Merge pull request #47 from yucongalicechen/keyvalue2

closes #26: loading user-specified key-value pairs

Author: sbillinge

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -3,12 +3,12 @@
 from pathlib import Path
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
-from diffpy.labpdfproc.tools import known_sources, set_output_directory, set_wavelength
+from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_output_directory, set_wavelength
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
 
 
-def get_args():
+def get_args(override_cli_inputs=None):
     p = ArgumentParser()
     p.add_argument("mud", help="Value of mu*D for your " "sample. Required.", type=float)
     p.add_argument("-i", "--input-file", help="The filename of the " "datafile to load.")
@@ -58,12 +58,25 @@ def get_args():
         action="store_true",
         help="Outputs will not overwrite existing file unless --force is specified.",
     )
-    args = p.parse_args()
+    p.add_argument(
+        "-u",
+        "--user-metadata",
+        metavar="KEY=VALUE",
+        nargs="+",
+        help="Specify key-value pairs to be loaded into metadata using the format key=value. "
+        "Separate pairs with whitespace, and ensure no whitespaces before or after the = sign. "
+        "Avoid using = in keys. If multiple = signs are present, only the first separates the key and value. "
+        "If a key or value contains whitespace, enclose it in quotes. "
+        "For example, facility='NSLS II', 'facility=NSLS II', beamline=28ID-2, "
+        "'beamline'='28ID-2', 'favorite color'=blue, are all valid key=value items. ",
+    )
+    args = p.parse_args(override_cli_inputs)
     return args
 
 
 def main():
     args = get_args()
+    args = load_user_metadata(args)
     args.output_directory = set_output_directory(args)
     args.wavelength = set_wavelength(args)
 

src/diffpy/labpdfproc/tests/test_tools.py

@@ -5,7 +5,8 @@
 
 import pytest
 
-from diffpy.labpdfproc.tools import known_sources, set_output_directory, set_wavelength
+from diffpy.labpdfproc.labpdfprocapp import get_args
+from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_output_directory, set_wavelength
 
 params1 = [
     ([None], ["."]),
@@ -76,3 +77,63 @@ def test_set_wavelength_bad(inputs, msg):
     actual_args = argparse.Namespace(wavelength=inputs[0], anode_type=inputs[1])
     with pytest.raises(ValueError, match=re.escape(msg[0])):
         actual_args.wavelength = set_wavelength(actual_args)
+
+
+params5 = [
+    ([], []),
+    (
+        ["--user-metadata", "facility=NSLS II", "beamline=28ID-2", "favorite color=blue"],
+        [["facility", "NSLS II"], ["beamline", "28ID-2"], ["favorite color", "blue"]],
+    ),
+    (["--user-metadata", "x=y=z"], [["x", "y=z"]]),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params5)
+def test_load_user_metadata(inputs, expected):
+    expected_args = get_args(["2.5"])
+    for expected_pair in expected:
+        setattr(expected_args, expected_pair[0], expected_pair[1])
+    delattr(expected_args, "user_metadata")
+
+    cli_inputs = ["2.5"] + inputs
+    actual_args = get_args(cli_inputs)
+    actual_args = load_user_metadata(actual_args)
+    assert actual_args == expected_args
+
+
+params6 = [
+    (
+        ["--user-metadata", "facility=", "NSLS II"],
+        [
+            "Please provide key-value pairs in the format key=value. "
+            "For more information, use `labpdfproc --help.`"
+        ],
+    ),
+    (
+        ["--user-metadata", "favorite", "color=blue"],
+        "Please provide key-value pairs in the format key=value. "
+        "For more information, use `labpdfproc --help.`",
+    ),
+    (
+        ["--user-metadata", "beamline", "=", "28ID-2"],
+        "Please provide key-value pairs in the format key=value. "
+        "For more information, use `labpdfproc --help.`",
+    ),
+    (
+        ["--user-metadata", "facility=NSLS II", "facility=NSLS III"],
+        "Please do not specify repeated keys: facility. ",
+    ),
+    (
+        ["--user-metadata", "wavelength=2"],
+        "wavelength is a reserved name.  Please rerun using a different key name. ",
+    ),
+]
+
+
+@pytest.mark.parametrize("inputs, msg", params6)
+def test_load_user_metadata_bad(inputs, msg):
+    cli_inputs = ["2.5"] + inputs
+    actual_args = get_args(cli_inputs)
+    with pytest.raises(ValueError, match=msg[0]):
+        actual_args = load_user_metadata(actual_args)

src/diffpy/labpdfproc/tools.py

@@ -60,3 +60,45 @@ def set_wavelength(args):
         return WAVELENGTHS[args.anode_type]
     else:
         return WAVELENGTHS["Mo"]
+
+
+def _load_key_value_pair(s):
+    items = s.split("=")
+    key = items[0].strip()
+    if len(items) > 1:
+        value = "=".join(items[1:])
+    return (key, value)
+
+
+def load_user_metadata(args):
+    """
+    Load user metadata into the provided argparse Namespace, raise ValueError if in incorrect format
+
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser
+
+    Returns
+    -------
+    the updated argparse Namespace with user metadata inserted as key-value pairs
+
+    """
+
+    reserved_keys = vars(args).keys()
+
+    if args.user_metadata:
+        for item in args.user_metadata:
+            if "=" not in item:
+                raise ValueError(
+                    "Please provide key-value pairs in the format key=value. "
+                    "For more information, use `labpdfproc --help.`"
+                )
+            key, value = _load_key_value_pair(item)
+            if key in reserved_keys:
+                raise ValueError(f"{key} is a reserved name.  Please rerun using a different key name. ")
+            if hasattr(args, key):
+                raise ValueError(f"Please do not specify repeated keys: {key}. ")
+            setattr(args, key, value)
+    delattr(args, "user_metadata")
+    return args