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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/libsis-jhdf5-java">Debian Med / libsis-jhdf5-java</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/10723447f1a67a8729fcd7f72213bf22bab5ec3f">10723447</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T21:49:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding final qualifier to some arguments of functions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/3ffb128b8f28b751604b823cafce3307d5001ca4">3ffb128b</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T21:50:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing hardening while compiling the jni part
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/1b85335af5d143318c5dacf04c874cf1395e4b2b">1b85335a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T21:52:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Changing syntax in override_dh_auto_clean
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/54310d4cc452404c2b5f82084d2718c560d4577d">54310d4c</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T21:57:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing the executable h5ar
Creating a new binary package with the executable and the jar that it wraps
Compiling this jar
Modifying the wrapper to incorporate Debian paths
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/1855adf0ecb98e6d3ce21e865cf7a6efbf22ad94">1855adf0</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T22:00:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing a manpage for h5ar
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/a490429d35726ce484dda4590c964b266b4d69b8">a490429d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T22:04:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Overriding jh_depends
The jni does not need jh_depends.
Moreover, having only the default call would lead to useless dependencies for
libsis-jhdf5-java.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/76476c05beda4b33a335a8b06806f0cb670457cd">76476c05</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T22:07:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding a test for h5ar to the testsuite
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/0b3be58d27c3cc63e2bee64ebc37bf797682057f">0b3be58d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T22:07:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating debian/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/3a87c74576ecaf06803ab5af0fed6407e78739b9">3a87c745</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T22:11:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating debian/rules to correctly build h5ar
override_dh_auto_clean has to treat more files
the building line for the jar of h5ar is now working
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/3470775498e6b57991700a1bf8705023e45f219c">34707754</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T22:29:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing tests of the testsuite as examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/d642cc72f3247f5f0192590c52bdb3c65738056a">d642cc72</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-05-12T22:45:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
</ul>
<h4>18 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#94619d79bf8da4f9fa0fecb627baa013382bc55e">
<span class="new-file">
+
debian/h5ar.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#67767a84d78fa871d44cd82e417eee657bacde12">
<span class="new-file">
+
debian/h5ar.examples
</span>
</a>
</li>
<li class="file-stats">
<a href="#0b879f70a76dd860c275c6c444ee989afbf05bba">
debian/libsis-jhdf5-java.install
→
debian/h5ar.install
</a>
</li>
<li class="file-stats">
<a href="#3fe2ac61700450a102427c79b9a66b4cb4f0b17f">
<span class="new-file">
+
debian/h5ar.jlibs
</span>
</a>
</li>
<li class="file-stats">
<a href="#97f8c00b616c52f6d118d6f3bd20edc17213ef41">
<span class="new-file">
+
debian/h5ar.manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#89f5427fa4c2c975bad14b1142829b17b6dd3325">
<span class="new-file">
+
debian/libsis-jhdf5-java.examples
</span>
</a>
</li>
<li class="file-stats">
<a href="#409518a0176558997c9daa6ad81fe4bbca902ea8">
<span class="new-file">
+
debian/patches/adapting_h5ar_script_to_debian.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#a0c3b79fbf11cb2c0b5aff3d40fa276618b23674">
<span class="new-file">
+
debian/patches/declaring_final_variables.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
<li class="file-stats">
<a href="#e4fae25747907519e311217bb7b55bd8a7d89975">
<span class="new-file">
+
debian/tests/run-unit-test-h5ar
</span>
</a>
</li>
<li class="file-stats">
<a href="#264939da03db78f479e0607871bcf16ceb129d17">
<span class="new-file">
+
debian/tests/run-unit-test-libsis-jhdf5-java
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</a>
</li>
<li class="file-stats">
<a href="#360ee7f5d66dc064a791afc9110fb750d663dba0">
<span class="new-file">
+
debian/tests/testWrappingExecutable
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" 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">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span><span class="o" style="font-weight: 600;">-</span><span class="nx">PACKAGE</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">where</span> <span class="nx">PACKAGE</span> <span class="nx">is</span> <span class="nx">the</span> <span class="nx">name</span> <span class="nx">of</span> <span class="nx">the</span> <span class="nb" style="color: #0086b3;">current</span> <span class="nx">package</span><span class="p">,</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">libsis</span><span class="p">-</span><span class="n" style="color: #333;">jhdf5</span><span class="p">-</span><span class="n" style="color: #333;">java</span> <span class="p">(</span><span class="m" style="color: #099;">19.04.0</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">UNRELEASED</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Changing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="p">.</span><span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">libsis</span><span class="p">-</span><span class="n" style="color: #333;">jhdf5</span><span class="p">-</span><span class="n" style="color: #333;">jni</span> <span class="p">(</span><span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">959955</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Providing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">executable</span> <span class="n" style="color: #333;">h5ar</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">manpage</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Adding</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">h5ar</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">testsuite</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Adding</span> <span class="n" style="color: #333;">final</span> <span class="n" style="color: #333;">qualifier</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">arguments</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">functions</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Providing</span> <span class="n" style="color: #333;">hardening</span> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">compiling</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">jni</span> <span class="n" style="color: #333;">part</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Providing</span> <span class="n" style="color: #333;">tests</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">testsuite</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">examples</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Pierre</span> <span class="n" style="color: #333;">Gruet</span> <span class="p"><</span><span class="n" style="color: #333;">pgtdebian</span><span class="p">@</span><span class="n" style="color: #333;">free</span><span class="p">.</span><span class="n" style="color: #333;">fr</span><span class="p">></span> <span class="n" style="color: #333;">T<span class="idiff left">hu</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">07</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">May</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2020</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">21</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">46</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">07</span></span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Pierre</span> <span class="n" style="color: #333;">Gruet</span> <span class="p"><</span><span class="n" style="color: #333;">pgtdebian</span><span class="p">@</span><span class="n" style="color: #333;">free</span><span class="p">.