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show existing confounding variables
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@KochTobi
KochTobi committed Jan 22, 2025
1 parent a518d71 commit 393fd53
Showing 1 changed file with 105 additions and 49 deletions.
154 changes: 105 additions & 49 deletions ...datamanager/views/projects/project/experiments/experiment/ExperimentDetailsComponent.java
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,9 @@
import life.qbic.datamanager.views.projects.project.experiments.experiment.update.EditExperimentDialog.ExperimentUpdateEvent;
import life.qbic.datamanager.views.projects.project.samples.SampleInformationMain;
import life.qbic.projectmanagement.application.DeletionService;
import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService;
import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService.ConfoundingVariableInformation;
import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService.ExperimentReference;
import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
import life.qbic.projectmanagement.application.experiment.ExperimentInformationService.ExperimentalGroupDTO;
import life.qbic.projectmanagement.application.ontology.SpeciesLookupService;
Expand Down Expand Up @@ -98,19 +101,21 @@ public class ExperimentDetailsComponent extends PageArea {
private final Span buttonBar = new Span();
private final Span sampleSourceComponent = new Span();
private final TabSheet experimentSheet = new TabSheet();
private final Div experimentalGroups = new Div();
private final Div experimentalVariables = new Div();
private final Div experimentalGroupsContainer = new Div();
private final Div experimentalVariablesContainer = new Div();
private final Div confoundingVariablesContainer = new Div();
private final CardCollection experimentalGroupsCollection = new CardCollection("GROUPS");
private final CardCollection experimentalVariableCollection = new CardCollection("VARIABLES");
private final CardCollection confoundingVariableCollection = new CardCollection(
"CONFOUNDING VARIABLES");
private final Disclaimer noExperimentalVariablesDefined;
private final Disclaimer noExperimentalGroupsDefined;
private final Disclaimer addExperimentalVariablesNote;
private final Disclaimer noConfoundingVariablesDefined;
private final transient DeletionService deletionService;
private final transient TerminologyService terminologyService;
private final transient MessageSourceNotificationFactory messageSourceNotificationFactory;
private final transient CancelConfirmationDialogFactory cancelConfirmationDialogFactory;
private final transient ConfoundingVariableService confoundingVariableService;
private Context context;
private int experimentalGroupCount;

Expand All @@ -122,7 +127,9 @@ public ExperimentDetailsComponent(
@Autowired SpeciesLookupService ontologyTermInformationService,
TerminologyService terminologyService,
MessageSourceNotificationFactory messageSourceNotificationFactory,
CancelConfirmationDialogFactory cancelConfirmationDialogFactory) {
CancelConfirmationDialogFactory cancelConfirmationDialogFactory,
ConfoundingVariableService confoundingVariableService) {
this.confoundingVariableService = requireNonNull(confoundingVariableService);
this.messageSourceNotificationFactory = requireNonNull(messageSourceNotificationFactory,
"messageSourceNotificationFactory must not be null");
this.experimentInformationService = requireNonNull(experimentInformationService);
Expand All @@ -131,14 +138,15 @@ public ExperimentDetailsComponent(
this.ontologyTermInformationService = requireNonNull(ontologyTermInformationService);
this.noExperimentalVariablesDefined = createNoVariableDisclaimer();
this.noExperimentalGroupsDefined = createNoGroupsDisclaimer();
this.addExperimentalVariablesNote = createNoVariableDisclaimer();
this.noConfoundingVariablesDefined = createNoConfoundingVariablesDisclaimer();
this.terminologyService = terminologyService;
this.cancelConfirmationDialogFactory = requireNonNull(cancelConfirmationDialogFactory);
this.addClassName("experiment-details-component");
layoutComponent();
configureComponent();
}


private static ComponentRenderer<Span, OntologyTerm> createOntologyRenderer() {
return new ComponentRenderer<>(ontologyClassDTO -> {
Span ontology = new Span();
Expand Down Expand Up @@ -178,6 +186,14 @@ private Disclaimer createNoVariableDisclaimer() {
return disclaimer;
}

private Disclaimer createNoConfoundingVariablesDisclaimer() {
var disclaimer = Disclaimer.createWithTitle("Define Confoungind Variables",
"Add confounding variables to your experiment to use them during sample registration",
"Add confounding variables");
disclaimer.addDisclaimerConfirmedListener(confirmed -> openConfoundingVariablesAddDialog());
return disclaimer;
}

private Disclaimer createNoGroupsDisclaimer() {
var disclaimer = Disclaimer.createWithTitle("Design your experiment",
"Create conditions for your samples by adding experimental groups", "Add groups");
Expand Down Expand Up @@ -281,7 +297,7 @@ private Map<SampleOriginType, Set<OntologyTerm>> getOntologyTermsUsedInSamples(

private void onExperimentUpdateEvent(ExperimentUpdateEvent event) {
ExperimentId experimentId = context.experimentId().orElseThrow();

