#374 - Extend API to save and load cohort and dataselection

- remove unused exception classes
- add DataqueryHandlerIT

src/main/java/de/numcodex/feasibility_gui_backend/query/dataquery/DataqueryHandler.java

@@ -57,7 +57,7 @@ public Long storeDataquery(@NonNull Dataquery dataquery, @NonNull String userId)
 
   public Dataquery getDataqueryById(Long dataqueryId, String userId) throws DataqueryException, JsonProcessingException {
     de.numcodex.feasibility_gui_backend.query.persistence.Dataquery dataquery = dataqueryRepository.findById(dataqueryId).orElseThrow(DataqueryException::new);
-    if (!dataquery.getCreatedBy().equals(userId)) {
+    if (dataquery.getCreatedBy() == null || !dataquery.getCreatedBy().equals(userId)) {
       throw new DataqueryException();
     }
     return convertPersistenceToApi(dataquery);
@@ -74,10 +74,10 @@ public void updateDataquery(Long queryId, Dataquery dataquery, String userId) th
       }
     }
 
-
     if (existingDataquery.getCreatedBy().equals(userId)) {
       var dataqueryToUpdate = convertApiToPersistence(dataquery);
       dataqueryToUpdate.setId(existingDataquery.getId());
+      dataqueryToUpdate.setCreatedBy(userId);
       dataqueryToUpdate.setLastModified(Timestamp.valueOf(LocalDateTime.now()));
       dataqueryRepository.save(dataqueryToUpdate);
     } else {
@@ -139,7 +139,7 @@ public de.numcodex.feasibility_gui_backend.query.api.Dataquery convertPersistenc
         .comment(in.getComment())
         .createdBy(in.getCreatedBy())
         .resultSize(in.getResultSize())
-        .lastModified(in.getLastModified().toString())
+        .lastModified(in.getLastModified() == null ? null : in.getLastModified().toString())
         .content(jsonUtil.readValue(in.getCrtdl(), Crtdl.class))
         .build();
   }

src/test/java/de/numcodex/feasibility_gui_backend/query/dataquery/DataqueryHandlerIT.java

