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TASK-5610 Create the CVDB endpoint analysis/clinical/cvdb/variant/summary and overwrite analysis/clinical/variant #102

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TASK-5610 Create the CVDB endpoint analysis/clinical/cvdb/variant/summary and overwrite analysis/clinical/variant #102

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3a6e5a9
solr: implement ORDER (asc and desc) for Solr facets, #TASK-7260, #TA…
jtarraga Dec 5, 2024
6f74a1f
datastore: fix order option in the facet query parser, #TASK-7260, #T…
jtarraga Jan 14, 2025
d6460be
Merge branch 'develop' into TASK-5610
jtarraga Jan 14, 2025
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2 changes: 2 additions & 0 deletions .../commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/QueryOptions.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,9 @@ public class QueryOptions extends ObjectMap {

public static final String SORT = "sort";
public static final String ORDER = "order";
public static final String ASC = "asc";
public static final String ASCENDING = "ascending";
public static final String DESC = "desc";
public static final String DESCENDING = "descending";

public static final String TIMEOUT = "timeout";
Expand Down
13 changes: 5 additions & 8 deletions ...astore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java
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Expand Up @@ -28,10 +28,7 @@
import org.opencb.commons.datastore.core.ComplexTypeConverter;
import org.opencb.commons.datastore.core.QueryOptions;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.*;
import java.util.concurrent.*;

import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.getProjection;
Expand Down Expand Up @@ -180,8 +177,8 @@ public FindIterable<Document> nativeFind(ClientSession clientSession, Bson query
if (sortObject instanceof Bson) {
findIterable.sort(((Bson) sortObject));
} else if (sortObject instanceof String) {
String order = options.getString(QueryOptions.ORDER, "DESC");
if (order.equalsIgnoreCase(QueryOptions.ASCENDING) || order.equalsIgnoreCase("ASC")
String order = options.getString(QueryOptions.ORDER, QueryOptions.DESC.toUpperCase(Locale.ROOT));
if (order.equalsIgnoreCase(QueryOptions.ASCENDING) || order.equalsIgnoreCase(QueryOptions.ASC)
|| order.equals("1")) {
findIterable.sort(Sorts.ascending(((String) sortObject)));
} else {
Expand All @@ -199,9 +196,9 @@ public FindIterable<Document> nativeFind(ClientSession clientSession, Bson query
order = fieldArray[1];
} else if (fieldArray.length == 1) {
sortField = field;
order = options.getString(QueryOptions.ORDER, "DESC");
order = options.getString(QueryOptions.ORDER, QueryOptions.DESC.toUpperCase(Locale.ROOT));
}
if (QueryOptions.ASCENDING.equalsIgnoreCase(order) || "ASC".equalsIgnoreCase(order)
if (QueryOptions.ASCENDING.equalsIgnoreCase(order) || QueryOptions.ASC.equalsIgnoreCase(order)
|| "1".equals(order)) {
sortedList.add(Sorts.ascending(sortField));
} else {
Expand Down
9 changes: 3 additions & 6 deletions ...tastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBQueryUtils.java
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Expand Up @@ -27,10 +27,7 @@
import java.time.LocalDateTime;
import java.time.ZoneId;
import java.time.format.DateTimeFormatter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