ProjectId projectId = context.projectId().orElseThrow();
ExperimentDraft experimentDraft = event.getExperimentDraft();
experimentInformationService.editExperimentInformation(
context.projectId().orElseThrow().value(),
Expand All @@ -292,7 +308,7 @@ private void onExperimentUpdateEvent(ExperimentUpdateEvent event) {
experimentDraft.getAnalytes(),
experimentDraft.getSpeciesIcon().getLabel(),
experimentDraft.getSpecimenIcon().getLabel());
reloadExperimentInfo(experimentId);
reloadExperimentInfo(projectId, experimentId);
event.getSource().close();
}

Expand Down Expand Up @@ -363,9 +379,8 @@ private void deleteExistingExperimentalVariables() {
});
}

private void reloadExperimentInfo(ExperimentId experimentId) {
experimentInformationService.find(context.projectId().orElseThrow().value(), experimentId)
.ifPresent(this::loadExperimentInformation);
private void reloadExperimentInfo(ProjectId projectId, ExperimentId experimentId) {
loadExperimentInformation(projectId, experimentId);
}

private void openExperimentalVariablesAddDialog() {
Expand All @@ -383,7 +398,7 @@ private void onExperimentalVariablesAddConfirmed(
ExperimentalVariablesDialog.ConfirmEvent confirmEvent) {
addExperimentalVariables(confirmEvent.getSource().definedVariables());
confirmEvent.getSource().close();
reloadExperimentInfo(context.experimentId().orElseThrow());
reloadExperimentInfo(context.projectId().orElseThrow(), context.experimentId().orElseThrow());
if (hasExperimentalGroups()) {
showSampleRegistrationPossibleNotification();
}
Expand Down Expand Up @@ -417,7 +432,8 @@ private void onExperimentalVariablesEditConfirmed(
deleteExistingExperimentalVariables();
addExperimentalVariables(confirmEvent.getSource().definedVariables());
confirmEvent.getSource().close();
reloadExperimentInfo(context.experimentId().orElseThrow());
reloadExperimentInfo(context.projectId().orElseThrow(),
context.experimentId().orElseThrow());
}

private boolean editVariablesNotAllowed() {
Expand Down Expand Up @@ -519,11 +535,12 @@ private void loadSampleSources(Experiment experiment) {

private void layoutTabSheet() {
experimentSheet.addClassName("experimental-sheet");
experimentSheet.add("Experimental Variables", experimentalVariables);
experimentalVariables.addClassName("experimental-groups-container");
experimentSheet.add("Experimental Groups", experimentalGroups);
experimentalGroups.addClassName("experimental-groups-container");
experimentSheet.add("Confounding Variables", confoundingVariableCollection);
experimentSheet.add("Experimental Variables", experimentalVariablesContainer);
experimentalVariablesContainer.addClassName("experimental-groups-container");
experimentSheet.add("Experimental Groups", experimentalGroupsContainer);
experimentalGroupsContainer.addClassName("experimental-groups-container");
experimentSheet.add("Confounding Variables", confoundingVariablesContainer);
confoundingVariablesContainer.add(confoundingVariableCollection);
content.add(experimentSheet);
}

Expand Down Expand Up @@ -641,18 +658,11 @@ private boolean hasExperimentalGroups() {
return this.experimentalGroupCount > 0;
}

private void loadExperimentalGroups() {
private List<ExperimentalGroup> loadExperimentalGroups() {
// We load the experimental groups of the experiment and render them as cards
List<ExperimentalGroup> groups = experimentInformationService.experimentalGroupsFor(
return experimentInformationService.experimentalGroupsFor(
context.projectId().orElseThrow().value(),
context.experimentId().orElseThrow());
Comparator<String> natOrder = Comparator.naturalOrder();
List<ExperimentalGroupCard> experimentalGroupsCards = groups.stream()
.sorted((g1, g2) -> natOrder.compare(g1.name(), g2.name()))
.map(ExperimentalGroupCard::new)
.toList();
experimentalGroupsCollection.setContent(experimentalGroupsCards);
this.experimentalGroupCount = experimentalGroupsCards.size();
}

private void addExperimentalVariables(
Expand All @@ -667,61 +677,107 @@ private void addExperimentalVariables(

