anon-iclr-submission/benchname-bug-localization huggingface dataset:
Repository: altbeacon/android-beacon-library
Issue: getInstanceForApplication should be renamed & is prone to context leaks

getInstanceForApplication or the BeaconManager class should probably call getApplicationContext on the application context to prevent leaks.

The suggested use for the BeaconManager is from an activity, like so:

`private BeaconManager beaconManager = BeaconManager.getInstanceForApplication(this);`

To prevent the activity being leaked, the beaconmanager should really make sure it calls `getApplicationContext` on the passed context.

Secondly `getInstanceForApplication` implies you should be passing an application to the method, simply `getInstance` might be better 


Changed files:
src/main/java/org/altbeacon/beacon/BeaconManager.java

diff --git a/src/main/java/org/altbeacon/beacon/BeaconManager.java b/src/main/java/org/altbeacon/beacon/BeaconManager.java
index 35b7df6..657d03b 100644
--- a/src/main/java/org/altbeacon/beacon/BeaconManager.java
+++ b/src/main/java/org/altbeacon/beacon/BeaconManager.java
@@ -246,7 +246,7 @@ public class BeaconManager {
     }
 
    protected BeaconManager(Context context) {
-      mContext = context;
+      mContext = context.getApplicationContext();
       if (!sManifestCheckingDisabled) {
          verifyServiceDeclaration();
       }
Repository: springdoc/springdoc-openapi
Issue: Commit 80bc5a75361d1689fa72099963db84bcd95b2068 breaks project with JDK 11 + Kotlin

The commit 80bc5a75361d1689fa72099963db84bcd95b2068 is breaking again our project built with JDK 11 and Kotlin.
Can you please revert this? Additionally, what is the purpose of using `LocalVariableTableParameterNameDiscoverer` just to get the name of the parameters that you can get from `java.lang.reflect.Parameter` array that you already have at that point?
I've removed this `LocalVariableTableParameterNameDiscoverer` and no test is breaking.
I hope you can remove this again. Thanks!

Best regards,
João Dias


Changed files:
springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java

diff --git a/springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java b/springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java
index 8063e23b..e18b05dd 100644
--- a/springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java
+++ b/springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java
@@ -59,8 +59,9 @@ public abstract class AbstractRequestBuilder {
         LocalVariableTableParameterNameDiscoverer d = parameterBuilder.getLocalSpringDocParameterNameDiscoverer();
         String[] pNames = d.getParameterNames(handlerMethod.getMethod());
         java.lang.reflect.Parameter[] parameters = handlerMethod.getMethod().getParameters();
+        String[] reflectionParametersNames = Arrays.stream(parameters).map(java.lang.reflect.Parameter::getName).toArray(String[]::new);
         if (pNames == null) {
-            pNames = Arrays.stream(parameters).map(java.lang.reflect.Parameter::getName).toArray(String[]::new);
+            pNames = reflectionParametersNames;
         }
         RequestBodyInfo requestBodyInfo = new RequestBodyInfo(methodAttributes);
         List<Parameter> operationParameters = (operation.getParameters() != null) ? operation.getParameters()
@@ -70,7 +71,7 @@ public abstract class AbstractRequestBuilder {
         for (int i = 0; i < pNames.length; i++) {
             // check if query param
             Parameter parameter = null;
-            final String pName = pNames[i];
+            final String pName = pNames[i] == null ? reflectionParametersNames[i] : pNames[i];
             io.swagger.v3.oas.annotations.Parameter parameterDoc = parameterBuilder.getParameterAnnotation(
                     handlerMethod, parameters[i], i, io.swagger.v3.oas.annotations.Parameter.class);
             if (parameterDoc == null) {
Repository: springdoc/springdoc-openapi
Issue: Commit 2594a276d97c8f4168f6f7aa22a00f8438f38dd5 broke Kotlin Coroutines support

This commit has changed the usage of `java.lang.reflect.Parameter` to `org.springframework.core.MethodParameter` and this broke Kotlin Coroutines support since with the second no parameter name is successfully retrieved.

Changed files:
springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java

diff --git a/springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java b/springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java
index adc9b904..62c168a4 100644
--- a/springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java
+++ b/springdoc-openapi-common/src/main/java/org/springdoc/core/AbstractRequestBuilder.java
@@ -160,8 +160,8 @@ public abstract class AbstractRequestBuilder {
 		// requests
 		String[] pNames = this.localSpringDocParameterNameDiscoverer.getParameterNames(handlerMethod.getMethod());
 		MethodParameter[] parameters = handlerMethod.getMethodParameters();
-		String[] reflectionParametersNames = Arrays.stream(parameters).map(MethodParameter::getParameterName).toArray(String[]::new);
-		if (pNames == null)
+		String[] reflectionParametersNames = Arrays.stream(handlerMethod.getMethod().getParameters()).map(java.lang.reflect.Parameter::getName).toArray(String[]::new);
+		if (pNames == null || Arrays.stream(pNames).anyMatch(Objects::isNull))
 			pNames = reflectionParametersNames;
 		parameters = DelegatingMethodParameter.customize(pNames, parameters);
 		RequestBodyInfo requestBodyInfo = new RequestBodyInfo();
Repository: square/keywhiz
Issue: Keywhiz has inconsistencies in filename enforcement

As evidenced by this output:

```
keywhiz.cli describe secret --name shh.2016-01-26T23:49:27Z.key
Exception in thread "main" java.lang.IllegalArgumentException: Invalid name, must match ^[a-zA-Z_0-9\\-.]+$
    at keywhiz.cli.commands.DescribeAction.run(DescribeAction.java:58)
    at keywhiz.cli.CommandExecutor.executeCommand(CommandExecutor.java:141)
    at keywhiz.cli.CliMain.main(CliMain.java:68)
```

This secret was added via the automation API and otherwise is served and is displayed correctly.


