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Chemometic Nucleoview: support for non-numeric values (#213)
Add support for non-numeric values in fields that are mapped to TQuantity type values.
1 parent a6b0152 commit 213bc43

10 files changed

+372
-1
lines changed

‎CHANGELOG.md

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@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Add calculated data documents to Unchained Labs Lunatic adapter
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- Parser for ChemoMetic NucleoView
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- Add non numeric options for tQuantityValue value property
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- Add support for non-numeric values to ChemoMetic NucleoView
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### Fixed
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### Changed
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- Simplify Moldev Softmax Pro parsing with dataclasses

‎src/allotropy/parsers/chemometec_nucleoview/nucleoview_parser.py

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@@ -24,7 +24,10 @@
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TQuantityValuePercent,
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TQuantityValueUnitless,
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)
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from allotropy.allotrope.models.shared.definitions.definitions import TDateTimeValue
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from allotropy.allotrope.models.shared.definitions.definitions import (
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TDateTimeValue,
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ValueEnum,
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)
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from allotropy.constants import ASM_CONVERTER_NAME, ASM_CONVERTER_VERSION
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from allotropy.named_file_contents import NamedFileContents
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from allotropy.parsers.chemometec_nucleoview.constants import (
@@ -60,6 +63,11 @@ def get_property_from_sample(
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property_type = _PROPERTY_LOOKUP[property_name]
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try:
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value = float(value)
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except ValueError:
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return property_type(value=ValueEnum.NaN)
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# if the porperty type is measured in million cells per ml convert cells per ml
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if property_type == TQuantityValueMillionCellsPerMilliliter:
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return property_type(value=float(value) / 1e6)

‎src/allotropy/parsers/chemometec_nucleoview/nucleoview_reader.py

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@@ -34,5 +34,9 @@ def read(cls, contents: IOType) -> pd.DataFrame:
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raw_data["Date time"] + raw_data["Time zone offset"]
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)
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raw_data["Sample ID"] = raw_data["Image"].str.split("-", n=3).str[3]
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raw_data = raw_data.rename(
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{"Estimated cell diameter [um]": "Estimated cell diameter (um)"},
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axis=1,
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)
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return raw_data

‎tests/parsers/chemometec_nucleoview/chemometec_nucleoview_parser_test.py

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@@ -7,6 +7,9 @@
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"chemometec_nucleoview_example01.csv",
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"chemometec_nucleoview_example02.csv",
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"chemometec_nucleoview_example03.csv",
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"chemometec_nucleoview_example04.csv",
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"chemometec_nucleoview_example05.csv",
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"chemometec_nucleoview_example06.csv",
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)
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VENDOR_TYPE = Vendor.CHEMOMETEC_NUCLEOVIEW

‎tests/parsers/chemometec_nucleoview/testdata/chemometec_nucleoview_example04.csv

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Viability and Cell Count Assay - example cell counting; ;
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Image;20231120-0012-c-cellsABCD;
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Operator;DrScientist;
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Viability (%);68.2;
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Live (cells/ml);2.45E6;
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Dead (cells/ml);1.14E6;
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Total (cells/ml);3.58E3 (Out of optimal range);
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; ;
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Estimated cell diameter [um];Not determined;
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Cell diameter standard deviation (um);6.9;
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(%) of cells in aggregates with five or more cells;3;
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Sample Volume (ul);200.0;
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Dilution Volume (ul);0.000;
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Multiplication factor;1.000;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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cm filename;20231120-0012-c-cellsABCD.cm
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Protocol template title;Viability and Cell Count Assay
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Protocol template purpose;Cell Count and Viability with AO and DAPI
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Protocol template filename;Viability and Cell Count Assay - NC-200.cmsx
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Protocol adaptation title;example cell counting
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Protocol adaptation purpose;Cell Count and Viability with AO and DAPI
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Protocol adaptation filename;94A29BE3f39d48cd8eb5cb9472add350.cmsu
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Instrument type;NucleoView NC-200
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Instrument s/n;s/n 9000201099909999
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Date time;20231120 163016
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Time zone offset;2
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Login ID;admin
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PC;DESKTOP-A678B9H
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Application SW version;1.4.2.0
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21 CFR Part 11;disabled
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Event log format;Plain text
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csv file version;2
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//[ECEC5A41]

‎tests/parsers/chemometec_nucleoview/testdata/chemometec_nucleoview_example04.json

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{
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"$asm.manifest": "http://purl.allotrope.org/manifests/cell-counting/BENCHLING/2023/11/cell-counting.manifest",
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"cell counting aggregate document": {
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"cell counting document": [
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{
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"measurement aggregate document": {
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"measurement document": [
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{
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"measurement time": "2023-11-20T16:30:16+02:00",
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"measurement identifier": "8b1c98f3-936b-47ac-aea3-98e1a9d18abb",
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "dark field imager (cell counter)",
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"detection type": "dark field"
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}
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]
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},
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"sample document": {
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"sample identifier": "cellsABCD"
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},
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"processed data aggregate document": {
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"processed data document": [
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{
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"viability (cell counter)": {
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"value": 68.2,
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"unit": "%"
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},
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"viable cell density (cell counter)": {
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"value": 2.45,
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"unit": "10^6 cells/mL"
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},
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"data processing document": {
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"cell density dilution factor": {
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"value": 1.0,
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"unit": "(unitless)"
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}
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},
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"total cell density (cell counter)": {
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"value": "NaN",
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"unit": "10^6 cells/mL"
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},
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"dead cell density (cell counter)": {
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"value": 1.14,
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"unit": "10^6 cells/mL"
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},
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"average total cell diameter": {
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"value": "NaN",
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"unit": "\u03bcm"
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}
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}
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]
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}
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}
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]
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},
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"analyst": "DrScientist"
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}
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],
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"device system document": {
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"model number": "NucleoView NC-200",
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"equipment serial number": "s/n 9000201099909999"
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},
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"data system document": {
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"file name": "chemometec_nucleoview_example04.csv",
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"software name": "NucleoView",
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"ASM converter name": "allotropy",
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"ASM converter version": "0.1.12"
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}
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}
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}

