@Test
public void testConvertNetworkMetaAnalysis()
throws Exception, InstantiationException, InvocationTargetException, NoSuchMethodException {
Domain domain = new DomainImpl();
ExampleData.initDefaultData(domain);
String name = "CGI network meta-analysis";
MetaAnalysisWithStudies ma = d_jaxbConverterTest.buildNetworkMetaAnalysis(name);
List<Study> studies = new ArrayList<Study>();
for (org.drugis.addis.entities.data.Study study : ma.d_studies) {
Study studyEnt = JAXBConvertor.convertStudy(study, domain);
domain.getStudies().add(studyEnt);
studies.add(studyEnt);
}
TreatmentDefinition combi =
TreatmentDefinition.createTrivial(
Arrays.asList(ExampleData.buildDrugFluoxetine(), ExampleData.buildDrugSertraline()));
TreatmentDefinition parox =
TreatmentDefinition.createTrivial(ExampleData.buildDrugParoxetine());
TreatmentDefinition sertr =
TreatmentDefinition.createTrivial(ExampleData.buildDrugSertraline());
SortedSet<TreatmentDefinition> alternatives = new TreeSet<TreatmentDefinition>();
alternatives.add(combi);
alternatives.add(parox);
alternatives.add(sertr);
Map<Study, Map<TreatmentDefinition, Arm>> armMap =
new HashMap<Study, Map<TreatmentDefinition, Arm>>();
Map<TreatmentDefinition, Arm> study1map = new HashMap<TreatmentDefinition, Arm>();
study1map.put(combi, studies.get(0).getArms().get(0));
study1map.put(sertr, studies.get(0).getArms().get(1));
armMap.put(studies.get(0), study1map);
Map<TreatmentDefinition, Arm> study2map = new HashMap<TreatmentDefinition, Arm>();
study2map.put(parox, studies.get(1).getArms().get(0));
study2map.put(sertr, studies.get(1).getArms().get(1));
armMap.put(studies.get(1), study2map);
Map<TreatmentDefinition, Arm> study3map = new HashMap<TreatmentDefinition, Arm>();
study3map.put(sertr, studies.get(2).getArms().get(0));
study3map.put(parox, studies.get(2).getArms().get(1));
study3map.put(combi, studies.get(2).getArms().get(2));
armMap.put(studies.get(2), study3map);
Collections.sort(
studies); // So the reading *by definition* puts the studies in their natural order
NetworkMetaAnalysis expected =
new NetworkMetaAnalysis(
name,
ExampleData.buildIndicationDepression(),
ExampleData.buildEndpointCgi(),
studies,
alternatives,
armMap);
assertEntityEquals(expected, NetworkMetaAnalysisConverter.load(ma.d_nwma, domain));
assertEquals(ma.d_nwma, NetworkMetaAnalysisConverter.save(expected));
}
private int createArmSelect(
PanelBuilder builder,
int row,
final Study curStudy,
TreatmentDefinition def,
CellConstraints cc) {
builder.addLabel(def.getLabel(), cc.xy(2, row));
ListModel arms = d_pm.getArmsPerStudyPerDefinition(curStudy, def);
final JComboBox drugBox =
AuxComponentFactory.createBoundComboBox(
arms, d_pm.getSelectedArmModel(curStudy, def), true);
if (arms.getSize() == 1) drugBox.setEnabled(false);
final JPanel drugAndDosePanel = new JPanel(new BorderLayout());
builder.add(drugBox, cc.xy(4, row));
drugBox.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
updateDrugAndDoseLabel(curStudy, drugBox, drugAndDosePanel);
}
});
row = LayoutUtil.addRow(builder.getLayout(), row);
updateDrugAndDoseLabel(curStudy, drugBox, drugAndDosePanel);
builder.add(drugAndDosePanel, cc.xy(4, row));
return LayoutUtil.addRow(builder.getLayout(), row);
}
@Test
public void testDependentsIncludeMetaStudies() throws Exception {
ExampleData.initDefaultData(d_domain);
List<Study> studies = new ArrayList<Study>();
studies.add(ExampleData.buildStudyChouinard());
studies.add(ExampleData.buildStudyDeWilde());
RandomEffectsMetaAnalysis ma =
ExampleData.buildRandomEffectsMetaAnalysis(
"meta",
ExampleData.buildEndpointHamd(),
studies,
TreatmentDefinition.createTrivial(ExampleData.buildDrugFluoxetine()),
TreatmentDefinition.createTrivial(ExampleData.buildDrugParoxetine()));
d_domain.getMetaAnalyses().add(ma);
Set<Entity> deps = d_domain.getDependents(ExampleData.buildDrugFluoxetine());
assertTrue(deps.contains(ma));
}
