Merge pull request #49 from TheJacksonLaboratory/enhancement/schema-s…

…earch

Enhancement/schema search

build.gradle

@@ -1,11 +1,12 @@
 plugins {
-    id("groovy") 
+    id("groovy")
     id("com.github.johnrengelman.shadow") version "8.1.1"
     id("io.micronaut.application") version "4.1.0"
     id("io.micronaut.test-resources") version "4.1.0"
+    id("jacoco")
 }
 
-version = "0.5.8"
+version = "0.5.9"
 group = "org.jacksonlaboratory"
 
 repositories {
@@ -103,5 +104,21 @@ tasks.withType(JavaCompile) {
     options.forkOptions.jvmArgs << "-Dmicronaut.openapi.views.spec=swagger-ui.enabled=true,swagger-ui.theme=flattop,swagger-ui.js.url=/api/${System.env.ONTOLOGY}/docs/res/,swagger-ui.theme.url=/api/${System.env.ONTOLOGY}/docs/,swagger-ui.spec.url=/api/${System.env.ONTOLOGY}/${project.name}-${System.env.ONTOLOGY}-${project.version}.yml".toString()
 }
 
+test {
+    finalizedBy("jacocoTestReport")
+}
+
+jacocoTestReport {
+    dependsOn("test")
+    afterEvaluate {
+        classDirectories.setFrom(files(classDirectories.files.collect {
+            fileTree(dir: it, exclude: [
+                    "org/jacksonlaboratory/view/*",
+                    "org/jacksonlaboratory/Application.class"
+            ])
+        }))
+    }
+}
+
 
 

src/main/java/org/jacksonlaboratory/Application.java

@@ -8,7 +8,7 @@
     info = @Info(
             title = "ontology-service-${ontology}",
             description = "A restful service for the ${ontology} ontology.",
-            version = "0.5.8",
+            version = "0.5.9",
             contact = @Contact(name = "Michael Gargano", email = "[email protected]")
     )
 )

src/main/java/org/jacksonlaboratory/controller/SearchController.java

@@ -31,13 +31,13 @@ public SearchController(TermService termService) {
 	public SearchDto search(
 			@QueryValue("q") @Schema(minLength = 3, maxLength = 250, type = "string", pattern = ".*")  String query,
 			@QueryValue(value = "page", defaultValue = "0") @Schema(maxLength = 1000, type = "number") int page,
-			@QueryValue(value = "limit", defaultValue = "10") @Schema(maxLength = 1, type = "number") int limit
+			@QueryValue(value = "limit", defaultValue = "10") @Schema(maxLength = 1000, type = "number") int limit
 	) {
-		page = page * limit;
 		List<OntologyTerm> terms = this.termService.searchOntologyTerm(query);
 		if (limit == -1) {
 			return new SearchDto(terms,  terms.size());
 		} else {
+			page = page * limit;
 			return new SearchDto(terms.stream().skip(page).limit(limit).collect(Collectors.toList()),  terms.size());
 		}
 	}

src/main/java/org/jacksonlaboratory/controller/TermController.java

@@ -66,4 +66,15 @@ public List<SimpleOntologyTerm> children(@Schema(minLength = 1, maxLength = 20,
         return this.graphService.getChildren(termId);
     }
 
+    /**
+     * Get the descendants of the ontology id
+     * @param id The ontology term id
+     * @return The descendants of the term id
+     */
+    @Get(uri="/{id}/descendants", produces="application/json")
+    public List<SimpleOntologyTerm> descendants(@Schema(minLength = 1, maxLength = 20, type = "string", pattern = ".*") @PathVariable String id){
+        TermId termId = TermId.of(id);
+        return this.graphService.getDescendants(termId);
+    }
+
 }

src/main/java/org/jacksonlaboratory/ingest/BabelonData.java

@@ -4,6 +4,9 @@
 
 import java.util.List;
 
+/**
+ *  A container of term and its babelon (translation) lines
+ */
 public class BabelonData {
 	private final TermId id;
 	private final List<BabelonLine> babelonLines;

src/main/java/org/jacksonlaboratory/ingest/BabelonIngestor.java

@@ -7,6 +7,7 @@
 import java.nio.file.Path;
 import java.util.zip.GZIPInputStream;
 
+
 public interface BabelonIngestor {
 
 	public static BabelonIngestor of() {

src/main/java/org/jacksonlaboratory/ingest/BabelonIngestorDefault.java

@@ -13,6 +13,9 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
+/**
+ * The default implementation of a babelon file file
+ */
 public class BabelonIngestorDefault implements BabelonIngestor {
 	private static final Logger LOGGER = LoggerFactory.getLogger(BabelonIngestorDefault.class);
 

src/main/java/org/jacksonlaboratory/ingest/BabelonLine.java

@@ -7,6 +7,9 @@
 
 import java.util.Objects;
 
+/**
+ * A representation of a line in a babelon (translation) file
+ */
 public class BabelonLine {
 
 	private final Language source_language;

src/main/java/org/jacksonlaboratory/ingest/BabelonNavigator.java

@@ -6,6 +6,9 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
+/**
+ * An access class for getting BabelonData
+ */
 public class BabelonNavigator {
 
 	private final List<BabelonData> babelonData;

src/main/java/org/jacksonlaboratory/ingest/OntologyDataResolver.java

@@ -0,0 +1,59 @@
+package org.jacksonlaboratory.ingest;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.Objects;
+
+/**
+ *  This builds the data directory path and validates required files exist
+ */
+public class OntologyDataResolver {
+		private static final Logger LOGGER = LoggerFactory.getLogger(OntologyDataResolver.class);
+
+		private final Path dataDirectory;
+		private final String ontology;
+
+		public static OntologyDataResolver of(Path dataDirectory, String ontology) throws RuntimeException {
+			return new OntologyDataResolver(dataDirectory, ontology);
+		}
+
+		private OntologyDataResolver(Path dataDirectory, String ontology) throws RuntimeException {
+			Objects.requireNonNull(dataDirectory, "Data directory must not be null!");
+			Objects.requireNonNull(ontology, "Ontology must be defined.");
+			this.dataDirectory = dataDirectory;
+			this.ontology = ontology;
+			validateHpoFiles();
+		}
+
+		private void validateHpoFiles() throws RuntimeException  {
+			boolean error = false;
+			List<Path> requiredFiles = List.of(ontologyJson());
+			for (Path file : requiredFiles) {
+				if (!Files.isRegularFile(file)) {
+					LOGGER.error("Missing required file `{}` in `{}`.", file.toFile().getName(), dataDirectory.toAbsolutePath());
+					error = true;
+				}
+			}
+			if (error) {
+				throw new RuntimeException("Missing one or more required files in OntologyAnnotationNetwork data directory!");
+			}
+		}
+
+
+		public Path dataDirectory() {
+			return dataDirectory;
+		}
+
+		public Path ontologyJson(){
+			return dataDirectory.resolve(String.format("%s-base.json", ontology));
+		}
+
+		public Path babelonFile(){
+		return dataDirectory.resolve(String.format("%s-all.babelon.tsv", ontology));
+	}
+}
+

src/main/java/org/jacksonlaboratory/ingest/TranslationProcessor.java

@@ -9,6 +9,9 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
+/**
+ * Create translations from babelon file
+ */
 public class TranslationProcessor {
 
 	/**

src/main/java/org/jacksonlaboratory/model/dto/SearchDto.java

@@ -3,6 +3,7 @@
 import org.jacksonlaboratory.model.entity.OntologyTerm;
 
 import java.util.List;
+import java.util.Objects;
 
 public class SearchDto {
 	private final List<OntologyTerm> terms;
@@ -20,4 +21,17 @@ public List<OntologyTerm> getTerms() {
 	public int getTotalCount() {
 		return totalCount;
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		SearchDto searchDto = (SearchDto) o;
+		return totalCount == searchDto.totalCount && Objects.equals(terms, searchDto.terms);
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(terms, totalCount);
+	}
 }

src/main/java/org/jacksonlaboratory/model/entity/OntologyTerm.java

@@ -7,17 +7,12 @@
 import io.swagger.v3.oas.annotations.media.ArraySchema;
 import jakarta.persistence.*;
 import org.jacksonlaboratory.model.converter.TermIdAttributeConverter;
-import org.monarchinitiative.phenol.ontology.data.Dbxref;
-import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
-import org.monarchinitiative.phenol.ontology.data.TermSynonym;
 
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.Objects;
-import java.util.function.Predicate;
-import java.util.stream.Collectors;
 
 @NamedNativeQuery(
 		name="searchQuery",
@@ -48,28 +43,31 @@ public class OntologyTerm {
 	private String xrefs;
 
 	@Column(columnDefinition = "int")
-	private int nDescendants;
+	private int descendantCount;
 
