Mercurial > repos > agpetit > calculate_diameter

annotate run_installed_tests.html @ 8:d45cecb7cfd0 draft

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
author agpetit
date Mon, 30 May 2022 15:56:59 +0000
parents a7128cd8f0e1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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1 <!DOCTYPE html>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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2 <html>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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3 <head>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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4 <meta charset="utf-8"/>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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5 <title>Test Report</title>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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6 <style>body {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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7 font-family: Helvetica, Arial, sans-serif;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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8 font-size: 12px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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9 /* do not increase min-width as some may use split screens */
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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10 min-width: 800px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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11 color: #999;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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12 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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13
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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14 h1 {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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15 font-size: 24px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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16 color: black;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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17 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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18
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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19 h2 {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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20 font-size: 16px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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21 color: black;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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22 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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23
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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24 p {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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25 color: black;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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26 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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27
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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28 a {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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29 color: #999;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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30 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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31
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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32 table {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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33 border-collapse: collapse;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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34 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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35
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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36 /******************************
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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37 * SUMMARY INFORMATION
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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38 ******************************/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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39 #environment td {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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40 padding: 5px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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41 border: 1px solid #E6E6E6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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42 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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43 #environment tr:nth-child(odd) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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44 background-color: #f6f6f6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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45 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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46
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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47 /******************************
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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48 * TEST RESULT COLORS
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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49 ******************************/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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50 span.passed,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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51 .passed .col-result {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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52 color: green;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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53 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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54
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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55 span.skipped,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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56 span.xfailed,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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57 span.rerun,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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58 .skipped .col-result,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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59 .xfailed .col-result,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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60 .rerun .col-result {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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61 color: orange;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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62 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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63
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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64 span.error,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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65 span.failed,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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66 span.xpassed,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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67 .error .col-result,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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68 .failed .col-result,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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69 .xpassed .col-result {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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70 color: red;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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71 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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72
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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73 /******************************
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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74 * RESULTS TABLE
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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75 *
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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76 * 1. Table Layout
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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77 * 2. Extra
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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78 * 3. Sorting items
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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79 *
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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80 ******************************/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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81 /*------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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82 * 1. Table Layout
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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83 *------------------*/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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84 #results-table {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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85 border: 1px solid #e6e6e6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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86 color: #999;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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87 font-size: 12px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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diff changeset
88 width: 100%;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
89 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
90 #results-table th,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
91 #results-table td {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
92 padding: 5px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
93 border: 1px solid #E6E6E6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
94 text-align: left;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
95 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
96 #results-table th {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
97 font-weight: bold;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
98 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
99
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
100 /*------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
101 * 2. Extra
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
102 *------------------*/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
103 .log {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
104 background-color: #e6e6e6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
105 border: 1px solid #e6e6e6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
106 color: black;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
107 display: block;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
108 font-family: "Courier New", Courier, monospace;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
109 height: 230px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
110 overflow-y: scroll;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
111 padding: 5px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
112 white-space: pre-wrap;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
113 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
114 .log:only-child {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
115 height: inherit;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
116 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
117
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
118 div.image {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
119 border: 1px solid #e6e6e6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
120 float: right;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
121 height: 240px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
122 margin-left: 5px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
123 overflow: hidden;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
124 width: 320px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
125 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
126 div.image img {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
127 width: 320px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
128 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
129
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
130 div.video {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
131 border: 1px solid #e6e6e6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
132 float: right;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
133 height: 240px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
134 margin-left: 5px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
135 overflow: hidden;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
136 width: 320px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
137 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
138 div.video video {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
139 overflow: hidden;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