Changed files:
cli/src/main/java/keywhiz/cli/Utilities.java, cli/src/test/java/keywhiz/cli/UtilitiesTest.java

diff --git a/cli/src/main/java/keywhiz/cli/Utilities.java b/cli/src/main/java/keywhiz/cli/Utilities.java
index 0871d598..2e1e6895 100644
--- a/cli/src/main/java/keywhiz/cli/Utilities.java
+++ b/cli/src/main/java/keywhiz/cli/Utilities.java
@@ -17,7 +17,7 @@ package keywhiz.cli;
 
 public class Utilities {
 
-  public static final String VALID_NAME_PATTERN = "^[a-zA-Z_0-9\\\\-.]+$";
+  public static final String VALID_NAME_PATTERN = "^[a-zA-Z_0-9\\\\-.:]+$";
 
   public static boolean validName(String name) {
     // "." is allowed at any position but the first.
diff --git a/cli/src/test/java/keywhiz/cli/UtilitiesTest.java b/cli/src/test/java/keywhiz/cli/UtilitiesTest.java
index 9788e8c1..d61d3a17 100644
--- a/cli/src/test/java/keywhiz/cli/UtilitiesTest.java
+++ b/cli/src/test/java/keywhiz/cli/UtilitiesTest.java
@@ -46,7 +46,7 @@ public class UtilitiesTest {
     assertThat(validName("bad\\tI-am-secret.yml")).isFalse();
 
     List<String> specialCharacters = Arrays.asList("&", "|", "(", ")", "[", "]", "{", "}", "^",
-        ";", ",", "\\\\", "/", "<", ">", "\\t", "\\n", "\\r", "`", "'", "\\"", "?", ":", "#", "%",
+        ";", ",", "\\\\", "/", "<", ">", "\\t", "\\n", "\\r", "`", "'", "\\"", "?", "#", "%",
         "*", "+", "=", "\\0", "\\u0002", "\\000");
 
     for (String name : specialCharacters) {
Repository: apache/netbeans
Issue: JavaDoc popup renders incorrectly

### Apache NetBeans version

Apache NetBeans 16

### What happened

The JavaDoc popup does not render the text in some tags. Specifically text in fixed-width code style appears to be missing.  For example references to system properties in the JavaDoc for ClassLoader.getSystemClassLoader().

### How to reproduce

In a Java editor type "ClassLoader." hit the autocompete shortcut and select the getSystemClassLoader() method such that the JavaDocs appear.  Notice that there are missing parts compared to viewing the same documentation in a web browser. Such as:

    If the system property "java.system.class.loader" is defined when...

appearing instead as:

    If the system property "" is defined when...

### Did this work correctly in an earlier version?

No / Don't know

### Operating System

macOS 13.2

### JDK

JDK 17.0.6

### Apache NetBeans packaging

Apache NetBeans binary zip

### Anything else

_No response_

### Are you willing to submit a pull request?

Yes

### Code of Conduct

Yes

Changed files:
java/java.sourceui/src/org/netbeans/api/java/source/ui/ElementJavadoc.java

diff --git a/java/java.sourceui/src/org/netbeans/api/java/source/ui/ElementJavadoc.java b/java/java.sourceui/src/org/netbeans/api/java/source/ui/ElementJavadoc.java
index ed8edb9fa3..6d1df08284 100644
--- a/java/java.sourceui/src/org/netbeans/api/java/source/ui/ElementJavadoc.java
+++ b/java/java.sourceui/src/org/netbeans/api/java/source/ui/ElementJavadoc.java
@@ -39,6 +39,7 @@ import com.sun.source.doctree.SinceTree;
 import com.sun.source.doctree.SnippetTree;
 import com.sun.source.doctree.StartElementTree;
 import com.sun.source.doctree.SummaryTree;
+import com.sun.source.doctree.SystemPropertyTree;
 import com.sun.source.doctree.TextTree;
 import com.sun.source.doctree.ThrowsTree;
 import com.sun.source.doctree.UnknownBlockTagTree;
@@ -1332,6 +1333,19 @@ public class ElementJavadoc {
                     List<? extends DocTree> summary = summaryTag.getSummary();
                     sb.append(inlineTags(summary, docPath, doc, trees, null));
                     break;
+                case SYSTEM_PROPERTY:
+                    SystemPropertyTree systemPropTag = (SystemPropertyTree) tag;
+                    sb.append("<code>"); //NOI18N
+                    sb.append(systemPropTag.getPropertyName());
+                    sb.append("</code>"); //NOI18N
+                    break;
+                default:
+                    sb.append("<code>"); //NOI18N
+                    try {
+                        sb.append(XMLUtil.toElementContent(tag.toString()));
+                    } catch (IOException ioe) {}
+                    sb.append("</code>"); //NOI18N
+                    break;
             }
         }
         return sb;
Repository: apache/netbeans
Issue: Netbeans dont Support WildFly 27

### Apache NetBeans version

Apache NetBeans 16

### What happened

Try to add WildFly 27 on Netbeans 16 and you get no imports of jakartaee.* to your project

### How to reproduce

Try to add WildFly 27 on Netbeans 16 and you get no imports of jakartaee.* to your project

### Did this work correctly in an earlier version?

No / Don't know

### Operating System

Windows

### JDK

JDK17

### Apache NetBeans packaging

Apache NetBeans provided installer

### Anything else

_No response_

### Are you willing to submit a pull request?

No

### Code of Conduct

Yes

Changed files:
enterprise/javaee.wildfly/src/org/netbeans/modules/javaee/wildfly/util/WildFlyProperties.java

diff --git a/enterprise/javaee.wildfly/src/org/netbeans/modules/javaee/wildfly/util/WildFlyProperties.java b/enterprise/javaee.wildfly/src/org/netbeans/modules/javaee/wildfly/util/WildFlyProperties.java
index 19bc47292e..711855ee35 100644
--- a/enterprise/javaee.wildfly/src/org/netbeans/modules/javaee/wildfly/util/WildFlyProperties.java
+++ b/enterprise/javaee.wildfly/src/org/netbeans/modules/javaee/wildfly/util/WildFlyProperties.java
@@ -232,12 +232,16 @@ public class WildFlyProperties {
     }
 
