Add fromwdl to janisdk

janisdk/fromwdl/__init__.py

@@ -0,0 +1,37 @@
+def add_fromwdl_args(parser):
+    parser.description = (
+        "Parse a WDL command line tool / workflow and write it as a Janis file"
+    )
+
+    parser.add_argument(
+        "-o",
+        "--output",
+        help="Directory to output the workflow / tools to, otherwise this is written to stdout",
+    )
+
+    parser.add_argument("wdlfile", help="The path to the WDL file")
+
+    parser.add_argument(
+        "translation", default="janis", choices=["wdl", "wdl", "janis"], nargs="?"
+    )
+
+    return parser
+
+
+def do_fromwdl(args):
+    from janis_core import WdlParser, Logger
+
+
+    Logger.info(f"Loading WDL file: {args.wdlfile}")
+    tool = WdlParser.from_doc(args.wdlfile)
+
+    Logger.info(f"Loaded {tool.type()}: {tool.versioned_id()}")
+
+    translated = tool.translate(
+        args.translation,
+        to_console=args.output is None,
+        to_disk=args.output is not None,
+        export_path=args.output,
+    )
+
+    return translated

janisdk/main.py

@@ -4,13 +4,14 @@
 
 from janisdk.container import do_container, add_container_args
 from janisdk.fromcwl import do_fromcwl, add_fromcwl_args
+from janisdk.fromwdl import do_fromwdl, add_fromwdl_args
 from janisdk.runtest import runner as test_runner
 
 from janis_assistant.management.configuration import JanisConfiguration
 
 
 def process_args():
-    cmds = {"container": do_container, "run-test": do_runtest, "fromcwl": do_fromcwl}
+    cmds = {"container": do_container, "run-test": do_runtest, "fromcwl": do_fromcwl, "fromwdl": do_fromwdl}
 
     parser = argparse.ArgumentParser(description="Execute a workflow")
     subparsers = parser.add_subparsers(help="subcommand help", dest="command")
@@ -20,6 +21,7 @@ def process_args():
     add_container_args(subparsers.add_parser("container"))
     test_runner.add_runtest_args(subparsers.add_parser("run-test"))
     add_fromcwl_args(subparsers.add_parser("fromcwl"))
+    add_fromwdl_args(subparsers.add_parser("fromwdl"))
 
     args = parser.parse_args()
     return cmds[args.command](args)

setup.py

@@ -3,7 +3,7 @@
 # Version information is found in the __init__ file of `janis/`
 DESCRIPTION = "Contains classes and helpers to build a workflow, and provide options to convert to CWL / WDL"
 
-JANIS_CORE_VERSION = "v0.11.4"
+JANIS_CORE_VERSION = "v0.11.5"
 JANIS_ASSISTANT_VERSION = "v0.11.7"
 JANIS_UNIX_VERSION = "v0.11.0"
 JANIS_BIOINFORMATICS_VERSION = "v0.11.1"