[ALS-7437] Switch study to dataset for concept node detail

code-formatting/pre-commit.sh

@@ -0,0 +1,28 @@
+#!/bin/sh -e
+CWD=$(pwd)
+cd $(git rev-parse --show-toplevel)
+format_cmd=""
+
+# skip if NO_VERIFY env var set
+if [ "$NO_VERIFY" ]; then
+    echo 'code formatting skipped' 1>&2
+    exit 0
+fi
+
+# I'm not great at bash, so this is a bit ugly, but I'll explain each pipe
+# 1. Get all staged files
+# 2. Reduce to just .java files
+# 3. Replace newlines with commas (this was really hard to do in sed)
+# 4. Replace commas with $,^.*
+# 5. Crop off the last 4 chars
+# This results in foo.java$,^.*bar.java$,^.*baz.java$
+# I then append ^.* to the beginning of that.
+STAGED_JAVA_FILES_AS_REGEX=$(git diff --staged --name-only --diff-filter=ACMR | grep '.java$' | tr '\n' ',' | sed -e 's/,/$,^.*/g' | sed 's/.\{4\}$//')
+FILES_TO_RESTAGE=$(git diff --staged --name-only --diff-filter=ACMR)
+if [ -n "$STAGED_JAVA_FILES_AS_REGEX" ]; then
+   echo "Found the following staged java files to format: $STAGED_JAVA_FILES_AS_REGEX"
+   mvn spotless:apply -DspotlessFiles=^.*$STAGED_JAVA_FILES_AS_REGEX
+   git add $FILES_TO_RESTAGE
+fi
+
+cd $CWD

pom.xml

@@ -15,6 +15,7 @@
 	<description>Data Dictionary API</description>
 	<properties>
 		<java.version>21</java.version>
+		<spotless.version>2.41.1</spotless.version>
 	</properties>
 	<dependencies>
 		<dependency>
@@ -74,6 +75,20 @@
 				<groupId>org.springframework.boot</groupId>
 				<artifactId>spring-boot-maven-plugin</artifactId>
 			</plugin>
+			<plugin>
+				<groupId>com.diffplug.spotless</groupId>
+				<artifactId>spotless-maven-plugin</artifactId>
+				<version>${spotless.version}</version>
+				<configuration>
+					<java>
+						<eclipse>
+							<version>4.26</version>
+							<file>code-formatting/eclipse-formatter.xml</file>
+						</eclipse>
+						<toggleOffOn />
+					</java>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

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

@@ -1,6 +1,8 @@
 package edu.harvard.dbmi.avillach.dictionary.concept;
 
 import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept;
+import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset;
+import edu.harvard.dbmi.avillach.dictionary.dataset.DatasetService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -9,6 +11,7 @@
 import org.springframework.stereotype.Service;
 
 import java.util.List;
+import java.util.Optional;
 import java.util.function.Predicate;
 import java.util.stream.Stream;
 
@@ -18,16 +21,18 @@ public class ConceptDecoratorService {
     private static final Logger LOG = LoggerFactory.getLogger(ConceptDecoratorService.class);
     private final boolean enabled;
     private final ConceptService conceptService;
+    private final DatasetService datasetService;
 
     private static final int COMPLIANT = 4, NON_COMPLIANT_TABLED = 3, NON_COMPLIANT_UNTABLED = 2;
 
     @Autowired
     public ConceptDecoratorService(
-        @Value("${dashboard.enable.extra_details}") boolean enabled,
-        @Lazy ConceptService conceptService // circular dep
+        @Value("${dashboard.enable.extra_details}") boolean enabled, @Lazy ConceptService conceptService, DatasetService datasetService // circular
+                                                                                                                                        // dep
     ) {
         this.enabled = enabled;
         this.conceptService = conceptService;
+        this.datasetService = datasetService;
     }
 
 
@@ -37,8 +42,20 @@ public Concept populateParentConcepts(Concept concept) {
         }
 
         // In some environments, certain parent concepts have critical details that we need to add to the detailed response
-        List<String> conceptNodes = Stream.of(concept.conceptPath()
-            .split("\\\\")).filter(Predicate.not(String::isBlank)).toList(); // you have to double escape the slash. Once for strings, and once for regex
+        List<String> conceptNodes = Stream.of(concept.conceptPath().split("\\\\")).filter(Predicate.not(String::isBlank)).toList(); // 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);
@@ -51,16 +68,14 @@ public Concept populateParentConcepts(Concept 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.conceptDetailWithoutAncestors(concept.dataset(), studyPath).orElse(null);
+        Dataset study = datasetService.getDataset(concept.dataset()).orElse(null);
         Concept table = conceptService.conceptDetailWithoutAncestors(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);
+        Dataset study = datasetService.getDataset(concept.dataset()).orElse(null);
         return concept.withStudy(study);
     }
 }

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

@@ -1,6 +1,7 @@
 package edu.harvard.dbmi.avillach.dictionary.concept.model;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
+import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset;
 import jakarta.annotation.Nullable;
 
 import java.util.List;
@@ -12,31 +13,27 @@ public record CategoricalConcept(
 
     List<String> values, boolean allowFiltering, String studyAcronym,
 
-    @Nullable
-    List<Concept> children,
+    @Nullable List<Concept> children,
 
-    @Nullable
-    Map<String, String> meta,
+    @Nullable Map<String, String> meta,
 
-    @Nullable
-    Concept table,
+    @Nullable Concept table,
 
-    @Nullable
-    Concept study
+    @Nullable Dataset study
 
 ) implements Concept {
 
     public CategoricalConcept(
-        String conceptPath, String name, String display, String dataset, String description, List<String> values,
-        boolean allowFiltering, String studyAcronym, @Nullable List<Concept> children, @Nullable Map<String, String> meta
+        String conceptPath, String name, String display, String dataset, String description, List<String> values, boolean allowFiltering,
+        String studyAcronym, @Nullable List<Concept> children, @Nullable Map<String, String> meta
     ) {
         this(conceptPath, name, display, dataset, description, values, allowFiltering, studyAcronym, 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.allowFiltering, core.studyAcronym, core.children, meta
+            core.conceptPath, core.name, core.display, core.dataset, core.description, core.values, core.allowFiltering, core.studyAcronym,
+            core.children, meta
         );
     }
 
@@ -66,7 +63,7 @@ public Concept withTable(Concept table) {
     }
 
     @Override
-    public Concept withStudy(Concept study) {
+    public Concept withStudy(Dataset study) {
         return new CategoricalConcept(
             conceptPath, name, display, dataset, description, values, allowFiltering, studyAcronym, children, meta, table, study
         );

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

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonSubTypes;
 import com.fasterxml.jackson.annotation.JsonTypeInfo;
+import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset;
 import jakarta.annotation.Nullable;
 
 import java.util.List;
@@ -16,12 +17,11 @@
 // - The name is set in the 'type' property
 // - For each possible Concept type, here is what the 'type' property will be
 @JsonTypeInfo(use = JsonTypeInfo.Id.NAME, property = "type")
-@JsonSubTypes({
-    @JsonSubTypes.Type(value = ContinuousConcept.class, name = "Continuous"),
-    @JsonSubTypes.Type(value = CategoricalConcept.class, name = "Categorical"),
-})
-public sealed interface Concept
-    permits CategoricalConcept, ConceptShell, ContinuousConcept {
+@JsonSubTypes(
+    {@JsonSubTypes.Type(value = ContinuousConcept.class, name = "Continuous"),
+        @JsonSubTypes.Type(value = CategoricalConcept.class, name = "Categorical"),}
+)
+public sealed interface Concept permits CategoricalConcept, ConceptShell, ContinuousConcept {
 
     /**
      * @return The complete concept path for this concept (// delimited)
@@ -53,7 +53,7 @@ public sealed interface Concept
 
     Concept table();
 
-    Concept study();
+    Dataset study();
 
     Map<String, String> meta();
 
@@ -68,7 +68,7 @@ default boolean allowFiltering() {
 
     Concept withTable(Concept table);
 
-    Concept withStudy(Concept study);
+    Concept withStudy(Dataset study);
 
     default boolean conceptEquals(Object object) {
         if (this == object) return true;

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

@@ -1,5 +1,6 @@
 package edu.harvard.dbmi.avillach.dictionary.concept.model;
 
+import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset;
 import jakarta.annotation.Nullable;
 
 import java.util.List;
@@ -33,7 +34,7 @@ public Concept table() {
     }
 
     @Override
-    public Concept study() {
+    public Dataset study() {
         return null;
     }
 
@@ -58,7 +59,7 @@ public Concept withTable(Concept table) {
     }
 
     @Override
-    public Concept withStudy(Concept study) {
+    public Concept withStudy(Dataset study) {
         return this;
     }
 

