First prototype of pypi2cwl

pypi2cwl/pypi2cwl.py

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+# /usr/bin/python3
+import imp
+import os
+import subprocess
+import sys
+
+import argparse as ap
+
+
+help_text = """
+pypi2cwl generates a bunch of  CWL command line tools out of scripts from a given PyPi package or GitHub repo
+Example: $ pypi2cwl PYPI_PACKAGE <options>
+"""
+parser = ap.ArgumentParser(description=help_text,
+                                   formatter_class=ap.RawDescriptionHelpFormatter)
+parser.add_argument('repo',
+                            help='PyPi repository or direct Github link')
+parser.add_argument('-d', '--directory',
+                            help='Directory to store CWL tool descriptions')
+parser.add_argument('-go', '--generate_outputs', action='store_true',
+                            help='Form output section from args than contain `output` keyword in their names')
+parser.add_argument('--no-install', action='store_true',
+                            help="Uninstall package after tool generation ")
+
+args = parser.parse_args()
+
+repo = args.repo
+if len(repo.split('/')) > 1:
+    # GitHub repo
+    pass
+else:
+    setuptools = imp.new_module('setuptools')
+    sys.modules['setuptools'] = setuptools
+    params = None
+
+    # TODO: cover all setuptools functions
+
+    def setup(*args, **kwargs):
+        global params
+        params = kwargs
+
+    def find_packages(*args, **kwargs):
+        return
+
+    setuptools.setup = setup
+    setuptools.find_packages = find_packages
+    subprocess.call(['sudo','pip2', 'install', repo])  # TODO: check pip version
+    """
+    TODO: Downloading repo from GitHub via API and unzipping
+    """
+    DIR = "/home/anton/phylotoast-master"  # has nothing to do with production version, just for the sake of quicker prototyping!
+    sys.path.insert(0, DIR)
+    os.chdir(DIR)
+    # importing setup from the target repo and parsing scripts
+    import setup
+    if params['scripts']:
+        for script in list(map(lambda script: script.split('/')[-1], params['scripts'])):
+            command = [script, '--generate_cwl_tool']
+            if args.directory:
+                command.extend(['-d', args.directory])
+            subprocess.call(command)