     public List<URL> getClasses() {
-        List<URL> list = selectJars(FileUtil.toFileObject(new File(getModulePath("javax"))));
+        List<URL> classes = new ArrayList<>();
+
+        classes.addAll(selectJars(FileUtil.toFileObject(new File(getModulePath("jakarta")))));
+        classes.addAll(selectJars(FileUtil.toFileObject(new File(getModulePath("javax")))));
+
         File glassfish = new File(getModulePath("org/glassfish/javax"));
         if(glassfish.exists()) {
-            list.addAll(selectJars(FileUtil.toFileObject(glassfish)));
+            classes.addAll(selectJars(FileUtil.toFileObject(glassfish)));
         }
-        return list;
+        return classes;
     }
 
     public List<URL> getSources() {
Repository: datalinkdc/dinky
Issue: [Bug] [core] program in loop when offline task failed

### Search before asking

- [X] I had searched in the [issues](https://github.com/DataLinkDC/dlink/issues?q=is%3Aissue) and found no similar issues.


### What happened

program in loop

### What you expected to happen

offline task succeed

### How to reproduce

submit task to online,
offline task when the jobinstant is high Backpressure
happen the issue

### Anything else

_No response_

### Version

0.6.1-SNAPSHOT

### Are you willing to submit PR?

- [X] Yes I am willing to submit a PR!

### Code of Conduct

- [X] I agree to follow this project's [Code of Conduct](https://www.apache.org/foundation/policies/conduct)


Changed files:
dlink-core/src/main/java/com/dlink/api/FlinkAPI.java, dlink-admin/src/main/java/com/dlink/service/impl/TaskServiceImpl.java

diff --git a/dlink-admin/src/main/java/com/dlink/service/impl/TaskServiceImpl.java b/dlink-admin/src/main/java/com/dlink/service/impl/TaskServiceImpl.java
index f49fe6e9..28754de4 100644
--- a/dlink-admin/src/main/java/com/dlink/service/impl/TaskServiceImpl.java
+++ b/dlink-admin/src/main/java/com/dlink/service/impl/TaskServiceImpl.java
@@ -463,7 +463,7 @@ public class TaskServiceImpl extends SuperServiceImpl<TaskMapper, Task> implemen
             return jobManager.cancel(jobId);
         }
         SavePointResult savePointResult = jobManager.savepoint(jobId, savePointType, null);
-        if (Asserts.isNotNull(savePointResult)) {
+        if (Asserts.isNotNull(savePointResult.getJobInfos())) {
             for (JobInfo item : savePointResult.getJobInfos()) {
                 if (Asserts.isEqualsIgnoreCase(jobId, item.getJobId()) && Asserts.isNotNull(jobConfig.getTaskId())) {
                     Savepoints savepoints = new Savepoints();
diff --git a/dlink-core/src/main/java/com/dlink/api/FlinkAPI.java b/dlink-core/src/main/java/com/dlink/api/FlinkAPI.java
index f841a0c6..605b62a0 100644
--- a/dlink-core/src/main/java/com/dlink/api/FlinkAPI.java
+++ b/dlink-core/src/main/java/com/dlink/api/FlinkAPI.java
@@ -97,7 +97,10 @@ public class FlinkAPI {
         Map<String, Object> paramMap = new HashMap<>();
         switch (type) {
             case CANCEL:
+                paramMap.put("cancel-job", true);
+                paramType = FlinkRestAPIConstant.SAVEPOINTS;
                 jobInfo.setStatus(JobInfo.JobStatus.CANCEL);
+                break;
             case STOP:
                 paramMap.put("drain", false);
                 paramType = FlinkRestAPIConstant.STOP;
@@ -127,7 +130,7 @@ public class FlinkAPI {
                     continue;
                 }
                 if (node.get("operation").has("failure-cause")) {
-                    String failureCause = node.get("operation").get("failure-cause").asText();
+                    String failureCause = node.get("operation").get("failure-cause").toString();
                     if (Asserts.isNotNullString(failureCause)) {
                         result.fail(failureCause);
                         break;
Repository: connectbot/connectbot
Issue: timers on the hosts list 

The timers displayed on the hosts list screen only seem to update after a failed login attempt.  So a newly created host displays as Never Connected and continues to do so (somewhat inaccurately) no matter how may times it has actually connected. Ironically, it only ever stops displaying Never Connected on the occasion that it fails to connect.   

It looks like the timer is zeroed on pressing the button to connect to a host.  Then it's like there is some back to front logic, such that it resets the timer to its previous value if a connection is successful, instead of unsuccessful. So a check to prevent the timer simply showing time-since-last-button-press has (inadvertently) resulted in it showing time-since-last-failed-connection.

Changed files:
app/src/main/java/org/connectbot/util/HostDatabase.java

diff --git a/app/src/main/java/org/connectbot/util/HostDatabase.java b/app/src/main/java/org/connectbot/util/HostDatabase.java
index 1e71b57c..2250b8e2 100644
--- a/app/src/main/java/org/connectbot/util/HostDatabase.java
+++ b/app/src/main/java/org/connectbot/util/HostDatabase.java
@@ -406,6 +406,7 @@ public class HostDatabase extends RobustSQLiteOpenHelper implements HostStorage,
 	@Override
 	public void touchHost(HostBean host) {
 		long now = System.currentTimeMillis() / 1000;
+		host.setLastConnect(now);
 
 		ContentValues values = new ContentValues();
 		values.put(FIELD_HOST_LASTCONNECT, now);
Repository: connectbot/connectbot
Issue: No ipv6 support

Inserting a sequence of ipv6 address such as 2620:0:1cfe:face:b00c::3 will result in connectbot warning about malformed hostname. Putting the ipv6 address in brackets has no effect. Connectbot still treats ipv6 in brackets as invalid hostname format.


