diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 5aae3b74700..b8bd30ce3be 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -17,7 +17,7 @@ org.opencb.opencga - opencga-lib + opencga-core org.opencb.opencga diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisJobExecuter.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisJobExecuter.java index 692d41a9445..57181b33c87 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisJobExecuter.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisJobExecuter.java @@ -8,15 +8,15 @@ import org.opencb.opencga.catalog.CatalogManager; import org.opencb.opencga.catalog.beans.File; import org.opencb.opencga.catalog.beans.Job; -import org.opencb.opencga.lib.SgeManager; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.SgeManager; +import org.opencb.opencga.core.common.Config; import org.opencb.opencga.analysis.beans.Analysis; import org.opencb.opencga.analysis.beans.Execution; import org.opencb.opencga.analysis.beans.Option; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.TimeUtils; -import org.opencb.opencga.lib.exec.Command; -import org.opencb.opencga.lib.exec.SingleProcess; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.TimeUtils; +import org.opencb.opencga.core.exec.Command; +import org.opencb.opencga.core.exec.SingleProcess; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -26,7 +26,6 @@ import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; -import java.text.SimpleDateFormat; import java.util.*; public class AnalysisJobExecuter { diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisOutputRecorder.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisOutputRecorder.java index 208e50c3e7b..9374e254791 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisOutputRecorder.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisOutputRecorder.java @@ -1,7 +1,5 @@ package org.opencb.opencga.analysis; -import com.mongodb.util.JSON; -import org.opencb.biodata.models.variant.VariantSource; import org.opencb.datastore.core.ObjectMap; import org.opencb.datastore.core.QueryOptions; import org.opencb.datastore.core.QueryResult; @@ -11,17 +9,11 @@ import org.opencb.opencga.catalog.beans.File; import org.opencb.opencga.catalog.beans.Index; import org.opencb.opencga.catalog.beans.Job; -import org.opencb.opencga.catalog.db.CatalogDBException; -import org.opencb.opencga.lib.common.TimeUtils; -import org.opencb.opencga.storage.core.StorageManagerFactory; -import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor; -import org.opencb.opencga.storage.core.variant.adaptors.VariantSourceDBAdaptor; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.IOException; import java.net.URI; -import java.net.UnknownHostException; import java.nio.file.*; import java.util.LinkedList; import java.util.List; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/AnalysisFileIndexer.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/AnalysisFileIndexer.java index 44ea32b32d6..c93e3ec73f0 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/AnalysisFileIndexer.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/AnalysisFileIndexer.java @@ -10,9 +10,9 @@ import org.opencb.opencga.catalog.CatalogManager; import org.opencb.opencga.catalog.beans.*; import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.TimeUtils; import org.opencb.opencga.storage.core.StorageManagerException; import org.opencb.opencga.storage.core.StorageManagerFactory; import org.opencb.opencga.storage.core.variant.VariantStorageManager; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/CatalogStudyConfigurationManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/CatalogStudyConfigurationManager.java index 5c0686ed574..45d473e2da0 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/CatalogStudyConfigurationManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/CatalogStudyConfigurationManager.java @@ -1,8 +1,5 @@ package org.opencb.opencga.analysis.storage; -import com.fasterxml.jackson.core.JsonParseException; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.ObjectMapper; import org.opencb.datastore.core.ObjectMap; import org.opencb.datastore.core.QueryOptions; @@ -12,7 +9,7 @@ import org.opencb.opencga.catalog.beans.Study; import org.opencb.opencga.catalog.db.CatalogDBException; import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.opencb.opencga.storage.core.StudyConfiguration; import org.opencb.opencga.storage.core.variant.StudyConfigurationManager; import org.slf4j.Logger; @@ -21,7 +18,6 @@ import java.io.IOException; import java.util.Arrays; import java.util.Collections; -import java.util.Map; /** * Created by hpccoll1 on 23/03/15. diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantStorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantStorageManager.java index d695773c4a3..a797d7a036a 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantStorageManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantStorageManager.java @@ -7,9 +7,7 @@ import org.opencb.opencga.catalog.CatalogException; import org.opencb.opencga.catalog.CatalogManager; import org.opencb.opencga.catalog.beans.File; -import org.opencb.opencga.catalog.db.CatalogDBException; -import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.opencb.opencga.storage.core.StorageManager; import org.opencb.opencga.storage.core.StorageManagerException; import org.opencb.opencga.storage.core.StorageManagerFactory; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/VariantStorage.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/VariantStorage.java index 9c99f506170..525bcaa698e 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/VariantStorage.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/VariantStorage.java @@ -9,8 +9,8 @@ import org.opencb.opencga.catalog.CatalogManager; import org.opencb.opencga.catalog.beans.*; import org.opencb.opencga.catalog.beans.File; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.StringUtils; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index dcc0a9577f9..690e371e095 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -27,7 +27,7 @@ org.opencb.opencga - opencga-lib + opencga-core commons-codec diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCGAMain.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCGAMain.java index 25b27b61222..04d96254f59 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCGAMain.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCGAMain.java @@ -18,7 +18,7 @@ import org.opencb.opencga.catalog.CatalogSampleAnnotationsLoader; import org.opencb.opencga.catalog.beans.*; import org.opencb.opencga.catalog.beans.File; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.opencb.opencga.storage.core.StorageManagerFactory; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/DaemonLoop.java b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/DaemonLoop.java index e0b29901cc0..cae25529e42 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/DaemonLoop.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/DaemonLoop.java @@ -18,9 +18,9 @@ import org.opencb.opencga.catalog.db.CatalogDBException; import org.opencb.opencga.catalog.io.CatalogIOManager; import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.SgeManager; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.SgeManager; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.TimeUtils; import org.slf4j.LoggerFactory; import org.slf4j.Logger; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/OpenCGADaemon.java b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/OpenCGADaemon.java index 81a376e1873..4fcd48a719f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/OpenCGADaemon.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/OpenCGADaemon.java @@ -1,7 +1,6 @@ package org.opencb.opencga.app.daemon; //import org.apache.catalina.Server; -import org.eclipse.jetty.server.Server; //import org.mortbay.jetty.Server; @@ -12,7 +11,7 @@ //import net.dpml.http.ServletContextHandler; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import java.io.File; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/localserver/FetchServlet.java b/opencga-app/src/main/java/org/opencb/opencga/app/localserver/FetchServlet.java index fcce68ef678..3c7065a10c8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/localserver/FetchServlet.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/localserver/FetchServlet.java @@ -1,6 +1,6 @@ package org.opencb.opencga.app.localserver; -import org.opencb.opencga.lib.common.StringUtils; +import org.opencb.opencga.core.common.StringUtils; import javax.servlet.ServletException; import javax.servlet.http.HttpServlet; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/localserver/LocalServer.java b/opencga-app/src/main/java/org/opencb/opencga/app/localserver/LocalServer.java index e899d0d22e5..2738956aaea 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/localserver/LocalServer.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/localserver/LocalServer.java @@ -3,8 +3,8 @@ import org.apache.catalina.Context; import org.apache.catalina.LifecycleException; import org.apache.catalina.startup.Tomcat; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.IOUtils; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.IOUtils; import java.io.File; import java.io.IOException; diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 2533d0c2ef0..883b4160cf0 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -17,7 +17,7 @@ org.opencb.opencga - opencga-lib + opencga-core diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogFileManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogFileManager.java index 31b150c3951..186a4f2b716 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogFileManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogFileManager.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.db.CatalogDBException; import org.opencb.opencga.catalog.io.CatalogIOManager; import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogManager.java index 099f76c6b64..2b753ef1b7e 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogManager.java @@ -1,6 +1,5 @@ package org.opencb.opencga.catalog; -import com.mongodb.MongoCredential; import org.opencb.datastore.core.ObjectMap; import org.opencb.datastore.core.QueryOptions; import org.opencb.datastore.core.QueryResult; @@ -17,9 +16,9 @@ import org.opencb.opencga.catalog.io.CatalogIOManagerException; import org.opencb.opencga.catalog.io.CatalogIOManagerFactory; -import org.opencb.opencga.lib.common.MailUtils; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.MailUtils; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.TimeUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Analysis.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Analysis.java index dbed71a4cfb..4bce887152a 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Analysis.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Analysis.java @@ -1,6 +1,6 @@ package org.opencb.opencga.catalog.beans; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import java.util.HashMap; import java.util.LinkedList; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/File.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/File.java index ee6599e2ab1..1ba76c1cb93 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/File.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/File.java @@ -1,7 +1,6 @@ package org.opencb.opencga.catalog.beans; -import org.opencb.datastore.core.ObjectMap; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import java.util.HashMap; import java.util.LinkedList; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Job.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Job.java index b7e6e9b5c79..045f70135a4 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Job.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Job.java @@ -1,6 +1,6 @@ package org.opencb.opencga.catalog.beans; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import java.net.URI; import java.util.HashMap; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Metadata.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Metadata.java index ca41b460c10..358eaa2595e 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Metadata.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Metadata.java @@ -1,6 +1,6 @@ package org.opencb.opencga.catalog.beans; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; /** * Created by imedina on 13/09/14. diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Project.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Project.java index a052946a6d8..cd620b890b9 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Project.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Project.java @@ -1,6 +1,6 @@ package org.opencb.opencga.catalog.beans; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import java.util.*; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Session.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Session.java index e4dd5f3eaa2..363f38f6281 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Session.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Session.java @@ -1,7 +1,7 @@ package org.opencb.opencga.catalog.beans; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.TimeUtils; /** * Created by jacobo on 11/09/14. diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Study.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Study.java index 6005c5d8ed6..2ec8cd40131 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Study.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Study.java @@ -1,6 +1,6 @@ package org.opencb.opencga.catalog.beans; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import java.net.URI; import java.util.*; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogMongoDBAdaptor.java index 00edac4c768..421ba08ad92 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogMongoDBAdaptor.java @@ -1,6 +1,5 @@ package org.opencb.opencga.catalog.db; -import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectReader; @@ -16,7 +15,7 @@ import org.opencb.datastore.mongodb.MongoDataStore; import org.opencb.datastore.mongodb.MongoDataStoreManager; import org.opencb.opencga.catalog.beans.*; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import org.slf4j.LoggerFactory; import java.io.IOException; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/PosixCatalogIOManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/PosixCatalogIOManager.java index 3351648bf5f..006528c1a96 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/PosixCatalogIOManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/PosixCatalogIOManager.java @@ -3,7 +3,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectWriter; import org.opencb.opencga.catalog.CatalogManager; -import org.opencb.opencga.lib.common.IOUtils; +import org.opencb.opencga.core.common.IOUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogFileManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogFileManagerTest.java index 3d72dbccf95..450eed9344f 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogFileManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogFileManagerTest.java @@ -1,6 +1,5 @@ package org.opencb.opencga.catalog; -import com.mongodb.MongoCredential; import org.junit.Before; import org.junit.Test; import org.opencb.datastore.core.ObjectMap; @@ -11,7 +10,7 @@ import org.opencb.opencga.catalog.beans.Study; import org.opencb.opencga.catalog.beans.User; import org.opencb.opencga.catalog.db.CatalogMongoDBAdaptor; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import java.io.IOException; import java.io.InputStream; diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogManagerTest.java index dccab40e183..e0c1557676f 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogManagerTest.java @@ -17,8 +17,8 @@ import org.opencb.opencga.catalog.beans.File; import org.opencb.opencga.catalog.db.CatalogDBException; import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.TimeUtils; import java.io.*; import java.net.URI; diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/CatalogMongoDBAdaptorTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/CatalogMongoDBAdaptorTest.java index cee9d56bb23..6632d06d3e9 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/CatalogMongoDBAdaptorTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/CatalogMongoDBAdaptorTest.java @@ -4,10 +4,8 @@ import com.mongodb.BasicDBObject; import com.mongodb.BasicDBObjectBuilder; import com.mongodb.DBObject; -import com.mongodb.MongoCredential; import org.junit.*; import org.junit.rules.ExpectedException; -import org.junit.rules.Timeout; import org.junit.runners.MethodSorters; import org.opencb.commons.test.GenericTest; import org.opencb.datastore.core.ObjectMap; @@ -19,8 +17,8 @@ import org.opencb.datastore.mongodb.MongoDataStoreManager; import org.opencb.opencga.catalog.CatalogManager; import org.opencb.opencga.catalog.beans.*; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.TimeUtils; import java.io.IOException; import java.io.InputStream; diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/io/PosixCatalogIOManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/io/PosixCatalogIOManagerTest.java index 25805397c81..ce315c80174 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/io/PosixCatalogIOManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/io/PosixCatalogIOManagerTest.java @@ -2,7 +2,7 @@ import org.junit.BeforeClass; import org.junit.Test; -import org.opencb.opencga.lib.common.IOUtils; +import org.opencb.opencga.core.common.IOUtils; import java.net.URI; import java.nio.file.Files; diff --git a/opencga-lib/pom.xml b/opencga-core/pom.xml similarity index 98% rename from opencga-lib/pom.xml rename to opencga-core/pom.xml index e5cba2a879d..72ff0982203 100644 --- a/opencga-lib/pom.xml +++ b/opencga-core/pom.xml @@ -10,7 +10,7 @@ .. - opencga-lib + opencga-core ${opencga.version} jar diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/SgeManager.java b/opencga-core/src/main/java/org/opencb/opencga/core/SgeManager.java similarity index 98% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/SgeManager.java rename to opencga-core/src/main/java/org/opencb/opencga/core/SgeManager.java index 543cd337e73..4f8c8a3ea5f 100755 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/SgeManager.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/SgeManager.java @@ -1,9 +1,9 @@ -package org.opencb.opencga.lib; +package org.opencb.opencga.core; import com.google.common.base.Splitter; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.exec.Command; -import org.opencb.opencga.lib.exec.SingleProcess; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.exec.Command; +import org.opencb.opencga.core.exec.SingleProcess; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.w3c.dom.Document; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/CellbaseCredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/CellbaseCredentials.java similarity index 96% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/auth/CellbaseCredentials.java rename to opencga-core/src/main/java/org/opencb/opencga/core/auth/CellbaseCredentials.java index 92722b1ba4d..43e04208850 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/CellbaseCredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/CellbaseCredentials.