From 39bc9bc97d06e6846eaf13b57a509996b6a918f8 Mon Sep 17 00:00:00 2001 From: imedina Date: Sun, 26 Apr 2015 20:58:29 +0100 Subject: [PATCH] License changed, Apache License v2 is now used --- opencga-analysis/pom.xml | 16 + .../analysis/AnalysisExecutionException.java | 16 + .../opencga/analysis/AnalysisJobExecuter.java | 16 + .../analysis/AnalysisOutputRecorder.java | 16 + .../opencb/opencga/analysis/beans/Acl.java | 16 + .../opencga/analysis/beans/Analysis.java | 16 + .../opencb/opencga/analysis/beans/Author.java | 16 + .../opencga/analysis/beans/ConfigAttr.java | 16 + .../opencga/analysis/beans/Example.java | 16 + .../opencga/analysis/beans/ExampleOption.java | 16 + .../opencga/analysis/beans/Execution.java | 16 + .../opencb/opencga/analysis/beans/Icon.java | 16 + .../opencga/analysis/beans/InputParam.java | 16 + .../opencb/opencga/analysis/beans/Option.java | 16 + .../analysis/storage/AnalysisFileIndexer.java | 16 + .../CatalogStudyConfigurationManager.java | 16 + .../variant/CatalogVariantDBAdaptor.java | 16 + .../variant/CatalogVariantStorageManager.java | 16 + .../storage/variant/VariantStorage.java | 16 + .../build/analysis/hpg-variant/results.js | 16 + .../build/analysis/network-miner/results.js | 16 + .../build/analysis/pathiways/results.js | 16 + .../build/analysis/reactome-fi/results.js | 16 + opencga-app/build/analysis/snow/results.js | 16 + opencga-app/build/analysis/variant/results.js | 16 + opencga-app/pom.xml | 16 + .../opencga/app/cli/main/OpenCGAMain.java | 16 + .../opencga/app/cli/main/OptionsParser.java | 16 + .../opencb/opencga/app/daemon/DaemonLoop.java | 16 + .../opencga/app/daemon/OpenCGADaemon.java | 16 + .../opencga/app/daemon/OptionParser.java | 16 + .../opencga/app/daemon/rest/AdminServlet.java | 16 + .../app/daemon/rest/DaemonServlet.java | 16 + .../opencga/app/daemon/rest/TestServlet.java | 16 + .../opencga/app/localserver/AdminServlet.java | 16 + .../opencga/app/localserver/FetchServlet.java | 16 + .../app/localserver/GetFoldersServlet.java | 16 + .../opencga/app/localserver/LocalServer.java | 16 + .../src/main/resources/account.properties | 16 + .../src/main/resources/analysis.properties | 16 + .../src/main/resources/catalog.properties | 16 + .../src/main/resources/daemon.properties | 16 + .../src/main/resources/log4j.properties | 16 + .../src/main/resources/storage.properties | 16 + opencga-catalog/pom.xml | 16 + .../opencga/catalog/CatalogException.java | 16 + .../opencga/catalog/CatalogFileManager.java | 16 + .../opencga/catalog/CatalogManager.java | 16 + .../CatalogSampleAnnotationsLoader.java | 16 + .../CatalogSampleAnnotationsValidator.java | 16 + .../org/opencb/opencga/catalog/beans/Acl.java | 16 + .../opencga/catalog/beans/Analysis.java | 16 + .../opencga/catalog/beans/Annotation.java | 16 + .../opencga/catalog/beans/AnnotationSet.java | 16 + .../opencb/opencga/catalog/beans/Cohort.java | 16 + .../opencga/catalog/beans/DataStore.java | 16 + .../opencb/opencga/catalog/beans/Dataset.java | 16 + .../opencga/catalog/beans/Experiment.java | 16 + .../opencb/opencga/catalog/beans/File.java | 16 + .../opencb/opencga/catalog/beans/Index.java | 16 + .../opencga/catalog/beans/Individual.java | 16 + .../org/opencb/opencga/catalog/beans/Job.java | 16 + .../opencga/catalog/beans/Metadata.java | 16 + .../opencb/opencga/catalog/beans/Project.java | 16 + .../opencb/opencga/catalog/beans/Sample.java | 16 + .../opencb/opencga/catalog/beans/Session.java | 16 + .../opencb/opencga/catalog/beans/Study.java | 16 + .../opencb/opencga/catalog/beans/Tool.java | 16 + .../opencb/opencga/catalog/beans/User.java | 16 + .../opencga/catalog/beans/Variable.java | 16 + .../opencga/catalog/beans/VariableSet.java | 16 + .../opencga/catalog/core/CatalogClient.java | 16 + .../opencga/catalog/core/CatalogDBClient.java | 16 + .../opencga/catalog/core/ICatalogManager.java | 16 + .../opencga/catalog/db/CatalogDBAdaptor.java | 16 + .../catalog/db/CatalogDBException.java | 16 + .../catalog/db/CatalogMongoDBAdaptor.java | 16 + .../catalog/db/CatalogMongoDBUtils.java | 16 + .../opencga/catalog/io/CatalogIOManager.java | 16 + .../catalog/io/CatalogIOManagerException.java | 16 + .../catalog/io/CatalogIOManagerFactory.java | 16 + .../catalog/io/HdfsCatalogIOManager.java | 16 + .../catalog/io/PosixCatalogIOManager.java | 16 + .../catalog/CatalogFileManagerTest.java | 16 + .../opencga/catalog/CatalogManagerTest.java | 16 + .../CatalogSampleAnnotationsLoaderTest.java | 16 + .../catalog/core/CatalogDBClientTest.java | 16 + .../catalog/db/CatalogMongoDBAdaptorTest.java | 16 + .../catalog/io/PosixCatalogIOManagerTest.java | 16 + .../src/test/resources/catalog.properties | 16 + opencga-core/pom.xml | 16 + .../org/opencb/opencga/core/SgeManager.java | 16 + .../core/auth/CellbaseCredentials.java | 16 + .../IllegalOpenCGACredentialsException.java | 16 + .../opencga/core/auth/MonbaseCredentials.java | 16 + .../opencga/core/auth/OpenCGACredentials.java | 16 + .../opencga/core/auth/SqliteCredentials.java | 16 + .../opencga/core/auth/TabixCredentials.java | 16 + .../opencga/core/common/ArrayUtils.java | 16 + .../opencb/opencga/core/common/Config.java | 16 + .../opencb/opencga/core/common/IOUtils.java | 16 + .../opencb/opencga/core/common/ListUtils.java | 16 + .../opencb/opencga/core/common/MailUtils.java | 16 + .../opencga/core/common/StringUtils.java | 16 + .../opencb/opencga/core/common/TimeUtils.java | 16 + .../opencb/opencga/core/common/XObject.java | 16 + .../opencga/core/common/networks/Layout.java | 16 + .../opencga/core/data/source/FileSource.java | 16 + .../opencga/core/data/source/S3Source.java | 16 + .../opencga/core/data/source/Source.java | 16 + .../opencga/core/data/source/UrlSource.java | 16 + .../org/opencb/opencga/core/exec/Command.java | 16 + .../opencga/core/exec/RunnableProcess.java | 16 + .../opencga/core/exec/SingleProcess.java | 16 + .../tools/accession/CombinationIterator.java | 16 + .../tools/accession/CreateAccessionTask.java | 16 + .../core/tools/accession/LRUCache.java | 16 + .../opencga/core/common/IOUtilsTest.java | 16 + .../opencga/core/common/StringUtilsTest.java | 16 + opencga-server/pom.xml | 16 + .../src/main/java/encryption/AESCipher.java | 16 + .../src/main/java/encryption/KeyEncoding.java | 16 + .../main/java/encryption/KeystoreUtil.java | 16 + .../opencga/server/AnalysisWSServer.java | 16 + .../opencga/server/AnalysisWSServerJob.java | 16 + .../opencb/opencga/server/CohortWSServer.java | 16 + .../opencb/opencga/server/FileWSServer.java | 16 + .../opencb/opencga/server/JobWSServer.java | 16 + .../opencga/server/OpenCGAWSServer.java | 16 + .../opencga/server/ProjectWSServer.java | 16 + .../opencb/opencga/server/SampleWSServer.java | 16 + .../opencb/opencga/server/StudyWSServer.java | 16 + .../opencb/opencga/server/TestWSServer.java | 16 + .../opencb/opencga/server/ToolWSServer.java | 16 + .../opencb/opencga/server/UserWSServer.java | 16 + .../opencb/opencga/server/UtilsWSServer.java | 16 + .../opencga/server/VariableWSServer.java | 16 + .../opencga/serverold/AccountWSServer.java | 16 + .../opencga/serverold/AdminWSServer.java | 16 + .../opencga/serverold/AnalysisWSServer.java | 16 + .../opencb/opencga/serverold/BamWSServer.java | 16 + .../opencga/serverold/GenericWSServer.java | 16 + .../serverold/GeocodingAddressService.java | 16 + .../opencb/opencga/serverold/GffWSServer.java | 16 + .../serverold/JobAnalysisWSServer.java | 16 + .../serverold/PublicStorageWSServer.java | 16 + .../opencga/serverold/StorageWSServer.java | 16 + .../opencga/serverold/UtilsWSServer.java | 16 + .../opencga/serverold/VariantWSServer.java | 16 + .../opencb/opencga/serverold/VcfWSServer.java | 16 + .../opencb/opencga/serverold/WSResponse.java | 16 + .../storage/VariantStorageService.java | 16 + .../src/main/resources/aes.properties | 16 + .../src/main/resources/application.properties | 16 + .../src/main/resources/catalog.properties | 16 + .../src/main/webapp/WEB-INF/web.xml | 16 + opencga-server/src/main/webapp/index.html | 16 + .../src/main/webapp/swagger-ui/css/reset.css | 16 + .../src/main/webapp/swagger-ui/css/screen.css | 16 + .../webapp/swagger-ui/lib/backbone-min.js | 16 + .../webapp/swagger-ui/lib/handlebars-1.0.0.js | 36 +- .../swagger-ui/lib/highlight.7.3.pack.js | 16 + .../webapp/swagger-ui/lib/jquery-1.8.0.min.js | 16 + .../swagger-ui/lib/jquery.ba-bbq.min.js | 19 +- .../swagger-ui/lib/jquery.slideto.min.js | 16 + .../swagger-ui/lib/jquery.wiggle.min.js | 16 + .../webapp/swagger-ui/lib/shred.bundle.js | 16 + .../webapp/swagger-ui/lib/shred/content.js | 16 + .../webapp/swagger-ui/lib/swagger-oauth.js | 16 + .../src/main/webapp/swagger-ui/lib/swagger.js | 16 + .../webapp/swagger-ui/lib/underscore-min.js | 16 + .../src/main/webapp/swagger-ui/o2c.html | 16 + .../src/main/webapp/swagger-ui/swagger-ui.js | 390 +++++++++--------- .../main/webapp/swagger-ui/swagger-ui.min.js | 16 + .../server/ws/GenericWSServerTest.java | 16 + .../server/ws/OpenCGAWSServerTest.java | 16 + .../server/ws/ProjectWSServerTest.java | 16 + .../opencga/server/ws/StudyWSServerTest.java | 16 + .../opencga/server/ws/UserWSServerTest.java | 16 + .../opencga/server/ws/WSServerTestUtils.java | 16 + opencga-storage/opencga-storage-app/pom.xml | 16 + .../storage/app/cli/CliOptionsParser.java | 16 + .../storage/app/cli/CommandExecutor.java | 16 + .../app/cli/IndexVariantsCommandExecutor.java | 16 + .../storage/app/cli/OpenCGAStorageMain.java | 16 + .../storage/app/cli/OptionsParser.java | 16 + .../opencga/storage/app/cli/StorageMain.java | 16 + .../app/service/OpenCGAStorageService.java | 16 + .../service/OpenCGAStorageServiceMain.java | 16 + .../storage/app/service/OptionParser.java | 16 + .../app/service/rest/DaemonServlet.java | 16 + .../app/service/rest/FilesServlet.java | 16 + .../storage/app/service/rest/TestServlet.java | 16 + .../app/service/rest/VariantsWSServer.java | 16 + .../src/main/resources/catalog.properties | 16 + .../src/main/resources/evs-mapping.properties | 16 + .../main/resources/storage-service.properties | 16 + .../src/main/resources/storage.properties | 16 + opencga-storage/opencga-storage-core/pom.xml | 16 + .../opencga/storage/core/StorageETL.java | 16 + .../opencga/storage/core/StorageManager.java | 16 + .../storage/core/StorageManagerException.java | 16 + .../storage/core/StorageManagerFactory.java | 16 + .../storage/core/StudyConfiguration.java | 16 + .../core/adaptors/ArchiveDBAdaptor.java | 16 + .../storage/core/adaptors/StudyDBAdaptor.java | 16 + .../alignment/AlignmentStorageManager.java | 16 + .../adaptors/AlignmentDBAdaptor.java | 16 + .../json/AlignmentCoverageJsonDataReader.java | 16 + .../json/AlignmentCoverageJsonDataWriter.java | 16 + .../json/AlignmentDifferenceJsonMixin.java | 16 + .../json/AlignmentJsonDataReader.java | 16 + .../json/AlignmentJsonDataWriter.java | 16 + .../tasks/AlignmentRegionCompactorTask.java | 16 + ...AlignmentRegionCoverageCalculatorTask.java | 16 + .../core/runner/SimpleThreadRunner.java | 16 + .../storage/core/runner/StringDataReader.java | 16 + .../storage/core/runner/StringDataWriter.java | 16 + .../storage/core/runner/ThreadRunner.java | 16 + .../sequence/SqliteSequenceDBAdaptor.java | 16 + .../storage/core/utils/SqliteManager.java | 16 + .../FileStudyConfigurationManager.java | 16 + .../variant/StudyConfigurationManager.java | 16 + .../variant/VariantJsonTransformTask.java | 16 + .../core/variant/VariantStorageManager.java | 16 + .../variant/adaptors/VariantDBAdaptor.java | 16 + .../variant/adaptors/VariantDBIterator.java | 16 + .../adaptors/VariantSourceDBAdaptor.java | 16 + .../annotation/CellBaseVariantAnnotator.java | 16 + .../annotation/VariantAnnotationManager.java | 16 + .../variant/annotation/VariantAnnotator.java | 16 + .../annotation/VariantAnnotatorException.java | 16 + .../annotation/VepVariantAnnotator.java | 16 + .../core/variant/io/VariantDBReader.java | 16 + .../core/variant/io/VariantDBWriter.java | 16 + .../core/variant/io/VariantEffectProtos.java | 16 + .../core/variant/io/VariantFieldsProtos.java | 16 + .../variant/io/json/GenotypeJsonMixin.java | 16 + .../io/json/VariantAnnotationMixin.java | 16 + .../variant/io/json/VariantJsonReader.java | 16 + .../variant/io/json/VariantJsonWriter.java | 16 + .../io/json/VariantSourceEntryJsonMixin.java | 16 + .../io/json/VariantSourceJsonMixin.java | 16 + .../io/json/VariantStatsJsonMixin.java | 16 + .../io/json/VariantStatsJsonSerializer.java | 16 + .../stats/VariantStatisticsCalculator.java | 16 + .../stats/VariantStatisticsManager.java | 16 + .../variant/stats/VariantStatsWrapper.java | 16 + .../storage/core/ThreadRunnerTest.java | 16 + .../sequence/SqliteSequenceDBAdaptorTest.java | 16 + .../variant/VariantStorageManagerTest.java | 16 + .../adaptors/VariantDBAdaptorTest.java | 16 + opencga-storage/opencga-storage-hbase/pom.xml | 16 + .../ArchivedVariantFileToHbaseConverter.java | 16 + .../HBaseToArchivedVariantFileConverter.java | 16 + .../variant/HBaseToVariantConverter.java | 16 + .../variant/HBaseToVariantStatsConverter.java | 16 + .../HbaseToVariantSourceConverter.java | 16 + .../hbase/variant/VariantHbaseDBAdaptor.java | 16 + .../hbase/variant/VariantHbaseWriter.java | 16 + .../VariantSourceToHbaseConverter.java | 16 + .../variant/VariantStatsToHbaseConverter.java | 16 + .../variant/VariantToHBaseConverter.java | 16 + .../variant/VariantHbaseDBAdaptorTest.java | 16 + .../hbase/variant/VariantHbaseWriterTest.java | 16 + .../VariantStatsToHbaseConverterTest.java | 16 + .../opencga-storage-mongodb/pom.xml | 16 + .../AlignmentIndexNotExistsException.java | 16 + .../alignment/AlignmentMetaDataDBAdaptor.java | 16 + .../storage/mongodb/alignment/BamManager.java | 16 + .../storage/mongodb/alignment/BamReader.java | 16 + .../alignment/CoverageMongoDBWriter.java | 16 + .../DBObjectToMeanCoverageConverter.java | 16 + .../DBObjectToRegionCoverageConverter.java | 16 + .../alignment/IndexedAlignmentDBAdaptor.java | 16 + .../MongoDBAlignmentStorageManager.java | 16 + .../alignment/TabixAlignmentDBAdaptor.java | 16 + .../mongodb/utils/MongoCredentials.java | 16 + .../storage/mongodb/utils/TabixReader.java | 39 +- .../variant/DBObjectToSamplesConverter.java | 16 + ...DBObjectToStudyConfigurationConverter.java | 16 + .../DBObjectToVariantAnnotationConverter.java | 16 + .../variant/DBObjectToVariantConverter.java | 16 + .../DBObjectToVariantSourceConverter.java | 16 + ...DBObjectToVariantSourceEntryConverter.java | 16 + .../DBObjectToVariantStatsConverter.java | 16 + .../MongoDBStudyConfigurationManager.java | 16 + .../variant/MongoDBVariantStorageManager.java | 16 + .../mongodb/variant/StudyMongoDBAdaptor.java | 16 + .../variant/VariantMongoDBAdaptor.java | 16 + .../variant/VariantMongoDBIterator.java | 16 + .../mongodb/variant/VariantMongoDBWriter.java | 16 + .../variant/VariantSourceMongoDBAdaptor.java | 16 + .../main/resources/storage-mongodb.properties | 16 + .../AlignmentMetaDataDBAdaptorTest.java | 16 + .../DBObjectToMeanCoverageConverterTest.java | 16 + .../IndexedAlignmentDBAdaptorTest.java | 16 + .../DBObjectToVariantConverterTest.java | 16 + .../DBObjectToVariantSourceConverterTest.java | 16 + ...jectToVariantSourceEntryConverterTest.java | 16 + .../DBObjectToVariantStatsConverterTest.java | 16 + .../MongoVariantStorageManagerTest.java | 16 + .../variant/VariantMongoDBAdaptorTest.java | 16 + .../variant/VariantMongoDBWriterTest.java | 16 + .../CellBaseVariantAnnotatorTest.java | 16 + .../resources/storage-mongo-test.properties | 16 + opencga-storage/pom.xml | 16 + .../AlignmentCoverageSqliteDataWriter.java | 16 + .../alignment/AlignmentHBaseDataWriter.java | 16 + .../storage/alignment/AlignmentSummary.java | 16 + .../alignment/hbase/AlignmentHBase.java | 16 + .../hbase/AlignmentHBaseDataReader.java | 16 + .../alignment/hbase/AlignmentHBaseHeader.java | 16 + .../hbase/AlignmentHBaseQueryBuilder.java | 16 + ...lignmentRegionCoverageHBaseDataWriter.java | 16 + .../hbase/AlignmentRegionHBaseDataWriter.java | 16 + .../storage/alignment/hbase/HBaseManager.java | 16 + .../alignment/json/AlignmentJsonMixin.java | 16 + .../alignment/proto/AlignmentProto.java | 16 + .../alignment/proto/AlignmentProtoHelper.java | 16 + .../AlignmentRegionCoverageFromJsonTask.java | 16 + .../tasks/AlignmentRegionSummarizeTask.java | 16 + .../storage/datamanagers/FeatureManager.java | 16 + .../storage/datamanagers/GffManager.java | 16 + .../storage/datamanagers/VcfManager.java | 16 + .../storage/indices/DefaultParser.java | 16 + .../sqlite/VariantSqliteDBAdaptor.java | 16 + .../variant/sqlite/VariantSqliteWriter.java | 16 + .../alignment/AlignmentProtoHelperTest.java | 16 + .../alignment/AlignmentRegionSummaryTest.java | 16 + ...mentRegionCoverageHBaseDataWriterTest.java | 16 + .../AlignmentRegionHBaseDataWriterTest.java | 16 + .../alignment/json/AlignmentJsonDataTest.java | 16 + .../VariantSqliteQueryBuilderTest.java | 16 + pom.xml | 16 + 335 files changed, 5541 insertions(+), 239 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index b8bd30ce3be..94f762c34fa 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -1,4 +1,20 @@ + + diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisExecutionException.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisExecutionException.java index d7e5e465ae8..6c4097290a6 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisExecutionException.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisExecutionException.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis; 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 57181b33c87..c33db62d96e 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis; import com.fasterxml.jackson.databind.ObjectMapper; 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 9374e254791..a6b1858afca 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis; import org.opencb.datastore.core.ObjectMap; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Acl.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Acl.java index 5bb7b9f654b..96ed4fc5036 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Acl.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Acl.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; public class Acl { diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Analysis.