Changed files:
app/src/main/java/org/connectbot/transport/SSH.java

diff --git a/app/src/main/java/org/connectbot/transport/SSH.java b/app/src/main/java/org/connectbot/transport/SSH.java
index 0867256b..89e2d8d1 100644
--- a/app/src/main/java/org/connectbot/transport/SSH.java
+++ b/app/src/main/java/org/connectbot/transport/SSH.java
@@ -101,7 +101,7 @@ public class SSH extends AbsTransport implements ConnectionMonitor, InteractiveC
 
 	static final Pattern hostmask;
 	static {
-		hostmask = Pattern.compile("^(.+)@([0-9a-z.-]+)(:(\\\\d+))?$", Pattern.CASE_INSENSITIVE);
+		hostmask = Pattern.compile("^(.+)@(([0-9a-z.-]+)|(\\\\[[a-f:0-9]+\\\\]))(:(\\\\d+))?$", Pattern.CASE_INSENSITIVE);
 	}
 
 	private boolean compression = false;
@@ -770,9 +770,9 @@ public class SSH extends AbsTransport implements ConnectionMonitor, InteractiveC
 			.append("://")
 			.append(Uri.encode(matcher.group(1)))
 			.append('@')
-			.append(matcher.group(2));
+			.append(Uri.encode(matcher.group(2)));
 
-		String portString = matcher.group(4);
+		String portString = matcher.group(6);
 		int port = DEFAULT_PORT;
 		if (portString != null) {
 			try {
Repository: connectbot/connectbot
Issue: Connection closed detection

This may be related to issue #227

1 - Start ConnectBot
2 - Open a connection
3 - Power off device
4 - Power on device
5 - Type "exit" to close the connection
6 - Console say "Connection closed" but no button yes/no to close the activity (need to menu -> Disconnect)


Changed files:
app/src/main/java/org/connectbot/ConsoleActivity.java

diff --git a/app/src/main/java/org/connectbot/ConsoleActivity.java b/app/src/main/java/org/connectbot/ConsoleActivity.java
index 0bb7858f..9cdb4a50 100644
--- a/app/src/main/java/org/connectbot/ConsoleActivity.java
+++ b/app/src/main/java/org/connectbot/ConsoleActivity.java
@@ -172,6 +172,10 @@ public class ConsoleActivity extends AppCompatActivity implements BridgeDisconne
 			adapter.notifyDataSetChanged();
 			final int requestedIndex = bound.getBridges().indexOf(requestedBridge);
 
+			if (requestedBridge != null)
+				requestedBridge.promptHelper.setHandler(promptHandler);
+
+
 			if (requestedIndex != -1) {
 				pager.post(new Runnable() {
 					@Override
Repository: connectbot/connectbot
Issue: Unable to show the ActionBar (when set to auto hide)

Since the very nice #277 when actionbar (Toolbar) is set to auto hide in settings, touching the screen does not show the action bar.


Changed files:
app/src/main/java/org/connectbot/ConsoleActivity.java

diff --git a/app/src/main/java/org/connectbot/ConsoleActivity.java b/app/src/main/java/org/connectbot/ConsoleActivity.java
index 440661a1..7c9ee056 100644
--- a/app/src/main/java/org/connectbot/ConsoleActivity.java
+++ b/app/src/main/java/org/connectbot/ConsoleActivity.java
@@ -661,7 +661,7 @@ public class ConsoleActivity extends AppCompatActivity implements BridgeDisconne
 			@Override
 			public void onClick(View v) {
 				if (keyboardGroup.getVisibility() == View.GONE) {
-					showEmulatedKeys(false);
+					showEmulatedKeys(true);
 				}
 			}
 		});
Repository: webbukkit/dynmap
Issue: Dynmap does not disable properly if using wrong platform

**Issue Description:** *Dynmap does not disable properly, when on the wrong version of bukkit forks*

* **Dynmap Version:** *3.0<version<3.6*
* **Server Version:** *1.20.1*
* **Steps to Replicate:** *Run dynmap 3.5 or lower for a unsupported platform, and have another plugin with dynmap as a dependency,*

Sorry for ruining your template. Doing this in DynmapPlugin#onEnable should work right? (this is really an issue in 3.6 as well, what I noticed):
```java
       if (helper == null) {
            Log.info("Dynmap is disabled (unsupported platform)");
            this.setEnabled(false); // Added this line
            return;
        }
```

 [x] *I have looked at all other issues and this is not a duplicate*  
 [x] *I have been able to replicate this*


Changed files:
spigot/src/main/java/org/dynmap/bukkit/DynmapPlugin.java

diff --git a/spigot/src/main/java/org/dynmap/bukkit/DynmapPlugin.java b/spigot/src/main/java/org/dynmap/bukkit/DynmapPlugin.java
index b2ad4e66..d54154fc 100644
--- a/spigot/src/main/java/org/dynmap/bukkit/DynmapPlugin.java
+++ b/spigot/src/main/java/org/dynmap/bukkit/DynmapPlugin.java
@@ -914,6 +914,7 @@ public class DynmapPlugin extends JavaPlugin implements DynmapAPI {
         }
         if (helper == null) {
             Log.info("Dynmap is disabled (unsupported platform)");
+            this.setEnabled(false);
             return;
         }
         PluginDescriptionFile pdfFile = this.getDescription();
Repository: webbukkit/dynmap
Issue: Schema version set wrong PostgreSQL

**Issue Description:** When using PostgreSQL as map storage the schema version gets misaligned which breaks markers

* **Dynmap Version:** version 3.4-beta-3 (core version 3.4-beta-3-774)
* **Server Version:** fabric 1.18.2 (0.51.1+1.18.2) PostgreSQL 14.2
* **Pastebin of Configuration.txt:** [click](https://gist.github.com/TheRijn/2d037d8e3e155c656cf2e2f83a8dce8a#file-config-yml)
* **Server Host (if applicable):** Selfhosted via Docker Compose
* **Pastebin of crashlogs or other relevant logs:** [click (part of the same Gist as above)](https://gist.github.com/TheRijn/2d037d8e3e155c656cf2e2f83a8dce8a#file-logs)

* **Steps to Replicate:** 

I had problems with markers sometime after migrating to PostgreSQL, so I started investigating by replacing my config.txt with a new one with a new database. This worked fine, I saw in the logs that it had problems with migrating so I paid particular attention to the schema version on the fresh start of Dynmap. It started with version 4. Everything was working again.

