Merge pull request #42 from saalfeldlab/fix/local-scripts-modules

fix: local script module issues for java 17

Author: bogovicj

startup-scripts/jar_path_util.py

@@ -6,6 +6,16 @@ def get_local_jar_path():
 def get_provided_jar_path():
 	return get_jar_path('-provided')
 
+
+def get_java_cmd_local(class_arg):
+    return [ 'java',
+        '--add-opens=java.base/java.nio=ALL-UNNAMED',
+        '--add-opens=java.base/java.lang.invoke=ALL-UNNAMED',
+        '--add-opens=java.base/java.util=ALL-UNNAMED',
+        '--add-exports=java.base/sun.nio.ch=ALL-UNNAMED',
+        '-Dspark.master=local[*]', '-cp', get_local_jar_path(),
+        class_arg]
+
 def get_jar_path(jar_suffix=None):
 	curr_script_dir = os.path.dirname(os.path.abspath(__file__))
 	base_folder = os.path.dirname(curr_script_dir)
@@ -29,4 +39,4 @@ def get_jar_path(jar_suffix=None):
 		jar_filename_ext = os.path.splitext(jar_filename)
 		jar_filename = jar_filename_ext[0] + jar_suffix + jar_filename_ext[1]
 
-	return os.path.join(target_folder, jar_filename)
+	return os.path.join(target_folder, jar_filename)

startup-scripts/spark-local/n5-connected-components.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.N5ConnectedComponentsSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.N5ConnectedComponentsSpark') + sys.argv[1:])

startup-scripts/spark-local/n5-convert.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.N5ConvertSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.N5ConvertSpark') + sys.argv[1:])

startup-scripts/spark-local/n5-downsample-label.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.downsample.N5LabelDownsamplerSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.downsample.N5LabelDownsamplerSpark') + sys.argv[1:])

startup-scripts/spark-local/n5-downsample-offset.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.downsample.N5OffsetDownsamplerSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.downsample.N5OffsetDownsamplerSpark') + sys.argv[1:])

startup-scripts/spark-local/n5-downsample.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.downsample.N5DownsamplerSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.downsample.N5DownsamplerSpark') + sys.argv[1:])

startup-scripts/spark-local/n5-mips.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.N5MaxIntensityProjectionSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.N5MaxIntensityProjectionSpark') + sys.argv[1:])

startup-scripts/spark-local/n5-remove.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.N5RemoveSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.N5RemoveSpark') + sys.argv[1:])

startup-scripts/spark-local/n5-scale-pyramid-nonisotropic.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.downsample.scalepyramid.N5NonIsotropicScalePyramidSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.downsample.scalepyramid.N5NonIsotropicScalePyramidSpark') + sys.argv[1:])

startup-scripts/spark-local/n5-scale-pyramid-offset.py

@@ -6,7 +6,6 @@
 
 sys.dont_write_bytecode = True
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-from jar_path_util import get_local_jar_path
-bin_path = get_local_jar_path()
+from jar_path_util import get_java_cmd_local
 
-subprocess.call(['java', '-Dspark.master=local[*]', '-cp', bin_path, 'org.janelia.saalfeldlab.n5.spark.downsample.scalepyramid.N5OffsetScalePyramidSpark'] + sys.argv[1:])
+subprocess.call(get_java_cmd_local('org.janelia.saalfeldlab.n5.spark.downsample.scalepyramid.N5OffsetScalePyramidSpark') + sys.argv[1:])