<div class="sourceCode" id="cb27"><pre class="sourceCode python"><code class="sourceCode python"><a class="sourceLine" id="cb27-1" title="1"><span class="im">import</span> sys</a>
<a class="sourceLine" id="cb27-2" title="2"><span class="im">import</span> io</a>
<a class="sourceLine" id="cb27-3" title="3"><span class="im">from</span> lxml <span class="im">import</span> etree</a>
<a class="sourceLine" id="cb27-4" title="4"><span class="im">import</span> optparse</a>
<a class="sourceLine" id="cb27-5" title="5"><span class="im">import</span> logging</a>
<a class="sourceLine" id="cb27-6" title="6"></a>
<a class="sourceLine" id="cb27-7" title="7"></a>
<a class="sourceLine" id="cb27-8" title="8"><span class="im">from</span> NAME_OF_MODULE <span class="im">import</span> predict_function</a>
<a class="sourceLine" id="cb27-9" title="9"></a>
<a class="sourceLine" id="cb27-10" title="10"></a>
<a class="sourceLine" id="cb27-11" title="11">logging.basicConfig(filename<span class="op">=</span><span class="st">'PythonScript.log'</span>,filemode<span class="op">=</span><span class="st">'a'</span>,level<span class="op">=</span>logging.DEBUG)</a>
<a class="sourceLine" id="cb27-12" title="12">log <span class="op">=</span> logging.getLogger(<span class="st">'bq.modules'</span>)</a>
<a class="sourceLine" id="cb27-13" title="13"></a>
<a class="sourceLine" id="cb27-14" title="14"></a>
<a class="sourceLine" id="cb27-15" title="15"><span class="im">from</span> bqapi.comm <span class="im">import</span> BQCommError</a>
<a class="sourceLine" id="cb27-16" title="16"><span class="im">from</span> bqapi.comm <span class="im">import</span> BQSession</a></code></pre></div>
</div>
<div id="python-script-wrapper-class" class="section level4 unnumbered">
<h4>Python Script Wrapper Class</h4>
<p>The class contains all of the functions needed to initialize, run, and save the module results back to BisQue as a resource. For instance, if the output is an image, the resource would be of type image and uploaded to BisQue as an image.</p>
<div class="sourceCode" id="cb28"><pre class="sourceCode python"><code class="sourceCode python"><a class="sourceLine" id="cb28-1" title="1"><span class="kw">class</span> PythonScriptWrapper(<span class="bu">object</span>):</a>
<a class="sourceLine" id="cb28-2" title="2"> <span class="kw">def</span> run(<span class="va">self</span>):</a>
<a class="sourceLine" id="cb28-3" title="3"> <span class="co">"""</span></a>
<a class="sourceLine" id="cb28-4" title="4"><span class="co"> Run Python script</span></a>
<a class="sourceLine" id="cb28-5" title="5"><span class="co"> """</span></a>
<a class="sourceLine" id="cb28-6" title="6"> bq <span class="op">=</span> <span class="va">self</span>.bqSession</a>
<a class="sourceLine" id="cb28-7" title="7"> </a>
<a class="sourceLine" id="cb28-8" title="8"> <span class="co"># call script</span></a>
<a class="sourceLine" id="cb28-9" title="9"> outputs <span class="op">=</span> predict_function( bq, log, <span class="op">**</span><span class="va">self</span>.options.__dict__ )</a>
<a class="sourceLine" id="cb28-10" title="10"> </a>
<a class="sourceLine" id="cb28-11" title="11"> <span class="co"># save output back to BisQue</span></a>
<a class="sourceLine" id="cb28-12" title="12"> <span class="cf">for</span> output <span class="kw">in</span> outputs:</a>
<a class="sourceLine" id="cb28-13" title="13"> <span class="va">self</span>.output_resources.append(output)</a>
<a class="sourceLine" id="cb28-14" title="14"> </a>
<a class="sourceLine" id="cb28-15" title="15"> <span class="kw">def</span> setup(<span class="va">self</span>):</a>