140 width: 320px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
141 height: 240px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
142 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
143
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
144 .collapsed {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
145 display: none;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
146 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
147
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
148 .expander::after {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
149 content: " (show details)";
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
150 color: #BBB;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
151 font-style: italic;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
152 cursor: pointer;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
153 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
154
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
155 .collapser::after {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
156 content: " (hide details)";
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
157 color: #BBB;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
158 font-style: italic;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
159 cursor: pointer;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
160 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
161
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
162 /*------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
163 * 3. Sorting items
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
164 *------------------*/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
165 .sortable {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
166 cursor: pointer;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
167 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
168
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
169 .sort-icon {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
170 font-size: 0px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
171 float: left;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
172 margin-right: 5px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
173 margin-top: 5px;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
174 /*triangle*/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
175 width: 0;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
176 height: 0;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
177 border-left: 8px solid transparent;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
178 border-right: 8px solid transparent;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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179 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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180 .inactive .sort-icon {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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181 /*finish triangle*/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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182 border-top: 8px solid #E6E6E6;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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183 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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184 .asc.active .sort-icon {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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185 /*finish triangle*/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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186 border-bottom: 8px solid #999;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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187 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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188 .desc.active .sort-icon {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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189 /*finish triangle*/
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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190 border-top: 8px solid #999;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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191 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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192 </style></head>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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193 <body onLoad="init()">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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194 <script>/* This Source Code Form is subject to the terms of the Mozilla Public
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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195 * License, v. 2.0. If a copy of the MPL was not distributed with this file,
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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196 * You can obtain one at http://mozilla.org/MPL/2.0/. */
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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197
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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198
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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199 function toArray(iter) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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200 if (iter === null) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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201 return null;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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202 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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203 return Array.prototype.slice.call(iter);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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204 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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205
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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206 function find(selector, elem) { // eslint-disable-line no-redeclare
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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207 if (!elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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208 elem = document;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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209 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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210 return elem.querySelector(selector);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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211 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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212
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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213 function findAll(selector, elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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214 if (!elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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215 elem = document;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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216 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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217 return toArray(elem.querySelectorAll(selector));
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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218 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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219
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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220 function sortColumn(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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221 toggleSortStates(elem);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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222 const colIndex = toArray(elem.parentNode.childNodes).indexOf(elem);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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223 let key;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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224 if (elem.classList.contains('result')) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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225 key = keyResult;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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226 } else if (elem.classList.contains('links')) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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227 key = keyLink;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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228 } else {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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229 key = keyAlpha;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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230 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
231 sortTable(elem, key(colIndex));
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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232 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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233
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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234 function showAllExtras() { // eslint-disable-line no-unused-vars
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
235 findAll('.col-result').forEach(showExtras);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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236 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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237
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
238 function hideAllExtras() { // eslint-disable-line no-unused-vars
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
239 findAll('.col-result').forEach(hideExtras);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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240 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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241
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
242 function showExtras(colresultElem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
243 const extras = colresultElem.parentNode.nextElementSibling;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
244 const expandcollapse = colresultElem.firstElementChild;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
245 extras.classList.remove('collapsed');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
246 expandcollapse.classList.remove('expander');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
247 expandcollapse.classList.add('collapser');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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248 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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249
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
250 function hideExtras(colresultElem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
251 const extras = colresultElem.parentNode.nextElementSibling;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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252 const expandcollapse = colresultElem.firstElementChild;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
253 extras.classList.add('collapsed');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
254 expandcollapse.classList.remove('collapser');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
255 expandcollapse.classList.add('expander');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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256 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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257
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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258 function showFilters() {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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259 const filterItems = document.getElementsByClassName('filter');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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260 for (let i = 0; i < filterItems.length; i++)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
261 filterItems[i].hidden = false;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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262 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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263
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
264 function addCollapse() {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
265 // Add links for show/hide all
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
266 const resulttable = find('table#results-table');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
267 const showhideall = document.createElement('p');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
268 showhideall.innerHTML = '<a href="javascript:showAllExtras()">Show all details</a> / ' +
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
269 '<a href="javascript:hideAllExtras()">Hide all details</a>';
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
270 resulttable.parentElement.insertBefore(showhideall, resulttable);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
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271
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
272 // Add show/hide link to each result
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
273 findAll('.col-result').forEach(function(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
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274 const collapsed = getQueryParameter('collapsed') || 'Passed';
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
275 const extras = elem.parentNode.nextElementSibling;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
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276 const expandcollapse = document.createElement('span');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
