Update file_setup Pipeline

Dockerfile

@@ -18,8 +18,8 @@ RUN apt-get update \
 
 
 # Install merge_images
-COPY setup_files /usr/local/bin
+COPY file_setup /usr/local/bin
 
 
-ENTRYPOINT ["setup_files"]
+ENTRYPOINT ["file_setup"]
 CMD ["--help"]

file_setup

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3.5
+# coding=utf-8
+
+
+"""
+merge_images
+
+Usage:  For usage instructions run with option --help
+Author: Stephan Porada <sporada@uni-bielefeld.de>
+
+"""
+
+from argparse import ArgumentParser
+import os
+import subprocess
+
+
+def parse_arguments():
+    parser = ArgumentParser(description='Merges images into one .pdf file.')
+    parser.add_argument('i', metavar='input directory')
+    parser.add_argument('o', metavar='output directory')
+    parser.add_argument('f', metavar='output file base')
+    parser.add_argument('--log-dir')
+    parser.add_argument('--zip')
+    return parser.parse_args()
+
+
+def merge_images(input_dir, output_dir, output_file_base, zip):
+    try:
+        os.mkdir(output_dir)
+    except FileExistsError:
+        pass
+    cmd = 'ls -Q -v "{i}"/*.* > "{i}"/file_list.txt'.format(i=input_dir)
+    subprocess.run(cmd, shell=True)
+    cmd = 'convert @"{}"/file_list.txt "{}"/"{}".pdf'.format(input_dir, output_dir, output_file_base)  # noqa
+    subprocess.run(cmd, shell=True)
+    cmd = 'rm "{}"/file_list.txt'.format(input_dir)
+    subprocess.run(cmd, shell=True)
+    if zip is not None:
+        cmd = 'cd "{}"'.format(output_dir)
+        cmd += ' && '
+        cmd += 'zip'
+        cmd += ' -m'
+        cmd += ' "{}"_-_pdf "{}".pdf'.format(zip, output_file_base)
+        cmd += ' && '
+        cmd += 'cd -'
+        subprocess.run(cmd, shell=True)
+
+
+def main():
+    args = parse_arguments()
+    print(args)
+    merge_images(args.i, args.o, args.f, args.zip)
+
+
+if __name__ == '__main__':
+    main()

setup_files

@@ -1,61 +0,0 @@
-#!/usr/bin/env python3.5
-# coding=utf-8
-
-
-"""
-merge_images
-
-Usage:  For usage instructions run with option --help
-Author: Stephan Porada <sporada@uni-bielefeld.de>
-
-"""
-
-import argparse
-import os
-import subprocess
-
-
-def parse_arguments():
-    parser = argparse.ArgumentParser(description='Merges given input images '
-                                                 'into one multipage tiff.')
-    parser.add_argument('-i',
-                        dest='input_dir',
-                        required=True,
-                        type=os.path.abspath)
-    parser.add_argument('-o',
-                        dest='output_dir',
-                        required=True,
-                        type=os.path.abspath)
-    parser.add_argument('--zip',
-                        default='combines-pictures',
-                        dest='zip',
-                        type=str,
-                        help='''package result files in zip bundles and set a
-                                filename prefix as a string.''',
-                        required=False)
-    return parser.parse_args()
-
-
-def merge_images(input_dir, output_dir, zip):
-    try:
-        os.mkdir(output_dir)
-    except FileExistsError:
-        pass
-    cmd = 'ls -Q -v {i}/*.* > {i}/file_list.txt'.format(i=input_dir)
-    subprocess.run(cmd, shell=True)
-    cmd = 'convert @{i}/file_list.txt {o}/combined.tif'.format(i=input_dir, o=output_dir)
-    subprocess.run(cmd, shell=True)
-    cmd = 'rm {i}/file_list.txt'.format(i=input_dir)
-    subprocess.run(cmd, shell=True)
-    if zip:
-        cmd = 'cd {o} && zip -m {f}-combined.zip combined.tif && cd -'.format(o=output_dir, f=zip)
-        subprocess.run(cmd, shell=True)
-
-
-def main():
-    args = parse_arguments()
-    merge_images(args.input_dir, args.output_dir, args.zip)
-
-
-if __name__ == '__main__':
-    main()

wrapper/file_setup

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+# coding=utf-8
+
+from argparse import ArgumentParser
+import os
+import subprocess
+
+CONTAINER_IMAGE = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/file_setup:latest'
+CONTAINER_INPUT_DIR = '/input'
+CONTAINER_OUTPUT_DIR = '/output'
+UID = str(os.getuid())
+GID = str(os.getgid())
+
+parser = ArgumentParser(add_help=False)
+parser.add_argument('-i')
+parser.add_argument('-o')
+args, remaining_args = parser.parse_known_args()
+
+cmd = ['docker', 'run', '--rm', '-it', '-u', '{}:{}'.format(UID, GID)]
+if args.o is not None:
+    cmd += ['-v', '{}:{}'.format(os.path.abspath(args.o), CONTAINER_OUTPUT_DIR)]
+    remaining_args.insert(0, CONTAINER_OUTPUT_DIR)
+if args.i is not None:
+    cmd += ['-v', '{}:{}'.format(os.path.abspath(args.i), CONTAINER_INPUT_DIR)]
+    remaining_args.insert(0, CONTAINER_INPUT_DIR)
+cmd.append(CONTAINER_IMAGE)
+cmd += remaining_args
+
+subprocess.run(cmd)

wrapper/setup_files

@@ -1,39 +0,0 @@
-#!/usr/bin/env python3
-# coding=utf-8
-
-import argparse
-import os
-import subprocess
-
-container_image = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/setup_files:latest'
-container_input_dir = '/input'
-container_output_dir = '/output'
-uid = str(os.getuid())
-gid = str(os.getgid())
-
-parser = argparse.ArgumentParser(add_help=False)
-parser.add_argument(
-    '-i',
-    dest='input_dir',
-    required=False
-)
-parser.add_argument(
-    '-o',
-    dest='output_dir',
-    required=False
-)
-args, remaining_args = parser.parse_known_args()
-
-cmd = ['docker', 'run', '--rm', '-it', '-u', uid + ':' + gid]
-if args.input_dir is not None:
-    host_input_dir = os.path.abspath(args.input_dir)
-    cmd += ['-v', host_input_dir + ':' + container_input_dir]
-    remaining_args += ['-i', container_input_dir]
-if args.output_dir is not None:
-    host_output_dir = os.path.abspath(args.output_dir)
-    cmd += ['-v', host_output_dir + ':' + container_output_dir]
-    remaining_args += ['-o', container_output_dir]
-cmd.append(container_image)
-cmd += remaining_args
-
-subprocess.run(cmd)