<a class="sourceLine" id="cb28-16" title="16"> <span class="co">"""</span></a>
<a class="sourceLine" id="cb28-17" title="17"><span class="co"> Pre-run initialization</span></a>
<a class="sourceLine" id="cb28-18" title="18"><span class="co"> """</span></a>
<a class="sourceLine" id="cb28-19" title="19"> <span class="va">self</span>.bqSession.update_mex(<span class="st">'Initializing...'</span>)</a>
<a class="sourceLine" id="cb28-20" title="20"> <span class="va">self</span>.mex_parameter_parser(<span class="va">self</span>.bqSession.mex.xmltree)</a>
<a class="sourceLine" id="cb28-21" title="21"> <span class="va">self</span>.output_resources <span class="op">=</span> []</a>
<a class="sourceLine" id="cb28-22" title="22"></a>
<a class="sourceLine" id="cb28-23" title="23"> <span class="kw">def</span> teardown(<span class="va">self</span>):</a>
<a class="sourceLine" id="cb28-24" title="24"> <span class="co">"""</span></a>
<a class="sourceLine" id="cb28-25" title="25"><span class="co"> Post the results to the mex xml</span></a>
<a class="sourceLine" id="cb28-26" title="26"><span class="co"> """</span></a>
<a class="sourceLine" id="cb28-27" title="27"> <span class="va">self</span>.bqSession.update_mex( <span class="st">'Returning results'</span>)</a>
<a class="sourceLine" id="cb28-28" title="28"></a>
<a class="sourceLine" id="cb28-29" title="29"> outputTag <span class="op">=</span> etree.Element(<span class="st">'tag'</span>, name <span class="op">=</span><span class="st">'outputs'</span>)</a>
<a class="sourceLine" id="cb28-30" title="30"> <span class="cf">for</span> r_xml <span class="kw">in</span> <span class="va">self</span>.output_resources:</a>
<a class="sourceLine" id="cb28-31" title="31"> <span class="cf">if</span> <span class="bu">isinstance</span>(r_xml, <span class="bu">basestring</span>):</a>
<a class="sourceLine" id="cb28-32" title="32"> r_xml <span class="op">=</span> etree.fromstring(r_xml) </a>
<a class="sourceLine" id="cb28-33" title="33"> res_type <span class="op">=</span> r_xml.get(<span class="st">'type'</span>, <span class="va">None</span>) <span class="kw">or</span> r_xml.get(<span class="st">'resource_type'</span>, <span class="va">None</span>) <span class="kw">or</span> r_xml.tag</a>
<a class="sourceLine" id="cb28-34" title="34"> <span class="co"># append reference to output</span></a>
<a class="sourceLine" id="cb28-35" title="35"> <span class="cf">if</span> res_type <span class="kw">in</span> [<span class="st">'table'</span>, <span class="st">'image'</span>]:</a>
<a class="sourceLine" id="cb28-36" title="36"> outputTag.append(r_xml)</a>
<a class="sourceLine" id="cb28-37" title="37"> <span class="co">#etree.SubElement(outputTag, 'tag', name='output_table' if res_type=='table' else 'output_image', type=res_type, value=r_xml.get('uri',''))</span></a>
<a class="sourceLine" id="cb28-38" title="38"> <span class="cf">else</span>:</a>
<a class="sourceLine" id="cb28-39" title="39"> outputTag.append(r_xml)</a>
<a class="sourceLine" id="cb28-40" title="40"> <span class="co">#etree.SubElement(outputTag, r_xml.tag, name=r_xml.get('name', '_'), type=r_xml.get('type', 'string'), value=r_xml.get('value', ''))</span></a>
<a class="sourceLine" id="cb28-41" title="41"> <span class="va">self</span>.bqSession.finish_mex(tags<span class="op">=</span>[outputTag])</a>
<a class="sourceLine" id="cb28-42" title="42"></a>
<a class="sourceLine" id="cb28-43" title="43"> <span class="kw">def</span> mex_parameter_parser(<span class="va">self</span>, mex_xml):</a>
<a class="sourceLine" id="cb28-44" title="44"> <span class="co">"""</span></a>
