diff --git a/LICENSE b/LICENSE
index 1b107ae65f117c26717ce8a3ccdabeb22ea0458c..4f4a877a1dd455ac1585209811bc07feb9664340 100644
--- a/LICENSE
+++ b/LICENSE
@@ -186,7 +186,7 @@
same "printed page" as the copyright notice for easier
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");
you may not use this file except in compliance with the License.
diff --git a/build.gradle b/build.gradle
index a2bc61022480d790df27c507608fc501c1af4e87..bcc3a32fb9a5e6af54be8bf0ebf89956a1287c52 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,6 +1,7 @@
plugins {
id 'org.springframework.boot' version '2.1.1.RELEASE'
id "io.github.ddimtirov.codacy" version "0.1.0"
+ id "com.diffplug.gradle.spotless" version "3.18.0"
}
apply plugin: 'java'
@@ -16,13 +17,31 @@ wrapper{
distributionType = Wrapper.DistributionType.BIN
}
-
group = 'uk.ac.ebi.ena.webin-cli'
ext.version_base = '1.7.1'
version = version_base
sourceCompatibility = '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 {
mainClassName = 'uk.ac.ebi.ena.webin.cli.WebinCli'
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/AbstractWebinCli.java b/src/main/java/uk/ac/ebi/ena/webin/cli/AbstractWebinCli.java
index 4ec1bcdf5c8c5b95c544294f021a1036d8b326bb..a31bd37bc10d0e86e4fce6d1a6856a25f0bc38c2 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/AbstractWebinCli.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/AbstractWebinCli.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
import java.io.File;
@@ -18,12 +18,12 @@ import java.security.NoSuchAlgorithmException;
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.reporter.ValidationMessageReporter;
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.utils.FileUtils;
-import uk.ac.ebi.ena.webin.cli.logger.ValidationMessageLogger;
-import uk.ac.ebi.ena.webin.cli.reporter.ValidationMessageReporter;
public abstract class
AbstractWebinCli<T extends ManifestReader>
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/ParameterDescriptor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/ParameterDescriptor.java
index f3257eb6715560a6d3fb4cacbfc4fb3b23e53924..638154412102928de9dc02a39bb795bbc17e75bc 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/ParameterDescriptor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/ParameterDescriptor.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
public interface ParameterDescriptor {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCli.java b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCli.java
index 50a7222a7327e4447efc2f73e3af3e87c26990e8..c6dfbe5146920ff42aded5fd851e3ca55eeecf44 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCli.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCli.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
import java.io.File;
@@ -35,6 +35,7 @@ import ch.qos.logback.classic.encoder.PatternLayoutEncoder;
import ch.qos.logback.classic.spi.ILoggingEvent;
import ch.qos.logback.core.FileAppender;
import ch.qos.logback.core.OutputStreamAppender;
+
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.ReportErrorType;
@@ -335,12 +336,12 @@ public class WebinCli { // implements CommandLineRunner
{
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
{
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() );
} catch( WebinCliException e )
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliContext.java b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliContext.java
index be09c540898255a88452e0f6563ca1d9f2ca3631..0ec3b941ff0bc382ba2ba19ce3354b3f4ab47689 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliContext.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliContext.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
import uk.ac.ebi.ena.webin.cli.assembly.GenomeAssemblyWebinCli;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliException.java b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliException.java
index 43de89fadf53871cdaa976fc0786fa41195690d5..abd817ce989cab534b9c2b86372b04ab2c77b9bc 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliException.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliException.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
public class
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliMessage.java b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliMessage.java
index 7767cf4728cfbabe1c32b821fde72868639ec39e..27b6657913d1129fb89e4bc6c32207772cdcb4d2 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliMessage.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliMessage.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,16 +9,15 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
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.Severity;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
-import java.lang.reflect.Field;
-import java.text.MessageFormat;
-
public interface WebinCliMessage {
// Messages.
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliParameters.java b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliParameters.java
index cd21d42c4fe87335d260b17d12e3f5381c1b2f37..ab740da6cf19fb92ef5e123e81be9a2f38e1e19f 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliParameters.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/WebinCliParameters.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
import java.io.File;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyManifest.java b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyManifest.java
index 37dcf687a41ca36131735ffbaa8d719d32399e88..ed402f4447faf316500d3d0ddf8580c21643e35c 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyManifest.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyManifest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.util.ArrayList;
@@ -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.SubmissionFiles;
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.ManifestFieldType;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFileCount;
@@ -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.SourceFeatureProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class
GenomeAssemblyManifest extends ManifestReader
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyWebinCli.java b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyWebinCli.java
index c3ddad80d336af32f7c2910343183e6789b5db15..efdd9d1a5c2c2911c29b29ad621894f012e548a7 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyWebinCli.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyWebinCli.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,20 +9,21 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.io.File;
import java.nio.file.Path;
import java.util.Optional;
+
import org.jdom2.Element;
+
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.ValidationEngineException;
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.SourceFeatureProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
-import uk.ac.ebi.ena.webin.cli.WebinCliContext;
public class
GenomeAssemblyWebinCli extends SequenceWebinCli<GenomeAssemblyManifest>
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyManifest.java b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyManifest.java
index b598c6c30cc503d5ffa014acd56523012b091466..c2aceaf5c3651f4d565822ab172eb177e134792a 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyManifest.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyManifest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.util.ArrayList;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyWebinCli.java b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyWebinCli.java
index d6d12a513278c1f962d3483fa6f017095b7fa031..42b16cab5bb41c5b0add3fe722816174b4145e64 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyWebinCli.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyWebinCli.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,18 +9,19 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.io.File;
import java.nio.file.Path;
import java.util.Optional;
+
import org.jdom2.Element;
+
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.ValidationEngineException;
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.manifest.processor.StudyProcessor;
public class SequenceAssemblyWebinCli extends SequenceWebinCli<SequenceAssemblyManifest> {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceWebinCli.java b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceWebinCli.java
index e8c1b68b12fd2f30a73dff36d82c25a1005bdc87..8c0d5d142d0a0d9062420f717f177ec35d68d658 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceWebinCli.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceWebinCli.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.io.File;
@@ -28,27 +28,27 @@ import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
-
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+
import uk.ac.ebi.embl.api.entry.feature.SourceFeature;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
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.FileType;
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.service.IgnoreErrorsService;
+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;
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.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.SubmissionXMLFile;
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.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
SequenceWebinCli<T extends ManifestReader> extends AbstractWebinCli<T>
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyManifest.java b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyManifest.java
index 1ac3ac47a1a97d15a6302fb9c86d0dbab2402508..949a58dfec405d4f41a77f70aa6a7fed11795c95 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyManifest.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyManifest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,17 +9,22 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
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 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.SubmissionFile;
+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.SubmissionOptions;
-import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.manifest.*;
import uk.ac.ebi.ena.webin.cli.manifest.processor.ASCIIFileNameProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.CVFieldProcessor;
@@ -26,12 +32,6 @@ 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.SourceFeatureProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Optional;
public class
TranscriptomeAssemblyManifest extends ManifestReader
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyWebinCli.java b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyWebinCli.java
index d5e6a05e5caf9c898fd9e7ad405aa8ba2cbbca1f..c9453460665bce0ff2ba40b40c8d5cf2fac6e9a4 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyWebinCli.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyWebinCli.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.io.File;
@@ -20,10 +20,10 @@ import org.jdom2.Element;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.ValidationEngineException;
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.SourceFeatureProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
-import uk.ac.ebi.ena.webin.cli.WebinCliContext;
public class TranscriptomeAssemblyWebinCli extends SequenceWebinCli<TranscriptomeAssemblyManifest> {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Sample.java b/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Sample.java
index 725aa12008bec0d6131358c50107139c3e97ca0d..fcc0e2021490589af71d010295f58f3a20adc58d 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Sample.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Sample.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.entity;
public class Sample {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Study.java b/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Study.java
index 54c34120d1942a0bbbfeb12729762c2e4847b8a0..39bdf5590886c37b478ef88b60992ec6ce15b776 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Study.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Study.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.entity;
import java.util.List;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Version.java b/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Version.java
index a63578bb516ba347b6faa5e84adeaa503c177072..43dce71610866de2188174855c9d6aaac53d59d0 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Version.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/entity/Version.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,14 +9,13 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.entity;
+import java.util.Date;
+
import com.fasterxml.jackson.databind.PropertyNamingStrategy;
import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import java.util.Date;
-
@JsonNaming(PropertyNamingStrategy.SnakeCaseStrategy.class)
public class Version {
public Boolean valid;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/logger/ValidationMessageLogger.java b/src/main/java/uk/ac/ebi/ena/webin/cli/logger/ValidationMessageLogger.java
index 4d15fa3bd7c43dffbaeb720e172d103c7df8aaac..975ce699fb58cfe8623cfcc0abdb7b0532f0f7d7 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/logger/ValidationMessageLogger.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/logger/ValidationMessageLogger.java
@@ -1,7 +1,19 @@
+
+/*
+ * 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.