</span><span class="n" style="color: #333;">fr</span><span class="p">></span> <span class="n" style="color: #333;">T<span class="idiff left">ue</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">12</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">May</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2020</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">22</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">37</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">32</span></span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">libsis</span><span class="p">-</span><span class="n" style="color: #333;">jhdf5</span><span class="p">-</span><span class="n" style="color: #333;">java</span> <span class="p">(</span><span class="m" style="color: #099;">19.04.0</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"></span>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" 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="28" 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">@@ -28,6 +28,22 @@ Vcs-Browser: https://salsa.debian.org/med-team/libsis-jhdf5-java</td>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libsis-jhdf5-java.git</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Homepage: https://sissource.ethz.ch/sispub/jhdf5</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Package: h5ar</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> ${java:Depends},</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> libsis-jhdf5-jni (>= ${binary:Version}),</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> libsis-jhdf5-jni (<< ${source:Version}.1~),</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> libargs4j-java,</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> jarwrapper</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Description: easy-to-use HDF archiver using Java</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> h5ar provides an archiver using a Java binding to the HDF Group library for</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> HDF5 focusing on ease-of-use, which was developed by CISD and is now</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> maintained by ETH SIS.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> The executable uses HDF5 1.8 from the HDF Group and files created with</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> h5ar are fully compatible with HDF5 1.6/1.8 (as you choose).</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Package: libsis-jhdf5-java</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,7 +82,8 @@ License: Apache</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">Copyright: 2015 Tim Booth <tbooth@ceh.ac.uk></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"> 2015 Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> 2016-2018 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> 2016-2020 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> 2020 Pierre Gruet <pgtdebian@free.fr></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext">License: GPL-3</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"> On Debian systems, the full text of the GNU General Public</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> License version 3 can be found in the file</span>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#94619d79bf8da4f9fa0fecb627baa013382bc55e"><strong>debian/h5ar.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH HDF5 "1" "May 2020" "HDF5 archiver version 19.04.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">h5ar \- HDF5 archiver</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.B h5ar</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">[ARCHIVE [option [...]] <archive_file> <item\-to\-archive> [...]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">| CAT [option [...]] <archive_file> <item\-to\-cat> [...]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">| EXTRACT [option [...]] <archive_file> [<item\-to\-unarchive> [...]]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">| DELETE [option [...]] <archive_file> <item\-to\-delete> [...]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">| LIST [option [...]] <archive_file> [<item\-to\-list> [...]]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">| VERIFY [option [...]] <archive_file> [<item\-to\-verify> [...]]]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">h5ar is a HDF5 archiver, which can create an HDF5 archive, extract it and manipulate it in various ways. It does to by calling an executable jar file.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-B\fR, \fB\-\-build\fR</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">prints out the build and environment information</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-C\fR, \fB\-\-compress\-all\fR</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">compresses all files</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-D\fR, \fB\-\-suppress\-directories\fR</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">suppresses output for directories itself for LIST</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">and VERIFY (default: false)</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-E\fR, \fB\-\-exclude\-dirs\fR REGEX</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">excludes directories according to provided regex</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-F\fR, \fB\-\-file\-format\fR N</span>
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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">specifies the file format version when creating</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">an archive (N=1 \-> HDF51.8 (default), N=2 \-></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">HDF51.10), N=99 \-> LATEST (default: 1)</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-H\fR, \fB\-\-help\fR</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">shows this help text</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-I\fR, \fB\-\-include\-dirs\fR REGEX</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">includes directories according to provided regex</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-N\fR, \fB\-\-no\-sync\fR</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">does not sync to disk before program exits (write</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">mode only) (default: false)</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-R\fR, \fB\-\-recursive\fR</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">recursive LIST and VERIFY (default: false)</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-S\fR, \fB\-\-stop\-on\-error\fR</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">stops on first error and gives detailed error</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">report (default: false)</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-V\fR, \fB\-\-version\fR</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">prints out the version information</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.TP</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">\fB\-a\fR, \fB\-\-verify\-attributes\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">considers file attributes for VERIFY (default:</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">false)</span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">\fB\-c\fR, \fB\-\-compress\fR REGEX</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">compresses files according to provided regex</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.TP</span>
