cleanups

Author: mr-c

cwl_utils/cite-extract.py

@@ -26,7 +26,7 @@ def extract_software_reqs(process: cwl.Process):
                                      process.id, process.loadingOptions)
 
 
-def process_software_requirement(req: cwl.SoftwarePackage):
+def process_software_requirement(req: cwl.SoftwareRequirement):
     for package in req.packages:
         print("Package: {}, version: {}, specs: {}".format(
             package.package, package.version, package.specs))

cwl_utils/docker-extract.py

@@ -7,8 +7,9 @@
 
 
 def parse_args():
-    parser = argparse.ArgumentParser(description='Tool to save docker images from a cwl workflow \n '
-                                                 'and generate udocker loading commands.')
+    parser = argparse.ArgumentParser(
+        description='Tool to save docker images from a cwl workflow \n '
+                    'and generate udocker loading commands.')
     parser.add_argument('dir', help='Directory in which to save images')
     parser.add_argument('input', help='Input CWL workflow')
     return parser.parse_args()
@@ -36,8 +37,17 @@ def load_docker_image(image_name):
 
 
 def save_docker_image(req, image_name, image_dir):
-    cmd = ['docker', 'save', '-o', os.path.join(image_dir, image_name), req]
-    subprocess.run(" ".join(cmd), shell=True, check=True)
+    cmd_pull = ['docker', 'pull', req]
+    try:
+        subprocess.run(cmd_pull, check=True, stdout=subprocess.PIPE,
+                       stderr=subprocess.STDOUT)
+    except subprocess.CalledProcessError as err:
+        if err.output:
+            raise subprocess.SubprocessError(err.output)
+        raise err
+    cmd_save = ['docker', 'save', '-o', os.path.join(image_dir, image_name),
+                req]
+    subprocess.run(cmd_save, check=True)
 
 
 def extract_docker_requirements(process: cwl.Process):
@@ -59,12 +69,6 @@ def extract_docker_reqs(process: cwl.Process):
                                      process.id, process.loadingOptions)
 
 
-def process_docker_requirement(req: cwl.SoftwarePackage):
-    if ':' not in req.dockerPull:
-        req.dockerPull += ':latest'
-    return req.dockerPull
-
-
 def traverse(process: cwl.Process):
     yield from extract_docker_requirements(process)
     if isinstance(process, cwl.Workflow):

setup.py

@@ -1,19 +1,18 @@
 from setuptools import setup, find_packages
 
 
-setup_requires = [
-    'ruamel.yaml',
-    'six',
-    'requests',
-    'cachecontrol',
-]
-
 setup(
     name='cwl-utils',
     version='0.1',
     author='Common workflow language working group',
     author_email='[email protected]',
     packages=find_packages(),
     python_requires='>=3.6',
-    setup_requires=setup_requires,
+    install_requires=[
+        'ruamel.yaml',
+        'six',
+        'requests',
+        'schema_salad',
+        'typing_extensions',
+    ],
 )