diff --git a/project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/SamplePreviewJpaRepository.java b/project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/SamplePreviewJpaRepository.java index fad7a1c595..dfb41e60fb 100644 --- a/project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/SamplePreviewJpaRepository.java +++ b/project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/SamplePreviewJpaRepository.java @@ -68,7 +68,7 @@ private Specification generateExperimentIdandFilterSpecification( Specification isBlankSpec = SamplePreviewSpecs.isBlank(filter); Specification experimentIdSpec = SamplePreviewSpecs.experimentIdEquals( experimentId); - Specification organismIdSpec = SamplePreviewSpecs.organismIdContains(filter); + Specification biologialReplicateSpec = SamplePreviewSpecs.biologicalReplicateContains(filter); Specification sampleCodeSpec = SamplePreviewSpecs.sampleCodeContains(filter); Specification sampleNameSpec = SamplePreviewSpecs.sampleNameContains(filter); Specification batchLabelSpec = SamplePreviewSpecs.batchLabelContains(filter); @@ -80,7 +80,7 @@ private Specification generateExperimentIdandFilterSpecification( filter); Specification commentSpec = SamplePreviewSpecs.commentContains(filter); Specification containsFilterSpec = Specification.anyOf(sampleCodeSpec, - sampleNameSpec, organismIdSpec, batchLabelSpec, conditionSpec, speciesSpec, + sampleNameSpec, biologialReplicateSpec, batchLabelSpec, conditionSpec, speciesSpec, specimenSpec, analyteSpec, analysisMethodContains, commentSpec); Specification isDistinctSpec = SamplePreviewSpecs.isDistinct(); return Specification.where(experimentIdSpec).and(isBlankSpec) @@ -158,9 +158,9 @@ private static Specification ontologyColumnContains(String col, S }; } - public static Specification organismIdContains(String filter) { + public static Specification biologicalReplicateContains(String filter) { return (root, query, builder) -> - builder.like(root.get("organismId"), "%" + filter + "%"); + builder.like(root.get("biologicalReplicate"), "%" + filter + "%"); } public static Specification speciesContains(String filter) { diff --git a/project-management/src/main/java/life/qbic/projectmanagement/application/batch/SampleUpdateRequest.java b/project-management/src/main/java/life/qbic/projectmanagement/application/batch/SampleUpdateRequest.java index 90044c4f61..71bf02e085 100644 --- a/project-management/src/main/java/life/qbic/projectmanagement/application/batch/SampleUpdateRequest.java +++ b/project-management/src/main/java/life/qbic/projectmanagement/application/batch/SampleUpdateRequest.java @@ -17,8 +17,9 @@ public record SampleUpdateRequest(SampleId sampleId, SampleInformation sampleInf /** * Sample update request. *

- * @param sampleName a human-readable semantic descriptor of the sample - * @param organismId optional identifier of the sample's source patient or organism + * @param sampleName a human-readable semantic descriptor of the sample + * @param biologicalReplicate optional identifier of the sample's source patient or organism, to + * be able to group biological replicates * @param analysisMethod analysis method to be performed * @param experimentalGroup the experimental group the sample is part of * @param species the species the sample belongs to @@ -26,7 +27,7 @@ public record SampleUpdateRequest(SampleId sampleId, SampleInformation sampleInf * @param analyte the analyte the sample belongs to * @param comment comment relating to the sample */ - public record SampleInformation(String sampleName, String organismId, + public record SampleInformation(String sampleName, String biologicalReplicate, AnalysisMethod analysisMethod, ExperimentalGroup experimentalGroup, OntologyTerm species, OntologyTerm specimen, OntologyTerm analyte, diff --git a/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java b/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java index fecc11bbe6..a9294c59fb 100644 --- a/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java +++ b/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java @@ -42,7 +42,7 @@ public class SamplePreview { private String sampleName; @Column(name = "organism_id") - private String organismId; + private String biologicalReplicate; private String comment; @Column(name = "analysis_method") private String analysisMethod; @@ -58,7 +58,7 @@ protected SamplePreview() { } private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampleCode, - String batchLabel, String sampleName, String organismId, + String batchLabel, String sampleName, String biologicalReplicate, ExperimentalGroup experimentalGroup, OntologyTerm species, OntologyTerm specimen, OntologyTerm analyte, String analysisMethod, String comment) { Objects.requireNonNull(experimentId); @@ -83,40 +83,40 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl this.analysisMethod = analysisMethod; // optional columns this.comment = comment; - this.organismId = organismId; + this.biologicalReplicate = biologicalReplicate; } /** * Creates a new instance of a SamplePreview object. * - * @param experimentId the {@link ExperimentId} of the associated experiment - * @param sampleId the {@link SampleId} from which this preview was created - * @param sampleCode the {@link SampleCode} associated with this SamplePreview - * @param batchLabel the label of the {@link Batch} which contains the {@link Sample} - * associated with this preview - * associated with this preview - * @param sampleName the name of the {@link Sample} associated with this preview - * @param organismId optional identifier of the patient or organism a {@link Sample} was taken of - * @param experimentalGroup the {@link ExperimentalGroup} for the {@link Sample} associated with - * this preview - * @param species the {@link OntologyTerm} for the species of this {@link Sample} - * associated with this preview - * @param specimen the {@link OntologyTerm} for the specimen of this {@link Sample} - * associated with this preview - * @param analyte the {@link OntologyTerm} for the analyte of this {@link Sample} - * associated with this preview - * @param analysisMethod the analysis method to be performed for this {@link Sample} - * @param comment an optional comment pertaining to the associated {@link Sample} + * @param experimentId the {@link ExperimentId} of the associated experiment + * @param sampleId the {@link SampleId} from which this preview was created + * @param sampleCode the {@link SampleCode} associated with this SamplePreview + * @param batchLabel the label of the {@link Batch} which contains the {@link Sample} + * associated with this preview + * @param sampleName the name of the {@link Sample} associated with this preview + * @param biologicalReplicate optional identifier of the patient or organism a {@link Sample} + * was taken of. Used to group biological replicates + * @param experimentalGroup the {@link ExperimentalGroup} for the {@link Sample} associated with + * this preview + * @param species the {@link OntologyTerm} for the species of this {@link Sample} + * associated with this preview + * @param specimen the {@link OntologyTerm} for the specimen of this {@link Sample} + * associated with this preview + * @param analyte the {@link OntologyTerm} for the analyte of this {@link Sample} + * associated with this preview + * @param analysisMethod the analysis method to be performed for this {@link Sample} + * @param comment an optional comment pertaining to the associated {@link Sample} * @return the sample preview */ public static SamplePreview create(ExperimentId experimentId, SampleId sampleId, String sampleCode, String batchLabel, - String sampleName, String organismId, ExperimentalGroup experimentalGroup, + String sampleName, String biologicalReplicate, ExperimentalGroup experimentalGroup, OntologyTerm species, OntologyTerm specimen, OntologyTerm analyte, String analysisMethod, String comment) { return new SamplePreview(experimentId, sampleId, sampleCode, batchLabel, - sampleName, organismId, experimentalGroup, species, specimen, analyte, analysisMethod, + sampleName, biologicalReplicate, experimentalGroup, species, specimen, analyte, analysisMethod, comment); } @@ -160,8 +160,8 @@ public String comment() { return comment; } - public String organismId() { - return organismId; + public String biologicalReplicate() { + return biologicalReplicate; } public ExperimentalGroup experimentalGroup() { @@ -180,7 +180,7 @@ public boolean equals(Object o) { return