After a server restart, I saw the same issues with markers again. And in the logs, I saw `[Dynmap] Updating database schema from version = 3` again. But I was sure it already was on version 4.

Logging in into the database I saw the `schemaversion` was indeed set 3, I changed it manually to 4 and everything worked again!

- [x] *I have looked at all other issues and this is not a duplicate*  
- [x] *I have been able to replicate this*

Changed files:
DynmapCore/src/main/java/org/dynmap/storage/postgresql/PostgreSQLMapStorage.java

diff --git a/DynmapCore/src/main/java/org/dynmap/storage/postgresql/PostgreSQLMapStorage.java b/DynmapCore/src/main/java/org/dynmap/storage/postgresql/PostgreSQLMapStorage.java
index 361e445a..533bd1e9 100644
--- a/DynmapCore/src/main/java/org/dynmap/storage/postgresql/PostgreSQLMapStorage.java
+++ b/DynmapCore/src/main/java/org/dynmap/storage/postgresql/PostgreSQLMapStorage.java
@@ -468,7 +468,7 @@ public class PostgreSQLMapStorage extends MapStorage {
                 doUpdate(c, "CREATE TABLE " + tableStandaloneFiles + " (FileName VARCHAR(128) NOT NULL, ServerID BIGINT NOT NULL DEFAULT 0, Content BYTEA, PRIMARY KEY (FileName, ServerID))");
                 doUpdate(c, "CREATE INDEX " + tableMaps + "_idx ON " + tableMaps + "(WorldID, MapID, Variant, ServerID)");  
                 doUpdate(c, "CREATE TABLE " + tableSchemaVersion + " (level INT PRIMARY KEY NOT NULL)");
-                doUpdate(c, "INSERT INTO " + tableSchemaVersion + " (level) VALUES (3)");
+                doUpdate(c, "INSERT INTO " + tableSchemaVersion + " (level) VALUES (4)");
                 version = 4;	// initialzed to current schema
             } catch (SQLException x) {
             	logSQLException("Error creating tables", x);
Repository: uwetrottmann/seriesguide
Issue: Writing to Storage Access Framework file does not replace existing data

`JsonExportTask` does not clear existing file contents before writing new data. If the written JSON is shorter than the existing file contents invalid JSON ends up in the file.

Changed files:
app/src/main/java/com/battlelancer/seriesguide/dataliberation/JsonExportTask.java

diff --git a/app/src/main/java/com/battlelancer/seriesguide/dataliberation/JsonExportTask.java b/app/src/main/java/com/battlelancer/seriesguide/dataliberation/JsonExportTask.java
index 786ea045f..f53d8ba49 100644
--- a/app/src/main/java/com/battlelancer/seriesguide/dataliberation/JsonExportTask.java
+++ b/app/src/main/java/com/battlelancer/seriesguide/dataliberation/JsonExportTask.java
@@ -258,6 +258,12 @@ public class JsonExportTask extends AsyncTask<Void, Integer, Integer> {
                 }
                 FileOutputStream out = new FileOutputStream(pfd.getFileDescriptor());
 
+                // Even though using streams and FileOutputStream does not append by
+                // default, using Storage Access Framework just overwrites existing
+                // bytes, potentially leaving old bytes hanging over:
+                // so truncate the file first to clear any existing bytes.
+                out.getChannel().truncate(0);
+
                 if (type == BACKUP_SHOWS) {
                     writeJsonStreamShows(out, data);
                 } else if (type == BACKUP_LISTS) {
Repository: jdbi/jdbi
Issue: PaginationParameterCustomizer warm() is never called

I have a custom binding annotation ala:

```
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.PARAMETER)
@SqlStatementCustomizingAnnotation(PaginationCustomizerFactory.class)
public @interface ApiBind
{
}
```

`PaginationCustomizerFactory` implements `createForParameter` and returns a `SqlStatementParameterCustomizer`. The `warm()` method of that parameter customizer is never called (`apply()` is correctly called however).

Changed files:
sqlobject/src/main/java/org/jdbi/v3/sqlobject/statement/internal/CustomizingStatementHandler.java
sqlobject/src/test/java/org/jdbi/v3/sqlobject/config/TestUseConfiguredDefaultParameterCustomizerFactory.java

diff --git a/sqlobject/src/main/java/org/jdbi/v3/sqlobject/statement/internal/CustomizingStatementHandler.java b/sqlobject/src/main/java/org/jdbi/v3/sqlobject/statement/internal/CustomizingStatementHandler.java
index ac3cffdd8..25fb4d8c0 100644
--- a/sqlobject/src/main/java/org/jdbi/v3/sqlobject/statement/internal/CustomizingStatementHandler.java
+++ b/sqlobject/src/main/java/org/jdbi/v3/sqlobject/statement/internal/CustomizingStatementHandler.java
@@ -75,6 +75,11 @@ abstract class CustomizingStatementHandler<StatementType extends SqlStatement<St
             .collect(Collectors.toList());
     }
 
+    @Override
+    public void warm(ConfigRegistry config) {
+        statementCustomizers.forEach(s -> s.warm(config));
+    }
+
     // duplicate implementation in SqlObjectFactory
     private static Stream<Class<?>> superTypes(Class<?> type) {
         Class<?>[] interfaces = type.getInterfaces();
diff --git a/sqlobject/src/test/java/org/jdbi/v3/sqlobject/config/TestUseConfiguredDefaultParameterCustomizerFactory.java b/sqlobject/src/test/java/org/jdbi/v3/sqlobject/config/TestUseConfiguredDefaultParameterCustomizerFactory.java
index 496a0e9b1..9f0de3246 100644
--- a/sqlobject/src/test/java/org/jdbi/v3/sqlobject/config/TestUseConfiguredDefaultParameterCustomizerFactory.java
+++ b/sqlobject/src/test/java/org/jdbi/v3/sqlobject/config/TestUseConfiguredDefaultParameterCustomizerFactory.java
@@ -59,7 +59,9 @@ public class TestUseConfiguredDefaultParameterCustomizerFactory {
         SomethingDao h = handle.attach(SomethingDao.class);
         h.findByNameAndIdNoBindAnnotation(1, "Joy");
 
