Mercurial > repos > yating-l > hubarchivecreator
annotate doc/_build/html/_modules/hubArchiveCreator.html @ 85:a65e52152476 draft default tip
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
| author | yating-l |
|---|---|
| date | Mon, 06 Nov 2017 13:13:01 -0500 |
| parents | 4ced8f116509 |
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| rev | line source |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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2 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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4 |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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5 <html xmlns="http://www.w3.org/1999/xhtml"> |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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6 <head> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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8 |
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9 <title>hubArchiveCreator — HubArchiveCreator 2.3 documentation</title> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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10 |
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4ced8f116509
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11 <link rel="stylesheet" href="../_static/classic.css" type="text/css" /> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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12 <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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13 |
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14 <script type="text/javascript"> |
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15 var DOCUMENTATION_OPTIONS = { |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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16 URL_ROOT: '../', |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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17 VERSION: '2.3', |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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18 COLLAPSE_INDEX: false, |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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19 FILE_SUFFIX: '.html', |
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20 HAS_SOURCE: true |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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21 }; |
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4ced8f116509
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22 </script> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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23 <script type="text/javascript" src="../_static/jquery.js"></script> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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24 <script type="text/javascript" src="../_static/underscore.js"></script> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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25 <script type="text/javascript" src="../_static/doctools.js"></script> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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26 <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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27 <link rel="index" title="Index" href="../genindex.html" /> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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28 <link rel="search" title="Search" href="../search.html" /> |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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29 <link rel="top" title="HubArchiveCreator 2.3 documentation" href="../index.html" /> |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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30 <link rel="up" title="Module code" href="index.html" /> |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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31 </head> |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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32 <body role="document"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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33 <div class="related" role="navigation" aria-label="related navigation"> |
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34 <h3>Navigation</h3> |
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35 <ul> |
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36 <li class="right" style="margin-right: 10px"> |
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4ced8f116509
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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37 <a href="../genindex.html" title="General Index" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
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38 accesskey="I">index</a></li> |
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39 <li class="right" > |
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40 <a href="../py-modindex.html" title="Python Module Index" |
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41 >modules</a> |</li> |
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42 <li class="nav-item nav-item-0"><a href="../index.html">HubArchiveCreator 2.3 documentation</a> »</li> |
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43 <li class="nav-item nav-item-1"><a href="index.html" accesskey="U">Module code</a> »</li> |
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44 </ul> |
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45 </div> |
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46 |
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47 <div class="document"> |
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48 <div class="documentwrapper"> |
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49 <div class="bodywrapper"> |
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50 <div class="body" role="main"> |
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51 |
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52 <h1>Source code for hubArchiveCreator</h1><div class="highlight"><pre> |
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53 <span></span><span class="ch">#!/usr/bin/python</span> |
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54 <span class="c1"># -*- coding: utf8 -*-</span> |
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55 |
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56 <span class="sd">"""</span> |
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57 <span class="sd">This Galaxy tool permits to prepare your files to be ready for</span> |
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58 <span class="sd">Assembly Hub visualization.</span> |
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59 <span class="sd">Program test arguments:</span> |
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60 <span class="sd">hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html</span> |
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61 <span class="sd">"""</span> |
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62 |
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63 <span class="kn">import</span> <span class="nn">argparse</span> |
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64 <span class="kn">import</span> <span class="nn">collections</span> |
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65 <span class="kn">import</span> <span class="nn">json</span> |
