[ALS-7336] Show specific ancestors in details

- Lots of weird BDC stuff. We decorate the concept with them

src/main/java/edu/harvard/dbmi/avillach/dictionary/ConceptDecoratorService.java

@@ -0,0 +1,65 @@
+package edu.harvard.dbmi.avillach.dictionary;
+
+import edu.harvard.dbmi.avillach.dictionary.concept.ConceptService;
+import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+
+@Service
+public class ConceptDecoratorService {
+
+    private static final Logger LOG = LoggerFactory.getLogger(ConceptDecoratorService.class);
+    private final boolean enabled;
+    private final ConceptService conceptService;
+
+    private static final int COMPLIANT = 4, NON_COMPLIANT_TABLED = 3, NON_COMPLIANT_UNTABLED = 2;
+
+    @Autowired
+    public ConceptDecoratorService(
+        @Value("${dashboard.enable.extra_details}") boolean enabled,
+        @Lazy ConceptService conceptService // circular dep
+    ) {
+        this.enabled = enabled;
+        this.conceptService = conceptService;
+    }
+
+
+    public Concept populateParentConcepts(Concept concept) {
+        if (!enabled) {
+            return concept;
+        }
+
+        // In some environments, certain parent concepts have critical details that we need to add to the detailed response
+        List<String> conceptNodes = List.of(concept.conceptPath()
+            .split("\\\\")); // you have to double escape the slash. Once for strings, and once for regex
+
+        return switch (conceptNodes.size()) {
+            case COMPLIANT, NON_COMPLIANT_TABLED -> populateTabledConcept(concept, conceptNodes);
+            case NON_COMPLIANT_UNTABLED -> populateNonCompliantTabledConcept(concept, conceptNodes);
+            default -> {
+                LOG.warn("Ignoring decoration request for weird concept path {}", concept.conceptPath());
+                yield concept;
+            }
+        };
+    }
+
+    private Concept populateTabledConcept(Concept concept, List<String> conceptNodes) {
+        String studyPath = String.join("\\", conceptNodes.subList(0, 1)) + "\\";
+        String tablePath = String.join("\\", conceptNodes.subList(0, 2)) + "\\";
+        Concept study = conceptService.conceptDetail(concept.dataset(), studyPath).orElse(null);
+        Concept table = conceptService.conceptDetail(concept.dataset(), tablePath).orElse(null);
+        return concept.withStudy(study).withTable(table);
+    }
+
+    private Concept populateNonCompliantTabledConcept(Concept concept, List<String> conceptNodes) {
+        String studyPath = String.join("\\", conceptNodes.subList(0, 1));
+        Concept study = conceptService.conceptDetail(concept.dataset(), studyPath).orElse(null);
+        return concept.withStudy(study);
+    }
+}

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptService.java

@@ -1,5 +1,6 @@
 package edu.harvard.dbmi.avillach.dictionary.concept;
 
+import edu.harvard.dbmi.avillach.dictionary.ConceptDecoratorService;
 import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept;
 import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept;
 import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptShell;
@@ -20,9 +21,12 @@ public class ConceptService {
 
     private final ConceptRepository conceptRepository;
 
+    private final ConceptDecoratorService conceptDecoratorService;
+
     @Autowired
-    public ConceptService(ConceptRepository conceptRepository) {
+    public ConceptService(ConceptRepository conceptRepository, ConceptDecoratorService conceptDecoratorService) {
         this.conceptRepository = conceptRepository;
+        this.conceptDecoratorService = conceptDecoratorService;
     }
 
     public List<Concept> listConcepts(Filter filter, Pageable page) {
@@ -53,7 +57,7 @@ public Optional<Concept> conceptDetail(String dataset, String conceptPath) {
                     case ConceptShell ignored -> throw new RuntimeException("Concept shell escaped to API");
                 };
             }
-        );
+        ).map(conceptDecoratorService::populateParentConcepts);
     }
 
     public Optional<Concept> conceptTree(String dataset, String conceptPath, int depth) {

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/CategoricalConcept.java

@@ -16,10 +16,23 @@ public record CategoricalConcept(
     List<Concept> children,
 
     @Nullable
-    Map<String, String> meta
+    Map<String, String> meta,
+
+    @Nullable
+    Concept table,
+
+    @Nullable
+    Concept study
 
 ) implements Concept {
 
+    public CategoricalConcept(
+        String conceptPath, String name, String display, String dataset, String description, List<String> values,
+        @Nullable List<Concept> children, @Nullable Map<String, String> meta
+    ) {
+        this(conceptPath, name, display, dataset, description, values, children, meta, null, null);
+    }
+
     public CategoricalConcept(CategoricalConcept core, Map<String, String> meta) {
         this(core.conceptPath, core.name, core.display, core.dataset, core.description, core.values, core.children, meta);
     }
@@ -44,6 +57,20 @@ public CategoricalConcept withChildren(List<Concept> children) {
         return new CategoricalConcept(this, children);
     }
 
