Feature/command completion (#344)

* Phase 1 implementation, Bash completion
* Knock down deprecation

Author: denis-yuen

seqware-common/src/main/java/net/sourceforge/seqware/common/util/filetools/ProvisionFilesUtil.java

@@ -512,7 +512,7 @@ private boolean putToS3(InputStream reader, String output, boolean fullOutputPat
             omd.setContentLength(this.inputSize);
             // just encrypt everything via Server-Side encryption, see
             // http://docs.amazonwebservices.com/AmazonS3/latest/dev/SSEUsingJavaSDK.html
-            omd.setServerSideEncryption(ObjectMetadata.AES_256_SERVER_SIDE_ENCRYPTION);
+            omd.setSSEAlgorithm(ObjectMetadata.AES_256_SERVER_SIDE_ENCRYPTION);
             BasicAWSCredentials credentials = new BasicAWSCredentials(accessKey, secretKey);
             ClientConfiguration config = new ClientConfiguration();
             config.setConnectionTimeout(connectionTimeout);
@@ -602,12 +602,12 @@ private boolean waitForS3Upload(Transfer myUpload) {
             // FIXME: this doesn't try to reconnect via a new reader if things go badly
             while (myUpload.isDone() == false) {
                 if (isVerbose()) {
-                    float percent = (myUpload.getProgress().getBytesTransfered() * 100.0f) / this.inputSize;
+                    float percent = (myUpload.getProgress().getBytesTransferred() * 100.0f) / this.inputSize;
                     System.out.printf("  + completed: %.2f", percent);
                     System.out.print("%\r");
                     Log.info("Transfer: " + myUpload.getDescription());
                     Log.info("  - State:    " + myUpload.getState());
-                    Log.info("  - Progress: " + myUpload.getProgress().getBytesTransfered() + " of " + this.inputSize);
+                    Log.info("  - Progress: " + myUpload.getProgress().getBytesTransferred() + " of " + this.inputSize);
                 }
                 // Do work while we wait for our upload to complete...
                 if (myUpload.getState() == TransferState.Failed) {

seqware-ext-admin-testing/src/main/java/net/sourceforge/seqware/pipeline/plugins/ITUtility.java

@@ -29,6 +29,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -196,11 +197,11 @@ public static String runArbitraryCommand(String line, int expectedReturnValue, F
             if (exitValue != expectedReturnValue){
                 throw new RuntimeException("exit value for full jar with no params should be " + expectedReturnValue + " was " + exitValue);
             }
-            String output = outputStream.toString();
+            String output = outputStream.toString(StandardCharsets.UTF_8);
             return output;
         } catch (ExecuteException e) {
             Log.error("Execution failed with:");
-            Log.error(outputStream.toString());
+            Log.error(outputStream.toString(StandardCharsets.UTF_8));
             throw e;
         }
     }

seqware-ext-admin-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/DeleteDBET.java

@@ -16,10 +16,6 @@
  */
 package net.sourceforge.seqware.pipeline.plugins;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 import io.seqware.common.model.WorkflowRunStatus;
 import net.sourceforge.seqware.common.module.ReturnValue;
 import org.apache.commons.dbutils.handlers.ArrayHandler;
@@ -28,6 +24,12 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
 /**
  * These tests support command-line tools found in the SeqWare User Tutorial, in this case, DeleteDB
  * 
@@ -129,7 +131,7 @@ public void testFailureDueToEmptyKeyFile() throws IOException {
     @Test
     public void testFailureDueToCorruptKeyFile() throws IOException {
         File createTempFile = File.createTempFile("deletion", "keyFile");
-        FileUtils.write(createTempFile, "crap data");
+        FileUtils.write(createTempFile, "crap data", StandardCharsets.UTF_8);
         String listCommand = "-p net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB " + "-- --r 6691 -k " + createTempFile;
         ITUtility.runSeqWareJar(listCommand, ReturnValue.INVALIDFILE, null);
     }

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/PluginRunnerET.java

@@ -2,10 +2,22 @@
 
 import com.google.common.io.Files;
 import io.seqware.pipeline.SqwKeys;
+import net.sourceforge.seqware.common.module.ReturnValue;
+import net.sourceforge.seqware.common.util.Log;
+import net.sourceforge.seqware.common.util.configtools.ConfigTools;
+import net.sourceforge.seqware.pipeline.runner.PluginRunner;
+import org.apache.commons.io.FileUtils;
+import org.junit.AfterClass;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.springframework.util.SerializationUtils;
+
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.PrintWriter;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -18,16 +30,6 @@
 import java.util.concurrent.ExecutorCompletionService;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
-import org.junit.Assert;
-import net.sourceforge.seqware.common.module.ReturnValue;
-import net.sourceforge.seqware.common.util.Log;
-import net.sourceforge.seqware.common.util.configtools.ConfigTools;
-import net.sourceforge.seqware.pipeline.runner.PluginRunner;
-import org.apache.commons.io.FileUtils;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.springframework.util.SerializationUtils;
 
 /*
  * Copyright (C) 2013 SeqWare
@@ -421,7 +423,7 @@ public File exportINIFile(String name, Integer accession, boolean newCLI) throws
             String listCommand = " workflow ini --accession " + accession + " --out " + workflowIni.getAbsolutePath();
             ITUtility.runSeqwareCLI(listCommand, ReturnValue.SUCCESS, null);
             // new command line does not go to stdout
-            listOutput = FileUtils.readFileToString(workflowIni);
+            listOutput = FileUtils.readFileToString(workflowIni, StandardCharsets.UTF_8);
         } else {
             Log.info("Attempting to export parameters for  " + name);
             String listCommand = "-p net.sourceforge.seqware.pipeline.plugins.BundleManager -- --list-workflow-params --workflow-accession "
@@ -475,7 +477,7 @@ public String call() {
                 String tOutput = ITUtility.runSeqWareJar("-p io.seqware.pipeline.plugins.WorkflowLifecycle -- " + command,
                         ReturnValue.SUCCESS, null);
                 Log.error(command + " completed, writing output to " + output.getAbsolutePath());
-                FileUtils.write(output, tOutput);
+                FileUtils.write(output, tOutput, StandardCharsets.UTF_8);
                 return tOutput;
             } catch (IOException ex) {
                 Log.error("IOException while running " + command, ex);

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/ProvisionFilesET.java

@@ -26,6 +26,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.util.Map;
 import java.util.Random;
 
@@ -85,14 +86,14 @@ public void provisionInAndOut() throws IOException {
         Assert.assertTrue("file locations do not differ: " + retrievedFile.getAbsolutePath() + "vs" + provisionedFile.getAbsolutePath(),
                 !retrievedFile.getAbsolutePath().equals(provisionedFile.getAbsolutePath()));
         Assert.assertTrue("file contents not the same",
-                FileUtils.readFileToString(retrievedFile).equals(FileUtils.readFileToString(provisionedFile)));
+                FileUtils.readFileToString(retrievedFile, StandardCharsets.UTF_8).equals(FileUtils.readFileToString(provisionedFile, StandardCharsets.UTF_8)));
     }
 
     public File provisionFileWithRandomInput(String sampleAccession) throws IOException {
         // create a random new file and check that the file we want to provision exists
         File inputFile = File.createTempFile("input", "out");
         final String content = "This is a funky funky test file";
-        FileUtils.write(inputFile, content);
+        FileUtils.write(inputFile, content, StandardCharsets.UTF_8);
 
         File metadataFile = File.createTempFile("metadata", "out");
 
@@ -112,11 +113,11 @@ public File provisionFileWithRandomInput(String sampleAccession) throws IOExcept
         // check that file was ended up being provisioned correctly
         File provisioned = new File(getDatastorePrefix() + inputFile.getName());
         Assert.assertTrue("file did not end up in final location", provisioned.exists());
-        String contents = FileUtils.readFileToString(provisioned).trim();
+        String contents = FileUtils.readFileToString(provisioned, StandardCharsets.UTF_8).trim();
         Assert.assertTrue("file contents not as expected", contents.equals(content));
 
         // check on metadata file
-        String metadataContent = FileUtils.readFileToString(metadataFile).trim();
+        String metadataContent = FileUtils.readFileToString(metadataFile, StandardCharsets.UTF_8).trim();
         try {
             int processingInt = Integer.parseInt(metadataContent);
             Log.info("provisioned file as sw_accession: " + processingInt);

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/WorkflowRunReporterET.java

@@ -162,10 +162,10 @@ public void emptyDateRange() throws IOException {
         File testOutFile = new File(createTempDir, randomString + ".txt");
         String listCommand = "-p net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter " + "-- --output-filename "
                 + testOutFile.getName() + " --workflow-accession 2861 --time-period 2014-01-01";
-        String listOutput = ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS, createTempDir);
+        ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS, createTempDir);
         File retrievedFile = new File(createTempDir, testOutFile.getName());
         Assert.assertTrue("output file does not exist", retrievedFile.exists());
-        List<String> readLines = FileUtils.readLines(testOutFile);
+        List<String> readLines = FileUtils.readLines(testOutFile, StandardCharsets.UTF_8);
         Assert.assertTrue("incorrect number of lines ", readLines.size() == 1);
         long checksumCRC32 = FileUtils.checksumCRC32(testOutFile);
         Assert.assertTrue("incorrect output checksum " + checksumCRC32, checksumCRC32 == 1649363086L);