</pre>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">\fB\-e\fR, \fB\-\-exclude\fR REGEX</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">excludes files according to provided regex</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.TP</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">\fB\-i\fR, \fB\-\-include\fR REGEX</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">includes files according to provided regex</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.TP</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">\fB\-m\fR, \fB\-\-check\-missing\-files\fR</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">checks for files present on the filesystem but</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">missing from the archive for VERIFY (default:</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">false)</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.TP</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">\fB\-n\fR, \fB\-\-numeric\fR</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">uses numeric values for mode, uid and gid for</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">LIST and VERIFY (default: false)</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.HP</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">\fB\-nc\fR, \fB\-\-no\-compression\fR REGEX</span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">does not compress files satisfying provided regex</span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">\fB\-q\fR, \fB\-\-quiet\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">quiet operation (only error output) (default:</span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">false)</span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">\fB\-r\fR, \fB\-\-root\-dir\fR DIR</span>
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<td class="diff-line-num new new_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">root directory for archiving / extracting /</span>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">verifying</span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">\fB\-t\fR, \fB\-\-test\-checksums\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">tests CRC32 checksums of files in archive for</span>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">LIST (default: false)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">\fB\-v\fR, \fB\-\-verbose\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">verbose output (all operations) (default: false)</span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">.SS "Modes (command capitalization ignored):"</span>
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">ARCHIVE (AR, A): add files on the file system to an archive (always recursive)</span>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.br</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">CAT (C): extract files from an archive to stdout</span>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.br</span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">EXTRACT (EX, E): extract files from an archive to the file system (always recursive)</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">.br</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">DELETE (REMOVE, RM, D): delete files from an archive</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">LIST (LS, S): list files in an archive</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.br</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">VERIFY (VF, V): verify the existence and integrity of files on the file system vs. the contents of an archive</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.SH EXAMPLES</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">.IP</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">h5ar ar /tmp/home \-r ~/ .</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">.IP</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">\- will create home.h5ar in /tmp containing all files of the user's home directory (note: ARCHIVE is always recursive).</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">.IP</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">h5ar ls \-v \-R \-t \-S /tmp/home</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">\- will list the full content of archive /tmp/home.h5ar recursively, with full detail and verify the checksums; stop if there is a checksum mismatch.</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.IP</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">h5ar vf \-r ~/ \-v \-R \-m /tmp/home foo bar</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">\- will verify the contents of directories foo/ and bar/ in archive /tmp/home.h5ar recursively against the user's home directory, detecting any missing files.</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">The full documentation for</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">.B HDF5</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">is maintained as a Texinfo manual. If the</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">.B info</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">and</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.B HDF5</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">programs are properly installed at your site, the command</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">.B info HDF5</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">.PP</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">should give you access to the complete manual.</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">.SH AUTHOR</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">This manual page was created by Pierre Gruet <pgtdebian@free.fr> for the Debian GNU/Linux distribution, because the original package does not have one.</span></pre>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#67767a84d78fa871d44cd82e417eee657bacde12"><strong>debian/h5ar.examples</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README.test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test-h5ar</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/testWrappingExecutable</span></pre>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#0b879f70a76dd860c275c6c444ee989afbf05bba"><strong>debian/libsis-jhdf5-java.install</strong>
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<strong>debian/h5ar.install</strong>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#3fe2ac61700450a102427c79b9a66b4cb4f0b17f"><strong>debian/h5ar.jlibs</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sis-jhdf5-h5ar-cli.jar</span></pre>
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<li id="97f8c00b616c52f6d118d6f3bd20edc17213ef41">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#97f8c00b616c52f6d118d6f3bd20edc17213ef41"><strong>debian/h5ar.manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/h5ar.1</span></pre>
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<li id="89f5427fa4c2c975bad14b1142829b17b6dd3325">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#89f5427fa4c2c975bad14b1142829b17b6dd3325"><strong>debian/libsis-jhdf5-java.examples</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test-libsis-jhdf5-java</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/readWriteTest</span></pre>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#409518a0176558997c9daa6ad81fe4bbca902ea8"><strong>debian/patches/adapting_h5ar_script_to_debian.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Adapting bindings to the location of files on a Debian system</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-05-12</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/dist/bin/h5ar</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/dist/bin/h5ar</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,23 +1,3 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #! /bin/bash</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# This script requires the readlink binary. If your system lacks this binary, $JHDFDIR needs to be hard-coded</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SCRIPT="$0"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ "${SCRIPT}" = "${SCRIPT#/}" ]; then</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SCRIPT="`pwd`/${SCRIPT#./}"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BINDIR="${SCRIPT%/*}"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LINK="`readlink $0`"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-while [ -n "${LINK}" ]; do</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [ "${LINK#/}" = "${LINK}" ]; then</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SCRIPT="${BINDIR}/${LINK}"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SCRIPT="${LINK}"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- BINDIR="${SCRIPT%/*}"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LINK="`readlink ${SCRIPT}`"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-done</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BINDIR="${SCRIPT%/*}"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JHDFDIR="${BINDIR%/*}"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-VERSION=`cat "${JHDFDIR}/version.txt"`</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-java -Dnative.libpath="${JHDFDIR}/lib/native" -jar "${JHDFDIR}/lib/sis-jhdf5-h5ar-cli-${VERSION}.jar" "$@"</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+java -Djava.library.path="/usr/lib/jni/" -jar "/usr/share/java/sis-jhdf5-h5ar-cli.jar" "$@"</span></span></pre>
