core: check verstion to use token or apiKey, and use param constants:…

… apiKey, token, dataRelease, #TASK-4791, #TASK-4641

cellbase-client/src/main/java/org/opencb/cellbase/client/rest/ParentRestClient.java

@@ -32,10 +32,13 @@
 import org.opencb.biodata.models.variant.avro.VariantAnnotation;
 import org.opencb.cellbase.client.config.ClientConfiguration;
 import org.opencb.cellbase.client.rest.models.mixin.DrugResponseClassificationMixIn;
-import org.opencb.cellbase.core.api.query.AbstractQuery;
 import org.opencb.cellbase.core.result.CellBaseDataResponse;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
-import org.opencb.commons.datastore.core.*;
+import org.opencb.commons.datastore.core.Event;
+import org.opencb.commons.datastore.core.ObjectMap;
+import org.opencb.commons.datastore.core.Query;
+import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.utils.VersionUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -53,6 +56,8 @@
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 
+import static org.opencb.cellbase.core.ParamConstants.*;
+
 /**
  * Created by imedina on 12/05/16.
  */
@@ -440,28 +445,36 @@ private <U> CellBaseDataResponse<U> restCall(List<String> hosts, String version,
         // Add the last URL part, the 'action' or 'resource'
         callUrl = callUrl.path(resource);
 
+        // Attention: parameter 'token' was renamed to 'apiKey' in CelBase v5.7
+        String apiKeyParam = null;
+        if (VersionUtils.isMinVersion("v5.7", configuration.getVersion())) {
+            apiKeyParam = API_KEY_PARAM;
+        } else if (VersionUtils.isMinVersion("v5.3", configuration.getVersion())) {
+            apiKeyParam = TOKEN_PARAM;
+        }
+
         if (queryOptions != null) {
             for (String s : queryOptions.keySet()) {
                 callUrl = callUrl.queryParam(s, queryOptions.get(s));
             }
             if (assembly != null && StringUtils.isEmpty(queryOptions.getString("assembly"))) {
                 callUrl = callUrl.queryParam("assembly", assembly);
             }
-            if (dataRelease != null && StringUtils.isEmpty(queryOptions.getString(AbstractQuery.DATA_RELEASE_PARAM))) {
-                callUrl = callUrl.queryParam(AbstractQuery.DATA_RELEASE_PARAM, dataRelease);
+            if (dataRelease != null && StringUtils.isEmpty(queryOptions.getString(DATA_RELEASE_PARAM))) {
+                callUrl = callUrl.queryParam(DATA_RELEASE_PARAM, dataRelease);
             }
-            if (apiKey != null && StringUtils.isEmpty(queryOptions.getString(AbstractQuery.API_KEY_PARAM))) {
-                callUrl = callUrl.queryParam(AbstractQuery.API_KEY_PARAM, apiKey);
+            if (apiKeyParam != null && apiKey != null && StringUtils.isEmpty(queryOptions.getString(API_KEY_PARAM))) {
+                callUrl = callUrl.queryParam(apiKeyParam, apiKey);
             }
         } else {
             if (assembly != null) {
                 callUrl = callUrl.queryParam("assembly", assembly);
             }
             if (dataRelease != null) {
-                callUrl = callUrl.queryParam(AbstractQuery.DATA_RELEASE_PARAM, dataRelease);
+                callUrl = callUrl.queryParam(DATA_RELEASE_PARAM, dataRelease);
             }
-            if (apiKey != null) {
-                callUrl = callUrl.queryParam(AbstractQuery.API_KEY_PARAM, apiKey);
+            if (apiKeyParam != null && apiKey != null) {
+                callUrl = callUrl.queryParam(apiKeyParam, apiKey);
             }
         }
 

cellbase-core/src/main/java/org/opencb/cellbase/core/ParamConstants.java

@@ -111,10 +111,18 @@ public Type type() {
             + "or dot notation (e.g. transcripts.biotype).";
     public static final String DEFAULT_VERSION = "v5.5";
     public static final String VERSION_DESCRIPTION = "API version, e.g.: " + DEFAULT_VERSION;
+
+    public static final String DATA_RELEASE_PARAM = "dataRelease";
     public static final String DATA_RELEASE_DESCRIPTION = "Data release. To use the default data release, set this to 0. To get the list"
             + " of available data release, please call the endpoint 'meta/dataReleases'";
-    public static final String API_KEY_DESCRIPTION = "Data token to allow access to licensed/restricted data sources such as"
+
+    public static final String API_KEY_PARAM = "apiKey";
+    public static final String API_KEY_DESCRIPTION = "API key to allow access to licensed/restricted data sources such as"
             + " Cosmic or HGMD";
+    // For backward-compatibility, but it should be deprecated
+    public static final String TOKEN_PARAM = "token";
+
+
     public static final String DEFAULT_ASSEMBLY = "grch38";
     public static final String ASSEMBLY_DESCRIPTION = "Set the reference genome assembly, e.g. grch38. For a full list of "
             + "potentially available assemblies, please call the endpoint 'meta/species'";
@@ -294,8 +302,6 @@ public Type type() {
             + " Exact text matches will be returned";
 