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Analysis.java index 356536582ac..21c9ba09156 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Analysis.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Analysis.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; import java.util.List; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Author.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Author.java index 4299ba31dbf..362857d2fe4 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Author.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Author.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; public class Author { diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/ConfigAttr.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/ConfigAttr.java index a5293b7776f..96a69bf84f9 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/ConfigAttr.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/ConfigAttr.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; public class ConfigAttr { diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Example.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Example.java index b6e9e0931ef..8ba29714563 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Example.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Example.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; import java.util.List; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/ExampleOption.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/ExampleOption.java index b0d89ab801a..3e065cb56aa 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/ExampleOption.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/ExampleOption.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Execution.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Execution.java index 29df60eb365..cedb24d87fa 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Execution.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Execution.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; import java.util.List; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Icon.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Icon.java index 9ff3d9f5d4d..26b0db9f12e 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Icon.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Icon.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; public class Icon { diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/InputParam.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/InputParam.java index b8916046223..03220f43075 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/InputParam.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/InputParam.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; public class InputParam { diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Option.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Option.java index c5f65a5d9f5..017b16aa236 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Option.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/beans/Option.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.beans; public class Option { 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 c93e3ec73f0..73468f1df16 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.storage; import org.opencb.biodata.models.variant.VariantSource; 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 45d473e2da0..28889c26bb6 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.storage; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantDBAdaptor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantDBAdaptor.java index e8b9810db99..9c81e1f1047 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantDBAdaptor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/storage/variant/CatalogVariantDBAdaptor.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.storage.variant; 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 a797d7a036a..81b2b56cdde 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.storage.variant; import org.opencb.biodata.formats.io.FileFormatException; 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 525bcaa698e..0d471d577b1 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.analysis.storage.variant; import org.opencb.datastore.core.QueryOptions; diff --git a/opencga-app/build/analysis/hpg-variant/results.js b/opencga-app/build/analysis/hpg-variant/results.js index 9d4fd53bcfe..88785810aae 100644 --- a/opencga-app/build/analysis/hpg-variant/results.js +++ b/opencga-app/build/analysis/hpg-variant/results.js @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + var RESULT = { "hpg-variant.effect": { "layout": { diff --git a/opencga-app/build/analysis/network-miner/results.js b/opencga-app/build/analysis/network-miner/results.js index e7134d5cfc7..16dda3664d6 100644 --- a/opencga-app/build/analysis/network-miner/results.js +++ b/opencga-app/build/analysis/network-miner/results.js @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + var RESULT = { "network-miner.default": { "layout": { diff --git a/opencga-app/build/analysis/pathiways/results.js b/opencga-app/build/analysis/pathiways/results.js index 6c9395ba574..612b0b7ec32 100644 --- a/opencga-app/build/analysis/pathiways/results.js +++ b/opencga-app/build/analysis/pathiways/results.js @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + var RESULT = { "pathiways": { "layout": { diff --git a/opencga-app/build/analysis/reactome-fi/results.js b/opencga-app/build/analysis/reactome-fi/results.js index e063e1b42ed..5bd00bdb915 100644 --- a/opencga-app/build/analysis/reactome-fi/results.js +++ b/opencga-app/build/analysis/reactome-fi/results.js @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + var RESULT = { "reactome-fi.default": { "layout": { diff --git a/opencga-app/build/analysis/snow/results.js b/opencga-app/build/analysis/snow/results.js index f9790c2cda0..b5c241fbca0 100644 --- a/opencga-app/build/analysis/snow/results.js +++ b/opencga-app/build/analysis/snow/results.js @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + var RESULT = { "snow.default": { "layout": { diff --git a/opencga-app/build/analysis/variant/results.js b/opencga-app/build/analysis/variant/results.js index c6563abd34f..7e04c4e7988 100644 --- a/opencga-app/build/analysis/variant/results.js +++ b/opencga-app/build/analysis/variant/results.js @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + var RESULT = { "variant": { "layout": { diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 690e371e095..81245f44b6c 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -1,4 +1,20 @@ + + 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 04d96254f59..f56a3515e29 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.cli.main; import com.beust.jcommander.ParameterException; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OptionsParser.java index f4fe10f18dd..f2d5cb7c18b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OptionsParser.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.cli.main; import com.beust.jcommander.*; 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 cae25529e42..7b8b296c101 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.daemon; import org.eclipse.jetty.server.Server; 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 4fcd48a719f..8eda1bf7e7d 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.daemon; //import org.apache.catalina.Server; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/OptionParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/OptionParser.java index 0b2ef14a535..7c43827364b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/OptionParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/OptionParser.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.daemon; import com.beust.jcommander.DynamicParameter; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/AdminServlet.java b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/AdminServlet.java index 3ec62b3eeb7..34d94f6db20 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/AdminServlet.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/AdminServlet.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.daemon.rest; import org.apache.catalina.LifecycleException; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/DaemonServlet.java b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/DaemonServlet.java index b97bb5014a4..e3db6fccac9 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/DaemonServlet.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/DaemonServlet.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.daemon.rest; import com.fasterxml.jackson.core.JsonProcessingException; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/TestServlet.java b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/TestServlet.java index 661c382f3be..4891bce7f24 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/TestServlet.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/daemon/rest/TestServlet.