..

petab/v2/petab1to2.py

@@ -3,6 +3,8 @@
 from itertools import chain
 from pathlib import Path
 
+from pandas.io.common import get_handle, is_url
+
 import petab.C
 from petab.yaml import get_path_prefix
 
@@ -56,38 +58,53 @@ def petab1to2(yaml_config: Path | str, output_dir: Path | str = None):
     # Write new YAML file
     output_dir = Path(output_dir)
     output_dir.mkdir(parents=True, exist_ok=True)
-    output_file = output_dir / Path(yaml_file).name
-    write_yaml(new_yaml_config, output_file)
+    new_yaml_file = output_dir / Path(yaml_file).name
+    write_yaml(new_yaml_config, new_yaml_file)
 
     # Update tables
     # condition tables, observable tables, SBML files, parameter table:
     #  no changes - just copy
     file = yaml_config[petab.C.PARAMETER_FILE]
-    shutil.copy(get_src_path(file), get_dest_path(file))
+    _copy_file(get_src_path(file), get_dest_path(file))
 
     for problem_config in yaml_config[petab.C.PROBLEMS]:
         for file in chain(
             problem_config[petab.C.CONDITION_FILES],
             problem_config[petab.C.OBSERVABLE_FILES],
             problem_config[petab.C.SBML_FILES],
         ):
-            shutil.copy(get_src_path(file), get_dest_path(file))
+            _copy_file(get_src_path(file), get_dest_path(file))
 
     # TODO: Measurements: preequilibration to experiments/timecourses
-    # TODO: ...
-    ...
+
+    # validate updated Problem
+    # TODO validate_problem(new_yaml_file)
 
 
 def _update_yaml(yaml_config: dict) -> dict:
     """Update PEtab 1.0 YAML to PEtab 2.0 format."""
     yaml_config = yaml_config.copy()
 
     # Update format_version
-    yaml_config["format_version"] = 2
+    yaml_config["format_version"] = "2.0.0"
 
     # Add extensions
     yaml_config["extensions"] = []
 
     # TODO models needs ID and format
 
     return yaml_config
+
+
+def _copy_file(src: Path | str, dest: Path | str):
+    """Copy file."""
+    src = str(src)
+    dest = str(dest)
+
+    if is_url(src):
+        with get_handle(src, mode="r") as src_handle:
+            with open(dest, "w") as dest_handle:
+                dest_handle.write(src_handle.handle.read())
+        return
+
+    shutil.copy(str(src), str(dest))