Mercurial > repos > agpetit > calculate_diameter

annotate run_installed_tests.html @ 3:b120a98cf623 draft

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
author agpetit
date Fri, 27 May 2022 07:36:52 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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1 <!DOCTYPE html>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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2 <html>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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3 <head>
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4 <meta charset="utf-8"/>
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5 <title>Test Report</title>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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6 <style>body {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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7 font-family: Helvetica, Arial, sans-serif;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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8 font-size: 12px;
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9 /* do not increase min-width as some may use split screens */
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10 min-width: 800px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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11 color: #999;
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12 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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13
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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14 h1 {
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15 font-size: 24px;
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16 color: black;
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17 }
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18
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19 h2 {
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20 font-size: 16px;
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21 color: black;
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22 }
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23
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24 p {
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25 color: black;
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26 }
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27
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28 a {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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29 color: #999;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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30 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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31
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32 table {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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33 border-collapse: collapse;
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34 }
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35
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36 /******************************
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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37 * SUMMARY INFORMATION
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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38 ******************************/
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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39 #environment td {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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40 padding: 5px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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41 border: 1px solid #E6E6E6;
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42 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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43 #environment tr:nth-child(odd) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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44 background-color: #f6f6f6;
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45 }
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46
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47 /******************************
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48 * TEST RESULT COLORS
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49 ******************************/
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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50 span.passed,
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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51 .passed .col-result {
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52 color: green;
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53 }
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54
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55 span.skipped,
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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56 span.xfailed,
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57 span.rerun,
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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58 .skipped .col-result,
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59 .xfailed .col-result,
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60 .rerun .col-result {
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61 color: orange;
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62 }
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63
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64 span.error,
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65 span.failed,
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66 span.xpassed,
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67 .error .col-result,
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68 .failed .col-result,
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69 .xpassed .col-result {
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70 color: red;
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71 }
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72
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73 /******************************
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74 * RESULTS TABLE
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75 *
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76 * 1. Table Layout
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77 * 2. Extra
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78 * 3. Sorting items
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79 *
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80 ******************************/
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81 /*------------------
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82 * 1. Table Layout
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83 *------------------*/
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84 #results-table {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
85 border: 1px solid #e6e6e6;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
86 color: #999;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
87 font-size: 12px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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88 width: 100%;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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89 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
90 #results-table th,
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
91 #results-table td {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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92 padding: 5px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
93 border: 1px solid #E6E6E6;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
94 text-align: left;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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95 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
96 #results-table th {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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97 font-weight: bold;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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98 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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99
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
100 /*------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
101 * 2. Extra
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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102 *------------------*/
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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103 .log {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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104 background-color: #e6e6e6;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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105 border: 1px solid #e6e6e6;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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106 color: black;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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107 display: block;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
108 font-family: "Courier New", Courier, monospace;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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109 height: 230px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
110 overflow-y: scroll;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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111 padding: 5px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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112 white-space: pre-wrap;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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113 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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114 .log:only-child {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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115 height: inherit;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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116 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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117
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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118 div.image {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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119 border: 1px solid #e6e6e6;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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120 float: right;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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121 height: 240px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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122 margin-left: 5px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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123 overflow: hidden;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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124 width: 320px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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125 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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126 div.image img {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
127 width: 320px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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128 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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129
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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130 div.video {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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131 border: 1px solid #e6e6e6;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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132 float: right;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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133 height: 240px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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134 margin-left: 5px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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135 overflow: hidden;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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136 width: 320px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
137 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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138 div.video video {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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139 overflow: hidden;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
140 width: 320px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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141 height: 240px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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142 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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143
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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144 .collapsed {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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145 display: none;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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146 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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147
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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148 .expander::after {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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149 content: " (show details)";
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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150 color: #BBB;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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151 font-style: italic;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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152 cursor: pointer;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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153 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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154
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
155 .collapser::after {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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156 content: " (hide details)";
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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157 color: #BBB;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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158 font-style: italic;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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159 cursor: pointer;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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160 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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161
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
162 /*------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
163 * 3. Sorting items
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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164 *------------------*/
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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165 .sortable {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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166 cursor: pointer;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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167 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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168
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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169 .sort-icon {
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170 font-size: 0px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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171 float: left;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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172 margin-right: 5px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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173 margin-top: 5px;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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174 /*triangle*/
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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175 width: 0;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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176 height: 0;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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177 border-left: 8px solid transparent;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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178 border-right: 8px solid transparent;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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179 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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180 .inactive .sort-icon {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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181 /*finish triangle*/
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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182 border-top: 8px solid #E6E6E6;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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183 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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184 .asc.active .sort-icon {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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185 /*finish triangle*/
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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186 border-bottom: 8px solid #999;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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187 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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188 .desc.active .sort-icon {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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189 /*finish triangle*/
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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190 border-top: 8px solid #999;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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191 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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192 </style></head>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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193 <body onLoad="init()">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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194 <script>/* This Source Code Form is subject to the terms of the Mozilla Public
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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195 * License, v. 2.0. If a copy of the MPL was not distributed with this file,
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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196 * You can obtain one at http://mozilla.org/MPL/2.0/. */
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197
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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198
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199 function toArray(iter) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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200 if (iter === null) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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201 return null;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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202 }
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203 return Array.prototype.slice.call(iter);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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204 }
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205
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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206 function find(selector, elem) { // eslint-disable-line no-redeclare
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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207 if (!elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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208 elem = document;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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209 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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210 return elem.querySelector(selector);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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211 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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212
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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213 function findAll(selector, elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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214 if (!elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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215 elem = document;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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216 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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217 return toArray(elem.querySelectorAll(selector));
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218 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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219
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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220 function sortColumn(elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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221 toggleSortStates(elem);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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222 const colIndex = toArray(elem.parentNode.childNodes).indexOf(elem);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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223 let key;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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224 if (elem.classList.contains('result')) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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225 key = keyResult;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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226 } else if (elem.classList.contains('links')) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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227 key = keyLink;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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228 } else {
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229 key = keyAlpha;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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230 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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231 sortTable(elem, key(colIndex));
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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232 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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233
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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234 function showAllExtras() { // eslint-disable-line no-unused-vars
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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235 findAll('.col-result').forEach(showExtras);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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236 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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237
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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238 function hideAllExtras() { // eslint-disable-line no-unused-vars
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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239 findAll('.col-result').forEach(hideExtras);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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240 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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241
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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242 function showExtras(colresultElem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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243 const extras = colresultElem.parentNode.nextElementSibling;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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244 const expandcollapse = colresultElem.firstElementChild;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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245 extras.classList.remove('collapsed');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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246 expandcollapse.classList.remove('expander');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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247 expandcollapse.classList.add('collapser');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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248 }
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249
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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250 function hideExtras(colresultElem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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251 const extras = colresultElem.parentNode.nextElementSibling;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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252 const expandcollapse = colresultElem.firstElementChild;
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253 extras.classList.add('collapsed');
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254 expandcollapse.classList.remove('collapser');
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255 expandcollapse.classList.add('expander');
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256 }
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257
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258 function showFilters() {
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259 const filterItems = document.getElementsByClassName('filter');
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260 for (let i = 0; i < filterItems.length; i++)
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261 filterItems[i].hidden = false;
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262 }
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263
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264 function addCollapse() {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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265 // Add links for show/hide all
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266 const resulttable = find('table#results-table');
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267 const showhideall = document.createElement('p');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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268 showhideall.innerHTML = '<a href="javascript:showAllExtras()">Show all details</a> / ' +
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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269 '<a href="javascript:hideAllExtras()">Hide all details</a>';
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270 resulttable.parentElement.insertBefore(showhideall, resulttable);
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271
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272 // Add show/hide link to each result
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273 findAll('.col-result').forEach(function(elem) {
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274 const collapsed = getQueryParameter('collapsed') || 'Passed';
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275 const extras = elem.parentNode.nextElementSibling;
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276 const expandcollapse = document.createElement('span');
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277 if (extras.classList.contains('collapsed')) {
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278 expandcollapse.classList.add('expander');
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279 } else if (collapsed.includes(elem.innerHTML)) {
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280 extras.classList.add('collapsed');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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281 expandcollapse.classList.add('expander');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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282 } else {
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283 expandcollapse.classList.add('collapser');
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284 }
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285 elem.appendChild(expandcollapse);
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286
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287 elem.addEventListener('click', function(event) {
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288 if (event.currentTarget.parentNode.nextElementSibling.classList.contains('collapsed')) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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289 showExtras(event.currentTarget);
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290 } else {
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291 hideExtras(event.currentTarget);
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292 }
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293 });
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294 });
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295 }
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296
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297 function getQueryParameter(name) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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298 const match = RegExp('[?&]' + name + '=([^&]*)').exec(window.location.search);
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299 return match && decodeURIComponent(match[1].replace(/\+/g, ' '));
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300 }
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301
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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302 function init () { // eslint-disable-line no-unused-vars
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303 resetSortHeaders();
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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304
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305 addCollapse();
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306
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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307 showFilters();
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308
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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309 sortColumn(find('.initial-sort'));
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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310
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311 findAll('.sortable').forEach(function(elem) {
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312 elem.addEventListener('click',
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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313 function() {
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314 sortColumn(elem);
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315 }, false);
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316 });
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317 }
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318
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319 function sortTable(clicked, keyFunc) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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320 const rows = findAll('.results-table-row');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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321 const reversed = !clicked.classList.contains('asc');
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322 const sortedRows = sort(rows, keyFunc, reversed);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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323 /* Whole table is removed here because browsers acts much slower
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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324 * when appending existing elements.