<a class="sourceLine" id="cb28-45" title="45"><span class="co"> Parses input of the xml and add it to options attribute (unless already set)</span></a>
<a class="sourceLine" id="cb28-46" title="46"></a>
<a class="sourceLine" id="cb28-47" title="47"><span class="co"> @param: mex_xml</span></a>
<a class="sourceLine" id="cb28-48" title="48"><span class="co"> """</span></a>
<a class="sourceLine" id="cb28-49" title="49"> <span class="co"># inputs are all non-"script_params" under "inputs" and all params under "script_params"</span></a>
<a class="sourceLine" id="cb28-50" title="50"> mex_inputs <span class="op">=</span> mex_xml.xpath(<span class="st">'tag[@name="inputs"]/tag[@name!="script_params"] | tag[@name="inputs"]/tag[@name="script_params"]/tag'</span>)</a>
<a class="sourceLine" id="cb28-51" title="51"> <span class="cf">if</span> mex_inputs:</a>
<a class="sourceLine" id="cb28-52" title="52"> <span class="cf">for</span> tag <span class="kw">in</span> mex_inputs:</a>
<a class="sourceLine" id="cb28-53" title="53"> <span class="cf">if</span> tag.tag <span class="op">==</span> <span class="st">'tag'</span> <span class="kw">and</span> tag.get(<span class="st">'type'</span>, <span class="st">''</span>) <span class="op">!=</span> <span class="st">'system-input'</span>: <span class="co">#skip system input values</span></a>
<a class="sourceLine" id="cb28-54" title="54"> <span class="cf">if</span> <span class="kw">not</span> <span class="bu">getattr</span>(<span class="va">self</span>.options,tag.get(<span class="st">'name'</span>, <span class="st">''</span>), <span class="va">None</span>):</a>
<a class="sourceLine" id="cb28-55" title="55"> log.debug(<span class="st">'Set options with </span><span class="sc">%s</span><span class="st"> as </span><span class="sc">%s</span><span class="st">'</span><span class="op">%</span>(tag.get(<span class="st">'name'</span>,<span class="st">''</span>),tag.get(<span class="st">'value'</span>,<span class="st">''</span>)))</a>
<a class="sourceLine" id="cb28-56" title="56"> <span class="bu">setattr</span>(<span class="va">self</span>.options,tag.get(<span class="st">'name'</span>,<span class="st">''</span>),tag.get(<span class="st">'value'</span>,<span class="st">''</span>))</a>
<a class="sourceLine" id="cb28-57" title="57"> <span class="cf">else</span>:</a>
<a class="sourceLine" id="cb28-58" title="58"> log.debug(<span class="st">'No Inputs Found on MEX!'</span>)</a>
<a class="sourceLine" id="cb28-59" title="59"></a>
<a class="sourceLine" id="cb28-60" title="60"> <span class="kw">def</span> validate_input(<span class="va">self</span>):</a>
<a class="sourceLine" id="cb28-61" title="61"> <span class="co">"""</span></a>
<a class="sourceLine" id="cb28-62" title="62"><span class="co"> Check to see if a mex with token or user with password was provided.</span></a>
<a class="sourceLine" id="cb28-63" title="63"></a>
<a class="sourceLine" id="cb28-64" title="64"><span class="co"> @return True is returned if validation credention was provided else</span></a>
<a class="sourceLine" id="cb28-65" title="65"><span class="co"> False is returned</span></a>
<a class="sourceLine" id="cb28-66" title="66"><span class="co"> """</span></a>
<a class="sourceLine" id="cb28-67" title="67"> <span class="cf">if</span> (<span class="va">self</span>.options.mexURL <span class="kw">and</span> <span class="va">self</span>.options.token): <span class="co">#run module through engine service</span></a>
<a class="sourceLine" id="cb28-68" title="68"> <span class="cf">return</span> <span class="va">True</span></a>
<a class="sourceLine" id="cb28-69" title="69"></a>
