[med-svn] [Git][med-team/sra-sdk][master] sra-sdk 2.10.6+dfsg-5: Reenable legacy schema for sra-load (#961347)

[Aaron M. Ucko]

Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk


Commits:
b36b20cb by Aaron M. Ucko at 2020-05-25T22:45:08-04:00
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.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/reenable_legacy_schema_in_sra_load.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+sra-sdk (2.10.6+dfsg-5) unstable; urgency=medium
+
+  * 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.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Mon, 25 May 2020 22:45:07 -0400
+
 sra-sdk (2.10.6+dfsg-4) unstable; urgency=medium
 
   * Account for new sratools setup.  (Closes: #961256.)


=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                libngs-sdk-dev (>= 2.9.0),
-               libncbi-vdb-dev (>= 2.10.6+dfsg-2~),
+               libncbi-vdb-dev (>= 2.10.6+dfsg-3~),
                libvdb-sqlite-dev,
                libfuse-dev,
                libhdf5-dev,
@@ -23,6 +23,7 @@ Rules-Requires-Root: no
 Package: sra-toolkit
 Architecture: amd64
 Depends: ${shlibs:Depends},
+         libncbi-wvdb2 (>= 2.10.6+dfsg-3~),
          ${misc:Depends}
 Recommends: med-config (>= 2.1)
 Description: utilities for the NCBI Sequence Read Archive


=====================================
debian/patches/reenable_legacy_schema_in_sra_load.patch
=====================================
@@ -0,0 +1,18 @@
+--- a/tools/sra-load/loader.c
++++ b/tools/sra-load/loader.c
+@@ -38,6 +38,7 @@
+ #include <kfs/directory.h>
+ #include <kdb/meta.h>
+ #include <kapp/loader-meta.h>
++#include <sra/sraschema.h>
+ #include <sra/wsradb.h>
+ 
+ #include <os-native.h>
+@@ -904,6 +905,7 @@ rc_t KMain(int argc, char *argv[])
+     if (rc == 0) {
+         rc = KDirectoryNativeDir(&s_Directory);
+     }
++    SRAUseLegacyDefaultSchema = true;
+     /* Parse command line arguments */
+     if (rc == 0) {
+         rc = TArgsMake(&args, argc, argv);


=====================================
debian/patches/series
=====================================
@@ -19,3 +19,4 @@ ignore_failing_test_for_the_moment_FIXME.patch
 python3
 use_exposed_headers.patch
 use_unversioned_tools.patch
+reenable_legacy_schema_in_sra_load.patch



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/b36b20cb22242853e29881740e1cdfc0893143cd

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/b36b20cb22242853e29881740e1cdfc0893143cd
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200526/8f7f97ed/attachment-0001.html>