277 if (extras.classList.contains('collapsed')) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
278 expandcollapse.classList.add('expander');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
279 } else if (collapsed.includes(elem.innerHTML)) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
280 extras.classList.add('collapsed');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
281 expandcollapse.classList.add('expander');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
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282 } else {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
283 expandcollapse.classList.add('collapser');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
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284 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
285 elem.appendChild(expandcollapse);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
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286
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
287 elem.addEventListener('click', function(event) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
288 if (event.currentTarget.parentNode.nextElementSibling.classList.contains('collapsed')) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
289 showExtras(event.currentTarget);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
290 } else {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
291 hideExtras(event.currentTarget);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
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292 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
293 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
294 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
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295 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
296
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
297 function getQueryParameter(name) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
298 const match = RegExp('[?&]' + name + '=([^&]*)').exec(window.location.search);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
299 return match && decodeURIComponent(match[1].replace(/\+/g, ' '));
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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300 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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diff changeset
301
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
302 function init () { // eslint-disable-line no-unused-vars
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
303 resetSortHeaders();
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
304
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
305 addCollapse();
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
306
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
307 showFilters();
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
308
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
309 sortColumn(find('.initial-sort'));
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
310
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
311 findAll('.sortable').forEach(function(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
312 elem.addEventListener('click',
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
313 function() {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
314 sortColumn(elem);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
315 }, false);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
316 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
317 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
318
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
319 function sortTable(clicked, keyFunc) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
320 const rows = findAll('.results-table-row');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
321 const reversed = !clicked.classList.contains('asc');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
322 const sortedRows = sort(rows, keyFunc, reversed);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
323 /* Whole table is removed here because browsers acts much slower
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
324 * when appending existing elements.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
325 */
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
326 const thead = document.getElementById('results-table-head');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
327 document.getElementById('results-table').remove();
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
328 const parent = document.createElement('table');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
329 parent.id = 'results-table';
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
330 parent.appendChild(thead);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
331 sortedRows.forEach(function(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
332 parent.appendChild(elem);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
333 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
334 document.getElementsByTagName('BODY')[0].appendChild(parent);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
335 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
336
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
337 function sort(items, keyFunc, reversed) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
338 const sortArray = items.map(function(item, i) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
339 return [keyFunc(item), i];
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
340 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
341
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
342 sortArray.sort(function(a, b) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
343 const keyA = a[0];
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
344 const keyB = b[0];
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
345
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
346 if (keyA == keyB) return 0;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
347
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
348 if (reversed) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
349 return keyA < keyB ? 1 : -1;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
350 } else {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
351 return keyA > keyB ? 1 : -1;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
352 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
353 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
354
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
355 return sortArray.map(function(item) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
356 const index = item[1];
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
357 return items[index];
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
358 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
359 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
360
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
361 function keyAlpha(colIndex) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
362 return function(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
363 return elem.childNodes[1].childNodes[colIndex].firstChild.data.toLowerCase();
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
364 };
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
365 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
366
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
367 function keyLink(colIndex) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
368 return function(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
369 const dataCell = elem.childNodes[1].childNodes[colIndex].firstChild;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
370 return dataCell == null ? '' : dataCell.innerText.toLowerCase();
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
371 };
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
372 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
373
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
374 function keyResult(colIndex) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
375 return function(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
376 const strings = ['Error', 'Failed', 'Rerun', 'XFailed', 'XPassed',
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
377 'Skipped', 'Passed'];
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
378 return strings.indexOf(elem.childNodes[1].childNodes[colIndex].firstChild.data);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
379 };
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
380 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
381
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
382 function resetSortHeaders() {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
383 findAll('.sort-icon').forEach(function(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
384 elem.parentNode.removeChild(elem);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
385 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
386 findAll('.sortable').forEach(function(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
387 const icon = document.createElement('div');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
388 icon.className = 'sort-icon';
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
389 icon.textContent = 'vvv';
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
390 elem.insertBefore(icon, elem.firstChild);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
391 elem.classList.remove('desc', 'active');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
392 elem.classList.add('asc', 'inactive');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
393 });
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
394 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
395
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
396 function toggleSortStates(elem) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
397 //if active, toggle between asc and desc
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
398 if (elem.classList.contains('active')) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
399 elem.classList.toggle('asc');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
400 elem.classList.toggle('desc');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
401 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
402
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
403 //if inactive, reset all other functions and add ascending active
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
404 if (elem.classList.contains('inactive')) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
405 resetSortHeaders();
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
406 elem.classList.remove('inactive');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
407 elem.classList.add('active');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
408 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
409 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
410
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
411 function isAllRowsHidden(value) {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
412 return value.hidden == false;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
413 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
414
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
415 function filterTable(elem) { // eslint-disable-line no-unused-vars
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
416 const outcomeAtt = 'data-test-result';
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
417 const outcome = elem.getAttribute(outcomeAtt);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
418 const classOutcome = outcome + ' results-table-row';
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
419 const outcomeRows = document.getElementsByClassName(classOutcome);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
420
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
421 for(let i = 0; i < outcomeRows.length; i++){
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
422 outcomeRows[i].hidden = !elem.checked;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
423 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
424
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
425 const rows = findAll('.results-table-row').filter(isAllRowsHidden);
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
426 const allRowsHidden = rows.length == 0 ? true : false;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
427 const notFoundMessage = document.getElementById('not-found-message');
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
428 notFoundMessage.hidden = !allRowsHidden;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
429 }
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
430 </script>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
431 <h1>run_installed_tests.html</h1>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
432 <p>Report generated on 30-May-2022 at 16:40:20 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a> v3.1.1</p>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
433 <h2>Environment</h2>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
434 <table id="environment">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
435 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
436 <td>Packages</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
437 <td>{"pluggy": "1.0.0", "py": "1.11.0", "pytest": "6.2.5"}</td></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
438 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