Expand Down Expand Up @@ -668,8 +665,8 @@ public static Bson getSort(QueryOptions options) {
if (sortObject instanceof Bson) {
return Aggregates.sort((Bson) sortObject);
} else if (sortObject instanceof String) {
String order = options.getString(QueryOptions.ORDER, "DESC");
if (order.equalsIgnoreCase(QueryOptions.ASCENDING) || order.equalsIgnoreCase("ASC") || order.equals("1")) {
String order = options.getString(QueryOptions.ORDER, QueryOptions.DESC.toUpperCase(Locale.ROOT));
if (order.equalsIgnoreCase(QueryOptions.ASCENDING) || order.equalsIgnoreCase(QueryOptions.ASC) || order.equals("1")) {
return Aggregates.sort(Sorts.ascending((String) sortObject));
} else {
return Aggregates.sort(Sorts.descending((String) sortObject));
Expand Down
7 changes: 4 additions & 3 deletions ...ore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/MongoDBCollectionTest.java
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Expand Up @@ -164,7 +164,7 @@ public void testDistinct() throws Exception {
public void testSortOrder() throws Exception {
Document query = new Document();
QueryOptions queryOptions = new QueryOptions(QueryOptions.LIMIT, 10).append(QueryOptions.SORT, "number")
.append(QueryOptions.ORDER, "asc");
.append(QueryOptions.ORDER, QueryOptions.ASC);
List<Document> result = mongoDBCollection.find(query, queryOptions).getResults();
assertEquals(0L, result.get(0).get("number"));
}
Expand All @@ -173,8 +173,9 @@ public void testSortOrder() throws Exception {
public void testMultipleSortOrder() throws Exception {
Document query = new Document();
QueryOptions queryOptions = new QueryOptions(QueryOptions.LIMIT, 500)
.append(QueryOptions.SORT, Arrays.asList("age:ASC", "number:DESC"))
.append(QueryOptions.ORDER, "asc");
.append(QueryOptions.SORT, Arrays.asList("age:" + QueryOptions.ASC.toUpperCase(Locale.ROOT),
"number:" + QueryOptions.DESC.toUpperCase(Locale.ROOT)))
.append(QueryOptions.ORDER, QueryOptions.ASC);
int age = 0;
long number = Long.MAX_VALUE;
List<Document> result = mongoDBCollection.find(query, queryOptions).getResults();
Expand Down
28 changes: 28 additions & 0 deletions ...mons-datastore-solr/src/main/java/org/opencb/commons/datastore/solr/FacetQueryParser.java
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Expand Up @@ -25,6 +25,8 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import static org.opencb.commons.datastore.core.QueryOptions.*;

public class FacetQueryParser {

public static final String FACET_SEPARATOR = ";";
Expand Down Expand Up @@ -252,6 +254,7 @@ private Map<String, Object> parseFacet(String facet, QueryOptions options) throw
auxMap.put("type", "terms");
setTermLimit(matcher.group(3), options, auxMap);
setTermSkip(options, auxMap);
setTermOrder(options, auxMap);

Map<String, Object> tmpMap = new HashMap<>();
tmpMap.put(matcher.group(1), auxMap);
Expand All @@ -261,6 +264,7 @@ private Map<String, Object> parseFacet(String facet, QueryOptions options) throw
outputMap.put("type", "terms");
setTermLimit(matcher.group(3), options, outputMap);
setTermSkip(options, outputMap);
setTermOrder(options, outputMap);
}
} else {
throw new Exception("Invalid categorical facet: " + facet);
Expand Down Expand Up @@ -290,6 +294,30 @@ private void setTermSkip(QueryOptions options, Map<String, Object> map) {
}
}

private void setTermOrder(QueryOptions options, Map<String, Object> map) throws Exception {
if (options.containsKey(QueryOptions.ORDER)) {
String order = options.getString(QueryOptions.ORDER);
switch (order.toLowerCase(Locale.ROOT)) {
case ASC:
case ASCENDING: {
map.put("sort", "count asc");
break;
}
case DESC:
case DESCENDING: {
map.put("sort", "count desc");
break;
}
default: {
throw new Exception("Invalid order value: '" + order + "'. Valid values are: "
+ StringUtils.join(Arrays.asList(ASC, ASCENDING, DESC, DESCENDING)));
}
}
} else {
map.put("sort", "count desc");
}
}

private void parseNestedFacet(String nestedFacet, QueryOptions options, Map<String, Object> jsonFacet)
throws Exception {
String[] split = nestedFacet.split(NESTED_FACET_SEPARATOR);
Expand Down
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