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.daemon.rest; import javax.ws.rs.GET; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/localserver/AdminServlet.java b/opencga-app/src/main/java/org/opencb/opencga/app/localserver/AdminServlet.java index 3200c2b246a..2762cf2d233 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/localserver/AdminServlet.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/localserver/AdminServlet.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.localserver; import org.apache.catalina.LifecycleException; 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 3c7065a10c8..99685caf066 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.localserver; import org.opencb.opencga.core.common.StringUtils; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/localserver/GetFoldersServlet.java b/opencga-app/src/main/java/org/opencb/opencga/app/localserver/GetFoldersServlet.java index 0eb140b0154..6921dff8ab3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/localserver/GetFoldersServlet.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/localserver/GetFoldersServlet.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.localserver; import javax.servlet.ServletException; 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 2738956aaea..3a8118f348e 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.app.localserver; import org.apache.catalina.Context; diff --git a/opencga-app/src/main/resources/account.properties b/opencga-app/src/main/resources/account.properties index f473ceeb325..3a3f67ebcd8 100644 --- a/opencga-app/src/main/resources/account.properties +++ b/opencga-app/src/main/resources/account.properties @@ -1,4 +1,20 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + ### Installation path must be OPENCGA.ENV.HOME = OPENCGA_HOME diff --git a/opencga-app/src/main/resources/analysis.properties b/opencga-app/src/main/resources/analysis.properties index 5a1e1cde51b..6dba13ffc15 100644 --- a/opencga-app/src/main/resources/analysis.properties +++ b/opencga-app/src/main/resources/analysis.properties @@ -1,3 +1,19 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + ############################################# # GENERAL PARAMETERS ############################################# diff --git a/opencga-app/src/main/resources/catalog.properties b/opencga-app/src/main/resources/catalog.properties index f380645bdca..4f68dea1f7f 100644 --- a/opencga-app/src/main/resources/catalog.properties +++ b/opencga-app/src/main/resources/catalog.properties @@ -1,4 +1,20 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + OPENCGA.CATALOG.DB.HOSTS = ${OPENCGA.CATALOG.DB.HOSTS} OPENCGA.CATALOG.DB.DATABASE = ${OPENCGA.CATALOG.DB.DATABASE} OPENCGA.CATALOG.DB.USER = ${OPENCGA.CATALOG.DB.USER} diff --git a/opencga-app/src/main/resources/daemon.properties b/opencga-app/src/main/resources/daemon.properties index c88fa6dcff3..f541aefaed9 100644 --- a/opencga-app/src/main/resources/daemon.properties +++ b/opencga-app/src/main/resources/daemon.properties @@ -1,6 +1,22 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + OPENCGA.APP.DAEMON.PORT = 50391 ## Sleep time diff --git a/opencga-app/src/main/resources/log4j.properties b/opencga-app/src/main/resources/log4j.properties index c6efc8224cb..e4531d4246d 100644 --- a/opencga-app/src/main/resources/log4j.properties +++ b/opencga-app/src/main/resources/log4j.properties @@ -1,3 +1,19 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + log4j.rootLogger=info, stdout, R log4j.appender.stdout=org.apache.log4j.ConsoleAppender diff --git a/opencga-app/src/main/resources/storage.properties b/opencga-app/src/main/resources/storage.properties index c812d90cfd1..5b5a72ba328 100644 --- a/opencga-app/src/main/resources/storage.properties +++ b/opencga-app/src/main/resources/storage.properties @@ -1,5 +1,21 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + ############################################# # STORAGE PARAMETERS # ############################################# diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 883b4160cf0..1d79dd1443c 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -1,4 +1,20 @@ + + diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogException.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogException.java index bc19da7955a..a6ac2162430 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogException.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogException.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog; /** 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 186a4f2b716..b43eae62618 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog; import org.opencb.datastore.core.ObjectMap; 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 2b753ef1b7e..2c16bb011a8 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog; import org.opencb.datastore.core.ObjectMap; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsLoader.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsLoader.java index 05095c73165..62d2733a9da 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsLoader.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsLoader.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog; import org.opencb.biodata.formats.pedigree.io.PedigreePedReader; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsValidator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsValidator.java index 19667b2c80c..b23995f6e9b 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsValidator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsValidator.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog; import org.opencb.opencga.catalog.CatalogException; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Acl.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Acl.java index 9256e2b6f92..0e4b0c4e604 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Acl.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Acl.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; /** 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 4bce887152a..50a4fd4771f 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import org.opencb.opencga.core.common.TimeUtils; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Annotation.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Annotation.java index 85044e0ac03..e2b43f1019c 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Annotation.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Annotation.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; /** diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/AnnotationSet.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/AnnotationSet.java index 86332661c1b..98eed79d688 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/AnnotationSet.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/AnnotationSet.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.Map; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Cohort.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Cohort.java index 49116d1c506..226b7382791 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Cohort.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Cohort.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.List; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/DataStore.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/DataStore.java index 6d6f5bbdc4b..ba612dc633b 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/DataStore.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/DataStore.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; /** diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Dataset.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Dataset.java index 7d08a979508..07b838fbb3c 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Dataset.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Dataset.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.List; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Experiment.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Experiment.java index d801ac396a0..57054b3235d 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Experiment.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Experiment.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.HashMap; 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 1ba76c1cb93..1fd4ce46ab0 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import org.opencb.opencga.core.common.TimeUtils; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Index.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Index.java index 0c6cdf1d003..e024c03da57 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Index.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Index.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.Map; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Individual.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Individual.java index 58afa23dbcb..2e228f76676 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Individual.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Individual.