Merge branch 'develop' for release 0.1.6

beeflow/client/bee_client.py

@@ -14,6 +14,7 @@
 import tempfile
 import textwrap
 import time
+import importlib.metadata
 import jsonpickle
 import requests
 import typer
@@ -174,8 +175,12 @@ def match_short_id(wf_id):
 @app.command()
 def submit(wf_name: str = typer.Argument(..., help='the workflow name'),  # pylint:disable=R0915
            wf_path: pathlib.Path = typer.Argument(..., help='path to the workflow .tgz or dir'),
-           main_cwl: str = typer.Argument(..., help='filename of main CWL file'),
-           yaml: str = typer.Argument(..., help='filename of YAML file'),
+           main_cwl: str = typer.Argument(...,
+           help='filename of main CWL (if using CWL tarball), '
+           + 'path of main CWL (if using CWL directory)'),
+           yaml: str = typer.Argument(...,
+           help='filename of yaml file (if using CWL tarball), '
+           + 'path of yaml file (if using CWL directory)'),
            workdir: pathlib.Path = typer.Argument(...,
            help='working directory for workflow containing input + output files',),
            no_start: bool = typer.Option(False, '--no-start', '-n',
@@ -189,7 +194,7 @@ def is_parent(parent, path):
 
     tarball_path = ""
     if os.path.exists(wf_path):
-        # Check to see if the wf_path is a tarball or a directory. Run package() if directory
+        # Check to see if the wf_path is a tarball or a directory. Package if directory
         if os.path.isdir(wf_path):
             print("Detected directory instead of packaged workflow. Packaging Directory...")
             main_cwl_path = pathlib.Path(main_cwl).resolve()
@@ -200,45 +205,37 @@ def is_parent(parent, path):
             if not yaml_path.exists():
                 error_exit(f'YAML file {yaml} does not exist')
 
-            # Parse workflow
-            parser = CwlParser()
-            workflow_id = generate_workflow_id()
-            workflow, tasks = parser.parse_workflow(workflow_id, str(main_cwl_path),
-                                                    job=str(yaml_path))
-            tasks = [jsonpickle.encode(task) for task in tasks]
-
+            # Packaging in temp dir, after copying alternate cwl_main or yaml file
             cwl_indir = is_parent(wf_path, main_cwl_path)
             yaml_indir = is_parent(wf_path, yaml_path)
-            # The CWL and YAML file are already in the workflow directory
-            # so we don't need to do anything
             tempdir_path = pathlib.Path(tempfile.mkdtemp())
             if cwl_indir and yaml_indir:
                 package_path = package(wf_path, tempdir_path)
             else:
-                # Create a temp wf directory
                 tempdir_wf_path = pathlib.Path(tempdir_path / wf_path.name)
                 shutil.copytree(wf_path, tempdir_wf_path, dirs_exist_ok=False)
                 if not cwl_indir:
                     shutil.copy2(main_cwl, tempdir_wf_path)
                 if not yaml_indir:
                     shutil.copy2(yaml, tempdir_wf_path)
                 package_path = package(tempdir_wf_path, tempdir_path)
-            wf_tarball = open(package_path, 'rb')
-            shutil.rmtree(tempdir_path)
         else:
-            # Untar and parse workflow
-            tempdir_path = pathlib.Path(tempfile.mkdtemp())
-            tempdir_wf_path = unpackage(wf_path, tempdir_path)
-            main_cwl_path = pathlib.Path(tempdir_wf_path / main_cwl).resolve()
-            yaml_path = pathlib.Path(tempdir_wf_path / yaml).resolve()
-
-            parser = CwlParser()
-            workflow_id = generate_workflow_id()
-            workflow, tasks = parser.parse_workflow(workflow_id, str(main_cwl_path),
-                                                    job=str(yaml_path))
-
+            package_path = wf_path
+        # Untar and parse workflow
+        untar_path = pathlib.Path(tempfile.mkdtemp())
+        untar_wf_path = unpackage(package_path, untar_path)
+        main_cwl_path = untar_wf_path / pathlib.Path(main_cwl).name
+        yaml_path = untar_wf_path / pathlib.Path(yaml).name
+        parser = CwlParser()
+        workflow_id = generate_workflow_id()
+        workflow, tasks = parser.parse_workflow(workflow_id, str(main_cwl_path),
+                                                job=str(yaml_path))
+        tasks = [jsonpickle.encode(task) for task in tasks]
+
+        wf_tarball = open(package_path, 'rb')
+        shutil.rmtree(untar_path)
+        if os.path.isdir(wf_path):
             shutil.rmtree(tempdir_path)
-            wf_tarball = open(wf_path, 'rb')
     else:
         error_exit(f'Workflow tarball {wf_path} cannot be found')
 
@@ -254,7 +251,8 @@ def is_parent(parent, path):
         'wf_filename': os.path.basename(wf_path).encode(),
         'workdir': workdir,
         'workflow': jsonpickle.encode(workflow),
-        'tasks': jsonpickle.encode(tasks, warn=True)
+        'tasks': jsonpickle.encode(tasks, warn=True),
+        'no_start': no_start,
     }
     files = {
         'workflow_archive': wf_tarball
@@ -283,10 +281,6 @@ def is_parent(parent, path):
     if tarball_path:
         os.remove(tarball_path)
 
-    # Start the workflow
-    if not no_start:
-        start(wf_id)
-
     return wf_id
 
 
@@ -354,7 +348,7 @@ def unpackage(package_path, dest_path):
     if not package_str.endswith('.tgz'):
         # No cleanup, maybe we should rm dest_path?
         error_exit("Invalid package name, please use the beeflow package command")
-    wf_dir = package_str[:-4]
+    wf_dir = pathlib.Path(package_path).stem
 
     return_code = subprocess.run(['tar', '-C', dest_path, '-xf', package_path],
                                  check=True).returncode
@@ -363,14 +357,12 @@ def unpackage(package_path, dest_path):
         error_exit("Unpackage failed")
     else:
         print(f"Package {package_str} unpackaged successfully")
-
-
-    return dest_path/wf_dir  # noqa: Not an arithmetic operation
+    return pathlib.Path(dest_path / wf_dir)
 
 
 @app.command('list')
 def list_workflows():
-    """List all worklfows."""
+    """List all workflows."""
     try:
         conn = _wfm_conn()
         resp = conn.get(_url(), timeout=60)
@@ -536,6 +528,16 @@ def reexecute(wf_name: str = typer.Argument(..., help='The workflow name'),
     return wf_id
 
 
+@app.callback(invoke_without_command=True)
+def version_callback(version: bool = False):
+    """Beeflow."""
+    # Print out the current version of the app, and then exit
+    # Note above docstring gets used in the help menu
+    if version:
+        version = importlib.metadata.version("hpc-beeflow")
+        print(version)
+
+
 def main():
     """Execute bee_client."""
     global _INTERACTIVE