@@ -0,0 +1,215 @@
+package de.numcodex.feasibility_gui_backend.query.dataquery;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import de.numcodex.feasibility_gui_backend.common.api.Criterion;
+import de.numcodex.feasibility_gui_backend.common.api.TermCode;
+import de.numcodex.feasibility_gui_backend.query.QueryHandlerService;
+import de.numcodex.feasibility_gui_backend.query.api.Crtdl;
+import de.numcodex.feasibility_gui_backend.query.api.Dataquery;
+import de.numcodex.feasibility_gui_backend.query.api.StructuredQuery;
+import de.numcodex.feasibility_gui_backend.query.api.status.SavedQuerySlots;
+import de.numcodex.feasibility_gui_backend.query.broker.BrokerSpringConfig;
+import de.numcodex.feasibility_gui_backend.query.collect.QueryCollectSpringConfig;
+import de.numcodex.feasibility_gui_backend.query.dispatch.QueryDispatchSpringConfig;
+import de.numcodex.feasibility_gui_backend.query.persistence.DataqueryRepository;
+import de.numcodex.feasibility_gui_backend.query.result.ResultServiceSpringConfig;
+import de.numcodex.feasibility_gui_backend.query.translation.QueryTranslatorSpringConfig;
+import de.numcodex.feasibility_gui_backend.terminology.validation.StructuredQueryValidation;
+import org.junit.jupiter.api.Tag;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase;
+import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest;
+import org.springframework.context.annotation.Import;
+import org.springframework.test.context.bean.override.mockito.MockitoBean;
+import org.testcontainers.junit.jupiter.Testcontainers;
+
+import java.net.URI;
+import java.sql.Timestamp;
+import java.util.List;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
+
+@Tag("query")
+@Tag("handler")
+@Import({
+    BrokerSpringConfig.class,
+    QueryTranslatorSpringConfig.class,
+    QueryDispatchSpringConfig.class,
+    QueryCollectSpringConfig.class,
+    QueryHandlerService.class,
+    ResultServiceSpringConfig.class,
+    DataquerySpringConfig.class
+})
+@DataJpaTest(
+    properties = {
+        "app.cqlTranslationEnabled=false",
+        "app.fhirTranslationEnabled=false",
+        "app.broker.mock.enabled=true",
+        "app.broker.direct.enabled=false",
+        "app.broker.aktin.enabled=false",
+        "app.broker.dsf.enabled=false"
+    }
+)
+@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
+@Testcontainers
+public class DataqueryHandlerIT {
+  public static final String SITE_NAME_1 = "site-name-114606";
+  public static final String SITE_NAME_2 = "site-name-114610";
+  public static final String CREATOR = "creator-114634";
+  public static final long UNKNOWN_QUERY_ID = 9999999L;
+  public static final String LABEL = "some-label";
+  public static final String COMMENT = "some-comment";
+  public static final String TIME_STRING = "1969-07-20 20:17:40.0";
+
+  @Autowired
+  private DataqueryHandler dataqueryHandler;
+
+  @Autowired
+  private DataqueryRepository dataqueryRepository;
+
+  @MockitoBean
+  private StructuredQueryValidation structuredQueryValidation;
+
+  @Autowired
+  @Qualifier("translation")
+  private ObjectMapper jsonUtil;
+
+  @Test
+  public void testStoreDataquery() throws DataqueryStorageFullException, DataqueryException {
+    var testDataquery = createDataquery(false);
+
+    dataqueryHandler.storeDataquery(testDataquery, "test");
+
+    assertThat(dataqueryRepository.count()).isOne();
+  }
+
+  @Test
+  public void testGetDataquery() throws JsonProcessingException {
+    var dataqueryEntity = createDataqueryEntity(false);
+    var dataqueryId = dataqueryRepository.save(dataqueryEntity).getId();
+
+    var loadedDataquery = assertDoesNotThrow(() -> dataqueryHandler.getDataqueryById(dataqueryId, dataqueryEntity.getCreatedBy()));
+
+    assertThat(loadedDataquery).isNotNull();
+    assertThat(jsonUtil.writeValueAsString(loadedDataquery.content())).isEqualTo(dataqueryEntity.getCrtdl());
+  }
+
+  @Test
+  public void testUpdateDataquery() throws JsonProcessingException, DataqueryStorageFullException, DataqueryException {
+    var dataquery = createDataquery(false);
+    var dataqueryWithResult = createDataquery(true);
+
+    var dataqueryId = dataqueryHandler.storeDataquery(dataquery, CREATOR);
+    var loadedDataqueryOld = assertDoesNotThrow(() -> dataqueryHandler.getDataqueryById(dataqueryId, CREATOR));