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.HashMap; 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 045f70135a4..665af52b9d2 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import org.opencb.opencga.core.common.TimeUtils; 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 358eaa2595e..1115415bc3f 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import org.opencb.opencga.core.common.TimeUtils; 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 cd620b890b9..2fc9d4ca138 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import org.opencb.opencga.core.common.TimeUtils; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Sample.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Sample.java index 485c3802119..f1d702ac89f 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Sample.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Sample.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; 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 363f38f6281..13170b116c6 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import org.opencb.opencga.core.common.StringUtils; 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 2ec8cd40131..5d61ec9284b 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import org.opencb.opencga.core.common.TimeUtils; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Tool.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Tool.java index 5b9da6ebf2e..bc84ec70dcc 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Tool.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Tool.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.LinkedList; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/User.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/User.java index ae01b17dfc8..88987c0243b 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/User.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/User.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.*; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Variable.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Variable.java index 9a5b2fec000..a067194ccac 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Variable.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/Variable.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.List; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/VariableSet.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/VariableSet.java index cf1d5dd23a1..4287506b73e 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/VariableSet.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/beans/VariableSet.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.beans; import java.util.Map; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/CatalogClient.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/CatalogClient.java index 43cc0ddac07..9234039517b 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/CatalogClient.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/CatalogClient.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.core; import org.opencb.datastore.core.QueryOptions; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/CatalogDBClient.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/CatalogDBClient.java index 95956219fef..03d68833311 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/CatalogDBClient.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/CatalogDBClient.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.core; import org.opencb.datastore.core.QueryOptions; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/ICatalogManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/ICatalogManager.java index 9219e37be8c..69d14348b6d 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/ICatalogManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/core/ICatalogManager.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.core; import org.opencb.datastore.core.ObjectMap; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBAdaptor.java index 79888219848..9857bc47760 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBAdaptor.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.db; import com.mongodb.WriteResult; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBException.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBException.java index 5ff3dbfa6bb..03f9e50564c 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBException.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBException.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.db; import org.opencb.opencga.catalog.CatalogException; 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 421ba08ad92..17529136ba5 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.db; import com.fasterxml.jackson.databind.DeserializationFeature; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogMongoDBUtils.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogMongoDBUtils.java index 292b9904f27..8138d45d0e1 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogMongoDBUtils.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogMongoDBUtils.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.db; import com.mongodb.BasicDBObject; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManager.java index 9c25a5e2e21..a3a34e69508 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManager.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.io; import org.slf4j.Logger; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManagerException.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManagerException.java index c7aee143a06..82d9d8e51c0 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManagerException.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManagerException.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.io; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManagerFactory.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManagerFactory.java index 18c7c143e47..1b9db4912e0 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManagerFactory.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/CatalogIOManagerFactory.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.io; import java.io.IOException; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/HdfsCatalogIOManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/HdfsCatalogIOManager.java index 6cc8a85f81e..107a5b4b5a7 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/HdfsCatalogIOManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/io/HdfsCatalogIOManager.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.io; import java.io.DataInputStream; 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 006528c1a96..78fd88b4326 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.io; import com.fasterxml.jackson.databind.ObjectMapper; 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 450eed9344f..8c95d46e3a6 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog; import org.junit.Before; 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 e0c1557676f..5012deed3ec 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog; import com.fasterxml.jackson.core.JsonProcessingException; diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsLoaderTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsLoaderTest.java index 8b7a92b5c33..c233da5c499 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsLoaderTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/CatalogSampleAnnotationsLoaderTest.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog; import junit.framework.Assert; diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/core/CatalogDBClientTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/core/CatalogDBClientTest.java index d20d7766d55..bcdb7302006 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/core/CatalogDBClientTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/core/CatalogDBClientTest.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.core; import org.junit.AfterClass; 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 6632d06d3e9..be9feb14bdd 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.db; import com.fasterxml.jackson.core.JsonProcessingException; 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 ce315c80174..f5473a73ec2 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.catalog.io; import org.junit.BeforeClass; diff --git a/opencga-catalog/src/test/resources/catalog.properties b/opencga-catalog/src/test/resources/catalog.properties index 4ea2002988e..0cc9faef54a 100644 --- a/opencga-catalog/src/test/resources/catalog.properties +++ b/opencga-catalog/src/test/resources/catalog.properties @@ -1,4 +1,20 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + OPENCGA.CATALOG.DB.HOSTS = ${OPENCGA.CATALOG.DB.HOSTS} OPENCGA.CATALOG.DB.DATABASE = ${OPENCGA.CATALOG.DB.TEST.DATABASE} OPENCGA.CATALOG.DB.USER = ${OPENCGA.CATALOG.DB.USER} diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 72ff0982203..c37b4761e72 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -1,4 +1,20 @@ + + diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/SgeManager.java b/opencga-core/src/main/java/org/opencb/opencga/core/SgeManager.java index 4f8c8a3ea5f..aecf8b044a9 100755 --- a/opencga-core/src/main/java/org/opencb/opencga/core/SgeManager.