[med-svn] [Git][med-team/sepp][master] Update a patch which induced a wrong behaviour when managing the built jar

[Pierre Gruet]

Pierre Gruet pushed to branch master at Debian Med / sepp


Commits:
41576940 by Pierre Gruet at 2020-08-19T10:24:01+02:00
Update a patch which induced a wrong behaviour when managing the built jar

- - - - -


1 changed file:

- debian/patches/use_debian_packaged_guppy_from_pplacer.patch


Changes:

=====================================
debian/patches/use_debian_packaged_guppy_from_pplacer.patch
=====================================
@@ -1,10 +1,12 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 22 Jul 2020 21:53:32 +0200
-Description: Use Debian packaged guppy
+Last-Update: Wed, 19 Aug 2020 10:20:03 +0200
+Description: Use Debian packaged guppy and hmm*
+ An if statement is added because copy_tool_to_lib is also called for the jar
+ that is generated before the Python part of the build.
 
 --- a/sepp-package/run-sepp.sh
 +++ b/sepp-package/run-sepp.sh
-@@ -146,7 +146,7 @@ cp $tmp/${name}_rename-json.py .
+@@ -146,7 +146,7 @@
  # we might want to split computation in two parts: a) obtaining placements and b) creation of an insertion tree.
  # If -n set to something, we stop after a) and leave it to the user to compute b) afterwards.
  if [ -z ${noTree+x} ]; then
@@ -15,7 +17,7 @@ Description: Use Debian packaged guppy
  
 --- a/setup.py
 +++ b/setup.py
-@@ -45,7 +45,7 @@ def get_tools_dir(where):
+@@ -45,7 +45,7 @@
  
  
  def get_tool_name(tool, bits):
@@ -24,12 +26,23 @@ Description: Use Debian packaged guppy
          return tool
      is_64bits = sys.maxsize > 2**32
      return "%s-%s" % (tool, "64" if is_64bits else "32")
-@@ -81,7 +81,7 @@ class ConfigSepp(Command):
+@@ -80,9 +80,16 @@
+         return os.path.join(self.basepath, "bundled-v%s" % version)
  
      def copy_tool_to_lib(self, tool, where=None, bits=True):
-         shutil.copy2(
+-        shutil.copy2(
 -            os.path.join(get_tools_dir(where), get_tool_name(tool, bits)),
-+            os.path.join("/usr/bin", get_tool_name(tool, bits)),
-             os.path.join(self.get_tools_dest(), tool))
+-            os.path.join(self.get_tools_dest(), tool))
++        # The jar just build is in a subdirectory, while we want to use
++        # Debian-provided binaries.
++        if get_tool_name(tool, bits).find(".jar") != -1:
++            shutil.copy2(
++                os.path.join(get_tools_dir(where), get_tool_name(tool, bits)),
++                os.path.join(self.get_tools_dest(), tool))
++        else:
++            shutil.copy2(
++                os.path.join("/usr/bin", get_tool_name(tool, bits)),
++                os.path.join(self.get_tools_dest(), tool))
  
      def initialize_options(self):
+         """init options"""



View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/41576940d19c7c01a019dbb8034eaed05c4e12df

-- 
View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/41576940d19c7c01a019dbb8034eaed05c4e12df
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