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feat: Migrate biorad_bioplex_manager to use SeriesData.get_unread #1100

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Merged
oscar-castro-bl merged 6 commits into from
Nov 12, 2025
Merged

feat: Migrate biorad_bioplex_manager to use SeriesData.get_unread #1100

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8902be5
Migrate biorad_bioplex_manager to use SeriesData.get_unread
oscar-castro-bl Oct 8, 2025
b17ffc4
merge main
oscar-castro-bl Nov 6, 2025
56f0883
fix unread warnings
oscar-castro-bl Nov 7, 2025
06c3fde
skip field, use recursive_find
oscar-castro-bl Nov 10, 2025
9ca8f12
more recursive_find implementation
oscar-castro-bl Nov 10, 2025
0e1faaf
Merge branch 'main' into biorad_bioplex_manager_get_unread
joshua-benchling Nov 11, 2025
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74 changes: 39 additions & 35 deletions ...schema_mappers/adm/multi_analyte_profiling/benchling/_2024/_09/multi_analyte_profiling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,7 @@ class Analyte:
statistics: list[StatisticsDocument] | None = None
statistic_datum_role: TStatisticDatumRole | None = None
fluorescence: float | None = None
custom_info: dict[str, Any] | None = None


@dataclass(frozen=True)
Expand Down Expand Up @@ -253,42 +254,45 @@ def _get_measurement_document(
assay_bead_count=TQuantityValueNumber(value=measurement.assay_bead_count),
analyte_aggregate_document=AnalyteAggregateDocument(
analyte_document=[
AnalyteDocumentItem(
analyte_identifier=analyte.identifier,
analyte_name=analyte.name,
assay_bead_identifier=analyte.assay_bead_identifier,
assay_bead_count=TQuantityValueNumber(
value=analyte.assay_bead_count
),
fluorescence=quantity_or_none(
TQuantityValueRelativeFluorescenceUnit,
analyte.fluorescence,
has_statistic_datum_role=analyte.statistic_datum_role,
),
statistics_aggregate_document=(
StatisticsAggregateDocument(
statistics_document=[
StatisticsDocumentItem(
statistical_feature=statistic.statistical_feature,
statistic_dimension_aggregate_document=StatisticDimensionAggregateDocument(
statistic_dimension_document=[
StatisticDimensionDocumentItem(
statistical_value=TQuantityValueModel(
value=dimension.value,
unit=dimension.unit,
has_statistic_datum_role=dimension.statistic_datum_role,
),
)
for dimension in statistic.statistic_dimensions
]
),
)
for statistic in analyte.statistics
]
)
if analyte.statistics
else None
add_custom_information_document(
AnalyteDocumentItem(
analyte_identifier=analyte.identifier,
analyte_name=analyte.name,
assay_bead_identifier=analyte.assay_bead_identifier,
assay_bead_count=TQuantityValueNumber(
value=analyte.assay_bead_count
),
fluorescence=quantity_or_none(
TQuantityValueRelativeFluorescenceUnit,
analyte.fluorescence,
has_statistic_datum_role=analyte.statistic_datum_role,
),
statistics_aggregate_document=(
StatisticsAggregateDocument(
statistics_document=[
StatisticsDocumentItem(
statistical_feature=statistic.statistical_feature,
statistic_dimension_aggregate_document=StatisticDimensionAggregateDocument(
statistic_dimension_document=[
StatisticDimensionDocumentItem(
statistical_value=TQuantityValueModel(
value=dimension.value,
unit=dimension.unit,
has_statistic_datum_role=dimension.statistic_datum_role,
),
)
for dimension in statistic.statistic_dimensions
]
),
)
for statistic in analyte.statistics
]
)
if analyte.statistics
else None
),
),
custom_info_doc=analyte.custom_info,
)
for analyte in measurement.analytes
]
Expand Down
18 changes: 11 additions & 7 deletions src/allotropy/parsers/biorad_bioplex_manager/biorad_bioplex_manager_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,11 @@ def create_data(self, named_file_contents: NamedFileContents) -> Data:

samples_dict = SampleMetadata.create_samples(reader["Samples"])
# Only parse system-level metadata once, from the first well.
system_metadata = SystemMetadata.create(reader["Wells"][0])
wells = reader["Wells"].findall("Well")
system_metadata = SystemMetadata.create(wells[0])
plate_dimensions = reader["PlateDimensions"]
plate_well_count = plate_dimensions.get_attr("TotalWells")
plate_dimensions.get_unread()

return Data(
create_metadata(
Expand All @@ -44,12 +48,12 @@ def create_data(self, named_file_contents: NamedFileContents) -> Data:
well,
samples_dict[well.name],
system_metadata,
experimental_data_id=reader["NativeDocumentLocation"].text,
experiment_type=reader["Description"].text,
plate_well_count=int(
reader.get_attribute("PlateDimensions", "TotalWells")
),
experimental_data_id=reader[
"NativeDocumentLocation"
].get_text_or_none(),
experiment_type=reader["Description"].get_text_or_none(),
plate_well_count=int(plate_well_count),
)
for well in [Well.create(well_xml) for well_xml in reader["Wells"]]
for well in [Well.create(well_xml) for well_xml in wells]
],
)
22 changes: 15 additions & 7 deletions src/allotropy/parsers/biorad_bioplex_manager/biorad_bioplex_manager_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,23 @@
)
from allotropy.named_file_contents import NamedFileContents
from allotropy.parsers.biorad_bioplex_manager import constants
from allotropy.parsers.utils.strict_xml_element import StrictXmlElement


class BioradBioplexReader:
def __init__(self, named_file_contents: NamedFileContents) -> None:
contents = named_file_contents.contents.read()
# Ensure contents is bytes for StrictXmlElement.create_from_bytes()
if isinstance(contents, str):
contents = contents.encode("utf-8")
try:
xml_tree = Et.ElementTree(Et.fromstring(contents)) # noqa: S314
self.root = xml_tree.getroot()
self.children = {child.tag: child for child in self.root}
self.root = StrictXmlElement.create_from_bytes(contents)
# Create a mapping of child tags to StrictXmlElement objects
self.children = {}
for child_tag in constants.EXPECTED_TAGS:
child_element = self.root.find_or_none(child_tag)
if child_element is not None:
self.children[child_tag] = child_element
except Et.ParseError as err:
# Return all expected tags if XML parsing fails
msg = "Error parsing xml"
Expand All @@ -31,12 +39,12 @@ def _validate(self) -> None:
msg = f"Missing expected tags in xml: {missing_tags}"
raise AllotropeConversionError(msg)

def __getitem__(self, child_tag: str) -> Et.Element:
def __getitem__(self, child_tag: str) -> StrictXmlElement:
return get_key_or_error("child tag of root", child_tag, self.children)

def get_attribute(self, child_tag: str, attribute: str) -> str:
try:
return self[child_tag].attrib[attribute]
except KeyError as e:
msg = f"Unable to find '{attribute}' in {self[child_tag].attrib}"
return self[child_tag].get_attr(attribute)
except Exception as e:
msg = f"Unable to find '{attribute}' in {self[child_tag].element.attrib}"
raise AllotropeConversionError(msg) from e
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