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/SgeManager.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core; import com.google.common.base.Splitter; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/auth/CellbaseCredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/CellbaseCredentials.java index 43e04208850..77694f305fa 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/auth/CellbaseCredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/CellbaseCredentials.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.auth; /** diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/auth/IllegalOpenCGACredentialsException.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/IllegalOpenCGACredentialsException.java index 90200e1c0ae..282180a924c 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/auth/IllegalOpenCGACredentialsException.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/IllegalOpenCGACredentialsException.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.auth; /** diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/auth/MonbaseCredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/MonbaseCredentials.java index 5421a098507..a7c031c3740 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/auth/MonbaseCredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/MonbaseCredentials.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.auth; //import com.mongodb.MongoCredential; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/auth/OpenCGACredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/OpenCGACredentials.java index ea6b36b93a7..591178628dc 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/auth/OpenCGACredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/OpenCGACredentials.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.auth; /** diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/auth/SqliteCredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/SqliteCredentials.java index fb960f664c9..cf4a08450d1 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/auth/SqliteCredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/SqliteCredentials.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.auth; import org.opencb.commons.utils.FileUtils; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/auth/TabixCredentials.java b/opencga-core/src/main/java/org/opencb/opencga/core/auth/TabixCredentials.java index a10f4d2835a..0d5b77bc4ba 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/auth/TabixCredentials.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/auth/TabixCredentials.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.auth; import java.io.IOException; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/ArrayUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/ArrayUtils.java index e8404c81d4f..c69100d3f90 100755 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/ArrayUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/ArrayUtils.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import java.lang.reflect.Array; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/Config.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/Config.java index 22d315dd954..d64fe9020b5 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/Config.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/Config.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import org.slf4j.Logger; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/IOUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/IOUtils.java index c3c83f72feb..caeee717106 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/IOUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/IOUtils.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import java.io.*; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/ListUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/ListUtils.java index d6e00279120..8ea38fb395e 100755 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/ListUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/ListUtils.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import java.lang.reflect.Array; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/MailUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/MailUtils.java index f52ff592012..869a5c09ffe 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/MailUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/MailUtils.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import javax.mail.*; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/StringUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/StringUtils.java index 37b93c16b6c..7d35c8054f1 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/StringUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/StringUtils.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import java.nio.file.Path; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/TimeUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/TimeUtils.java index def03d8313c..27849716924 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/TimeUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/TimeUtils.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import java.text.ParseException; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/XObject.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/XObject.java index 7b92ebc776e..739cbecf2f3 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/XObject.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/XObject.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/networks/Layout.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/networks/Layout.java index b3fb319943a..351340ff7c1 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/networks/Layout.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/networks/Layout.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common.networks; import org.apache.commons.codec.binary.Base64; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/data/source/FileSource.java b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/FileSource.java index 1b0578f001c..610c7234c38 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/data/source/FileSource.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/FileSource.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.data.source; import java.io.File; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/data/source/S3Source.java b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/S3Source.java index 9d467cee843..29cb5d9e90d 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/data/source/S3Source.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/S3Source.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.data.source; import com.amazonaws.auth.AWSCredentials; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/data/source/Source.java b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/Source.java index a69027712ba..a9d8f9329c4 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/data/source/Source.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/Source.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.data.source; import java.io.InputStream; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/data/source/UrlSource.java b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/UrlSource.java index f5e00cbaee9..3d3bc08973b 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/data/source/UrlSource.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/data/source/UrlSource.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.data.source; import javax.net.ssl.HttpsURLConnection; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/exec/Command.java b/opencga-core/src/main/java/org/opencb/opencga/core/exec/Command.java index 562d5b0634a..da7f3734f7f 100755 --- a/opencga-core/src/main/java/org/opencb/opencga/core/exec/Command.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/exec/Command.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.exec; import org.apache.tools.ant.types.Commandline; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/exec/RunnableProcess.java b/opencga-core/src/main/java/org/opencb/opencga/core/exec/RunnableProcess.java index b436e2f25e8..113619c3c53 100755 --- a/opencga-core/src/main/java/org/opencb/opencga/core/exec/RunnableProcess.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/exec/RunnableProcess.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.exec; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/exec/SingleProcess.java b/opencga-core/src/main/java/org/opencb/opencga/core/exec/SingleProcess.java index 6cb9a34bc5f..a4360b9d339 100755 --- a/opencga-core/src/main/java/org/opencb/opencga/core/exec/SingleProcess.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/exec/SingleProcess.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.exec; import org.slf4j.Logger; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CombinationIterator.java b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CombinationIterator.java index 0b51eb66ac9..5aaf8b60c26 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CombinationIterator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CombinationIterator.