DDP-7121 | add filter parser to handle numeric values in the same man…

…ner as text values

src/main/java/org/broadinstitute/dsm/model/elastic/export/parse/BaseParser.java

@@ -11,6 +11,7 @@ public abstract class BaseParser implements Parser {
 
     @Override
     public Object parse(String value) {
+        value = convertString(value);
         Object result = forString(value);
         if (StringUtils.isNumeric(value)) {
             result = forNumeric(value);
@@ -77,8 +78,12 @@ public String convertBoolean(String value) {
     }
 
     public String convertString(String value) {
-        if (value.charAt(0) == '\'' && value.charAt(value.length() - 1) == '\'')
+        if (isWrappedByChar(value))
             return value.substring(1, value.length() - 1);
         return value;
     }
+
+    private boolean isWrappedByChar(String value) {
+        return StringUtils.isNotBlank(value) && value.charAt(0) == '\'' && value.charAt(value.length() - 1) == '\'';
+    }
 }

src/main/java/org/broadinstitute/dsm/model/elastic/filter/CollectionQueryBuilder.java

@@ -1,27 +1,29 @@
 package org.broadinstitute.dsm.model.elastic.filter;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.lucene.search.Query;
 import org.apache.lucene.search.join.ScoreMode;
 import org.broadinstitute.dsm.model.Filter;
 import org.broadinstitute.dsm.model.elastic.Util;
+import org.broadinstitute.dsm.model.elastic.export.parse.Parser;
 import org.elasticsearch.index.query.*;
 
 import java.util.*;
 
 public class CollectionQueryBuilder extends DsmAbstractQueryBuilder {
 
-    public CollectionQueryBuilder(String filter) {
-        super(filter);
+    public CollectionQueryBuilder(String filter, Parser parser) {
+        super(filter, parser);
     }
 
+    public CollectionQueryBuilder() {}
+
     @Override
     public AbstractQueryBuilder build() {
         Map<String, List<String>> parsedFilters = parseFiltersByLogicalOperators();
         BoolQueryBuilder boolQueryBuilder = new BoolQueryBuilder();
         for (Map.Entry<String, List<String>> parsedFilter: parsedFilters.entrySet()) {
             List<String> filterValues = parsedFilter.getValue();
-            if (parsedFilter.getKey().equals(Filter.AND)) {
+            if (parsedFilter.getKey().equals(Filter.AND_TRIMMED)) {
                 buildUpNestedQuery(boolQueryBuilder, filterValues, BoolQueryBuilder::must);
             } else {
                 buildUpNestedQuery(boolQueryBuilder, filterValues, BoolQueryBuilder::should);
@@ -37,7 +39,7 @@ private void buildUpNestedQuery(BoolQueryBuilder boolQueryBuilder, List<String>
             splitter.setFilter(filterValue);
             String outerProperty = Util.TABLE_ALIAS_MAPPINGS.get(splitter.getAlias()).getPropertyName(); //medicalRecord
             String nestedPath = DSM_WITH_DOT + outerProperty;
-            QueryPayload queryPayload = new QueryPayload(nestedPath + "." + splitter.getInnerProperty(), splitter.getValue());
+            QueryPayload queryPayload = new QueryPayload(nestedPath + "." + splitter.getInnerProperty(), parser.parse(splitter.getValue()));
             QueryBuilder queryBuilder = QueryBuilderFactory.buildQueryBuilder(operator, queryPayload);
             filterStrategy.build(boolQueryBuilder, new NestedQueryBuilder(nestedPath, queryBuilder, ScoreMode.Avg));
         }

src/main/java/org/broadinstitute/dsm/model/elastic/filter/DsmAbstractQueryBuilder.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.dsm.model.elastic.filter;
 