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66 <span class="kn">import</span> <span class="nn">logging</span> |
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67 <span class="kn">import</span> <span class="nn">os</span> |
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68 <span class="kn">import</span> <span class="nn">sys</span> |
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69 |
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70 <span class="c1"># Internal dependencies</span> |
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71 <span class="kn">from</span> <span class="nn">Bam</span> <span class="k">import</span> <span class="n">Bam</span> |
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72 <span class="kn">from</span> <span class="nn">BedSimpleRepeats</span> <span class="k">import</span> <span class="n">BedSimpleRepeats</span> |
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73 <span class="kn">from</span> <span class="nn">Bed</span> <span class="k">import</span> <span class="n">Bed</span> |
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74 <span class="kn">from</span> <span class="nn">BigWig</span> <span class="k">import</span> <span class="n">BigWig</span> |
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75 <span class="kn">from</span> <span class="nn">util.Fasta</span> <span class="k">import</span> <span class="n">Fasta</span> |
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76 <span class="kn">from</span> <span class="nn">util.Filters</span> <span class="k">import</span> <span class="n">TraceBackFormatter</span> |
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77 <span class="kn">from</span> <span class="nn">Gff3</span> <span class="k">import</span> <span class="n">Gff3</span> |
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78 <span class="kn">from</span> <span class="nn">Gtf</span> <span class="k">import</span> <span class="n">Gtf</span> |
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79 <span class="kn">from</span> <span class="nn">Psl</span> <span class="k">import</span> <span class="n">Psl</span> |
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80 <span class="kn">from</span> <span class="nn">TrackHub</span> <span class="k">import</span> <span class="n">TrackHub</span> |
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81 |
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82 <span class="c1"># TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort</span> |
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83 |
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84 |
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85 <span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="n">argv</span><span class="p">):</span> |
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86 <span class="c1"># Command Line parsing init</span> |
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87 <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s1">'Create a foo.txt inside the given folder.'</span><span class="p">)</span> |
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88 |
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89 <span class="c1"># Reference genome mandatory</span> |
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90 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-f'</span><span class="p">,</span> <span class="s1">'--fasta'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Fasta file of the reference genome'</span><span class="p">)</span> |
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91 |
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92 <span class="c1"># GFF3 Management</span> |
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93 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--gff3'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'GFF3 format'</span><span class="p">)</span> |
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94 |
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95 <span class="c1"># GTF Management</span> |
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96 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--gtf'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'GTF format'</span><span class="p">)</span> |
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97 |
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98 <span class="c1"># Bed4+12 (TrfBig)</span> |
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99 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--bedSimpleRepeats'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Bed4+12 format, using simpleRepeats.as'</span><span class="p">)</span> |
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100 |
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101 <span class="c1"># Generic Bed (Blastx transformed to bed)</span> |
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102 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--bed'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Bed generic format'</span><span class="p">)</span> |
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103 |
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104 <span class="c1"># BigWig Management</span> |
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105 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--bigwig'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'BigWig format'</span><span class="p">)</span> |
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106 |
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107 <span class="c1"># Bam Management</span> |
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108 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--bam'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Bam format'</span><span class="p">)</span> |
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109 |
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110 <span class="c1"># Psl Management</span> |
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111 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--psl'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Psl format'</span><span class="p">)</span> |
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112 |
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113 <span class="c1"># TODO: Check if the running directory can have issues if we run the tool outside</span> |
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114 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-d'</span><span class="p">,</span> <span class="s1">'--directory'</span><span class="p">,</span> |
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115 <span class="n">help</span><span class="o">=</span><span class="s1">'Running tool directory, where to find the templates. Default is running directory'</span><span class="p">)</span> |
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116 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-u'</span><span class="p">,</span> <span class="s1">'--ucsc_tools_path'</span><span class="p">,</span> |
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117 <span class="n">help</span><span class="o">=</span><span class="s1">'Directory where to find the executables needed to run this tool'</span><span class="p">)</span> |
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118 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-e'</span><span class="p">,</span> <span class="s1">'--extra_files_path'</span><span class="p">,</span> |
