Merge pull request #31 from TheJacksonLaboratory/bugfix/queries

Bugfix/queries
TheJacksonLaboratory · Sep 25, 2024 · 8923412 · 8923412
2 parents f6a71da + 3e3c3f9
commit 8923412
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Showing 11 changed files with 74 additions and 12 deletions.
diff --git a/oan-etl/pom.xml b/oan-etl/pom.xml
@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.jax.oan</groupId>
         <artifactId>ontology-annotation-network</artifactId>
-        <version>1.0.8</version>
+        <version>1.0.9</version>
     </parent>
 
     <artifactId>oan-etl</artifactId>

diff --git a/oan-model/pom.xml b/oan-model/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.jax.oan</groupId>
         <artifactId>ontology-annotation-network</artifactId>
-        <version>1.0.8</version>
+        <version>1.0.9</version>
     </parent>
 
     <artifactId>oan-model</artifactId>

diff --git a/oan-rest/pom.xml b/oan-rest/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.jax.oan</groupId>
         <artifactId>ontology-annotation-network</artifactId>
-        <version>1.0.8</version>
+        <version>1.0.9</version>
     </parent>
 
     <artifactId>oan-rest</artifactId>

diff --git a/oan-rest/src/main/java/org/jax/oan/Application.java b/oan-rest/src/main/java/org/jax/oan/Application.java
@@ -12,7 +12,7 @@
 @OpenAPIDefinition(
     info = @Info(
             title = "ontology-annotation-network",
-            version = "1.0.7",
+            version = "1.0.9",
             description = "A restful service for access to the ontology annotation network.",
             contact = @Contact(name = "Michael Gargano", email = "[email protected]")
     ), servers = {@Server(url = "https://ontology.jax.org/api/network", description = "Production Server URL")

diff --git a/oan-rest/src/main/java/org/jax/oan/controller/SearchController.java b/oan-rest/src/main/java/org/jax/oan/controller/SearchController.java
@@ -16,6 +16,7 @@
 import org.jax.oan.exception.OntologyAnnotationNetworkRuntimeException;
 import org.jax.oan.service.DiseaseService;
 import org.jax.oan.service.SearchService;
+import org.jax.oan.utils.QueryCleaner;
 import org.monarchinitiative.phenol.base.PhenolRuntimeException;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
@@ -46,9 +47,9 @@ public HttpResponse<?> searchEntity(@Schema(minLength = 1, maxLength = 20, type
 											@QueryValue(value = "limit", defaultValue = "10") int limit) {
 
 		if (entity.equalsIgnoreCase("GENE")){
-			return HttpResponse.ok(this.searchService.searchGene(q.toUpperCase(), page, limit));
+			return HttpResponse.ok(this.searchService.searchGene(QueryCleaner.clean(q.toUpperCase()), page, limit));
 		} else if (entity.equalsIgnoreCase("DISEASE")){
-			return HttpResponse.ok(this.searchService.searchDisease(q.toUpperCase(), page, limit));
+			return HttpResponse.ok(this.searchService.searchDisease(QueryCleaner.clean(q.toUpperCase()), page, limit));
 		} else {
 			return HttpResponse.badRequest();
 		}

diff --git a/oan-rest/src/main/java/org/jax/oan/repository/DiseaseRepository.java b/oan-rest/src/main/java/org/jax/oan/repository/DiseaseRepository.java
@@ -39,6 +39,9 @@ public Optional<Disease> findDiseaseById(TermId termId){
 			}
 			return Optional.empty();
 		}
+		catch (Exception e){
+			return Optional.empty();
+		}
 	}
 
 	/**
@@ -57,6 +60,9 @@ public Collection<Disease> findDiseases(String query) {
 				diseases.add(disease);
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return diseases.stream().sorted(Comparator.comparing((Disease d) -> !d.getName().toLowerCase()
 				.startsWith(query.toLowerCase()))).toList();
 	}
@@ -76,6 +82,9 @@ public Collection<Gene> findGenesByDisease(TermId termId) {
 				genes.add(gene);
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return genes;
 	}
 
@@ -97,6 +106,9 @@ public Collection<PhenotypeExtended> findPhenotypesByDisease(TermId termId){
 				phenotypes.add(phenotype);
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return phenotypes;
 	}
 