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<li id="a0c3b79fbf11cb2c0b5aff3d40fa276618b23674">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#a0c3b79fbf11cb2c0b5aff3d40fa276618b23674"><strong>debian/patches/declaring_final_variables.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Adding final qualifier for some variables used by an inner class</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-05-12</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5BaseWriter.java</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5BaseWriter.java</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1038,7 +1038,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> HDF5DataSet createDataSet(final String objectPath, final long storageDataTypeId,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> final HDF5AbstractStorageFeatures features, final long[] dimensions,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final long[] chunkSizeOrNull, int elementLength)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final long[] chunkSizeOrNull, final int elementLength)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> openDataSetCallable =</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> new ICallableWithCleanUp<HDF5DataSet>()</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5IntWriter.java</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5IntWriter.java</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> assert objectPath != null;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -659,7 +659,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> @Override</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDIntArray data, HDF5DataSetTemplate template)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDIntArray data, final HDF5DataSetTemplate template)</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> {</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> assert data != null;</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> baseWriter.checkOpen();</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -787,7 +787,7 @@</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> }</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> @Override</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> {</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> baseWriter.checkOpen();</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -824,7 +824,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> baseWriter.checkOpen();</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5ShortWriter.java</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5ShortWriter.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> }</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> @Override</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> {</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> assert objectPath != null;</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -659,7 +659,7 @@</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> }</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDShortArray data, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDShortArray data, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> assert data != null;</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> baseWriter.checkOpen();</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="p">@@ -787,7 +787,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> @Override</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> {</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> baseWriter.checkOpen();</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -824,7 +824,7 @@</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> }</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> @Override</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> {</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> baseWriter.checkOpen();</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5ByteWriter.java</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5ByteWriter.java</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> {</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> assert objectPath != null;</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -659,7 +659,7 @@</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> }</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> @Override</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDByteArray data, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDByteArray data, final HDF5DataSetTemplate template)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> {</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> assert data != null;</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> baseWriter.checkOpen();</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -787,7 +787,7 @@</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> }</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> @Override</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> {</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> baseWriter.checkOpen();</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -824,7 +824,7 @@</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> }</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> </span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> @Override</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> {</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> baseWriter.checkOpen();</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5FloatWriter.java</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5FloatWriter.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="p">@@ -280,7 +280,7 @@</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> }</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> {</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> assert objectPath != null;</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="p">@@ -658,7 +658,7 @@</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> }</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> @Override</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDFloatArray data, HDF5DataSetTemplate template)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDFloatArray data, final HDF5DataSetTemplate template)</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> {</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> assert data != null;</span>
</pre>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> baseWriter.checkOpen();</span>
</pre>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="p">@@ -786,7 +786,7 @@</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> }</span>