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325 */
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326 const thead = document.getElementById('results-table-head');
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327 document.getElementById('results-table').remove();
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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328 const parent = document.createElement('table');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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329 parent.id = 'results-table';
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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330 parent.appendChild(thead);
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331 sortedRows.forEach(function(elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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332 parent.appendChild(elem);
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333 });
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diff changeset
334 document.getElementsByTagName('BODY')[0].appendChild(parent);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
335 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
336
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
337 function sort(items, keyFunc, reversed) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
338 const sortArray = items.map(function(item, i) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
339 return [keyFunc(item), i];
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
340 });
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
341
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
342 sortArray.sort(function(a, b) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
343 const keyA = a[0];
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
344 const keyB = b[0];
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
345
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
346 if (keyA == keyB) return 0;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
347
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
348 if (reversed) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
349 return keyA < keyB ? 1 : -1;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
350 } else {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
351 return keyA > keyB ? 1 : -1;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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352 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
353 });
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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354
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
355 return sortArray.map(function(item) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
356 const index = item[1];
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
357 return items[index];
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
358 });
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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359 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
360
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
361 function keyAlpha(colIndex) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
362 return function(elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
363 return elem.childNodes[1].childNodes[colIndex].firstChild.data.toLowerCase();
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
364 };
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
365 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
366
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
367 function keyLink(colIndex) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
368 return function(elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
369 const dataCell = elem.childNodes[1].childNodes[colIndex].firstChild;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
370 return dataCell == null ? '' : dataCell.innerText.toLowerCase();
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
371 };
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
372 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
373
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
374 function keyResult(colIndex) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
375 return function(elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
376 const strings = ['Error', 'Failed', 'Rerun', 'XFailed', 'XPassed',
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
377 'Skipped', 'Passed'];
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
378 return strings.indexOf(elem.childNodes[1].childNodes[colIndex].firstChild.data);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
379 };
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
380 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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381
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
382 function resetSortHeaders() {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
383 findAll('.sort-icon').forEach(function(elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
384 elem.parentNode.removeChild(elem);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
385 });
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
386 findAll('.sortable').forEach(function(elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
387 const icon = document.createElement('div');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
388 icon.className = 'sort-icon';
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
389 icon.textContent = 'vvv';
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
390 elem.insertBefore(icon, elem.firstChild);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
391 elem.classList.remove('desc', 'active');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
392 elem.classList.add('asc', 'inactive');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
393 });
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
394 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
395
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
396 function toggleSortStates(elem) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
397 //if active, toggle between asc and desc
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
398 if (elem.classList.contains('active')) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
399 elem.classList.toggle('asc');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
400 elem.classList.toggle('desc');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
401 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
402
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
403 //if inactive, reset all other functions and add ascending active
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
404 if (elem.classList.contains('inactive')) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
405 resetSortHeaders();
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
406 elem.classList.remove('inactive');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
407 elem.classList.add('active');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
408 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
409 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
410
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
411 function isAllRowsHidden(value) {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
412 return value.hidden == false;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
413 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
414
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
415 function filterTable(elem) { // eslint-disable-line no-unused-vars
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
416 const outcomeAtt = 'data-test-result';
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
417 const outcome = elem.getAttribute(outcomeAtt);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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418 const classOutcome = outcome + ' results-table-row';
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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419 const outcomeRows = document.getElementsByClassName(classOutcome);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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420
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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421 for(let i = 0; i < outcomeRows.length; i++){
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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422 outcomeRows[i].hidden = !elem.checked;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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423 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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424
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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425 const rows = findAll('.results-table-row').filter(isAllRowsHidden);
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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426 const allRowsHidden = rows.length == 0 ? true : false;
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427 const notFoundMessage = document.getElementById('not-found-message');
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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428 notFoundMessage.hidden = !allRowsHidden;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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429 }
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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430 </script>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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431 <h1>run_installed_tests.html</h1>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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432 <p>Report generated on 27-May-2022 at 09:08:27 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a> v3.1.1</p>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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433 <h2>Environment</h2>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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434 <table id="environment">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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435 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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436 <td>Packages</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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437 <td>{"pluggy": "1.0.0", "py": "1.11.0", "pytest": "6.2.5"}</td></tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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438 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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439 <td>Platform</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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440 <td>Linux-5.13.0-44-generic-x86_64-with-glibc2.29</td></tr>
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441 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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442 <td>Plugins</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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443 <td>{"anyio": "3.5.0", "asyncio": "0.17.2", "celery": "0.0.0", "cov": "3.0.0", "html": "3.1.1", "json-report": "1.4.1", "metadata": "1.11.0", "mock": "3.7.0", "postgresql": "4.1.0", "pythonpath": "0.7.3", "shard": "0.1.2"}</td></tr>