439 <td>Platform</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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440 <td>Linux-5.13.0-44-generic-x86_64-with-glibc2.29</td></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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441 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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442 <td>Plugins</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-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>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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444 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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445 <td>Python</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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446 <td>3.8.10</td></tr></table>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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447 <h2>Summary</h2>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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448 <p>6 tests ran in 207.85 seconds. </p>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-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">4 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>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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450 <h2>Results</h2>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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451 <table id="results-table">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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452 <thead id="results-table-head">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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453 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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454 <th class="sortable result initial-sort" col="result">Result</th>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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455 <th class="sortable" col="name">Test</th>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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456 <th class="sortable" col="duration">Duration</th>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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457 <th class="sortable links" col="links">Links</th></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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458 <tr hidden="true" id="not-found-message">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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459 <th colspan="4">No results found. Try to check the filters</th></tr></thead>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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460 <tbody class="failed results-table-row">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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461 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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462 <td class="col-result">Failed</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-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/cut_trajectory/cut_trajectory/0.1.0_test_1]</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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464 <td class="col-duration">41.70</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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465 <td class="col-links"></td></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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466 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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467 <td class="extra" colspan="4">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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468 <div class="log">testcases = (&#x27;testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0_test_1&#x27;, &lt;functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0 testMethod=runTest&gt;, 0)<br/>driver = &lt;functional.test_toolbox_pytest.DefaultGalaxyTestDriver object at 0x7fbd7dccadc0&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 0x7fbd717e2400&gt;, history = &#x27;54f2a3a23292eb07&#x27;<br/>jobs = [{&#x27;create_time&#x27;: &#x27;2022-05-30T14:38:35.742760&#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;2022-05-30T14:38:35.746121&#x27;, &#x27;data_type&#x27;: &#x27;galaxy.datatypes.data.Text&#x27;, &#x27;deleted&#x27;: False,...b446aa50-6cfd-42d4-a1ed-d388b4035422&#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;2022-05-30T14:38:35.744675&#x27;, &#x27;deleted&#x27;: False, ...}}<br/>galaxy_interactor = &lt;galaxy.tool_util.verify.interactor.GalaxyInteractorApi object at 0x7fbd2509c1f0&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, difference (using diff):</span><br/><span class="error">E ( /tmp/tmppchetkzbcut_trajectories_file.log v. /tmp/tmpt35t2o_2cut_trajectories_file.log )</span><br/><span class="error">E --- local_file</span><br/><span class="error">E +++ history_data</span><br/><span class="error">E @@ -25,9 +25,9 @@</span><br/><span class="error">E </span><br/><span class="error">E :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:</span><br/><span class="error">E </span><br/><span class="error">E -Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx</span><br/><span class="error">E -Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1</span><br/><span class="error">E -Working dir: /tmp/tmp87fei_xs/job_working_directory/000/5/working</span><br/><span class="error">E +Executable: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296/bin.AVX2_256/gmx</span><br/><span class="error">E +Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296</span><br/><span class="error">E +Working dir: /tmp/tmpudbcnm66/job_working_directory/000/11/working</span><br/><span class="error">E Command line:</span><br/><span class="error">E gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 0 -e 20 -o out/PIP2.1_test_traj_1.xtc</span><br/><span class="error">E </span><br/><span class="error">E @@ -63,16 +63,16 @@</span><br/><span class="error">E Last written: frame 2 time 20.000</span><br/><span class="error">E </span><br/><span class="error">E </span><br/><span class="error">E -GROMACS reminds you: &quot;The Microsecond is Within Reach&quot; (P.J. Van Maaren)</span><br/><span class="error">E +GROMACS reminds you: &quot;Unlike teachers or doctors, our efforts improve the lives of people we&#x27;ll never meet.&quot; (Katie Busch-Sorensen)</span><br/><span class="error">E </span><br/><span class="error">E Note that major changes are planned in future for trjconv, to improve usability and utility.</span><br/><span class="error">E Select group for output</span><br/><span class="error">E Selected 0: &#x27;System&#x27;</span><br/><span class="error">E ********</span><br/><span class="error">E *SNIP *</span><br/><span class="error">E ********</span><br/><span class="error">E +GROMACS reminds you: &quot;What about my nose?&quot; (Aneesur Rahman, responding to an Argonne manager arguing the long hair of Charles Bennett in his group was disreputing the lab; Retold by Michael Klein)</span><br/><span class="error">E </span><br/><span class="error">E Note that major changes are planned in future for trjconv, to improve usability and utility.</span><br/><span class="error">E Select group for output</span><br/><span class="error">E Selected 0: &#x27;System&#x27;</span><br/><span class="error">E :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:</span><br/><span class="error">E </span><br/><span class="error">E -Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx</span><br/><span class="error">E -Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1</span><br/><span class="error">E -Working dir: /tmp/tmp87fei_xs/job_working_directory/000/5/working</span><br/><span class="error">E +Executable: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296/bin.AVX2_256/gmx</span><br/><span class="error">E +Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296</span><br/><span class="error">E +Working dir: /tmp/tmpudbcnm66/job_working_directory/000/11/working</span><br/><span class="error">E Command line:</span><br/><span class="error">E gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc</span><br/><span class="error">E </span><br/><span class="error">E @@ -155,7 +155,7 @@</span><br/><span class="error">E Last written: frame 2 time 80.000</span><br/><span class="error">E </span><br/><span class="error">E </span><br/><span class="error">E -GROMACS reminds you: &quot;Furious activity is no substitute for understanding.&quot; (H.H. Williams)</span><br/><span class="error">E +GROMACS reminds you: &quot;There&#x27;s so many shades of black&quot; (The Raconteurs)</span><br/><span class="error">E </span><br/><span class="error">E Note that major changes are planned in future for trjconv, to improve usability and utility.</span><br/><span class="error">E Select group for output</span><br/><br/>lib/galaxy/tool_util/verify/interactor.py:1299: JobOutputsError<br/> ------------------------------Captured stderr call------------------------------ <br/>2022-05-30 16:38:07,832 DEBUG [multipart.multipart] Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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469 2022-05-30 16:38:07,832 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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470 2022-05-30 16:38:07,833 DEBUG [multipart.multipart] Calling on_field_data with data[5:123]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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471 2022-05-30 16:38:07,833 DEBUG [multipart.multipart] Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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472 2022-05-30 16:38:07,833 DEBUG [multipart.multipart] Calling on_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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473 2022-05-30 16:38:08,953 INFO [galaxy.tools] Validated and populated state for tool request (29.050 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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474 2022-05-30 16:38:08,960 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.145 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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475 2022-05-30 16:38:09,092 DEBUG [galaxy.tools.actions.upload] Checked uploads (132.576 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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476 2022-05-30 16:38:09,098 DEBUG [galaxy.tools.actions.upload] Created upload job (6.056 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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477 2022-05-30 16:38:09,122 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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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478 2022-05-30 16:38:09,852 INFO [galaxy.jobs.handler] (8) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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479 2022-05-30 16:38:10,126 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/8/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/8/registry.xml&#x27; &#x27;/tmp/upload_params_i5a_w25s&#x27; &#x27;9:/tmp/tmpudbcnm66/job_working_directory/000/8/working/dataset_23d2a6f5-94b1-4d86-9f3f-a265f3acfe63_files:/tmp/tmpudbcnm66/files/2/3/d/dataset_23d2a6f5-94b1-4d86-9f3f-a265f3acfe63.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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480 2022-05-30 16:38:18,031 INFO [galaxy.tools] Validated and populated state for tool request (29.267 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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481 2022-05-30 16:38:18,038 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.146 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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482 2022-05-30 16:38:18,189 DEBUG [galaxy.tools.actions.upload] Checked uploads (150.477 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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483 2022-05-30 16:38:18,195 DEBUG [galaxy.tools.actions.upload] Created upload job (6.006 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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484 2022-05-30 16:38:18,222 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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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485 2022-05-30 16:38:19,453 INFO [galaxy.jobs.handler] (9) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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486 2022-05-30 16:38:19,600 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/9/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/9/registry.xml&#x27; &#x27;/tmp/upload_params_f8bxg9_p&#x27; &#x27;10:/tmp/tmpudbcnm66/job_working_directory/000/9/working/dataset_db8cec7e-182c-4956-ab6d-92d9562a59a0_files:/tmp/tmpudbcnm66/files/d/b/8/dataset_db8cec7e-182c-4956-ab6d-92d9562a59a0.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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487 2022-05-30 16:38:26,862 INFO [galaxy.tools] Validated and populated state for tool request (22.705 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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488 2022-05-30 16:38:26,868 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.148 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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489 2022-05-30 16:38:26,990 DEBUG [galaxy.tools.actions.upload] Checked uploads (121.841 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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490 2022-05-30 16:38:26,997 DEBUG [galaxy.tools.actions.upload] Created upload job (6.363 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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491 2022-05-30 16:38:27,045 INFO [galaxy.web_stack.handlers] (Job[id=10,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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492 2022-05-30 16:38:28,374 INFO [galaxy.jobs.handler] (10) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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493 2022-05-30 16:38:28,534 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/10/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/10/registry.xml&#x27; &#x27;/tmp/upload_params_ta376p5u&#x27; &#x27;11:/tmp/tmpudbcnm66/job_working_directory/000/10/working/dataset_3d11862f-97ea-4b1f-9042-90ff10bf136a_files:/tmp/tmpudbcnm66/files/3/d/1/dataset_3d11862f-97ea-4b1f-9042-90ff10bf136a.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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494 2022-05-30 16:38:35,702 INFO [galaxy.tools] Validated and populated state for tool request (25.700 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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495 2022-05-30 16:38:35,716 INFO [galaxy.tools.actions] Handled collection output named output_traj for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0 (2.649 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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496 2022-05-30 16:38:35,718 INFO [galaxy.tools.actions] Handled output named cut_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0 (2.191 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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497 2022-05-30 16:38:35,729 INFO [galaxy.tools.actions] Added output datasets to history (10.524 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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498 2022-05-30 16:38:35,731 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0] complete, ready to be enqueued (1.911 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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499 2022-05-30 16:38:35,771 INFO [galaxy.web_stack.handlers] (Job[id=11,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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500 2022-05-30 16:38:36,103 INFO [galaxy.jobs.handler] (11) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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501 2022-05-30 16:38:36,326 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/11/tool_script.sh] for tool command [[ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296&#x27;)&quot; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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502 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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503 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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diff changeset
