Commit 3e870002 authored by Rasko Leinonen's avatar Rasko Leinonen

Added spotless plugin to automatically add license to source files and to...

Added spotless plugin to automatically add license to source files and to order and remove unused imports.
parent 454f1bc8
...@@ -186,7 +186,7 @@ ...@@ -186,7 +186,7 @@
same "printed page" as the copyright notice for easier same "printed page" as the copyright notice for easier
identification within third-party archives. identification within third-party archives.
Copyright 2018 EMBL - European Bioinformatics Institute Copyright 2018-2019 EMBL - European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License. you may not use this file except in compliance with the License.
......
plugins { plugins {
id 'org.springframework.boot' version '2.1.1.RELEASE' id 'org.springframework.boot' version '2.1.1.RELEASE'
id "io.github.ddimtirov.codacy" version "0.1.0" id "io.github.ddimtirov.codacy" version "0.1.0"
id "com.diffplug.gradle.spotless" version "3.18.0"
} }
apply plugin: 'java' apply plugin: 'java'
...@@ -16,13 +17,31 @@ wrapper{ ...@@ -16,13 +17,31 @@ wrapper{
distributionType = Wrapper.DistributionType.BIN distributionType = Wrapper.DistributionType.BIN
} }
group = 'uk.ac.ebi.ena.webin-cli' group = 'uk.ac.ebi.ena.webin-cli'
ext.version_base = '1.7.1' ext.version_base = '1.7.1'
version = version_base version = version_base
sourceCompatibility = '1.8' sourceCompatibility = '1.8'
targetCompatibility = '1.8' targetCompatibility = '1.8'
spotless {
java {
licenseHeader('''
/*
* Copyright 2018-2019 EMBL - European Bioinformatics Institute
* 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.
*/
''')
importOrder 'java', 'javax', 'org', 'com', '', 'uk'
removeUnusedImports()
}
}
bootJar { bootJar {
mainClassName = 'uk.ac.ebi.ena.webin.cli.WebinCli' mainClassName = 'uk.ac.ebi.ena.webin.cli.WebinCli'
......
/* /*
* Copyright 2018 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli; package uk.ac.ebi.ena.webin.cli;
import java.io.File; import java.io.File;
...@@ -18,12 +18,12 @@ import java.security.NoSuchAlgorithmException; ...@@ -18,12 +18,12 @@ import java.security.NoSuchAlgorithmException;
import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.StringUtils;
import uk.ac.ebi.ena.webin.cli.logger.ValidationMessageLogger;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestReader; import uk.ac.ebi.ena.webin.cli.manifest.ManifestReader;
import uk.ac.ebi.ena.webin.cli.reporter.ValidationMessageReporter;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle; import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundleHelper; import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundleHelper;
import uk.ac.ebi.ena.webin.cli.utils.FileUtils; import uk.ac.ebi.ena.webin.cli.utils.FileUtils;
import uk.ac.ebi.ena.webin.cli.logger.ValidationMessageLogger;
import uk.ac.ebi.ena.webin.cli.reporter.ValidationMessageReporter;
public abstract class public abstract class
AbstractWebinCli<T extends ManifestReader> AbstractWebinCli<T extends ManifestReader>
......
/* /*
* Copyright 2018 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli; package uk.ac.ebi.ena.webin.cli;
public interface ParameterDescriptor { public interface ParameterDescriptor {
......
/* /*
* Copyright 2018 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli; package uk.ac.ebi.ena.webin.cli;
import java.io.File; import java.io.File;
...@@ -35,6 +35,7 @@ import ch.qos.logback.classic.encoder.PatternLayoutEncoder; ...@@ -35,6 +35,7 @@ import ch.qos.logback.classic.encoder.PatternLayoutEncoder;
import ch.qos.logback.classic.spi.ILoggingEvent; import ch.qos.logback.classic.spi.ILoggingEvent;
import ch.qos.logback.core.FileAppender; import ch.qos.logback.core.FileAppender;
import ch.qos.logback.core.OutputStreamAppender; import ch.qos.logback.core.OutputStreamAppender;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry; import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.ValidationEngineException; import uk.ac.ebi.embl.api.validation.ValidationEngineException;
import uk.ac.ebi.embl.api.validation.ValidationEngineException.ReportErrorType; import uk.ac.ebi.embl.api.validation.ValidationEngineException.ReportErrorType;
...@@ -335,12 +336,12 @@ public class WebinCli { // implements CommandLineRunner ...@@ -335,12 +336,12 @@ public class WebinCli { // implements CommandLineRunner
{ {
SubmissionBundle bundle = validator.getSubmissionBundle(); SubmissionBundle bundle = validator.getSubmissionBundle();
UploadService ftpService = params.ascp && new ASCPService().isAvaliable() ? new ASCPService() : new FtpService(); UploadService ftpService = params.ascp && new ASCPService().isAvailable() ? new ASCPService() : new FtpService();
try try
{ {
ftpService.connect( params.userName, params.password ); ftpService.connect( params.userName, params.password );
ftpService.ftpDirectory( bundle.getUploadFileList(), bundle.getUploadDirectory(), validator.getParameters().getInputDir().toPath() ); ftpService.upload( bundle.getUploadFileList(), bundle.getUploadDirectory(), validator.getParameters().getInputDir().toPath() );
log.info( WebinCliMessage.Cli.UPLOAD_SUCCESS.format() ); log.info( WebinCliMessage.Cli.UPLOAD_SUCCESS.format() );
} catch( WebinCliException e ) } catch( WebinCliException e )
......
