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Edit templates for measurement registration #832

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merged 20 commits into from
Sep 17, 2024
Merged

Edit templates for measurement registration #832

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2b9dc75
WIP
KochTobi Sep 10, 2024
7ca7d72
wip
KochTobi Sep 10, 2024
d45eb87
make it work
KochTobi Sep 13, 2024
f0e073b
Extract behaviour
KochTobi Sep 13, 2024
82f0b1d
remove unused method
KochTobi Sep 13, 2024
265accb
Adapt proteomics template
KochTobi Sep 16, 2024
f278e28
Make ngs row creation simpler
KochTobi Sep 16, 2024
9ce0bc3
remove duplicate row creation for ngs
KochTobi Sep 16, 2024
c5b7496
Rename `Instrument` to `MS Device` in template
KochTobi Sep 16, 2024
eb906f2
Fix column name
KochTobi Sep 16, 2024
ea44f52
Fix sheet locking
KochTobi Sep 16, 2024
5965ca5
replace instrument by ms device for proteomics
KochTobi Sep 16, 2024
19568fc
correct spelling
KochTobi Sep 16, 2024
df82459
fix jpa access
KochTobi Sep 16, 2024
4c5bccd
solves #747 add technical replicate
KochTobi Sep 16, 2024
aec0f86
fix constructors in tests
KochTobi Sep 16, 2024
5cdefa3
use correct methods
KochTobi Sep 17, 2024
4294945
Fix wrong imports
KochTobi Sep 17, 2024
bbdfa72
move test
KochTobi Sep 17, 2024
b81cef4
Add QBIC_SAMPLE_ID
KochTobi Sep 17, 2024
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106 changes: 61 additions & 45 deletions user-interface/src/main/java/life/qbic/datamanager/parser/MetadataConverter.java
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Original file line number Diff line number Diff line change
@@ -1,22 +1,5 @@
package life.qbic.datamanager.parser;

import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.COMMENT;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.CYCLE;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.DIGESTION_ENZYME;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.DIGESTION_METHOD;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.ENRICHMENT_METHOD;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.FACILITY;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.INJECTION_VOLUME;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.LABEL;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.LABELING_TYPE;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.LCMS_METHOD;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.LC_COLUMN;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.MEASUREMENT_ID;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.MS_DEVICE;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.ORGANISATION_ID;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.QBIC_SAMPLE_ID;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.SAMPLE_POOL_GROUP;
import static life.qbic.datamanager.parser.MetadataConverter.ProteomicsMeasurementProperty.TECHNICAL_REPLICATE_NAME;
import static life.qbic.logging.service.LoggerFactory.logger;

import java.util.ArrayList;
Expand Down Expand Up @@ -133,39 +116,66 @@ private List<MeasurementMetadata> convertProteomicsMeasurement(ParsingResult par
for (ParsingResult.Row row : parsingResult.rows()) {
// we us -1 as default value if a property cannot be accessed, thus ending up in an empty String
var pxpMetaDatum = new ProteomicsMeasurementMetadata(
safeListAccess(row.values(), keyIndices.getOrDefault(MEASUREMENT_ID.propertyName(), -1),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.MEASUREMENT_ID.propertyName(),
-1),
""),
SampleCode.create(
safeListAccess(row.values(),
keyIndices.getOrDefault(QBIC_SAMPLE_ID.propertyName(), -1),
keyIndices.getOrDefault(
ProteomicsMeasurementProperty.QBIC_SAMPLE_ID.propertyName(), -1),
"")),
safeListAccess(row.values(),
keyIndices.getOrDefault(TECHNICAL_REPLICATE_NAME.propertyName(), -1), ""),
safeListAccess(row.values(), keyIndices.getOrDefault(ORGANISATION_ID.propertyName(), -1),
keyIndices.getOrDefault(
ProteomicsMeasurementProperty.TECHNICAL_REPLICATE_NAME.propertyName(), -1), ""),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.ORGANISATION_ID.propertyName(),
-1),
""),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.MS_DEVICE.propertyName(), -1),
""),
safeListAccess(row.values(),
keyIndices.getOrDefault(
ProteomicsMeasurementProperty.SAMPLE_POOL_GROUP.propertyName(), -1),
""),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.FACILITY.propertyName(), -1),
""),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.CYCLE.propertyName(), -1), ""),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.DIGESTION_ENZYME.propertyName(),
-1),
""),
safeListAccess(row.values(), keyIndices.getOrDefault(MS_DEVICE.propertyName(), -1), ""),
safeListAccess(row.values(),
keyIndices.getOrDefault(SAMPLE_POOL_GROUP.propertyName(), -1),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.DIGESTION_METHOD.propertyName(),
-1),
""),
safeListAccess(row.values(), keyIndices.getOrDefault(FACILITY.propertyName(), -1), ""),
safeListAccess(row.values(), keyIndices.getOrDefault(CYCLE.propertyName(), -1), ""),
safeListAccess(row.values(), keyIndices.getOrDefault(DIGESTION_ENZYME.propertyName(), -1),
safeListAccess(row.values(),
keyIndices.getOrDefault(
ProteomicsMeasurementProperty.ENRICHMENT_METHOD.propertyName(), -1),
""),
safeListAccess(row.values(), keyIndices.getOrDefault(DIGESTION_METHOD.propertyName(), -1),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.INJECTION_VOLUME.propertyName(),
-1),
""),
safeListAccess(row.values(),
keyIndices.getOrDefault(ENRICHMENT_METHOD.propertyName(), -1),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.LC_COLUMN.propertyName(), -1),
""),
safeListAccess(row.values(), keyIndices.getOrDefault(INJECTION_VOLUME.propertyName(), -1),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.LCMS_METHOD.propertyName(), -1),
""),
safeListAccess(row.values(), keyIndices.getOrDefault(LC_COLUMN.propertyName(), -1), ""),
safeListAccess(row.values(), keyIndices.getOrDefault(LCMS_METHOD.propertyName(), -1), ""),
new Labeling(
safeListAccess(row.values(),
keyIndices.getOrDefault(LABELING_TYPE.propertyName(), -1),
keyIndices.getOrDefault(
ProteomicsMeasurementProperty.LABELING_TYPE.propertyName(), -1),
""),
safeListAccess(row.values(), keyIndices.getOrDefault(LABEL.propertyName(), -1), "")),
safeListAccess(row.values(), keyIndices.getOrDefault(COMMENT.propertyName(), -1), "")
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.LABEL.propertyName(), -1),
"")),
safeListAccess(row.values(),
keyIndices.getOrDefault(ProteomicsMeasurementProperty.COMMENT.propertyName(), -1), "")
);
result.add(pxpMetaDatum);
}
Expand All @@ -184,16 +194,20 @@ private List<MeasurementMetadata> convertNGSMeasurement(ParsingResult parsingRes
var keyIndices = parsingResult.keys();
for (Row row : parsingResult.rows()) {
var ngsMeasurementMetadata = new NGSMeasurementMetadata(
safeListAccess(row.values(), keyIndices.getOrDefault(MEASUREMENT_ID.propertyName(), -1),
safeListAccess(row.values(),
keyIndices.getOrDefault(NGSMeasurementProperty.MEASUREMENT_ID.propertyName(), -1),
""),
List.of(SampleCode.create(
safeListAccess(row.values(),
keyIndices.getOrDefault(QBIC_SAMPLE_ID.propertyName(), -1),
keyIndices.getOrDefault(NGSMeasurementProperty.SAMPLE_CODE.propertyName(), -1),
""))),
safeListAccess(row.values(), keyIndices.getOrDefault(ORGANISATION_ID.propertyName(), -1),
safeListAccess(row.values(),
keyIndices.getOrDefault(NGSMeasurementProperty.ORGANISATION_ID.propertyName(), -1),
""),
safeListAccess(row.values(), keyIndices.getOrDefault(MS_DEVICE.propertyName(), -1), ""),
safeListAccess(row.values(), keyIndices.getOrDefault(FACILITY.propertyName(), -1), ""),
safeListAccess(row.values(),
keyIndices.getOrDefault(NGSMeasurementProperty.INSTRUMENT.propertyName(), -1), ""),
safeListAccess(row.values(),
keyIndices.getOrDefault(NGSMeasurementProperty.FACILITY.propertyName(), -1), ""),
safeListAccess(row.values(), keyIndices.getOrDefault(
NGSMeasurementProperty.SEQUENCING_READ_TYPE.propertyName(), -1), ""),
safeListAccess(row.values(),
Expand All @@ -205,15 +219,16 @@ private List<MeasurementMetadata> convertNGSMeasurement(ParsingResult parsingRes
NGSMeasurementProperty.SEQUENCING_RUN_PROTOCOL.propertyName(), -1),
""),
safeListAccess(row.values(),
keyIndices.getOrDefault(SAMPLE_POOL_GROUP.propertyName(), -1),
keyIndices.getOrDefault(NGSMeasurementProperty.SAMPLE_POOL_GROUP.propertyName(), -1),
""),
safeListAccess(row.values(),
keyIndices.getOrDefault(NGSMeasurementProperty.INDEX_I7.propertyName(), -1),
""),
safeListAccess(row.values(),
keyIndices.getOrDefault(NGSMeasurementProperty.INDEX_I5.propertyName(), -1),
""),
safeListAccess(row.values(), keyIndices.getOrDefault(COMMENT.propertyName(), -1), "")
safeListAccess(row.values(),
keyIndices.getOrDefault(NGSMeasurementProperty.COMMENT.propertyName(), -1), "")
);
result.add(ngsMeasurementMetadata);
}
Expand All @@ -225,11 +240,11 @@ private boolean looksLikeNgsMeasurement(Collection<String> properties, boolean i
.collect(Collectors.toList());
Map<String, Integer> hitMap;
if (ignoreID) {
formattedProperties.remove(MEASUREMENT_ID.propertyName());
formattedProperties.remove(NGSMeasurementProperty.MEASUREMENT_ID.propertyName());
hitMap = countHits(formattedProperties,
Arrays.stream(NGSMeasurementProperty.values())
.map(NGSMeasurementProperty::propertyName).collect(
Collectors.toSet()), MEASUREMENT_ID.propertyName());
Collectors.toSet()), NGSMeasurementProperty.MEASUREMENT_ID.propertyName());
} else {
hitMap = countHits(formattedProperties,
Arrays.stream(NGSMeasurementProperty.values())
Expand All @@ -255,11 +270,11 @@ private boolean looksLikeProteomicsMeasurement(Collection<String> properties, bo
.collect(Collectors.toList());
Map<String, Integer> hitMap;
if (ignoreID) {
formattedProperties.remove(MEASUREMENT_ID.propertyName());
formattedProperties.remove(ProteomicsMeasurementProperty.MEASUREMENT_ID.propertyName());
hitMap = countHits(formattedProperties,
Arrays.stream(ProteomicsMeasurementProperty.values())
.map(ProteomicsMeasurementProperty::propertyName).collect(
Collectors.toSet()), MEASUREMENT_ID.propertyName());
Collectors.toSet()), ProteomicsMeasurementProperty.MEASUREMENT_ID.propertyName());
} else {
hitMap = countHits(formattedProperties,
Arrays.stream(ProteomicsMeasurementProperty.values())
Expand Down Expand Up @@ -327,6 +342,7 @@ public String propertyName() {

enum NGSMeasurementProperty {
MEASUREMENT_ID("measurement id"),
SAMPLE_CODE("sample code"),
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This property does not exist in the template sheets for ngs registration and editing, which leads to the issue that no measurements can be registered or edited.
Did you mean QBiC Sample Id ?

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Yes I did. The issue with the wrong properties being used seems to have been in the code already. It should be fixed now.

ORGANISATION_ID("organisation id"),
SAMPLE_POOL_GROUP("sample pool group"),
FACILITY("facility"),
Expand Down