+ */
package uk.ac.ebi.ena.webin.cli.logger;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestCVList.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestCVList.java
index dbb04dea1cdfdf2b80ee33f4556364099d5794e4..7b29153b1bf5a05e9f263cdc36b1facdfead4cf8 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestCVList.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestCVList.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
import java.io.File;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldDefinition.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldDefinition.java
index fc8b8fdf8e4759c02ed290e1eb55ce305ba0dd4a..8965a9406e3a75dd74b6a8ff57152683b1b36cdf 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldDefinition.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldDefinition.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
import java.util.Arrays;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldProcessor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldProcessor.java
index 3717a9c2b0a5d12770eaf6acb519f3280b3712e7..182ff3fd8cfe93092012ee0d8242b87f909637be 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldProcessor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldProcessor.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
import uk.ac.ebi.embl.api.validation.Origin;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldType.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldType.java
index 7705ccc1226026eb4d0a7627e2200d333c6183d8..47f50e5d57e4cccaaafb6f1e50d4834a2e2bd8d3 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldType.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldType.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
public enum ManifestFieldType {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldValue.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldValue.java
index 002ec355eb6cbacda697450d005101db74dc57c6..9e39d03d7a3c3f958b48027624a450204e9057a5 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldValue.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFieldValue.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
import uk.ac.ebi.embl.api.validation.Origin;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFileCount.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFileCount.java
index 72fd6f5e6c7b68c0787518a6829a8ccd7c6bd543..f4983843ea34073b5ed5ab2845e2fe357c2bd744 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFileCount.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFileCount.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
public class ManifestFileCount {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFileSuffix.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFileSuffix.java
index 847c3eae884d1793604b3eb5c060658480718e15..aa6ec9665eda56632ac46865c641ae26cf226fd1 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFileSuffix.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestFileSuffix.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
import java.util.Arrays;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReader.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReader.java
index 2f6cec02b3b5579ed35f2c06f8c9a93e6656875b..9f1bf4e8a0194b31d26fa5d760daf8e687b2072c 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReader.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReader.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,9 +9,12 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
+import static uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.Fields.INFO;
+import static uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.ManifestReaderState.State.PARSE;
+import static uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.ManifestReaderState.State.VALIDATE;
+
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
@@ -27,10 +31,6 @@ import org.apache.commons.lang.StringUtils;
import uk.ac.ebi.embl.api.validation.*;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-import static uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.Fields.INFO;
-import static uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.ManifestReaderState.State.PARSE;
-import static uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.ManifestReaderState.State.VALIDATE;
-
public abstract class
ManifestReader
{
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReaderResult.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReaderResult.java
index 671598da52a6c2596f12d4fbbfab1742909b56c2..f5348c52b93c64bfd12503309224a33d7c11851d 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReaderResult.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReaderResult.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,16 +9,15 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
-import uk.ac.ebi.embl.api.validation.ValidationResult;
-
import java.util.ArrayList;
import java.util.Collection;
import java.util.NoSuchElementException;
import java.util.stream.Collectors;
+import uk.ac.ebi.embl.api.validation.ValidationResult;
+
public class
ManifestReaderResult
{
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ASCIIFileNameProcessor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ASCIIFileNameProcessor.java
index 1a052a58463b24409c58eec0007173be2c2ea1f1..1e3926652eead80f4e9af88c12899bc9996991e6 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ASCIIFileNameProcessor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ASCIIFileNameProcessor.java
@@ -1,12 +1,23 @@
+
+/*
+ * 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.
+ */
package uk.ac.ebi.ena.webin.cli.manifest.processor;
import java.util.regex.Pattern;
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class
ASCIIFileNameProcessor implements ManifestFieldProcessor
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/CVFieldProcessor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/CVFieldProcessor.java
index e0894e16094e05bc17c55e0ccc96deb6624c5a20..8a46a6df25b70773c931bdc95ba40693ed7218c6 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/CVFieldProcessor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/CVFieldProcessor.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,15 +9,14 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
+import uk.ac.ebi.ena.webin.cli.manifest.ManifestCVList;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import uk.ac.ebi.ena.webin.cli.manifest.ManifestCVList;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class
CVFieldProcessor implements ManifestFieldProcessor
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/FileSuffixProcessor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/FileSuffixProcessor.java
index fb46382f3a28eebc58c186af554835203b4adb39..3ebcf98a3398fbace0cb7e096f6a49e8f1cc65a5 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/FileSuffixProcessor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/FileSuffixProcessor.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,16 +9,15 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
+import java.util.List;
+
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-
-import java.util.List;
public class FileSuffixProcessor implements ManifestFieldProcessor {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SampleProcessor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SampleProcessor.java
index 8c03b36ac1292fa8f691a172bfb86c84e2561e51..4ffff338d95da86557d34d76126c18e7bb764962 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SampleProcessor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SampleProcessor.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,18 +9,17 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
-import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
-import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import uk.ac.ebi.ena.webin.cli.entity.Sample;
-import uk.ac.ebi.ena.webin.cli.service.SampleService;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
+import uk.ac.ebi.ena.webin.cli.entity.Sample;
+import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
+import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
+import uk.ac.ebi.ena.webin.cli.service.SampleService;
public class
SampleProcessor implements ManifestFieldProcessor
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SourceFeatureProcessor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SourceFeatureProcessor.java
index 563de006f4859495c3f9f4e76b0bfc1f130274ec..14e4ea4589d466580deefdaf3870ff8f2dc967fb 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SourceFeatureProcessor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SourceFeatureProcessor.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,18 +9,17 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