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119 <span class="n">help</span><span class="o">=</span><span class="s1">'Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive'</span><span class="p">)</span> |
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120 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-o'</span><span class="p">,</span> <span class="s1">'--output'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Name of the HTML summarizing the content of the Track Hub Archive'</span><span class="p">)</span> |
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121 |
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122 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-j'</span><span class="p">,</span> <span class="s1">'--data_json'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Json containing the metadata of the inputs'</span><span class="p">)</span> |
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123 |
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124 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--user_email'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Email of the user who launched the Hub Archive Creation'</span><span class="p">)</span> |
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125 |
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126 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--genome_name'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'UCSC Genome Browser assembly ID'</span><span class="p">)</span> |
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127 |
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128 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--debug_mode'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'store_true'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Allow more details about the errors'</span><span class="p">)</span> |
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129 |
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130 <span class="c1"># Begin init variables</span> |
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131 |
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132 <span class="n">toolDirectory</span> <span class="o">=</span> <span class="s1">'.'</span> |
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133 <span class="n">extra_files_path</span> <span class="o">=</span> <span class="s1">'.'</span> |
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134 |
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135 <span class="c1"># Get the args passed in parameter</span> |
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136 <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span> |
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137 |
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138 <span class="n">extra_files_path</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">extra_files_path</span> |
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139 <span class="n">toolDirectory</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">directory</span> |
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140 |
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141 <span class="c1">#### Logging management ####</span> |
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142 <span class="c1"># If we are in Debug mode, also print in stdout the debug dump</span> |
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144 <span class="n">configure_logger</span><span class="p">(</span><span class="n">extra_files_path</span><span class="o">=</span><span class="n">extra_files_path</span><span class="p">,</span> <span class="n">debug</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">debug_mode</span><span class="p">)</span> |
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146 <span class="c1">#### END Logging management ####</span> |
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148 <span class="n">array_inputs_reference_genome</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">fasta</span><span class="p">)</span> |
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149 |
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150 <span class="c1"># TODO: Replace these with the object Fasta</span> |
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151 <span class="n">input_fasta_file</span> <span class="o">=</span> <span class="n">array_inputs_reference_genome</span><span class="p">[</span><span class="s2">"false_path"</span><span class="p">]</span> |
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152 <span class="n">input_fasta_file_name</span> <span class="o">=</span> <span class="n">sanitize_name_input</span><span class="p">(</span><span class="n">array_inputs_reference_genome</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span> |
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153 <span class="n">genome_name</span> <span class="o">=</span> <span class="n">sanitize_name_input</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">genome_name</span><span class="p">)</span> |
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154 |
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155 <span class="n">reference_genome</span> <span class="o">=</span> <span class="n">Fasta</span><span class="p">(</span><span class="n">input_fasta_file</span><span class="p">,</span> |
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156 <span class="n">input_fasta_file_name</span><span class="p">,</span> <span class="n">genome_name</span><span class="p">)</span> |
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157 |
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158 <span class="n">user_email</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">user_email</span> |
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159 |
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160 |
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161 <span class="c1"># TODO: Use a class to have a better management of the structure of these inputs</span> |
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162 <span class="c1"># These inputs are populated in the Galaxy Wrapper xml and are in this format:</span> |
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163 <span class="c1"># ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]</span> |
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164 <span class="c1"># EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}</span> |
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165 <span class="n">array_inputs_bam</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">bam</span> |
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166 <span class="n">array_inputs_bed_generic</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">bed</span> |
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167 <span class="n">array_inputs_bed_simple_repeats</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">bedSimpleRepeats</span> |
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168 <span class="n">array_inputs_bigwig</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">bigwig</span> |
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169 <span class="n">array_inputs_gff3</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">gff3</span> |
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170 <span class="n">array_inputs_gtf</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">gtf</span> |
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171 <span class="n">array_inputs_psl</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">psl</span> |
