Merge branch 'develop' into TASK-5392

opencb · Jan 26, 2024 · ffdf27a · ffdf27a
2 parents 5d00721 + 8faeba2
commit ffdf27a
Show file tree

Hide file tree

Showing 10 changed files with 45 additions and 41 deletions.
diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.9.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.9.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.9.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.9.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -137,10 +137,10 @@
             <groupId>com.github.samtools</groupId>
             <artifactId>htsjdk</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>io.jsonwebtoken</groupId>
             <artifactId>jjwt-api</artifactId>

diff --git a/...base-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java b/...base-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java
@@ -167,7 +167,7 @@ private boolean updateRocksDB(Variant variant) throws RocksDBException, IOExcept
 
         if (normalisedVariantStringList != null) {
             for (String normalisedVariantString : normalisedVariantStringList) {
-                VariantAnnotation variantAnnotation = getVariantAnnotation(variant.toString().getBytes());
+                VariantAnnotation variantAnnotation = getVariantAnnotation(normalisedVariantString.getBytes());
 
                 // Add haplotype property to all EvidenceEntry objects in variant if there are more than 1 variants in
                 // normalisedVariantStringList, i.e. if this variant is part of an MNV (haplotype)

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/MetaMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/MetaMongoDBAdaptor.java
@@ -16,17 +16,20 @@
 
 package org.opencb.cellbase.lib.impl.core;
 
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.mongodb.ReadPreference;
+import com.mongodb.WriteConcern;
 import com.mongodb.client.model.Filters;
 import com.mongodb.client.model.Updates;
 import org.bson.BsonDocument;
 import org.bson.Document;
 import org.bson.conversions.Bson;
-import org.codehaus.jackson.map.ObjectMapper;
+import org.opencb.cellbase.core.api.key.ApiKeyStats;
 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;
-import org.opencb.cellbase.core.api.key.ApiKeyStats;
 import org.opencb.cellbase.lib.iterator.CellBaseIterator;
 import org.opencb.commons.datastore.core.FacetField;
 import org.opencb.commons.datastore.core.QueryOptions;
@@ -55,7 +58,7 @@ public MetaMongoDBAdaptor(MongoDataStore mongoDataStore) {
     private void init() {
         logger.debug("MetaMongoDBAdaptor: in 'constructor'");
         mongoDBCollection = mongoDataStore.getCollection("metadata");
-        apiKeyStatsMongoDBCollection = mongoDataStore.getCollection("apikey_stats");
+        apiKeyStatsMongoDBCollection = mongoDataStore.getCollection("apikey_stats", WriteConcern.ACKNOWLEDGED, ReadPreference.primary());
     }
 
     public CellBaseDataResult getAll() {

diff --git a/...src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java b/...src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
@@ -431,6 +431,7 @@ private List<GeneMirnaTarget> getTargets(Gene mirna) throws QueryException, Ille
             }
         }
         GeneQuery geneQuery = new GeneQuery();
+        geneQuery.setDataRelease(dataRelease);
         geneQuery.setAnnotationTargets(new LogicalList<>(mirnas, false));
         List<GeneMirnaTarget> geneMirnaTargets = new ArrayList<>();
         List<Gene> genes = (geneManager.search(geneQuery)).getResults();
@@ -679,9 +680,9 @@ public List<Gene> getBatchGeneList(List<Variant> variantList)
 
         List<Gene> geneList = new ArrayList<>();
         GeneQuery geneQuery = new GeneQuery();
+        geneQuery.setDataRelease(dataRelease);
         geneQuery.setIncludes(includeGeneFields);
         geneQuery.setRegions(regionList);
-        geneQuery.setDataRelease(dataRelease);
 
         if (StringUtils.isNotEmpty(consequenceTypeSource)) {
             // sources can be "ensembl" and/or "refseq". query is validated before execution, will fail if invalid value
@@ -1354,6 +1355,7 @@ private boolean[] getRegulatoryRegionOverlaps(String chromosome, Integer start,
         boolean[] overlapsRegulatoryRegion = {false, false};
 
         RegulationQuery query = new RegulationQuery();
+        query.setDataRelease(dataRelease);
         query.setExcludes(Collections.singletonList("_id"));
         query.setIncludes(Collections.singletonList("chromosome"));
         query.setLimit(1);

diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.9.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java
@@ -116,16 +116,18 @@ public GenericRestWSServer(@PathParam("version") String version, @PathParam("spe
         this.species = species;
 
         try {
-            init();
+            if (!INITIALIZED.get()) {
+                init();
+            }
             initQuery();
         } catch (Exception e) {
             throw new CellBaseServerException(e.getMessage());
         }
     }
 
-    private void init() throws IOException, CellBaseException {
+    private synchronized void init() throws IOException, CellBaseException {
         // we need to make sure we only init one single time
-        if (INITIALIZED.compareAndSet(false, true)) {
+        if (!INITIALIZED.get()) {
             SERVICE_START_DATE = new SimpleDateFormat("yyyyMMdd_HHmmss").format(Calendar.getInstance().getTime());
             WATCH = new StopWatch();
             WATCH.start();
@@ -159,19 +161,21 @@ private void init() throws IOException, CellBaseException {
             cellBaseManagerFactory = new CellBaseManagerFactory(cellBaseConfiguration);
             logger.info("***************************************************");
 