import uk.ac.ebi.embl.api.entry.feature.SourceFeature;
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
-import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
-import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import uk.ac.ebi.ena.webin.cli.service.SourceFeatureService;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
+import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
+import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
+import uk.ac.ebi.ena.webin.cli.service.SourceFeatureService;
public class
SourceFeatureProcessor implements ManifestFieldProcessor
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/StudyProcessor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/StudyProcessor.java
index ba1c86c095fa1aa91bdb03a46c99f655f8918c5a..d71cc7e6d9df378d4c465f2387e7ac239332be03 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/StudyProcessor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/manifest/processor/StudyProcessor.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,18 +9,17 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
-import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
-import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import uk.ac.ebi.ena.webin.cli.entity.Study;
-import uk.ac.ebi.ena.webin.cli.service.StudyService;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
+import uk.ac.ebi.ena.webin.cli.entity.Study;
+import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldProcessor;
+import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
+import uk.ac.ebi.ena.webin.cli.service.StudyService;
public class
StudyProcessor implements ManifestFieldProcessor
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/BloomWrapper.java b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/BloomWrapper.java
index 03276afd2ea996b6c64b39029b81c9ba81e0453b..4c7ff0a68f730b80a41f1a54d104a284757e3470 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/BloomWrapper.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/BloomWrapper.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.util.HashMap;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/DelegateIterator.java b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/DelegateIterator.java
index f3bc7ed79bcf2cb841db6a738e3ccdb1fcf18ef1..3eb808e1624a25780fb1e09989e33bc54c01a1e1 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/DelegateIterator.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/DelegateIterator.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.util.Iterator;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/FastqScanner.java b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/FastqScanner.java
index ab69285f725a6c506cbe7a3e74b3fa89153369f1..e41d566a5d91470e2a34ce2f379b15eb6623da02 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/FastqScanner.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/FastqScanner.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.io.BufferedInputStream;
@@ -33,9 +33,9 @@ import java.util.stream.Collectors;
import java.util.zip.GZIPInputStream;
import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
-
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+
import uk.ac.ebi.embl.api.validation.DefaultOrigin;
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.Severity;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsFile.java b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsFile.java
index 81d66c424f0371c74ec060cb06b93990706f2a25..9edfd8931e165df09253b54f2aa73b2ea24229da 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsFile.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsFile.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.nio.file.Path;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsManifest.java b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsManifest.java
index d33a60917700a6f1cfa677369c11db7558aea119..333e185c08d5be26a372643da7f59c77d1b5004f 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsManifest.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsManifest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.io.File;
@@ -22,6 +22,7 @@ import java.util.stream.Stream;
import org.apache.commons.lang.StringUtils;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestCVList;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldDefinition;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldType;
@@ -37,7 +38,6 @@ import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsFile.AsciiOffset;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsFile.Filetype;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsFile.QualityScoringSystem;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class
RawReadsManifest extends ManifestReader {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsWebinCli.java b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsWebinCli.java
index 9ef3a462e06154ec8da15c3e67802f0d3e32d45f..75a11f19a96553a4c8b7c22ba9d9cf02430369a7 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsWebinCli.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsWebinCli.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.io.File;
@@ -31,6 +31,8 @@ import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import htsjdk.samtools.DefaultSAMRecordFactory;
import htsjdk.samtools.SAMFormatException;
@@ -44,26 +46,25 @@ import htsjdk.samtools.cram.CRAMException;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.Log.LogLevel;
import net.sf.cram.ref.ENAReferenceSource;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+
import uk.ac.ebi.embl.api.validation.DefaultOrigin;
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
import uk.ac.ebi.embl.api.validation.ValidationResult;
+import uk.ac.ebi.ena.webin.cli.*;
+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.manifest.processor.SampleProcessor;
import uk.ac.ebi.ena.webin.cli.manifest.processor.StudyProcessor;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsFile.ChecksumMethod;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsFile.Filetype;
import uk.ac.ebi.ena.webin.cli.rawreads.refs.CramReferenceInfo;
-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.*;
+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.SubmissionXMLFile;
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.reporter.ValidationMessageReporter;
public class
RawReadsWebinCli extends AbstractWebinCli<RawReadsManifest>
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/CramReferenceInfo.java b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/CramReferenceInfo.java
index a684947681df5a2e11dcebc93552b740c165d8bc..ef66a55954a65aafca24399059a59299dce386b0 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/CramReferenceInfo.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/CramReferenceInfo.java
@@ -1,19 +1,14 @@
-/*******************************************************************************
- * Copyright 2013 EMBL-EBI
- *
- * 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.
- ******************************************************************************/
+/*
+ * 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.
+ */
package uk.ac.ebi.ena.webin.cli.rawreads.refs;
import java.io.BufferedReader;
@@ -41,6 +36,9 @@ import javax.script.ScriptEngine;
import javax.script.ScriptEngineManager;
import javax.script.ScriptException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.SamFiles;
import htsjdk.samtools.SamInputResource;
@@ -51,8 +49,6 @@ import htsjdk.samtools.cram.ref.ReferenceSource;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.Log.LogLevel;
import net.sf.cram.ref.PathPattern;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
public class
CramReferenceInfo
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/reporter/ValidationMessageReporter.java b/src/main/java/uk/ac/ebi/ena/webin/cli/reporter/ValidationMessageReporter.java
index c3aa1a7a7c75c938b9b562e7817a99b7602e3522..9efa314b8c4a30c1c62cad069eb8836e558cc3bd 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/reporter/ValidationMessageReporter.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/reporter/ValidationMessageReporter.java
@@ -1,11 +1,15 @@
-package uk.ac.ebi.ena.webin.cli.reporter;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import uk.ac.ebi.embl.api.validation.Origin;
-import uk.ac.ebi.embl.api.validation.Severity;
-import uk.ac.ebi.embl.api.validation.ValidationMessage;
-import uk.ac.ebi.embl.api.validation.ValidationResult;
+/*
+ * 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.