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

@@ -1,6 +1,7 @@
 package edu.harvard.dbmi.avillach.dictionary.concept.model;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
+import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset;
 import jakarta.annotation.Nullable;
 
 import java.util.ArrayList;
@@ -11,32 +12,24 @@
 public record ContinuousConcept(
     String conceptPath, String name, String display, String dataset, String description, boolean allowFiltering,
 
-    @Nullable Float min, @Nullable Float max,  String studyAcronym,
-    Map<String, String> meta,
-    @Nullable
-    List<Concept> children,
+    @Nullable Float min, @Nullable Float max, String studyAcronym, Map<String, String> meta, @Nullable List<Concept> children,
 
-    @Nullable
-    Concept table,
+    @Nullable Concept table,
 
-    @Nullable
-    Concept study
+    @Nullable Dataset study
 ) implements Concept {
 
     public ContinuousConcept(
-        String conceptPath, String name, String display, String dataset, String description, boolean allowFiltering,
-        @Nullable Float min, @Nullable Float max,  String studyAcronym, Map<String, String> meta, @Nullable List<Concept> children
+        String conceptPath, String name, String display, String dataset, String description, boolean allowFiltering, @Nullable Float min,
+        @Nullable Float max, String studyAcronym, Map<String, String> meta, @Nullable List<Concept> children
     ) {
-        this(
-            conceptPath, name, display, dataset, description, allowFiltering,
-            min, max, studyAcronym, meta, children, null, null
-        );
+        this(conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, children, null, null);
     }
 
     public ContinuousConcept(ContinuousConcept core, Map<String, String> meta) {
         this(
-            core.conceptPath, core.name, core.display, core.dataset, core.description, core.allowFiltering,
-            core.min, core.max, core.studyAcronym, meta, core.children
+            core.conceptPath, core.name, core.display, core.dataset, core.description, core.allowFiltering, core.min, core.max,
+            core.studyAcronym, meta, core.children
         );
     }
 
@@ -45,8 +38,8 @@ public ContinuousConcept(String conceptPath, String dataset) {
     }
 
     public ContinuousConcept(
-        String conceptPath, String name, String display, String dataset, String description, boolean allowFiltering,
-        @Nullable Float min, @Nullable Float max,  String studyAcronym, Map<String, String> meta
+        String conceptPath, String name, String display, String dataset, String description, boolean allowFiltering, @Nullable Float min,
+        @Nullable Float max, String studyAcronym, Map<String, String> meta
     ) {
         this(conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, null);
     }
@@ -67,16 +60,14 @@ public ContinuousConcept withChildren(List<Concept> children) {
     @Override
     public Concept withTable(Concept table) {
         return new ContinuousConcept(
-            conceptPath, name, display, dataset, description, allowFiltering,
-            min, max, studyAcronym, meta, children, table, study
+            conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, children, table, study
         );
     }
 
     @Override
-    public Concept withStudy(Concept study) {
+    public Concept withStudy(Dataset study) {
         return new ContinuousConcept(
-            conceptPath, name, display, dataset, description, allowFiltering,
-            min, max, studyAcronym, meta, children, table, study
+            conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, children, table, study
         );
     }
 

src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/Dataset.java

@@ -0,0 +1,16 @@
+package edu.harvard.dbmi.avillach.dictionary.dataset;
+
+import jakarta.annotation.Nullable;
+
+import java.util.Map;
+
+public record Dataset(String ref, String fullName, String abbreviation, String description, @Nullable Map<String, String> meta) {
+
+    public Dataset(String ref, String fullName, String abbreviation, String description) {
+        this(ref, fullName, abbreviation, description, null);
+    }
+
+    public Dataset withMeta(Map<String, String> meta) {
+        return new Dataset(ref, fullName, abbreviation, description, meta);
+    }
+}

src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetMapper.java

@@ -0,0 +1,15 @@
+package edu.harvard.dbmi.avillach.dictionary.dataset;
+
+import org.springframework.jdbc.core.RowMapper;
+import org.springframework.stereotype.Component;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+
+@Component
+public class DatasetMapper implements RowMapper<Dataset> {
+    @Override
+    public Dataset mapRow(ResultSet rs, int rowNum) throws SQLException {
+        return new Dataset(rs.getString("ref"), rs.getString("full_name"), rs.getString("abbreviation"), rs.getString("description"));
+    }
+}