[med-svn] [Git][med-team/sra-sdk][master] 3 commits: Marking the -java package as Architecture: all, making it binNMU-able

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / sra-sdk


Commits:
323619d7 by Pierre Gruet at 2022-10-12T16:59:50+02:00
Marking the -java package as Architecture: all, making it binNMU-able

- - - - -
acae3fb0 by Pierre Gruet at 2022-10-12T17:02:03+02:00
Adding a Lintian override for the embedded JS code

- - - - -
d147fc46 by Pierre Gruet at 2022-10-13T22:54:52+02:00
Providing a symlink to the shared lib in a new -jni binary package

- - - - -


4 changed files:

- debian/control
- + debian/libngs-java-doc.lintian-overrides
- + debian/libngs-jni.links.in
- debian/rules


Changes:

=====================================
debian/control
=====================================
@@ -163,12 +163,12 @@ Description: Next Generation Sequencing language Bindings (C++ development)
  This is the full development package.
 
 Package: libngs-java
-Multi-Arch: same
-Architecture: any
+Multi-Arch: foreign
+Architecture: all
 Section: java
-Depends: ${misc:Depends},
-         ${java:Depends},
-         libncbi-ngs-dev (= ${binary:Version})
+Depends: ${java:Depends},
+         libngs-jni (>= ${source:Version}),
+         libngs-jni (<< ${source:Version}.1~)
 Recommends: ${java:Recommends}
 Suggests: libngs-java-doc
 Description: Next Generation Sequencing language Bindings (Java bindings)
@@ -186,6 +186,27 @@ Description: Next Generation Sequencing language Bindings (Java bindings)
  .
  Java bindings.
 
+Package: libngs-jni
+Architecture: any
+Section: java
+Depends: ${shlibs:Depends},
+         libncbi-ngs3 (= ${binary:Version}),
+         ${misc:Depends}
+Description: Next Generation Sequencing language Bindings (Java native binding)
+ NGS is a new, domain-specific API for accessing reads, alignments and
+ pileups produced from Next Generation Sequencing. The API itself is
+ independent from any particular back-end implementation, and supports
+ use of multiple back-ends simultaneously. It also provides a library for
+ building new back-end "engines". The engine for accessing SRA data is
+ contained within the sister repository ncbi-vdb.
+ .
+ The API is currently expressed in C++, Java and Python languages. The
+ design makes it possible to maintain a high degree of similarity between
+ the code in one language and code in another - especially between C++
+ and Java.
+ .
+ Java native bindings.
+
 Package: libngs-java-doc
 Multi-Arch: foreign
 Architecture: all


=====================================
debian/libngs-java-doc.lintian-overrides
=====================================
@@ -0,0 +1,4 @@
+# It would be too complicated to remove the javascript that is included in
+# javadocs, see the discussion on Debian Java mailing list starting at 
+# https://lists.debian.org/debian-java/2018/06/msg00020.html.
+embedded-javascript-library please use * [usr/share/doc/libngs-java/api/*/jquery*.*s]


=====================================
debian/libngs-jni.links.in
=====================================
@@ -0,0 +1 @@
+usr/lib/${DEB_HOST_MULTIARCH}/libncbi-ngs.so.#STRIPPED_UPSTREAM_VERSION# usr/lib/jni/libncbi-ngs.so


=====================================
debian/rules
=====================================
@@ -10,6 +10,7 @@ pkg := sra-toolkit
 
 include /usr/share/dpkg/architecture.mk
 include /usr/share/dpkg/buildflags.mk
+include /usr/share/dpkg/pkg-info.mk
 
 build3vers := $(shell py3versions -sv)
 
@@ -32,6 +33,8 @@ override_dh_auto_clean:
 	rm -rf ngs/ngs-sdk/$(DEB_HOST_MULTIARCH)
 	rm -rf ngs/ngs-python/build
 
+	-rm debian/libngs-jni.links
+
 override_dh_auto_configure:
 	dh_auto_configure -- -DVDB_LIBDIR=/usr/lib/${DEB_HOST_MULTIARCH} \
 	    -DVDB_INCDIR=/usr/include/ncbi-vdb
@@ -121,6 +124,11 @@ endif
 override_dh_prep:
 	dh_prep -X debian/tmp
 
+execute_before_dh_link:
+	# Putting the upstream version number (without the dfsg part) at the end of
+	# symlink source in the -jni package.
+	sed 's/\(#STRIPPED_UPSTREAM_VERSION#\)/\1$(DEB_VERSION_UPSTREAM)/; s/#STRIPPED_UPSTREAM_VERSION#\(.*\)+dfsg[0-9]*/\1/' debian/libngs-jni.links.in > debian/libngs-jni.links
+
 # require network, not automatically run
 # use it when the pom file must be re-downloaded from maven repo
 BASE_URL:=https://repo.maven.apache.org/maven2/gov/nih/nlm/ncbi/ngs-java



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/744618d2a40015f728ce1a973f44207c7564f7b0...d147fc46f80e014d62da2ac36f19ec1a645aee59

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/744618d2a40015f728ce1a973f44207c7564f7b0...d147fc46f80e014d62da2ac36f19ec1a645aee59
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