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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/libsonlib">Debian Med / libsonlib</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/libsonlib/-/commit/e99bb276b45fbbaa46bf85b01acc8dce9c95652c">e99bb276</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-06-23T16:10:37+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include sonLib_daemonize.py into missing-sources
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<h4>2 changed files:</h4>
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debian/missing-sources/sonLib_daemonize.py
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debian/source/include-binaries
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<h4>Changes:</h4>
<li id="9c397f49010613099dc4b72bd47669ce5eff78e7">
<a href="https://salsa.debian.org/med-team/libsonlib/-/commit/e99bb276b45fbbaa46bf85b01acc8dce9c95652c#9c397f49010613099dc4b72bd47669ce5eff78e7"><strong>debian/missing-sources/sonLib_daemonize.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Glenn Hickey 2011</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#Released under the MIT license, see LICENSE.txt</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">launch a command as a daemon. </span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">mostly copied from (and see for comments & explanation):</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">########################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (C) 2005 Chad J. Schroeder</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">http://code.activestate.com/recipes/278731/</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">Disk And Execution MONitor (Daemon)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">Configurable daemon behaviors:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> 1.) The current working directory set to the "/" directory.</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> 2.) The current file creation mode mask set to 0.</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> 3.) Close all open files (1024). </span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> 4.) Redirect standard I/O streams to "/dev/null".</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;">A failed call to fork() now raises an exception.</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;">References:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> 1) Advanced Programming in the Unix Environment: W. Richard Stevens</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> 2) Unix Programming Frequently Asked Questions:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> http://www.erlenstar.demon.co.uk/unix/faq_toc.html</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">########################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;">handy to break out of a jobTree dependence (which the regular </span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">os.system and subprocess.Popen can't do on their own)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;">takes single argument: the command line to execute</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">be careful: the command line is not executed in a shell</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;">example: sonLib_daemonize.py 'ktserver -port 26'</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">resource</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">signal</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sonLib.bioio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">system</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Default daemon parameters.</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># File mode creation mask of the daemon.</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># use sonLib.bioio.spawnDaemon() for a python interface</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="n" style="color: #333;">UMASK</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Default working directory for the daemon.</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">WORKDIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/"</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Default maximum for the number of available file descriptors.</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="n" style="color: #333;">MAXFD</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The standard I/O file descriptors are redirected to /dev/null by default.</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="s" style="color: #d14;">"devnull"</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">REDIRECT_TO</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">REDIRECT_TO</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/dev/null"</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s: Wrong number of arguments"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">fork</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">_exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">setsid</span><span class="p">()</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> </span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIGHUP</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIG_IGN</span><span class="p">)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">umask</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">fork</span><span class="p">()</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">_exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">maxfd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">getrlimit</span><span class="p">(</span><span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">RLIMIT_NOFILE</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxfd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">RLIM_INFINITY</span><span class="p">):</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">maxfd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAXFD</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Iterate through and close all file descriptors.</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">maxfd</span><span class="p">):</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># ERROR, fd wasn't open to begin with (ignored)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Redirect the standard I/O file descriptors to the specified file. Since</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">REDIRECT_TO</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">O_RDWR</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># standard input (0)</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Duplicate standard input to standard output and standard error.</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">dup2</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># standard output (1)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">dup2</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># standard error (2)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> </span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">retVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(),</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">bufsize</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">retVal</span><span class="p">)</span> </span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/missing-sources/sonLib_daemonize.py</span></pre>
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