<a class="sourceLine" id="cb28-70" title="70"> <span class="cf">if</span> (<span class="va">self</span>.options.user <span class="kw">and</span> <span class="va">self</span>.options.pwd <span class="kw">and</span> <span class="va">self</span>.options.root): <span class="co">#run module locally (note: to test module)</span></a>
<a class="sourceLine" id="cb28-71" title="71"> <span class="cf">return</span> <span class="va">True</span></a>
<a class="sourceLine" id="cb28-72" title="72"></a>
<a class="sourceLine" id="cb28-73" title="73"> log.debug(<span class="st">'Insufficient options or arguments to start this module'</span>)</a>
<a class="sourceLine" id="cb28-74" title="74"> <span class="cf">return</span> <span class="va">False</span></a></code></pre></div>
</div>
<div id="main-function" class="section level4 unnumbered">
<h4>Main Function</h4>
<p>The main function enables the communication between BisQue and the module. For example, when a module is run under a user, we need to make sure that the unique ID is registered with the user.</p>
<div class="sourceCode" id="cb29"><pre class="sourceCode python"><code class="sourceCode python"><a class="sourceLine" id="cb29-1" title="1"><span class="kw">def</span> main(<span class="va">self</span>):</a>
<a class="sourceLine" id="cb29-2" title="2"> parser <span class="op">=</span> optparse.OptionParser()</a>
<a class="sourceLine" id="cb29-3" title="3"> parser.add_option(<span class="st">'--mex_url'</span> , dest<span class="op">=</span><span class="st">"mexURL"</span>)</a>
<a class="sourceLine" id="cb29-4" title="4"> parser.add_option(<span class="st">'--module_dir'</span> , dest<span class="op">=</span><span class="st">"modulePath"</span>)</a>
<a class="sourceLine" id="cb29-5" title="5"> parser.add_option(<span class="st">'--staging_path'</span> , dest<span class="op">=</span><span class="st">"stagingPath"</span>)</a>
<a class="sourceLine" id="cb29-6" title="6"> parser.add_option(<span class="st">'--bisque_token'</span> , dest<span class="op">=</span><span class="st">"token"</span>)</a>
<a class="sourceLine" id="cb29-7" title="7"> parser.add_option(<span class="st">'--user'</span> , dest<span class="op">=</span><span class="st">"user"</span>)</a>
<a class="sourceLine" id="cb29-8" title="8"> parser.add_option(<span class="st">'--pwd'</span> , dest<span class="op">=</span><span class="st">"pwd"</span>)</a>
<a class="sourceLine" id="cb29-9" title="9"> parser.add_option(<span class="st">'--root'</span> , dest<span class="op">=</span><span class="st">"root"</span>)</a>
<a class="sourceLine" id="cb29-10" title="10"> </a>
<a class="sourceLine" id="cb29-11" title="11"> (options, args) <span class="op">=</span> parser.parse_args()</a>
<a class="sourceLine" id="cb29-12" title="12"></a>
<a class="sourceLine" id="cb29-13" title="13"> fh <span class="op">=</span> logging.FileHandler(<span class="st">'scriptrun.log'</span>, mode<span class="op">=</span><span class="st">'a'</span>)</a>
<a class="sourceLine" id="cb29-14" title="14"> fh.setLevel(logging.DEBUG)</a>
<a class="sourceLine" id="cb29-15" title="15"> formatter <span class="op">=</span> logging.Formatter(<span class="st">'[</span><span class="sc">%(asctime)s</span><span class="st">] </span><span class="sc">%(levelname)8s</span><span class="st"> --- </span><span class="sc">%(message)s</span><span class="st"> '</span> <span class="op">+</span></a>
<a class="sourceLine" id="cb29-16" title="16"> <span class="st">'(</span><span class="sc">%(filename)s</span><span class="st">:</span><span class="sc">%(lineno)s</span><span class="st">)'</span>,datefmt<span class="op">=</span><span class="st">'%Y-%m-</span><span class="sc">%d</span><span class="st"> %H:%M:%S'</span>)</a>
