Merge branch 'develop'

commons-datastore/commons-datastore-core/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>3.4.0</version>
+        <version>3.4.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/ComplexTypeConverter.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/DataStoreServerAddress.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/ObjectMap.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/Query.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.datastore.core;
 
 import java.util.Arrays;

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/QueryOptions.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -27,8 +27,9 @@ public class QueryOptions extends ObjectMap {
 
     public static final String INCLUDE = "include";
     public static final String EXCLUDE = "exclude";
-    public static final String LIMIT = "limit";
     public static final String SKIP = "skip";
+    public static final String LIMIT = "limit";
+    public static final String COUNT = "count";
 
     public static final String SORT = "sort";
     public static final String ORDER = "order";

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/QueryParam.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.datastore.core;
 
 /**
@@ -24,4 +40,36 @@ enum Type {
 
     Type type();
 
+    static QueryParam create(String key, String description, Type type) {
+        return new QueryParamImpl(key, description, type);
+    }
+
+    class QueryParamImpl implements QueryParam {
+
+        private final String key;
+        private final String description;
+        private final Type type;
+
+        private QueryParamImpl(String key, String description, Type type) {
+            this.key = key;
+            this.description = description;
+            this.type = type;
+        }
+
+        @Override
+        public String key() {
+            return key;
+        }
+
+        @Override
+        public String description() {
+            return description;
+        }
+
+        @Override
+        public Type type() {
+            return type;
+        }
+    }
+
 }

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/QueryResponse.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/QueryResult.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/QueryResultWriter.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-mongodb/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>3.4.0</version>
+        <version>3.4.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -23,7 +23,7 @@
         <dependency>
             <groupId>org.mongodb</groupId>
             <artifactId>mongo-java-driver</artifactId>
-            <version>3.2.2</version>
+            <version>3.4.2</version>
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/GenericDocumentComplexConverter.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.datastore.mongodb;
 
 import com.fasterxml.jackson.core.JsonProcessingException;

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBCollection.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBConfiguration.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBQueryUtils.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.datastore.mongodb;
 
 import com.mongodb.client.model.Accumulators;
@@ -141,7 +157,7 @@ public static Bson createAutoFilter(String mongoDbField, String queryParam, Quer
                     break;
                 case INTEGER:
                 case INTEGER_ARRAY:
-                    bsonList.add(createFilter(mongoDbField, Integer.parseInt(queryValueString), comparator));
+                    bsonList.add(createFilter(mongoDbField, Long.parseLong(queryValueString), comparator));
                     break;
                 case DOUBLE:
                 case DECIMAL:

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDataStore.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDataStoreManager.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2015 OpenCB
+ * Copyright 2015-2017 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoPersistentCursor.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.datastore.mongodb;
 
 import com.mongodb.MongoCursorNotFoundException;

commons-datastore/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons</artifactId>
-        <version>3.4.0</version>
+        <version>3.4.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

commons-lib/pom.xml

@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons</artifactId>
-        <version>3.4.0</version>
+        <version>3.4.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

commons-lib/src/main/java/org/opencb/commons/containers/DataItem.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.containers;
 
 /**

commons-lib/src/main/java/org/opencb/commons/containers/DataRW.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.containers;
 
 import java.util.concurrent.BlockingQueue;

commons-lib/src/main/java/org/opencb/commons/containers/list/IncrementalList.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.containers.list;
 
 import java.util.*;

commons-lib/src/main/java/org/opencb/commons/containers/list/SortedList.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.containers.list;
 
 import java.util.ArrayList;

commons-lib/src/main/java/org/opencb/commons/db/SqliteSingletonConnection.java

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2015-2017 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.opencb.commons.db;
 
 import java.sql.Connection;