-        assertThat(invocationCounter.get()).isEqualTo(2);
+        // factory is called twice for each parameters, once in
+        // warm() and once in apply()
+        assertThat(invocationCounter.get()).isEqualTo(4);
     }
 
     @Test
Repository: jdbi/jdbi
Issue: JdbiRule fails to clean on flyway 9+ due to cleanDisabled defaulting to true

`JdbiRule` needs a fix equivalent to the one in https://github.com/jdbi/jdbi/pull/2179

Changed files:
testing/src/main/java/org/jdbi/v3/testing/JdbiRule.java, testing/src/main/java/org/jdbi/v3/testing/Migration.java

diff --git a/testing/src/main/java/org/jdbi/v3/testing/JdbiRule.java b/testing/src/main/java/org/jdbi/v3/testing/JdbiRule.java
index 8fcb22b57..cdd04c0ba 100644
--- a/testing/src/main/java/org/jdbi/v3/testing/JdbiRule.java
+++ b/testing/src/main/java/org/jdbi/v3/testing/JdbiRule.java
@@ -154,6 +154,7 @@ public abstract class JdbiRule extends ExternalResource {
                 .dataSource(getDataSource())
                 .locations(migration.paths.toArray(new String[0]))
                 .schemas(migration.schemas.toArray(new String[0]))
+                .cleanDisabled(!migration.cleanAfter)
                 .load();
             flyway.migrate();
         }
diff --git a/testing/src/main/java/org/jdbi/v3/testing/Migration.java b/testing/src/main/java/org/jdbi/v3/testing/Migration.java
index 18268c592..32a57b4ea 100644
--- a/testing/src/main/java/org/jdbi/v3/testing/Migration.java
+++ b/testing/src/main/java/org/jdbi/v3/testing/Migration.java
@@ -75,6 +75,15 @@ public class Migration {
         return this;
     }
 
+    /**
+     * Controls whether to drop all objects in the configured schemas after running the tests using Flyway.
+     */
+    @SuppressWarnings("HiddenField")
+    public Migration cleanAfter(boolean cleanAfter) {
+        this.cleanAfter = cleanAfter;
+        return this;
+    }
+
     /**
      * Create new Migration.
      */
Repository: synthetichealth/synthea
Issue: Providers CSV exports UUIDs with duplicates

Hello, it seems that even with a small population of 10 that the id of some providers is not unique in the csv export. Is this possibly the line of code that is the cause for that
https://github.com/synthetichealth/synthea/blob/bcb17a9532645f03f6410b7d5cf67092592842e7/src/main/java/org/mitre/synthea/world/agents/Provider.java#L476
or am I doing something wrong?

Changed files:
src/main/java/org/mitre/synthea/world/agents/Clinician.java

diff --git a/src/main/java/org/mitre/synthea/world/agents/Clinician.java b/src/main/java/org/mitre/synthea/world/agents/Clinician.java
index 50902977e..352f3d84c 100644
--- a/src/main/java/org/mitre/synthea/world/agents/Clinician.java
+++ b/src/main/java/org/mitre/synthea/world/agents/Clinician.java
@@ -54,7 +54,9 @@ public class Clinician implements Serializable, QuadTreeElement {
    */
   public Clinician(long clinicianSeed, Random clinicianRand,
       long identifier, Provider organization) {
-    this.uuid =  new UUID(clinicianSeed, identifier).toString();    
+    String base = clinicianSeed + ":" + identifier + ":" +
+      organization.id + ":" + clinicianRand.nextLong();
+    this.uuid = UUID.nameUUIDFromBytes(base.getBytes()).toString();
     this.random = clinicianRand;
     this.identifier = identifier;
     this.organization = organization;
Repository: naver/ngrinder
Issue: Fix plugins loading conflict in the clustered mode 

When multiple instances in clustered mode boot up at the same time, each instances tries to expand the plugin jar file  at the same time and at the same place. This causes plugin loading error.


Changed files:
ngrinder-controller/src/main/java/org/ngrinder/common/model/Home.java
ngrinder-controller/src/main/java/org/ngrinder/infra/plugin/extension/NGrinderDefaultPluginManager.java

diff --git a/ngrinder-controller/src/main/java/org/ngrinder/common/model/Home.java b/ngrinder-controller/src/main/java/org/ngrinder/common/model/Home.java
index a35dd0aa9..588fe4fb9 100644
--- a/ngrinder-controller/src/main/java/org/ngrinder/common/model/Home.java
+++ b/ngrinder-controller/src/main/java/org/ngrinder/common/model/Home.java
@@ -99,15 +99,6 @@ public class Home {
 		return directory;
 	}
 
-	/**
-	 * Get the plugin directory.
-	 *
-	 * @return the plugin directory
-	 */
-	public File getPluginDirectory() {
-		return new File(directory, PATH_PLUGIN);
-	}
-
 	/**
 	 * Copy the given file from given location.
 	 *
@@ -182,7 +173,9 @@ public class Home {
 	 * @return plugin cache directory.
 	 */
 	public File getPluginsCacheDirectory() {
-		return getSubFile(PATH_PLUGIN + "_cache");
+		File cacheDir =  getSubFile(PATH_PLUGIN + "_cache");
+		cacheDir.mkdirs();
+		return cacheDir;
 	}
 