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.auth; +package org.opencb.opencga.core.auth; /** * diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/IllegalOpenCGACredentialsException.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/IllegalOpenCGACredentialsException.java similarity index 95% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/auth/IllegalOpenCGACredentialsException.java rename to opencga-core/src/main/java/org/opencb/opencga/core/auth/IllegalOpenCGACredentialsException.java index 6440f97e879..90200e1c0ae 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/IllegalOpenCGACredentialsException.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/IllegalOpenCGACredentialsException.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.auth; +package org.opencb.opencga.core.auth; /** * diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/MonbaseCredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/MonbaseCredentials.java similarity index 98% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/auth/MonbaseCredentials.java rename to opencga-core/src/main/java/org/opencb/opencga/core/auth/MonbaseCredentials.java index 0575a5c723e..5421a098507 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/MonbaseCredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/MonbaseCredentials.java @@ -1,7 +1,6 @@ -package org.opencb.opencga.lib.auth; +package org.opencb.opencga.core.auth; //import com.mongodb.MongoCredential; -import java.util.Map; import java.util.Properties; /** diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/OpenCGACredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/OpenCGACredentials.java similarity index 95% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/auth/OpenCGACredentials.java rename to opencga-core/src/main/java/org/opencb/opencga/core/auth/OpenCGACredentials.java index 2267f3f6c83..ea6b36b93a7 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/OpenCGACredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/OpenCGACredentials.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.auth; +package org.opencb.opencga.core.auth; /** * A set of credentials to access a data source, such as: user, diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/SqliteCredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/SqliteCredentials.java similarity index 96% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/auth/SqliteCredentials.java rename to opencga-core/src/main/java/org/opencb/opencga/core/auth/SqliteCredentials.java index 0a8459c5e1c..fb960f664c9 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/SqliteCredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/SqliteCredentials.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.auth; +package org.opencb.opencga.core.auth; import org.opencb.commons.utils.FileUtils; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/TabixCredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/TabixCredentials.java similarity index 95% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/auth/TabixCredentials.java rename to opencga-core/src/main/java/org/opencb/opencga/core/auth/TabixCredentials.java index 0ca7fecd278..a10f4d2835a 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/auth/TabixCredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/TabixCredentials.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.auth; +package org.opencb.opencga.core.auth; import java.io.IOException; import java.nio.file.Path; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/ArrayUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/ArrayUtils.java similarity index 99% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/ArrayUtils.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/ArrayUtils.java index a243081d11e..e8404c81d4f 100755 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/ArrayUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/ArrayUtils.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import java.lang.reflect.Array; import java.text.DecimalFormat; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/Config.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/Config.java similarity index 99% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/Config.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/Config.java index cfd5b305d7c..22d315dd954 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/Config.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/Config.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/IOUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/IOUtils.java similarity index 99% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/IOUtils.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/IOUtils.java index 59fa801f35b..c3c83f72feb 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/IOUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/IOUtils.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import java.io.*; import java.nio.charset.Charset; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/ListUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/ListUtils.java similarity index 99% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/ListUtils.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/ListUtils.java index e1821b5ed10..d6e00279120 100755 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/ListUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/ListUtils.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import java.lang.reflect.Array; import java.util.*; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/MailUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/MailUtils.java similarity index 98% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/MailUtils.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/MailUtils.java index cfbd5f3285b..f52ff592012 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/MailUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/MailUtils.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import javax.mail.*; import javax.mail.internet.InternetAddress; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/StringUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/StringUtils.java similarity index 95% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/StringUtils.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/StringUtils.java index cffc22c4ea1..37b93c16b6c 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/StringUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/StringUtils.java @@ -1,10 +1,9 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import java.nio.file.Path; import java.nio.file.Paths; import java.security.MessageDigest; import java.security.NoSuchAlgorithmException; -import java.security.SecureRandom; import java.util.Random; public class StringUtils { diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/TimeUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/TimeUtils.java similarity index 96% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/TimeUtils.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/TimeUtils.java index 3cfda6cd5d3..def03d8313c 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/TimeUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/TimeUtils.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import java.text.ParseException; import java.text.SimpleDateFormat; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/XObject.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/XObject.java similarity index 99% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/XObject.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/XObject.java index 53e90edf5c1..7b92ebc776e 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/XObject.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/XObject.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import java.util.LinkedHashMap; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/networks/Layout.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/networks/Layout.java similarity index 99% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/common/networks/Layout.java rename to opencga-core/src/main/java/org/opencb/opencga/core/common/networks/Layout.java index 6502e045441..b3fb319943a 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/common/networks/Layout.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/networks/Layout.java @@ -1,7 +1,7 @@ -package org.opencb.opencga.lib.common.networks; +package org.opencb.opencga.core.common.networks; import org.apache.commons.codec.binary.Base64; -import org.opencb.opencga.lib.common.StringUtils; +import org.opencb.opencga.core.common.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/FileSource.java b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/FileSource.java similarity index 90% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/FileSource.java rename to opencga-core/src/main/java/org/opencb/opencga/core/data/source/FileSource.java index 1ef087ce792..1b0578f001c 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/FileSource.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/FileSource.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.data.source; +package org.opencb.opencga.core.data.source; import java.io.File; import java.io.FileInputStream; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/S3Source.java b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/S3Source.java similarity index 94% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/S3Source.java rename to opencga-core/src/main/java/org/opencb/opencga/core/data/source/S3Source.java index 16b00d7275f..9d467cee843 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/S3Source.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/S3Source.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.data.source; +package org.opencb.opencga.core.data.source; import com.amazonaws.auth.AWSCredentials; import com.amazonaws.auth.BasicAWSCredentials; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/Source.java b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/Source.java similarity index 70% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/Source.java rename to opencga-core/src/main/java/org/opencb/opencga/core/data/source/Source.java index 640cc820770..a69027712ba 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/Source.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/Source.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.data.source; +package org.opencb.opencga.core.data.source; import java.io.InputStream; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/UrlSource.java b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/UrlSource.java similarity index 94% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/UrlSource.java rename to opencga-core/src/main/java/org/opencb/opencga/core/data/source/UrlSource.java index e554b920016..f5e00cbaee9 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/data/source/UrlSource.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/UrlSource.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.data.source; +package org.opencb.opencga.core.data.source; import javax.net.ssl.HttpsURLConnection; import java.io.InputStream; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/exec/Command.java b/opencga-core/src/main/java/org/opencb/opencga/core/exec/Command.java similarity index 98% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/exec/Command.java rename to opencga-core/src/main/java/org/opencb/opencga/core/exec/Command.java index 1158fef3697..562d5b0634a 100755 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/exec/Command.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/exec/Command.java @@ -1,7 +1,7 @@ -package org.opencb.opencga.lib.exec; +package org.opencb.opencga.core.exec; import org.apache.tools.ant.types.Commandline; -import org.opencb.opencga.lib.common.ListUtils; +import org.opencb.opencga.core.common.ListUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/exec/RunnableProcess.java b/opencga-core/src/main/java/org/opencb/opencga/core/exec/RunnableProcess.java similarity index 98% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/exec/RunnableProcess.java rename to opencga-core/src/main/java/org/opencb/opencga/core/exec/RunnableProcess.java index 5a21ba626d3..b436e2f25e8 100755 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/exec/RunnableProcess.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/exec/RunnableProcess.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.exec; +package org.opencb.opencga.core.exec; public abstract class RunnableProcess implements Runnable { diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/exec/SingleProcess.java b/opencga-core/src/main/java/org/opencb/opencga/core/exec/SingleProcess.java similarity index 98% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/exec/SingleProcess.java rename to opencga-core/src/main/java/org/opencb/opencga/core/exec/SingleProcess.java index 469da8188a0..6cb9a34bc5f 100755 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/exec/SingleProcess.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/exec/SingleProcess.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.exec; +package org.opencb.opencga.core.exec; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/CombinationIterator.java b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CombinationIterator.java similarity index 98% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/CombinationIterator.java rename to opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CombinationIterator.java index 13dfcb7099b..0b51eb66ac9 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/CombinationIterator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CombinationIterator.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.tools.accession; +package org.opencb.opencga.core.tools.accession; import java.util.Iterator; import java.util.NoSuchElementException; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/CreateAccessionTask.java b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CreateAccessionTask.java similarity index 99% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/CreateAccessionTask.java rename to opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CreateAccessionTask.java index 3d2a2ccd48c..053255626b2 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/CreateAccessionTask.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CreateAccessionTask.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.tools.accession; +package org.opencb.opencga.core.tools.accession; import java.io.IOException; import java.util.HashMap; diff --git a/opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/LRUCache.java b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/LRUCache.java similarity index 91% rename from opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/LRUCache.java rename to opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/LRUCache.java index 65bbfa6091e..3dc871c75f2 100644 --- a/opencga-lib/src/main/java/org/opencb/opencga/lib/tools/accession/LRUCache.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/LRUCache.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.tools.accession; +package org.opencb.opencga.core.tools.accession; import java.util.LinkedHashMap; import java.util.Map.Entry; diff --git a/opencga-lib/src/test/java/org/opencb/opencga/lib/common/IOUtilsTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/common/IOUtilsTest.java similarity index 96% rename from opencga-lib/src/test/java/org/opencb/opencga/lib/common/IOUtilsTest.java rename to opencga-core/src/test/java/org/opencb/opencga/core/common/IOUtilsTest.java index f877df25bab..2a7ee36ed78 100644 --- a/opencga-lib/src/test/java/org/opencb/opencga/lib/common/IOUtilsTest.java +++ b/opencga-core/src/test/java/org/opencb/opencga/core/common/IOUtilsTest.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; import org.junit.Test; diff --git a/opencga-lib/src/test/java/org/opencb/opencga/lib/common/StringUtilsTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/common/StringUtilsTest.java similarity index 73% rename from opencga-lib/src/test/java/org/opencb/opencga/lib/common/StringUtilsTest.java rename to opencga-core/src/test/java/org/opencb/opencga/core/common/StringUtilsTest.java index 0865e8c742d..6b02d59e907 100644 --- a/opencga-lib/src/test/java/org/opencb/opencga/lib/common/StringUtilsTest.java +++ b/opencga-core/src/test/java/org/opencb/opencga/core/common/StringUtilsTest.java @@ -1,15 +1,10 @@ -package org.opencb.opencga.lib.common; +package org.opencb.opencga.core.common; -import com.google.common.primitives.Bytes; import org.junit.Test; import org.opencb.commons.test.GenericTest; -import java.io.BufferedOutputStream; import java.io.DataOutputStream; import java.io.FileOutputStream; -import java.io.OutputStream; - -import static org.junit.Assert.*; public class StringUtilsTest extends GenericTest { diff --git a/opencga-lib/src/test/resources/file.txt b/opencga-core/src/test/resources/file.txt similarity index 100% rename from opencga-lib/src/test/resources/file.txt rename to opencga-core/src/test/resources/file.txt diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 7d46ee75622..f3f0ab3b737 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -21,7 +21,7 @@ org.opencb.opencga - opencga-lib + opencga-core org.opencb.opencga diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/AnalysisWSServerJob.java b/opencga-server/src/main/java/org/opencb/opencga/server/AnalysisWSServerJob.java index 16a07f543d3..244adbab639 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/AnalysisWSServerJob.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/AnalysisWSServerJob.java @@ -1,7 +1,7 @@ package org.opencb.opencga.server; import org.opencb.opencga.analysis.AnalysisJobExecuter; -import org.opencb.opencga.lib.SgeManager; +import org.opencb.opencga.core.SgeManager; import javax.servlet.http.HttpServletRequest; import javax.ws.rs.*; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/FileWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/FileWSServer.java index 9341b566e72..1b6d1393232 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/FileWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/FileWSServer.java @@ -10,14 +10,13 @@ import org.opencb.datastore.core.QueryResult; import org.opencb.opencga.analysis.AnalysisExecutionException; import org.opencb.opencga.analysis.storage.AnalysisFileIndexer; -import org.opencb.opencga.analysis.storage.variant.CatalogVariantDBAdaptor; import org.opencb.opencga.catalog.CatalogException; import org.opencb.opencga.catalog.beans.DataStore; import org.opencb.opencga.catalog.beans.File; import org.opencb.opencga.catalog.beans.Job; import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.IOUtils; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.IOUtils; import org.opencb.opencga.storage.core.StorageManagerException; import org.opencb.opencga.storage.core.StorageManagerFactory; import org.opencb.opencga.storage.core.alignment.AlignmentStorageManager; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/JobWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/JobWSServer.java index 66c9ab2f830..160b51582bb 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/JobWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/JobWSServer.java @@ -13,7 +13,7 @@ import org.opencb.opencga.catalog.beans.File; import org.opencb.opencga.catalog.beans.Job; import org.opencb.opencga.catalog.beans.Tool; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import javax.servlet.http.HttpServletRequest; import javax.ws.rs.*; @@ -21,7 +21,6 @@ import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; import java.io.IOException; -import java.nio.file.Files; import java.nio.file.Paths; import java.util.*; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/OpenCGAWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/OpenCGAWSServer.java index 55d7b486b98..c527f1e1324 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/OpenCGAWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/OpenCGAWSServer.java @@ -17,7 +17,7 @@ import org.opencb.opencga.catalog.CatalogManager; import org.opencb.opencga.catalog.db.CatalogDBException; import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.opencb.opencga.storage.core.alignment.json.AlignmentDifferenceJsonMixin; import org.opencb.opencga.storage.core.variant.io.json.VariantSourceEntryJsonMixin; import org.opencb.opencga.storage.core.variant.io.json.VariantSourceJsonMixin; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/UtilsWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/UtilsWSServer.java index d6f4b862533..85bcd2170a1 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/UtilsWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/UtilsWSServer.java @@ -4,15 +4,13 @@ import com.fasterxml.jackson.core.JsonParser; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import org.glassfish.jersey.client.ClientConfig; import org.glassfish.jersey.media.multipart.FormDataParam; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.StringUtils; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.StringUtils; import javax.servlet.http.HttpServletRequest; import javax.ws.rs.*; import javax.ws.rs.client.ClientBuilder; -import javax.ws.rs.client.WebTarget; import javax.ws.rs.core.Context; import javax.ws.rs.core.MediaType; import javax.ws.rs.core.Response; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/AnalysisWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/AnalysisWSServer.java index c7fe704e3df..6d9fe666780 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/AnalysisWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/AnalysisWSServer.java @@ -11,9 +11,8 @@ import org.opencb.opencga.analysis.beans.Analysis; import org.opencb.opencga.analysis.beans.Execution; import org.opencb.opencga.analysis.beans.InputParam; -import org.opencb.opencga.lib.SgeManager; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.server.OpenCGAWSServer; +import org.opencb.opencga.core.SgeManager; +import org.opencb.opencga.core.common.StringUtils; import javax.servlet.http.HttpServletRequest; import javax.ws.rs.*; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/GenericWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/GenericWSServer.java index 7f24f37a11a..bd782f8ca98 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/GenericWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/GenericWSServer.java @@ -10,7 +10,7 @@ import org.opencb.datastore.core.QueryResponse; import org.opencb.opencga.account.CloudSessionManager; import org.opencb.opencga.account.io.IOManagementException; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/PublicStorageWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/PublicStorageWSServer.java index 83064926970..312441170fe 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/PublicStorageWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/PublicStorageWSServer.java @@ -17,9 +17,8 @@ import org.opencb.commons.containers.QueryResult; import org.opencb.commons.utils.FileUtils; import org.opencb.opencga.account.db.AccountManagementException; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.server.OpenCGAWSServer; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.StringUtils; /** * diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/StorageWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/StorageWSServer.java index e44c8f1010f..031142bca91 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/StorageWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/StorageWSServer.java @@ -5,9 +5,9 @@ import org.glassfish.jersey.media.multipart.FormDataParam; import org.opencb.opencga.account.beans.ObjectItem; import org.opencb.opencga.account.db.AccountManagementException; -import org.opencb.opencga.lib.common.IOUtils; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.IOUtils; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.TimeUtils; import javax.servlet.http.HttpServletRequest; import javax.ws.rs.*; @@ -27,7 +27,6 @@ import java.util.List; import org.opencb.commons.containers.QueryResult; -import org.opencb.opencga.server.OpenCGAWSServer; @Path("/account/{accountId}/storage/{bucketId}/{objectId}") public class StorageWSServer extends GenericWSServer { diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/UtilsWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/UtilsWSServer.java index 8199de09c18..4bbba980b09 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/UtilsWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/UtilsWSServer.java @@ -5,12 +5,10 @@ import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; //import org.opencb.cellbase.core.lib.dbquery.DBObjectMap; -import org.opencb.datastore.core.QueryResult; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.networks.Layout; -import org.opencb.opencga.lib.common.networks.Layout.LayoutResp; -import org.opencb.opencga.server.OpenCGAWSServer; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.networks.Layout; +import org.opencb.opencga.core.common.networks.Layout.LayoutResp; import javax.servlet.http.HttpServletRequest; import javax.ws.rs.*; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/VariantWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/VariantWSServer.java index 3998539c275..7932707070c 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/VariantWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/VariantWSServer.java @@ -7,7 +7,7 @@ import org.opencb.biodata.models.variant.VariantSource; import org.opencb.biodata.models.variant.stats.VariantStats; import org.opencb.datastore.core.QueryResult; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; import org.opencb.opencga.storage.core.variant.io.json.VariantSourceEntryJsonMixin; import org.opencb.opencga.storage.core.variant.io.json.GenotypeJsonMixin; import org.opencb.opencga.storage.core.variant.io.json.VariantSourceJsonMixin; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/WSResponse.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/WSResponse.java index 5c41e57c3cf..cbb14a1180d 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/WSResponse.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/WSResponse.java @@ -1,6 +1,6 @@ package org.opencb.opencga.serverold; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.common.XObject; public class WSResponse { String error = "None"; diff --git a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/IndexVariantsCommandExecutor.java b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/IndexVariantsCommandExecutor.java index 38d87d3c58f..73c95a3d637 100644 --- a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/IndexVariantsCommandExecutor.java +++ b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/IndexVariantsCommandExecutor.java @@ -3,11 +3,10 @@ import org.opencb.biodata.formats.io.FileFormatException; import org.opencb.biodata.models.variant.VariantSource; import org.opencb.datastore.core.ObjectMap; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.opencb.opencga.storage.core.StorageManagerException; import org.opencb.opencga.storage.core.StorageManagerFactory; import org.opencb.opencga.storage.core.variant.VariantStorageManager; -import org.opencb.opencga.storage.core.variant.annotation.