+ */
+package uk.ac.ebi.ena.webin.cli.reporter;
import java.io.*;
import java.nio.charset.StandardCharsets;
@@ -14,6 +18,14 @@ import java.nio.file.StandardOpenOption;
import java.util.Arrays;
import java.util.HashSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import uk.ac.ebi.embl.api.validation.Origin;
+import uk.ac.ebi.embl.api.validation.Severity;
+import uk.ac.ebi.embl.api.validation.ValidationMessage;
+import uk.ac.ebi.embl.api.validation.ValidationResult;
+
public class ValidationMessageReporter implements Closeable {
protected final OutputStream strm;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/AbstractService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/AbstractService.java
index ae3c252aa30cf7f7859f534aac7170282c5632c9..433924bd3103acd83c88d874477502561f3d70f5 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/AbstractService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/AbstractService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
public class
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/IgnoreErrorsService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/IgnoreErrorsService.java
index d28021b768830f345d7cbd3e56ebf2011053845f..69e1027d8251e81179273d11e4ef70edcb64508a 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/IgnoreErrorsService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/IgnoreErrorsService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
import org.springframework.http.HttpEntity;
@@ -17,9 +17,9 @@ import org.springframework.http.HttpMethod;
import org.springframework.http.ResponseEntity;
import org.springframework.web.client.RestTemplate;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.service.handler.DefaultErrorHander;
import uk.ac.ebi.ena.webin.cli.service.utils.HttpHeaderBuilder;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class
IgnoreErrorsService extends AbstractService {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/SampleService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/SampleService.java
index d322ea8db56ab65e5bc5a72590bfac00c3662905..c0c5e6ca53949b9d7afadc8b87ae0216b736daa1 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/SampleService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/SampleService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
import org.springframework.http.HttpEntity;
@@ -16,11 +16,11 @@ import org.springframework.http.HttpMethod;
import org.springframework.http.ResponseEntity;
import org.springframework.web.client.RestTemplate;
+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.service.handler.NotFoundErrorHandler;
import uk.ac.ebi.ena.webin.cli.service.utils.HttpHeaderBuilder;
-import uk.ac.ebi.ena.webin.cli.WebinCliException;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class
SampleService extends AbstractService
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/SourceFeatureService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/SourceFeatureService.java
index 06177f327be1b18873d1727bd2674c5e4b5a23b8..f4296f50cafdf8a4344650c46d9d1e32e188715e 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/SourceFeatureService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/SourceFeatureService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
import java.io.StringReader;
@@ -32,10 +32,10 @@ import uk.ac.ebi.embl.api.entry.feature.SourceFeature;
import uk.ac.ebi.embl.api.entry.qualifier.Qualifier;
import uk.ac.ebi.embl.api.validation.helper.MasterSourceFeatureUtils;
import uk.ac.ebi.embl.api.validation.helper.taxon.TaxonHelperImpl;
-import uk.ac.ebi.ena.webin.cli.service.handler.NotFoundErrorHandler;
-import uk.ac.ebi.ena.webin.cli.service.utils.HttpHeaderBuilder;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
+import uk.ac.ebi.ena.webin.cli.service.handler.NotFoundErrorHandler;
+import uk.ac.ebi.ena.webin.cli.service.utils.HttpHeaderBuilder;
public class
SourceFeatureService extends AbstractService
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/StudyService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/StudyService.java
index 859e9e93d4c7faf0857e41a21342fe583e85cbc2..94255a02ab9da8ad4eea02f35f906d74849f4f97 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/StudyService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/StudyService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,21 +9,21 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
+import java.util.List;
+
import org.springframework.http.HttpEntity;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpMethod;
import org.springframework.http.ResponseEntity;
import org.springframework.web.client.RestTemplate;
+
+import uk.ac.ebi.ena.webin.cli.WebinCliException;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.entity.Study;
import uk.ac.ebi.ena.webin.cli.service.handler.NotFoundErrorHandler;
import uk.ac.ebi.ena.webin.cli.service.utils.HttpHeaderBuilder;
-import uk.ac.ebi.ena.webin.cli.WebinCliException;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-
-import java.util.List;
public class StudyService extends AbstractService {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/SubmitService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/SubmitService.java
index b6d3e3d1641c401af688bc2e50276740580a83c7..e9b71c4cd6cbb1c5c43dd69105455e64a274b0c0 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/SubmitService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/SubmitService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
import java.io.File;
@@ -37,11 +37,11 @@ import org.springframework.util.LinkedMultiValueMap;
import org.springframework.util.MultiValueMap;
import org.springframework.web.client.RestTemplate;
+import uk.ac.ebi.ena.webin.cli.WebinCliException;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.service.handler.DefaultErrorHander;
import uk.ac.ebi.ena.webin.cli.service.utils.HttpHeaderBuilder;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle.SubmissionXMLFile;
-import uk.ac.ebi.ena.webin.cli.WebinCliException;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class SubmitService extends AbstractService {
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/VersionService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/VersionService.java
index a8d428f2ff792fc94861d892fb7f80407c28bdc7..0137029724b2ce0f1144f302812f017b5e2d47ab 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/VersionService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/VersionService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,14 +9,13 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
import org.springframework.web.client.RestTemplate;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
import uk.ac.ebi.ena.webin.cli.entity.Version;
import uk.ac.ebi.ena.webin.cli.service.handler.DefaultErrorHander;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class
VersionService extends AbstractService
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/handler/DefaultErrorHander.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/handler/DefaultErrorHander.java
index 62e8b0fa7736d2795903ff65977277c397b9b172..0a838fbecbe3f4af47a22df780e0f1f802dd835b 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/handler/DefaultErrorHander.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/handler/DefaultErrorHander.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,19 +9,19 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service.handler;
+import static org.springframework.http.HttpStatus.Series.CLIENT_ERROR;
+import static org.springframework.http.HttpStatus.Series.SERVER_ERROR;
+
+import java.io.IOException;
+
import org.springframework.http.client.ClientHttpResponse;
import org.springframework.web.client.ResponseErrorHandler;
+
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-import java.io.IOException;
-
-import static org.springframework.http.HttpStatus.Series.CLIENT_ERROR;
-import static org.springframework.http.HttpStatus.Series.SERVER_ERROR;
-
public class DefaultErrorHander implements ResponseErrorHandler {
private final String systemError;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/handler/NotFoundErrorHandler.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/handler/NotFoundErrorHandler.java
index c74ea663fc1ddc2256ff8abeb378f7cdca86d3af..a55eb6940f56e592ef81e5336aa24e0e22727caa 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/handler/NotFoundErrorHandler.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/handler/NotFoundErrorHandler.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,19 +9,19 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service.handler;
+import static org.springframework.http.HttpStatus.Series.CLIENT_ERROR;
+import static org.springframework.http.HttpStatus.Series.SERVER_ERROR;
+
+import java.io.IOException;
+
import org.springframework.http.client.ClientHttpResponse;
import org.springframework.web.client.ResponseErrorHandler;
+
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-import java.io.IOException;
-
-import static org.springframework.http.HttpStatus.Series.CLIENT_ERROR;
-import static org.springframework.http.HttpStatus.Series.SERVER_ERROR;
-
public class NotFoundErrorHandler implements ResponseErrorHandler {
private final String validationError;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/utils/HttpHeaderBuilder.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/utils/HttpHeaderBuilder.java
index 6069b641903ab18e9b4f0fcb2608c30fd472f346..b39901928b284c5fb25f127d834a50c58cfab6ae 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/utils/HttpHeaderBuilder.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/utils/HttpHeaderBuilder.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,14 +9,13 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service.utils;
+import java.util.Base64;
+
import org.springframework.http.HttpHeaders;
import org.springframework.http.MediaType;
-import java.util.Base64;
-
public class HttpHeaderBuilder {
private final HttpHeaders headers = new HttpHeaders();
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/service/utils/HttpLoggingInterceptor.java b/src/main/java/uk/ac/ebi/ena/webin/cli/service/utils/HttpLoggingInterceptor.java