+            // Get default API key (for anonymous queries)
+            if (apiKeyManager == null) {
+                apiKeyManager = new ApiKeyManager(cellBaseConfiguration.getSecretKey());
+                defaultApiKey = apiKeyManager.getDefaultApiKey();
+                logger.info("default API key {}", defaultApiKey);
+            }
+
             // Initialize Monitor
             monitor = new Monitor(cellBaseManagerFactory.getMetaManager());
+
+            INITIALIZED.set(true);
         }
     }
 
     private void initQuery() throws CellBaseException {
-        // Get default API key (for anonymous queries)
-        if (apiKeyManager == null) {
-            apiKeyManager = new ApiKeyManager(cellBaseConfiguration.getSecretKey());
-            defaultApiKey = apiKeyManager.getDefaultApiKey();
-            logger.info("default API key {}", defaultApiKey);
-        }
-
         startTime = System.currentTimeMillis();
         query = new Query();
         uriParams = convertMultiToMap(uriInfo.getQueryParameters());
@@ -184,12 +188,10 @@ private void initQuery() throws CellBaseException {
 
         // Set default API key, if necessary
         String apiKey = uriParams.getOrDefault(API_KEY_PARAM, null);
-        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));
 
         checkLimit();
 
@@ -228,11 +230,6 @@ protected int getDataRelease() throws CellBaseException {
                 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
-        if (!DONT_CHECK_SPECIES.equals(species)) {
-            logger.info("No data release present in query: using the default data release '" + defaultDataRelease + "' for CellBase version"
-                    + " '" + version + "'");
-        }
         return defaultDataRelease;
     }
 
@@ -273,7 +270,8 @@ private void checkVersion() throws CellBaseException {
     }
 
     private void checkApiKey() throws CellBaseException {
-        if (!uriInfo.getPath().contains("health")) {
+        // Update the API key content only for non-meta endpoints
+        if (!uriInfo.getPath().contains("/meta/")) {
             String apiKey = getApiKey();
             ApiKeyJwtPayload payload = apiKeyManager.decode(apiKey);
 
@@ -414,7 +412,7 @@ protected Response createOkResponse(Object obj) {
 
         // Update API key stats, if necessary
         try {
-            if (!uriInfo.getPath().contains("health")) {
+            if (!uriInfo.getPath().contains("/meta/")) {
                 String apiKey = getApiKey();
                 MetaManager metaManager = cellBaseManagerFactory.getMetaManager();
                 long bytes = (jsonResponse.getEntity() != null) ? jsonResponse.getEntity().toString().length() : 0;

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase</artifactId>
-    <version>5.9.0-SNAPSHOT</version>
+    <version>6.0.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>CellBase project</name>
@@ -23,18 +23,20 @@
 
     <properties>
         <pycellbase.version>${project.version}</pycellbase.version>
-        <java-common-libs.version>4.13.0-SNAPSHOT</java-common-libs.version>
-        <biodata.version>2.13.0-SNAPSHOT</biodata.version>
+        <java-common-libs.version>5.0.0-SNAPSHOT</java-common-libs.version>
+        <biodata.version>3.0.0-SNAPSHOT</biodata.version>
         <bionetdb.version>0.1.0</bionetdb.version>
-        <jackson.version>2.11.4</jackson.version>
-        <jackson-asl.version>1.9.13</jackson-asl.version>
+        <jetty.version>9.4.51.v20230217</jetty.version>
+
+        <jackson.version>2.14.3</jackson.version>
+        <commons-lang3.version>3.14.0</commons-lang3.version>
+        <slf4j.version>1.7.36</slf4j.version>
+
         <jersey.version>2.30.1</jersey.version>
-        <slf4j.version>1.7.32</slf4j.version>
         <log4j.version>2.17.2</log4j.version>
         <junit.platform.version>1.5.2</junit.platform.version>
         <junit.jupiter.version>5.5.2</junit.jupiter.version>
         <jacoco.version>0.8.8</jacoco.version>
-        <jetty.version>9.4.17.v20190418</jetty.version>
         <jjwt.version>0.11.5</jjwt.version>
         <swagger-annotations.version>1.6.5</swagger-annotations.version>
         <javax.servlet-api.version>3.1.0</javax.servlet-api.version>
@@ -50,7 +52,6 @@
         <grpc.version>1.48.0</grpc.version>
         <commons-lang.version>2.4</commons-lang.version>
         <commons-io.version>2.4</commons-io.version>
-        <commons-lang3.version>3.12.0</commons-lang3.version>
         <jakarta.ws.rs-api.version>2.1.6</jakarta.ws.rs-api.version>
         <commons-collections4.version>4.4</commons-collections4.version>
         <jcommander.version>1.69</jcommander.version>
@@ -412,11 +413,11 @@
                 <artifactId>swagger-annotations</artifactId>
                 <version>${swagger-annotations.version}</version>
             </dependency>
-            <dependency>
+<!--            <dependency>
                 <groupId>org.codehaus.jackson</groupId>
                 <artifactId>jackson-mapper-asl</artifactId>
                 <version>${jackson-asl.version}</version>
-            </dependency>
+            </dependency>-->
             <dependency>
                 <groupId>io.jsonwebtoken</groupId>
                 <artifactId>jjwt-jackson</artifactId>