+import org.broadinstitute.dsm.model.elastic.export.parse.Parser;
 import org.broadinstitute.dsm.statics.DBConstants;
 import org.broadinstitute.dsm.statics.ESObjectConstants;
 import org.elasticsearch.index.query.AbstractQueryBuilder;
@@ -8,10 +9,22 @@ public abstract class DsmAbstractQueryBuilder {
 
     protected static final String DSM_WITH_DOT = ESObjectConstants.DSM + DBConstants.ALIAS_DELIMITER;
     protected String filter;
+    protected Parser parser;
 
-    public DsmAbstractQueryBuilder(String filter) {
+    public DsmAbstractQueryBuilder(String filter, Parser parser) {
+        this.parser = parser;
         this.filter = filter;
     }
 
+    public DsmAbstractQueryBuilder() {}
+
+    public void setFilter(String filter) {
+        this.filter = filter;
+    }
+
+    public void setParser(Parser parser) {
+        this.parser = parser;
+    }
+
     public abstract AbstractQueryBuilder build();
 }

src/main/java/org/broadinstitute/dsm/model/elastic/filter/FilterParser.java

@@ -0,0 +1,11 @@
+package org.broadinstitute.dsm.model.elastic.filter;
+
+import org.broadinstitute.dsm.model.elastic.export.parse.ValueParser;
+
+public class FilterParser extends ValueParser {
+
+    @Override
+    protected Object forNumeric(String value) {
+        return value;
+    }
+}

src/test/java/org/broadinstitute/dsm/model/elastic/export/parse/BaseParserTest.java

@@ -27,7 +27,13 @@ public void isBoolean() {
     @Test
     public void parse() {
         String value = "'15'";
+        String value1 = "'ASCProject_PZ8GJC_SALIVA'";
+        String value2 = "'2015-01-01'";
         String convertedValue = valueParser.convertString(value);
+        String convertedValue1 = valueParser.convertString(value1);
+        String convertedValue2 = valueParser.convertString(value2);
         Assert.assertEquals("15", convertedValue);
+        Assert.assertEquals("ASCProject_PZ8GJC_SALIVA", convertedValue1);
+        Assert.assertEquals("2015-01-01", convertedValue2);
     }
 }

src/test/java/org/broadinstitute/dsm/model/elastic/filter/CollectionQueryBuilderTest.java

@@ -1,22 +1,34 @@
 package org.broadinstitute.dsm.model.elastic.filter;
 
-import org.apache.lucene.search.join.ScoreMode;
-import org.elasticsearch.index.query.*;
-import org.junit.Assert;
-import org.junit.Test;
-
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
-import static org.junit.Assert.*;
+import org.apache.lucene.search.join.ScoreMode;
+import org.elasticsearch.index.query.AbstractQueryBuilder;
+import org.elasticsearch.index.query.BoolQueryBuilder;
+import org.elasticsearch.index.query.ExistsQueryBuilder;
+import org.elasticsearch.index.query.MatchQueryBuilder;
+import org.elasticsearch.index.query.NestedQueryBuilder;
+import org.elasticsearch.index.query.RangeQueryBuilder;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
 
 public class CollectionQueryBuilderTest {
 
+    static CollectionQueryBuilder collectionQueryBuilder;
+
+    @BeforeClass
+    public static void setUp() {
+        collectionQueryBuilder = new CollectionQueryBuilder();
+        collectionQueryBuilder.setParser(new FilterParser());
+    }
+
     @Test
     public void parseFiltersByLogicalOperators() {
         String filter = "AND m.medicalRecordId = '15' OR m.medicalRecordSomething LIKE '55555' OR m.medicalRecordSomethingg = '55552' AND m.dynamicFields.ragac = '55' OR m.medicalRecordName = '213'";
-        CollectionQueryBuilder collectionQueryBuilder = new CollectionQueryBuilder(filter);
+        collectionQueryBuilder.setFilter(filter);
         Map<String, List<String>> parsedFilters = collectionQueryBuilder.parseFiltersByLogicalOperators();
         for (Map.Entry<String, List<String>> eachFilter: parsedFilters.entrySet()) {
             if (eachFilter.getKey().equals("AND")) {
@@ -33,9 +45,8 @@ public void collectionBuild() {
 