+    dataqueryHandler.updateDataquery(dataqueryId, dataqueryWithResult, CREATOR);
+    var loadedDataqueryUpdated = assertDoesNotThrow(() -> dataqueryHandler.getDataqueryById(dataqueryId, CREATOR));
+
+    assertThat(loadedDataqueryUpdated).isNotNull();
+    assertThat(loadedDataqueryUpdated.resultSize()).isEqualTo(dataqueryWithResult.resultSize());
+    assertThat(loadedDataqueryUpdated.resultSize()).isNotEqualTo(loadedDataqueryOld.resultSize());
+  }
+
+  @Test
+  public void testGetDataqueriesByAuthor() throws JsonProcessingException {
+    var listSize = 10;
+
+    for (int i = 0; i < listSize; ++i) {
+      dataqueryRepository.save(createDataqueryEntity(false));
+    }
+
+    var dataqueryList = assertDoesNotThrow(() -> dataqueryHandler.getDataqueriesByAuthor(CREATOR));
+    var dataqueryListOtherAuthor = assertDoesNotThrow(() -> dataqueryHandler.getDataqueriesByAuthor("other-" + CREATOR));
+
+    assertThat(dataqueryList.size()).isEqualTo(listSize);
+    assertThat(dataqueryListOtherAuthor).isEmpty();
+  }
+
+  @Test
+  public void testDeleteDataquery() throws JsonProcessingException {
+    var listSize = 10;
+
+    for (int i = 0; i < listSize; ++i) {
+      dataqueryRepository.save(createDataqueryEntity(false));
+    }
+
+    var dataqueryListBeforeDelete = assertDoesNotThrow(() -> dataqueryHandler.getDataqueriesByAuthor(CREATOR));
+
+    assertDoesNotThrow(() -> dataqueryHandler.deleteDataquery(1L, CREATOR));
+
+    var dataqueryListAfterDelete = assertDoesNotThrow(() -> dataqueryHandler.getDataqueriesByAuthor(CREATOR));
+
+    assertThat(dataqueryListBeforeDelete.size()).isEqualTo(listSize);
+    assertThat(dataqueryListAfterDelete.size()).isEqualTo(listSize - 1);
+  }
+
+  @Test
+  public void testGetDataquerySlotsJson() throws JsonProcessingException, DataqueryException {
+    var dataqueriesWithResult = 3;
+    var dataqueriesWithoutResult = 5;
+
+    for (int i = 0; i < dataqueriesWithResult; ++i) {
+      dataqueryRepository.save(createDataqueryEntity(true));
+    }
+
+    for (int i = 0; i < dataqueriesWithoutResult; ++i) {
+      dataqueryRepository.save(createDataqueryEntity(false));
+    }
+
+    var dataqueryList = dataqueryHandler.getDataqueriesByAuthor(CREATOR);
+    var dataquerySlots = assertDoesNotThrow(() -> dataqueryHandler.getDataquerySlotsJson(CREATOR));
+
+    assertThat(dataqueryList.size()).isEqualTo(dataqueriesWithoutResult + dataqueriesWithResult);
+    assertThat(dataquerySlots).isInstanceOf(SavedQuerySlots.class);
+    assertThat(dataquerySlots.used()).isEqualTo(dataqueriesWithResult);
+  }
+
+  private Dataquery createDataquery(boolean withResult) {
+    var testDataquery = Dataquery.builder()
+        .label("test")
+        .comment("test")
+        .content(createCrtdl())
+        .resultSize(withResult ? 123L : null)
+        .build();
+    return testDataquery;
+  }
+
+  private Crtdl createCrtdl() {
+    return Crtdl.builder()
+        .cohortDefinition(createValidStructuredQuery())
+        .display("foo")
+        .build();
+  }
+
+  private StructuredQuery createValidStructuredQuery() {
+    var termCode = TermCode.builder()
+        .code("LL2191-6")
+        .system("http://loinc.org")
+        .display("Geschlecht")
+        .build();
+    var inclusionCriterion = Criterion.builder()
+        .termCodes(List.of(termCode))
+        .attributeFilters(List.of())
+        .build();
+    return StructuredQuery.builder()
+        .version(URI.create("http://to_be_decided.com/draft-2/schema#"))
+        .inclusionCriteria(List.of(List.of(inclusionCriterion)))
+        .exclusionCriteria(null)
+        .display("foo")
+        .build();
+  }
+
+  private de.numcodex.feasibility_gui_backend.query.persistence.Dataquery createDataqueryEntity(boolean withResult) throws JsonProcessingException {
+    de.numcodex.feasibility_gui_backend.query.persistence.Dataquery out = new de.numcodex.feasibility_gui_backend.query.persistence.Dataquery();
+    out.setLabel(LABEL);
+    out.setComment(COMMENT);
+    out.setLastModified(Timestamp.valueOf(TIME_STRING));
+    out.setCreatedBy(CREATOR);
+    out.setResultSize(withResult ? 123L : null);
+    out.setCrtdl(jsonUtil.writeValueAsString(createCrtdl()));
+    return out;
+  }
+}