‎tests/parsers/chemometec_nucleoview/testdata/chemometec_nucleoview_example05.csv

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Viability and Cell Count Assay - example cell counting; ;
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Image;20231120-0012-c-cellsABCD;
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Operator;DrScientist;
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Viability (%);68.2;
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Live (cells/ml);2.45E6;
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Dead (cells/ml);1.14E6;
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Total (cells/ml);3.58E6;
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; ;
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Estimated cell diameter [um];<8;
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Cell diameter standard deviation (um);6.9;
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(%) of cells in aggregates with five or more cells;3;
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Sample Volume (ul);200.0;
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Dilution Volume (ul);0.000;
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Multiplication factor;1.000;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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cm filename;20231120-0012-c-cellsABCD.cm
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Protocol template title;Viability and Cell Count Assay
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Protocol template purpose;Cell Count and Viability with AO and DAPI
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Protocol template filename;Viability and Cell Count Assay - NC-200.cmsx
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Protocol adaptation title;example cell counting
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Protocol adaptation purpose;Cell Count and Viability with AO and DAPI
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Protocol adaptation filename;94A29BE3f39d48cd8eb5cb9472add350.cmsu
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Instrument type;NucleoView NC-200
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Instrument s/n;s/n 9000201099909999
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Date time;20231120 163016
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Time zone offset;2
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Login ID;admin
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PC;DESKTOP-A678B9H
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Application SW version;1.4.2.0
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21 CFR Part 11;disabled
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Event log format;Plain text
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csv file version;2
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//[ECEC5A41]

‎tests/parsers/chemometec_nucleoview/testdata/chemometec_nucleoview_example05.json

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{
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"$asm.manifest": "http://purl.allotrope.org/manifests/cell-counting/BENCHLING/2023/11/cell-counting.manifest",
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"cell counting aggregate document": {
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"cell counting document": [
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{
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"measurement aggregate document": {
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"measurement document": [
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{
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"measurement time": "2023-11-20T16:30:16+02:00",
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"measurement identifier": "08222a88-7587-492c-8812-9a1930bcec98",
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "dark field imager (cell counter)",
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"detection type": "dark field"
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}
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]
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},
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"sample document": {
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"sample identifier": "cellsABCD"
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},
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"processed data aggregate document": {
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"processed data document": [
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{
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"viability (cell counter)": {
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"value": 68.2,
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"unit": "%"
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},
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"viable cell density (cell counter)": {
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"value": 2.45,
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"unit": "10^6 cells/mL"
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},
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"data processing document": {
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"cell density dilution factor": {
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"value": 1.0,
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"unit": "(unitless)"
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}
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},
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"total cell density (cell counter)": {
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"value": 3.58,
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"unit": "10^6 cells/mL"
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},
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"dead cell density (cell counter)": {
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"value": 1.14,
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"unit": "10^6 cells/mL"
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},
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"average total cell diameter": {
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"value": "NaN",
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"unit": "\u03bcm"
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}
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}
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]
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}
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}
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]
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},
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"analyst": "DrScientist"
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}
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],
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"device system document": {
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"model number": "NucleoView NC-200",
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"equipment serial number": "s/n 9000201099909999"
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},
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"data system document": {
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"file name": "chemometec_nucleoview_example05.csv",
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"software name": "NucleoView",
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"ASM converter name": "allotropy",
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"ASM converter version": "0.1.12"
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}
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}
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}

‎tests/parsers/chemometec_nucleoview/testdata/chemometec_nucleoview_example06.csv

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Viability and Cell Count Assay - example cell counting; ;
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Image;20231120-0002-c-cellsABCD;
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Operator;DrScientist;
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Viability (%);92.8;
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Live (cells/ml);1.58E6;
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Dead (cells/ml);1.22E5;
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Total (cells/ml);1.70E6;
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; ;
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Estimated cell diameter (um);13.2 (Uncertain
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determination);
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Cell diameter standard deviation (um);7.7;
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(%) of cells in aggregates with five or more cells;5;
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Sample Volume (ul);200.0;
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Dilution Volume (ul);0.000;
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Multiplication factor;1.000;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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cm filename;20231120-0039-c-cellsABCD.cm
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Protocol template title;Viability and Cell Count Assay
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Protocol template purpose;Cell Count and Viability with AO and DAPI
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Protocol template filename;Viability and Cell Count Assay - NC-200.cmsx
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Protocol adaptation title;example cell counting
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Protocol adaptation purpose;Cell Count and Viability with AO and DAPI
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Protocol adaptation filename;287764ADc8824786b882bfc202a12044.cmsu
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Instrument type;NucleoView NC-200
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Instrument s/n;s/n 9000201099909999
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Date time;20231120 110300
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Time zone offset;-7
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Login ID;admin
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PC;ABC0-NBBS-FQ01
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Application SW version;1.4.0.0
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21 CFR Part 11;disabled
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Event log format;Plain text
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csv file version;2
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//[25FDBA08]

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