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allow for multiple options in config file
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@lukaspie
lukaspie committed Feb 20, 2024
1 parent f5667c7 commit d3bfd73
Showing 1 changed file with 105 additions and 36 deletions.
141 changes: 105 additions & 36 deletions pynxtools_xps/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@
XPS_TOKEN = "@xps_token:"
XPS_DATA_TOKEN = "@data:"
XPS_DETECTOR_TOKEN = "@detector_data:"
XPS_METADATA_TOKEN = "@metadata:"
ELN_TOKEN = "@eln"
LINK_TOKEN = "link"
TOKEN_SET = {XPS_TOKEN, XPS_DATA_TOKEN, XPS_DETECTOR_TOKEN, ELN_TOKEN}
Expand Down Expand Up @@ -291,38 +292,52 @@ def fill_template_with_xps_data(config_dict, xps_data_dict, template):
and store them into template. We use searching_keys
for separating the data from xps_data_dict.
"""
for key, config_value in config_dict.items():
if isinstance(config_value, str) and any(
token in config_value for token in TOKEN_SET
):
if XPS_DATA_TOKEN in str(config_value):
key_part = config_value.split(XPS_DATA_TOKEN)[-1]
entries_values = find_entry_and_value(
xps_data_dict, key_part, dt_typ=XPS_DATA_TOKEN
)
fill_data_group(key, key_part, entries_values, config_dict, template)
for key, config_values in config_dict.items():
config_value_list = values_to_list(config_values)

for config_value in config_value_list:
if isinstance(config_value, str) and any(
token in config_value for token in TOKEN_SET
):
if XPS_DATA_TOKEN in str(config_value):
key_part = config_value.split(XPS_DATA_TOKEN)[-1]
entries_values = find_entry_and_value(
xps_data_dict, key_part, dt_typ=XPS_DATA_TOKEN
)
fill_data_group(
key, key_part, entries_values, config_dict, template
)

elif XPS_DETECTOR_TOKEN in str(config_value):
key_part = config_value.split(XPS_DATA_TOKEN)[-1]
entries_values = find_entry_and_value(
xps_data_dict, key_part, dt_typ=XPS_DETECTOR_TOKEN
)
elif XPS_DETECTOR_TOKEN in str(config_value):
key_part = config_value.split(XPS_DATA_TOKEN)[-1]
entries_values = find_entry_and_value(
xps_data_dict, key_part, dt_typ=XPS_DETECTOR_TOKEN
)

fill_detector_group(
key, entries_values, config_dict, xps_data_dict, template
)
fill_detector_group(
key, entries_values, config_dict, xps_data_dict, template
)

elif XPS_TOKEN in str(config_value):
key_part = config_value.split(XPS_TOKEN)[-1]
entries_values = find_entry_and_value(
xps_data_dict, key_part, dt_typ=XPS_TOKEN
)
for entry, ent_value in entries_values.items():
modified_key = key.replace("[entry]", f"[{entry}]")
fill_template_with_value(modified_key, ent_value, template)
elif XPS_TOKEN in str(config_value):
key_part = config_value.split(XPS_TOKEN)[-1]
entries_values = find_entry_and_value(
xps_data_dict, key_part, dt_typ=XPS_TOKEN
)
for entry, ent_value in entries_values.items():
modified_key = key.replace("[entry]", f"[{entry}]")
fill_template_with_value(modified_key, ent_value, template)

elif XPS_METADATA_TOKEN in str(config_value):
token = config_value.split(XPS_METADATA_TOKEN)[-1]
entries_values = find_entry_and_value(
xps_data_dict, token, dt_typ=XPS_METADATA_TOKEN
)
for entry, ent_value in entries_values.items():
modified_key = key.replace("[entry]", f"[{entry}]")
fill_template_with_value(modified_key, ent_value, template)

else:
fill_template_with_value(key, config_value, template)
else:
fill_template_with_value(key, config_value, template)


def fill_template_with_eln_data(eln_data_dict, config_dict, template):
Expand All @@ -339,6 +354,22 @@ def fill_template_with_eln_data(eln_data_dict, config_dict, template):
fill_template_with_value(key, field_value, template)


def values_to_list(values):
"""
Return a list of the values object, independent of its intial type
Parameters
----------
values :
Dictionary values.
Returns
-------
list.
"""
if isinstance(values, bool):
return [values]
return list(values)


def concatenate_values(value1, value2):
"""
Concatenate two values of same type to be stored
Expand All @@ -358,6 +389,51 @@ def concatenate_values(value1, value2):
return concatenated


def _concatenate_values(value1, value2):
"""
Concatenate two values of same type to be stored
in xps_data_dict. Dicts are merged and every other object is
appended to a list.
"""
if isinstance(value1, dict) and isinstance(value2, dict):
concatenated = {**value1, **value2}
else:
if not isinstance(value1, list):
value1 = [value1]
if not isinstance(value2, list):
value2 = [value2]
concatenated = value1 + value2
return concatenated


def update_dict_without_replacing(existing_dict, new_dict):
"""
Update an existing dictionary with a new dict,
without overwriting existing keys.
Parameters
----------
existing_dict : dict
Dictionary contain XPS data.
new_dict : dict
Dictionary containining similar XPS data, used to update the
first dict.
Returns
-------
updated_dict : dict
Existing dictionary, updated with new dict.
"""
existing = [
(key, existing_dict[key], new_dict[key])
for key in set(existing_dict).intersection(new_dict)
]

updated_dict = {**existing_dict, **new_dict}
for key, value1, value2 in existing:
updated_dict[key] = _concatenate_values(value1, value2)

return updated_dict


# pylint: disable=too-few-public-methods
class XPSReader(BaseReader):
"""Reader for XPS."""
Expand Down Expand Up @@ -399,14 +475,7 @@ def read(

# If there are multiple input data files of the same type,
# make sure that existing keys are not overwritten.
existing = [
(key, xps_data_dict[key], data_dict[key])
for key in set(xps_data_dict).intersection(data_dict)
]

xps_data_dict = {**xps_data_dict, **data_dict}
for key, value1, value2 in existing:
xps_data_dict[key] = concatenate_values(value1, value2)
xps_data_dict = update_dict_without_replacing(xps_data_dict, data_dict)

config_file = reader_dir.joinpath(f"config/{config_file}")
elif file_ext in XpsDataFileParser.__prmt_metadata_file_ext__:
Expand Down

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