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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-tools6">Debian Med / ncbi-tools6</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/fac5500e8e9b2339d2c9d2a5f534022ba8a0ebe2">fac5500e</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-04-13T18:37:49+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest: check if NCBI is available to start testing
</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
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<h4>Changes:</h4>
<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/fac5500e8e9b2339d2c9d2a5f534022ba8a0ebe2#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="LC2" class="line" lang="plaintext">Depends: <span class="idiff left right">netcat, </span>@</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/fac5500e8e9b2339d2c9d2a5f534022ba8a0ebe2#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,21 +113,22 @@ end_out="$(grep -c "<Object-id_id>${last_id}</Object-id_id>" dsRNA_viruses.xgs)"</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$end_in</span> <span class="nt" style="color: navy;">-eq</span> <span class="nv" style="color: teal;">$end_out</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## _insdseqget_ and _idfetch_ testing requires internet connection.</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Uncomment the lines below to run the tests provided.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt</span></span>
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<pre style="margin: 0;">-<span id="LC119" 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="LC120" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#echo '---insdseqget test---'</span></span>
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<pre style="margin: 0;">-<span id="LC121" 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="LC122" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/usr/bin/insdseqget -i GIs.txt > insdset.xml</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#[ -s insdset.xml ]</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#check_GI insdset.xml GIs.txt</span></span>
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<pre style="margin: 0;">-<span id="LC125" 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="LC126" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#echo '---idfetch test---'</span></span>
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<pre style="margin: 0;">-<span id="LC127" 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="LC128" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/usr/bin/idfetch -G GIs.txt -o idfetch.text</span></span>
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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#[ -s idfetch.text ]</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#check_GI idfetch.text GIs.txt</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span>nc <span class="nt" style="color: navy;">-z</span> <span class="nt" style="color: navy;">-w</span> 1 www.ncbi.nlm.nih.gov 80<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'GI:'</span> nc0225.gbk | head | sed <span class="s1" style="color: #d14;">'s/.*GI://'</span> <span class="o" style="font-weight: 600;">></span> GIs.txt</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---insdseqget test---'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" 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">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"> /usr/bin/insdseqget <span class="nt" style="color: navy;">-i</span> GIs.txt <span class="o" style="font-weight: 600;">></span> insdset.xml</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> insdset.xml <span class="o" style="font-weight: 600;">]</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"> check_GI insdset.xml GIs.txt</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---idfetch test---'</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"> /usr/bin/idfetch <span class="nt" style="color: navy;">-G</span> GIs.txt <span class="nt" style="color: navy;">-o</span> idfetch.text</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> idfetch.text <span class="o" style="font-weight: 600;">]</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"> check_GI idfetch.text GIs.txt</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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131
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="shell"></span>
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132
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="shell"></span>
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133
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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