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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/fsm-lite">Debian Med / fsm-lite</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/fsm-lite/-/commit/539ada1b52b4eb9e8d6458de7ba785a992fdc48c">539ada1b</a></strong>
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<span>by Lance Lin</span>
<i>at 2021-12-20T20:07:08+07:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added a start to autopkgtest framework
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<h4>2 changed files:</h4>
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debian/tests/control
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/fsm-lite/-/commit/539ada1b52b4eb9e8d6458de7ba785a992fdc48c#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/fsm-lite/-/commit/539ada1b52b4eb9e8d6458de7ba785a992fdc48c#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Lance Lin <LQi254@protonmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Date: 20 December 2021</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># File: run-unit-test</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Purpose: run a simple-unit test for the fsm-lite package</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Details:</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Use a publicly accessible .fasta file format example. There are others, but they quite large (>30MB)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Execute fsm-lite on the sample data and verify the resulting generated files are the correct length</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Verify the two ouptut is correct:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># tmp.meta should look like: "testfile 1508 ", which is {inputFileName, filesize}</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># tmp.tmp will have the sequencing and should be 1508 bytes in length, as reported by tmp.meta</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nv" style="color: #008080;">WORKDIR</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span><span class="si" style="color: #d14;">)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$WORKDIR</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$WORKDIR</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run-unit-test: generating data"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># FASTA format file from "UT Southwestern Medical Center"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># URL: http://prodata.swmed.edu/promals/info/fasta_format_file_example.htm</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Website title: Fasta format file example</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Date accessed: 20 December 2021</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > testfile.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq0</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="sh" style="color: #d14;">FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq1</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="sh" style="color: #d14;">KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq2</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="sh" style="color: #d14;">EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq3</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="sh" style="color: #d14;">MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq4</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="sh" style="color: #d14;">EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq5</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="sh" style="color: #d14;">SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq6</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="sh" style="color: #d14;">FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq7</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="sh" style="color: #d14;">SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq8</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="sh" style="color: #d14;">SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq9</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="sh" style="color: #d14;">KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="sh" style="color: #d14;">>seq10</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="sh" style="color: #d14;">FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run-unit-test: generating test input list file"</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > input.list</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="sh" style="color: #d14;">testfile </span><span class="nv" style="color: #008080;">$WORKDIR</span><span class="sh" style="color: #d14;">/testfile.fasta</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run-unit-test: running fsm-lite"</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell">fsm-lite <span class="nt" style="color: #000080;">-l</span> input.list <span class="nt" style="color: #000080;">-t</span> tmp | <span class="nb" style="color: #0086b3;">gzip</span> - <span class="o" style="font-weight: 600;">></span> output.txt.gz</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run-unit-test: verifying output"</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Output in tmp.meta should contain "1508", the file size/output of tmp.tmp in bytes</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The test will capture the file size from tmp.meta and compare the output file length</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="nv" style="color: #008080;">fileSizeMeta</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>tmp.meta | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f2</span><span class="si" style="color: #d14;">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Check file size of tmp.tmp matches what is reported by tmp.meta</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="nv" style="color: #008080;">fileSize</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">du</span> <span class="nt" style="color: #000080;">-b</span> tmp.tmp | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1</span><span class="si" style="color: #d14;">)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$fileSize</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$metaFileSize</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]]</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run-unit-test: Failure - output file size does not match expected: </span><span class="nv" style="color: #008080;">$fileSize</span><span class="s2" style="color: #d14;"> (generated) instead of </span><span class="nv" style="color: #008080;">$fileSizeMeta</span><span class="s2" style="color: #d14;"> (expected)"</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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