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444 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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445 <td>Python</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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446 <td>3.8.10</td></tr></table>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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447 <h2>Summary</h2>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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448 <p>5 tests ran in 162.57 seconds. </p>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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449 <p class="filter" hidden="true">(Un)check the boxes to filter the results.</p><input checked="true" class="filter" data-test-result="passed" hidden="true" name="filter_checkbox" onChange="filterTable(this)" type="checkbox"/><span class="passed">3 passed</span>, <input checked="true" class="filter" data-test-result="skipped" disabled="true" hidden="true" name="filter_checkbox" onChange="filterTable(this)" type="checkbox"/><span class="skipped">0 skipped</span>, <input checked="true" class="filter" data-test-result="failed" hidden="true" name="filter_checkbox" onChange="filterTable(this)" type="checkbox"/><span class="failed">2 failed</span>, <input checked="true" class="filter" data-test-result="error" disabled="true" hidden="true" name="filter_checkbox" onChange="filterTable(this)" type="checkbox"/><span class="error">0 errors</span>, <input checked="true" class="filter" data-test-result="xfailed" disabled="true" hidden="true" name="filter_checkbox" onChange="filterTable(this)" type="checkbox"/><span class="xfailed">0 expected failures</span>, <input checked="true" class="filter" data-test-result="xpassed" disabled="true" hidden="true" name="filter_checkbox" onChange="filterTable(this)" type="checkbox"/><span class="xpassed">0 unexpected passes</span>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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450 <h2>Results</h2>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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451 <table id="results-table">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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452 <thead id="results-table-head">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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453 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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454 <th class="sortable result initial-sort" col="result">Result</th>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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455 <th class="sortable" col="name">Test</th>
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456 <th class="sortable" col="duration">Duration</th>
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457 <th class="sortable links" col="links">Links</th></tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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458 <tr hidden="true" id="not-found-message">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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459 <th colspan="4">No results found. Try to check the filters</th></tr></thead>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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460 <tbody class="failed results-table-row">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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461 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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462 <td class="col-result">Failed</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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463 <td class="col-name">test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_2]</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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464 <td class="col-duration">38.80</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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465 <td class="col-links"></td></tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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466 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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467 <td class="extra" colspan="4">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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468 <div class="log">testcases = (&#x27;testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_2&#x27;, ...d.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 testMethod=runTest&gt;, 1)<br/>driver = &lt;functional.test_toolbox_pytest.DefaultGalaxyTestDriver object at 0x7f227250c280&gt;<br/><br/> @pytest.mark.parametrize(&quot;testcases&quot;, cases(), ids=idfn)<br/> def test_tool(testcases, driver):<br/> test = testcases[1]<br/>&gt; test.do_it(test_index=testcases[2])<br/><br/>test/functional/test_toolbox_pytest.py:84: <br/>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ <br/>test/functional/test_toolbox.py:35: in do_it<br/> verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)<br/>lib/galaxy/tool_util/verify/interactor.py:1127: in verify_tool<br/> raise e<br/>lib/galaxy/tool_util/verify/interactor.py:1123: in verify_tool<br/> job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet)<br/>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ <br/><br/>testdef = &lt;galaxy.tool_util.verify.interactor.ToolTestDescription object at 0x7f226f4f3c40&gt;, history = &#x27;54f2a3a23292eb07&#x27;<br/>jobs = [{&#x27;create_time&#x27;: &#x27;2022-05-27T07:07:09.529613&#x27;, &#x27;exit_code&#x27;: None, &#x27;galaxy_version&#x27;: &#x27;22.01&#x27;, &#x27;history_id&#x27;: &#x27;54f2a3a23292eb07&#x27;, ...}]<br/>data_list = {&#x27;cut_log&#x27;: {&#x27;create_time&#x27;: &#x27;2022-05-27T07:07:09.533075&#x27;, &#x27;data_type&#x27;: &#x27;galaxy.datatypes.data.Text&#x27;, &#x27;deleted&#x27;: False,...157069a5-6727-4eb8-9d80-8a551afe1093&#x27;, &#x27;validated_state&#x27;: &#x27;unknown&#x27;, &#x27;validated_state_message&#x27;: None, &#x27;visible&#x27;: True}}<br/>data_collection_list = {&#x27;output_traj&#x27;: {&#x27;collection_type&#x27;: &#x27;list&#x27;, &#x27;contents_url&#x27;: &#x27;/api/dataset_collections/5729865256bc2525/contents/5729865256bc2525&#x27;, &#x27;create_time&#x27;: &#x27;2022-05-27T07:07:09.531693&#x27;, &#x27;deleted&#x27;: False, ...}}<br/>galaxy_interactor = &lt;galaxy.tool_util.verify.interactor.GalaxyInteractorApi object at 0x7f2214721b50&gt;, quiet = False<br/><br/> def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=False):<br/> assert len(jobs) == 1, &quot;Test framework logic error, somehow tool test resulted in more than one job.&quot;<br/> job = jobs[0]<br/> <br/> found_exceptions = []<br/> <br/> def register_exception(e):<br/> if not found_exceptions and not quiet:<br/> # Only print this stuff out once.<br/> for stream in [&#x27;stdout&#x27;, &#x27;stderr&#x27;]:<br/> if stream in job_stdio:<br/> print(_format_stream(job_stdio[stream], stream=stream, format=True), file=sys.stderr)<br/> found_exceptions.append(e)<br/> <br/> if testdef.expect_failure:<br/> if testdef.outputs:<br/> raise Exception(&quot;Cannot specify outputs in a test expecting failure.&quot;)<br/> <br/> maxseconds = testdef.maxseconds<br/> # Wait for the job to complete and register expections if the final<br/> # status was not what test was expecting.<br/> job_failed = False<br/> try:<br/> galaxy_interactor.wait_for_job(job[&#x27;id&#x27;], history, maxseconds)<br/> except Exception as e:<br/> job_failed = True<br/> if not testdef.expect_failure:<br/> found_exceptions.append(e)<br/> <br/> job_stdio = galaxy_interactor.get_job_stdio(job[&#x27;id&#x27;])<br/> <br/> if testdef.num_outputs is not None:<br/> expected = testdef.num_outputs<br/> actual = len(data_list) + len(data_collection_list)<br/> if expected != actual:<br/> message = f&quot;Incorrect number of outputs - expected {expected}, found {actual}: datasets {data_list.keys()} collections {data_collection_list.keys()}&quot;<br/> error = AssertionError(message)<br/> register_exception(error)<br/> <br/> if not job_failed and testdef.expect_failure:<br/> error = AssertionError(&quot;Expected job to fail but Galaxy indicated the job successfully completed.&quot;)<br/> register_exception(error)<br/> <br/> expect_exit_code = testdef.expect_exit_code<br/> if expect_exit_code is not None:<br/> exit_code = job_stdio[&quot;exit_code&quot;]<br/> if str(expect_exit_code) != str(exit_code):<br/> error = AssertionError(f&quot;Expected job to complete with exit code {expect_exit_code}, found {exit_code}&quot;)<br/> register_exception(error)<br/> <br/> for output_index, output_dict in enumerate(testdef.outputs):<br/> # Get the correct hid<br/> name = output_dict[&quot;name&quot;]<br/> outfile = output_dict[&quot;value&quot;]<br/> attributes = output_dict[&quot;attributes&quot;]<br/> output_testdef = Bunch(name=name, outfile=outfile, attributes=attributes)<br/> try:<br/> output_data = data_list[name]<br/> except (TypeError, KeyError):<br/> # Legacy - fall back on ordered data list access if data_list is<br/> # just a list (case with twill variant or if output changes its<br/> # name).<br/> if hasattr(data_list, &quot;values&quot;):<br/> output_data = list(data_list.values())[output_index]<br/> else:<br/> output_data = data_list[len(data_list) - len(testdef.outputs) + output_index]<br/> assert output_data is not None<br/> try:<br/> galaxy_interactor.verify_output(history, jobs, output_data, output_testdef=output_testdef, tool_id=job[&#x27;tool_id&#x27;], maxseconds=maxseconds, tool_version=testdef.tool_version)<br/> except Exception as e:<br/> register_exception(e)<br/> <br/> other_checks = {<br/> &quot;command_line&quot;: &quot;Command produced by the job&quot;,<br/> &quot;command_version&quot;: &quot;Tool version indicated during job execution&quot;,<br/> &quot;stdout&quot;: &quot;Standard output of the job&quot;,<br/> &quot;stderr&quot;: &quot;Standard error of the job&quot;,<br/> }<br/> # TODO: Only hack the stdio like this for older profile, for newer tool profiles<br/> # add some syntax for asserting job messages maybe - or just drop this because exit<br/> # code and regex on stdio can be tested directly - so this is really testing Galaxy<br/> # core handling more than the tool.<br/> job_messages = job_stdio.get(&quot;job_messages&quot;) or []<br/> stdout_prefix = &quot;&quot;<br/> stderr_prefix = &quot;&quot;<br/> for job_message in job_messages:<br/> message_type = job_message.get(&quot;type&quot;)<br/> if message_type == &quot;regex&quot; and job_message.get(&quot;stream&quot;) == &quot;stderr&quot;:<br/> stderr_prefix += f&quot;{job_message.get(&#x27;desc&#x27;) or &#x27;&#x27;}\n&quot;<br/> elif message_type == &quot;regex&quot; and job_message.get(&quot;stream&quot;) == &quot;stdout&quot;:<br/> stdout_prefix += f&quot;{job_message.get(&#x27;desc&#x27;) or &#x27;&#x27;}\n&quot;<br/> elif message_type == &quot;exit_code&quot;:<br/> stderr_prefix += f&quot;{job_message.get(&#x27;desc&#x27;) or &#x27;&#x27;}\n&quot;<br/> else:<br/> raise Exception(f&quot;Unknown job message type [{message_type}] in [{job_message}]&quot;)<br/> <br/> for what, description in other_checks.items():<br/> if getattr(testdef, what, None) is not None:<br/> try:<br/> raw_data = job_stdio[what]<br/> assertions = getattr(testdef, what)<br/> if what == &quot;stdout&quot;:<br/> data = stdout_prefix + raw_data<br/> elif what == &quot;stderr&quot;:<br/> data = stderr_prefix + raw_data<br/> else:<br/> data = raw_data<br/> verify_assertions(data, assertions)<br/> except AssertionError as err:<br/> errmsg = f&#x27;{description} different than expected\n&#x27;<br/> errmsg += util.unicodify(err)<br/> register_exception(AssertionError(errmsg))<br/> <br/> for output_collection_def in testdef.output_collections:<br/> try:<br/> name = output_collection_def.name<br/> # TODO: data_collection_list is clearly a bad name for dictionary.<br/> if name not in data_collection_list:<br/> message = f&quot;Failed to find output [{name}], tool outputs include [{&#x27;,&#x27;.join(data_collection_list.keys())}]&quot;<br/> raise AssertionError(message)<br/> <br/> # Data collection returned from submission, elements may have been populated after<br/> # the job completed so re-hit the API for more information.<br/> data_collection_id = data_collection_list[name][&quot;id&quot;]<br/> galaxy_interactor.verify_output_collection(output_collection_def, data_collection_id, history, job[&#x27;tool_id&#x27;])<br/> except Exception as e:<br/> register_exception(e)<br/> <br/> if found_exceptions and not testdef.expect_test_failure:<br/>&gt; raise JobOutputsError(found_exceptions, job_stdio)<br/><span class="error">E galaxy.tool_util.verify.interactor.JobOutputsError: Output cut_log: different than expected</span><br/><span class="error">E Expected 241+-0 lines in the output found 163</span><br/><br/>lib/galaxy/tool_util/verify/interactor.py:1299: JobOutputsError<br/> ------------------------------Captured stderr call------------------------------ <br/>2022-05-27 09:06:44,120 DEBUG [multipart.multipart] Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
469 2022-05-27 09:06:44,121 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
470 2022-05-27 09:06:44,121 DEBUG [multipart.multipart] Calling on_field_data with data[5:153]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
471 2022-05-27 09:06:44,121 DEBUG [multipart.multipart] Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
472 2022-05-27 09:06:44,121 DEBUG [multipart.multipart] Calling on_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
473 2022-05-27 09:06:45,213 INFO [galaxy.tools] Validated and populated state for tool request (21.598 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