504 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
505 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
506 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
507 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
508 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
509 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
510 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
511 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
512 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
513 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
514 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
515 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
516 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
517 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
518 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296&#x27;)&quot; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
519 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
520 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
521 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
522 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
523 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
524 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
525 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
526 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
527 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
528 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
529 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
530 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
531 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
532 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
533 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
534 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
535 } ; ln -s &#x27;/tmp/tmpudbcnm66/files/2/3/d/dataset_23d2a6f5-94b1-4d86-9f3f-a265f3acfe63.dat&#x27; &#x27;PIP2.1_test.gro&#x27; &amp;&amp; ln -s &#x27;/tmp/tmpudbcnm66/files/d/b/8/dataset_db8cec7e-182c-4956-ab6d-92d9562a59a0.dat&#x27; &#x27;PIP2.1_test.xtc&#x27; &amp;&amp; ln -s &#x27;/tmp/tmpudbcnm66/files/3/d/1/dataset_3d11862f-97ea-4b1f-9042-90ff10bf136a.dat&#x27; &#x27;estimated_number_of_sub_trajectories.tsv&#x27; &amp;&amp; python &#x27;/tmp/tmpudbcnm66/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/b9fb306ccb2a/cut_trajectory/cut_trajectory.py&#x27; --verbose --gro_file &#x27;PIP2.1_test.gro&#x27; --xtc_file &#x27;PIP2.1_test.xtc&#x27; --log_output &#x27;out_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;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
536 2022-05-30 16:38:47,856 INFO [galaxy.tool_util.verify] ## files diff on &#x27;/tmp/tmppchetkzbcut_trajectories_file.log&#x27; and &#x27;/tmp/tmpt35t2o_2cut_trajectories_file.log&#x27;: lines_diff = 12, found diff = 24
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
537 ---------------------- &gt;&gt; begin tool stdout &lt;&lt; -----------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
538
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
539 ----------------------- &gt;&gt; end tool stdout &lt;&lt; ------------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
540
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
541 ---------------------- &gt;&gt; begin tool stderr &lt;&lt; -----------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
542
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
543 ----------------------- &gt;&gt; end tool stderr &lt;&lt; ------------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
544
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
545 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
546 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
547 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:123]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
548 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
549 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
550 <tbody class="failed results-table-row">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
551 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
552 <td class="col-result">Failed</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
553 <td class="col-name">test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0_test_2]</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
554 <td class="col-duration">45.94</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
555 <td class="col-links"></td></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
556 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
557 <td class="extra" colspan="4">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
558 <div class="log">testcases = (&#x27;testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0_test_2&#x27;, &lt;functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0 testMethod=runTest&gt;, 1)<br/>driver = &lt;functional.test_toolbox_pytest.DefaultGalaxyTestDriver object at 0x7fbd7dccadc0&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 0x7fbd7aaba0d0&gt;, history = &#x27;8155e4b4bf1581ff&#x27;<br/>jobs = [{&#x27;create_time&#x27;: &#x27;2022-05-30T14:39:20.051320&#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;2022-05-30T14:39:20.055030&#x27;, &#x27;data_type&#x27;: &#x27;galaxy.datatypes.data.Text&#x27;, &#x27;deleted&#x27;: False,...9bcf1c61-a26b-4578-9eb2-b93eb3b0d2d9&#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;2022-05-30T14:39:20.052784&#x27;, &#x27;deleted&#x27;: False, ...}}<br/>galaxy_interactor = &lt;galaxy.tool_util.verify.interactor.GalaxyInteractorApi object at 0x7fbd2509c1f0&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, difference (using diff):</span><br/><span class="error">E ( /tmp/tmp64i094o0cut_trajectories_no_file.log v. /tmp/tmpmbp6yd0kcut_trajectories_no_file.log )</span><br/><span class="error">E --- local_file</span><br/><span class="error">E +++ history_data</span><br/><span class="error">E @@ -23,9 +23,9 @@</span><br/><span class="error">E </span><br/><span class="error">E :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:</span><br/><span class="error">E </span><br/><span class="error">E -Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx</span><br/><span class="error">E -Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1</span><br/><span class="error">E -Working dir: /tmp/tmp87fei_xs/job_working_directory/000/7/working</span><br/><span class="error">E +Executable: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296/bin.AVX2_256/gmx</span><br/><span class="error">E +Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296</span><br/><span class="error">E +Working dir: /tmp/tmpudbcnm66/job_working_directory/000/15/working</span><br/><span class="error">E Command line:</span><br/><span class="error">E gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 0 -e 20 -o out/PIP2.1_test_traj_1.xtc</span><br/><span class="error">E </span><br/><span class="error">E @@ -61,16 +61,16 @@</span><br/><span class="error">E Last written: frame 2 time 20.000</span><br/><span class="error">E </span><br/><span class="error">E </span><br/><span class="error">E -GROMACS reminds you: &quot;It is now quite lawful for a Catholic woman to avoid pregnancy by a resort to mathematics, though she is still forbidden to resort to physics and chemistry.&quot; (Henry Louis Mencken)</span><br/><span class="error">E +GROMACS reminds you: &quot;Pretend That You&#x27;re Hercule Poirot&quot; (TeX)</span><br/><span class="error">E </span><br/><span class="error">E Note that major changes are planned in future for trjconv, to improve usability and utility.</span><br/><span class="error">E Select group for output</span><br/><span class="error">E Selected 0: &#x27;System&#x27;</span><br/><span class="error">E ********</span><br/><span class="error">E *SNIP *</span><br/><span class="error">E ********</span><br/><span class="error">E +GROMACS reminds you: &quot;If it&#x27;s a good idea, go ahead and do it. It&#x27;s much easier to apologize than it is to get permission.&quot; (Grace Hopper, developer of COBOL)</span><br/><span class="error">E </span><br/><span class="error">E Note that major changes are planned in future for trjconv, to improve usability and utility.</span><br/><span class="error">E Select group for output</span><br/><span class="error">E Selected 0: &#x27;System&#x27;</span><br/><span class="error">E :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:</span><br/><span class="error">E </span><br/><span class="error">E -Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx</span><br/><span class="error">E -Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1</span><br/><span class="error">E -Working dir: /tmp/tmp87fei_xs/job_working_directory/000/7/working</span><br/><span class="error">E +Executable: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296/bin.AVX2_256/gmx</span><br/><span class="error">E +Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296</span><br/><span class="error">E +Working dir: /tmp/tmpudbcnm66/job_working_directory/000/15/working</span><br/><span class="error">E Command line:</span><br/><span class="error">E gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc</span><br/><span class="error">E </span><br/><span class="error">E @@ -153,7 +153,7 @@</span><br/><span class="error">E Last written: frame 2 time 80.000</span><br/><span class="error">E </span><br/><span class="error">E </span><br/><span class="error">E -GROMACS reminds you: &quot;Whatever Happened to Pong ?&quot; (F. Black)</span><br/><span class="error">E +GROMACS reminds you: &quot;Oh My God ! It&#x27;s the Funky Shit&quot; (Beastie Boys)</span><br/><span class="error">E </span><br/><span class="error">E Note that major changes are planned in future for trjconv, to improve usability and utility.</span><br/><span class="error">E Select group for output</span><br/><br/>lib/galaxy/tool_util/verify/interactor.py:1299: JobOutputsError<br/> ------------------------------Captured stderr call------------------------------ <br/>2022-05-30 16:38:49,689 DEBUG [multipart.multipart] Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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559 2022-05-30 16:38:49,689 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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560 2022-05-30 16:38:49,689 DEBUG [multipart.multipart] Calling on_field_data with data[5:123]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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561 2022-05-30 16:38:49,689 DEBUG [multipart.multipart] Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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562 2022-05-30 16:38:49,690 DEBUG [multipart.multipart] Calling on_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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563 2022-05-30 16:38:50,819 INFO [galaxy.tools] Validated and populated state for tool request (23.182 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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564 2022-05-30 16:38:50,825 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.158 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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565 2022-05-30 16:38:50,943 DEBUG [galaxy.tools.actions.upload] Checked uploads (118.175 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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566 2022-05-30 16:38:50,952 DEBUG [galaxy.tools.actions.upload] Created upload job (8.520 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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567 2022-05-30 16:38:50,974 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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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568 2022-05-30 16:38:51,873 INFO [galaxy.jobs.handler] (12) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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569 2022-05-30 16:38:52,023 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/12/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/12/registry.xml&#x27; &#x27;/tmp/upload_params_fm4vkooe&#x27; &#x27;16:/tmp/tmpudbcnm66/job_working_directory/000/12/working/dataset_835311dd-d3e5-4db2-bd98-274b2aa04186_files:/tmp/tmpudbcnm66/files/8/3/5/dataset_835311dd-d3e5-4db2-bd98-274b2aa04186.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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570 2022-05-30 16:39:00,135 INFO [galaxy.tools] Validated and populated state for tool request (22.401 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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571 2022-05-30 16:39:00,141 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.169 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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572 2022-05-30 16:39:00,253 DEBUG [galaxy.tools.actions.upload] Checked uploads (111.316 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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573 2022-05-30 16:39:00,260 DEBUG [galaxy.tools.actions.upload] Created upload job (7.542 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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574 2022-05-30 16:39:00,290 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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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575 2022-05-30 16:39:00,589 INFO [galaxy.jobs.handler] (13) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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576 2022-05-30 16:39:00,789 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/13/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/13/registry.xml&#x27; &#x27;/tmp/upload_params_porkb1x0&#x27; &#x27;17:/tmp/tmpudbcnm66/job_working_directory/000/13/working/dataset_93d9a3db-08e5-4c64-b4b8-6ea194b2ec67_files:/tmp/tmpudbcnm66/files/9/3/d/dataset_93d9a3db-08e5-4c64-b4b8-6ea194b2ec67.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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577 2022-05-30 16:39:07,852 INFO [galaxy.tools] Validated and populated state for tool request (23.241 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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578 2022-05-30 16:39:07,858 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.145 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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579 2022-05-30 16:39:07,983 DEBUG [galaxy.tools.actions.upload] Checked uploads (124.879 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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parents:
diff changeset
580 2022-05-30 16:39:07,994 DEBUG [galaxy.tools.actions.upload] Created upload job (10.361 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
581 2022-05-30 16:39:08,024 INFO [galaxy.web_stack.handlers] (Job[id=14,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
582 2022-05-30 16:39:09,254 INFO [galaxy.jobs.handler] (14) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
583 2022-05-30 16:39:09,407 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/14/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/14/registry.xml&#x27; &#x27;/tmp/upload_params_zlwcb6g0&#x27; &#x27;18:/tmp/tmpudbcnm66/job_working_directory/000/14/working/dataset_89419396-ffd3-496c-9421-9534fdcdfb7b_files:/tmp/tmpudbcnm66/files/8/9/4/dataset_89419396-ffd3-496c-9421-9534fdcdfb7b.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
584 2022-05-30 16:39:20,011 INFO [galaxy.tools] Validated and populated state for tool request (25.260 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
585 2022-05-30 16:39:20,024 INFO [galaxy.tools.actions] Handled collection output named output_traj for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0 (0.951 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
586 2022-05-30 16:39:20,025 INFO [galaxy.tools.actions] Handled output named cut_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0 (0.960 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
587 2022-05-30 16:39:20,036 INFO [galaxy.tools.actions] Added output datasets to history (11.339 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
588 2022-05-30 16:39:20,039 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0] complete, ready to be enqueued (1.890 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
589 2022-05-30 16:39:20,079 INFO [galaxy.web_stack.handlers] (Job[id=15,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/cut_trajectory/0.1.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
590 2022-05-30 16:39:21,134 INFO [galaxy.jobs.handler] (15) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
591 2022-05-30 16:39:21,441 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/15/tool_script.sh] for tool command [[ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296&#x27;)&quot; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
592 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
593 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
594 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
595 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
596 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
597 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
598 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
599 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
600 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
601 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
602 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
603 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
604 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
605 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
606 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
607 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
608 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296&#x27;)&quot; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
609 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
610 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
611 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
612 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
613 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
614 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
615 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
616 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
617 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
618 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
619 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
620 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
621 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
622 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
623 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
624 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
625 } ; ln -s &#x27;/tmp/tmpudbcnm66/files/8/3/5/dataset_835311dd-d3e5-4db2-bd98-274b2aa04186.dat&#x27; &#x27;PIP2.1_test.gro&#x27; &amp;&amp; ln -s &#x27;/tmp/tmpudbcnm66/files/9/3/d/dataset_93d9a3db-08e5-4c64-b4b8-6ea194b2ec67.dat&#x27; &#x27;PIP2.1_test.xtc&#x27; &amp;&amp; ln -s &#x27;/tmp/tmpudbcnm66/files/8/9/4/dataset_89419396-ffd3-496c-9421-9534fdcdfb7b.dat&#x27; &#x27;PIP2.1_test_check.txt&#x27; &amp;&amp; python &#x27;/tmp/tmpudbcnm66/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/cut_trajectory/b9fb306ccb2a/cut_trajectory/cut_trajectory.py&#x27; --verbose --gro_file &#x27;PIP2.1_test.gro&#x27; --xtc_file &#x27;PIP2.1_test.xtc&#x27; --log_output &#x27;out_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;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
626 2022-05-30 16:39:33,777 INFO [galaxy.tool_util.verify] ## files diff on &#x27;/tmp/tmp64i094o0cut_trajectories_no_file.log&#x27; and &#x27;/tmp/tmpmbp6yd0kcut_trajectories_no_file.log&#x27;: lines_diff = 12, found diff = 24
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
627 ---------------------- &gt;&gt; begin tool stdout &lt;&lt; -----------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
628
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
629 ----------------------- &gt;&gt; end tool stdout &lt;&lt; ------------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
630
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
631 ---------------------- &gt;&gt; begin tool stderr &lt;&lt; -----------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
632
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
633 ----------------------- &gt;&gt; end tool stderr &lt;&lt; ------------------------
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
634
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
635 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
636 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
637 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:123]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
638 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
639 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
640 <tbody class="passed results-table-row">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
641 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
642 <td class="col-result">Passed</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
643 <td class="col-name">test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/calculate_diameter/calculate_diameter/1.0.0_test_1]</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
644 <td class="col-duration">30.87</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
645 <td class="col-links"></td></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
646 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
647 <td class="extra" colspan="4">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
648 <div class="log"> ------------------------------Captured stderr call------------------------------ <br/>2022-05-30 16:37:05,655 DEBUG [multipart.multipart] Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
649 2022-05-30 16:37:05,655 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
650 2022-05-30 16:37:05,655 DEBUG [multipart.multipart] Calling on_field_data with data[5:131]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
651 2022-05-30 16:37:05,655 DEBUG [multipart.multipart] Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
652 2022-05-30 16:37:05,655 DEBUG [multipart.multipart] Calling on_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
653 2022-05-30 16:37:05,796 INFO [galaxy.managers.configuration] Galaxy extra version JSON file /tmp/tmpudbcnm66/galaxy-dev/version.json not loaded.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
654 2022-05-30 16:37:06,804 INFO [galaxy.tools] Validated and populated state for tool request (24.171 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
655 2022-05-30 16:37:06,821 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.159 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
656 2022-05-30 16:37:06,969 DEBUG [galaxy.tools.actions.upload] Checked uploads (147.872 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
657 2022-05-30 16:37:06,975 DEBUG [galaxy.tools.actions.upload] Created upload job (5.802 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
658 2022-05-30 16:37:07,006 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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
659 2022-05-30 16:37:07,656 INFO [galaxy.jobs.handler] (1) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
660 2022-05-30 16:37:07,917 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/1/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/1/registry.xml&#x27; &#x27;/tmp/upload_params_b__72u_9&#x27; &#x27;1:/tmp/tmpudbcnm66/job_working_directory/000/1/working/dataset_fa99edec-859c-4f92-a5c3-df96305c5bb8_files:/tmp/tmpudbcnm66/files/f/a/9/dataset_fa99edec-859c-4f92-a5c3-df96305c5bb8.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
661 2022-05-30 16:37:15,524 INFO [galaxy.tools] Validated and populated state for tool request (24.286 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
662 2022-05-30 16:37:15,531 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.453 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
663 2022-05-30 16:37:15,643 DEBUG [galaxy.tools.actions.upload] Checked uploads (112.079 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
664 2022-05-30 16:37:15,650 DEBUG [galaxy.tools.actions.upload] Created upload job (6.610 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
665 2022-05-30 16:37:15,678 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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
666 2022-05-30 16:37:16,066 INFO [galaxy.jobs.handler] (2) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
667 2022-05-30 16:37:16,315 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/2/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/2/registry.xml&#x27; &#x27;/tmp/upload_params_tk7_ntpu&#x27; &#x27;2:/tmp/tmpudbcnm66/job_working_directory/000/2/working/dataset_428a901e-46dd-433f-aa38-040834923c53_files:/tmp/tmpudbcnm66/files/4/2/8/dataset_428a901e-46dd-433f-aa38-040834923c53.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
668 2022-05-30 16:37:23,491 INFO [galaxy.tools] Validated and populated state for tool request (28.958 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
669 2022-05-30 16:37:23,505 INFO [galaxy.tools.actions] Handled output named table for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/calculate_diameter/calculate_diameter/1.0.0 (2.815 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
670 2022-05-30 16:37:23,507 INFO [galaxy.tools.actions] Handled output named tool_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/calculate_diameter/calculate_diameter/1.0.0 (2.062 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
671 2022-05-30 16:37:23,523 INFO [galaxy.tools.actions] Added output datasets to history (15.846 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
672 2022-05-30 16:37:23,527 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/calculate_diameter/calculate_diameter/1.0.0] complete, ready to be enqueued (3.520 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
673 2022-05-30 16:37:23,568 INFO [galaxy.web_stack.handlers] (Job[id=3,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/calculate_diameter/calculate_diameter/1.0.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
674 2022-05-30 16:37:24,549 INFO [galaxy.jobs.handler] (3) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
675 2022-05-30 16:37:24,812 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/3/tool_script.sh] for tool command [[ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/__mdanalysis@2.1.0&#x27;)&quot; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
676 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
677 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
678 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
679 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/__mdanalysis@2.1.0&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
680 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
681 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
682 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
683 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
684 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
685 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