<a class="sourceLine" id="cb29-17" title="17"> fh.setFormatter(formatter)</a>
<a class="sourceLine" id="cb29-18" title="18"> log.addHandler(fh)</a>
<a class="sourceLine" id="cb29-19" title="19"></a>
<a class="sourceLine" id="cb29-20" title="20"> <span class="cf">try</span>: <span class="co">#pull out the mex</span></a>
<a class="sourceLine" id="cb29-21" title="21"></a>
<a class="sourceLine" id="cb29-22" title="22"> <span class="cf">if</span> <span class="kw">not</span> options.mexURL:</a>
<a class="sourceLine" id="cb29-23" title="23"> options.mexURL <span class="op">=</span> sys.argv[<span class="op">-</span><span class="dv">2</span>]</a>
<a class="sourceLine" id="cb29-24" title="24"> <span class="cf">if</span> <span class="kw">not</span> options.token:</a>
<a class="sourceLine" id="cb29-25" title="25"> options.token <span class="op">=</span> sys.argv[<span class="op">-</span><span class="dv">1</span>]</a>
<a class="sourceLine" id="cb29-26" title="26"></a>
<a class="sourceLine" id="cb29-27" title="27"> <span class="cf">except</span> <span class="pp">IndexError</span>: <span class="co">#no argv were set</span></a>
<a class="sourceLine" id="cb29-28" title="28"> <span class="cf">pass</span></a>
<a class="sourceLine" id="cb29-29" title="29"></a>
<a class="sourceLine" id="cb29-30" title="30"> <span class="cf">if</span> <span class="kw">not</span> options.stagingPath:</a>
<a class="sourceLine" id="cb29-31" title="31"> options.stagingPath <span class="op">=</span> <span class="st">''</span></a>
<a class="sourceLine" id="cb29-32" title="32"></a>
<a class="sourceLine" id="cb29-33" title="33"> log.info(<span class="st">'</span><span class="ch">\n\n</span><span class="st">PARAMS : </span><span class="sc">%s</span><span class="st"> </span><span class="ch">\n\n</span><span class="st"> Options: </span><span class="sc">%s</span><span class="st">'</span> <span class="op">%</span> (args, options))</a>
<a class="sourceLine" id="cb29-34" title="34"> <span class="va">self</span>.options <span class="op">=</span> options</a>
<a class="sourceLine" id="cb29-35" title="35"></a>
<a class="sourceLine" id="cb29-36" title="36"> <span class="cf">if</span> <span class="va">self</span>.validate_input():</a>
<a class="sourceLine" id="cb29-37" title="37"></a>
<a class="sourceLine" id="cb29-38" title="38"> <span class="co">#initalizes if user and password are provided</span></a>
<a class="sourceLine" id="cb29-39" title="39"> <span class="cf">if</span> (<span class="va">self</span>.options.user <span class="kw">and</span> <span class="va">self</span>.options.pwd <span class="kw">and</span> <span class="va">self</span>.options.root):</a>
<a class="sourceLine" id="cb29-40" title="40"> <span class="va">self</span>.bqSession <span class="op">=</span> BQSession().init_local( <span class="va">self</span>.options.user, <span class="va">self</span>.options.pwd, bisque_root<span class="op">=</span><span class="va">self</span>.options.root)</a>
<a class="sourceLine" id="cb29-41" title="41"> <span class="va">self</span>.options.mexURL <span class="op">=</span> <span class="va">self</span>.bqSession.mex.uri</a>
<a class="sourceLine" id="cb29-42" title="42"></a>
<a class="sourceLine" id="cb29-43" title="43"> <span class="co">#initalizes if mex and mex token is provided</span></a>
<a class="sourceLine" id="cb29-44" title="44"> <span class="cf">elif</span> (<span class="va">self</span>.options.mexURL <span class="kw">and</span> <span class="va">self</span>.options.token):</a>
