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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/sra-sdk">Debian Med / sra-sdk</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/b36b20cb22242853e29881740e1cdfc0893143cd">b36b20cb</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2020-05-25T22:45:08-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sra-sdk 2.10.6+dfsg-5: Reenable legacy schema for sra-load (#961347)
* debian/patches/reenable_legacy_schema_in_sra_load.patch: New patch to
make use of ncbi-vdb's new SRAUseLegacyDefaultSchema toggle,
unbreaking tools/sra-load (fastq-load et al.) (Closes: #961347.)
* debian/control: Ensure that this toggle is available at build time and
at runtime.
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<h4>4 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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+
debian/patches/reenable_legacy_schema_in_sra_load.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/b36b20cb22242853e29881740e1cdfc0893143cd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sra-sdk (2.10.6+dfsg-5) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * debian/patches/reenable_legacy_schema_in_sra_load.patch: New patch to</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> make use of ncbi-vdb's new SRAUseLegacyDefaultSchema toggle,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> unbreaking tools/sra-load (fastq-load et al.) (Closes: #961347.)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debian/control: Ensure that this toggle is available at build time and</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> at runtime.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Mon, 25 May 2020 22:45:07 -0400</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">sra-sdk (2.10.6+dfsg-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Account for new sratools setup. (Closes: #961256.)</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/b36b20cb22242853e29881740e1cdfc0893143cd#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -7,7 +7,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libngs-sdk-dev (>= 2.9.0),</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> libncbi-vdb-dev (>= 2.10.6+dfsg-<span class="idiff left right">2</span>~),</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> libncbi-vdb-dev (>= 2.10.6+dfsg-<span class="idiff left right">3</span>~),</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libvdb-sqlite-dev,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libfuse-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libhdf5-dev,</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">@@ -23,6 +23,7 @@ Rules-Requires-Root: no</td>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Package: sra-toolkit</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Architecture: amd64</span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> libncbi-wvdb2 (>= 2.10.6+dfsg-3~),</span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> ${misc:Depends}</span>
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27
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Recommends: med-config (>= 2.1)</span>
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28
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Description: utilities for the NCBI Sequence Read Archive</span>
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<li id="d684839504edbccea0b8237f38a2b741d36f5ef3">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/b36b20cb22242853e29881740e1cdfc0893143cd#d684839504edbccea0b8237f38a2b741d36f5ef3"><strong>debian/patches/reenable_legacy_schema_in_sra_load.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/sra-load/loader.c</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/sra-load/loader.c</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -38,6 +38,7 @@</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> #include <kfs/directory.h></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> #include <kdb/meta.h></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> #include <kapp/loader-meta.h></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <sra/sraschema.h></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #include <sra/wsradb.h></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"> #include <os-native.h></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -904,6 +905,7 @@</span> rc_t KMain(int argc, char *argv[])</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> if (rc == 0) {</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> rc = KDirectoryNativeDir(&s_Directory);</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SRAUseLegacyDefaultSchema = true;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> /* Parse command line arguments */</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if (rc == 0) {</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> rc = TArgsMake(&args, argc, argv);</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/b36b20cb22242853e29881740e1cdfc0893143cd#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -19,3 +19,4 @@ ignore_failing_test_for_the_moment_FIXME.patch</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">python3</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">use_exposed_headers.patch</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">use_unversioned_tools.patch</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">reenable_legacy_schema_in_sra_load.patch</span></pre>
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