474 2022-05-27 09:06:45,219 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.142 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
475 2022-05-27 09:06:45,353 DEBUG [galaxy.tools.actions.upload] Checked uploads (134.155 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
476 2022-05-27 09:06:45,360 DEBUG [galaxy.tools.actions.upload] Created upload job (6.274 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
477 2022-05-27 09:06:45,381 INFO [galaxy.web_stack.handlers] (Job[id=7,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
478 2022-05-27 09:06:46,309 INFO [galaxy.jobs.handler] (7) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
479 2022-05-27 09:06:46,485 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/7/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/7/registry.xml&#x27; &#x27;/tmp/upload_params_n9cdh_8t&#x27; &#x27;8:/tmp/tmptoruqmiy/job_working_directory/000/7/working/dataset_af8d1b0c-d748-4b88-935e-429302b926ec_files:/tmp/tmptoruqmiy/files/a/f/8/dataset_af8d1b0c-d748-4b88-935e-429302b926ec.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
480 2022-05-27 09:06:54,095 INFO [galaxy.tools] Validated and populated state for tool request (24.710 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
481 2022-05-27 09:06:54,102 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.144 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
482 2022-05-27 09:06:54,215 DEBUG [galaxy.tools.actions.upload] Checked uploads (113.287 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
483 2022-05-27 09:06:54,221 DEBUG [galaxy.tools.actions.upload] Created upload job (5.835 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
484 2022-05-27 09:06:54,242 INFO [galaxy.web_stack.handlers] (Job[id=8,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
485 2022-05-27 09:06:54,873 INFO [galaxy.jobs.handler] (8) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
486 2022-05-27 09:06:55,123 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/8/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/8/registry.xml&#x27; &#x27;/tmp/upload_params__n8zpgmo&#x27; &#x27;9:/tmp/tmptoruqmiy/job_working_directory/000/8/working/dataset_2f2d7be8-929e-4b65-a898-06a921300c73_files:/tmp/tmptoruqmiy/files/2/f/2/dataset_2f2d7be8-929e-4b65-a898-06a921300c73.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
487 2022-05-27 09:07:01,790 INFO [galaxy.tools] Validated and populated state for tool request (23.541 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
488 2022-05-27 09:07:01,796 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.142 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
489 2022-05-27 09:07:01,908 DEBUG [galaxy.tools.actions.upload] Checked uploads (112.494 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
490 2022-05-27 09:07:01,916 DEBUG [galaxy.tools.actions.upload] Created upload job (7.217 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
491 2022-05-27 09:07:01,941 INFO [galaxy.web_stack.handlers] (Job[id=9,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
492 2022-05-27 09:07:02,320 INFO [galaxy.jobs.handler] (9) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
493 2022-05-27 09:07:02,533 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/9/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/9/registry.xml&#x27; &#x27;/tmp/upload_params_d9ksd_uu&#x27; &#x27;10:/tmp/tmptoruqmiy/job_working_directory/000/9/working/dataset_1cbe15a0-33cd-4c77-a7eb-cfce8034f2bb_files:/tmp/tmptoruqmiy/files/1/c/b/dataset_1cbe15a0-33cd-4c77-a7eb-cfce8034f2bb.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
494 2022-05-27 09:07:09,478 INFO [galaxy.tools] Validated and populated state for tool request (23.189 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
495 2022-05-27 09:07:09,492 INFO [galaxy.tools.actions] Handled collection output named output_traj for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (2.367 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
496 2022-05-27 09:07:09,494 INFO [galaxy.tools.actions] Handled output named cut_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (1.967 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
497 2022-05-27 09:07:09,511 INFO [galaxy.tools.actions] Added output datasets to history (17.096 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
498 2022-05-27 09:07:09,515 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0] complete, ready to be enqueued (3.762 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
499 2022-05-27 09:07:09,558 INFO [galaxy.web_stack.handlers] (Job[id=10,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
500 2022-05-27 09:07:09,901 INFO [galaxy.jobs.handler] (10) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
501 2022-05-27 09:07:10,139 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/10/tool_script.sh] for tool command [[ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
502 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
503 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
504 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
505 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
506 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
507 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
508 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
509 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
510 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
511 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
512 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
513 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
514 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
515 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
516 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
517 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
518 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
519 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
520 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
521 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
522 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
523 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
524 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
525 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
526 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
527 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
528 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
529 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
530 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
531 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
532 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
533 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
534 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
535 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
536 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
537 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
538 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
539 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
540 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
541 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
542 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
543 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
544 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
545 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
546 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
547 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
548 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
549 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
550 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
551 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
552 } ; ln -s &#x27;/tmp/tmptoruqmiy/files/a/f/8/dataset_af8d1b0c-d748-4b88-935e-429302b926ec.dat&#x27; &#x27;PIP2.1_test.gro&#x27; &amp;&amp; ln -s &#x27;/tmp/tmptoruqmiy/files/2/f/2/dataset_2f2d7be8-929e-4b65-a898-06a921300c73.dat&#x27; &#x27;PIP2.1_test.xtc&#x27; &amp;&amp; ln -s &#x27;/tmp/tmptoruqmiy/files/1/c/b/dataset_1cbe15a0-33cd-4c77-a7eb-cfce8034f2bb.dat&#x27; &#x27;estimated_number_of_sub_trajectories.tsv&#x27; &amp;&amp; python &#x27;/tmp/tmptoruqmiy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/c09cf8acc4de/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories.py&#x27; --verbose --gro_file &#x27;PIP2.1_test.gro&#x27; --xtc_file &#x27;PIP2.1_test.xtc&#x27; --log_output &#x27;log/cut_trajectories.log&#x27; --output_directory &#x27;out/&#x27; --nbr_sub_traj &#x27;estimated_number_of_sub_trajectories.tsv&#x27; --group_output 0 --number_cpus &quot;${GALAXY_SLOTS:-1}&quot;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
553 ---------------------- &gt;&gt; begin tool stdout &lt;&lt; -----------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
554
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
555 ----------------------- &gt;&gt; end tool stdout &lt;&lt; ------------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
556
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
557 ---------------------- &gt;&gt; begin tool stderr &lt;&lt; -----------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
558
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
559 ----------------------- &gt;&gt; end tool stderr &lt;&lt; ------------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
560
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
561 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
562 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
563 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:153]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
564 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
565 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
566 <tbody class="failed results-table-row">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
567 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
568 <td class="col-result">Failed</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
569 <td class="col-name">test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_3]</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
570 <td class="col-duration">40.43</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
571 <td class="col-links"></td></tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
572 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
573 <td class="extra" colspan="4">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
574 <div class="log">testcases = (&#x27;testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_3&#x27;, ...d.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 testMethod=runTest&gt;, 2)<br/>driver = &lt;functional.test_toolbox_pytest.DefaultGalaxyTestDriver object at 0x7f227250c280&gt;<br/><br/> @pytest.mark.parametrize(&quot;testcases&quot;, cases(), ids=idfn)<br/> def test_tool(testcases, driver):<br/> test = testcases[1]<br/>&gt; test.do_it(test_index=testcases[2])<br/><br/>test/functional/test_toolbox_pytest.py:84: <br/>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ <br/>test/functional/test_toolbox.py:35: in do_it<br/> verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)<br/>lib/galaxy/tool_util/verify/interactor.py:1127: in verify_tool<br/> raise e<br/>lib/galaxy/tool_util/verify/interactor.py:1123: in verify_tool<br/> job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet)<br/>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ <br/><br/>testdef = &lt;galaxy.tool_util.verify.interactor.ToolTestDescription object at 0x7f226f22bd30&gt;, history = &#x27;8155e4b4bf1581ff&#x27;<br/>jobs = [{&#x27;create_time&#x27;: &#x27;2022-05-27T07:07:50.059003&#x27;, &#x27;exit_code&#x27;: None, &#x27;galaxy_version&#x27;: &#x27;22.01&#x27;, &#x27;history_id&#x27;: &#x27;8155e4b4bf1581ff&#x27;, ...}]<br/>data_list = {&#x27;cut_log&#x27;: {&#x27;create_time&#x27;: &#x27;2022-05-27T07:07:50.063180&#x27;, &#x27;data_type&#x27;: &#x27;galaxy.datatypes.data.Text&#x27;, &#x27;deleted&#x27;: False,...11db857f-5e9e-40b7-ab71-3aba6213bc8b&#x27;, &#x27;validated_state&#x27;: &#x27;unknown&#x27;, &#x27;validated_state_message&#x27;: None, &#x27;visible&#x27;: True}}<br/>data_collection_list = {&#x27;output_traj&#x27;: {&#x27;collection_type&#x27;: &#x27;list&#x27;, &#x27;contents_url&#x27;: &#x27;/api/dataset_collections/54f2a3a23292eb07/contents/54f2a3a23292eb07&#x27;, &#x27;create_time&#x27;: &#x27;2022-05-27T07:07:50.061399&#x27;, &#x27;deleted&#x27;: False, ...}}<br/>galaxy_interactor = &lt;galaxy.tool_util.verify.interactor.GalaxyInteractorApi object at 0x7f2214721b50&gt;, quiet = False<br/><br/> def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=False):<br/> assert len(jobs) == 1, &quot;Test framework logic error, somehow tool test resulted in more than one job.