<a class="sourceLine" id="cb29-45" title="45"> <span class="va">self</span>.bqSession <span class="op">=</span> BQSession().init_mex(<span class="va">self</span>.options.mexURL, <span class="va">self</span>.options.token)</a>
<a class="sourceLine" id="cb29-46" title="46"></a>
<a class="sourceLine" id="cb29-47" title="47"> <span class="cf">else</span>:</a>
<a class="sourceLine" id="cb29-48" title="48"> <span class="cf">raise</span> ScriptError(<span class="st">'Insufficient options or arguments to start this module'</span>)</a>
<a class="sourceLine" id="cb29-49" title="49"></a>
<a class="sourceLine" id="cb29-50" title="50"> <span class="cf">try</span>:</a>
<a class="sourceLine" id="cb29-51" title="51"> <span class="va">self</span>.setup()</a>
<a class="sourceLine" id="cb29-52" title="52"> <span class="cf">except</span> <span class="pp">Exception</span> <span class="im">as</span> e:</a>
<a class="sourceLine" id="cb29-53" title="53"> log.exception(<span class="st">"Exception during setup"</span>)</a>
<a class="sourceLine" id="cb29-54" title="54"> <span class="va">self</span>.bqSession.fail_mex(msg <span class="op">=</span> <span class="st">"Exception during setup: </span><span class="sc">%s</span><span class="st">"</span> <span class="op">%</span> <span class="bu">str</span>(e))</a>
<a class="sourceLine" id="cb29-55" title="55"> <span class="cf">return</span></a>
<a class="sourceLine" id="cb29-56" title="56"></a>
<a class="sourceLine" id="cb29-57" title="57"> <span class="cf">try</span>:</a>
<a class="sourceLine" id="cb29-58" title="58"> <span class="va">self</span>.run()</a>
<a class="sourceLine" id="cb29-59" title="59"> <span class="cf">except</span> (<span class="pp">Exception</span>, ScriptError) <span class="im">as</span> e:</a>
<a class="sourceLine" id="cb29-60" title="60"> log.exception(<span class="st">"Exception during run"</span>)</a>
<a class="sourceLine" id="cb29-61" title="61"> <span class="va">self</span>.bqSession.fail_mex(msg <span class="op">=</span> <span class="st">"Exception during run: </span><span class="sc">%s</span><span class="st">"</span> <span class="op">%</span> <span class="bu">str</span>(e))</a>
<a class="sourceLine" id="cb29-62" title="62"> <span class="cf">return</span></a>
<a class="sourceLine" id="cb29-63" title="63"></a>
<a class="sourceLine" id="cb29-64" title="64"> <span class="cf">try</span>:</a>
<a class="sourceLine" id="cb29-65" title="65"> <span class="va">self</span>.teardown()</a>
<a class="sourceLine" id="cb29-66" title="66"> <span class="cf">except</span> (<span class="pp">Exception</span>, ScriptError) <span class="im">as</span> e:</a>
<a class="sourceLine" id="cb29-67" title="67"> log.exception(<span class="st">"Exception during teardown"</span>)</a>
<a class="sourceLine" id="cb29-68" title="68"> <span class="va">self</span>.bqSession.fail_mex(msg <span class="op">=</span> <span class="st">"Exception during teardown: </span><span class="sc">%s</span><span class="st">"</span> <span class="op">%</span> <span class="bu">str</span>(e))</a>
<a class="sourceLine" id="cb29-69" title="69"> <span class="cf">return</span></a>
<a class="sourceLine" id="cb29-70" title="70"> </a>
<a class="sourceLine" id="cb29-71" title="71"> <span class="va">self</span>.bqSession.close()</a>
<a class="sourceLine" id="cb29-72" title="72"></a>
<a class="sourceLine" id="cb29-73" title="73"><span class="cf">if</span> <span class="va">__name__</span><span class="op">==</span><span class="st">"__main__"</span>:</a>
<a class="sourceLine" id="cb29-74" title="74"> PythonScriptWrapper().main()</a></code></pre></div>
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