+    @Override
+    public Concept withTable(Concept table) {
+        return new CategoricalConcept(
+            conceptPath, name, display, dataset, description, values, children, meta, table, study
+        );
+    }
+
+    @Override
+    public Concept withStudy(Concept study) {
+        return new CategoricalConcept(
+            conceptPath, name, display, dataset, description, values, children, meta, table, study
+        );
+    }
+
     @Override
     public boolean equals(Object object) {
         return conceptEquals(object);

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/Concept.java

@@ -49,13 +49,21 @@ public sealed interface Concept
      */
     ConceptType type();
 
+    Concept table();
+
+    Concept study();
+
     Map<String, String> meta();
 
     @Nullable
     List<Concept> children();
 
     Concept withChildren(List<Concept> children);
 
+    Concept withTable(Concept table);
+
+    Concept withStudy(Concept study);
+
     default boolean conceptEquals(Object object) {
         if (this == object) return true;
         if (!(object instanceof Concept)) return false;

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptShell.java

@@ -22,6 +22,16 @@ public ConceptType type() {
         return ConceptType.Continuous;
     }
 
+    @Override
+    public Concept table() {
+        return null;
+    }
+
+    @Override
+    public Concept study() {
+        return null;
+    }
+
     @Override
     public Map<String, String> meta() {
         return Map.of();
@@ -37,6 +47,16 @@ public ConceptShell withChildren(List<Concept> children) {
         return this;
     }
 
+    @Override
+    public Concept withTable(Concept table) {
+        return this;
+    }
+
+    @Override
+    public Concept withStudy(Concept study) {
+        return this;
+    }
+
     @Override
     public boolean equals(Object object) {
         return conceptEquals(object);

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ContinuousConcept.java

@@ -14,9 +14,22 @@ public record ContinuousConcept(
     @Nullable Integer min, @Nullable Integer max,
     Map<String, String> meta,
     @Nullable
-    List<Concept> children
+    List<Concept> children,
+
+    @Nullable
+    Concept table,
+
+    @Nullable
+    Concept study
 ) implements Concept {
 
+    public ContinuousConcept(
+        String conceptPath, String name, String display, String dataset, String description,
+        @Nullable Integer min, @Nullable Integer max, Map<String, String> meta, @Nullable List<Concept> children
+    ) {
+        this(conceptPath, name, display, dataset, description, min, max, meta, children, null, null);
+    }
+
     public ContinuousConcept(ContinuousConcept core, Map<String, String> meta) {
         this(core.conceptPath, core.name, core.display, core.dataset, core.description, core.min, core.max, meta, core.children);
     }
@@ -47,6 +60,20 @@ public ContinuousConcept withChildren(List<Concept> children) {
         return new ContinuousConcept(this, children);
     }
 
+    @Override
+    public Concept withTable(Concept table) {
+        return new ContinuousConcept(
+            conceptPath, name, display, dataset, description, min, max, meta, children, table, study
+        );
+    }
+
+    @Override
+    public Concept withStudy(Concept study) {
+        return new ContinuousConcept(
+            conceptPath, name, display, dataset, description, min, max, meta, children, table, study
+        );
+    }
+
     @Override
     public boolean equals(Object object) {
         return conceptEquals(object);

src/main/resources/application-bdc.properties

@@ -4,3 +4,5 @@ spring.datasource.driver-class-name=com.amazonaws.secretsmanager.sql.AWSSecretsM
 spring.datasource.url=jdbc-secretsmanager:postgresql://${DATASOURCE_URL}/picsure?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&autoReconnectForPools=true&currentSchema=dict
 spring.datasource.username=${DATASOURCE_USERNAME}
 server.port=80
+
+dashboard.enable.extra_details=true

src/main/resources/application.properties

@@ -7,4 +7,5 @@ server.port=80
 
 dashboard.columns={abbreviation:'Abbreviation',name:'Name',clinvars:'Clinical Variables'}
 dashboard.column-order=abbreviation,name,clinvars
-dashboard.nonmeta-columns=abbreviation,name
+dashboard.nonmeta-columns=abbreviation,name
+dashboard.enable.extra_details=true

src/test/java/edu/harvard/dbmi/avillach/dictionary/ConceptDecoratorServiceTest.java