</pre>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> {</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> baseWriter.checkOpen();</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="p">@@ -823,7 +823,7 @@</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> }</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> @Override</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> {</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> baseWriter.checkOpen();</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedByteWriter.java</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedByteWriter.java</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="p">@@ -280,7 +280,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> @Override</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> {</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> assert objectPath != null;</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="p">@@ -658,7 +658,7 @@</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> }</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> </span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDByteArray data, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDByteArray data, final HDF5DataSetTemplate template)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> {</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> assert data != null;</span>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> baseWriter.checkOpen();</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="p">@@ -786,7 +786,7 @@</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> }</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> </span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> @Override</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> {</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> baseWriter.checkOpen();</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="p">@@ -823,7 +823,7 @@</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> }</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> </span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> @Override</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> {</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> baseWriter.checkOpen();</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5DoubleWriter.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5DoubleWriter.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" 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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="p">@@ -280,7 +280,7 @@</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> }</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> </span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="212" 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">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> {</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> assert objectPath != null;</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="217" 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">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="p">@@ -658,7 +658,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> }</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> </span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDDoubleArray data, HDF5DataSetTemplate template)</span></span>
</pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDDoubleArray data, final HDF5DataSetTemplate template)</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> {</span>
</pre>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> assert data != null;</span>
</pre>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> baseWriter.checkOpen();</span>
</pre>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="p">@@ -786,7 +786,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> }</span>
</pre>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> baseWriter.checkOpen();</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="p">@@ -823,7 +823,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> baseWriter.checkOpen();</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5LongWriter.java</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5LongWriter.java</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> assert objectPath != null;</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="p">@@ -659,7 +659,7 @@</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> }</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> </span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDLongArray data, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDLongArray data, final HDF5DataSetTemplate template)</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> {</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> assert data != null;</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> baseWriter.checkOpen();</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="p">@@ -787,7 +787,7 @@</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> }</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> </span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> @Override</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> {</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> baseWriter.checkOpen();</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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<td class="diff-line-num new new_line" data-linenumber="273" 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">
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="p">@@ -824,7 +824,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> </span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> {</span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> baseWriter.checkOpen();</span>
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<td class="diff-line-num new new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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<td class="diff-line-num new new_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedShortWriter.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedShortWriter.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="p">@@ -280,7 +280,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" 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">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> @Override</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="289" 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">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> {</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="291" 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">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> assert objectPath != null;</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="293" 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">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="p">@@ -658,7 +658,7 @@</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> }</span>
</pre>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> </span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> @Override</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDShortArray data, HDF5DataSetTemplate template)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDShortArray data, final HDF5DataSetTemplate template)</span></span>
</pre>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> {</span>
</pre>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> assert data != null;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> baseWriter.checkOpen();</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
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<td class="diff-line-num new new_line" data-linenumber="302" 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">
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="p">@@ -786,7 +786,7 @@</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="303" 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">
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="304" 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">
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> </span>
</pre>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> baseWriter.checkOpen();</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="p">@@ -823,7 +823,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" 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">