index f559beb7e740c646eb6ee8fc9709362c8ba2e73f..deb999b691f36c146deb1ba4a869edc73823385f 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/service/utils/HttpLoggingInterceptor.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/service/utils/HttpLoggingInterceptor.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,9 +9,12 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service.utils;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.http.HttpRequest;
@@ -19,10 +23,6 @@ import org.springframework.http.client.ClientHttpRequestInterceptor;
import org.springframework.http.client.ClientHttpResponse;
import org.springframework.util.StreamUtils;
-import java.io.IOException;
-import java.nio.charset.Charset;
-import java.nio.charset.StandardCharsets;
-
public class HttpLoggingInterceptor implements ClientHttpRequestInterceptor {
private final Logger log = LoggerFactory.getLogger(this.getClass());
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundle.java b/src/main/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundle.java
index b7a3a4095917270896121d25f26cbb7c4e7eca5b..c975482c65f9093c3dfd9a664ab05e64b25a159a 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundle.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundle.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.submit;
import java.io.File;
@@ -21,9 +21,9 @@ import java.util.stream.Collectors;
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.ValidationResult;
-import uk.ac.ebi.ena.webin.cli.utils.FileUtils;
import uk.ac.ebi.ena.webin.cli.WebinCli;
import uk.ac.ebi.ena.webin.cli.reporter.ValidationMessageReporter;
+import uk.ac.ebi.ena.webin.cli.utils.FileUtils;
public class
SubmissionBundle implements Serializable
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundleHelper.java b/src/main/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundleHelper.java
index 642bfa623dd181124fd6c7c6fad51dff111cdbbd..bac99ccef260f863927d339337c030589ef3f28e 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundleHelper.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundleHelper.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.submit;
import java.io.FileInputStream;
@@ -19,6 +19,7 @@ import java.io.ObjectOutputStream;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+
import uk.ac.ebi.embl.api.validation.DefaultOrigin;
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.ValidationResult;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/upload/ASCPService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/upload/ASCPService.java
index 9136ea3a0ae25751ed48f768883824e4e24b7438..1b329ff5cbaf879ae890ea9bc6233d10ba9d15ba 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/upload/ASCPService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/upload/ASCPService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.upload;
import java.io.File;
@@ -19,9 +19,9 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import uk.ac.ebi.ena.webin.cli.utils.ShellExec;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
+import uk.ac.ebi.ena.webin.cli.utils.ShellExec;
public class
@@ -32,7 +32,7 @@ ASCPService implements UploadService
private String password;
@Override public boolean
- isAvaliable()
+ isAvailable()
{
try
{
@@ -89,9 +89,9 @@ ASCPService implements UploadService
@Override public void
- ftpDirectory( List<File> uploadFilesList,
- String uploadDir,
- Path inputDir )
+ upload(List<File> uploadFilesList,
+ String uploadDir,
+ Path inputDir )
{
try
{
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/upload/FtpService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/upload/FtpService.java
index 3588c766ac50dc95612b92ad47d31640f939903c..0700d05e303c52352ea6acb294c4aefb0d9ee12b 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/upload/FtpService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/upload/FtpService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.upload;
import java.io.BufferedInputStream;
@@ -24,9 +24,9 @@ import java.util.stream.Stream;
import org.apache.commons.net.ftp.FTP;
import org.apache.commons.net.ftp.FTPClient;
import org.apache.commons.net.ftp.FTPFile;
-
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
@@ -106,7 +106,7 @@ public class FtpService implements UploadService {
//TODO verbose possible issues with file/folder permissions
@Override public void
- ftpDirectory( List<File> uploadFilesList, String uploadDir, Path inputDir )
+ upload(List<File> uploadFilesList, String uploadDir, Path inputDir )
{
if( null == uploadDir || uploadDir.isEmpty() )
throw WebinCliException.userError( WebinCliMessage.Ftp.UPLOAD_DIR_ERROR.format());
@@ -156,7 +156,7 @@ public class FtpService implements UploadService {
@Override public boolean
- isAvaliable()
+ isAvailable()
{
return true;
}
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/upload/UploadService.java b/src/main/java/uk/ac/ebi/ena/webin/cli/upload/UploadService.java
index 0d6923e1bcb1c8c2d3d7cc7cd79c1523adc1ec33..add8018ac7bb98990d79fa4ff0f01bc87b5ad754 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/upload/UploadService.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/upload/UploadService.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,18 +9,17 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.upload;
import java.io.File;
import java.nio.file.Path;
import java.util.List;
-public interface
+public interface
UploadService
{
void connect( String userName, String password );
- void ftpDirectory( List<File> uploadFilesList, String uploadDir, Path inputDir );
+ void upload(List<File> uploadFilesList, String uploadDir, Path inputDir );
void disconnect();
- boolean isAvaliable();
-}
\ No newline at end of file
+ boolean isAvailable();
+}
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/utils/FileUtils.java b/src/main/java/uk/ac/ebi/ena/webin/cli/utils/FileUtils.java
index eaaef699e5a701a1e5fda1069ef56af34c9b0e68..b1e6124fa9cf26e316b8661403a25720864d9573 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/utils/FileUtils.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/utils/FileUtils.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.utils;
import java.io.BufferedInputStream;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/utils/ShellExec.java b/src/main/java/uk/ac/ebi/ena/webin/cli/utils/ShellExec.java
index 744df83ebc742e785d0525f7bf09a298b1df51eb..289a11ca5ae460445bb0f676ce5e21058f7abc8f 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/utils/ShellExec.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/utils/ShellExec.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.utils;
import java.io.IOException;
diff --git a/src/main/java/uk/ac/ebi/ena/webin/cli/version/HotSpotRuntimeVersion.java b/src/main/java/uk/ac/ebi/ena/webin/cli/version/HotSpotRuntimeVersion.java
index 3eb04ec08b6e113fe5f1d6bba4c8a5c71d47cb1e..793d39c8358d7362d9c1f91213872b08d7f5663d 100644
--- a/src/main/java/uk/ac/ebi/ena/webin/cli/version/HotSpotRuntimeVersion.java
+++ b/src/main/java/uk/ac/ebi/ena/webin/cli/version/HotSpotRuntimeVersion.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.version;
import java.util.regex.Matcher;
diff --git a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/instrument.properties b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/instrument.properties
index e2863e52028bf812c5fe620ebdd244fc95f7a8bb..e3de301a21ea4abd4274543990ec5d88afb4cecd 100644
--- a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/instrument.properties
+++ b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/instrument.properties
@@ -1,14 +1,3 @@
-#
-# Copyright 2018 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.
-#
-
unspecified=LS454,ILLUMINA,PACBIO_SMRT,ION_TORRENT
454\ GS=LS454
454\ GS\ 20=LS454
diff --git a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/platform.properties b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/platform.properties
index fa81a84e0867738a6b2521ccc93a4ff281494157..70b757b20e06aac488c935f59ebb36e6c4974405 100644
--- a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/platform.properties
+++ b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/platform.properties
@@ -1,14 +1,3 @@
-#
-# Copyright 2018 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.
-#
-
LS454=454 technology use 1-color sequential flows
ILLUMINA=Illumina is 4-channel flowgram with 1-to-1 mapping between basecalls and flows
PACBIO_SMRT=PacificBiosciences platform type for the single molecule real time (SMRT) technology.
diff --git a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/selection.properties b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/selection.properties
index f722574e1090fca3c361724fe2fe21948ac2a787..8dc8f844e6af09e61eb9e762f3843eb383023a93 100644
--- a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/selection.properties
+++ b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/selection.properties
@@ -1,14 +1,3 @@
-#
-# Copyright 2018 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.
-#
-
RANDOM=No Selection or Random selection
PCR=target enrichment via PCR
RANDOM\ PCR=Source material was selected by randomly generated primers.
diff --git a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/source.properties b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/source.properties
index f4fdbae3a28b1a775c892eb985510e7054714afd..bfaf1bc0ffaa8e4cfeafd303418b875562743240 100644
--- a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/source.properties
+++ b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/source.properties
@@ -1,14 +1,3 @@
-#
-# Copyright 2018 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.
-#
-
GENOMIC=Genomic DNA (includes PCR products from genomic DNA).
GENOMIC\ SINGLE\ CELL=
TRANSCRIPTOMIC=Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
diff --git a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/strategy.properties b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/strategy.properties
index a7fd983e2d6edfe3bef4b6efe0506ff92afa1d68..fff66fe052af3335f240eaa1dc8bc4a03519c4ef 100644
--- a/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/strategy.properties
+++ b/src/main/resources/uk/ac/ebi/ena/webin/cli/rawreads/strategy.properties
@@ -1,14 +1,3 @@
-#
-# Copyright 2018 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.