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172 |
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173 <span class="n">outputFile</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">output</span> |
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174 |
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175 <span class="n">json_inputs_data</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">data_json</span> |
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176 |
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177 <span class="n">inputs_data</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">json_inputs_data</span><span class="p">)</span> |
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178 <span class="c1"># We remove the spaces in ["name"] of inputs_data</span> |
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179 <span class="n">sanitize_name_inputs</span><span class="p">(</span><span class="n">inputs_data</span><span class="p">)</span> |
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180 |
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181 <span class="c1"># TODO: Check here all the binaries / tools we need. Exception if missing</span> |
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182 |
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183 <span class="c1"># Create the Track Hub folder</span> |
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184 <span class="n">trackHub</span> <span class="o">=</span> <span class="n">TrackHub</span><span class="p">(</span><span class="n">reference_genome</span><span class="p">,</span> <span class="n">user_email</span><span class="p">,</span> <span class="n">outputFile</span><span class="p">,</span> <span class="n">extra_files_path</span><span class="p">,</span> <span class="n">toolDirectory</span><span class="p">)</span> |
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185 |
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186 <span class="n">all_datatype_dictionary</span> <span class="o">=</span> <span class="p">{}</span> |
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187 |
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188 <span class="k">for</span> <span class="p">(</span><span class="n">inputs</span><span class="p">,</span> <span class="n">datatype_class</span><span class="p">)</span> <span class="ow">in</span> <span class="p">[</span> |
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189 <span class="p">(</span><span class="n">array_inputs_bam</span><span class="p">,</span> <span class="n">Bam</span><span class="p">),</span> |
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190 <span class="p">(</span><span class="n">array_inputs_bed_generic</span><span class="p">,</span> <span class="n">Bed</span><span class="p">),</span> |
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191 <span class="p">(</span><span class="n">array_inputs_bigwig</span><span class="p">,</span> <span class="n">BigWig</span><span class="p">),</span> |
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192 <span class="p">(</span><span class="n">array_inputs_bed_simple_repeats</span><span class="p">,</span> <span class="n">BedSimpleRepeats</span><span class="p">),</span> |
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193 <span class="p">(</span><span class="n">array_inputs_gff3</span><span class="p">,</span> <span class="n">Gff3</span><span class="p">),</span> |
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194 <span class="p">(</span><span class="n">array_inputs_gtf</span><span class="p">,</span> <span class="n">Gtf</span><span class="p">),</span> |
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195 <span class="p">(</span><span class="n">array_inputs_psl</span><span class="p">,</span> <span class="n">Psl</span><span class="p">)]:</span> |
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196 <span class="k">if</span> <span class="n">inputs</span><span class="p">:</span> |
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197 <span class="n">all_datatype_dictionary</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">create_ordered_datatype_objects</span><span class="p">(</span><span class="n">datatype_class</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">inputs_data</span><span class="p">))</span> |
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198 |
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199 <span class="c1"># Create Ordered Dictionary to add the tracks in the tool form order</span> |
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200 <span class="n">all_datatype_ordered_dictionary</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">(</span><span class="n">all_datatype_dictionary</span><span class="p">)</span> |
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201 |
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202 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"----- End of all_datatype_dictionary processing -----"</span><span class="p">)</span> |
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203 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"all_datatype_ordered_dictionary keys are: </span><span class="si">{0}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">all_datatype_ordered_dictionary</span><span class="o">.</span><span class="n">values</span><span class="p">()))</span> |
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204 |
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205 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"----- Beginning of Track adding processing -----"</span><span class="p">)</span> |
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206 <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">datatypeObject</span> <span class="ow">in</span> <span class="n">all_datatype_ordered_dictionary</span><span class="o">.</span><span class="n">iteritems</span><span class="p">():</span> |
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207 <span class="n">trackHub</span><span class="o">.</span><span class="n">addTrack</span><span class="p">(</span><span class="n">datatypeObject</span><span class="o">.</span><span class="n">track</span><span class="o">.</span><span class="n">trackDb</span><span class="p">)</span> |
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208 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"----- End of Track adding processing -----"</span><span class="p">)</span> |
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209 |
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210 <span class="c1"># We process all the modifications to create the zip file</span> |
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211 <span class="c1">#trackHub.createZip()</span> |
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212 |
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213 <span class="c1"># We terminate le process and so create a HTML file summarizing all the files</span> |
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214 <span class="n">trackHub</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span> |
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215 |
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216 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s1">'#### End of HubArchiveCreator Debug Mode: Bye! ####'</span><span class="p">)</span> |
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217 |
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218 <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
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219 |