&quot;<br/> job = jobs[0]<br/> <br/> found_exceptions = []<br/> <br/> def register_exception(e):<br/> if not found_exceptions and not quiet:<br/> # Only print this stuff out once.<br/> for stream in [&#x27;stdout&#x27;, &#x27;stderr&#x27;]:<br/> if stream in job_stdio:<br/> print(_format_stream(job_stdio[stream], stream=stream, format=True), file=sys.stderr)<br/> found_exceptions.append(e)<br/> <br/> if testdef.expect_failure:<br/> if testdef.outputs:<br/> raise Exception(&quot;Cannot specify outputs in a test expecting failure.&quot;)<br/> <br/> maxseconds = testdef.maxseconds<br/> # Wait for the job to complete and register expections if the final<br/> # status was not what test was expecting.<br/> job_failed = False<br/> try:<br/> galaxy_interactor.wait_for_job(job[&#x27;id&#x27;], history, maxseconds)<br/> except Exception as e:<br/> job_failed = True<br/> if not testdef.expect_failure:<br/> found_exceptions.append(e)<br/> <br/> job_stdio = galaxy_interactor.get_job_stdio(job[&#x27;id&#x27;])<br/> <br/> if testdef.num_outputs is not None:<br/> expected = testdef.num_outputs<br/> actual = len(data_list) + len(data_collection_list)<br/> if expected != actual:<br/> message = f&quot;Incorrect number of outputs - expected {expected}, found {actual}: datasets {data_list.keys()} collections {data_collection_list.keys()}&quot;<br/> error = AssertionError(message)<br/> register_exception(error)<br/> <br/> if not job_failed and testdef.expect_failure:<br/> error = AssertionError(&quot;Expected job to fail but Galaxy indicated the job successfully completed.&quot;)<br/> register_exception(error)<br/> <br/> expect_exit_code = testdef.expect_exit_code<br/> if expect_exit_code is not None:<br/> exit_code = job_stdio[&quot;exit_code&quot;]<br/> if str(expect_exit_code) != str(exit_code):<br/> error = AssertionError(f&quot;Expected job to complete with exit code {expect_exit_code}, found {exit_code}&quot;)<br/> register_exception(error)<br/> <br/> for output_index, output_dict in enumerate(testdef.outputs):<br/> # Get the correct hid<br/> name = output_dict[&quot;name&quot;]<br/> outfile = output_dict[&quot;value&quot;]<br/> attributes = output_dict[&quot;attributes&quot;]<br/> output_testdef = Bunch(name=name, outfile=outfile, attributes=attributes)<br/> try:<br/> output_data = data_list[name]<br/> except (TypeError, KeyError):<br/> # Legacy - fall back on ordered data list access if data_list is<br/> # just a list (case with twill variant or if output changes its<br/> # name).<br/> if hasattr(data_list, &quot;values&quot;):<br/> output_data = list(data_list.values())[output_index]<br/> else:<br/> output_data = data_list[len(data_list) - len(testdef.outputs) + output_index]<br/> assert output_data is not None<br/> try:<br/> galaxy_interactor.verify_output(history, jobs, output_data, output_testdef=output_testdef, tool_id=job[&#x27;tool_id&#x27;], maxseconds=maxseconds, tool_version=testdef.tool_version)<br/> except Exception as e:<br/> register_exception(e)<br/> <br/> other_checks = {<br/> &quot;command_line&quot;: &quot;Command produced by the job&quot;,<br/> &quot;command_version&quot;: &quot;Tool version indicated during job execution&quot;,<br/> &quot;stdout&quot;: &quot;Standard output of the job&quot;,<br/> &quot;stderr&quot;: &quot;Standard error of the job&quot;,<br/> }<br/> # TODO: Only hack the stdio like this for older profile, for newer tool profiles<br/> # add some syntax for asserting job messages maybe - or just drop this because exit<br/> # code and regex on stdio can be tested directly - so this is really testing Galaxy<br/> # core handling more than the tool.<br/> job_messages = job_stdio.get(&quot;job_messages&quot;) or []<br/> stdout_prefix = &quot;&quot;<br/> stderr_prefix = &quot;&quot;<br/> for job_message in job_messages:<br/> message_type = job_message.get(&quot;type&quot;)<br/> if message_type == &quot;regex&quot; and job_message.get(&quot;stream&quot;) == &quot;stderr&quot;:<br/> stderr_prefix += f&quot;{job_message.get(&#x27;desc&#x27;) or &#x27;&#x27;}\n&quot;<br/> elif message_type == &quot;regex&quot; and job_message.get(&quot;stream&quot;) == &quot;stdout&quot;:<br/> stdout_prefix += f&quot;{job_message.get(&#x27;desc&#x27;) or &#x27;&#x27;}\n&quot;<br/> elif message_type == &quot;exit_code&quot;:<br/> stderr_prefix += f&quot;{job_message.get(&#x27;desc&#x27;) or &#x27;&#x27;}\n&quot;<br/> else:<br/> raise Exception(f&quot;Unknown job message type [{message_type}] in [{job_message}]&quot;)<br/> <br/> for what, description in other_checks.items():<br/> if getattr(testdef, what, None) is not None:<br/> try:<br/> raw_data = job_stdio[what]<br/> assertions = getattr(testdef, what)<br/> if what == &quot;stdout&quot;:<br/> data = stdout_prefix + raw_data<br/> elif what == &quot;stderr&quot;:<br/> data = stderr_prefix + raw_data<br/> else:<br/> data = raw_data<br/> verify_assertions(data, assertions)<br/> except AssertionError as err:<br/> errmsg = f&#x27;{description} different than expected\n&#x27;<br/> errmsg += util.unicodify(err)<br/> register_exception(AssertionError(errmsg))<br/> <br/> for output_collection_def in testdef.output_collections:<br/> try:<br/> name = output_collection_def.name<br/> # TODO: data_collection_list is clearly a bad name for dictionary.<br/> if name not in data_collection_list:<br/> message = f&quot;Failed to find output [{name}], tool outputs include [{&#x27;,&#x27;.join(data_collection_list.keys())}]&quot;<br/> raise AssertionError(message)<br/> <br/> # Data collection returned from submission, elements may have been populated after<br/> # the job completed so re-hit the API for more information.<br/> data_collection_id = data_collection_list[name][&quot;id&quot;]<br/> galaxy_interactor.verify_output_collection(output_collection_def, data_collection_id, history, job[&#x27;tool_id&#x27;])<br/> except Exception as e:<br/> register_exception(e)<br/> <br/> if found_exceptions and not testdef.expect_test_failure:<br/>&gt; raise JobOutputsError(found_exceptions, job_stdio)<br/><span class="error">E galaxy.tool_util.verify.interactor.JobOutputsError: Output cut_log: different than expected</span><br/><span class="error">E Expected 239+-0 lines in the output found 161</span><br/><br/>lib/galaxy/tool_util/verify/interactor.py:1299: JobOutputsError<br/> ------------------------------Captured stderr call------------------------------ <br/>2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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575 2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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576 2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_field_data with data[5:153]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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577 2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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578 2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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579 2022-05-27 09:07:24,155 INFO [galaxy.tools] Validated and populated state for tool request (22.557 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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580 2022-05-27 09:07:24,161 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.147 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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581 2022-05-27 09:07:24,267 DEBUG [galaxy.tools.actions.upload] Checked uploads (105.875 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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582 2022-05-27 09:07:24,273 DEBUG [galaxy.tools.actions.upload] Created upload job (6.109 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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583 2022-05-27 09:07:24,304 INFO [galaxy.web_stack.handlers] (Job[id=11,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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584 2022-05-27 09:07:24,687 INFO [galaxy.jobs.handler] (11) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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585 2022-05-27 09:07:24,908 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/11/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/11/registry.xml&#x27; &#x27;/tmp/upload_params_149iajw4&#x27; &#x27;15:/tmp/tmptoruqmiy/job_working_directory/000/11/working/dataset_77bd9b6c-523e-47cf-9eab-81619349d30f_files:/tmp/tmptoruqmiy/files/7/7/b/dataset_77bd9b6c-523e-47cf-9eab-81619349d30f.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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586 2022-05-27 09:07:32,387 INFO [galaxy.tools] Validated and populated state for tool request (22.918 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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587 2022-05-27 09:07:32,394 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.147 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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588 2022-05-27 09:07:32,506 DEBUG [galaxy.tools.actions.upload] Checked uploads (111.673 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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589 2022-05-27 09:07:32,512 DEBUG [galaxy.tools.actions.upload] Created upload job (6.064 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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590 2022-05-27 09:07:32,540 INFO [galaxy.web_stack.handlers] (Job[id=12,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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591 2022-05-27 09:07:33,244 INFO [galaxy.jobs.handler] (12) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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592 2022-05-27 09:07:33,510 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/12/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/12/registry.xml&#x27; &#x27;/tmp/upload_params_t99uz5pr&#x27; &#x27;16:/tmp/tmptoruqmiy/job_working_directory/000/12/working/dataset_18454cb5-4d92-467e-a6fe-92717ffffe40_files:/tmp/tmptoruqmiy/files/1/8/4/dataset_18454cb5-4d92-467e-a6fe-92717ffffe40.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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593 2022-05-27 09:07:40,449 INFO [galaxy.tools] Validated and populated state for tool request (22.896 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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594 2022-05-27 09:07:40,456 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.352 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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595 2022-05-27 09:07:40,576 DEBUG [galaxy.tools.actions.upload] Checked uploads (119.159 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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596 2022-05-27 09:07:40,584 DEBUG [galaxy.tools.actions.upload] Created upload job (8.363 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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597 2022-05-27 09:07:40,608 INFO [galaxy.web_stack.handlers] (Job[id=13,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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598 2022-05-27 09:07:40,935 INFO [galaxy.jobs.handler] (13) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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599 2022-05-27 09:07:41,109 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/13/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/13/registry.xml&#x27; &#x27;/tmp/upload_params_e61k8ex6&#x27; &#x27;17:/tmp/tmptoruqmiy/job_working_directory/000/13/working/dataset_745f4487-3b81-44f5-9eb8-9d76e882a98a_files:/tmp/tmptoruqmiy/files/7/4/5/dataset_745f4487-3b81-44f5-9eb8-9d76e882a98a.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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600 2022-05-27 09:07:50,014 INFO [galaxy.tools] Validated and populated state for tool request (24.877 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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601 2022-05-27 09:07:50,027 INFO [galaxy.tools.actions] Handled collection output named output_traj for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (0.776 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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602 2022-05-27 09:07:50,028 INFO [galaxy.tools.actions] Handled output named cut_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (0.902 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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603 2022-05-27 09:07:50,042 INFO [galaxy.tools.actions] Added output datasets to history (13.785 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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604 2022-05-27 09:07:50,045 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0] complete, ready to be enqueued (2.064 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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diff changeset