*; import org.opencb.opencga.storage.core.variant.annotation.VariantAnnotationManager; import java.io.FileInputStream; diff --git a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/OpenCGAStorageMain.java b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/OpenCGAStorageMain.java index 73d91147de2..d97fb8b41f8 100644 --- a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/OpenCGAStorageMain.java +++ b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/OpenCGAStorageMain.java @@ -5,7 +5,6 @@ import com.fasterxml.jackson.core.JsonFactory; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.ObjectWriter; import com.google.common.io.Files; import org.opencb.biodata.formats.feature.gff.Gff; import org.opencb.biodata.formats.feature.gff.io.GffReader; @@ -24,9 +23,9 @@ import org.opencb.datastore.core.ObjectMap; import org.opencb.datastore.core.QueryOptions; import org.opencb.datastore.core.QueryResult; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.TimeUtils; -import org.opencb.opencga.lib.tools.accession.CreateAccessionTask; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.TimeUtils; +import org.opencb.opencga.core.tools.accession.CreateAccessionTask; import org.opencb.opencga.storage.core.StorageManagerException; import org.opencb.opencga.storage.core.StorageManagerFactory; import org.opencb.opencga.storage.core.StudyConfiguration; diff --git a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/service/OpenCGAStorageService.java b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/service/OpenCGAStorageService.java index ffc37c41ac2..5f926ca90a0 100644 --- a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/service/OpenCGAStorageService.java +++ b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/service/OpenCGAStorageService.java @@ -9,8 +9,7 @@ //import org.opencb.opencga.catalog.CatalogManager; //import org.opencb.opencga.catalog.db.CatalogDBException; //import org.opencb.opencga.catalog.io.CatalogIOManagerException; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/service/OpenCGAStorageServiceMain.java b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/service/OpenCGAStorageServiceMain.java index 0671ae10c5c..cf75de13c1f 100644 --- a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/service/OpenCGAStorageServiceMain.java +++ b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/service/OpenCGAStorageServiceMain.java @@ -1,6 +1,6 @@ package org.opencb.opencga.storage.app.service; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 33f06d1c7ea..fc8a1b9e813 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -17,7 +17,7 @@ org.opencb.opencga - opencga-lib + opencga-core org.opencb.cellbase diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/StorageManagerFactory.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/StorageManagerFactory.java index 26b9a513ed3..28a6b113f0f 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/StorageManagerFactory.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/StorageManagerFactory.java @@ -1,12 +1,11 @@ package org.opencb.opencga.storage.core; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.opencb.opencga.storage.core.alignment.AlignmentStorageManager; import org.opencb.opencga.storage.core.variant.VariantStorageManager; import java.net.URI; -import java.nio.file.Paths; import java.util.HashMap; import java.util.Map; import java.util.Properties; diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/sequence/SqliteSequenceDBAdaptor.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/sequence/SqliteSequenceDBAdaptor.java index 1e51940e2cf..b82079c8705 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/sequence/SqliteSequenceDBAdaptor.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/sequence/SqliteSequenceDBAdaptor.java @@ -5,7 +5,7 @@ import org.opencb.biodata.formats.sequence.fasta.dbadaptor.SequenceDBAdaptor; import org.opencb.biodata.formats.sequence.fasta.io.FastaReader; import org.opencb.biodata.models.feature.Region; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.common.XObject; import org.opencb.opencga.storage.core.utils.SqliteManager; import java.io.File; diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/utils/SqliteManager.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/utils/SqliteManager.java index 4dbe0a4d089..7e8ad50dbab 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/utils/SqliteManager.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/utils/SqliteManager.java @@ -1,6 +1,6 @@ package org.opencb.opencga.storage.core.utils; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.common.XObject; import org.sqlite.SQLiteConfig; import java.nio.file.Path; diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageManager.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageManager.java index 3e6adbef445..3638b27847a 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageManager.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageManager.java @@ -11,7 +11,7 @@ import org.opencb.commons.run.Task; import org.opencb.datastore.core.ObjectMap; import org.opencb.datastore.core.QueryOptions; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import org.opencb.opencga.storage.core.StorageManager; import org.opencb.opencga.storage.core.StorageManagerException; import org.opencb.opencga.storage.core.StudyConfiguration; @@ -31,7 +31,6 @@ import java.io.FileInputStream; import java.io.IOException; import java.io.InputStreamReader; -import java.lang.reflect.InvocationTargetException; import java.net.URI; import java.nio.file.Path; import java.nio.file.Paths; diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/VariantAnnotationManager.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/VariantAnnotationManager.java index 0723d0c9ac6..dbef0f77990 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/VariantAnnotationManager.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/VariantAnnotationManager.java @@ -9,7 +9,7 @@ import org.opencb.commons.io.DataReader; import org.opencb.commons.io.DataWriter; import org.opencb.datastore.core.QueryOptions; -import org.opencb.opencga.lib.common.TimeUtils; +import org.opencb.opencga.core.common.TimeUtils; import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor; import org.opencb.opencga.storage.core.variant.adaptors.VariantDBIterator; import org.slf4j.Logger; diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/ThreadRunnerTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/ThreadRunnerTest.java index 13bb73b60b7..16f53a89651 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/ThreadRunnerTest.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/ThreadRunnerTest.java @@ -9,7 +9,7 @@ import org.opencb.commons.run.Task; import org.opencb.commons.test.GenericTest; import org.opencb.datastore.core.ObjectMap; -import org.opencb.opencga.lib.common.StringUtils; +import org.opencb.opencga.core.common.StringUtils; import org.opencb.opencga.storage.core.runner.ThreadRunner; import java.io.FileOutputStream; diff --git a/opencga-storage/opencga-storage-hbase/pom.xml b/opencga-storage/opencga-storage-hbase/pom.xml index 2d39734a37a..ac609890d72 100644 --- a/opencga-storage/opencga-storage-hbase/pom.xml +++ b/opencga-storage/opencga-storage-hbase/pom.xml @@ -21,7 +21,7 @@ org.opencb.opencga - opencga-lib + opencga-core org.opencb.datastore diff --git a/opencga-storage/opencga-storage-hbase/src/main/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseDBAdaptor.java b/opencga-storage/opencga-storage-hbase/src/main/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseDBAdaptor.java index e2d199a9d21..07a2b1aec9a 100644 --- a/opencga-storage/opencga-storage-hbase/src/main/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseDBAdaptor.java +++ b/opencga-storage/opencga-storage-hbase/src/main/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseDBAdaptor.java @@ -9,7 +9,7 @@ import org.apache.hadoop.hbase.ZooKeeperConnectionException; import org.apache.hadoop.hbase.client.*; -import org.opencb.opencga.lib.auth.MonbaseCredentials; +import org.opencb.opencga.core.auth.MonbaseCredentials; import java.io.IOException; import java.net.UnknownHostException; diff --git a/opencga-storage/opencga-storage-hbase/src/main/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseWriter.java b/opencga-storage/opencga-storage-hbase/src/main/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseWriter.java index 55e6613c711..c56f4da5c23 100644 --- a/opencga-storage/opencga-storage-hbase/src/main/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseWriter.java +++ b/opencga-storage/opencga-storage-hbase/src/main/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseWriter.java @@ -24,7 +24,7 @@ import org.opencb.biodata.models.variant.protobuf.VariantStatsProtos; import org.opencb.biodata.models.variant.stats.VariantStats; import org.opencb.commons.utils.CryptoUtils; -import org.opencb.opencga.lib.auth.MonbaseCredentials; +import org.opencb.opencga.core.auth.MonbaseCredentials; import org.opencb.opencga.storage.core.variant.io.VariantDBWriter; import org.opencb.opencga.storage.core.variant.io.VariantEffectProtos; diff --git a/opencga-storage/opencga-storage-hbase/src/test/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseDBAdaptorTest.java b/opencga-storage/opencga-storage-hbase/src/test/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseDBAdaptorTest.java index 5333e3f59af..77bf7e4864f 100644 --- a/opencga-storage/opencga-storage-hbase/src/test/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseDBAdaptorTest.java +++ b/opencga-storage/opencga-storage-hbase/src/test/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseDBAdaptorTest.java @@ -17,8 +17,8 @@ import org.opencb.biodata.models.variant.stats.VariantStats; import org.opencb.commons.containers.QueryResult; import org.opencb.commons.containers.map.QueryOptions; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; -import