-#
-
WGS=Whole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details)
WGA=Whole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details)
WXS=Random sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details)
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/AbstractWebinCliTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/AbstractWebinCliTest.java
index 44a9ec1c292b7701a43e0119bb4b5a435922c10a..a3c1e020f41618995b6134be28ce3c4c7521882c 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/AbstractWebinCliTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/AbstractWebinCliTest.java
@@ -1,12 +1,24 @@
+
+/*
+ * 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.
+ */
package uk.ac.ebi.ena.webin.cli;
+import static org.junit.Assert.assertEquals;
+
import org.junit.Test;
+
import uk.ac.ebi.ena.webin.cli.assembly.GenomeAssemblyWebinCli;
import uk.ac.ebi.ena.webin.cli.assembly.TranscriptomeAssemblyWebinCli;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsWebinCli;
-import static org.junit.Assert.assertEquals;
-
public class AbstractWebinCliTest {
@Test
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliContextTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliContextTest.java
index 035346d960d55e21b8daf0d50fe6234eeea5d694..a943802e8b43223b3ddaad8aa63a24385d320981 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliContextTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliContextTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,13 +9,12 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
-import org.junit.Test;
-
import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
+import org.junit.Test;
+
public class
WebinCliContextTest
{
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliMessageTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliMessageTest.java
index 0fa6f6d3045820ca41d8bf96661a1e3935a79ca2..97aa45dafa3ca8e9ab3ce4b00b2f0a13b5234d7f 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliMessageTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliMessageTest.java
@@ -1,14 +1,26 @@
+
+/*
+ * 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.
+ */
package uk.ac.ebi.ena.webin.cli;
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.lang.reflect.Modifier;
+
import org.junit.Test;
+
import uk.ac.ebi.embl.api.validation.Origin;
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
-import java.lang.reflect.Modifier;
-
-import static org.assertj.core.api.Assertions.assertThat;
-
public class WebinCliMessageTest {
@Test
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliTest.java
index f4824e0d9afa8b87e6c5d6330f4b643bfe9d1481..f383af97196deb8b7f579ac479bcb1bbd826ca49 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,9 +9,10 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
+import static org.junit.Assert.assertEquals;
+
import java.nio.file.Path;
import org.junit.Assert;
@@ -23,8 +25,6 @@ import uk.ac.ebi.ena.webin.cli.manifest.ManifestReader;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsManifest;
import uk.ac.ebi.ena.webin.cli.upload.ASCPService;
-import static org.junit.Assert.assertEquals;
-
public class
WebinCliTest
{
@@ -130,7 +130,7 @@ WebinCliTest
{
Path input_dir = WebinCliTestUtils.createTempDir().toPath();
Path cram_file = WebinCliTestUtils.createTempFileFromResource( "uk/ac/ebi/ena/webin/cli/rawreads/18045_1#93.cram", input_dir, false );
- Assert.assertTrue( new ASCPService().isAvaliable() );
+ Assert.assertTrue( new ASCPService().isAvailable() );
testWebinCli( WebinCliContext.reads,
input_dir,
RawReadsManifest.Fields.CRAM + " " + cram_file.getFileName() + "\n" + getRawReadsInfoFields(),
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliTestUtils.java b/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliTestUtils.java
index 4331c927782cf1b9afee754fbd4bba8593a56724..c3085ac9f92dd8f693bf4c62ae67471a1e88bbee 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliTestUtils.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/WebinCliTestUtils.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli;
import java.io.ByteArrayInputStream;
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/AssemblyTestUtils.java b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/AssemblyTestUtils.java
index a8c591816bf6b77e8684050213c8dd0ed47eda91..dbb49940cb19916ff6a29439f412e510e8d4862b 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/AssemblyTestUtils.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/AssemblyTestUtils.java
@@ -1,13 +1,24 @@
+
+/*
+ * 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.
+ */
package uk.ac.ebi.ena.webin.cli.assembly;
+import java.io.File;
+import java.nio.file.Path;
+
import uk.ac.ebi.embl.api.entry.feature.FeatureFactory;
import uk.ac.ebi.embl.api.entry.feature.SourceFeature;
+import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
import uk.ac.ebi.ena.webin.cli.entity.Sample;
-import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
-
-import java.io.File;
-import java.nio.file.Path;
class AssemblyTestUtils {
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyValidationTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyValidationTest.java
index 0203c315bbd4a55e1760e6128f8147f0b8f25197..ce6c5535efbfe05eace23fc984a9c15eba85a30b 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyValidationTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyValidationTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,9 +9,11 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
+import static org.assertj.core.api.Assertions.assertThatThrownBy;
+import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
+
import java.io.File;
import java.nio.file.Path;
import java.util.Arrays;
@@ -22,13 +25,10 @@ import org.junit.Test;
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFiles;
-import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
-import uk.ac.ebi.ena.webin.cli.entity.Study;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-
-import static org.assertj.core.api.Assertions.assertThatThrownBy;
-import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
+import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
+import uk.ac.ebi.ena.webin.cli.entity.Study;
public class GenomeAssemblyValidationTest {
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyXmlTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyXmlTest.java
index a25c3604219955b312ca2f9a144133103314df84..b6c22130965932e563e56f2a86f819bf2bf9b041 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyXmlTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/GenomeAssemblyXmlTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,14 +9,15 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.nio.file.Path;
import java.util.Locale;
import java.util.Optional;
+
import org.junit.Before;
import org.junit.Test;
+
import uk.ac.ebi.embl.api.entry.feature.FeatureFactory;
import uk.ac.ebi.embl.api.entry.feature.SourceFeature;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
@@ -23,11 +25,11 @@ 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.SubmissionFiles;
import uk.ac.ebi.embl.api.validation.submission.SubmissionOptions;
+import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
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.submit.SubmissionBundle;
-import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
public class
GenomeAssemblyXmlTest
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyValidationTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyValidationTest.java
index 24f99c2fda6f4f1cb89fd474766a070d165a167f..534eb530bdd44080ef26cbff3ae960442ba0f41c 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyValidationTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyValidationTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import static org.assertj.core.api.Assertions.assertThat;
@@ -29,17 +29,17 @@ import org.junit.Test;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
import uk.ac.ebi.embl.api.validation.Severity;
+import uk.ac.ebi.embl.api.validation.ValidationMessage;
+import uk.ac.ebi.embl.api.validation.ValidationResult;
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.FileType;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFiles;
import uk.ac.ebi.embl.api.validation.submission.SubmissionOptions;
-import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
-import uk.ac.ebi.ena.webin.cli.entity.Study;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
-import uk.ac.ebi.embl.api.validation.ValidationMessage;
-import uk.ac.ebi.embl.api.validation.ValidationResult;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
+import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
+import uk.ac.ebi.ena.webin.cli.entity.Study;
public class SequenceAssemblyValidationTest {
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyXmlTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyXmlTest.java
index 111e36d0bb48f5f1169d556ee91081b268e34f8e..b44b28a9029bf04e3f492f565b7eafeb722b1445 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyXmlTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/SequenceAssemblyXmlTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.nio.file.Path;
@@ -23,10 +23,10 @@ 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.SubmissionFiles;
import uk.ac.ebi.embl.api.validation.submission.SubmissionOptions;
+import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
import uk.ac.ebi.ena.webin.cli.entity.Study;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle;
-import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
public class
SequenceAssemblyXmlTest
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyValidationTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyValidationTest.java
index 6992b1ce341f510ec9f7a00b964bdac07c9781dc..3709f0995148518b9cc83bd75f96c58c16f5676b 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyValidationTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyValidationTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,9 +9,11 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
