diff env/lib/python3.9/site-packages/gxformat2/main.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/gxformat2/main.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,61 @@
+"""Module containing :func:`convert_and_import_workflow`."""
+import os
+
+from .converter import python_to_workflow, yaml_to_workflow
+from .interface import BioBlendImporterGalaxyInterface
+from .yaml import ordered_load
+
+
+def convert_and_import_workflow(has_workflow, **kwds):
+    """Conversion and import Format 2 workflows into a target Galaxy instance."""
+    galaxy_interface = kwds.get("galaxy_interface", None)
+    if galaxy_interface is None:
+        galaxy_interface = BioBlendImporterGalaxyInterface(**kwds)
+
+    source_type = kwds.get("source_type", None)
+    workflow_directory = kwds.get("workflow_directory", None)
+    if source_type == "path":
+        workflow_path = has_workflow
+        if workflow_directory is None:
+            workflow_directory = os.path.dirname(has_workflow)
+        with open(workflow_path, "r") as f:
+            has_workflow = ordered_load(f)
+
+    if workflow_directory is not None:
+        workflow_directory = os.path.abspath(workflow_directory)
+
+    convert = kwds.get("convert", True)
+    raw_yaml = kwds.get("raw_yaml", False)
+    if raw_yaml and convert:
+        raise Exception("Incompatible options selected.")
+    if convert:
+        if isinstance(has_workflow, dict):
+            workflow = python_to_workflow(has_workflow, galaxy_interface, workflow_directory)
+        else:
+            workflow = yaml_to_workflow(has_workflow, galaxy_interface, workflow_directory)
+    else:
+        workflow = has_workflow
+        if not isinstance(workflow, dict) and not raw_yaml:
+            workflow = ordered_load(workflow)
+        else:
+            workflow = {"yaml_content": workflow}
+
+    name = kwds.get("name", None)
+    if name is not None:
+        workflow["name"] = name
+    publish = kwds.get("publish", False)
+    exact_tools = kwds.get("exact_tools", False)
+    fill_defaults = kwds.get("fill_defaults", True)
+    import_kwds = {
+        "fill_defaults": fill_defaults
+    }
+    if publish:
+        import_kwds["publish"] = True
+    if exact_tools:
+        import_kwds["exact_tools"] = True
+    return galaxy_interface.import_workflow(workflow, **import_kwds)
+
+
+__all__ = (
+    'convert_and_import_workflow',
+)