 	/**
diff --git a/ngrinder-controller/src/main/java/org/ngrinder/infra/plugin/extension/NGrinderDefaultPluginManager.java b/ngrinder-controller/src/main/java/org/ngrinder/infra/plugin/extension/NGrinderDefaultPluginManager.java
index 1aeb08f0d..f3af53965 100644
--- a/ngrinder-controller/src/main/java/org/ngrinder/infra/plugin/extension/NGrinderDefaultPluginManager.java
+++ b/ngrinder-controller/src/main/java/org/ngrinder/infra/plugin/extension/NGrinderDefaultPluginManager.java
@@ -30,8 +30,8 @@ public class NGrinderDefaultPluginManager extends DefaultPluginManager {
 
 	@Autowired
 	public NGrinderDefaultPluginManager(Config config, ApplicationContext applicationContext) throws MalformedURLException {
-		super(config.getHome().getPluginsDirectory());
-		super.pluginRepository = new DefaultPluginRepository(pluginsDirectory, new JarFileFilter());
+		super(config.isClustered() ? config.getExHome().getPluginsCacheDirectory() : config.getHome().getPluginsCacheDirectory());
+		super.pluginRepository = new DefaultPluginRepository(config.getHome().getPluginsDirectory(), new JarFileFilter());
 	}
 
 	@Autowired
Repository: hapifhir/hapi-fhir
Issue: TestUtil should check Embeddable not just Entity

TestUtil.scanEntities()  only considers Entity classes, need to add also Embeddable classes

Changed files:
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java
index f878494e559..3b1ed6553fd 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java
@@ -35,6 +35,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.InstantType;
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Embedded;
 import javax.persistence.EmbeddedId;
 import javax.persistence.Entity;
@@ -106,7 +107,8 @@ public class TestUtil {
 		for (ClassInfo classInfo : classes) {
 			Class<?> clazz = Class.forName(classInfo.getName());
 			Entity entity = clazz.getAnnotation(Entity.class);
-			if (entity == null) {
+			Embeddable embeddable = clazz.getAnnotation(Embeddable.class);
+			if (entity == null && embeddable == null) {
 				continue;
 			}
Repository: gchq/gaffer
Issue: Parquet store fails to addElements when using HDFS

The final task for the addElements operations is to move the data from the tempDir/sorted to the dataDir/timestamp, which works fine when working on the local file system. However if you are working on HDFS then the files will be moved to dataDir/timestamp/sorted.

Changed files:
store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/AddElementsHandler.java
store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/ImportRDDOfElementsHandler.java

diff --git a/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/AddElementsHandler.java b/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/AddElementsHandler.java
index 2e69c31142..bc8cf94b84 100755
--- a/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/AddElementsHandler.java
+++ b/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/AddElementsHandler.java
@@ -111,7 +111,7 @@ public class AddElementsHandler implements OperationHandler<AddElements> {
         final long snapshot = System.currentTimeMillis();
         final String destPath = dataDirString + "/" + snapshot;
         LOGGER.debug("Creating directory {}", destPath);
-        fs.mkdirs(new Path(destPath));
+        fs.mkdirs(new Path(destPath).getParent());
         final String tempPath = tempDataDirString + "/" + ParquetStoreConstants.SORTED;
         LOGGER.debug("Renaming {} to {}", tempPath, destPath);
         fs.rename(new Path(tempPath), new Path(destPath));
diff --git a/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/ImportRDDOfElementsHandler.java b/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/ImportRDDOfElementsHandler.java
index 25dc58c4c7..0d37fd93ca 100644
--- a/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/ImportRDDOfElementsHandler.java
+++ b/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/addelements/handler/ImportRDDOfElementsHandler.java
@@ -105,7 +105,7 @@ public class ImportRDDOfElementsHandler implements OperationHandler<ImportRDDOfE
         // Move data from temp to data
         final long snapshot = System.currentTimeMillis();
         final String destPath = rootDataDirString + "/" + snapshot;
-        fs.mkdirs(new Path(destPath));
+        fs.mkdirs(new Path(destPath).getParent());
         fs.rename(new Path(tempDataDirString + "/" + ParquetStoreConstants.SORTED), new Path(destPath));
         // Reload indices
         newGraphIndex.setSnapshotTimestamp(snapshot);
Repository: gchq/gaffer
Issue: SplitTableTool ignores first split in file and only reads half the splits

The following reads the first line then reads the next and adds it to the set:

```
String line = br.readLine();
while (line != null) {
     splits.add(new Text(br.readLine()));
     line = br.readLine();
}
```


Changed files:
accumulo-store/src/main/java/gaffer/accumulostore/operation/hdfs/handler/tool/SplitTableTool.java

diff --git a/accumulo-store/src/main/java/gaffer/accumulostore/operation/hdfs/handler/tool/SplitTableTool.java b/accumulo-store/src/main/java/gaffer/accumulostore/operation/hdfs/handler/tool/SplitTableTool.java
index 7ef29b307f..5e95e010b5 100644
--- a/accumulo-store/src/main/java/gaffer/accumulostore/operation/hdfs/handler/tool/SplitTableTool.java
+++ b/accumulo-store/src/main/java/gaffer/accumulostore/operation/hdfs/handler/tool/SplitTableTool.java
@@ -65,7 +65,7 @@ public class SplitTableTool extends Configured implements Tool {
                 new InputStreamReader(fs.open(new Path(operation.getInputPath())), CommonConstants.UTF_8))) {
             String line = br.readLine();
             while (line != null) {
-                splits.add(new Text(br.readLine()));
+                splits.add(new Text(line));
                 line = br.readLine();
             }
         } catch (final IOException e) {
Repository: gchq/gaffer
Issue: ImportRDDOfElements on Parquet store fails when used on a HDFS cluster

The `ImportRDDOfElements` operation on the Parquet store passes all the unit tests which run on a local file system but fails when run on HDFS running on a cluster. The line

    fs.rename(new Path(tempDir + "/AddElementsFromRDDTemp/sorted_aggregated_new/"), new Path(newDataDir));

in `AddElementsFromRDD` fails to move the directory as intended (the sorted_aggregated_new directory is moved into the new directory). This means that the group directories cannot be found when the partition is calculated.