+import static org.assertj.core.api.Assertions.assertThatThrownBy;
+import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
+
import java.io.File;
import java.nio.file.Path;
import java.util.Arrays;
@@ -22,13 +25,10 @@ import org.junit.Test;
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType;
import uk.ac.ebi.embl.api.validation.submission.SubmissionFiles;
-import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
-import uk.ac.ebi.ena.webin.cli.entity.Study;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-
-import static org.assertj.core.api.Assertions.assertThatThrownBy;
-import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
+import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
+import uk.ac.ebi.ena.webin.cli.entity.Study;
public class TranscriptomeAssemblyValidationTest {
@@ -216,4 +216,3 @@ public class TranscriptomeAssemblyValidationTest {
validator.validate();
}
}
-
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyXmlTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyXmlTest.java
index 3b15ec0969c42af660c752eee86d34ffb18d98a7..65157fe0be1e2221216a0ad1b3561a35355a6b59 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyXmlTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/assembly/TranscriptomeAssemblyXmlTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.assembly;
import java.nio.file.Path;
@@ -20,14 +20,14 @@ import org.junit.Test;
import uk.ac.ebi.embl.api.entry.genomeassembly.AssemblyInfoEntry;
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.SubmissionFiles;
import uk.ac.ebi.embl.api.validation.submission.SubmissionOptions;
-import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType;
+import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
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.submit.SubmissionBundle;
-import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
public class
TranscriptomeAssemblyXmlTest {
@@ -148,4 +148,3 @@ TranscriptomeAssemblyXmlTest {
}
}
}
-
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestCVListTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestCVListTest.java
index 91174dddbb5a17041324d421f98b281068f39b5b..ad91180558fb453d3be4892e95c72a2daa74a413 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestCVListTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestCVListTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,11 +9,11 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
import org.junit.Assert;
import org.junit.Test;
+
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsManifest;
public class
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReaderTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReaderTest.java
index 024b183ea95fd97ba1bad3202806d89f52dde3a4..b151e44bb3889a31864cc3f427180f9d396ac955 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReaderTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/ManifestReaderTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,16 +9,8 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
-import org.junit.Assert;
-import org.junit.Test;
-import uk.ac.ebi.embl.api.validation.Severity;
-import uk.ac.ebi.ena.webin.cli.manifest.processor.CVFieldProcessor;
-import uk.ac.ebi.ena.webin.cli.manifest.processor.FileSuffixProcessor;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
@@ -29,6 +22,14 @@ import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
+import org.junit.Assert;
+import org.junit.Test;
+
+import uk.ac.ebi.embl.api.validation.Severity;
+import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
+import uk.ac.ebi.ena.webin.cli.manifest.processor.CVFieldProcessor;
+import uk.ac.ebi.ena.webin.cli.manifest.processor.FileSuffixProcessor;
+
public class ManifestReaderTest {
private final Path inputDir = Paths.get( "." );
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/TestManifestReader.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/TestManifestReader.java
index d6718676cfd3cda85632b91145b8b2a58a140ed9..b0070db203e0bf7befd5ee852ad0b12c243b3be0 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/TestManifestReader.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/TestManifestReader.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest;
import java.util.List;
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ASCIIFileNameProcessorTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ASCIIFileNameProcessorTest.java
index 36eff5ace36901e737cf71322c5b1b8c34ae0c3f..58e2168c54f42bb35d1be923eb734a06579ce316 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ASCIIFileNameProcessorTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ASCIIFileNameProcessorTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,17 +9,17 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
+import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
+
import org.junit.Assert;
import org.junit.Test;
+
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldType;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
-
public class
ASCIIFileNameProcessorTest
{
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/CVFieldProcessorTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/CVFieldProcessorTest.java
index da6e04fe5bfeb46cc5037f9c465c8eee573333fa..85289d211c0107458ac72b2bc5b007610f574146 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/CVFieldProcessorTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/CVFieldProcessorTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,18 +9,18 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
+import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
+
import org.junit.Assert;
import org.junit.Test;
+
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestCVList;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldType;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
-
public class CVFieldProcessorTest {
@Test public void test()
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/FileSuffixProcessorTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/FileSuffixProcessorTest.java
index 0a2a5cef3eaa61eb4583ba023b3b69c00d2b7483..d745fe7e19b2c42f0a59b0b47f5efe435b9cad73 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/FileSuffixProcessorTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/FileSuffixProcessorTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,18 +9,18 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
+import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
+
import org.junit.Assert;
import org.junit.Test;
+
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldType;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFileSuffix;
-import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
-
public class FileSuffixProcessorTest {
@Test
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ProcessorTestUtils.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ProcessorTestUtils.java
index c7b8f19be06a8107836878975659b910b0e760a3..b907db6b4008f4f07e2f87592285b9ad8932dd87 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ProcessorTestUtils.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/ProcessorTestUtils.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldDefinition;
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SampleProcessorTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SampleProcessorTest.java
index 6d1429dd19d5de30af94b1beaea7073fd3ef6f11..db3bc18f3b534671ffe45fa57eab4410590d07ca 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SampleProcessorTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/SampleProcessorTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,20 +9,19 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
+import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
+
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import uk.ac.ebi.embl.api.validation.Severity;
+import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
+import uk.ac.ebi.ena.webin.cli.entity.Sample;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldType;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import uk.ac.ebi.ena.webin.cli.entity.Sample;
-import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
-
-import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
public class
SampleProcessorTest
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/StudyProcessorTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/StudyProcessorTest.java
index d24db0e98c06255ff7fe6cfd8c306cff4a0b5c29..5aca597b4d2307f17b96662617b1ff01c9e2ea74 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/StudyProcessorTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/manifest/processor/StudyProcessorTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,20 +9,19 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.manifest.processor;
+import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
+
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import uk.ac.ebi.embl.api.validation.Severity;
+import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
+import uk.ac.ebi.ena.webin.cli.entity.Study;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldType;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
-import uk.ac.ebi.ena.webin.cli.entity.Study;
-import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
-
-import static uk.ac.ebi.ena.webin.cli.manifest.processor.ProcessorTestUtils.createFieldValue;
public class
StudyProcessorTest
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/BloomWrapperTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/BloomWrapperTest.java
index ae650d1f8c0d41bdc2b7bcacd23a90db72a750c9..2f974a5ea2c90b8ead3c590ff049d5d549f8cbb0 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/BloomWrapperTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/BloomWrapperTest.java
@@ -1,3 +1,14 @@
+
+/*
+ * 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.