org.opencb.opencga.lib.auth.MonbaseCredentials; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.MonbaseCredentials; import java.io.IOException; import java.net.UnknownHostException; diff --git a/opencga-storage/opencga-storage-hbase/src/test/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseWriterTest.java b/opencga-storage/opencga-storage-hbase/src/test/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseWriterTest.java index d45feef6192..a458f3ad161 100644 --- a/opencga-storage/opencga-storage-hbase/src/test/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseWriterTest.java +++ b/opencga-storage/opencga-storage-hbase/src/test/java/org/opencb/opencga/storage/hbase/variant/VariantHbaseWriterTest.java @@ -11,8 +11,8 @@ import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.VariantFactory; import org.opencb.biodata.models.variant.VariantSource; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; -import org.opencb.opencga.lib.auth.MonbaseCredentials; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.MonbaseCredentials; import java.io.IOException; import java.util.Arrays; diff --git a/opencga-storage/opencga-storage-mongodb/pom.xml b/opencga-storage/opencga-storage-mongodb/pom.xml index 626e1fc5f07..227d56ad390 100644 --- a/opencga-storage/opencga-storage-mongodb/pom.xml +++ b/opencga-storage/opencga-storage-mongodb/pom.xml @@ -17,7 +17,7 @@ org.opencb.opencga - opencga-lib + opencga-core org.opencb.opencga diff --git a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/BamManager.java b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/BamManager.java index db33cce1199..8cd21983488 100644 --- a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/BamManager.java +++ b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/BamManager.java @@ -11,11 +11,11 @@ import net.sf.samtools.*; import net.sf.samtools.SAMRecord.SAMTagAndValue; import org.opencb.biodata.models.feature.Region; -import org.opencb.opencga.lib.SgeManager; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.IOUtils; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.SgeManager; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.IOUtils; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.XObject; import org.opencb.opencga.storage.core.utils.SqliteManager; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/IndexedAlignmentDBAdaptor.java b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/IndexedAlignmentDBAdaptor.java index 084ecc2ca5f..7d0dc09e44d 100644 --- a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/IndexedAlignmentDBAdaptor.java +++ b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/IndexedAlignmentDBAdaptor.java @@ -18,12 +18,10 @@ import org.opencb.datastore.core.ComplexTypeConverter; import org.opencb.datastore.core.QueryOptions; import org.opencb.datastore.core.QueryResult; -import org.opencb.datastore.core.config.DataStoreServerAddress; import org.opencb.datastore.mongodb.MongoDBCollection; -import org.opencb.datastore.mongodb.MongoDBConfiguration; import org.opencb.datastore.mongodb.MongoDataStore; import org.opencb.datastore.mongodb.MongoDataStoreManager; -import org.opencb.opencga.lib.common.IOUtils; +import org.opencb.opencga.core.common.IOUtils; import org.opencb.opencga.storage.core.alignment.adaptors.AlignmentDBAdaptor; import org.opencb.opencga.storage.core.alignment.tasks.AlignmentRegionCoverageCalculatorTask; import org.opencb.opencga.storage.mongodb.utils.MongoCredentials; diff --git a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/MongoDBAlignmentStorageManager.java b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/MongoDBAlignmentStorageManager.java index 234d9dc92bd..fc7e5a65177 100644 --- a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/MongoDBAlignmentStorageManager.java +++ b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/MongoDBAlignmentStorageManager.java @@ -7,7 +7,7 @@ import org.opencb.commons.run.Runner; import org.opencb.commons.run.Task; import org.opencb.datastore.core.ObjectMap; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; import org.opencb.opencga.storage.core.alignment.AlignmentStorageManager; import org.opencb.opencga.storage.core.alignment.adaptors.AlignmentDBAdaptor; import org.opencb.opencga.storage.core.alignment.json.AlignmentCoverageJsonDataReader; diff --git a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/TabixAlignmentDBAdaptor.java b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/TabixAlignmentDBAdaptor.java index 3884ea9eca5..31f1b893c6a 100644 --- a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/TabixAlignmentDBAdaptor.java +++ b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/alignment/TabixAlignmentDBAdaptor.java @@ -26,11 +26,11 @@ import org.opencb.datastore.core.ObjectMap; import org.opencb.datastore.core.QueryOptions; import org.opencb.datastore.core.QueryResult; -import org.opencb.opencga.lib.auth.CellbaseCredentials; -import org.opencb.opencga.lib.auth.SqliteCredentials; -import org.opencb.opencga.lib.auth.TabixCredentials; -import org.opencb.opencga.lib.common.IOUtils; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.auth.CellbaseCredentials; +import org.opencb.opencga.core.auth.SqliteCredentials; +import org.opencb.opencga.core.auth.TabixCredentials; +import org.opencb.opencga.core.common.IOUtils; +import org.opencb.opencga.core.common.XObject; import org.opencb.opencga.storage.core.alignment.adaptors.AlignmentDBAdaptor; import org.opencb.opencga.storage.core.utils.SqliteManager; import org.slf4j.LoggerFactory; diff --git a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/utils/MongoCredentials.java b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/utils/MongoCredentials.java index 4328ed2e03b..69d8b1d9f64 100644 --- a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/utils/MongoCredentials.java +++ b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/utils/MongoCredentials.java @@ -3,8 +3,8 @@ import com.mongodb.MongoCredential; import org.opencb.datastore.core.config.DataStoreServerAddress; import org.opencb.datastore.mongodb.MongoDBConfiguration; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; -import org.opencb.opencga.lib.auth.OpenCGACredentials; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.OpenCGACredentials; import java.util.LinkedList; import java.util.List; diff --git a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/MongoDBStudyConfigurationManager.java b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/MongoDBStudyConfigurationManager.java index 9edb58bed2f..0e7baa4efc0 100644 --- a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/MongoDBStudyConfigurationManager.java +++ b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/MongoDBStudyConfigurationManager.java @@ -7,10 +7,9 @@ import org.opencb.datastore.core.QueryOptions; import org.opencb.datastore.core.QueryResult; import org.opencb.datastore.mongodb.MongoDBCollection; -import org.opencb.datastore.mongodb.MongoDBConfiguration; import org.opencb.datastore.mongodb.MongoDataStore; import org.opencb.datastore.mongodb.MongoDataStoreManager; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; import org.opencb.opencga.storage.core.StudyConfiguration; import org.opencb.opencga.storage.core.variant.StudyConfigurationManager; import org.opencb.opencga.storage.mongodb.utils.MongoCredentials; diff --git a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/MongoDBVariantStorageManager.java b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/MongoDBVariantStorageManager.java index f53abcd0eea..ab8b6818765 100644 --- a/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/MongoDBVariantStorageManager.java +++ b/opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/MongoDBVariantStorageManager.java @@ -8,7 +8,6 @@ import java.util.*; import java.util.concurrent.atomic.AtomicBoolean; -import org.opencb.biodata.formats.io.FileFormatException; import org.opencb.biodata.formats.variant.io.VariantReader; import org.opencb.biodata.formats.variant.io.VariantWriter; import org.opencb.biodata.models.variant.Variant; @@ -19,7 +18,7 @@ import org.opencb.commons.run.Task; import org.opencb.datastore.core.ObjectMap; import org.opencb.datastore.core.config.DataStoreServerAddress; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; import org.opencb.opencga.storage.core.StudyConfiguration; import org.opencb.opencga.storage.core.StorageManagerException; diff --git a/opencga-storage/opencga-storage-mongodb/src/test/java/org/opencb/opencga/storage/mongodb/variant/annotator/CellBaseVariantAnnotatorTest.java b/opencga-storage/opencga-storage-mongodb/src/test/java/org/opencb/opencga/storage/mongodb/variant/annotator/CellBaseVariantAnnotatorTest.java index f397aead5cc..9589909f3ab 100644 --- a/opencga-storage/opencga-storage-mongodb/src/test/java/org/opencb/opencga/storage/mongodb/variant/annotator/CellBaseVariantAnnotatorTest.java +++ b/opencga-storage/opencga-storage-mongodb/src/test/java/org/opencb/opencga/storage/mongodb/variant/annotator/CellBaseVariantAnnotatorTest.java @@ -2,10 +2,9 @@ import org.junit.Test; import org.opencb.cellbase.core.client.CellBaseClient; -import org.opencb.cellbase.core.common.core.CellbaseConfiguration; import org.opencb.commons.test.GenericTest; import org.opencb.datastore.core.QueryOptions; -import org.opencb.opencga.lib.common.Config; +import org.opencb.opencga.core.common.Config; import org.opencb.opencga.storage.core.StorageManagerException; import