605 2022-05-27 09:07:50,082 INFO [galaxy.web_stack.handlers] (Job[id=14,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
606 2022-05-27 09:07:50,482 INFO [galaxy.jobs.handler] (14) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
607 2022-05-27 09:07:50,758 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/14/tool_script.sh] for tool command [[ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
608 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
609 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
610 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
611 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
612 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
613 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
614 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
615 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
616 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
617 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
618 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
619 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
620 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
621 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
622 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
623 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
624 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
625 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
626 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
627 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
628 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
629 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
630 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
631 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
632 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
633 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
634 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
635 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
636 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
637 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
638 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
639 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
640 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
641 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
642 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
643 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
644 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
645 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
646 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
647 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
648 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
649 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
650 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
651 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
652 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
653 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
654 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
655 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
656 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
657 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
658 } ; ln -s &#x27;/tmp/tmptoruqmiy/files/7/7/b/dataset_77bd9b6c-523e-47cf-9eab-81619349d30f.dat&#x27; &#x27;PIP2.1_test.gro&#x27; &amp;&amp; ln -s &#x27;/tmp/tmptoruqmiy/files/1/8/4/dataset_18454cb5-4d92-467e-a6fe-92717ffffe40.dat&#x27; &#x27;PIP2.1_test.xtc&#x27; &amp;&amp; ln -s &#x27;/tmp/tmptoruqmiy/files/7/4/5/dataset_745f4487-3b81-44f5-9eb8-9d76e882a98a.dat&#x27; &#x27;PIP2.1_test_check.txt&#x27; &amp;&amp; python &#x27;/tmp/tmptoruqmiy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/c09cf8acc4de/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories.py&#x27; --verbose --gro_file &#x27;PIP2.1_test.gro&#x27; --xtc_file &#x27;PIP2.1_test.xtc&#x27; --log_output &#x27;log/cut_trajectories.log&#x27; --output_directory &#x27;out/&#x27; --nbr_sub_traj &#x27;3&#x27; --input_check &#x27;PIP2.1_test_check.txt&#x27; --start_traj &#x27;0&#x27; --end_traj &#x27;10&#x27; --group_output 0 --number_cpus &quot;${GALAXY_SLOTS:-1}&quot;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
659 ---------------------- &gt;&gt; begin tool stdout &lt;&lt; -----------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
660
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
661 ----------------------- &gt;&gt; end tool stdout &lt;&lt; ------------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
662
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
663 ---------------------- &gt;&gt; begin tool stderr &lt;&lt; -----------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
664
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
665 ----------------------- &gt;&gt; end tool stderr &lt;&lt; ------------------------
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
666
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
667 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
668 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
669 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:153]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
670 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
671 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
672 <tbody class="passed results-table-row">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
673 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
674 <td class="col-result">Passed</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
675 <td class="col-name">test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/concatenate_table/concatenate_table/1.0.0_test_1]</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
676 <td class="col-duration">30.08</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
677 <td class="col-links"></td></tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
678 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
679 <td class="extra" colspan="4">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
680 <div class="log"> ------------------------------Captured stderr call------------------------------ <br/>2022-05-27 09:05:57,130 DEBUG [multipart.multipart] Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
681 2022-05-27 09:05:57,130 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
682 2022-05-27 09:05:57,131 DEBUG [multipart.multipart] Calling on_field_data with data[5:129]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
683 2022-05-27 09:05:57,131 DEBUG [multipart.multipart] Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
684 2022-05-27 09:05:57,131 DEBUG [multipart.multipart] Calling on_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
685 2022-05-27 09:05:57,282 INFO [galaxy.managers.configuration] Galaxy extra version JSON file /tmp/tmptoruqmiy/galaxy-dev/version.json not loaded.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
686 2022-05-27 09:05:57,369 INFO [galaxy.tools] Validated and populated state for tool request (23.134 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
687 2022-05-27 09:05:57,383 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.163 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
688 2022-05-27 09:05:57,525 DEBUG [galaxy.tools.actions.upload] Checked uploads (141.865 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
689 2022-05-27 09:05:57,531 DEBUG [galaxy.tools.actions.upload] Created upload job (5.830 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
690 2022-05-27 09:05:57,566 INFO [galaxy.web_stack.handlers] (Job[id=1,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
691 2022-05-27 09:05:58,195 INFO [galaxy.jobs.handler] (1) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
692 2022-05-27 09:05:58,387 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/1/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/1/registry.xml&#x27; &#x27;/tmp/upload_params_7yd43mro&#x27; &#x27;1:/tmp/tmptoruqmiy/job_working_directory/000/1/working/dataset_97392d40-4be1-455b-b5a1-d46e4721e0d8_files:/tmp/tmptoruqmiy/files/9/7/3/dataset_97392d40-4be1-455b-b5a1-d46e4721e0d8.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
693 2022-05-27 09:06:05,465 INFO [galaxy.tools] Validated and populated state for tool request (29.005 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
694 2022-05-27 09:06:05,474 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.156 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
695 2022-05-27 09:06:05,608 DEBUG [galaxy.tools.actions.upload] Checked uploads (133.631 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
696 2022-05-27 09:06:05,614 DEBUG [galaxy.tools.actions.upload] Created upload job (5.702 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
697 2022-05-27 09:06:05,635 INFO [galaxy.web_stack.handlers] (Job[id=2,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
698 2022-05-27 09:06:06,681 INFO [galaxy.jobs.handler] (2) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
699 2022-05-27 09:06:06,896 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/2/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/2/registry.xml&#x27; &#x27;/tmp/upload_params_niqt66u4&#x27; &#x27;2:/tmp/tmptoruqmiy/job_working_directory/000/2/working/dataset_cb889cdf-730a-428f-b94b-82c19b5bb4f4_files:/tmp/tmptoruqmiy/files/c/b/8/dataset_cb889cdf-730a-428f-b94b-82c19b5bb4f4.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
700 2022-05-27 09:06:13,887 INFO [galaxy.tools] Validated and populated state for tool request (21.823 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
701 2022-05-27 09:06:13,893 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.140 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
702 2022-05-27 09:06:14,001 DEBUG [galaxy.tools.actions.upload] Checked uploads (108.369 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
703 2022-05-27 09:06:14,007 DEBUG [galaxy.tools.actions.upload] Created upload job (5.655 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
704 2022-05-27 09:06:14,035 INFO [galaxy.web_stack.handlers] (Job[id=3,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
705 2022-05-27 09:06:14,310 INFO [galaxy.jobs.handler] (3) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
706 2022-05-27 09:06:14,453 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/3/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/3/registry.xml&#x27; &#x27;/tmp/upload_params_4_iqbmvk&#x27; &#x27;3:/tmp/tmptoruqmiy/job_working_directory/000/3/working/dataset_30dd8d24-f614-4ac7-8cd6-a4e18b4f1f3e_files:/tmp/tmptoruqmiy/files/3/0/d/dataset_30dd8d24-f614-4ac7-8cd6-a4e18b4f1f3e.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
707 2022-05-27 09:06:21,302 INFO [galaxy.tools] Validated and populated state for tool request (28.288 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
708 2022-05-27 09:06:21,362 INFO [galaxy.tools.actions] Handled output named sort_file for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/concatenate_table/concatenate_table/1.0.0 (3.760 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
709 2022-05-27 09:06:21,377 INFO [galaxy.tools.actions] Added output datasets to history (14.220 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
710 2022-05-27 09:06:21,379 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/concatenate_table/concatenate_table/1.0.0] complete, ready to be enqueued (1.770 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
711 2022-05-27 09:06:21,418 INFO [galaxy.web_stack.handlers] (Job[id=4,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/concatenate_table/concatenate_table/1.0.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
712 2022-05-27 09:06:21,724 INFO [galaxy.jobs.handler] (4) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
713 2022-05-27 09:06:22,041 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/4/tool_script.sh] for tool command [cat /tmp/tmptoruqmiy/files/9/7/3/dataset_97392d40-4be1-455b-b5a1-d46e4721e0d8.dat | awk -F&#x27;\t&#x27; &#x27;BEGIN{mean=&quot;Time (ps)&quot;; std=&quot;&quot;} /^Time/ {for (i=2; i&lt;(NF+1); i++) gsub(&quot; &quot;, &quot;,mean &quot;,$i) ; for (i=2; i&lt;(NF+1); i++) mean=mean &quot;\t&quot; $i ; for (i=2; i&lt;(NF+1); i++) gsub(&quot;,mean&quot;, &quot;,std &quot;,$i); for (i=2; i&lt;(NF+1); i++) std=std &quot;\t&quot; $i } END{print (mean std)}&#x27; &amp;&gt;&gt; &#x27;/tmp/tmptoruqmiy/files/e/e/c/dataset_eec2e4de-bddf-4d25-b9b2-aa655cfec902.dat&#x27; ; cat /tmp/tmptoruqmiy/files/9/7/3/dataset_97392d40-4be1-455b-b5a1-d46e4721e0d8.dat | awk -F&#x27;\t&#x27; -v min=200.0 &#x27;BEGIN{min_val=min ; max_val=0 ; means=&quot;&quot;; std=&quot;&quot;} /^[0-9]/ {if ($1 &lt;= min_val) {min_val=$1} ; if ($1 &gt;= max_val) {max_val=$1}} ; /Mean/ {for (i=2; i&lt;NF; i++) means=means&quot;\t&quot;$i ;means=means&quot;\t&quot;$NF } ; /Std/ {for (i=2; i&lt;NF; i++) std=std&quot;\t&quot;$i; ;std=std&quot;\t&quot;$NF} END {print (min_val &quot;-&quot; max_val means std)}&#x27; &amp;&gt;&gt; &#x27;test.tabular&#x27; ; cat /tmp/tmptoruqmiy/files/c/b/8/dataset_cb889cdf-730a-428f-b94b-82c19b5bb4f4.dat | awk -F&#x27;\t&#x27; -v min=500.0 &#x27;BEGIN{min_val=min ; max_val=0 ; means=&quot;&quot;; std=&quot;&quot;} /^[0-9]/ {if ($1 &lt;= min_val) {min_val=$1} ; if ($1 &gt;= max_val) {max_val=$1}} ; /Mean/ {for (i=2; i&lt;NF; i++) means=means&quot;\t&quot;$i ;means=means&quot;\t&quot;$NF } ; /Std/ {for (i=2; i&lt;NF; i++) std=std&quot;\t&quot;$i; ;std=std&quot;\t&quot;$NF} END {print (min_val &quot;-&quot; max_val means std)}&#x27; &amp;&gt;&gt; &#x27;test.tabular&#x27; ; cat /tmp/tmptoruqmiy/files/3/0/d/dataset_30dd8d24-f614-4ac7-8cd6-a4e18b4f1f3e.dat | awk -F&#x27;\t&#x27; -v min=1000.0 &#x27;BEGIN{min_val=min ; max_val=0 ; means=&quot;&quot;; std=&quot;&quot;} /^[0-9]/ {if ($1 &lt;= min_val) {min_val=$1} ; if ($1 &gt;= max_val) {max_val=$1}} ; /Mean/ {for (i=2; i&lt;NF; i++) means=means&quot;\t&quot;$i ;means=means&quot;\t&quot;$NF } ; /Std/ {for (i=2; i&lt;NF; i++) std=std&quot;\t&quot;$i; ;std=std&quot;\t&quot;$NF} END {print (min_val &quot;-&quot; max_val means std)}&#x27; &amp;&gt;&gt; &#x27;test.tabular&#x27; ; cat &#x27;test.tabular&#x27; | sort -k1 -n &amp;&gt;&gt; &#x27;/tmp/tmptoruqmiy/files/e/e/c/dataset_eec2e4de-bddf-4d25-b9b2-aa655cfec902.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
714 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
715 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
716 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:129]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
717 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
718 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
719 <tbody class="passed results-table-row">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
720 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
721 <td class="col-result">Passed</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
722 <td class="col-name">test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_1]</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
723 <td class="col-duration">16.85</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
724 <td class="col-links"></td></tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
725 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
726 <td class="extra" colspan="4">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
727 <div class="log"> ------------------------------Captured stderr call------------------------------ <br/>2022-05-27 09:06:27,235 DEBUG [multipart.multipart] Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
728 2022-05-27 09:06:27,236 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
729 2022-05-27 09:06:27,236 DEBUG [multipart.multipart] Calling on_field_data with data[5:153]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
730 2022-05-27 09:06:27,237 DEBUG [multipart.multipart] Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
731 2022-05-27 09:06:27,237 DEBUG [multipart.multipart] Calling on_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
732 2022-05-27 09:06:27,445 INFO [galaxy.tools] Validated and populated state for tool request (22.082 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
733 2022-05-27 09:06:27,453 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.154 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
734 2022-05-27 09:06:27,567 DEBUG [galaxy.tools.actions.upload] Checked uploads (113.879 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
735 2022-05-27 09:06:27,572 DEBUG [galaxy.tools.actions.upload] Created upload job (5.676 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
736 2022-05-27 09:06:27,592 INFO [galaxy.web_stack.handlers] (Job[id=5,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
737 2022-05-27 09:06:28,223 INFO [galaxy.jobs.handler] (5) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
738 2022-05-27 09:06:28,370 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/5/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/5/registry.xml&#x27; &#x27;/tmp/upload_params_3z8ry2g5&#x27; &#x27;5:/tmp/tmptoruqmiy/job_working_directory/000/5/working/dataset_fedb0d1a-a7bd-401b-86ba-117e6751df12_files:/tmp/tmptoruqmiy/files/f/e/d/dataset_fedb0d1a-a7bd-401b-86ba-117e6751df12.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
739 2022-05-27 09:06:37,473 INFO [galaxy.tools] Validated and populated state for tool request (22.142 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
740 2022-05-27 09:06:37,488 INFO [galaxy.tools.actions] Handled output named sub_trajectories_out_file for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (2.549 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
741 2022-05-27 09:06:37,490 INFO [galaxy.tools.actions] Handled output named estimate_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (1.954 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
742 2022-05-27 09:06:37,505 INFO [galaxy.tools.actions] Added output datasets to history (15.426 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
743 2022-05-27 09:06:37,508 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0] complete, ready to be enqueued (2.166 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
744 2022-05-27 09:06:37,543 INFO [galaxy.web_stack.handlers] (Job[id=6,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
745 2022-05-27 09:06:37,847 INFO [galaxy.jobs.handler] (6) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
746 2022-05-27 09:06:37,982 WARNI [galaxy.security.object_wrapper] Unable to create dynamic subclass SafeStringWrapper(galaxy.model.none_like.None:&lt;class &#x27;NoneType&#x27;&gt;,&lt;class &#x27;NotImplementedType&#x27;&gt;,&lt;class &#x27;bool&#x27;&gt;,&lt;class &#x27;bytearray&#x27;&gt;,&lt;class &#x27;ellipsis&#x27;&gt;,&lt;class &#x27;galaxy.security.object_wrapper.SafeStringWrapper&#x27;&gt;,&lt;class &#x27;galaxy.tools.wrappers.ToolParameterValueWrapper&#x27;&gt;,&lt;class &#x27;numbers.Number&#x27;&gt;) for &lt;class &#x27;galaxy.model.none_like.NoneDataset&#x27;&gt;, None: type() doesn&#x27;t support MRO entry resolution; use types.new_class()
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
747 2022-05-27 09:06:38,056 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/6/tool_script.sh] for tool command [[ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
748 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
749 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
750 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
751 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
752 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
753 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
754 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
755 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
756 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
757 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
758 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
759 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
760 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
761 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
762 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
763 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
764 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
765 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
766 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
767 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
768 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
769 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
770 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
771 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
772 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
773 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
774 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
775 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
776 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
777 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
778 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
779 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
780 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
781 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
782 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
783 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
784 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
785 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
786 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
787 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
788 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
789 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
790 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
791 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
792 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
793 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
794 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
795 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
796 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
797 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
798 } ; ln -s &#x27;/tmp/tmptoruqmiy/files/f/e/d/dataset_fedb0d1a-a7bd-401b-86ba-117e6751df12.dat&#x27; &#x27;PIP2.1_test_check.txt&#x27; &amp;&amp; ln -s &#x27;/tmp/tmptoruqmiy/files/5/8/a/dataset_58ab194a-5436-4b35-aea0-6b66530a0562.dat&#x27; &#x27;estimated_number_of_sub_trajectories.tsv&#x27; &amp;&amp; python &#x27;/tmp/tmptoruqmiy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/c09cf8acc4de/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories.py&#x27; --input_check &#x27;PIP2.1_test_check.txt&#x27; --verbose --output_file &#x27;estimated_number_of_sub_trajectories.tsv&#x27; --log_output &#x27;log/estimated_number_of_sub_trajectories.log&#x27; --nb_frames &#x27;3&#x27; --start_traj &#x27;&#x27; --end_traj &#x27;&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
799 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
800 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
801 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:153]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
802 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
803 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
804 <tbody class="passed results-table-row">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
805 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
806 <td class="col-result">Passed</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
807 <td class="col-name">test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0_test_1]</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
808 <td class="col-duration">23.96</td>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
809 <td class="col-links"></td></tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
810 <tr>
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
811 <td class="extra" colspan="4">
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
812 <div class="log"> ------------------------------Captured stderr call------------------------------ <br/>2022-05-27 09:08:03,555 DEBUG [multipart.multipart] Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
813 2022-05-27 09:08:03,556 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
814 2022-05-27 09:08:03,556 DEBUG [multipart.multipart] Calling on_field_data with data[5:149]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
815 2022-05-27 09:08:03,557 DEBUG [multipart.multipart] Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
816 2022-05-27 09:08:03,557 DEBUG [multipart.multipart] Calling on_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
817 2022-05-27 09:08:03,766 INFO [galaxy.tools] Validated and populated state for tool request (22.328 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
818 2022-05-27 09:08:03,772 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.146 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
819 2022-05-27 09:08:03,874 DEBUG [galaxy.tools.actions.upload] Checked uploads (101.847 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
820 2022-05-27 09:08:03,880 DEBUG [galaxy.tools.actions.upload] Created upload job (5.943 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
821 2022-05-27 09:08:03,908 INFO [galaxy.web_stack.handlers] (Job[id=15,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