+ */
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.math.BigInteger;
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/FastqScannerTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/FastqScannerTest.java
index 01d888e5efa77e1d0b45610e08518a15b968ba79..5057aa8b9a8e7f47b06e232c55caf4f1e4fbbb61 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/FastqScannerTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/FastqScannerTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.io.File;
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsManifestTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsManifestTest.java
index 8e13585cc8d9d315ede0abd854552ab4d8568c76..bcb60034d3d32e70748dc5393b1728c6a01e5eb0 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsManifestTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsManifestTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import java.io.IOException;
@@ -25,12 +25,12 @@ import org.junit.Test;
import uk.ac.ebi.embl.api.validation.Severity;
import uk.ac.ebi.embl.api.validation.ValidationMessage;
import uk.ac.ebi.embl.api.validation.ValidationResult;
+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.ManifestFieldType;
import uk.ac.ebi.ena.webin.cli.manifest.ManifestFieldValue;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsFile.Filetype;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsManifest.Fields;
-import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
public class
RawReadsManifestTest
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsWebinCliTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsWebinCliTest.java
index 45f485a604d23431af577b8ed6a8e77c105b0e59..ab8a9b56755ea34d4c697d98fb098cfacf16b177 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsWebinCliTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/RawReadsWebinCliTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads;
import static org.junit.Assert.fail;
@@ -38,14 +38,15 @@ import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.ValidationStringency;
import net.sf.cram.ref.ENAReferenceSource;
import net.sf.cram.ref.ENAReferenceSource.LoggerWrapper;
+
import uk.ac.ebi.embl.api.validation.ValidationMessage;
import uk.ac.ebi.embl.api.validation.ValidationResult;
+import uk.ac.ebi.ena.webin.cli.WebinCliException;
+import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
import uk.ac.ebi.ena.webin.cli.rawreads.RawReadsManifest.Fields;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle;
import uk.ac.ebi.ena.webin.cli.submit.SubmissionBundle.SubmissionXMLFileType;
-import uk.ac.ebi.ena.webin.cli.WebinCliException;
-import uk.ac.ebi.ena.webin.cli.WebinCliParameters;
public class
RawReadsWebinCliTest
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/CramReferenceInfoTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/CramReferenceInfoTest.java
index 4533ece1029c5229735b14d4f7c48ec88c794edd..b270b543eebfd2682e61bf34ea713b2435792831 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/CramReferenceInfoTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/CramReferenceInfoTest.java
@@ -1,3 +1,14 @@
+
+/*
+ * 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.
+ */
package uk.ac.ebi.ena.webin.cli.rawreads.refs;
import org.junit.Assert;
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/ENAReferenceSourceTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/ENAReferenceSourceTest.java
index 5d57d444450d7c623d2ae11c3d64fdefda72da1b..5e4f1f3a733c7ec5aa969fcaf05d88b33233e2c3 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/ENAReferenceSourceTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/rawreads/refs/ENAReferenceSourceTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.rawreads.refs;
import java.io.IOException;
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/reporter/ValidationMessageReporterTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/reporter/ValidationMessageReporterTest.java
index 77b5f623abfcd14a2084a8883e0481fc69012a2b..845d5077e08534ff0c4c2df70032de839e7655b5 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/reporter/ValidationMessageReporterTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/reporter/ValidationMessageReporterTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,21 +9,21 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.reporter;
-import org.junit.Test;
-import uk.ac.ebi.embl.api.validation.DefaultOrigin;
-import uk.ac.ebi.embl.api.validation.Origin;
-import uk.ac.ebi.embl.api.validation.Severity;
-import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
+import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
-import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
+import org.junit.Test;
+
+import uk.ac.ebi.embl.api.validation.DefaultOrigin;
+import uk.ac.ebi.embl.api.validation.Origin;
+import uk.ac.ebi.embl.api.validation.Severity;
+import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
public class ValidationMessageReporterTest {
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/service/IgnoreErrorsServiceTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/service/IgnoreErrorsServiceTest.java
index 5cc4c9267d3f9db15e307af0f4ce9453f499d89e..afc6b7e623619406883267af90b100c12bfe9680 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/service/IgnoreErrorsServiceTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/service/IgnoreErrorsServiceTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,13 +9,13 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
+import static org.assertj.core.api.Assertions.assertThat;
+
import org.junit.Test;
-import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
-import static org.assertj.core.api.Assertions.assertThat;
+import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
public class
IgnoreErrorsServiceTest
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/service/SampleServiceTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/service/SampleServiceTest.java
index f696371b9d9f80b241af88fb74122c3dbd225af9..cdf06abdd7e34ec08b139eb5019d976a7a1e5fa1 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/service/SampleServiceTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/service/SampleServiceTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
import static org.assertj.core.api.Assertions.assertThatThrownBy;
@@ -16,10 +16,10 @@ import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
import org.junit.Test;
-import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
-import uk.ac.ebi.ena.webin.cli.entity.Sample;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
+import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
+import uk.ac.ebi.ena.webin.cli.entity.Sample;
public class
SampleServiceTest {
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/service/SourceFeatureServiceTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/service/SourceFeatureServiceTest.java
index b54ee9809b5410612d3a2a91e361f15298f0f910..ea1dbecfb02c9439eecfaf2f601b9e1d9635464c 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/service/SourceFeatureServiceTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/service/SourceFeatureServiceTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
import static org.assertj.core.api.Assertions.assertThatThrownBy;
@@ -17,9 +17,9 @@ import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
import org.junit.Test;
import uk.ac.ebi.embl.api.entry.feature.SourceFeature;
-import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
+import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
public class
SourceFeatureServiceTest {
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/service/StudyServiceTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/service/StudyServiceTest.java
index ef54d41fb9c24feebe08f957092bfd0c28b7a313..b5d58bdbc944c5207e92da6102f6d1c605869577 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/service/StudyServiceTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/service/StudyServiceTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,18 +9,17 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.assertThatThrownBy;
+
import org.junit.Test;
-import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
-import uk.ac.ebi.ena.webin.cli.entity.Study;
import uk.ac.ebi.ena.webin.cli.WebinCliException;
import uk.ac.ebi.ena.webin.cli.WebinCliMessage;
-
-import static org.assertj.core.api.Assertions.assertThat;
-import static org.assertj.core.api.Assertions.assertThatThrownBy;
+import uk.ac.ebi.ena.webin.cli.WebinCliTestUtils;
+import uk.ac.ebi.ena.webin.cli.entity.Study;
public class
StudyServiceTest {
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/service/VersionServiceTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/service/VersionServiceTest.java
index bcd27642957e6541c1c9a02572a32a9ed1681743..16d406cb517dcbfb31fbba55ee0b32a30eaf2d2d 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/service/VersionServiceTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/service/VersionServiceTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,14 +9,14 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.service;
+import static org.assertj.core.api.Assertions.assertThat;
+
import org.junit.BeforeClass;
import org.junit.Test;
-import uk.ac.ebi.ena.webin.cli.entity.Version;
-import static org.assertj.core.api.Assertions.assertThat;
+import uk.ac.ebi.ena.webin.cli.entity.Version;
public class
VersionServiceTest {
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundleTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundleTest.java
index c8b8817c54f14185599be5854d4eb730a5ded793..f2526215f789ae6f1d70a0d0d0d1cc0777c3b057 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundleTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/submit/SubmissionBundleTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.submit;
import java.io.File;
diff --git a/src/test/java/uk/ac/ebi/ena/webin/cli/version/HotSpotRuntimeVersionTest.java b/src/test/java/uk/ac/ebi/ena/webin/cli/version/HotSpotRuntimeVersionTest.java
index e23e546603b6a784ee89096073bf4aa28772238c..5816cb965b13cc15c8bfe748e1c5f2772aed1980 100644
--- a/src/test/java/uk/ac/ebi/ena/webin/cli/version/HotSpotRuntimeVersionTest.java
+++ b/src/test/java/uk/ac/ebi/ena/webin/cli/version/HotSpotRuntimeVersionTest.java
@@ -1,5 +1,6 @@
+
/*
- * 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
* file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
@@ -8,7 +9,6 @@
* CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
-
package uk.ac.ebi.ena.webin.cli.version;
import org.junit.Assert;