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.tools.accession; import java.util.Iterator; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CreateAccessionTask.java b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CreateAccessionTask.java index 053255626b2..19b42b26093 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CreateAccessionTask.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/CreateAccessionTask.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.tools.accession; import java.io.IOException; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/LRUCache.java b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/LRUCache.java index 3dc871c75f2..106e2ecb230 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/LRUCache.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/tools/accession/LRUCache.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.tools.accession; import java.util.LinkedHashMap; diff --git a/opencga-core/src/test/java/org/opencb/opencga/core/common/IOUtilsTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/common/IOUtilsTest.java index 2a7ee36ed78..e42e71c46fd 100644 --- a/opencga-core/src/test/java/org/opencb/opencga/core/common/IOUtilsTest.java +++ b/opencga-core/src/test/java/org/opencb/opencga/core/common/IOUtilsTest.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import org.junit.Test; diff --git a/opencga-core/src/test/java/org/opencb/opencga/core/common/StringUtilsTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/common/StringUtilsTest.java index 6b02d59e907..0407d70208f 100644 --- a/opencga-core/src/test/java/org/opencb/opencga/core/common/StringUtilsTest.java +++ b/opencga-core/src/test/java/org/opencb/opencga/core/common/StringUtilsTest.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.core.common; import org.junit.Test; diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f3f0ab3b737..a2bc6f22fa8 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -1,4 +1,20 @@ + + diff --git a/opencga-server/src/main/java/encryption/AESCipher.java b/opencga-server/src/main/java/encryption/AESCipher.java index 3ed1d87f2e5..50041534ca0 100644 --- a/opencga-server/src/main/java/encryption/AESCipher.java +++ b/opencga-server/src/main/java/encryption/AESCipher.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package encryption; import com.google.common.base.Throwables; diff --git a/opencga-server/src/main/java/encryption/KeyEncoding.java b/opencga-server/src/main/java/encryption/KeyEncoding.java index 81b41026b04..e9ef1db327a 100644 --- a/opencga-server/src/main/java/encryption/KeyEncoding.java +++ b/opencga-server/src/main/java/encryption/KeyEncoding.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package encryption; public enum KeyEncoding { diff --git a/opencga-server/src/main/java/encryption/KeystoreUtil.java b/opencga-server/src/main/java/encryption/KeystoreUtil.java index 08be262858d..d3c4cfd7863 100644 --- a/opencga-server/src/main/java/encryption/KeystoreUtil.java +++ b/opencga-server/src/main/java/encryption/KeystoreUtil.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package encryption; import com.google.common.io.BaseEncoding; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/AnalysisWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/AnalysisWSServer.java index 7e38a02b05e..2f7f16f4541 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/AnalysisWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/AnalysisWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; 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 244adbab639..13a262587b3 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; import org.opencb.opencga.analysis.AnalysisJobExecuter; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/CohortWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/CohortWSServer.java index 6c276c5bb65..d4845297742 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/CohortWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/CohortWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; import com.wordnik.swagger.annotations.Api; 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 1b6d1393232..f221c067669 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; import com.wordnik.swagger.annotations.*; 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 160b51582bb..a00c2ad47ac 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; 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 c527f1e1324..d02c210febc 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/ProjectWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/ProjectWSServer.java index 9ff166e6bdc..15b62684b6d 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/ProjectWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/ProjectWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/SampleWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/SampleWSServer.java index c900666e5ec..45f7cee8df6 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/SampleWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/SampleWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; import com.wordnik.swagger.annotations.Api; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/StudyWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/StudyWSServer.java index bca3696a217..732d5230237 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/StudyWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/StudyWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/TestWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/TestWSServer.java index 7e7a29b46db..8468a7f2cea 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/TestWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/TestWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/ToolWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/ToolWSServer.java index a2fe4fab958..23218f5afa4 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/ToolWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/ToolWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; import com.wordnik.swagger.annotations.Api; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/UserWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/UserWSServer.java index bab1aac46ff..3221f72d4d5 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/UserWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/UserWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; 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 85bcd2170a1..880d854280c 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; import com.fasterxml.jackson.core.JsonFactory; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/VariableWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/VariableWSServer.java index ee1e37762da..352eab659a0 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/VariableWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/VariableWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.server; import com.wordnik.swagger.annotations.Api; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/AccountWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/AccountWSServer.java index d41ce3eb9da..930700efdc8 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/AccountWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/AccountWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import org.opencb.commons.containers.QueryResult; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/AdminWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/AdminWSServer.java index 47fc1b13332..f226c200fdc 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/AdminWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/AdminWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import java.io.IOException; 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 6d9fe666780..74fbfa49a74 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import org.opencb.commons.containers.QueryResult; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/BamWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/BamWSServer.java index 37d0d54c598..e212b39c04d 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/BamWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/BamWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import java.io.IOException; 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 bd782f8ca98..42b6e300303 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import com.fasterxml.jackson.core.JsonProcessingException; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/GeocodingAddressService.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/GeocodingAddressService.java index da5390f3521..6b201beb3be 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/GeocodingAddressService.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/GeocodingAddressService.