@@ -130,6 +142,9 @@ public Collection<MedicalActionTargetExtended> findMedicalActionsByDisease(TermI
 				actions.add(new MedicalActionTargetExtended(TermId.of(m.get("id").asString()), m.get("name").asString(), relations, targets ));
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return actions;
 	}
 }
diff --git a/oan-rest/src/main/java/org/jax/oan/repository/GeneRepository.java b/oan-rest/src/main/java/org/jax/oan/repository/GeneRepository.java
@@ -10,10 +10,7 @@
 import org.neo4j.driver.Transaction;
 import org.neo4j.driver.Value;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
+import java.util.*;
 
 import static org.neo4j.driver.Values.parameters;
 
@@ -41,7 +38,10 @@ public Collection<Gene> findGenes(String query){
 					Gene gene = new Gene(TermId.of(value.get("id").asString()), value.get("name").asString());
 					genes.add(gene);
 				}
-			}
+		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return genes.stream().sorted(Comparator.comparing((Gene g) -> !g.getName().toLowerCase()
 				.startsWith(query.toLowerCase()))).toList();
 	}
@@ -60,6 +60,8 @@ public Collection<Phenotype> findPhenotypesByGene(TermId termId){
 				Phenotype phenotype = new Phenotype(TermId.of(value.get("id").asString()), value.get("name").asString());
 				phenotypes.add(phenotype);
 			}
+		} catch (Exception e){
+			return Collections.emptyList();
 		}
 		return phenotypes;
 	}
@@ -80,6 +82,9 @@ public Collection<Disease> findDiseasesByGene(TermId termId) {
 				diseases.add(disease);
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return diseases;
 	}
 }
diff --git a/oan-rest/src/main/java/org/jax/oan/repository/PhenotypeRepository.java b/oan-rest/src/main/java/org/jax/oan/repository/PhenotypeRepository.java
@@ -36,6 +36,9 @@ public Collection<Disease> findDiseasesByTerm(TermId termId){
 				diseases.add(disease);
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return diseases;
 	}
 
@@ -56,6 +59,9 @@ public Collection<Gene> findGenesByTerm(TermId termId) {
 				genes.add(gene);
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return genes;
 	}
 
@@ -75,6 +81,9 @@ public Collection<Assay> findAssaysByTerm(TermId termId){
 				assays.add(assay);
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return assays;
 	}
 
@@ -101,6 +110,9 @@ public Collection<MedicalActionSourceExtended> findMedicalActionsByTerm(TermId t
 				medicalActions.add(new MedicalActionSourceExtended(TermId.of(subject.get("id").asString()), subject.get("name").asString(), relations, sources));
 			}
 		}
+		catch (Exception e){
+			return Collections.emptyList();
+		}
 		return medicalActions;
 	}
 }
diff --git a/oan-rest/src/main/java/org/jax/oan/utils/QueryCleaner.java b/oan-rest/src/main/java/org/jax/oan/utils/QueryCleaner.java
@@ -0,0 +1,13 @@
+package org.jax.oan.utils;
+
+public class QueryCleaner {
+
+	/**
+	 * This method cleans the query string from any special characters
+	 * @param query the query string
+	 * @return the cleaned query string
+	 */
+	public static String clean(String query) {
+		return query.replaceAll("[^a-zA-Z0-9\\-:\\s]", "");
+	}
+}
diff --git a/oan-rest/src/test/java/org/jax/oan/utils/QueryCleanerTest.java b/oan-rest/src/test/java/org/jax/oan/utils/QueryCleanerTest.java
@@ -0,0 +1,16 @@
+package org.jax.oan.utils;
+
+import org.junit.jupiter.api.Test;
+import static org.junit.jupiter.api.Assertions.*;
+
+class QueryCleanerTest {
+
+	@Test
+	void clean() {
+		String query = "HP:0000001";
+		String badQuery = "HP:0000001!)";
+		assertEquals("HP:0000001", QueryCleaner.clean(query));
+		assertEquals("HP:0000001", QueryCleaner.clean(badQuery));
+	}
+
+}
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
   <groupId>org.jax.oan</groupId>
   <artifactId>ontology-annotation-network</artifactId>
   <packaging>pom</packaging>
-  <version>1.0.8</version>
+  <version>1.0.9</version>
 
   <name>ontology-annotation-network</name>
   <url>https://github.com/TheJacksonLaboratory/ontology-annotation-network</url>