pwwang · June 11, 2020 19:41 · Jun 11, 2020
diff --git a/sift4g_annotator b/sift4g_annotator
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+#
+# Wrapper script for SIFT4G_annotator
+#
+
+#
+# Program Parameters
+#
+import os
+import subprocess
+import sys
+from os import access
+from os import getenv
+from os import X_OK
+jar_file = 'SIFT4G_Annotator.jar'
+
+default_jvm_mem_opts = ['-Xms512m', '-Xmx1g']
+
+# !!! End of parameter section. No user-serviceable code below this line !!!
+
+
+def real_dirname(path):
+    """Return the symlink-resolved, canonicalized directory-portion of path."""
+    return os.path.dirname(os.path.realpath(path))
+
+
+def java_executable():
+    """Return the executable name of the Java interpreter."""
+    java_home = getenv('JAVA_HOME')
+    java_bin = os.path.join('bin', 'java')
+    env_prefix = os.path.dirname(os.path.dirname(real_dirname(sys.argv[0])))
+
+    if java_home and access(os.path.join(java_home, java_bin), X_OK):
+        return os.path.join(java_home, java_bin)
+    else:
+        # Use Java installed with Anaconda to ensure correct version
+        return os.path.join(env_prefix, 'bin', 'java')
+
+
+def jvm_opts(argv):
+    """Construct list of Java arguments based on our argument list.
+
+    The argument list passed in argv must not include the script name.
+    The return value is a 3-tuple lists of strings of the form:
+      (memory_options, prop_options, passthrough_options)
+    """
+    mem_opts = []
+    prop_opts = []
+    pass_args = []
+
+    for arg in argv:
+        if arg.startswith('-D'):
+            prop_opts.append(arg)
+        elif arg.startswith('-XX'):
+            prop_opts.append(arg)
+        elif arg.startswith('-Xm'):
+            mem_opts.append(arg)
+        else:
+            pass_args.append(arg)
+
+    # In the original shell script the test coded below read:
+    #   if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ]
+    # To reproduce the behaviour of the above shell code fragment
+    # it is important to explictly check for equality with None
+    # in the second condition, so a null envar value counts as True!
+
+    if mem_opts == [] and getenv('_JAVA_OPTIONS') is None:
+        mem_opts = default_jvm_mem_opts
+
+    return (mem_opts, prop_opts, pass_args)
+
+
+def main():
+    java = java_executable()
+    jar_dir = real_dirname(sys.argv[0])
+    (mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:])
+
+    if pass_args != [] and pass_args[0].startswith('org'):
+        jar_arg = '-cp'
+    else:
+        jar_arg = '-jar'
+
+    if '-c' not in pass_args:
+        pass_args.append('-c')
+
+    jar_path = os.path.join(jar_dir, jar_file)
+
+    if not os.path.isfile(jar_path):
+        sys.stderr.write(f'{jar_file} file not found.\n')
+        sys.exit(1)
+
+    java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args
+    sys.stdout.write(f'Running: {java_args}\n')
+    sys.exit(subprocess.call(java_args))
+
+
+if __name__ == '__main__':
+    main()