     // ---------------------------------------------
-    public static final String DATA_TOKEN_DESCRIPTION = "Token to allow access to licensed/restricted data sources";
-    public static final String DATA_TOKEN_PARAM = "dataToken";
 
     public static final String SOURCE_DESCRIPTION = "Comma separated list of database sources of the documents to be returned."
             + " Possible values are clinvar or cosmic";

cellbase-core/src/main/java/org/opencb/cellbase/core/api/query/AbstractQuery.java

@@ -33,6 +33,9 @@
 import java.lang.reflect.Field;
 import java.util.*;
 
+import static org.opencb.cellbase.core.ParamConstants.API_KEY_PARAM;
+import static org.opencb.cellbase.core.ParamConstants.DATA_RELEASE_PARAM;
+
 /**
  * Helper object used to construct queries consumed by the dbadapters.
  */
@@ -45,11 +48,6 @@ public abstract class AbstractQuery extends CellBaseQueryOptions {
     //    public static final int DEFAULT_LIMIT = 50;
     public static final int DEFAULT_SKIP = 0;
 
-    public static final String DATA_RELEASE_PARAM = "dataRelease";
-    public static final String API_KEY_PARAM = "apiKey";
-//    @Deprecated
-//    public static final String TOKEN_PARAM = "token";
-
     // list of fields in this class
     private Map<String, Field> classFields;
     // key = transcripts.biotype, value = transcriptsBiotype

cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ClinicalMongoDBAdaptor.java

@@ -26,7 +26,6 @@
 import org.opencb.biodata.models.variant.avro.VariantType;
 import org.opencb.cellbase.core.ParamConstants;
 import org.opencb.cellbase.core.api.ClinicalVariantQuery;
-import org.opencb.cellbase.core.api.query.AbstractQuery;
 import org.opencb.cellbase.core.api.query.ProjectionQueryOptions;
 import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
@@ -46,6 +45,8 @@
 import java.util.*;
 import java.util.function.Consumer;
 
+import static org.opencb.cellbase.core.ParamConstants.DATA_RELEASE_PARAM;
+
 /**
  * Created by fjlopez on 06/12/16.
  */
@@ -103,15 +104,15 @@ public CellBaseDataResult<Long> count(Query query) throws CellBaseException {
         Bson bson = parseQuery(query);
 
         MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
-                (Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
+                (Integer) query.getOrDefault(DATA_RELEASE_PARAM, 0));
         return new CellBaseDataResult<>(mongoDBCollection.count(bson));
     }
 
     public CellBaseDataResult distinct(Query query, String field) throws CellBaseException {
         Bson bson = parseQuery(query);
 
         MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
-                (Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
+                (Integer) query.getOrDefault(DATA_RELEASE_PARAM, 0));
         return new CellBaseDataResult<>(mongoDBCollection.distinct(field, bson));
     }
 
@@ -128,7 +129,7 @@ public CellBaseDataResult<Variant> get(Query query, QueryOptions options) throws
         logger.debug("queryOptions: {}", options.toJson());
 
         MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
-                (Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
+                (Integer) query.getOrDefault(DATA_RELEASE_PARAM, 0));
         return new CellBaseDataResult<>(mongoDBCollection.find(bson, null, Variant.class, parsedOptions));
     }
 
@@ -140,7 +141,7 @@ public CellBaseDataResult nativeGet(Query query, QueryOptions options) throws Ce
         logger.debug("queryOptions: {}", options.toJson());
 
         MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
-                (Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
+                (Integer) query.getOrDefault(DATA_RELEASE_PARAM, 0));
         return new CellBaseDataResult<>(mongoDBCollection.find(bson, parsedOptions));
     }
 
@@ -152,7 +153,7 @@ public Iterator nativeIterator(Query query, QueryOptions options) throws CellBas
         Bson bson = parseQuery(query);
 
         MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
-                (Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
+                (Integer) query.getOrDefault(DATA_RELEASE_PARAM, 0));
         return mongoDBCollection.nativeQuery().find(bson, options);
     }
 
@@ -417,8 +418,8 @@ private CellBaseDataResult<Variant> getClinicalVariant(Variant variant, GenomeMa
             }
 
             // Add data release to query
-            if (!query.containsKey(AbstractQuery.DATA_RELEASE_PARAM)) {
-                query.put(AbstractQuery.DATA_RELEASE_PARAM, dataRelease);
+            if (!query.containsKey(DATA_RELEASE_PARAM)) {
+                query.put(DATA_RELEASE_PARAM, dataRelease);
             }
         }
 

cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptor.java

@@ -50,6 +50,7 @@
 import java.util.*;
 import java.util.function.Consumer;
 
+import static org.opencb.cellbase.core.ParamConstants.DATA_RELEASE_PARAM;
 import static org.opencb.cellbase.lib.MongoDBCollectionConfiguration.VARIATION_FUNCTIONAL_SCORE_CHUNK_SIZE;
 
 /**
@@ -252,7 +253,7 @@ public Bson parseQuery(VariantQuery query) {
                     case "region":
                         createRegionQuery(query, query.getRegions(), MongoDBCollectionConfiguration.VARIATION_CHUNK_SIZE, andBsonList);
                         break;
-                    case VariantQuery.DATA_RELEASE_PARAM:
+                    case DATA_RELEASE_PARAM:
                     case "svType":
                         // don't do anything, this is parsed later
                         break;

cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/AbstractManager.java

@@ -32,7 +32,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import static org.opencb.cellbase.core.api.query.AbstractQuery.API_KEY_PARAM;
+import static org.opencb.cellbase.core.ParamConstants.API_KEY_PARAM;
 
 public class AbstractManager implements AutoCloseable {
 

cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptorTest.java

@@ -23,7 +23,6 @@
 import org.opencb.biodata.models.variant.avro.Expression;
 import org.opencb.biodata.models.variant.avro.ExpressionCall;
 import org.opencb.cellbase.core.api.GeneQuery;
-import org.opencb.cellbase.core.api.query.AbstractQuery;
 import org.opencb.cellbase.core.api.query.LogicalList;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
 import org.opencb.cellbase.lib.GenericMongoDBAdaptorTest;
@@ -36,6 +35,7 @@
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.opencb.cellbase.core.ParamConstants.DATA_RELEASE_PARAM;
 
 /**
  * Created by fjlopez on 08/10/15.
@@ -53,7 +53,7 @@ public void testQueryId() throws Exception {
         Map<String, String> paramMap = new HashMap<>();
         paramMap.put("id", "ENSG00000248746");
         paramMap.put("include", "id,name,start,end");
-        paramMap.put(AbstractQuery.DATA_RELEASE_PARAM, String.valueOf(dataRelease));
+        paramMap.put(DATA_RELEASE_PARAM, String.valueOf(dataRelease));
 
         GeneQuery geneQuery = new GeneQuery(paramMap);
         geneQuery.setCount(Boolean.TRUE);
@@ -73,7 +73,7 @@ public void testQuery() throws Exception {
         paramMap.put("annotation.expression.tissue", "brain");
         paramMap.put("annotation.expression.value", "UP");
         paramMap.put("include", "id,name");
-        paramMap.put(AbstractQuery.DATA_RELEASE_PARAM, String.valueOf(dataRelease));
+        paramMap.put(DATA_RELEASE_PARAM, String.valueOf(dataRelease));
 
         GeneQuery geneQuery = new GeneQuery(paramMap);
         geneQuery.setCount(Boolean.TRUE);
@@ -125,7 +125,7 @@ public void testConstraints() throws Exception {
 
         Map<String, String> paramMap = new HashMap<>();
         paramMap.put("constraints", "oe_lof<=0.85585");
-        paramMap.put(AbstractQuery.DATA_RELEASE_PARAM, String.valueOf(dataRelease));
+        paramMap.put(DATA_RELEASE_PARAM, String.valueOf(dataRelease));
         GeneQuery geneQuery = new GeneQuery(paramMap);
         CellBaseDataResult<Gene> cellBaseDataResult = geneManager.search(geneQuery);
         assertEquals(12, cellBaseDataResult.getNumResults());
@@ -134,28 +134,28 @@ public void testConstraints() throws Exception {
 