public void setContext(Context context) {
this.context = requireNonNull(context);
if (context.projectId().isEmpty()) {
throw new ApplicationException("no project id in context " + context);
}
ExperimentId experimentId = context.experimentId()
var projectId = context.projectId()
.orElseThrow(() -> new ApplicationException("no project id in context " + context));
var experimentId = context.experimentId()
.orElseThrow(() -> new ApplicationException("no experiment id in context " + context));
reloadExperimentInfo(experimentId);
reloadExperimentInfo(projectId, experimentId);
}

private void loadExperimentInformation(Experiment experiment) {
private void loadExperimentInformation(ProjectId projectId, ExperimentId experimentId) {
Experiment experiment = experimentInformationService.find(projectId.value(), experimentId)
.orElseThrow();
title.setText(experiment.getName());
loadSampleSources(experiment);
loadExperimentalVariables(experiment);
loadExperimentalGroups();
// We load the experimental variables of the experiment and render them as cards
var experimentalVariables = experiment.variables();
fillExperimentalVariablesCollection(experimentalVariables);
if (experiment.variables().isEmpty()) {
onNoVariablesDefined();
return;
} else {
onVariablesDefined();
}

var experimentalGroups = loadExperimentalGroups();
fillExperimentalGroupCollection(experimentalGroups);
if (experiment.getExperimentalGroups().isEmpty()) {
onNoGroupsDefined();
} else {
onGroupsDefined();
}

var confoundingVariables = loadConfoundingVariables(projectId.value(), experimentId);
fillConfoundingVariablesCollection(confoundingVariables);
if (confoundingVariables.isEmpty()) {
onNoConfoundingDefined();
} else {
onConfoundingDefined();
}
}

private void loadExperimentalVariables(Experiment experiment) {
this.experimentalVariables.removeAll();
// We load the experimental variables of the experiment and render them as cards
List<ExperimentalVariable> variables = experiment.variables();
private void onVariablesDefined() {
experimentalVariablesContainer.removeAll();
experimentalVariablesContainer.add(experimentalVariableCollection);
}

private void fillExperimentalGroupCollection(List<ExperimentalGroup> groups) {
Comparator<String> natOrder = Comparator.naturalOrder();
List<ExperimentalGroupCard> experimentalGroupsCards = groups.stream()
.sorted((g1, g2) -> natOrder.compare(g1.name(), g2.name()))
.map(ExperimentalGroupCard::new)
.toList();
experimentalGroupsCollection.setContent(experimentalGroupsCards);
this.experimentalGroupCount = experimentalGroupsCards.size();
}

private void fillExperimentalVariablesCollection(List<ExperimentalVariable> variables) {
this.experimentalVariablesContainer.removeAll();

Comparator<String> natOrder = Comparator.naturalOrder();
List<ExperimentalVariableCard> experimentalVariableCards = variables.stream()
.sorted((var1, var2) -> natOrder.compare(var1.name().value(), var2.name().value()))
.map(ExperimentalVariableCard::new).toList();

experimentalVariableCollection.setContent(experimentalVariableCards);
}

if (variables.isEmpty()) {
this.experimentalVariables.add(addExperimentalVariablesNote);
} else {
this.experimentalVariables.add(experimentalVariableCollection);
private void fillConfoundingVariablesCollection(
List<ConfoundingVariableInformation> confoundingVariables) {
this.confoundingVariableCollection.removeAll();
for (ConfoundingVariableInformation confoundingVariable : confoundingVariables) {
confoundingVariableCollection.add(new Div(confoundingVariable.variableName()));
}
}

private List<ConfoundingVariableInformation> loadConfoundingVariables(String projectId,
ExperimentId experimentId) {
return confoundingVariableService.listConfoundingVariablesForExperiment(projectId,
new ExperimentReference(experimentId.value()));
}

private void onNoVariablesDefined() {
experimentalGroups.removeAll();
experimentalGroups.add(noExperimentalVariablesDefined);
experimentalGroupsContainer.removeAll();
experimentalGroupsContainer.add(noExperimentalVariablesDefined);
}

private void onNoGroupsDefined() {
experimentalGroups.removeAll();
experimentalGroups.add(noExperimentalGroupsDefined);
experimentalGroupsContainer.removeAll();
experimentalGroupsContainer.add(noExperimentalGroupsDefined);
}

private void onGroupsDefined() {
experimentalGroups.removeAll();
experimentalGroups.add(experimentalGroupsCollection);
experimentalGroupsContainer.removeAll();
experimentalGroupsContainer.add(experimentalGroupsCollection);
}

private void onNoConfoundingDefined() {
confoundingVariablesContainer.removeAll();
confoundingVariablesContainer.add(noConfoundingVariablesDefined);
}

private void onConfoundingDefined() {
confoundingVariablesContainer.removeAll();
confoundingVariablesContainer.add(confoundingVariableCollection);
}

/**
Expand Down

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