/* /*
* Copyright 2018 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli; package uk.ac.ebi.ena.webin.cli;
import uk.ac.ebi.ena.webin.cli.assembly.GenomeAssemblyWebinCli; import uk.ac.ebi.ena.webin.cli.assembly.GenomeAssemblyWebinCli;
......
/* /*
* Copyright 2018 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli; package uk.ac.ebi.ena.webin.cli;
public class public class
......
/* /*
* Copyright 2019 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,16 +9,15 @@ ...@@ -8,16 +9,15 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli; package uk.ac.ebi.ena.webin.cli;
import java.lang.reflect.Field;
import java.text.MessageFormat;
import uk.ac.ebi.embl.api.validation.Origin; import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.Severity; import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.ValidationMessage; import uk.ac.ebi.embl.api.validation.ValidationMessage;
import java.lang.reflect.Field;
import java.text.MessageFormat;
public interface WebinCliMessage { public interface WebinCliMessage {
// Messages. // Messages.
......
/* /*
* Copyright 2018 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli; package uk.ac.ebi.ena.webin.cli;
import java.io.File; import java.io.File;
......
/* /*
* Copyright 2019 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli.assembly; package uk.ac.ebi.ena.webin.cli.assembly;
import java.util.ArrayList; import java.util.ArrayList;
...@@ -24,6 +24,7 @@ import uk.ac.ebi.embl.api.validation.submission.SubmissionFile; ...@@ -24,6 +24,7 @@ import uk.ac.ebi.embl.api.validation.submission.SubmissionFile;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType; import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFiles; import uk.ac.ebi.embl.api.validation.submission.SubmissionFiles;
import uk.ac.ebi.embl.api.validation.submission.SubmissionOptions; import uk.ac.ebi.embl.api.validation.submission.SubmissionOptions;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldDefinition; import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldDefinition;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldType; import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldType;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFileCount; import uk.ac.ebi.ena.webin.cli.manifest.ManifestFileCount;
...@@ -35,7 +36,6 @@ import uk.ac.ebi.ena.webin.cli.manifest.processor.FileSuffixProcessor; ...@@ -35,7 +36,6 @@ import uk.ac.ebi.ena.webin.cli.manifest.processor.FileSuffixProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.SampleProcessor; import uk.ac.ebi.ena.webin.cli.manifest.processor.SampleProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.SourceFeatureProcessor; import uk.ac.ebi.ena.webin.cli.manifest.processor.SourceFeatureProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor; import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class public class
GenomeAssemblyManifest extends ManifestReader GenomeAssemblyManifest extends ManifestReader
......
/* /*
* Copyright 2018 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,20 +9,21 @@ ...@@ -8,20 +9,21 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli.assembly; package uk.ac.ebi.ena.webin.cli.assembly;
import java.io.File; import java.io.File;
import java.nio.file.Path; import java.nio.file.Path;
import java.util.Optional; import java.util.Optional;
import org.jdom2.Element; import org.jdom2.Element;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry; import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.ValidationEngineException; import uk.ac.ebi.embl.api.validation.ValidationEngineException;
import uk.ac.ebi.embl.api.validation.submission.SubmissionValidator; import uk.ac.ebi.embl.api.validation.submission.SubmissionValidator;
import uk.ac.ebi.ena.webin.cli.WebinCliContext;
import uk.ac.ebi.ena.webin.cli.manifest.processor.SampleProcessor; import uk.ac.ebi.ena.webin.cli.manifest.processor.SampleProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.SourceFeatureProcessor; import uk.ac.ebi.ena.webin.cli.manifest.processor.SourceFeatureProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor; import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
import uk.ac.ebi.ena.webin.cli.WebinCliContext;
public class public class
GenomeAssemblyWebinCli extends SequenceWebinCli<GenomeAssemblyManifest> GenomeAssemblyWebinCli extends SequenceWebinCli<GenomeAssemblyManifest>
......
