8000 Fixes interface for failing nomad tests by domna · Pull Request #119 · FAIRmat-NFDI/pynxtools · GitHub
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Fixes interface for failing nomad tests #119

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Merged
merged 3 commits into from
May 30, 2023
Merged

Fixes interface for failing nomad tests #119

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1054984
Fixes interface for failing nomad tests
domna May 30, 2023
8267a26
Fixes linting
domna May 30, 2023
3a64cf5
Allow input file name to be a list or a str
domna May 30, 2023
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13 changes: 11 additions & 2 deletions pynxtools/nexus/nexus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1021,7 +1021,12 @@ def process_node(hdf_node, hdf_path, parser, logger, doc=True):
logger.debug(f'value: {val[0]} {"..." if len(val) > 1 else ""}')
(req_str, nxdef, nxdl_path) = \
get_nxdl_doc(hdf_info, logger, doc, attr=key)
if parser is not None and 'NOT IN SCHEMA' not in req_str and 'None' not in req_str:
if (
parser is not None
and req_str is not None
and 'NOT IN SCHEMA' not in req_str
and 'None' not in req_str
):
parser({"hdf_info": hdf_info,
"nxdef": nxdef,
"nxdl_path": nxdl_path,
Expand Down Expand Up @@ -1325,7 +1330,11 @@ def full_visit(self, root, hdf_node, name, func):
def process_nexus_master_file(self, parser):
"""Process a nexus master file by processing all its nodes and their attributes"""
self.parser = parser
self.in_file = h5py.File(self.input_file_name, 'r')
self.in_file = h5py.File(
self.input_file_name[0]
if isinstance(self.input_file_name, list)
else self.input_file_name, 'r'
)
self.full_visit(self.in_file, self.in_file, '', self.visit_node)
if self.d_inq_nd is None and self.c_inq_nd is None:
get_default_plotable(self.in_file, self.logger)
Expand Down
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