Objects.equals(experimentId, that.experimentId) && Objects.equals( sampleCode, that.sampleCode) && Objects.equals(sampleId, that.sampleId) && Objects.equals(batchLabel, that.batchLabel) && Objects.equals(sampleName, - that.sampleName) && Objects.equals(organismId, that.organismId) + that.sampleName) && Objects.equals(biologicalReplicate, that.biologicalReplicate) && Objects.equals(species, that.species) && Objects.equals(specimen, that.specimen) && Objects.equals(analyte, that.analyte) && Objects.equals( experimentalGroup, that.experimentalGroup) && Objects.equals(analysisMethod, @@ -190,7 +190,7 @@ public boolean equals(Object o) { @Override public int hashCode() { return Objects.hash(experimentId, sampleCode, sampleId, batchLabel, - sampleName, organismId, + sampleName, biologicalReplicate, species, specimen, analyte, experimentalGroup, analysisMethod, comment); } @@ -202,7 +202,7 @@ public String toString() { ", sampleId='" + sampleId + '\'' + ", batchLabel='" + batchLabel + '\'' + ", sampleName='" + sampleName + '\'' + - ", organismId='" + organismId + '\'' + + ", biologicalReplicate='" + biologicalReplicate + '\'' + ", species='" + species + '\'' + ", specimen='" + specimen + '\'' + ", analyte='" + analyte + '\'' + diff --git a/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/Sample.java b/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/Sample.java index 3fd34e5942..2c20ea509c 100644 --- a/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/Sample.java +++ b/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/Sample.java @@ -44,7 +44,7 @@ public class Sample { private SampleId id; private String label; @Column(name = "organism_id") - private String organismId; + private String biologicalReplicate; private String comment; @Column(name = "analysis_method") @@ -58,13 +58,13 @@ public class Sample { private SampleOrigin sampleOrigin; private Sample(SampleId id, SampleCode sampleCode, BatchId assignedBatch, String label, - String organismId, ExperimentId experimentId, Long experimentalGroupId, + String biologicalReplicate, ExperimentId experimentId, Long experimentalGroupId, SampleOrigin sampleOrigin, AnalysisMethod analysisMethod, String comment) { this.id = id; this.sampleCode = Objects.requireNonNull(sampleCode); this.label = label; - this.organismId = organismId; + this.biologicalReplicate = biologicalReplicate; this.experimentId = experimentId; this.experimentalGroupId = experimentalGroupId; this.sampleOrigin = sampleOrigin; @@ -89,7 +89,7 @@ public static Sample create(SampleCode sampleCode, Objects.requireNonNull(sampleRegistrationRequest); SampleId sampleId = SampleId.create(); return new Sample(sampleId, sampleCode, sampleRegistrationRequest.assignedBatch(), - sampleRegistrationRequest.label(), sampleRegistrationRequest.organismId(), + sampleRegistrationRequest.label(), sampleRegistrationRequest.biologicalReplicate(), sampleRegistrationRequest.experimentId(), sampleRegistrationRequest.experimentalGroupId(), sampleRegistrationRequest.sampleOrigin(), sampleRegistrationRequest.analysisMethod(), sampleRegistrationRequest.comment()); @@ -119,8 +119,8 @@ public String label() { return this.label; } - public String organismId() { - return this.organismId; + public String biologicalReplicate() { + return this.biologicalReplicate; } public Optional comment() { @@ -147,8 +147,8 @@ public void setLabel(String label) { this.label = label; } - public void setOrganismId(String organismId) { - this.organismId = organismId; + public void setBiologicalReplicate(String biologicalReplicate) { + this.biologicalReplicate = biologicalReplicate; } public void setComment(String comment) { @@ -165,7 +165,7 @@ public void setSampleOrigin(SampleOrigin sampleOrigin) { public void update(SampleUpdateRequest sampleInfo) { setLabel(sampleInfo.sampleInformation().sampleName()); - setOrganismId(sampleInfo.sampleInformation().organismId()); + setBiologicalReplicate(sampleInfo.sampleInformation().biologicalReplicate()); setAnalysisMethod(sampleInfo.sampleInformation().analysisMethod()); setSampleOrigin(SampleOrigin.create(sampleInfo.sampleInformation().species(), sampleInfo.sampleInformation().specimen(), sampleInfo.sampleInformation().analyte())); diff --git