org.opencb.opencga.storage.core.StorageManagerFactory; import org.opencb.opencga.storage.core.variant.VariantStorageManager; diff --git a/opencga-storage/src/main/java/org/opencb/opencga/storage/alignment/hbase/AlignmentHBaseQueryBuilder.java b/opencga-storage/src/main/java/org/opencb/opencga/storage/alignment/hbase/AlignmentHBaseQueryBuilder.java index 86299269811..c2cf4af986c 100644 --- a/opencga-storage/src/main/java/org/opencb/opencga/storage/alignment/hbase/AlignmentHBaseQueryBuilder.java +++ b/opencga-storage/src/main/java/org/opencb/opencga/storage/alignment/hbase/AlignmentHBaseQueryBuilder.java @@ -21,7 +21,7 @@ import org.opencb.biodata.models.feature.Region; import org.opencb.commons.containers.QueryResult; import org.opencb.commons.containers.map.QueryOptions; -import org.opencb.opencga.lib.auth.MonbaseCredentials; +import org.opencb.opencga.core.auth.MonbaseCredentials; import org.opencb.opencga.storage.alignment.AlignmentQueryBuilder; import org.opencb.opencga.storage.alignment.AlignmentSummary; import org.opencb.opencga.storage.alignment.proto.AlignmentProto; diff --git a/opencga-storage/src/main/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionHBaseDataWriter.java b/opencga-storage/src/main/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionHBaseDataWriter.java index c62381c49f5..8215dbed420 100644 --- a/opencga-storage/src/main/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionHBaseDataWriter.java +++ b/opencga-storage/src/main/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionHBaseDataWriter.java @@ -2,7 +2,6 @@ import java.io.IOException; import java.io.InterruptedIOException; -import java.util.ArrayList; import java.util.LinkedList; import java.util.List; import java.util.Properties; @@ -19,7 +18,7 @@ import org.opencb.biodata.models.alignment.AlignmentRegion; import org.opencb.commons.containers.map.ObjectMap; import org.opencb.commons.io.DataWriter; -import org.opencb.opencga.lib.auth.MonbaseCredentials; +import org.opencb.opencga.core.auth.MonbaseCredentials; import org.opencb.opencga.storage.alignment.AlignmentSummary; import org.opencb.opencga.storage.alignment.AlignmentSummary.AlignmentRegionSummaryBuilder; import org.opencb.opencga.storage.alignment.proto.AlignmentProto; diff --git a/opencga-storage/src/main/java/org/opencb/opencga/storage/datamanagers/GffManager.java b/opencga-storage/src/main/java/org/opencb/opencga/storage/datamanagers/GffManager.java index d2259f44d2c..e39ae5b4d2e 100644 --- a/opencga-storage/src/main/java/org/opencb/opencga/storage/datamanagers/GffManager.java +++ b/opencga-storage/src/main/java/org/opencb/opencga/storage/datamanagers/GffManager.java @@ -1,6 +1,6 @@ package org.opencb.opencga.storage.datamanagers; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.common.XObject; import org.opencb.opencga.storage.indices.DefaultParser; import org.opencb.opencga.storage.indices.SqliteManager; diff --git a/opencga-storage/src/main/java/org/opencb/opencga/storage/datamanagers/VcfManager.java b/opencga-storage/src/main/java/org/opencb/opencga/storage/datamanagers/VcfManager.java index a331ea47c48..abfebd1497a 100644 --- a/opencga-storage/src/main/java/org/opencb/opencga/storage/datamanagers/VcfManager.java +++ b/opencga-storage/src/main/java/org/opencb/opencga/storage/datamanagers/VcfManager.java @@ -5,11 +5,11 @@ import com.fasterxml.jackson.databind.ObjectWriter; import org.opencb.cellbase.core.common.Region; import org.opencb.commons.bioformats.variant.vcf4.VcfRecord; -import org.opencb.opencga.lib.SgeManager; -import org.opencb.opencga.lib.common.Config; -import org.opencb.opencga.lib.common.IOUtils; -import org.opencb.opencga.lib.common.StringUtils; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.SgeManager; +import org.opencb.opencga.core.common.Config; +import org.opencb.opencga.core.common.IOUtils; +import org.opencb.opencga.core.common.StringUtils; +import org.opencb.opencga.core.common.XObject; import org.opencb.opencga.storage.TabixReader; import org.opencb.opencga.storage.indices.SqliteManager; import org.slf4j.Logger; diff --git a/opencga-storage/src/main/java/org/opencb/opencga/storage/indices/DefaultParser.java b/opencga-storage/src/main/java/org/opencb/opencga/storage/indices/DefaultParser.java index a23be65a22f..c9e50428882 100644 --- a/opencga-storage/src/main/java/org/opencb/opencga/storage/indices/DefaultParser.java +++ b/opencga-storage/src/main/java/org/opencb/opencga/storage/indices/DefaultParser.java @@ -1,6 +1,6 @@ package org.opencb.opencga.storage.indices; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.common.XObject; import java.util.Set; diff --git a/opencga-storage/src/main/java/org/opencb/opencga/storage/variant/sqlite/VariantSqliteDBAdaptor.java b/opencga-storage/src/main/java/org/opencb/opencga/storage/variant/sqlite/VariantSqliteDBAdaptor.java index 50c182f3d62..b6b4a3611c6 100644 --- a/opencga-storage/src/main/java/org/opencb/opencga/storage/variant/sqlite/VariantSqliteDBAdaptor.java +++ b/opencga-storage/src/main/java/org/opencb/opencga/storage/variant/sqlite/VariantSqliteDBAdaptor.java @@ -11,8 +11,8 @@ import org.opencb.commons.containers.QueryResult; import org.opencb.commons.containers.map.ObjectMap; import org.opencb.commons.containers.map.QueryOptions; -import org.opencb.opencga.lib.auth.SqliteCredentials; -import org.opencb.opencga.lib.common.XObject; +import org.opencb.opencga.core.auth.SqliteCredentials; +import org.opencb.opencga.core.common.XObject; import org.opencb.opencga.storage.indices.SqliteManager; import java.io.IOException; diff --git a/opencga-storage/src/main/java/org/opencb/opencga/storage/variant/sqlite/VariantSqliteWriter.java b/opencga-storage/src/main/java/org/opencb/opencga/storage/variant/sqlite/VariantSqliteWriter.java index 863f5478e66..cd89371069d 100644 --- a/opencga-storage/src/main/java/org/opencb/opencga/storage/variant/sqlite/VariantSqliteWriter.java +++ b/opencga-storage/src/main/java/org/opencb/opencga/storage/variant/sqlite/VariantSqliteWriter.java @@ -15,7 +15,7 @@ import org.opencb.biodata.models.variant.stats.VariantStats; import org.opencb.commons.db.SqliteSingletonConnection; -import org.opencb.opencga.lib.auth.SqliteCredentials; +import org.opencb.opencga.core.auth.SqliteCredentials; /** * @author Alejandro Aleman Ramos diff --git a/opencga-storage/src/test/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionCoverageHBaseDataWriterTest.java b/opencga-storage/src/test/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionCoverageHBaseDataWriterTest.java index c19962393b1..6a3aad8dccf 100644 --- a/opencga-storage/src/test/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionCoverageHBaseDataWriterTest.java +++ b/opencga-storage/src/test/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionCoverageHBaseDataWriterTest.java @@ -11,8 +11,8 @@ import org.opencb.commons.run.Runner; import org.opencb.commons.run.Task; import org.opencb.commons.test.GenericTest; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; -import org.opencb.opencga.lib.auth.MonbaseCredentials; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.MonbaseCredentials; import org.opencb.opencga.storage.alignment.hbase.AlignmentRegionCoverageHBaseDataWriter; import java.io.IOException; diff --git a/opencga-storage/src/test/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionHBaseDataWriterTest.java b/opencga-storage/src/test/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionHBaseDataWriterTest.java index 2c271db4f5b..8c485fa66cb 100644 --- a/opencga-storage/src/test/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionHBaseDataWriterTest.java +++ b/opencga-storage/src/test/java/org/opencb/opencga/storage/alignment/hbase/AlignmentRegionHBaseDataWriterTest.java @@ -14,8 +14,8 @@ import org.opencb.commons.containers.QueryResult; import org.opencb.commons.containers.map.QueryOptions; import org.opencb.commons.test.GenericTest; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; -import org.opencb.opencga.lib.auth.MonbaseCredentials; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.MonbaseCredentials; import org.opencb.opencga.storage.alignment.hbase.AlignmentHBaseQueryBuilder; import org.opencb.opencga.storage.alignment.hbase.AlignmentRegionHBaseDataWriter; diff --git a/opencga-storage/src/test/java/org/opencb/opencga/storage/variant/VariantSqliteQueryBuilderTest.java b/opencga-storage/src/test/java/org/opencb/opencga/storage/variant/VariantSqliteQueryBuilderTest.java index 9a0d303f571..b9870fd3c12 100644 --- a/opencga-storage/src/test/java/org/opencb/opencga/storage/variant/VariantSqliteQueryBuilderTest.java +++ b/opencga-storage/src/test/java/org/opencb/opencga/storage/variant/VariantSqliteQueryBuilderTest.java @@ -6,8 +6,8 @@ import org.opencb.commons.containers.QueryResult; import org.opencb.commons.containers.map.QueryOptions; import org.opencb.commons.test.GenericTest; -import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; -import org.opencb.opencga.lib.auth.SqliteCredentials; +import org.opencb.opencga.core.auth.IllegalOpenCGACredentialsException; +import org.opencb.opencga.core.auth.SqliteCredentials; import java.io.IOException; import java.nio.file.Paths; diff --git a/pom.xml b/pom.xml index 665a69d2614..32ddb69376e 100644 --- a/pom.xml +++ b/pom.xml @@ -11,7 +11,7 @@ opencga-app - opencga-lib + opencga-core opencga-storage opencga-analysis opencga-server @@ -107,7 +107,7 @@ org.opencb.opencga - opencga-lib + opencga-core ${opencga.version}