822 2022-05-27 09:08:04,251 INFO [galaxy.jobs.handler] (15) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
823 2022-05-27 09:08:04,484 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/15/tool_script.sh] for tool command [python &#x27;/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmptoruqmiy/galaxy-dev&#x27; &#x27;/tmp/tmptoruqmiy/job_working_directory/000/15/registry.xml&#x27; &#x27;/tmp/upload_params_fom2zjay&#x27; &#x27;22:/tmp/tmptoruqmiy/job_working_directory/000/15/working/dataset_14d25761-af75-46cc-b88e-fff28f41b237_files:/tmp/tmptoruqmiy/files/1/4/d/dataset_14d25761-af75-46cc-b88e-fff28f41b237.dat&#x27;]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
824 2022-05-27 09:08:11,110 INFO [galaxy.tools] Validated and populated state for tool request (11.546 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
825 2022-05-27 09:08:11,124 INFO [galaxy.tools.actions] Handled output named out_file for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0 (2.658 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
826 2022-05-27 09:08:11,126 INFO [galaxy.tools.actions] Handled output named out_file2 for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0 (1.971 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
827 2022-05-27 09:08:11,128 INFO [galaxy.tools.actions] Handled output named out_file3 for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0 (1.959 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
828 2022-05-27 09:08:11,131 INFO [galaxy.tools.actions] Handled output named out_file4 for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0 (2.792 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
829 2022-05-27 09:08:11,148 INFO [galaxy.tools.actions] Added output datasets to history (16.256 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
830 2022-05-27 09:08:11,150 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0] complete, ready to be enqueued (2.459 ms)
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
831 2022-05-27 09:08:11,183 INFO [galaxy.web_stack.handlers] (Job[id=16,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
832 2022-05-27 09:08:11,681 INFO [galaxy.jobs.handler] (16) Job dispatched
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
833 2022-05-27 09:08:11,940 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/16/tool_script.sh] for tool command [[ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
834 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
835 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
836 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
837 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
838 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
839 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
840 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
841 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
842 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
843 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
844 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
845 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
846 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
847 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
848 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
849 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
850 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
851 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
852 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
853 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
854 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
855 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
856 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
857 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
858 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
859 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
860 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
861 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
862 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
863 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
864 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
865 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
866 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
867 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
868 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
869 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
870 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
871 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
872 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
873 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
874 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
875 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
876 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
877 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
878 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
879 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
880 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
881 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
882 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
883 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
884 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27;)&quot; ] || {
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
885 MAX_TRIES=3
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
886 COUNT=0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
887 while [ $COUNT -lt $MAX_TRIES ]; do
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
888 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27; &gt; conda_activate.log 2&gt;&amp;1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
889 if [ $? -eq 0 ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
890 break
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
891 else
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
892 let COUNT=COUNT+1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
893 if [ $COUNT -eq $MAX_TRIES ];then
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
894 echo &quot;Failed to activate conda environment! Error was:&quot;
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
895 cat conda_activate.log
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
896 exit 1
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
897 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
898 sleep 10s
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
899 fi
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
900 done
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
901 } ; ln -s &#x27;/tmp/tmptoruqmiy/files/1/4/d/dataset_14d25761-af75-46cc-b88e-fff28f41b237.dat&#x27; &#x27;table_sort_pore_diameter_aqp.tabular&#x27; &amp;&amp; Rscript &#x27;/tmp/tmptoruqmiy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/3cdcc6eeb3ec/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp.R&#x27; -i &#x27;table_sort_pore_diameter_aqp.tabular&#x27; -a TRUE -p TRUE -d TRUE -f TRUE]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
902 2022-05-27 09:08:24,745 INFO [galaxy.tool_util.verify] ## files diff on &#x27;/tmp/tmpher3091iall_graphics_distribution.pdf&#x27; and &#x27;/tmp/tmpc_uqkw8kall_graphics_distribution.pdf&#x27;: lines_diff = 0, found diff = 4, found pdf invalid diff = 0
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
903 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
904 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
905 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:149]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
906 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
907 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/> ----------------------------Captured stderr teardown---------------------------- <br/>2022-05-27 09:08:24,841 INFO [test_driver] 21 threads were active before stopping embedded server
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
908 2022-05-27 09:08:24,841 INFO [test_driver] Shutting down embedded galaxy uvicorn server
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
909 2022-05-27 09:08:24,841 INFO [test_driver] Embedded web server galaxy stopped
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
910 2022-05-27 09:08:24,841 INFO [test_driver] Stopping embedded server thread
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
911 INFO: Shutting down
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
912 2022-05-27 09:08:24,911 INFO [uvicorn.error] Shutting down
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
913 INFO: Waiting for application shutdown.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
914 2022-05-27 09:08:25,013 INFO [uvicorn.error] Waiting for application shutdown.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
915 INFO: Application shutdown complete.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
916 2022-05-27 09:08:25,013 INFO [uvicorn.error] Application shutdown complete.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
917 INFO: Finished server process [23683]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
918 2022-05-27 09:08:25,014 INFO [uvicorn.error] Finished server process [23683]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
919 2022-05-27 09:08:25,015 INFO [test_driver] Event loop for uvicorn closed
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
920 2022-05-27 09:08:25,016 INFO [test_driver] Embedded server thread stopped
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
921 2022-05-27 09:08:25,016 INFO [test_driver] Stopping application galaxy
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
922 2022-05-27 09:08:26,298 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
923 2022-05-27 09:08:26,325 INFO [galaxy.jobs.handler] sending stop signal to worker thread
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
924 2022-05-27 09:08:27,337 INFO [galaxy.jobs.handler] job handler queue stopped
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
925 2022-05-27 09:08:27,338 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
926 2022-05-27 09:08:27,338 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
927 2022-05-27 09:08:27,339 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
928 2022-05-27 09:08:27,340 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
929 2022-05-27 09:08:27,340 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
930 2022-05-27 09:08:27,468 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
931 2022-05-27 09:08:27,469 INFO [galaxy.jobs.handler] sending stop signal to worker thread
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
932 2022-05-27 09:08:27,469 INFO [galaxy.jobs.handler] job handler stop queue stopped
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
933 2022-05-27 09:08:27,470 INFO [test_driver] Application galaxy stopped.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
934 2022-05-27 09:08:27,471 INFO [test_driver] 2 active after stopping embedded server
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
935 <br/> -----------------------------Captured log teardown------------------------------ <br/>INFO test_driver:driver_util.py:747 21 threads were active before stopping embedded server
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
936 INFO test_driver:driver_util.py:755 Shutting down embedded galaxy uvicorn server
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
937 INFO test_driver:driver_util.py:757 Embedded web server galaxy stopped
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
938 INFO test_driver:driver_util.py:760 Stopping embedded server thread
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
939 INFO uvicorn.error:server.py:252 Shutting down
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
940 INFO uvicorn.error:on.py:64 Waiting for application shutdown.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
941 INFO uvicorn.error:on.py:75 Application shutdown complete.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
942 INFO uvicorn.error:server.py:85 Finished server process [23683]
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
943 INFO test_driver:driver_util.py:587 Event loop for uvicorn closed
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
944 INFO test_driver:driver_util.py:762 Embedded server thread stopped
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
945 INFO test_driver:driver_util.py:765 Stopping application galaxy
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
946 INFO test_driver:driver_util.py:767 Application galaxy stopped.
b120a98cf623 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
947 INFO test_driver:driver_util.py:769 2 active after stopping embedded server<br/></div></td></tr></tbody></table></body></html>