         String filter = "AND m.medicalRecordId = '15' AND m.type = 'PHYSICIAN' OR k.bspCollaboratorSampleId = 'ASCProject_PZ8GJC_SALIVA'";
 
-        DsmAbstractQueryBuilder dsmAbstractQueryBuilder = new CollectionQueryBuilder(filter);
-
-        AbstractQueryBuilder actual = dsmAbstractQueryBuilder.build();
+        collectionQueryBuilder.setFilter(filter);
+        AbstractQueryBuilder actual = collectionQueryBuilder.build();
 
         AbstractQueryBuilder<BoolQueryBuilder> expected = new BoolQueryBuilder().must(new NestedQueryBuilder("dsm.medicalRecord", new MatchQueryBuilder("dsm.medicalRecord.medicalRecordId", "15"), ScoreMode.Avg))
                 .must(new NestedQueryBuilder("dsm.medicalRecord", new MatchQueryBuilder("dsm.medicalRecord.type", "PHYSICIAN"), ScoreMode.Avg))
@@ -49,9 +60,8 @@ public void collectionBuild2() {
 
         String filter = "AND m.medicalRecordId >= '15' AND m.type LIKE 'PHYSICIAN' OR k.bspCollaboratorSampleId = 'ASCProject_PZ8GJC_SALIVA' AND t.returnDate <= '2015-01-01' AND p.participantId IS NOT NULL";
 
-        DsmAbstractQueryBuilder dsmAbstractQueryBuilder = new CollectionQueryBuilder(filter);
-
-        AbstractQueryBuilder actual = dsmAbstractQueryBuilder.build();
+        collectionQueryBuilder.setFilter(filter);
+        AbstractQueryBuilder actual = collectionQueryBuilder.build();
 
         AbstractQueryBuilder<BoolQueryBuilder> expected = new BoolQueryBuilder().must(new NestedQueryBuilder("dsm.medicalRecord", new RangeQueryBuilder("dsm.medicalRecord.medicalRecordId").gte("15"), ScoreMode.Avg))
                 .must(new NestedQueryBuilder("dsm.medicalRecord", new MatchQueryBuilder("dsm.medicalRecord.type", "PHYSICIAN"), ScoreMode.Avg))
@@ -67,9 +77,8 @@ public void collectionBuildAgeRange() {
 
         String filter = "AND m.age >= '15' AND m.age <= '30'";
 
-        DsmAbstractQueryBuilder dsmAbstractQueryBuilder = new CollectionQueryBuilder(filter);
-
-        AbstractQueryBuilder actual = dsmAbstractQueryBuilder.build();
+        collectionQueryBuilder.setFilter(filter);
+        AbstractQueryBuilder actual = collectionQueryBuilder.build();
 
         AbstractQueryBuilder<BoolQueryBuilder> expected = new BoolQueryBuilder().must(new NestedQueryBuilder("dsm.medicalRecord",
                         new RangeQueryBuilder("dsm.medicalRecord.age").gte("15"), ScoreMode.Avg))
@@ -84,12 +93,11 @@ public void collectionBuildBoolean() {
 
         String filter = "AND m.followUp LIKE '1'";
 
-        DsmAbstractQueryBuilder dsmAbstractQueryBuilder = new CollectionQueryBuilder(filter);
-
-        AbstractQueryBuilder actual = dsmAbstractQueryBuilder.build();
+        collectionQueryBuilder.setFilter(filter);
+        AbstractQueryBuilder actual = collectionQueryBuilder.build();
 
         AbstractQueryBuilder<BoolQueryBuilder> expected = new BoolQueryBuilder().must(new NestedQueryBuilder("dsm.medicalRecord",
-                        new MatchQueryBuilder("dsm.medicalRecord.followUp", "'1'"), ScoreMode.Avg));
+                        new MatchQueryBuilder("dsm.medicalRecord.followUp", "1"), ScoreMode.Avg));
 
         Assert.assertEquals(expected, actual);
     }