start sorting feature

alliance-genome · Mar 4, 2024 · 63b9a5d · 63b9a5d
1 parent 5549455
commit 63b9a5d
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Showing 5 changed files with 44 additions and 5 deletions.
diff --git a/agr_api/src/main/java/org/alliancegenome/api/service/DiseaseESService.java b/agr_api/src/main/java/org/alliancegenome/api/service/DiseaseESService.java
@@ -390,10 +390,23 @@ public JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsWi
 		bool2.should(new MatchQueryBuilder("parentSlimIDs.keyword", diseaseID));
 
 		// create histogram of select columns of unfiltered query
-
 		addTableFilter(pagination, bool);
-		LinkedHashMap <String, SortOrder> sortingMap = new LinkedHashMap<>();
-		sortingMap.put("phylogeneticSortingIndex", SortOrder.ASC);
+
+		// Sorting sets for different names of the sorting selection box
+		Map<String, List<String>> sortingSetMap = new HashMap<>();
+		sortingSetMap.put("default", List.of("phylogeneticSortingIndex",
+			"subject.geneSymbol.displayText.keyword"));
+		sortingSetMap.put("gene", List.of("subject.geneSymbol.displayText.keyword", "phylogeneticSortingIndex"));
+		sortingSetMap.put("disease", List.of("object.name.keyword", "phylogeneticSortingIndex","subject.geneSymbol.displayText.keyword"));
+		sortingSetMap.put("species", List.of("subject.taxon.name.keyword", "subject.geneSymbol.displayText.keyword"));
+
+		LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();
+
+		List<String> sortFields = sortingSetMap.get(pagination.getSortBy());
+		if (sortFields == null) {
+			sortFields = sortingSetMap.get("default");
+		}
+		sortFields.forEach(sortField -> sortingMap.put(sortField, SortOrder.ASC));
 
 		SearchResponse searchResponse = getSearchResponse(bool, pagination, sortingMap, debug);
 

diff --git a/...n/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java b/...n/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java
@@ -142,6 +142,7 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationViaOrthol
 						stringListMap.forEach((basedOnGenesList, diseaseAnnotations1) -> {
 							DiseaseAnnotation diseaseAnnotation = diseaseAnnotations1.get(0);
 							GeneDiseaseAnnotationDocument gdad = new GeneDiseaseAnnotationDocument();
+							gdad.setViaOrthologyAnnotation(true);
 							gdad.setSubject(gene);
 							gdad.setRelation(associationType);
 							String generatedRelationString = getGeneratedRelationString(gdad.getRelation().getName(), diseaseAnnotation.getNegated());

diff --git a/...va/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java b/...va/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java
@@ -44,7 +44,7 @@ public List<GeneDiseaseAnnotation> getFiltered() {
 		params.put("internal", false);
 		params.put("obsolete", false);
 		//params.put("subject.curie", "MGI:2140175");
-		// params.put("subject.curie", "HGNC:6893");
+		//params.put("subject.curie", "HGNC:13625");
 //		params.put("subject.curie", "HGNC:40");
 
 		do {

diff --git a/agr_java_core/src/main/java/org/alliancegenome/api/entity/GeneDiseaseAnnotationDocument.java b/agr_java_core/src/main/java/org/alliancegenome/api/entity/GeneDiseaseAnnotationDocument.java
@@ -1,5 +1,7 @@
 package org.alliancegenome.api.entity;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import com.fasterxml.jackson.annotation.JsonView;
 import lombok.Data;
@@ -18,4 +20,26 @@ public class GeneDiseaseAnnotationDocument extends DiseaseAnnotationDocument {
 	public GeneDiseaseAnnotationDocument() {
 		setCategory("gene_disease_annotation");
 	}
+
+	// 1 true
+	// 0 false
+	@JsonIgnore
+	private boolean isViaOrthologyAnnotation;
+
+	@JsonView({View.DiseaseAnnotationAll.class})
+	@JsonProperty("viaOrthologyOrder")
+	public int getViaOrthologyOrder() {
+		return isViaOrthologyAnnotation ? 1 : 0;
+	}
+
+	@JsonView({View.DiseaseAnnotationAll.class})
+	@JsonProperty("viaOrthologyOrder")
+	public void setViaOrthologyOrder(int order) {
+		isViaOrthologyAnnotation = order == 1;
+	}
+
+	@Override
+	public String toString() {
+		return subject.getCurie() + " | " + getRelation().getName() + " | " + getObject().getCurie();
+	}
 }
diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java b/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java
@@ -114,7 +114,8 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
 		new FieldBuilder(builder, "soTermName", "text").keyword().letterText().build();
 		new FieldBuilder(builder, "soTermId", "keyword").build();
 		new FieldBuilder(builder, "species", "text").keyword().synonym().sort().build();
-
+		new FieldBuilder(builder, "displayText", "text").keyword().sort().build();
+
 		// speciesOrder will generate properly and it will be of type: long
 
 		// new FieldBuilder(builder, "stage", "text").keyword().build();