686 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
687 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
688 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
689 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
690 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
691 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
692 } ; python &#x27;/tmp/tmpudbcnm66/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/calculate_diameter/e504457035e5/calculate_diameter/calculate_pore_diameter_aqp.py&#x27; --arr_one &#x27;HSD LEU ALA THR&#x27; --arr_second &#x27;ARG SER PHE GLY&#x27; --gro_file &#x27;/tmp/tmpudbcnm66/files/f/a/9/dataset_fa99edec-859c-4f92-a5c3-df96305c5bb8.dat&#x27; --xtc_file &#x27;/tmp/tmpudbcnm66/files/4/2/8/dataset_428a901e-46dd-433f-aa38-040834923c53.dat&#x27; --gro_file_ext &#x27;gro&#x27; --xtc_file_ext &#x27;xtc&#x27; --output &#x27;/tmp/tmpudbcnm66/files/9/7/7/dataset_977de3e3-d359-4a40-8a4b-7c51d4262504.dat&#x27; --verbose --log_output &#x27;/tmp/tmpudbcnm66/files/4/5/1/dataset_451a5cfb-9113-4c26-83ee-01449cf245c7.dat&#x27; --output_directory &#x27;out&#x27; 2&gt;&amp;1]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
693 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
694 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
695 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:131]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
696 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
697 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
698 <tbody class="passed results-table-row">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
699 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
700 <td class="col-result">Passed</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
701 <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>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
702 <td class="col-duration">31.28</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
703 <td class="col-links"></td></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
704 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
705 <td class="extra" colspan="4">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
706 <div class="log"> ------------------------------Captured stderr call------------------------------ <br/>2022-05-30 16:37:36,534 DEBUG [multipart.multipart] Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
707 2022-05-30 16:37:36,535 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
708 2022-05-30 16:37:36,535 DEBUG [multipart.multipart] Calling on_field_data with data[5:129]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
709 2022-05-30 16:37:36,535 DEBUG [multipart.multipart] Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
710 2022-05-30 16:37:36,535 DEBUG [multipart.multipart] Calling on_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
711 2022-05-30 16:37:36,751 INFO [galaxy.tools] Validated and populated state for tool request (22.588 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
712 2022-05-30 16:37:36,757 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.152 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
713 2022-05-30 16:37:36,869 DEBUG [galaxy.tools.actions.upload] Checked uploads (111.983 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
714 2022-05-30 16:37:36,876 DEBUG [galaxy.tools.actions.upload] Created upload job (6.364 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
715 2022-05-30 16:37:36,905 INFO [galaxy.web_stack.handlers] (Job[id=4,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
716 2022-05-30 16:37:37,198 INFO [galaxy.jobs.handler] (4) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
717 2022-05-30 16:37:37,368 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/4/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/4/registry.xml&#x27; &#x27;/tmp/upload_params_86aigh4i&#x27; &#x27;5:/tmp/tmpudbcnm66/job_working_directory/000/4/working/dataset_31f0355f-84ac-411f-97a3-0ac90eb23f59_files:/tmp/tmpudbcnm66/files/3/1/f/dataset_31f0355f-84ac-411f-97a3-0ac90eb23f59.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
718 2022-05-30 16:37:44,495 INFO [galaxy.tools] Validated and populated state for tool request (22.079 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
719 2022-05-30 16:37:44,502 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.148 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
720 2022-05-30 16:37:44,627 DEBUG [galaxy.tools.actions.upload] Checked uploads (125.252 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
721 2022-05-30 16:37:44,636 DEBUG [galaxy.tools.actions.upload] Created upload job (8.474 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
722 2022-05-30 16:37:44,669 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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
723 2022-05-30 16:37:45,610 INFO [galaxy.jobs.handler] (5) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
724 2022-05-30 16:37:45,851 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/5/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/5/registry.xml&#x27; &#x27;/tmp/upload_params_wrbilm9o&#x27; &#x27;6:/tmp/tmpudbcnm66/job_working_directory/000/5/working/dataset_3698b34a-13cb-49f7-a025-b7c5874abd65_files:/tmp/tmpudbcnm66/files/3/6/9/dataset_3698b34a-13cb-49f7-a025-b7c5874abd65.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
725 2022-05-30 16:37:53,123 INFO [galaxy.tools] Validated and populated state for tool request (26.199 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
726 2022-05-30 16:37:53,129 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.147 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
727 2022-05-30 16:37:53,247 DEBUG [galaxy.tools.actions.upload] Checked uploads (117.795 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
728 2022-05-30 16:37:53,253 DEBUG [galaxy.tools.actions.upload] Created upload job (5.870 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
729 2022-05-30 16:37:53,281 INFO [galaxy.web_stack.handlers] (Job[id=6,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
730 2022-05-30 16:37:54,076 INFO [galaxy.jobs.handler] (6) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
731 2022-05-30 16:37:54,263 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/6/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/6/registry.xml&#x27; &#x27;/tmp/upload_params_a2trnhop&#x27; &#x27;7:/tmp/tmpudbcnm66/job_working_directory/000/6/working/dataset_8eed8997-0952-492c-82cf-ec9c086fbdc2_files:/tmp/tmpudbcnm66/files/8/e/e/dataset_8eed8997-0952-492c-82cf-ec9c086fbdc2.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
732 2022-05-30 16:38:01,685 INFO [galaxy.tools] Validated and populated state for tool request (28.588 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
733 2022-05-30 16:38:01,747 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 (3.914 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
734 2022-05-30 16:38:01,762 INFO [galaxy.tools.actions] Added output datasets to history (14.449 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
735 2022-05-30 16:38:01,763 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 (1.467 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
736 2022-05-30 16:38:01,798 INFO [galaxy.web_stack.handlers] (Job[id=7,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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
737 2022-05-30 16:38:02,505 INFO [galaxy.jobs.handler] (7) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
738 2022-05-30 16:38:02,788 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/7/tool_script.sh] for tool command [cat /tmp/tmpudbcnm66/files/3/1/f/dataset_31f0355f-84ac-411f-97a3-0ac90eb23f59.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/tmpudbcnm66/files/2/d/6/dataset_2d6d52d2-777e-48e6-b725-28a364f4e52c.dat&#x27; ; cat /tmp/tmpudbcnm66/files/3/1/f/dataset_31f0355f-84ac-411f-97a3-0ac90eb23f59.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/tmpudbcnm66/files/3/6/9/dataset_3698b34a-13cb-49f7-a025-b7c5874abd65.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/tmpudbcnm66/files/8/e/e/dataset_8eed8997-0952-492c-82cf-ec9c086fbdc2.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/tmpudbcnm66/files/2/d/6/dataset_2d6d52d2-777e-48e6-b725-28a364f4e52c.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
739 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
740 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
741 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:129]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
742 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
743 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
744 <tbody class="passed results-table-row">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
745 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
746 <td class="col-result">Passed</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
747 <td class="col-name">test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_nb_sub_trajectories/estimate_nb_sub_trajectories/0.1.0_test_1]</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
748 <td class="col-duration">18.87</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
749 <td class="col-links"></td></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
750 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
751 <td class="extra" colspan="4">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
752 <div class="log"> ------------------------------Captured stderr call------------------------------ <br/>2022-05-30 16:39:35,689 DEBUG [multipart.multipart] Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
753 2022-05-30 16:39:35,689 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
754 2022-05-30 16:39:35,689 DEBUG [multipart.multipart] Calling on_field_data with data[5:151]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
755 2022-05-30 16:39:35,689 DEBUG [multipart.multipart] Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
756 2022-05-30 16:39:35,689 DEBUG [multipart.multipart] Calling on_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
757 2022-05-30 16:39:35,939 INFO [galaxy.tools] Validated and populated state for tool request (22.631 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
758 2022-05-30 16:39:35,946 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.145 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
759 2022-05-30 16:39:36,081 DEBUG [galaxy.tools.actions.upload] Checked uploads (135.506 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
760 2022-05-30 16:39:36,091 DEBUG [galaxy.tools.actions.upload] Created upload job (9.617 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
761 2022-05-30 16:39:36,127 INFO [galaxy.web_stack.handlers] (Job[id=16,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
762 2022-05-30 16:39:37,095 INFO [galaxy.jobs.handler] (16) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
763 2022-05-30 16:39:37,276 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/16/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/16/registry.xml&#x27; &#x27;/tmp/upload_params_yw33j4zk&#x27; &#x27;23:/tmp/tmpudbcnm66/job_working_directory/000/16/working/dataset_5b800b43-9848-4d53-9323-c6aceb22f262_files:/tmp/tmpudbcnm66/files/5/b/8/dataset_5b800b43-9848-4d53-9323-c6aceb22f262.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
764 2022-05-30 16:39:47,071 INFO [galaxy.tools] Validated and populated state for tool request (13.357 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
765 2022-05-30 16:39:47,085 INFO [galaxy.tools.actions] Handled output named sub_trajectories_out_file for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_nb_sub_trajectories/estimate_nb_sub_trajectories/0.1.0 (2.867 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
766 2022-05-30 16:39:47,087 INFO [galaxy.tools.actions] Handled output named estimate_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_nb_sub_trajectories/estimate_nb_sub_trajectories/0.1.0 (1.940 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
767 2022-05-30 16:39:47,102 INFO [galaxy.tools.actions] Added output datasets to history (14.826 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
768 2022-05-30 16:39:47,105 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_nb_sub_trajectories/estimate_nb_sub_trajectories/0.1.0] complete, ready to be enqueued (1.997 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
769 2022-05-30 16:39:47,141 INFO [galaxy.web_stack.handlers] (Job[id=17,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_nb_sub_trajectories/estimate_nb_sub_trajectories/0.1.0]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
770 2022-05-30 16:39:47,780 INFO [galaxy.jobs.handler] (17) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
771 2022-05-30 16:39:48,028 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/17/tool_script.sh] for tool command [ln -s &#x27;/tmp/tmpudbcnm66/files/5/b/8/dataset_5b800b43-9848-4d53-9323-c6aceb22f262.dat&#x27; &#x27;PIP2.1_test_check.txt&#x27; &amp;&amp; ln -s &#x27;/tmp/tmpudbcnm66/files/c/5/6/dataset_c56e8bb6-ce7d-4267-8564-4773459f1129.dat&#x27; &#x27;estimated_number_of_sub_trajectories.tsv&#x27; &amp;&amp; python &#x27;/tmp/tmpudbcnm66/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_nb_sub_trajectories/5fcbf7af809c/estimate_nb_sub_trajectories/estimate_nb_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;out_log/estimated_number_of_sub_trajectories.log&#x27; --nb_frames &#x27;3&#x27; --start_traj &#x27;&#x27; --end_traj &#x27;&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
772 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
773 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
774 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:151]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
775 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
776 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/></div></td></tr></tbody>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
777 <tbody class="passed results-table-row">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
778 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
779 <td class="col-result">Passed</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
780 <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>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
781 <td class="col-duration">26.28</td>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
782 <td class="col-links"></td></tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
783 <tr>
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