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220 |
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221 <div class="viewcode-block" id="sanitize_name_input"><a class="viewcode-back" href="../code.html#hubArchiveCreator.sanitize_name_input">[docs]</a><span class="k">def</span> <span class="nf">sanitize_name_input</span><span class="p">(</span><span class="n">string_to_sanitize</span><span class="p">):</span> |
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222 <span class="sd">"""</span> |
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223 <span class="sd"> Sanitize the string passed in parameter by replacing '/' and ' ' by '_'</span> |
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224 |
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225 <span class="sd"> :param string_to_sanitize:</span> |
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226 <span class="sd"> :return :</span> |
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227 |
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228 <span class="sd"> :Example:</span> |
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229 |
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230 <span class="sd"> >>> sanitize_name_input('this/is an//example')</span> |
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231 <span class="sd"> this_is_an__example</span> |
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232 <span class="sd"> """</span> |
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233 <span class="k">return</span> <span class="n">string_to_sanitize</span> \ |
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234 <span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"/"</span><span class="p">,</span> <span class="s2">"_"</span><span class="p">)</span> \ |
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235 <span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">" "</span><span class="p">,</span> <span class="s2">"_"</span><span class="p">)</span></div> |
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236 |
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237 |
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238 <div class="viewcode-block" id="sanitize_name_inputs"><a class="viewcode-back" href="../code.html#hubArchiveCreator.sanitize_name_inputs">[docs]</a><span class="k">def</span> <span class="nf">sanitize_name_inputs</span><span class="p">(</span><span class="n">inputs_data</span><span class="p">):</span> |
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239 <span class="sd">"""</span> |
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240 <span class="sd"> Sanitize value of the keys "name" of the dictionary passed in parameter.</span> |
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241 |
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242 <span class="sd"> Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.</span> |
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243 <span class="sd"> Also, it can contain '/' character and could break the use of os.path function.</span> |
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244 |
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245 <span class="sd"> :param inputs_data: dict[string, dict[string, string]]</span> |
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246 <span class="sd"> """</span> |
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247 <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">inputs_data</span><span class="p">:</span> |
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248 <span class="n">inputs_data</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s2">"name"</span><span class="p">]</span> <span class="o">=</span> <span class="n">sanitize_name_input</span><span class="p">(</span><span class="n">inputs_data</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s2">"name"</span><span class="p">])</span></div> |
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249 |
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250 |
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251 <div class="viewcode-block" id="create_ordered_datatype_objects"><a class="viewcode-back" href="../code.html#hubArchiveCreator.create_ordered_datatype_objects">[docs]</a><span class="k">def</span> <span class="nf">create_ordered_datatype_objects</span><span class="p">(</span><span class="n">ExtensionClass</span><span class="p">,</span> <span class="n">array_inputs</span><span class="p">,</span> <span class="n">inputs_data</span><span class="p">):</span> |
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252 <span class="sd">"""</span> |
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253 <span class="sd"> Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub</span> |
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254 <span class="sd"> and update the dictionary of datatype</span> |
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255 |
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256 <span class="sd"> :param ExtensionClass:</span> |
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257 <span class="sd"> :param array_inputs:</span> |
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258 <span class="sd"> :param inputs_data:</span> |
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259 <span class="sd"> :type ExtensionClass: Datatype</span> |
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260 <span class="sd"> :type array_inputs: list[string]</span> |
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261 <span class="sd"> :type inputs_data: dict</span> |
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262 <span class="sd"> :rtype: dict</span> |
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263 <span class="sd"> """</span> |
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264 |
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265 <span class="n">datatype_dictionary</span> <span class="o">=</span> <span class="p">{}</span> |
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266 |
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267 <span class="c1"># TODO: Optimize this double loop</span> |
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268 <span class="k">for</span> <span class="n">input_false_path</span> <span class="ow">in</span> <span class="n">array_inputs</span><span class="p">:</span> |
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269 <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">data_value</span> <span class="ow">in</span> <span class="n">inputs_data</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> |
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270 <span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="n">input_false_path</span><span class="p">:</span> |
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271 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"input_false_path: "</span> <span class="o">+</span> <span class="n">input_false_path</span><span class="p">)</span> |
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272 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"data_value: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">data_value</span><span class="p">))</span> |
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273 <span class="n">extensionObject</span> <span class="o">=</span> <span class="n">ExtensionClass</span><span class="p">(</span><span class="n">input_false_path</span><span class="p">,</span> <span class="n">data_value</span><span class="p">)</span> |