/* /*
* Copyright 2019 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli.assembly; package uk.ac.ebi.ena.webin.cli.assembly;
import java.util.ArrayList; import java.util.ArrayList;
......
/* /*
* Copyright 2019 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,18 +9,19 @@ ...@@ -8,18 +9,19 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli.assembly; package uk.ac.ebi.ena.webin.cli.assembly;
import java.io.File; import java.io.File;
import java.nio.file.Path; import java.nio.file.Path;
import java.util.Optional; import java.util.Optional;
import org.jdom2.Element; import org.jdom2.Element;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry; import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.ValidationEngineException; import uk.ac.ebi.embl.api.validation.ValidationEngineException;
import uk.ac.ebi.embl.api.validation.submission.SubmissionValidator; import uk.ac.ebi.embl.api.validation.submission.SubmissionValidator;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
import uk.ac.ebi.ena.webin.cli.WebinCliContext; import uk.ac.ebi.ena.webin.cli.WebinCliContext;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
public class SequenceAssemblyWebinCli extends SequenceWebinCli<SequenceAssemblyManifest> { public class SequenceAssemblyWebinCli extends SequenceWebinCli<SequenceAssemblyManifest> {
......
/* /*
* Copyright 2018 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,7 +9,6 @@ ...@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli.assembly; package uk.ac.ebi.ena.webin.cli.assembly;
import java.io.File; import java.io.File;
...@@ -28,27 +28,27 @@ import org.jdom2.Document; ...@@ -28,27 +28,27 @@ import org.jdom2.Document;
import org.jdom2.Element; import org.jdom2.Element;
import org.jdom2.output.Format; import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter; import org.jdom2.output.XMLOutputter;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import uk.ac.ebi.embl.api.entry.feature.SourceFeature; import uk.ac.ebi.embl.api.entry.feature.SourceFeature;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry; import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.ValidationEngineException; import uk.ac.ebi.embl.api.validation.ValidationEngineException;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFile; import uk.ac.ebi.embl.api.validation.submission.SubmissionFile;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType; import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType;
import uk.ac.ebi.embl.api.validation.submission.SubmissionOptions; import uk.ac.ebi.embl.api.validation.submission.SubmissionOptions;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestReader; import uk.ac.ebi.ena.webin.cli.AbstractWebinCli;
import uk.ac.ebi.ena.webin.cli.service.IgnoreErrorsService; import uk.ac.ebi.ena.webin.cli.WebinCli;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.entity.Sample; import uk.ac.ebi.ena.webin.cli.entity.Sample;
import uk.ac.ebi.ena.webin.cli.entity.Study; import uk.ac.ebi.ena.webin.cli.entity.Study;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestReader;
import uk.ac.ebi.ena.webin.cli.service.IgnoreErrorsService;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle; import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle.SubmissionXMLFile; import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle.SubmissionXMLFile;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle.SubmissionXMLFileType; import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle.SubmissionXMLFileType;
import uk.ac.ebi.ena.webin.cli.utils.FileUtils; import uk.ac.ebi.ena.webin.cli.utils.FileUtils;
import uk.ac.ebi.ena.webin.cli.AbstractWebinCli;
import uk.ac.ebi.ena.webin.cli.WebinCli;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public abstract class public abstract class
SequenceWebinCli<T extends ManifestReader> extends AbstractWebinCli<T> SequenceWebinCli<T extends ManifestReader> extends AbstractWebinCli<T>
......
/* /*
* Copyright 2019 EMBL - European Bioinformatics Institute * Copyright 2018-2019 EMBL - European Bioinformatics Institute
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * 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 * file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
...@@ -8,17 +9,22 @@ ...@@ -8,17 +9,22 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the * CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License. * specific language governing permissions and limitations under the License.
*/ */
package uk.ac.ebi.ena.webin.cli.assembly; package uk.ac.ebi.ena.webin.cli.assembly;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.StringUtils;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry; import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.submission.Context; import uk.ac.ebi.embl.api.validation.submission.Context;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFile; import uk.ac.ebi.embl.api.validation.submission.SubmissionFile;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType;