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TASK-7881 - Can't filter by "not equals" with an "AND" operator #120

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Merged
merged 2 commits into from
Aug 20, 2025
Merged

TASK-7881 - Can't filter by "not equals" with an "AND" operator #120

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77f2812
datastore: add smart splitter that would consider quotes, #TASK-7881
pfurio Aug 12, 2025
6a637e3
Merge branch 'release-6.x.x' into TASK-7881
pfurio Aug 12, 2025
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1 change: 0 additions & 1 deletion ...ore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/ObjectMap.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,6 @@ public class ObjectMap implements Map<String, Object>, Serializable {

private static final Pattern KEY_SPLIT_PATTERN = Pattern.compile("(^[^\\[\\].]+(?:\\[[^\\]]+\\])?)(?:\\.(.*))*");
private static final Pattern LIST_FILTER_PATTERN = Pattern.compile("([^\\[\\]]+)\\[([^=]*?)(?:[=]?)([^=]+)\\]$");
public static final Pattern COMMA_SEPARATED_LIST_SPLIT_PATTERN = Pattern.compile("((?:(?!,\\S).)+)+");

public ObjectMap() {
objectMap = new LinkedHashMap<>();
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31 changes: 0 additions & 31 deletions ...commons-datastore-core/src/test/java/org/opencb/commons/datastore/core/ObjectMapTest.java
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Expand Up @@ -263,35 +263,4 @@ public void testGetWithFilterFromList() {
assertEquals("CGHI", objectMap.get("nestedList[nested.value=G].nested.list[id=Cghi].name"));
}

@Test
public void testPatternListSplit() {
List<String> originalValues = Arrays.asList("disorder1", "disorder2, blabla", "disorder3");
objectMap.put("key", StringUtils.join(originalValues, ","));
objectMap.put("key1", "");
objectMap.put("key2", "my value");
objectMap.put("key3", Arrays.asList("1", "2"));
objectMap.put("key4", Arrays.asList(1, 2));

List<String> values = objectMap.getAsStringList("key", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
assertEquals(originalValues.size(), values.size());
assertTrue(originalValues.containsAll(values));

values = objectMap.getAsStringList("key1", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
assertEquals(1, values.size());
assertEquals("", values.get(0));

values = objectMap.getAsStringList("key2", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
assertEquals(1, values.size());
assertEquals("my value", values.get(0));

values = objectMap.getAsStringList("key3", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
assertEquals(2, values.size());
assertEquals("1", values.get(0));
assertEquals("2", values.get(1));

values = objectMap.getAsStringList("key4", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
assertEquals(2, values.size());
assertEquals("1", values.get(0));
assertEquals("2", values.get(1));
}
}
58 changes: 55 additions & 3 deletions ...tastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBQueryUtils.java
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Expand Up @@ -36,9 +36,9 @@

import static com.mongodb.client.model.Aggregates.*;
import static com.mongodb.client.model.Projections.*;
import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.*;
import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.bucket;
import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.count;
import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.*;

/**
* Created by imedina on 17/01/16.
Expand Down Expand Up @@ -178,6 +178,53 @@ public static Bson createFilter(String mongoDbField, String queryParam, Query qu
return filter;
}

/**
* Splits a string by the given separator, handling quoted values properly.
* Quoted values can contain the separator character without being split.
* Removes surrounding quotes and trims whitespace from each value.
*
* @param input the input string to split
* @param separator the separator to split by ("," or ";")
* @return list of trimmed, unquoted values
*/
public static List<String> smartSplit(String input, String separator) {
List<String> result = new ArrayList<>();
if (input == null || input.isEmpty()) {
return result;
}

boolean inQuotes = false;
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What if there are unbalanced quotes?

"value1","value 2","value3

StringBuilder currentValue = new StringBuilder();

for (int i = 0; i < input.length(); i++) {
char c = input.charAt(i);

if (c == '"') {
inQuotes = !inQuotes;
} else if (!inQuotes && input.substring(i).startsWith(separator)) {
// Found separator outside quotes
String value = currentValue.toString().trim();
if (value.startsWith("\"") && value.endsWith("\"") && value.length() > 1) {
value = value.substring(1, value.length() - 1);
}
result.add(value.trim());
currentValue = new StringBuilder();
i += separator.length() - 1; // Skip the separator
} else {
currentValue.append(c);
}
}

// Add the last value
String value = currentValue.toString().trim();
if (value.startsWith("\"") && value.endsWith("\"") && value.length() > 1) {
value = value.substring(1, value.length() - 1);
}
result.add(value.trim());

return result;
}

private static String getLogicalSeparator(LogicalOperator operator) {
return (operator != null && operator.equals(LogicalOperator.AND)) ? AND : OR;
}
Expand Down Expand Up @@ -258,8 +305,13 @@ protected static String getOp2(String op, String value) {

public static Bson createAutoFilter(String mongoDbField, String queryParam, Query query, QueryParam.Type type, LogicalOperator operator)
throws NumberFormatException {

List<String> queryParamList = query.getAsStringList(queryParam, getLogicalSeparator(operator));
List<String> queryParamList;
String value = query.getString(queryParam);
if (StringUtils.isNotEmpty(value) && value.contains("\"")) {
queryParamList = smartSplit(value, getLogicalSeparator(operator));
} else {
queryParamList = query.getAsStringList(queryParam, getLogicalSeparator(operator));
}
return createAutoFilter(mongoDbField, queryParam, type, operator, queryParamList);
}

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63 changes: 63 additions & 0 deletions ...-datastore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/SmartSplitTest.java
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@@ -0,0 +1,63 @@
package org.opencb.commons.datastore.mongodb;

import org.junit.Test;
import java.util.List;
import static org.junit.Assert.assertEquals;

public class SmartSplitTest {

@Test
public void testSmartSplitWithQuotedCommaValues() {
String input = "\"a \",\" b\",\" c \"";
List<String> result = MongoDBQueryUtils.smartSplit(input, ",");

assertEquals(3, result.size());
assertEquals("a", result.get(0));
assertEquals("b", result.get(1));
assertEquals("c", result.get(2));
}

@Test
public void testSmartSplitWithQuotedSemicolonValues() {
String input = "\"a \";\" b\";\" c \"";
List<String> result = MongoDBQueryUtils.smartSplit(input, ";");

assertEquals(3, result.size());
assertEquals("a", result.get(0));
assertEquals("b", result.get(1));
assertEquals("c", result.get(2));
}

@Test
public void testSmartSplitWithNonQuotedValues() {
String input = "a,b,c";
List<String> result = MongoDBQueryUtils.smartSplit(input, ",");

assertEquals(3, result.size());
assertEquals("a", result.get(0));
assertEquals("b", result.get(1));
assertEquals("c", result.get(2));
}

@Test
public void testSmartSplitWithNonQuotedValuesAndSpaces() {
String input = "a, b,c ";
List<String> result = MongoDBQueryUtils.smartSplit(input, ",");

assertEquals(3, result.size());
assertEquals("a", result.get(0));
assertEquals("b", result.get(1));
assertEquals("c", result.get(2));
}

@Test
public void testSmartSplitWithMixedValues() {
String input = "\"a, with comma\",b,\"c\"";
List<String> result = MongoDBQueryUtils.smartSplit(input, ",");

assertEquals(3, result.size());
assertEquals("a, with comma", result.get(0));
assertEquals("b", result.get(1));
assertEquals("c", result.get(2));
}
}
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