diff --git a/src/main/java/caosdb/server/accessControl/UserSources.java b/src/main/java/caosdb/server/accessControl/UserSources.java index 7a0298f6ddb7722eecbb1cf8c0cd115bbedb5b7e..a3f35c11b0f3bcc10e67397bd8c48c6e969fcc7d 100644 --- a/src/main/java/caosdb/server/accessControl/UserSources.java +++ b/src/main/java/caosdb/server/accessControl/UserSources.java @@ -1,28 +1,36 @@ /* - * ** header v3.0 This file is a part of the CaosDB Project. + * ** header v3.0 + * This file is a part of the CaosDB Project. * - * Copyright (C) 2018 Research Group Biomedical Physics, Max-Planck-Institute for Dynamics and - * Self-Organization Göttingen + * Copyright (C) 2018 Research Group Biomedical Physics, + * Max-Planck-Institute for Dynamics and Self-Organization Göttingen * - * This program is free software: you can redistribute it and/or modify it under the terms of the - * GNU Affero General Public License as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. * - * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without - * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Affero General Public License for more details. + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. * - * You should have received a copy of the GNU Affero General Public License along with this program. - * If not, see <https://www.gnu.org/licenses/>. + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <https://www.gnu.org/licenses/>. * * ** end header */ package caosdb.server.accessControl; +import caosdb.server.CaosDBServer; +import caosdb.server.ServerProperties; +import caosdb.server.entity.Message; +import caosdb.server.transaction.RetrieveRoleTransaction; +import caosdb.server.transaction.RetrieveUserTransaction; +import caosdb.server.utils.ServerMessages; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.IOException; -import java.lang.reflect.InvocationTargetException; import java.util.HashMap; import java.util.HashSet; import java.util.Set; @@ -31,12 +39,6 @@ import org.apache.shiro.config.Ini; import org.apache.shiro.subject.PrincipalCollection; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import caosdb.server.CaosDBServer; -import caosdb.server.ServerProperties; -import caosdb.server.entity.Message; -import caosdb.server.transaction.RetrieveRoleTransaction; -import caosdb.server.transaction.RetrieveUserTransaction; -import caosdb.server.utils.ServerMessages; public class UserSources extends HashMap<String, UserSource> { @@ -58,8 +60,10 @@ public class UserSources extends HashMap<String, UserSource> { private UserSources() { initMap(); this.put(getInternalRealm()); - final String[] realms = this.map.getSectionProperty(Ini.DEFAULT_SECTION_NAME, KEY_REALMS) - .split("(\\s*,\\s*)|(\\s+)"); + final String[] realms = + this.map + .getSectionProperty(Ini.DEFAULT_SECTION_NAME, KEY_REALMS) + .split("(\\s*,\\s*)|(\\s+)"); for (final String realm : realms) { if (realm != null && !realm.isEmpty()) { final String className = this.map.getSectionProperty(realm, KEY_REALM_CLASS); @@ -68,10 +72,12 @@ public class UserSources extends HashMap<String, UserSource> { @SuppressWarnings("unchecked") final Class<? extends UserSource> clazz = (Class<? extends UserSource>) Class.forName(className); - this.put(clazz.getDeclaredConstructor().newInstance()); - } catch (IllegalArgumentException | InvocationTargetException | NoSuchMethodException - | SecurityException | ClassNotFoundException | InstantiationException - | IllegalAccessException e) { + this.put(clazz.newInstance()); + } catch (final ClassNotFoundException e) { + logger.error("LOAD_USER_SOURCE", e); + } catch (final InstantiationException e) { + logger.error("LOAD_USER_SOURCE", e); + } catch (final IllegalAccessException e) { logger.error("LOAD_USER_SOURCE", e); } } @@ -99,8 +105,9 @@ public class UserSources extends HashMap<String, UserSource> { public void initMap() { this.map = null; try { - final FileInputStream f = new FileInputStream( - CaosDBServer.getServerProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE)); + final FileInputStream f = + new FileInputStream( + CaosDBServer.getServerProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE)); this.map = new Ini(); this.map.load(f); f.close(); diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java index a7a5c607df280a29c89a947e276bfdb789d11baa..0e557da58074729b9c3635453dd4b84b657599bb 100644 --- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java +++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java @@ -22,14 +22,14 @@ */ package caosdb.server.database.backend.implementation.MySQL; -import java.sql.PreparedStatement; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.util.Iterator; import caosdb.server.database.access.Access; import caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl; import caosdb.server.database.exceptions.TransactionException; import caosdb.server.database.proto.SparseEntity; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Iterator; public class MySQLRetrieveAllUncheckedFiles extends MySQLTransaction implements RetrieveAllUncheckedFilesImpl { diff --git a/src/main/java/caosdb/server/datatype/AbstractDatatype.java b/src/main/java/caosdb/server/datatype/AbstractDatatype.java index 81072a72f2026c8b6fa4dbea65a3e99b85b513e4..0cde534aa74a05e33591d5e8d719316e7f1704f6 100644 --- a/src/main/java/caosdb/server/datatype/AbstractDatatype.java +++ b/src/main/java/caosdb/server/datatype/AbstractDatatype.java @@ -22,11 +22,11 @@ */ package caosdb.server.datatype; -import java.util.HashMap; -import org.reflections.Reflections; import caosdb.server.entity.EntityInterface; import caosdb.server.entity.Message; import caosdb.server.entity.container.Container; +import java.util.HashMap; +import org.reflections.Reflections; public abstract class AbstractDatatype { diff --git a/src/main/java/caosdb/server/jobs/Job.java b/src/main/java/caosdb/server/jobs/Job.java index fb6b4aeb91e4d3227fb6b773dae26118c115b92a..110809e77ae0d40076642d953c15b0d9566eddd6 100644 --- a/src/main/java/caosdb/server/jobs/Job.java +++ b/src/main/java/caosdb/server/jobs/Job.java @@ -22,16 +22,6 @@ */ package caosdb.server.jobs; -import java.lang.reflect.InvocationTargetException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.LinkedList; -import java.util.List; -import java.util.Set; -import org.apache.shiro.SecurityUtils; -import org.apache.shiro.authz.Permission; -import org.apache.shiro.subject.Subject; -import org.reflections.Reflections; import caosdb.server.CaosDBException; import caosdb.server.database.BackendTransaction; import caosdb.server.database.backend.transaction.GetIDByName; @@ -54,6 +44,16 @@ import caosdb.server.utils.EntityStatus; import caosdb.server.utils.Observable; import caosdb.server.utils.Observer; import caosdb.server.utils.ServerMessages; +import java.lang.reflect.InvocationTargetException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.LinkedList; +import java.util.List; +import java.util.Set; +import org.apache.shiro.SecurityUtils; +import org.apache.shiro.authz.Permission; +import org.apache.shiro.subject.Subject; +import org.reflections.Reflections; public abstract class Job extends AbstractObservable implements Observer { private Transaction<? extends TransactionContainer> transaction = null; @@ -88,7 +88,12 @@ public abstract class Job extends AbstractObservable implements Observer { final Job job = clazz.getDeclaredConstructor().newInstance(); job.init(getMode(), entity, getTransaction()); return getTransaction().getSchedule().add(job); - } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException | SecurityException e) { + } catch (InstantiationException + | IllegalAccessException + | IllegalArgumentException + | InvocationTargetException + | NoSuchMethodException + | SecurityException e) { throw new CaosDBException(e); } } @@ -332,7 +337,12 @@ public abstract class Job extends AbstractObservable implements Observer { return ret; } return null; - } catch (final InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException | SecurityException e) { + } catch (final InstantiationException + | IllegalAccessException + | IllegalArgumentException + | InvocationTargetException + | NoSuchMethodException + | SecurityException e) { throw new TransactionException(e); } } diff --git a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanModel.java b/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanModel.java index 92fdfed58f921db27471e7eb457529628ca7b516..92a8a240363cf8659e0d3526dec1c5fcac8ddd11 100644 --- a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanModel.java +++ b/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanModel.java @@ -1,6 +1,5 @@ package caosdb.server.jobs.extension; -import java.util.Objects; import caosdb.server.CaosDBServer; import