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> baseWriter.checkOpen();</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedIntWriter.java</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedIntWriter.java</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="p">@@ -280,7 +280,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> assert objectPath != null;</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="p">@@ -658,7 +658,7 @@</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> }</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> </span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> @Override</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDIntArray data, HDF5DataSetTemplate template)</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDIntArray data, final HDF5DataSetTemplate template)</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> {</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> assert data != null;</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> baseWriter.checkOpen();</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="p">@@ -786,7 +786,7 @@</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> }</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> @Override</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> {</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> baseWriter.checkOpen();</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="p">@@ -823,7 +823,7 @@</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> }</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> </span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> @Override</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> {</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> baseWriter.checkOpen();</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedLongWriter.java</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedLongWriter.java</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="p">@@ -280,7 +280,7 @@</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> }</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> </span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> @Override</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> {</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> assert objectPath != null;</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> </span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="p">@@ -658,7 +658,7 @@</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> }</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> </span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> @Override</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void writeMDArray(String objectPath, MDLongArray data, HDF5DataSetTemplate template)</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeMDArray(final String objectPath, final MDLongArray data, final HDF5DataSetTemplate template)</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> {</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> assert data != null;</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> baseWriter.checkOpen();</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="p">@@ -786,7 +786,7 @@</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> }</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> @Override</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void createMDArray(String objectPath, HDF5DataSetTemplate template)</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void createMDArray(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> {</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> baseWriter.checkOpen();</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> final ICallableWithCleanUp<Void> createRunnable = new ICallableWithCleanUp<Void>()</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="p">@@ -823,7 +823,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> }</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> </span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public HDF5DataSet createMDArrayAndOpen(String objectPath, HDF5DataSetTemplate template)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public HDF5DataSet createMDArrayAndOpen(final String objectPath, final HDF5DataSetTemplate template)</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> {</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> baseWriter.checkOpen();</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> final ICallableWithCleanUp<HDF5DataSet> createRunnable = new ICallableWithCleanUp<HDF5DataSet>()</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,3 +3,5 @@ use_jaxb.patch</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">avoid_using_private_hdf5_header.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">using_h5util_definitions.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">loading_jni_in_java_file.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">declaring_final_variables.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">adapting_h5ar_script_to_debian.patch</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="9" 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">@@ -9,6 +9,7 @@ export TESTCLASSPATH=/usr/share/java/junit4.jar:/usr/share/java/testng.jar:/usr/</td>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">DPKG_EXPORT_BUILDFLAGS = 1</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">include /usr/share/dpkg/buildflags.mk</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">include /usr/share/java/java_defaults.mk</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">CPPFLAGS += ${jvm_includes} -Ijni</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,13 +18,19 @@ CPPFLAGS += ${jvm_includes} -Ijni</td>
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17
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">override_dh_auto_clean:</span>
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19
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> -rm -rf debian/libsis-jhdf5-java/ debian/libsis-jhdf5-jni/ debian/tmp/ debian/.debhelper/</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> -rm debian/*debhelper* debian/files debian/*.substvars</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> -rm -rf targets/ test-output/</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> -rm source/c/libsis-jhdf5.so</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> $(RM) -rf debian/libsis-jhdf5-java/ debian/libsis-jhdf5-jni/ debian/tmp/ debian/.debhelper/</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> $(RM) debian/*debhelper* debian/files debian/*.substvars</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> $(RM) -rf targets/ test-output/</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> $(RM) source/c/libsis-jhdf5.so</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> $(RM) -rf debian/_jh*</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> $(RM) -rf debian/h5ar/</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> $(RM) sis-jhdf5-h5ar-cli.jar</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> # The jar needed by the h5ar wrapper is not built by the call to gradle.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> # We thus do it manually.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> CLASSPATH="$(CLASSPATH):/usr/share/java/args4j.jar:/usr/share/java/jaxb-runtime.jar" jh_build sis-jhdf5-h5ar-cli.jar $$(find source/java/ -name *.java) --main ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverMain</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> # Create JNI manually since this is not part of the build system</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> # Upsteam seems to `cd source/c` and call a script which in turn calls compile_hdf5_gcc.sh</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> # In this script hdf5 source is unpacked, possibly patched, build and used for the JNI build</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,6 +48,12 @@ override_jh_installlibs:</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> mv $$GENERATEDJARPATH targets/gradle/libs/sis-jhdf5.jar</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> jh_installlibs --version-strip='[~pre1]*[+]git[.0-9a-f]*[+]dfsg[.0-9]*'</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">override_jh_depends:</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> # We do two successive calls because the library does not need to depend on</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> # the jre as the program package does, and the jni does not need jh_depends.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> jh_depends --package=h5ar</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> jh_depends --package=libsis-jhdf5-java</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> # Run the tests that come with the upstream source.</span>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: providedTests</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, default-jdk, junit4, testng, libjmock2-java, libjcommander-java</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: libsis-jhdf5-java, libsis-jhdf5-jni, default-jdk, junit4, testng, libjmock2-java, libjcommander-java</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Tests: testWrappingExecutable</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Depends: h5ar, libsis-jhdf5-jni, jarwrapper</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Tests: readWriteTest</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Depends: <span class="idiff left right">@</span>, default-jdk</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Depends: <span class="idiff left right">libsis-jhdf5-java, libsis-jhdf5-jni</span>, default-jdk</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Restrictions: superficial</span></pre>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#e4fae25747907519e311217bb7b55bd8a7d89975"><strong>debian/tests/run-unit-test-h5ar</strong></a>
