.

.gitignore

@@ -0,0 +1,10 @@
+__pycache__
+*egg-info*
+.DS_Store
+.coverage
+build
+dist
+.eggs
+_build
+_static
+_templates

VERSION

@@ -0,0 +1 @@
+1.0

pipeline_utils/__main__.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python3
+
+################################################
+#
+#   __main__
+#     this is the entry point for command line
+#
+#   Michele Berselli - [email protected]
+#   Phil Grayson - [email protected]
+#
+################################################
+
+################################################
+#   Libraries
+################################################
+import sys, os
+import argparse
+
+# Commands
+from pipeline_utils import deploy_pipeline
+
+################################################
+#   Functions
+################################################
+################################################
+#   main
+################################################
+def main(args=None):
+    '''
+        command line wrapper around available commands
+    '''
+    # Adding parser and subparsers
+    parser = argparse.ArgumentParser(prog='pipeline_utils', description='Collection of utilities for cgap-pipeline')
+    subparsers = parser.add_subparsers(dest='func', metavar="<command>")
+
+    # Add deploy_pipeline to subparsers
+    deploy_pipeline_parser = subparsers.add_parser('deploy_pipeline', description='Utility to automatically deploy a pipeline',
+                                                help='Utility to automatically deploy a pipeline')
+
+    # Required args
+    deploy_pipeline_parser.add_argument('--ff-env', required=True)
+    deploy_pipeline_parser.add_argument('--cwl-bucket', required=False)
+    deploy_pipeline_parser.add_argument('--account', required=False)
+    deploy_pipeline_parser.add_argument('--region', required=False)
+    deploy_pipeline_parser.add_argument('--project-uuid', required=False)
+    deploy_pipeline_parser.add_argument('--institution-uuid', required=False)
+
+    # Optional args
+    deploy_pipeline_parser.add_argument('--post-software', action='store_true')
+    deploy_pipeline_parser.add_argument('--post-file-format', action='store_true')
+    deploy_pipeline_parser.add_argument('--post-file-reference', action='store_true')
+    deploy_pipeline_parser.add_argument('--post-workflow', action='store_true')
+    deploy_pipeline_parser.add_argument('--post-metaworkflow', action='store_true')
+    deploy_pipeline_parser.add_argument('--post-cwl', action='store_true')
+    deploy_pipeline_parser.add_argument('--post-ecr', action='store_true')
+    deploy_pipeline_parser.add_argument('--del-prev-version', action='store_true')
+
+    # Subparsers map
+    subparser_map = {
+                    'deploy_pipeline': deploy_pipeline_parser
+                    }
+
+    # Checking arguments
+    if len(sys.argv) == 1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+    elif len(sys.argv) == 2:
+        if sys.argv[1] in subparser_map:
+            subparser_map[sys.argv[1]].print_help(sys.stderr)
+            sys.exit(1)
+        else:
+            parser.print_help(sys.stderr)
+            sys.exit(1)
+        #end if
+    #end if
+    args = vars(parser.parse_args())
+
+    print(args)
+    sys.exit()
+
+    # Call the right tool
+    if args['func'] == 'deploy_pipeline':
+        deploy_pipeline.main(args)
+
+#################################################################
+#
+#    MAIN
+#
+#################################################################
+if __name__ == "__main__":
+
+    main()
+
+#end if

pipeline_utils/deploy_pipeline.py

@@ -330,14 +330,17 @@ def _post_patch_repo(ff_key, cwl_bucket, account, region,
 
 
 ################################################
-#   main
+#   runner
 ################################################
 def main(args):
     '''
         deploy cgap pipeline
         post | patch metadata and dockers in the specified environment from repos
     '''
 
+    print(args)
+    return
+
     # Get env variables
     if os.environ.get('GLOBAL_BUCKET_ENV', ''):  # new cgap account
         s3 = s3_utils.s3Utils(env=ff_env)
@@ -380,28 +383,13 @@ def main(args):
                      args.post_cwl, args.post_ecr, args.del_prev_version)
 
 
-if __name__ == '__main__':
-
-    parser = argparse.ArgumentParser()
-
-    # Required args
-    parser.add_argument('--ff-env', required=True)
-    parser.add_argument('--cwl-bucket', required=False)
-    parser.add_argument('--account', required=False)
-    parser.add_argument('--region', required=False)
-    parser.add_argument('--project-uuid', required=False)
-    parser.add_argument('--institution-uuid', required=False)
-
-    # Optional args
-    parser.add_argument('--post-software', action='store_true')
-    parser.add_argument('--post-file-format', action='store_true')
-    parser.add_argument('--post-file-reference', action='store_true')
-    parser.add_argument('--post-workflow', action='store_true')
-    parser.add_argument('--post-metaworkflow', action='store_true')
-    parser.add_argument('--post-cwl', action='store_true')
-    parser.add_argument('--post-ecr', action='store_true')
-    parser.add_argument('--del-prev-version', action='store_true')
+#################################################################
+#
+#    MAIN
+#
+#################################################################
+if __name__ == "__main__":
 
-    args = parser.parse_args()
+    main()
 
-    main(args)
+#end if

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup, find_packages
 
 # Description
-with open('README_utils.md') as fd:
+with open('README.md') as fd:
     long_description = fd.read()
 #end with
 
@@ -20,13 +20,13 @@
 
 setup(
     name='cgap-pipeline-utils',
-    version=open('VERSION').readlines()[-1].replace('v', '').strip() + '.0', # VERSION.release
+    version=open('VERSION').readlines()[-1],
     description = 'Collection of utilities for cgap-pipeline',
     long_description = long_description,
     long_description_content_type = 'text/markdown',
-    author = 'Michele Berselli, Soo Lee',
+    author = 'Michele Berselli, Phil Grayson',
     author_email = '[email protected]',
-    url='https://github.com/dbmi-bgm/cgap-pipeline',
+    url='https://github.com/dbmi-bgm/cgap-pipeline-utils',
     include_package_data=True,
     packages=['pipeline_utils'],
     classifiers=[
@@ -35,6 +35,11 @@
             'Programming Language :: Python',
             'Programming Language :: Python :: 3'
             ],
+    entry_points = {
+        'console_scripts': [
+            'pipeline_utils = pipeline_utils.__main__:main',
+        ]
+    },
     install_requires=install_requires,
     setup_requires=install_requires,
     tests_require=tests_requires,