Module opencga-lib has been renamed to opencga-core, closes #39

opencb · Apr 26, 2015 · ee7bcb0 · ee7bcb0
1 parent 8fdbd81
commit ee7bcb0
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Showing 108 changed files with 158 additions and 207 deletions.
diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml
@@ -17,7 +17,7 @@
     <dependencies>
         <dependency>
             <groupId>org.opencb.opencga</groupId>
-            <artifactId>opencga-lib</artifactId>
+            <artifactId>opencga-core</artifactId>
         </dependency>
         <dependency>
             <groupId>org.opencb.opencga</groupId>

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
@@ -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
@@ -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
@@ -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/...s/src/main/java/org/opencb/opencga/analysis/storage/CatalogStudyConfigurationManager.java b/...s/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/...c/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantStorageManager.java b/...c/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/...ga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/VariantStorage.java b/...ga-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
@@ -27,7 +27,7 @@
         </dependency>
         <dependency>
             <groupId>org.opencb.opencga</groupId>
-            <artifactId>opencga-lib</artifactId>
+            <artifactId>opencga-core</artifactId>
             <exclusions>
                 <exclusion>
                     <artifactId>commons-codec</artifactId>

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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -17,7 +17,7 @@
     <dependencies>
         <dependency>
             <groupId>org.opencb.opencga</groupId>
-            <artifactId>opencga-lib</artifactId>
+            <artifactId>opencga-core</artifactId>
         </dependency>
 
         <dependency>

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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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 → opencga-core/pom.xml b/opencga-lib/pom.xml → opencga-core/pom.xml
@@ -10,7 +10,7 @@
         <relativePath>..</relativePath>
     </parent>
 
-    <artifactId>opencga-lib</artifactId>
+    <artifactId>opencga-core</artifactId>
     <version>${opencga.version}</version>
     <packaging>jar</packaging>
 

diff --git a/...va/org/opencb/opencga/lib/SgeManager.java → ...a/org/opencb/opencga/core/SgeManager.java b/...va/org/opencb/opencga/lib/SgeManager.java → ...a/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;