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274 <span class="n">datatype_dictionary</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="n">data_value</span><span class="p">[</span><span class="s2">"order_index"</span><span class="p">]:</span> <span class="n">extensionObject</span><span class="p">})</span> |
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275 <span class="k">return</span> <span class="n">datatype_dictionary</span></div> |
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276 |
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277 <span class="k">def</span> <span class="nf">configure_logger</span><span class="p">(</span><span class="n">extra_files_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">debug</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> |
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278 <span class="k">if</span> <span class="ow">not</span> <span class="n">extra_files_path</span><span class="p">:</span> |
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279 <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Extra files path is not set. Stopping the application"</span><span class="p">)</span> |
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280 |
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281 |
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282 <span class="c1"># All case log: log everything in a .log file</span> |
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283 <span class="n">logger_file_name</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">__name__</span><span class="p">,</span> <span class="s1">'.log'</span><span class="p">])</span> |
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284 <span class="n">logging_file_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extra_files_path</span><span class="p">,</span> <span class="n">logger_file_name</span><span class="p">)</span> |
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285 |
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286 <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">logging_file_path</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span> |
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287 |
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288 <span class="n">log_stdout</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span> |
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289 <span class="k">if</span> <span class="ow">not</span> <span class="n">debug</span><span class="p">:</span> |
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290 <span class="n">configure_logger_user</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span> |
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291 <span class="k">else</span><span class="p">:</span> |
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292 <span class="n">configure_logger_dev</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span> |
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293 |
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294 <span class="c1"># stderr configuration</span> |
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295 <span class="n">configure_logger_stderr</span><span class="p">()</span> |
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296 |
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297 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s1">'#### Welcome in HubArchiveCreator Debug Mode ####</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> |
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298 |
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299 <div class="viewcode-block" id="configure_logger_user"><a class="viewcode-back" href="../code.html#hubArchiveCreator.configure_logger_user">[docs]</a><span class="k">def</span> <span class="nf">configure_logger_user</span><span class="p">(</span><span class="n">log_stdout</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> |
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300 <span class="sd">"""</span> |
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301 <span class="sd"> User Logger is defined as following:</span> |
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302 <span class="sd"> - User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback</span> |
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303 <span class="sd"> in STDOUT</span> |
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304 <span class="sd"> - Still access to full, brute and traceback for errors</span> |
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305 <span class="sd"> in STDERR</span> |
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306 <span class="sd"> - And further access to debug if needed</span> |
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307 <span class="sd"> in .log</span> |
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308 |
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309 <span class="sd"> """</span> |
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310 |
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311 <span class="k">if</span> <span class="ow">not</span> <span class="n">log_stdout</span><span class="p">:</span> |
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312 <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"No log_stdout given. Stopping the application"</span><span class="p">)</span> |
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313 |
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314 <span class="c1"># stdout for INFO / WARN / ERROR / CRITICAL</span> |
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315 <span class="n">log_stdout</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span> |
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316 |
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317 <span class="n">formatter</span> <span class="o">=</span> <span class="n">TraceBackFormatter</span><span class="p">(</span><span class="s1">'</span><span class="si">%(message)s</span><span class="s1">'</span><span class="p">)</span> |
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318 |
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319 <span class="n">log_stdout</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span> |
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320 |
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321 <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span></div> |
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322 |
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323 <div class="viewcode-block" id="configure_logger_dev"><a class="viewcode-back" href="../code.html#hubArchiveCreator.configure_logger_dev">[docs]</a><span class="k">def</span> <span class="nf">configure_logger_dev</span><span class="p">(</span><span class="n">log_stdout</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> |
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324 <span class="sd">"""</span> |
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325 <span class="sd"> Dev Logger is defined as following:</span> |
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326 <span class="sd"> - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout</span> |
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327 <span class="sd"> - Still access to full, brute and traceback in stderr for errors</span> |
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328 <span class="sd"> - And further access to debug if needed</span> |
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329 |
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330 <span class="sd"> """</span> |
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331 <span class="k">if</span> <span class="ow">not</span> <span class="n">log_stdout</span><span class="p">:</span> |
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332 <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"No log_stdout given. Stopping the application"</span><span class="p">)</span> |
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333 <span class="n">log_format</span> <span class="o">=</span> <span class="s1">'</span><span class="si">%(message)s</span><span class="s1">'</span> |
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334 |
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335 <span class="c1"># stdout and stderr and both identical for INFO / WARN / ERROR / CRITICAL</span> |
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336 <span class="n">log_stdout</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span> |
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337 |
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338 <span class="n">formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="n">log_format</span><span class="p">)</span> |
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339 |
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340 <span class="n">log_stdout</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span> |
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341 |
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342 <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span></div> |
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343 |
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344 <div class="viewcode-block" id="configure_logger_stderr"><a class="viewcode-back" href="../code.html#hubArchiveCreator.configure_logger_stderr">[docs]</a><span class="k">def</span> <span class="nf">configure_logger_stderr</span><span class="p">():</span> |
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345 <span class="sd">"""</span> |
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346 <span class="sd"> Configure what should be logged in stderr</span> |
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347 <span class="sd"> """</span> |
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348 <span class="n">log_error</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span> |
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349 <span class="n">log_error</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">ERROR</span><span class="p">)</span> |
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350 <span class="n">log_error_format</span> <span class="o">=</span> <span class="s1">'</span><span class="si">%(message)s</span><span class="s1">'</span> |
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351 |
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352 <span class="n">formatter_error</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="n">log_error_format</span><span class="p">)</span> |
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353 |
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354 <span class="n">log_error</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter_error</span><span class="p">)</span> |
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355 |
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356 <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">log_error</span><span class="p">)</span></div> |
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357 |
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358 <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span> |
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359 <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="n">__name__</span><span class="p">)</span> |
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360 <span class="n">main</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> |
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361 </pre></div> |
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362 |
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363 </div> |
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364 </div> |
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365 </div> |
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366 <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> |
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367 <div class="sphinxsidebarwrapper"> |
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368 <div id="searchbox" style="display: none" role="search"> |
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369 <h3>Quick search</h3> |
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370 <form class="search" action="../search.html" method="get"> |
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371 <div><input type="text" name="q" /></div> |
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372 <div><input type="submit" value="Go" /></div> |
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373 <input type="hidden" name="check_keywords" value="yes" /> |
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374 <input type="hidden" name="area" value="default" /> |
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375 </form> |
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376 </div> |
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377 <script type="text/javascript">$('#searchbox').show(0);</script> |
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378 </div> |
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379 </div> |
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380 <div class="clearer"></div> |
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381 </div> |
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382 <div class="related" role="navigation" aria-label="related navigation"> |
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383 <h3>Navigation</h3> |
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384 <ul> |
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385 <li class="right" style="margin-right: 10px"> |
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386 <a href="../genindex.html" title="General Index" |
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387 >index</a></li> |
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388 <li class="right" > |
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389 <a href="../py-modindex.html" title="Python Module Index" |
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390 >modules</a> |</li> |
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391 <li class="nav-item nav-item-0"><a href="../index.html">HubArchiveCreator 2.3 documentation</a> »</li> |
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392 <li class="nav-item nav-item-1"><a href="index.html" >Module code</a> »</li> |
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393 </ul> |
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394 </div> |
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395 <div class="footer" role="contentinfo"> |
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396 © Copyright 2016, Remi Marenco. |
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397 Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8. |
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398 </div> |
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399 </body> |
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400 </html> |