Merge pull request #82 from yucongalicechen/metadata3

load args into DO metadata

Author: sbillinge

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -2,15 +2,7 @@
 from argparse import ArgumentParser
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
-from diffpy.labpdfproc.tools import (
-    known_sources,
-    load_package_info,
-    load_user_info,
-    load_user_metadata,
-    set_input_lists,
-    set_output_directory,
-    set_wavelength,
-)
+from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
 
@@ -112,12 +104,7 @@ def get_args(override_cli_inputs=None):
 
 def main():
     args = get_args()
-    args = load_package_info(args)
-    args = load_user_info(args)
-    args = set_input_lists(args)
-    args.output_directory = set_output_directory(args)
-    args = set_wavelength(args)
-    args = load_user_metadata(args)
+    args = preprocessing_args(args)
 
     for filepath in args.input_paths:
         outfilestem = filepath.stem + "_corrected"
@@ -144,7 +131,7 @@ def main():
             "tth",
             scat_quantity="x-ray",
             name=filepath.stem,
-            metadata={"muD": args.mud, "anode_type": args.anode_type},
+            metadata=load_metadata(args, filepath),
         )
 
         absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength)

src/diffpy/labpdfproc/tests/test_tools.py

@@ -7,9 +7,11 @@
 from diffpy.labpdfproc.labpdfprocapp import get_args
 from diffpy.labpdfproc.tools import (
     known_sources,
+    load_metadata,
     load_package_info,
     load_user_info,
     load_user_metadata,
+    preprocessing_args,
     set_input_lists,
     set_output_directory,
     set_wavelength,
@@ -278,3 +280,41 @@ def test_load_package_info(mocker):
     actual_args = get_args(cli_inputs)
     actual_args = load_package_info(actual_args)
     assert actual_args.package_info == {"diffpy.labpdfproc": "1.2.3", "diffpy.utils": "3.3.0"}
+
+
+def test_load_metadata(mocker, user_filesystem):
+    cwd = Path(user_filesystem)
+    home_dir = cwd / "home_dir"
+    mocker.patch("pathlib.Path.home", lambda _: home_dir)
+    os.chdir(cwd)
+    mocker.patch(
+        "importlib.metadata.version",
+        side_effect=lambda package_name: "3.3.0" if package_name == "diffpy.utils" else "1.2.3",
+    )
+    cli_inputs = [
+        "2.5",
+        ".",
+        "--user-metadata",
+        "key=value",
+        "--username",
+        "cli_username",
+        "--email",
+        "[email protected]",
+    ]
+    actual_args = get_args(cli_inputs)
+    actual_args = preprocessing_args(actual_args)
+    for filepath in actual_args.input_paths:
+        actual_metadata = load_metadata(actual_args, filepath)
+        expected_metadata = {
+            "mud": 2.5,
+            "input_directory": str(filepath),
+            "anode_type": "Mo",
+            "wavelength": 0.71,
+            "output_directory": str(Path.cwd().resolve()),
+            "xtype": "tth",
+            "key": "value",
+            "username": "cli_username",
+            "email": "[email protected]",
+            "package_info": {"diffpy.labpdfproc": "1.2.3", "diffpy.utils": "3.3.0"},
+        }
+        assert actual_metadata == expected_metadata

src/diffpy/labpdfproc/tools.py

@@ -1,9 +1,11 @@
+import copy
 from pathlib import Path
 
 from diffpy.utils.tools import get_package_info, get_user_info
 
 WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
 known_sources = [key for key in WAVELENGTHS.keys()]
+METADATA_KEYS_TO_EXCLUDE = ["output_correction", "force_overwrite", "input", "input_paths"]
 
 
 def set_output_directory(args):
@@ -110,7 +112,7 @@ def set_wavelength(args):
 
     Returns
     -------
-        float: the wavelength value
+    args argparse.Namespace
 
     we raise an ValueError if the input wavelength is non-positive
     or if the input anode_type is not one of the known sources
@@ -214,3 +216,47 @@ def load_package_info(args):
     metadata = get_package_info("diffpy.labpdfproc")
     setattr(args, "package_info", metadata["package_info"])
     return args
+
+
+def preprocessing_args(args):
+    """
+    Perform preprocessing on the provided argparse Namespace
+
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser, default is None
+
+    Returns
+    -------
+    the updated argparse Namespace with arguments preprocessed
+    """
+    args = load_package_info(args)
+    args = load_user_info(args)
+    args = set_input_lists(args)
+    args.output_directory = set_output_directory(args)
+    args = set_wavelength(args)
+    args = load_user_metadata(args)
+    return args
+
+
+def load_metadata(args, filepath):
+    """
+    Load relevant metadata from args
+
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser
+
+    Returns
+    -------
+    A dictionary with relevant arguments from the parser
+    """
+
+    metadata = copy.deepcopy(vars(args))
+    for key in METADATA_KEYS_TO_EXCLUDE:
+        metadata.pop(key, None)
+    metadata["input_directory"] = str(filepath)
+    metadata["output_directory"] = str(metadata["output_directory"])
+    return metadata