Merge pull request #25 from unity-sds/optional_stage_inout

Remove bundling of stage in/out from unity-app-generator by default

Author: mcduffie

requirements.txt

@@ -1,2 +1,2 @@
-app_pack_generator>=0.4.3
-unity-sds-client==0.2.0
+app_pack_generator>=1.0.0
+unity-sds-client>=0.2.0

unity_app_generator/__main__.py

@@ -79,7 +79,7 @@ def build_cwl(args):
 
     app_gen = UnityApplicationGenerator(state_dir)
 
-    app_gen.create_cwl(cwl_output_path=args.cwl_output_path, docker_url=args.image_url)
+    app_gen.create_cwl(cwl_output_path=args.cwl_output_path, docker_url=args.image_url, monolithic=args.monolithic)
 
 def push_app_registry(args):
     state_dir = check_state_directory(state_directory_path(args))
@@ -152,6 +152,9 @@ def main():
     parser_build_cwl.add_argument("-u", "--image_url", 
         help="Docker image tag or remote registry URL to be included in the generated CWL files if not using the build_docker and/or push_docker subcommands") 
 
+    parser_build_cwl.add_argument("--monolithic", action="store_true",
+        help="Use the deprecated 'monolithic' approach to generating CWL where stage in and out are bundled inside the application")
+
     parser_build_cwl.set_defaults(func=build_cwl)
 
     # push_app_registry

unity_app_generator/generator.py

@@ -6,7 +6,8 @@
 
 from .state import ApplicationState
 
-from app_pack_generator import GitManager, DockerUtil, ApplicationNotebook, CWL, Descriptor
+from app_pack_generator import GitManager, DockerUtil, ApplicationNotebook
+from app_pack_generator import ProcessCWL, DataStagingCWL, Descriptor
 
 from unity_sds_client.services.application_service import DockstoreAppCatalog
 
@@ -55,9 +56,9 @@ def push_to_docker_registry(self, docker_registry, image_tag=None):
         # Push to remote repository
         self.app_state.docker_url = self.docker_util.push_image(docker_registry, self.app_state.docker_image_tag)
 
-    def _generate_dockstore_cwl(self, cwl_output_path):
+    def _generate_dockstore_cwl(self, cwl_output_path, target_cwl_filename):
 
-        template = """
+        template = f"""
 cwlVersion: v1.0
 
 class: Workflow
@@ -66,14 +67,15 @@ def _generate_dockstore_cwl(self, cwl_output_path):
 
 steps:
 step:
-    run: workflow.cwl
+    run: {target_cwl_filename}
 """
+        
         # Hard code file name because it is a hard coded re
         dockstore_cwl_filename = os.path.join(cwl_output_path, "Dockstore.cwl")
         with open(dockstore_cwl_filename, "w") as cwl_file:
             cwl_file.write(template.lstrip())
 
-    def create_cwl(self, cwl_output_path=None, docker_url=None):
+    def create_cwl(self, cwl_output_path=None, docker_url=None, monolithic=False):
 
         # Fall through using docker_image_tag if docker_url does not exist because no push has occurred
         # Or if docker_url is supplied as an argument use that
@@ -99,14 +101,26 @@ def create_cwl(self, cwl_output_path=None, docker_url=None):
         app = ApplicationNotebook(notebook_filename)
 
         logger.info("Parameters:\n" + app.parameter_summary())
+            
+        # Create CWL files depending on the mode of production
+        cwl_generators = [ ProcessCWL(app) ]
 
-        cwl = CWL(app)
-        desc = Descriptor(app, self.repo_info)
+        if monolithic:
+            cwl_generators.append( DataStagingCWL(app) )
 
-        files = cwl.generate_all(cwl_output_path, docker_url)
-        files.append(desc.generate_descriptor(cwl_output_path, docker_url))
+        files_created = []
+        for cwl_gen in cwl_generators:
+            files_created += cwl_gen.generate_all(cwl_output_path, dockerurl=docker_url)
+        
+        # Add the JSON descriptor file
+        desc = Descriptor(app, self.repo_info)
+        files_created.append(desc.generate_descriptor(cwl_output_path, docker_url))
 
-        self._generate_dockstore_cwl(cwl_output_path)
+        # Add Dockstore.cwl, point it to the appropriate entry point
+        if monolithic:
+            self._generate_dockstore_cwl(cwl_output_path, "workflow.cwl")
+        else:
+            self._generate_dockstore_cwl(cwl_output_path, "process.cwl")
 
     def notebook_parameters(self):
 

unity_app_generator/version.py

@@ -1 +1 @@
-__version__="0.3.2"
+__version__="1.0.0"