784 <td class="extra" colspan="4">
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
785 <div class="log"> ------------------------------Captured stderr call------------------------------ <br/>2022-05-30 16:39:54,571 DEBUG [multipart.multipart] Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
786 2022-05-30 16:39:54,571 DEBUG [multipart.multipart] Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
787 2022-05-30 16:39:54,571 DEBUG [multipart.multipart] Calling on_field_data with data[5:149]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
788 2022-05-30 16:39:54,571 DEBUG [multipart.multipart] Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
789 2022-05-30 16:39:54,571 DEBUG [multipart.multipart] Calling on_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
790 2022-05-30 16:39:54,792 INFO [galaxy.tools] Validated and populated state for tool request (26.681 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
791 2022-05-30 16:39:54,798 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.150 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
792 2022-05-30 16:39:54,915 DEBUG [galaxy.tools.actions.upload] Checked uploads (116.261 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
793 2022-05-30 16:39:54,921 DEBUG [galaxy.tools.actions.upload] Created upload job (6.361 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
794 2022-05-30 16:39:54,943 INFO [galaxy.web_stack.handlers] (Job[id=18,tool_id=upload1]) Handler &#x27;_default_&#x27; assigned using &#x27;HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED&#x27; assignment method
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
795 2022-05-30 16:39:55,282 INFO [galaxy.jobs.handler] (18) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
796 2022-05-30 16:39:55,521 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/18/tool_script.sh] for tool command [python &#x27;/tmp/tmpudbcnm66/galaxy-dev/tools/data_source/upload.py&#x27; &#x27;/tmp/tmpudbcnm66/galaxy-dev&#x27; &#x27;/tmp/tmpudbcnm66/job_working_directory/000/18/registry.xml&#x27; &#x27;/tmp/upload_params_tj6wy_cu&#x27; &#x27;26:/tmp/tmpudbcnm66/job_working_directory/000/18/working/dataset_12912b09-e396-43d6-afbb-14e2260e8be3_files:/tmp/tmpudbcnm66/files/1/2/9/dataset_12912b09-e396-43d6-afbb-14e2260e8be3.dat&#x27;]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
797 2022-05-30 16:40:03,597 INFO [galaxy.tools] Validated and populated state for tool request (16.995 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
798 2022-05-30 16:40:03,623 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 (4.741 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
799 2022-05-30 16:40:03,628 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 (4.097 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
800 2022-05-30 16:40:03,630 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 (2.331 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
801 2022-05-30 16:40:03,634 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 (3.048 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
802 2022-05-30 16:40:03,656 INFO [galaxy.tools.actions] Added output datasets to history (22.238 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
803 2022-05-30 16:40:03,659 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 (2.452 ms)
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
804 2022-05-30 16:40:03,721 INFO [galaxy.web_stack.handlers] (Job[id=19,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
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
805 2022-05-30 16:40:04,091 INFO [galaxy.jobs.handler] (19) Job dispatched
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
806 2022-05-30 16:40:04,375 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpudbcnm66/job_working_directory/000/19/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; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
807 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
808 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
809 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
810 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
811 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
812 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
813 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
814 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
815 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
816 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
817 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
818 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
819 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
820 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
821 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
822 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
823 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27;)&quot; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
824 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
825 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
826 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
827 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
828 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
829 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
830 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
831 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
832 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
833 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
834 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
835 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
836 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
837 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
838 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
839 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
840 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27;)&quot; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
841 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
842 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
843 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
844 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
845 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
846 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
847 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
848 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
849 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
850 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
851 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
852 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
853 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
854 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
855 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
856 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
857 } ; [ &quot;$(basename &quot;$CONDA_DEFAULT_ENV&quot;)&quot; = &quot;$(basename &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27;)&quot; ] || {
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
858 MAX_TRIES=3
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
859 COUNT=0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
860 while [ $COUNT -lt $MAX_TRIES ]; do
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
861 . &#x27;/home/aepetit/miniconda3/bin/activate&#x27; &#x27;/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f&#x27; &gt; conda_activate.log 2&gt;&amp;1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
862 if [ $? -eq 0 ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
863 break
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
864 else
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
865 let COUNT=COUNT+1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
866 if [ $COUNT -eq $MAX_TRIES ];then
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
867 echo &quot;Failed to activate conda environment! Error was:&quot;
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
868 cat conda_activate.log
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
869 exit 1
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
870 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
871 sleep 10s
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
872 fi
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
873 done
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
874 } ; ln -s &#x27;/tmp/tmpudbcnm66/files/1/2/9/dataset_12912b09-e396-43d6-afbb-14e2260e8be3.dat&#x27; &#x27;table_sort_pore_diameter_aqp.tabular&#x27; &amp;&amp; Rscript &#x27;/tmp/tmpudbcnm66/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/7f1b1530d0fb/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]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
875 2022-05-30 16:40:19,428 INFO [galaxy.tool_util.verify] ## files diff on &#x27;/tmp/tmpaz27gu1ball_graphics_distribution.pdf&#x27; and &#x27;/tmp/tmphrnvqxzjall_graphics_distribution.pdf&#x27;: lines_diff = 0, found diff = 4, found pdf invalid diff = 0
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
876 <br/> -------------------------------Captured log call-------------------------------- <br/>DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
877 DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
878 DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:149]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
879 DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
880 DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data<br/> ----------------------------Captured stderr teardown---------------------------- <br/>2022-05-30 16:40:19,530 INFO [test_driver] 21 threads were active before stopping embedded server
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
881 2022-05-30 16:40:19,530 INFO [test_driver] Shutting down embedded galaxy uvicorn server
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
882 2022-05-30 16:40:19,530 INFO [test_driver] Embedded web server galaxy stopped
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
883 2022-05-30 16:40:19,531 INFO [test_driver] Stopping embedded server thread
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
884 INFO: Shutting down
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
885 2022-05-30 16:40:19,532 INFO [uvicorn.error] Shutting down
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
886 INFO: Waiting for application shutdown.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
887 2022-05-30 16:40:19,632 INFO [uvicorn.error] Waiting for application shutdown.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
888 INFO: Application shutdown complete.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
889 2022-05-30 16:40:19,633 INFO [uvicorn.error] Application shutdown complete.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
890 INFO: Finished server process [39518]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
891 2022-05-30 16:40:19,633 INFO [uvicorn.error] Finished server process [39518]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
892 2022-05-30 16:40:19,633 INFO [test_driver] Event loop for uvicorn closed
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
893 2022-05-30 16:40:19,633 INFO [test_driver] Embedded server thread stopped
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
894 2022-05-30 16:40:19,634 INFO [test_driver] Stopping application galaxy
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
895 2022-05-30 16:40:20,509 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
896 2022-05-30 16:40:20,524 INFO [galaxy.jobs.handler] sending stop signal to worker thread
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
897 2022-05-30 16:40:20,525 INFO [galaxy.jobs.handler] job handler queue stopped
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
898 2022-05-30 16:40:20,525 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
899 2022-05-30 16:40:20,525 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
900 2022-05-30 16:40:20,526 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
901 2022-05-30 16:40:20,526 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
902 2022-05-30 16:40:20,526 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
903 2022-05-30 16:40:20,800 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
904 2022-05-30 16:40:20,801 INFO [galaxy.jobs.handler] sending stop signal to worker thread
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
905 2022-05-30 16:40:20,801 INFO [galaxy.jobs.handler] job handler stop queue stopped
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
906 2022-05-30 16:40:20,802 INFO [test_driver] Application galaxy stopped.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
907 2022-05-30 16:40:20,803 INFO [test_driver] 2 active after stopping embedded server
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
908 <br/> -----------------------------Captured log teardown------------------------------ <br/>INFO test_driver:driver_util.py:747 21 threads were active before stopping embedded server
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
909 INFO test_driver:driver_util.py:755 Shutting down embedded galaxy uvicorn server
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
910 INFO test_driver:driver_util.py:757 Embedded web server galaxy stopped
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
911 INFO test_driver:driver_util.py:760 Stopping embedded server thread
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
912 INFO uvicorn.error:server.py:252 Shutting down
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
913 INFO uvicorn.error:on.py:64 Waiting for application shutdown.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
914 INFO uvicorn.error:on.py:75 Application shutdown complete.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
915 INFO uvicorn.error:server.py:85 Finished server process [39518]
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
916 INFO test_driver:driver_util.py:587 Event loop for uvicorn closed
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
917 INFO test_driver:driver_util.py:762 Embedded server thread stopped
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
918 INFO test_driver:driver_util.py:765 Stopping application galaxy
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
919 INFO test_driver:driver_util.py:767 Application galaxy stopped.
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
920 INFO test_driver:driver_util.py:769 2 active after stopping embedded server<br/></div></td></tr></tbody></table></body></html>