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26 changes: 26 additions & 0 deletions
26
.../src/main/java/bio/terra/workspace/azureDatabaseUtils/process/LaunchProcessException.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| package bio.terra.workspace.azureDatabaseUtils.process; | ||
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| /** | ||
| * Custom exception class for system or internal exceptions. These represent errors that the user | ||
| * cannot fix. | ||
| */ | ||
| public class LaunchProcessException extends RuntimeException { | ||
| /** | ||
| * Constructs an exception with the given message. The cause is set to null. | ||
| * | ||
| * @param message description of error that may help with debugging | ||
| */ | ||
| public LaunchProcessException(String message) { | ||
| super(message); | ||
| } | ||
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|
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| /** | ||
| * Constructs an exception with the given message and cause. | ||
| * | ||
| * @param message description of error that may help with debugging | ||
| * @param cause underlying exception that can be logged for debugging purposes | ||
| */ | ||
| public LaunchProcessException(String message, Throwable cause) { | ||
| super(message, cause); | ||
| } | ||
| } |
89 changes: 89 additions & 0 deletions
89
...ls/src/main/java/bio/terra/workspace/azureDatabaseUtils/process/LocalProcessLauncher.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| package bio.terra.workspace.azureDatabaseUtils.process; | ||
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| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.io.OutputStream; | ||
| import java.nio.file.Path; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
|
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| /** This class provides utility methods for launching local child processes. */ | ||
| public class LocalProcessLauncher { | ||
| private Process process; | ||
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| public enum Output { | ||
| OUT, | ||
| ERROR | ||
| } | ||
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|
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| /** | ||
| * Executes a command in a separate process from the current working directory (i.e. the same | ||
| * place as this Java process is running). | ||
| * | ||
| * @param command the command and arguments to execute | ||
| * @param envVars the environment variables to set or overwrite if already defined | ||
| */ | ||
| public void launchProcess(List<String> command, Map<String, String> envVars) { | ||
| launchProcess(command, envVars, null); | ||
| } | ||
|
|
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| /** | ||
| * Executes a command in a separate process from the given working directory, with the given | ||
| * environment variables set beforehand. | ||
| * | ||
| * @param command the command and arguments to execute | ||
| * @param envVars the environment variables to set or overwrite if already defined | ||
| * @param workingDirectory the working directory to launch the process from | ||
| */ | ||
| public void launchProcess( | ||
| List<String> command, Map<String, String> envVars, Path workingDirectory) { | ||
| // build and run process from the specified working directory | ||
| ProcessBuilder procBuilder = new ProcessBuilder(command); | ||
| if (workingDirectory != null) { | ||
| procBuilder.directory(workingDirectory.toFile()); | ||
| } | ||
| if (envVars != null) { | ||
| Map<String, String> procEnvVars = procBuilder.environment(); | ||
| procEnvVars.putAll(envVars); | ||
| } | ||
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| try { | ||
| process = procBuilder.start(); | ||
| } catch (IOException ioEx) { | ||
| throw new LaunchProcessException("Error launching local process", ioEx); | ||
| } | ||
| } | ||
|
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| /** | ||
| * Stream standard out/err from the child process to the CLI console. | ||
| * | ||
| * @param type specifies which process stream to get data from | ||
| */ | ||
| public InputStream getOutputForProcess(Output type) { | ||
| if (type == Output.ERROR) { | ||
| return process.getErrorStream(); | ||
| } | ||
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| return process.getInputStream(); | ||
| } | ||
|
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| /** Block until the child process terminates, then return its exit code. */ | ||
| public int waitForTerminate() { | ||
| try { | ||
| return process.waitFor(); | ||
| } catch (InterruptedException intEx) { | ||
| Thread.currentThread().interrupt(); | ||
| throw new LaunchProcessException("Error waiting for child process to terminate", intEx); | ||
| } | ||
| } | ||
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| /** Get stdout input stream from the child process. */ | ||
| public InputStream getInputStream() { | ||
| return process.getInputStream(); | ||
| } | ||
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| /** Get stdin output stream from the child process. */ | ||
| public OutputStream getOutputStream() { | ||
| return process.getOutputStream(); | ||
| } | ||
| } |
53 changes: 53 additions & 0 deletions
53
...ls/src/main/java/bio/terra/workspace/azureDatabaseUtils/runners/PgDumpDatabaseRunner.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| package bio.terra.workspace.azureDatabaseUtils.runners; | ||
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| import bio.terra.workspace.azureDatabaseUtils.database.DatabaseService; | ||
| import org.springframework.beans.factory.annotation.Value; | ||
| import org.springframework.boot.ApplicationArguments; | ||
| import org.springframework.boot.ApplicationRunner; | ||
| import org.springframework.context.annotation.Profile; | ||
| import org.springframework.stereotype.Component; | ||
|
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| @Profile("PgDumpDatabase") | ||
| @Component | ||
| public class PgDumpDatabaseRunner implements ApplicationRunner { | ||
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| @Value("${env.db.connectToDatabase}") | ||
| private String sourceDbName; | ||
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| @Value("${env.db.url}") | ||
| private String sourceDbHost; | ||
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| @Value("${env.db.port}") | ||
| private String sourceDbPort; | ||
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| @Value("${env.db.user}") | ||
| private String sourceDbUser; | ||
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| @Value("${env.params.dumpfileName}") | ||
| private String dumpfileName; | ||
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| @Value("${env.params.destinationWorkspaceId}") | ||
| private String destinationWorkspaceId; | ||
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| @Value("${env.params.blobstorageDetails}") | ||
| private String blobstorageDetails; | ||
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| private final DatabaseService databaseService; | ||
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| public PgDumpDatabaseRunner(DatabaseService databaseService) { | ||
| this.databaseService = databaseService; | ||
| } | ||
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| @Override | ||
| public void run(ApplicationArguments args) { | ||
| // should I reuse `newDbName`, or create a new param `cloneDbName`? | ||
| databaseService.pgDump( | ||
| sourceDbName, | ||
| sourceDbHost, | ||
| sourceDbPort, | ||
| sourceDbUser, | ||
| dumpfileName, | ||
| destinationWorkspaceId, | ||
| blobstorageDetails); | ||
| } | ||
| } |
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