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1
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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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2
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<pre style="margin: 0;">+<span id="LC2" 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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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>h5ar</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" 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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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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;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">sh testWrappingExecutable</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" 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;">"Test testWrappingExecutable PASSED"</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" 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;">"Test testWrappingExecutable FAILED"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#264939da03db78f479e0607871bcf16ceb129d17"><strong>debian/tests/run-unit-test-libsis-jhdf5-java</strong></a>
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1
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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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2
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<pre style="margin: 0;">+<span id="LC2" 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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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>libsis-jhdf5-java</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" 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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">sh readWriteTest</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" 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;">"Test readWriteTest PASSED"</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" 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;">"Test readWriteTest FAILED"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/compare/4d1d27836208c0a4a36a18df2826ffbdd95861c1...d642cc72f3247f5f0192590c52bdb3c65738056a#360ee7f5d66dc064a791afc9110fb750d663dba0"><strong>debian/tests/testWrappingExecutable</strong></a>
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1
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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/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: Create an archive with both the wrapper and the jar, </span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># then compare their contents. Extract one of them and check that the outfiles</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># are the same as the original ones.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># (C) 2020 Pierre Gruet.</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;"># Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" 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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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" 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;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span><span class="si" style="color: #d14;">)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$WORKDIR</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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12
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<pre style="margin: 0;">+<span id="LC12" 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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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" 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;"> > firstFile</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="sh" style="color: #d14;">Contents of file 1</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="se" style="color: #d14;">\[</span><span class="sh" style="color: #d14;">e^{i</span><span class="se" style="color: #d14;">\p</span><span class="sh" style="color: #d14;">i}+1=0</span><span class="se" style="color: #d14;">\]</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</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="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;"> > secondFile.tex</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="sh" style="color: #d14;">Contents of file 2</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="se" style="color: #d14;">\[\s</span><span class="sh" style="color: #d14;">um_{n=1}^{+</span><span class="se" style="color: #d14;">\i</span><span class="sh" style="color: #d14;">nfty}</span><span class="se" style="color: #d14;">\f</span><span class="sh" style="color: #d14;">rac{1}{n^2}=</span><span class="se" style="color: #d14;">\f</span><span class="sh" style="color: #d14;">rac{</span><span class="se" style="color: #d14;">\p</span><span class="sh" style="color: #d14;">i^2}{6}</span><span class="se" style="color: #d14;">\]</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#Creating an archive</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">h5ar ar arch1 firstFile secondFile.tex</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></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;">#The result must be the same if we directly call the wrapped jar.</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">java <span class="nt" style="color: #000080;">-jar</span> /usr/share/java/sis-jhdf5-h5ar-cli.jar ar arch2 firstFile secondFile.tex</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#To check it, we get a listing of the files in the two archives and see that they are equal.</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">java <span class="nt" style="color: #000080;">-jar</span> /usr/share/java/sis-jhdf5-h5ar-cli.jar <span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-R</span> <span class="nt" style="color: #000080;">-t</span> <span class="nt" style="color: #000080;">-S</span> arch1.h5ar | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> 2 <span class="o" style="font-weight: 600;">></span> outLs1</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">h5ar <span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-R</span> <span class="nt" style="color: #000080;">-t</span> <span class="nt" style="color: #000080;">-S</span> arch2.h5ar | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> 2 <span class="o" style="font-weight: 600;">></span> outLs2</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">diff outLs1 outLs2</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#Finally, we make a copy of the original files and delete them.</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#Then we extract the archive and compare the outfiles to the copies we made.</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp </span>firstFile firstFileCp</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp </span>secondFile.tex secondFileCp.tex</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm </span>firstFile secondFile.tex</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">h5ar ex arch1.h5ar</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell">diff firstFile firstFileCp <span class="o" style="font-weight: 600;">&&</span> diff secondFile.tex secondFileCp.tex</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"></span></pre>
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