         paramMap = new HashMap<>();
         paramMap.put("constraints", "oe_mis>0.8");
-        paramMap.put(AbstractQuery.DATA_RELEASE_PARAM, String.valueOf(dataRelease));
+        paramMap.put(DATA_RELEASE_PARAM, String.valueOf(dataRelease));
         geneQuery = new GeneQuery(paramMap);
         cellBaseDataResult = geneManager.search(geneQuery);
         assertEquals(9, cellBaseDataResult.getNumResults());
 
         paramMap = new HashMap<>();
         paramMap.put("constraints", "oe_syn=0.91766");
-        paramMap.put(AbstractQuery.DATA_RELEASE_PARAM, String.valueOf(dataRelease));
+        paramMap.put(DATA_RELEASE_PARAM, String.valueOf(dataRelease));
         geneQuery = new GeneQuery(paramMap);
         cellBaseDataResult = geneManager.search(geneQuery);
         assertEquals(0, cellBaseDataResult.getNumResults());
 
         paramMap = new HashMap<>();
         paramMap.put("constraints", " exac_pLI<0.17633");
-        paramMap.put(AbstractQuery.DATA_RELEASE_PARAM, String.valueOf(dataRelease));
+        paramMap.put(DATA_RELEASE_PARAM, String.valueOf(dataRelease));
         geneQuery = new GeneQuery(paramMap);
         cellBaseDataResult = geneManager.search(geneQuery);
         assertEquals(0, cellBaseDataResult.getNumResults());
 
         paramMap = new HashMap<>();
         paramMap.put("constraints", "exac_oe_lof>=0.45091");
-        paramMap.put(AbstractQuery.DATA_RELEASE_PARAM, String.valueOf(dataRelease));
+        paramMap.put(DATA_RELEASE_PARAM, String.valueOf(dataRelease));
         geneQuery = new GeneQuery(paramMap);
         cellBaseDataResult = geneManager.search(geneQuery);
         assertEquals(7, cellBaseDataResult.getNumResults());

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java

@@ -60,7 +60,7 @@
 import java.util.*;
 import java.util.concurrent.atomic.AtomicBoolean;
 
-import static org.opencb.cellbase.core.api.query.AbstractQuery.API_KEY_PARAM;
+import static org.opencb.cellbase.core.ParamConstants.*;
 
 @Path("/{version}/{species}")
 @Produces("text/plain")
@@ -179,13 +179,13 @@ private void initQuery() throws CellBaseException {
 
         // Set default API key, if necessary
         // For back-compatibility, we get 'token' parameter after checking 'apiKey' parameter
-        String apiKey = uriParams.containsKey(API_KEY_PARAM) ? uriParams.get(API_KEY_PARAM) : uriParams.get("token");
-        logger.info("before checking, API key {}", apiKey);
+        String apiKey = uriParams.containsKey(API_KEY_PARAM) ? uriParams.get(API_KEY_PARAM) : uriParams.get(TOKEN_PARAM);
+        logger.info("Before checking, API key {}", apiKey);
         if (StringUtils.isEmpty(apiKey)) {
             apiKey = defaultApiKey;
         }
         uriParams.put(API_KEY_PARAM, apiKey);
-        logger.info("after checking, API key {}", uriParams.get(API_KEY_PARAM));
+        logger.info("After checking, API key {}", uriParams.get(API_KEY_PARAM));
 
         checkLimit();
 
@@ -209,9 +209,9 @@ private void initQuery() throws CellBaseException {
     }
 
     protected int getDataRelease() throws CellBaseException {
-        if (uriParams.containsKey("dataRelease") && StringUtils.isNotEmpty(uriParams.get("dataRelease"))) {
+        if (uriParams.containsKey(DATA_RELEASE_PARAM) && StringUtils.isNotEmpty(uriParams.get(DATA_RELEASE_PARAM))) {
             try {
-                int dataRelease = Integer.parseInt(uriParams.get("dataRelease"));
+                int dataRelease = Integer.parseInt(uriParams.get(DATA_RELEASE_PARAM));
                 // If data release is 0, then use the default data release
                 if (dataRelease == 0) {
                     logger.info("Using data release 0 in query: using the default data release '" + defaultDataRelease + "' for CellBase"
@@ -221,7 +221,7 @@ protected int getDataRelease() throws CellBaseException {
                     return dataRelease;
                 }
             } catch (NumberFormatException e) {
-                throw new CellBaseException("Invalid data release number '" + uriParams.get("dataRelease") + "'");
+                throw new CellBaseException("Invalid data release number '" + uriParams.get(DATA_RELEASE_PARAM) + "'");
             }
         }
         // If no data release is present in the query, then use the default data release