@@ -0,0 +1,72 @@
+package edu.harvard.dbmi.avillach.dictionary;
+
+import edu.harvard.dbmi.avillach.dictionary.concept.ConceptService;
+import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept;
+import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+
+import java.util.Optional;
+
+
+@SpringBootTest
+class ConceptDecoratorServiceTest {
+
+    @MockBean
+    ConceptService conceptService;
+
+    @Autowired
+    ConceptDecoratorService subject;
+
+    @Test
+    void shouldPopulateCompliantStudy() {
+        CategoricalConcept concept = new CategoricalConcept("\\study\\table\\idk\\concept\\", "dataset");
+        CategoricalConcept table = new CategoricalConcept("\\study\\table\\", "dataset");
+        CategoricalConcept study = new CategoricalConcept("\\study\\", "dataset");
+
+        Mockito.when(conceptService.conceptDetail("dataset", table.dataset()))
+            .thenReturn(Optional.of(table));
+        Mockito.when(conceptService.conceptDetail("dataset", study.dataset()))
+            .thenReturn(Optional.of(study));
+
+        Concept actual = subject.populateParentConcepts(concept);
+        Concept expected = concept.withStudy(study).withTable(table);
+
+        Assertions.assertEquals(expected, actual);
+    }
+
+    @Test
+    void shouldPopulateNonCompliantTabledStudy() {
+        CategoricalConcept concept = new CategoricalConcept("\\study\\table\\concept\\", "dataset");
+        CategoricalConcept table = new CategoricalConcept("\\study\\table\\", "dataset");
+        CategoricalConcept study = new CategoricalConcept("\\study\\", "dataset");
+
+        Mockito.when(conceptService.conceptDetail("dataset", table.dataset()))
+            .thenReturn(Optional.of(table));
+        Mockito.when(conceptService.conceptDetail("dataset", study.dataset()))
+            .thenReturn(Optional.of(study));
+
+        Concept actual = subject.populateParentConcepts(concept);
+        Concept expected = concept.withStudy(study).withTable(table);
+
+        Assertions.assertEquals(expected, actual);
+    }
+
+    @Test
+    void shouldPopulateNonCompliantUnTabledStudy() {
+        CategoricalConcept concept = new CategoricalConcept("\\study\\concept\\", "dataset");
+        CategoricalConcept study = new CategoricalConcept("\\study\\", "dataset");
+
+        Mockito.when(conceptService.conceptDetail("dataset", study.dataset()))
+            .thenReturn(Optional.of(study));
+
+        Concept actual = subject.populateParentConcepts(concept);
+        Concept expected = concept.withStudy(study);
+
+        Assertions.assertEquals(expected, actual);
+    }
+}

src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptServiceTest.java

@@ -1,5 +1,6 @@
 package edu.harvard.dbmi.avillach.dictionary.concept;
 
+import edu.harvard.dbmi.avillach.dictionary.ConceptDecoratorService;
 import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept;
 import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept;
 import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptShell;
@@ -24,6 +25,9 @@ class ConceptServiceTest {
     @MockBean
     ConceptRepository repository;
 
+    @MockBean
+    ConceptDecoratorService decoratorService;
+
     @Autowired
     ConceptService subject;
 
@@ -59,6 +63,8 @@ void shouldShowDetailForContinuous() {
         Map<String, String> meta = Map.of("MIN", "0", "MAX", "1", "stigmatizing", "true");
         Mockito.when(repository.getConcept("dataset", "path"))
             .thenReturn(Optional.of(concept));
+        Mockito.when(decoratorService.populateParentConcepts(Mockito.any()))
+            .thenAnswer(i -> i.getArguments()[0]);
         Mockito.when(repository.getConceptMeta("dataset", "path"))
             .thenReturn(meta);
 
@@ -74,6 +80,8 @@ void shouldShowDetailForCategorical() {
         Map<String, String> meta = Map.of("VALUES", "a", "stigmatizing", "true");
         Mockito.when(repository.getConcept("dataset", "path"))
             .thenReturn(Optional.of(concept));
+        Mockito.when(decoratorService.populateParentConcepts(Mockito.any()))
+            .thenAnswer(i -> i.getArguments()[0]);
         Mockito.when(repository.getConceptMeta("dataset", "path"))
             .thenReturn(meta);
 

src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptTest.java

@@ -75,7 +75,7 @@ void shouldIncludeTypeInList() throws JsonProcessingException {
         );
 
         String actual = new ObjectMapper().writeValueAsString(concepts);
-        String expected = "[{\"conceptPath\":\"/foo//baz\",\"name\":\"baz\",\"display\":\"Baz\",\"dataset\":\"study_a\",\"description\":null,\"min\":0,\"max\":1,\"meta\":{},\"children\":null,\"type\":\"Continuous\"},{\"conceptPath\":\"/foo//bar\",\"name\":\"bar\",\"display\":\"Bar\",\"dataset\":\"study_a\",\"description\":null,\"values\":[\"a\",\"b\"],\"children\":null,\"meta\":{},\"type\":\"Categorical\"}]";
+        String expected = "[{\"conceptPath\":\"/foo//baz\",\"name\":\"baz\",\"display\":\"Baz\",\"dataset\":\"study_a\",\"description\":null,\"min\":0,\"max\":1,\"meta\":{},\"children\":null,\"table\":null,\"study\":null,\"type\":\"Continuous\"},{\"conceptPath\":\"/foo//bar\",\"name\":\"bar\",\"display\":\"Bar\",\"dataset\":\"study_a\",\"description\":null,\"values\":[\"a\",\"b\"],\"children\":null,\"meta\":{},\"table\":null,\"study\":null,\"type\":\"Categorical\"}]";
 
         Assertions.assertEquals(expected, actual);
     }

src/test/resources/application.properties

@@ -7,3 +7,5 @@ spring.datasource.driver-class-name=org.postgresql.Driver
 dashboard.columns={abbreviation:'Abbreviation',melast:'This one goes last',name:'Name',clinvars:'Clinical Variables',participants:'Participants'}
 dashboard.column-order=abbreviation,name,clinvars
 dashboard.nonmeta-columns=abbreviation,name
+
+dashboard.enable.extra_details=true