caosdb.server.database.exceptions.EntityDoesNotExistException; import caosdb.server.entity.EntityInterface; @@ -8,6 +7,7 @@ import caosdb.server.entity.Role; import caosdb.server.entity.wrapper.Property; import caosdb.server.jobs.ContainerJob; import caosdb.server.utils.Utils; +import java.util.Objects; public abstract class AWIBoxLoanModel extends ContainerJob { diff --git a/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java b/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java index 41778ac6ca184d819b42954a80369df813373297..4882f0aff290cc53f80372f1451b538c664dae56 100644 --- a/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java +++ b/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java @@ -22,6 +22,11 @@ */ package caosdb.server.jobs.extension; +import caosdb.server.CaosDBException; +import caosdb.server.entity.FileProperties; +import caosdb.server.entity.Message; +import caosdb.server.jobs.EntityJob; +import caosdb.server.utils.FileUtils; import java.io.IOException; import java.security.NoSuchAlgorithmException; import java.sql.Connection; @@ -34,11 +39,6 @@ import java.util.Collections; import java.util.HashMap; import java.util.List; import java.util.concurrent.locks.ReentrantLock; -import caosdb.server.CaosDBException; -import caosdb.server.entity.FileProperties; -import caosdb.server.entity.Message; -import caosdb.server.jobs.EntityJob; -import caosdb.server.utils.FileUtils; public class SQLiteTransaction extends EntityJob { private static HashMap<String, ReentrantLock> lockedTables = new HashMap<String, ReentrantLock>(); diff --git a/src/main/java/caosdb/server/query/StoredAt.java b/src/main/java/caosdb/server/query/StoredAt.java index 243822f740f0410345fe322e472146d4a965039b..b16bb83f2f95c4da1f86292a7d0f17e73f8150d4 100644 --- a/src/main/java/caosdb/server/query/StoredAt.java +++ b/src/main/java/caosdb/server/query/StoredAt.java @@ -23,6 +23,8 @@ package caosdb.server.query; import static java.sql.Types.VARCHAR; + +import caosdb.server.query.Query.QueryException; import java.nio.file.Path; import java.nio.file.Paths; import java.sql.CallableStatement; @@ -30,7 +32,6 @@ import java.sql.SQLException; import java.util.regex.Matcher; import java.util.regex.Pattern; import org.jdom2.Element; -import caosdb.server.query.Query.QueryException; public class StoredAt implements EntityFilterInterface { diff --git a/src/main/java/caosdb/server/utils/mail/Mail.java b/src/main/java/caosdb/server/utils/mail/Mail.java index 36d5e9332ff33c925c8b04c8ae44d0e4e5120537..c2036f909009a5ac0f294c6b0abed572e2d45790 100644 --- a/src/main/java/caosdb/server/utils/mail/Mail.java +++ b/src/main/java/caosdb/server/utils/mail/Mail.java @@ -22,9 +22,9 @@ */ package caosdb.server.utils.mail; -import java.util.Date; import caosdb.server.CaosDBServer; import caosdb.server.ServerProperties; +import java.util.Date; public class Mail { diff --git a/src/test/java/caosdb/server/query/TestCQL.java b/src/test/java/caosdb/server/query/TestCQL.java index ebe1cc8c53b5beaeb3762565f351fe801d20f649..37bb5e59cbeef858392293253d4382e7e2f044ae 100644 --- a/src/test/java/caosdb/server/query/TestCQL.java +++ b/src/test/java/caosdb/server/query/TestCQL.java @@ -28,6 +28,15 @@ import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; + +import caosdb.server.CaosDBServer; +import caosdb.server.database.access.Access; +import caosdb.server.database.backend.implementation.MySQL.ConnectionException; +import caosdb.server.database.exceptions.TransactionException; +import caosdb.server.query.CQLParser.CqContext; +import caosdb.server.query.Query.Pattern; +import caosdb.server.query.Query.QueryException; +import caosdb.server.utils.Initialization; import java.io.IOException; import java.sql.SQLException; import java.util.LinkedList; @@ -38,14 +47,6 @@ import org.antlr.v4.runtime.Token; import org.antlr.v4.runtime.tree.ParseTree; import org.junit.BeforeClass; import org.junit.Test; -import caosdb.server.CaosDBServer; -import caosdb.server.database.access.Access; -import caosdb.server.database.backend.implementation.MySQL.ConnectionException; -import caosdb.server.database.exceptions.TransactionException; -import caosdb.server.query.CQLParser.CqContext; -import caosdb.server.query.Query.Pattern; -import caosdb.server.query.Query.QueryException; -import caosdb.server.utils.Initialization; public class TestCQL {