Changed files:
store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/handler/spark/AddElementsFromRDD.java

diff --git a/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/handler/spark/AddElementsFromRDD.java b/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/handler/spark/AddElementsFromRDD.java
index d782452152..293e0f39b5 100644
--- a/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/handler/spark/AddElementsFromRDD.java
+++ b/store-implementation/parquet-store/src/main/java/uk/gov/gchq/gaffer/parquetstore/operation/handler/spark/AddElementsFromRDD.java
@@ -170,11 +170,16 @@ public class AddElementsFromRDD {
             // the replacement of the old data with the new data an atomic operation and ensures that a get operation
             // against the store will not read the directory when only some of the data has been moved there).
             final long snapshot = System.currentTimeMillis();
-            final String newDataDir = store.getDataDir() + "/" + ParquetStore.getSnapshotPath(snapshot) + "-tmp";
+            final String newDataDir = store.getDataDir() + "/" + ParquetStore.getSnapshotPath(snapshot) + "-tmp/";
             LOGGER.info("Moving aggregated and sorted data to new snapshot directory {}", newDataDir);
+            LOGGER.info("Making directory {}", newDataDir);
             fs.mkdirs(new Path(newDataDir));
-            fs.rename(new Path(tempDir + "/AddElementsFromRDDTemp/sorted_aggregated_new/"),
-                    new Path(newDataDir));
+            final FileStatus[] fss = fs.listStatus(new Path(tempDir + "/AddElementsFromRDDTemp/sorted_aggregated_new/"));
+            for (int i = 0; i < fss.length; i++) {
+                final Path destination = new Path(newDataDir, fss[i].getPath().getName());
+                fs.rename(fss[i].getPath(), destination);
+                LOGGER.info("Renamed {} to {}", fss[i].getPath(), destination);
+            }
 
             // Move snapshot-tmp directory to snapshot
             final String directoryWithoutTmp = newDataDir.substring(0, newDataDir.lastIndexOf("-tmp"));
Repository: embulk/embulk
Issue: Use Ruby's timezone names instead of Joda-Time's

While I was walking-through and trying to refactor our Ruby-compatible date/time parser, I'm afraid I found that we may not using Ruby's timezone names (`TimeZoneConverter`), but using Joda-Time's.

* https://github.com/embulk/embulk/blob/v0.8.36/embulk-core/src/main/java/org/embulk/spi/time/TimestampParser.java#L188
* https://github.com/embulk/embulk/blob/v0.8.36/embulk-core/src/main/java/org/embulk/spi/time/TimestampFormat.java#L58-L88

@muga Can you check it? If it's true, I'd fix it throughout my refactoring.

Changed files:
embulk-core/src/main/java/org/embulk/spi/time/TimestampFormat.java

diff --git a/embulk-core/src/main/java/org/embulk/spi/time/TimestampFormat.java b/embulk-core/src/main/java/org/embulk/spi/time/TimestampFormat.java
index 2a634b1f..857001f1 100644
--- a/embulk-core/src/main/java/org/embulk/spi/time/TimestampFormat.java
+++ b/embulk-core/src/main/java/org/embulk/spi/time/TimestampFormat.java
@@ -57,6 +57,12 @@ public class TimestampFormat
 
     public static DateTimeZone parseDateTimeZone(String s)
     {
+        final int rubyStyleTimeOffsetInSecond = TimeZoneConverter.dateZoneToDiff(s);
+
+        if (rubyStyleTimeOffsetInSecond != Integer.MIN_VALUE) {
+            return DateTimeZone.forOffsetMillis(rubyStyleTimeOffsetInSecond * 1000);
+        }
+
         if(s.startsWith("+") || s.startsWith("-")) {
             return DateTimeZone.forID(s);
Repository: embulk/embulk
Issue: embulk v0.8.28 bundle command is not working.

embulk v0.8.28  breaking bundle command. Maybe related to https://github.com/embulk/embulk/issues/748

- 0.8.28
```
embulk bundle
2017-07-28 09:38:46.392 +0000: Embulk v0.8.28
Exception in thread "main" java.lang.NullPointerException
	at org.embulk.cli.EmbulkRun.runSubcommand(EmbulkRun.java:401)
	at org.embulk.cli.EmbulkRun.run(EmbulkRun.java:80)
	at org.embulk.cli.EmbulkBundle.checkBundleWithEmbulkVersion(EmbulkBundle.java:42)
	at org.embulk.cli.EmbulkBundle.checkBundle(EmbulkBundle.java:15)
	at org.embulk.cli.Main.main(Main.java:26)
```

- 0.8.27
```
embulk bundle install
2017-07-28 09:43:55.455 +0000: Embulk v0.8.27
Using embulk-executor-mapreduce 0.3.0
```



Changed files:
embulk-cli/src/main/java/org/embulk/cli/EmbulkRun.java

diff --git a/embulk-cli/src/main/java/org/embulk/cli/EmbulkRun.java b/embulk-cli/src/main/java/org/embulk/cli/EmbulkRun.java
index 9bc2ae60..c5933a8a 100644
--- a/embulk-cli/src/main/java/org/embulk/cli/EmbulkRun.java
+++ b/embulk-cli/src/main/java/org/embulk/cli/EmbulkRun.java
@@ -398,14 +398,14 @@ public class EmbulkRun
             }
             return 0;
         case BUNDLE:
-            if (!commandLine.getArguments().isEmpty() && commandLine.getArguments().get(0).equals("new")) {
-                if (commandLine.getArguments().size() != 2) {
+            if (!subcommandArguments.isEmpty() && subcommandArguments.get(0).equals("new")) {
+                if (subcommandArguments.size() != 2) {
                     printGeneralUsage(System.err);
                     System.err.println("");
                     System.err.println("Use `<command> --help` to see description of the commands.");
                     return 1;
                 }
-                newBundle(commandLine.getArguments().get(1), null);
+                newBundle(subcommandArguments.get(1), null);
                 System.err.println("'embulk bundle new' is deprecated. This will be removed in future release. Please use 'embulk mkbundle' instead.");
             }
             else {