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import org.opencb.opencga.server.OpenCGAWSServer; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/GffWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/GffWSServer.java index 12b89bfeeae..49d12d7c026 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/GffWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/GffWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import org.opencb.opencga.server.OpenCGAWSServer; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/JobAnalysisWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/JobAnalysisWSServer.java index c141ec69ed6..c4dc49856cc 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/JobAnalysisWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/JobAnalysisWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import org.opencb.commons.containers.QueryResult; 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 312441170fe..f78a68ec413 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import com.google.common.base.Splitter; 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 031142bca91..11e25a6ce93 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import com.google.common.base.Splitter; 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 4bbba980b09..bdfc1cbad79 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import com.fasterxml.jackson.core.JsonFactory; 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 7932707070c..b77549de2ea 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/VcfWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/VcfWSServer.java index 96fb67143ee..73d60f5f967 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/VcfWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/VcfWSServer.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import org.opencb.opencga.server.OpenCGAWSServer; 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 cbb14a1180d..1d3318ccd9c 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 @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold; import org.opencb.opencga.core.common.XObject; diff --git a/opencga-server/src/main/java/org/opencb/opencga/serverold/storage/VariantStorageService.java b/opencga-server/src/main/java/org/opencb/opencga/serverold/storage/VariantStorageService.java index f950804a31f..c5962ed7a79 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/serverold/storage/VariantStorageService.java +++ b/opencga-server/src/main/java/org/opencb/opencga/serverold/storage/VariantStorageService.java @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + package org.opencb.opencga.serverold.storage; diff --git a/opencga-server/src/main/resources/aes.properties b/opencga-server/src/main/resources/aes.properties index 881e4ee6b8a..746ff56ac09 100644 --- a/opencga-server/src/main/resources/aes.properties +++ b/opencga-server/src/main/resources/aes.properties @@ -1,3 +1,19 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + # To add new # http://www.ensor.cc/2014/02/aes-256-encryption-with-java-and-jceks.html # key keytool -genseckey -keystore aes-keystore.jck -storetype jceks -storepass mystorepass -keyalg AES -keysize 256 -alias jceksaes -keypass mykeypass diff --git a/opencga-server/src/main/resources/application.properties b/opencga-server/src/main/resources/application.properties index f974e4f7f9d..3833a0a080c 100755 --- a/opencga-server/src/main/resources/application.properties +++ b/opencga-server/src/main/resources/application.properties @@ -1,3 +1,19 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + OPENCGA.INSTALLATION.DIR = ${OPENCGA.INSTALLATION.DIR} ####################################################################### diff --git a/opencga-server/src/main/resources/catalog.properties b/opencga-server/src/main/resources/catalog.properties index 95b3522f616..22a5f484822 100644 --- a/opencga-server/src/main/resources/catalog.properties +++ b/opencga-server/src/main/resources/catalog.properties @@ -1,4 +1,20 @@ +# +# Copyright 2015 OpenCB +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + OPENCGA.CATALOG.DB.HOSTS = ${OPENCGA.CATALOG.DB.HOSTS} OPENCGA.CATALOG.DB.DATABASE = ${OPENCGA.CATALOG.DB.DATABASE} OPENCGA.CATALOG.DB.USER = ${OPENCGA.CATALOG.DB.USER} diff --git a/opencga-server/src/main/webapp/WEB-INF/web.xml b/opencga-server/src/main/webapp/WEB-INF/web.xml index 232e180ad52..4d7b0f1b019 100755 --- a/opencga-server/src/main/webapp/WEB-INF/web.xml +++ b/opencga-server/src/main/webapp/WEB-INF/web.xml @@ -1,4 +1,20 @@ + + + + OpenCGA WS API diff --git a/opencga-server/src/main/webapp/swagger-ui/css/reset.css b/opencga-server/src/main/webapp/swagger-ui/css/reset.css index b2b078943c4..a523789b45a 100644 --- a/opencga-server/src/main/webapp/swagger-ui/css/reset.css +++ b/opencga-server/src/main/webapp/swagger-ui/css/reset.css @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + /* http://meyerweb.com/eric/tools/css/reset/ v2.0 | 20110126 */ html, body, diff --git a/opencga-server/src/main/webapp/swagger-ui/css/screen.css b/opencga-server/src/main/webapp/swagger-ui/css/screen.css index 478b99837d7..1ec6b9de85d 100644 --- a/opencga-server/src/main/webapp/swagger-ui/css/screen.css +++ b/opencga-server/src/main/webapp/swagger-ui/css/screen.css @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + /* Original style from softwaremaniacs.org (c) Ivan Sagalaev */ .swagger-section pre code { display: block; diff --git a/opencga-server/src/main/webapp/swagger-ui/lib/backbone-min.js b/opencga-server/src/main/webapp/swagger-ui/lib/backbone-min.js index c1c0d4fff28..8216d3cf4f4 100644 --- a/opencga-server/src/main/webapp/swagger-ui/lib/backbone-min.js +++ b/opencga-server/src/main/webapp/swagger-ui/lib/backbone-min.js @@ -1,3 +1,19 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // Backbone.js 0.9.2 // (c) 2010-2012 Jeremy Ashkenas, DocumentCloud Inc. diff --git a/opencga-server/src/main/webapp/swagger-ui/lib/handlebars-1.0.0.js b/opencga-server/src/main/webapp/swagger-ui/lib/handlebars-1.0.0.js index c70f09d1de6..5d43088a06a 100644 --- a/opencga-server/src/main/webapp/swagger-ui/lib/handlebars-1.0.0.js +++ b/opencga-server/src/main/webapp/swagger-ui/lib/handlebars-1.0.0.js @@ -1,26 +1,18 @@ /* - -Copyright (C) 2011 by Yehuda Katz - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. - -*/ + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ // lib/handlebars/browser-prefix.js var Handlebars = {}; diff --git a/opencga-server/src/main/webapp/swagger-ui/lib/highlight.7.3.pack.js b/opencga-server/src/main/webapp/swagger-ui/lib/highlight.7.3.pack.js index 9a95a75ea16..9bad0f90192 100644 --- a/opencga-server/src/main/webapp/swagger-ui/lib/highlight.7.3.pack.js +++ b/opencga-server/src/main/webapp/swagger-ui/lib/highlight.7.3.pack.js @@ -1 +1,17 @@ +/* + * Copyright 2015 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + var hljs=new function(){function l(o){return o.replace(/&/gm,"&").replace(//gm,">")}function b(p){for(var o=p.firstChild;o;o=o.nextSibling){if(o.nodeName=="CODE"){return o}if(!(o.nodeType==3&&o.nodeValue.match(/\s+/))){break}}}function h(p,o){return Array.prototype.map.call(p.childNodes,function(q){if(q.nodeType==3){return o?q.nodeValue.replace(/\n/g,""):q.nodeValue}if(q.nodeName=="BR"){return"\n"}return h(q,o)}).join("")}function a(q){var p=(q.className+" "+q.parentNode.className).split(/\s+/);p=p.map(function(r){return r.replace(/^language-/,"")});for(var o=0;o"}while(x.length||v.length){var u=t().splice(0,1)[0];y+=l(w.substr(p,u.offset-p));p=u.offset;if(u.event=="start"){y+=s(u.node);r.push(u.node)}else{if(u.event=="stop"){var o,q=r.length;do{q--;o=r[q];y+=("")}while(o!=u.node);r.splice(q,1);while(q'+L[0]+""}else{r+=L[0]}N=A.lR.lastIndex;L=A.lR.exec(K)}return r+K.substr(N)}function z(){if(A.sL&&!e[A.sL]){return l(w)}var r=A.sL?d(A.sL,w):g(w);if(A.r>0){v+=r.keyword_count;B+=r.r}return''+r.value+""}function J(){return A.sL!==undefined?z():G()}function I(L,r){var K=L.cN?'':"";if(L.rB){x+=K;w=""}else{if(L.eB){x+=l(r)+K;w=""}else{x+=K;w=r}}A=Object.create(L,{parent:{value:A}});B+=L.r}function C(K,r){w+=K;if(r===undefined){x+=J();return 0}var L=o(r,A);if(L){x+=J();I(L,r);return L.rB?0:r.length}var M=s(A,r);if(M){if(!(M.rE||M.eE)){w+=r}x+=J();do{if(A.cN){x+=""}A=A.parent}while(A!=M.parent);if(M.eE){x+=l(r)}w="";if(M.starts){I(M.starts,"")}return M.rE?0:r.length}if(t(r,A)){throw"Illegal"}w+=r;return r.length||1}var F=e[D];f(F);var A=F;var w="";var B=0;var v=0;var x="";try{var u,q,p=0;while(true){A.t.lastIndex=p;u=A.t.exec(E);if(!u){break}q=C(E.substr(p,u.index-p),u[0]);p=u.index+q}C(E.substr(p));return{r:B,keyword_count:v,value:x,language:D}}catch(H){if(H=="Illegal"){return{r:0,keyword_count:0,value:l(E)}}else{throw H}}}function g(s){var o={keyword_count:0,r:0,value:l(s)};var q=o;for(var p in e){if(!e.hasOwnProperty(p)){continue}var r=d(p,s);r.language=p;if(r.keyword_count+r.r>q.keyword_count+q.r){q=r}if(r.keyword_count+r.r>o.keyword_count+o.r){q=o;o=r}}if(q.language){o.second_best=q}return o}function i(q,p,o){if(p){q=q.replace(/^((<[^>]+>|\t)+)/gm,function(r,v,u,t){return v.replace(/\t/g,p)})}if(o){q=q.replace(/\n/g,"
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