private EntityType createCategoricalRefEntityType(String entityName) {
EntityType targetRefEntityType = entityTypeFactory.create(entityName);
Attribute targetCodeAttribute = attrMetaFactory.create().setName("code").setDataType(INT);
Attribute targetLabelAttribute = attrMetaFactory.create().setName("label");
targetRefEntityType.addAttribute(targetCodeAttribute, ROLE_ID);
targetRefEntityType.addAttribute(targetLabelAttribute, ROLE_LABEL);
return targetRefEntityType;
}
public Attribute getTermsAttr() {
return attributeFactory
.create()
.setName(HPO_TERMS)
.setDataType(TEXT)
.setDescription("HPO terms");
}
public Attribute getIdsAttr() {
return attributeFactory
.create()
.setName(HPO_IDS)
.setDataType(TEXT)
.setDescription("HPO identifiers");
}
@Test
public void testGenerateRules() {
EntityType targetRefEntityType = createCategoricalRefEntityType("HOP_HYPERTENSION");
Entity targetEntity1 =
new DynamicEntity(
targetRefEntityType, of("code", 0, "label", "Never had high blood pressure "));
Entity targetEntity2 =
new DynamicEntity(
targetRefEntityType, of("code", 1, "label", "Ever had high blood pressure "));
Entity targetEntity3 =
new DynamicEntity(targetRefEntityType, of("code", 9, "label", "Missing"));
Mockito.when(dataService.findAll(targetRefEntityType.getName()))
.thenReturn(Stream.of(targetEntity1, targetEntity2, targetEntity3));
targetAttribute =
attrMetaFactory.create().setName("History of Hypertension").setDataType(CATEGORICAL);
targetAttribute.setRefEntity(targetRefEntityType);
EntityType sourceRefEntityType = createCategoricalRefEntityType("High_blood_pressure_ref");
Entity sourceEntity1 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "yes"));
Entity sourceEntity2 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "no"));
Entity sourceEntity3 =
new DynamicEntity(targetRefEntityType, of("code", 3, "label", "I do not know"));
Mockito.when(dataService.findAll(sourceRefEntityType.getName()))
.thenReturn(Stream.of(sourceEntity1, sourceEntity2, sourceEntity3));
sourceAttribute =
attrMetaFactory.create().setName("High_blood_pressure").setDataType(CATEGORICAL);
sourceAttribute.setRefEntity(sourceRefEntityType);
String generatedAlgorithm =
categoryAlgorithmGenerator.generate(
targetAttribute, singletonList(sourceAttribute), targetEntityType, sourceEntityType);
String expectedAlgorithm =
"$('High_blood_pressure').map({\"1\":\"1\",\"2\":\"0\",\"3\":\"9\"}, null, null).value();";
Assert.assertEquals(generatedAlgorithm, expectedAlgorithm);
}
@BeforeMethod
public void init() {
dataService = Mockito.mock(DataService.class);
categoryAlgorithmGenerator = new OneToOneCategoryAlgorithmGenerator(dataService);
EntityType targetRefEntityType = createCategoricalRefEntityType("POTATO_REF");
Entity targetEntity1 =
new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Almost daily + daily"));
Entity targetEntity2 =
new DynamicEntity(targetRefEntityType, of("code", 2, "label", "Several times a week"));
Entity targetEntity3 =
new DynamicEntity(targetRefEntityType, of("code", 3, "label", "About once a week"));
Entity targetEntity4 =
new DynamicEntity(
targetRefEntityType, of("code", 4, "label", "Never + fewer than once a week"));
Entity targetEntity5 =
new DynamicEntity(targetRefEntityType, of("code", 9, "label", "missing"));
targetAttribute =
attrMetaFactory
.create()
.setName("Current Consumption Frequency of Potatoes")
.setDataType(CATEGORICAL);
targetAttribute.setRefEntity(targetRefEntityType);
Mockito.when(dataService.findAll(targetRefEntityType.getName()))
.thenReturn(
Stream.of(targetEntity1, targetEntity2, targetEntity3, targetEntity4, targetEntity5));
targetEntityType = entityTypeFactory.create("target");
targetEntityType.addAttribute(targetAttribute);
EntityType sourceRefEntityType = createCategoricalRefEntityType("LifeLines_POTATO_REF");
Entity sourceEntity1 =
new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Not this month"));
Entity sourceEntity2 =
new DynamicEntity(targetRefEntityType, of("code", 2, "label", "1 day per month"));
Entity sourceEntity3 =
new DynamicEntity(targetRefEntityType, of("code", 3, "label", "2-3 days per month"));
Entity sourceEntity4 =
new DynamicEntity(targetRefEntityType, of("code", 4, "label", "1 day per week"));
Entity sourceEntity5 =
new DynamicEntity(targetRefEntityType, of("code", 5, "label", "2-3 days per week"));
Entity sourceEntity6 =
new DynamicEntity(targetRefEntityType, of("code", 6, "label", "4-5 days per week"));
Entity sourceEntity7 =
new DynamicEntity(targetRefEntityType, of("code", 7, "label", "6-7 days per week"));
Entity sourceEntity8 =
new DynamicEntity(targetRefEntityType, of("code", 8, "label", "9 days per week"));
sourceAttribute = attrMetaFactory.create().setName("MESHED_POTATO").setDataType(CATEGORICAL);
sourceAttribute.setLabel(
"How often did you eat boiled or mashed potatoes (also in stew) in the past month? Baked potatoes are asked later");
sourceAttribute.setRefEntity(sourceRefEntityType);
Mockito.when(dataService.findAll(sourceRefEntityType.getName()))
.thenReturn(
Stream.of(
sourceEntity1,
sourceEntity2,
sourceEntity3,
sourceEntity4,
sourceEntity5,
sourceEntity6,
sourceEntity7,
sourceEntity8));
sourceEntityType = entityTypeFactory.create("source");
sourceEntityType.addAttributes(Lists.newArrayList(sourceAttribute));
}