 	@Transient
 	private List<Translation> translations;
 
 	@Creator
-	public OntologyTerm(TermId id, String name, String definition, String comment) {
+	public OntologyTerm(TermId id, String name, String definition, String comment, String synonyms, String xrefs, int descendantCount) {
 		this.id = id;
 		this.name = name;
 		this.definition = definition;
 		this.comment = comment;
-		this.synonyms = null;
-		this.xrefs = null;
+		this.synonyms = synonyms;
+		this.xrefs = xrefs;
+		this.descendantCount = descendantCount;
 	}
 
-	public OntologyTerm(Term term) {
-		this.id = term.id();
-		this.name = term.getName();
-		this.definition = term.getDefinition();
-		this.comment = term.getComment();
-		this.synonyms = term.getSynonyms().stream().filter(Predicate.not(TermSynonym::isObsoleteSynonym)).map(TermSynonym::getValue).collect(Collectors.joining(";"));
-		this.xrefs = term.getXrefs().stream().map(Dbxref::getName).collect(Collectors.joining(";"));
+	public OntologyTerm(TermId id, String name, String definition, String comment, String synonyms, String xrefs, int descendantCount, List<Translation> translations) {
+		this.id = id;
+		this.name = name;
+		this.definition = definition;
+		this.comment = comment;
+		this.synonyms = synonyms;
+		this.xrefs = xrefs;
+		this.descendantCount = descendantCount;
+		this.translations = translations;
 	}
 
 	public OntologyTerm() {
@@ -106,7 +104,7 @@ public String getComment() {
 	}
 
 	public int getDescendantCount() {
-		return nDescendants;
+		return descendantCount;
 	}
 
 	@ArraySchema(maxItems = 25)
@@ -133,14 +131,6 @@ public List<Translation> getTranslations() {
 		return translations;
 	}
 
-	public void setTranslation(List<Translation> translations) {
-		this.translations = translations;
-	}
-
-	public void setDescendantCount(int count) {
-		this.nDescendants = count;
-	}
-
 	@Override
 	public boolean equals(Object o) {
 		if (this == o) return true;
@@ -153,4 +143,5 @@ public boolean equals(Object o) {
 	public int hashCode() {
 		return Objects.hash(uid, id, name, definition, comment, synonyms, xrefs, translations);
 	}
+
 }

src/main/java/org/jacksonlaboratory/model/entity/OntologyTermBuilder.java

@@ -0,0 +1,72 @@
+package org.jacksonlaboratory.model.entity;
+
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import java.util.List;
+
+public class OntologyTermBuilder {
+	private TermId id;
+	private String name;
+	private String definition;
+	private String comment;
+	private String synonyms;
+	private String xrefs;
+	private int nDescendants;
+	private List<Translation> translations;
+
+	public OntologyTermBuilder setId(TermId id) {
+		this.id = id;
+		return this;
+	}
+
+	public OntologyTermBuilder setName(String name) {
+		this.name = name;
+		return this;
+	}
+
+	public OntologyTermBuilder setDefinition(String definition) {
+		this.definition = definition;
+		return this;
+	}
+
+	public OntologyTermBuilder setComment(String comment) {
+		this.comment = comment;
+		return this;
+	}
+
+	public OntologyTermBuilder setSynonyms(String synonyms) {
+		this.synonyms = synonyms;
+		return this;
+	}
+
+	public OntologyTermBuilder setXrefs(String xrefs) {
+		this.xrefs = xrefs;
+		return this;
+	}
+
+	public OntologyTermBuilder setDescendantCount(int nDescendants) {
+		this.nDescendants = nDescendants;
+		return this;
+	}
+
+	public OntologyTermBuilder setTranslations(List<Translation> translations) {
+		this.translations = translations;
+		return this;
+	}
+
+	public OntologyTerm createOntologyTerm() {
+		return new OntologyTerm(id, name, definition, comment, synonyms, xrefs, nDescendants, translations);
+	}
+
+	public OntologyTermBuilder fromOntologyTerm(OntologyTerm term) {
+		this.id = term.getTermId();
+		this.name = term.getName();
+		this.definition = term.getDefinition();
+		this.comment = term.getComment();
+		this.synonyms = String.join(";", term.getSynonyms());
+		this.xrefs = String.join(";", term.getXrefs());
+		this.nDescendants = term.getDescendantCount();
+		this.translations = term.getTranslations();
+		return this;
+	}
+}