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use pynxtools.nomad.schema.Root #513

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use pynxtools.nomad.schema.Root #513

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22 changes: 16 additions & 6 deletions src/pynxtools/nomad/entrypoints.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ def load(self):
SearchQuantities,
)

schema = "pynxtools.nomad.schema.NeXus"
schema = "pynxtools.nomad.schema.Root"

nexus_app = AppEntryPoint(
name="NexusApp",
Expand Down Expand Up @@ -105,17 +105,17 @@ def load(self):
Column(quantity=f"entry_type", selected=True),
Column(
title="definition",
quantity=f"data.*.ENTRY[*].definition__field#{schema}",
quantity=f"data.ENTRY[*].definition__field#{schema}",
selected=True,
),
Column(
title="start_time",
quantity=f"data.*.ENTRY[*].start_time__field#{schema}",
quantity=f"data.ENTRY[*].start_time__field#{schema}",
selected=True,
),
Column(
title="title",
quantity=f"data.*.ENTRY[*].title__field#{schema}",
quantity=f"data.ENTRY[*].title__field#{schema}",
selected=True,
),
],
Expand Down Expand Up @@ -161,8 +161,8 @@ def load(self):
"autorange": True,
"nbins": 30,
"scale": "linear",
"quantity": f"data.Root.datetime#{schema}",
"title": "Procesing Time",
"quantity": f"data.ENTRY.start_time__field#{schema}",
"title": "Start Time",
"layout": {
"lg": {"minH": 3, "minW": 3, "h": 4, "w": 12, "y": 0, "x": 0}
},
Expand All @@ -177,6 +177,16 @@ def load(self):
"lg": {"minH": 3, "minW": 3, "h": 8, "w": 4, "y": 0, "x": 12}
},
},
{
"type": "terms",
"show_input": False,
"scale": "linear",
"quantity": f"data.ENTRY.definition__field#{schema}",
"title": "Definition",
"layout": {
"lg": {"minH": 3, "minW": 3, "h": 8, "w": 4, "y": 0, "x": 16}
},
},
{
"type": "periodic_table",
"scale": "linear",
Expand Down
49 changes: 27 additions & 22 deletions src/pynxtools/nomad/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,7 @@ def _to_section(
nx_def: str,
nx_node: Optional[ET.Element],
current: MSection,
nx_root,
) -> MSection:
"""
Args:
Expand Down Expand Up @@ -105,7 +106,17 @@ def _to_section(
new_section = section
break

if new_section is None:
if new_section is not None:
return new_section
if current == nx_root:
cls = getattr(nexus_schema, nx_def, None)
sec = cls()
new_def_spec = sec.m_def.all_sub_sections[nomad_def_name]
sec.m_create(new_def_spec.section_def.section_cls)
new_section = sec.m_get_sub_section(new_def_spec, -1)
current.ENTRY.append(new_section)
new_section.__dict__["nx_name"] = hdf_name
else:
current.m_create(new_def.section_def.section_cls)
new_section = current.m_get_sub_section(new_def, -1)
new_section.__dict__["nx_name"] = hdf_name
Expand Down Expand Up @@ -194,7 +205,7 @@ def _populate_data(
# so values of non-scalar attribute will not end up in metainfo!

attr_name = attr_name + "__attribute"
current = _to_section(attr_name, nx_def, nx_attr, current)
current = _to_section(attr_name, nx_def, nx_attr, current, self.nx_root)

try:
if nx_root or nx_parent.tag.endswith("group"):
Expand Down Expand Up @@ -332,12 +343,13 @@ def __nexus_populate(self, params: dict, attr=None): # pylint: disable=W0613
if nx_path is None or nx_path == "/":
return

current: MSection = _to_section(None, nx_def, None, self.nx_root)
# current: MSection = _to_section(None, nx_def, None, self.nx_root)
current = self.nx_root
depth: int = 1
current_hdf_path = ""
for name in hdf_path.split("/")[1:]:
nx_node = nx_path[depth] if depth < len(nx_path) else name
current = _to_section(name, nx_def, nx_node, current)
current = _to_section(name, nx_def, nx_node, current, self.nx_root)
self._collect_class(current)
depth += 1
if depth < len(nx_path):
Expand Down Expand Up @@ -468,7 +480,7 @@ def parse(
child_archives: Dict[str, EntryArchive] = None,
) -> None:
self.archive = archive
self.nx_root = nexus_schema.NeXus() # type: ignore # pylint: disable=no-member
self.nx_root = nexus_schema.Root() # type: ignore # pylint: disable=no-member

self.archive.data = self.nx_root
self._logger = logger if logger else get_logger(__name__)
Expand All @@ -483,25 +495,18 @@ def parse(
archive.metadata = EntryMetadata()

# Normalise experiment type
app_defs = str(self.nx_root).split("(")[1].split(")")[0].split(",")
app_def_list = []
for app_elem in app_defs:
app = app_elem.lstrip()
try:
app_sec = getattr(self.nx_root, app)
# app_defs = str(self.nx_root).split("(")[1].split(")")[0].split(",")
app_def_list = set()
try:
app_entries = getattr(self.nx_root, "ENTRY")
for entry in app_entries:
try:
app_entry = getattr(app_sec, "ENTRY")
if len(app_entry) < 1:
raise AttributeError()
app = entry.definition__field
app_def_list.add(rename_nx_for_nomad(app) if app else "Generic")
except (AttributeError, TypeError):
app_entry = getattr(app_sec, "entry")
if len(app_entry) < 1:
raise AttributeError()
app_def_list.append(
app if app != rename_nx_for_nomad("NXroot") else "Generic"
)
except (AttributeError, TypeError):
pass
pass
except (AttributeError, TypeError):
pass
if len(app_def_list) == 0:
app_def = "Experiment"
else:
Expand Down
2 changes: 1 addition & 1 deletion src/pynxtools/nomad/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@
}


class NexusMeasurement(Measurement):
class NexusMeasurement(Measurement, Schema):
def normalize(self, archive, logger):
try:
app_entry = getattr(self, "ENTRY")
Expand Down
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