a/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/SampleRegistrationRequest.java b/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/SampleRegistrationRequest.java index 5a1ded365c..b30637acc3 100644 --- a/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/SampleRegistrationRequest.java +++ b/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/SampleRegistrationRequest.java @@ -9,7 +9,8 @@ * Serves as a parameter object for sample creation. * * @param label a human-readable semantic descriptor of the sample - * @param organismId optional identifier of the patient or organism a sample was taken of + * @param biologicalReplicate optional identifier of the patient or organism a sample was taken of. + * Used to group biological replicates * @param assignedBatch the assigned batch * @param experimentId the experiment reference * @param experimentalGroupId the experimental group id the sample is part of @@ -19,16 +20,16 @@ * * @since 1.0.0 */ -public record SampleRegistrationRequest(String label, String organismId, BatchId assignedBatch, +public record SampleRegistrationRequest(String label, String biologicalReplicate, BatchId assignedBatch, ExperimentId experimentId, Long experimentalGroupId, SampleOrigin sampleOrigin, AnalysisMethod analysisMethod, String comment) { - public SampleRegistrationRequest(String label, String organismId, BatchId assignedBatch, + public SampleRegistrationRequest(String label, String biologicalReplicate, BatchId assignedBatch, ExperimentId experimentId, Long experimentalGroupId, SampleOrigin sampleOrigin, AnalysisMethod analysisMethod, String comment) { this.label = Objects.requireNonNull(label); - this.organismId = organismId; + this.biologicalReplicate = biologicalReplicate; this.assignedBatch = Objects.requireNonNull(assignedBatch); this.experimentId = Objects.requireNonNull(experimentId); this.experimentalGroupId = Objects.requireNonNull(experimentalGroupId); diff --git a/project-management/src/main/java/life/qbic/projectmanagement/domain/service/SampleDomainService.java b/project-management/src/main/java/life/qbic/projectmanagement/domain/service/SampleDomainService.java index 668d622c0a..1dfac717bb 100644 --- a/project-management/src/main/java/life/qbic/projectmanagement/domain/service/SampleDomainService.java +++ b/project-management/src/main/java/life/qbic/projectmanagement/domain/service/SampleDomainService.java @@ -86,7 +86,7 @@ public void updateSamples(Project project, Collection updat .filter(sampleUpdateRequest -> sampleUpdateRequest.sampleId().equals(sample.sampleId())) .findFirst().orElseThrow(); sample.setLabel(sampleInfo.sampleInformation().sampleName()); - sample.setOrganismId(sampleInfo.sampleInformation().organismId()); + sample.setBiologicalReplicate(sampleInfo.sampleInformation().biologicalReplicate()); sample.setAnalysisMethod(sampleInfo.sampleInformation().analysisMethod()); sample.setSampleOrigin(SampleOrigin.create(sampleInfo.sampleInformation().species(), sampleInfo.sampleInformation().specimen(), sampleInfo.sampleInformation().analyte())); diff --git a/user-interface/src/main/bundles/dev.bundle b/user-interface/src/main/bundles/dev.bundle index 5fc7639209..a4d4c8af6e 100644 Binary files a/user-interface/src/main/bundles/dev.bundle and b/user-interface/src/main/bundles/dev.bundle differ diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java index 746c76be64..3be5cd3062 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java +++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java @@ -104,10 +104,10 @@ private static Grid createSampleGrid() { .setTooltipGenerator(SamplePreview::sampleName) .setAutoWidth(true) .setResizable(true); - sampleGrid.addColumn(SamplePreview::organismId) - .setHeader("Organism ID") - .setSortProperty("organismId") - .setTooltipGenerator(SamplePreview::organismId) + sampleGrid.addColumn(SamplePreview::biologicalReplicate) + .setHeader("Biological Replicate") + .setSortProperty("biologicalReplicate") + .setTooltipGenerator(SamplePreview::biologicalReplicate) .setAutoWidth(true) .setResizable(true); sampleGrid.addColumn(SamplePreview::batchLabel) diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java index 7db3a19d09..d8dd51c6e5 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java +++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java @@ -233,7 +233,7 @@ private List generateSampleRequestsFromSampleInfo(Bat List sampleRegistrationRequests; sampleRegistrationRequests = sampleInfos.stream() .map(sample -> new SampleRegistrationRequest( - sample.getSampleName(), sample.getOrganismId(), + sample.getSampleName(), sample.getBiologicalReplicate(), batchId, context.experimentId().orElseThrow(), sample.getExperimentalGroup().id(), @@ -247,7 +247,7 @@ private List generateSampleRequestsFromSampleInfo(Bat private SampleUpdateRequest generateSampleUpdateRequestFromSampleInfo( SampleInfo sampleInfo) { return new SampleUpdateRequest(sampleInfo.getSampleId(), new SampleInformation( - sampleInfo.getSampleName(), sampleInfo.getOrganismId(), + sampleInfo.getSampleName(), sampleInfo.getBiologicalReplicate(), sampleInfo.getAnalysisToBePerformed(), sampleInfo.getExperimentalGroup(), sampleInfo.getSpecies(), sampleInfo.getSpecimen(), sampleInfo.getAnalyte(), @@ -353,7 +353,7 @@ private SampleBatchInformationSpreadsheet.SampleInfo convertSampleToSampleInfo(S /*We currently allow replicates independent of experimental groups which is why we have to parse all replicates */ return SampleBatchInformationSpreadsheet.SampleInfo.create(sample.sampleId(), sample.sampleCode(), sample.analysisMethod(), - sample.label(), sample.organismId(), experimentalGroup, sample.sampleOrigin() + sample.label(), sample.biologicalReplicate(), experimentalGroup, sample.sampleOrigin() .getSpecies(), sample.sampleOrigin().getSpecimen(), sample.sampleOrigin().getAnalyte(), sample.comment().orElse("")); } diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java index 85d7646b0c..10ca48ced7 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java +++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java @@ -32,7 +32,7 @@ public byte[] getContent() { TSVBuilder tsvBuilder = new TSVBuilder<>(samples); tsvBuilder.addColumn("Sample ID", SamplePreview::sampleCode); tsvBuilder.addColumn("Sample Name", SamplePreview::sampleName); - tsvBuilder.addColumn("Organism ID", SamplePreview::organismId); + tsvBuilder.addColumn("Biological Replicate", SamplePreview::biologicalReplicate); tsvBuilder.addColumn("Batch", SamplePreview::batchLabel); tsvBuilder.addColumn("Species", sample -> sample.species().getLabel()); tsvBuilder.addColumn("Specimen", sample -> sample.specimen().getLabel()); diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java index 866050ab4a..68b209a0cc 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java +++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java @@ -119,8 +119,8 @@ private void createSampleInfoEntry(SamplePreview sample, Row sampleRow, var labelCol = sampleRow.createCell(SamplePreviewColumn.LABEL.column()); labelCol.setCellValue(sample.sampleName()); - var organismIdCol = sampleRow.createCell(SamplePreviewColumn.ORGANISM_ID.column()); - organismIdCol.setCellValue(sample.organismId()); + var bioRepCol = sampleRow.createCell(SamplePreviewColumn.BIOLOGICAL_REPLICATE.column()); + bioRepCol.setCellValue(sample.biologicalReplicate()); var batchCol = sampleRow.createCell(SamplePreviewColumn.BATCH.column()); batchCol.setCellValue(sample.batchLabel()); @@ -162,7 +162,7 @@ enum SamplePreviewColumn { SAMPLE_ID("Sample ID", 0), LABEL("Sample Name", 1), - ORGANISM_ID("Organism ID", 2), + BIOLOGICAL_REPLICATE("Biological Replicate", 2), BATCH("Batch", 3), SPECIES("Species", 4), SPECIMEN("Specimen", 5), diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/SampleBatchInformationSpreadsheet.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/SampleBatchInformationSpreadsheet.java index 59256c9e01..3a8e3fdcd3 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/SampleBatchInformationSpreadsheet.java +++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/SampleBatchInformationSpreadsheet.java @@ -58,7 +58,8 @@ public SampleBatchInformationSpreadsheet(List experimentalGro .requireDistinctValues() .setRequired(); - addColumn("Organism ID", SampleInfo::getOrganismId, SampleInfo::setOrganismId); + addColumn("Biological Replicate", SampleInfo::getBiologicalReplicate, + SampleInfo::setBiologicalReplicate); addColumn("Condition", SampleInfo::getExperimentalGroup, experimentalGroup -> formatConditionString(experimentalGroup.condition()), @@ -108,7 +109,7 @@ public static class SampleInfo { private SampleCode sampleCode; private AnalysisMethod analysisToBePerformed; private String sampleName; - private String organismId; + private String biologicalReplicate; private ExperimentalGroup experimentalGroup; private OntologyTerm species; private OntologyTerm specimen; @@ -116,15 +117,15 @@ public static class SampleInfo { private String customerComment; public static SampleInfo create(AnalysisMethod analysisMethod, String sampleName, - String organismId, ExperimentalGroup experimentalGroup, OntologyTerm species, + String biologicalReplicate, ExperimentalGroup experimentalGroup, OntologyTerm species, OntologyTerm specimen, OntologyTerm analyte, String customerComment) { - return create(null, null, analysisMethod, sampleName, organismId, + return create(null, null, analysisMethod, sampleName, biologicalReplicate, experimentalGroup, species, specimen, analyte, customerComment); } public static SampleInfo create(SampleId sampleId, SampleCode sampleCode, - AnalysisMethod analysisMethod, String sampleName, String organismId, + AnalysisMethod analysisMethod, String sampleName, String biologicalReplicate, ExperimentalGroup experimentalGroup, OntologyTerm species, OntologyTerm specimen, OntologyTerm analyte, String customerComment) { @@ -133,7 +134,7 @@ public static SampleInfo create(SampleId sampleId, SampleCode sampleCode, sampleInfo.setSampleCode(sampleCode); sampleInfo.setAnalysisToBePerformed(analysisMethod); sampleInfo.setSampleName(sampleName); - sampleInfo.setOrganismId(organismId); + sampleInfo.setBiologicalReplicate(biologicalReplicate); sampleInfo.setExperimentalGroup(experimentalGroup); sampleInfo.setSpecies(species); sampleInfo.setSpecimen(specimen); @@ -174,12 +175,12 @@ public void setSampleName(String sampleName) { this.sampleName = sampleName; } - public String getOrganismId() { - return organismId; + public String getBiologicalReplicate() { + return biologicalReplicate; } - public void setOrganismId(String organismId) { - this.organismId = organismId; + public void setBiologicalReplicate(String biologicalReplicate) { + this.biologicalReplicate = biologicalReplicate; } public OntologyTerm getSpecies() { @@ -226,7 +227,7 @@ public void setCustomerComment(String customerComment) { public String toString() { return new StringJoiner(", ", SampleInfo.class.getSimpleName() + "[", "]").add( "analysisToBePerformed=" + analysisToBePerformed).add("sampleName='" + sampleName + "'") - .add("organismId='" + organismId + "'") + .add("biologicalReplicate='" + biologicalReplicate + "'") .add("experimentalGroup=" + experimentalGroup).add("species=" + species) .add("specimen=" + specimen).add("analyte=" + analyte) .add("customerComment='" + customerComment + "'").toString(); @@ -241,7 +242,7 @@ public static SampleInfo copy(SampleInfo original) { sampleInfo.sampleCode = original.sampleCode; sampleInfo.sampleId = original.sampleId; sampleInfo.sampleName = original.sampleName; - sampleInfo.organismId = original.organismId; + sampleInfo.biologicalReplicate = original.biologicalReplicate; sampleInfo.species = original.species; sampleInfo.specimen = original.specimen; return sampleInfo; @@ -270,7 +271,7 @@ public boolean equals(Object object) { if (!Objects.equals(sampleName, that.sampleName)) { return false; } - if (!Objects.equals(organismId, that.organismId)) { + if (!Objects.equals(biologicalReplicate, that.biologicalReplicate)) { return false; } if (!Objects.equals(experimentalGroup, that.experimentalGroup)) { @@ -294,7 +295,7 @@ public int hashCode() { result = 31 * result + (sampleCode != null ? sampleCode.hashCode() : 0); result = 31 * result + (analysisToBePerformed != null ? analysisToBePerformed.hashCode() : 0); result = 31 * result + (sampleName != null ? sampleName.hashCode() : 0); - result = 31 * result + (organismId != null ? organismId.hashCode() : 0); + result = 31 * result + (biologicalReplicate != null ? biologicalReplicate.hashCode() : 0); result = 31 * result + (experimentalGroup != null ? experimentalGroup.hashCode() : 0); result = 31 * result + (species != null ? species.hashCode() : 0); result = 31 * result + (specimen != null ? specimen.hashCode() : 0);