Closed sanbrock closed 3 months ago
This seems to be picked up by CI/CD now, too: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/jobs/2122024
Here is the error trace:
=================================== FAILURES =================================== _ /builds/nomad-lab/nomad-remote-tools-hub/docker/xps/example/XPS workflow and fitting example.ipynb _ --------------------------------------------------------------------------- convert(input_file=["In-situ PBTTT XPS (SPECS).xml", "eln_data.yaml", "config_file.json"], reader='xps', nxdl='NXmpes', output='PBTTT.nxs') --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /tmp/ipykernel_29/3962228810.py in <cell line: 1>() ----> 1 convert(input_file=["In-situ PBTTT XPS (SPECS).xml", "eln_data.yaml", "config_file.json"], 2 reader='xps', 3 nxdl='NXmpes', 4 output='PBTTT.nxs') /opt/conda/lib/python3.10/site-packages/nexusutils/dataconverter/convert.py in convert(input_file, reader, nxdl, output, generate_template, fair, **kwargs) 106 raise Exception("The chosen NXDL isn't supported by the selected reader.") 107 --> 108 data = data_reader().read( # type: ignore[operator] 109 template=Template(template), 110 file_paths=input_file, /opt/conda/lib/python3.10/site-packages/nexusutils/dataconverter/readers/xps/reader.py in read(self, template, file_paths, objects) 392 ENTRY_SET) 393 if eln_data_dict: --> 394 fill_template_with_eln_data(eln_data_dict, 395 config_dict, 396 template, /opt/conda/lib/python3.10/site-packages/nexusutils/dataconverter/readers/xps/reader.py in fill_template_with_eln_data(eln_data_dict, config_dict, template, entry_set) 343 for key, val in config_dict.items(): 344 if ELN_TOCKEN in val: --> 345 fill_from_file(key) 346 elif key in list(eln_data_dict.keys()): 347 fill_from_value(key) /opt/conda/lib/python3.10/site-packages/nexusutils/dataconverter/readers/xps/reader.py in fill_from_file(key) 307 def fill_from_file(key): 308 atom_types: List = [] --> 309 field_value = eln_data_dict[key] 310 311 if "chemical_formula" in key: KeyError: '/ENTRY[entry]/SAMPLE[sample]/chemical_formula'
@sanbrock and @RubelMozumder I think this is solved with the fix I did in the ci-cd branch of the north repository.
This seems to be picked up by CI/CD now, too: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/jobs/2122024
Here is the error trace: