Add saveResultsToBundle() for -bundle option
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
index 3473297..dd8e20f 100644
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
@@ -95,6 +95,8 @@
public boolean hasLogFile();
public boolean hasOption(String option);
+
+ public boolean hasSaveResultsToBundle() ;
public String inputDelimiter(String inputName);
@@ -112,4 +114,6 @@
*/
public boolean saveResultsToDirectory();
+ public String saveResultsToBundle();
+
}
\ No newline at end of file
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
index 9d8c5fc..368527d 100644
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
@@ -26,6 +26,7 @@
import java.net.URISyntaxException;
import java.net.URL;
import java.nio.file.Path;
+import java.nio.file.Paths;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.Map;
@@ -170,6 +171,15 @@
setupDatabase(commandLineOptions);
if (commandLineOptions.getWorkflow() != null) {
+
+ /* Set context class loader to us,
+ * so that things such as JSON-LD caching of
+ * robundle works.
+ */
+
+ Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
+
+
/*
* Initialise Credential Manager and SSL stuff quite early as
* parsing and validating the workflow may require it
@@ -251,7 +261,8 @@
try {
Thread.sleep(500);
} catch (InterruptedException e) {
- // Ignore
+ System.err.println("Interrupted while waiting for workflow to finish");
+ return 1;
}
}
@@ -278,6 +289,16 @@
}
}
}
+ if (commandLineOptions.saveResultsToBundle() != null) {
+ Path bundlePath = Paths.get(commandLineOptions.saveResultsToBundle());
+ DataBundles.closeAndSaveBundle(runService.getDataBundle(runId), bundlePath);
+ System.out.println("Workflow Run Bundle saved to: " + bundlePath.toAbsolutePath());
+ } else {
+ System.out.println("Workflow Run Bundle: " + runService.getDataBundle(runId).getSource());
+ // For debugging we'll leave it in /tmp for now
+ runService.getDataBundle(runId).setDeleteOnClose(false);
+ DataBundles.closeBundle(runService.getDataBundle(runId));
+ }
if (report.getState().equals(State.FAILED)) {
System.out.println("Workflow failed - see report below.");
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
index 795376a..bcaa7fb 100644
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
@@ -27,6 +27,7 @@
import java.net.URL;
import java.nio.file.Files;
import java.nio.file.Path;
+import java.nio.file.Paths;
import java.nio.file.StandardOpenOption;
import java.util.ArrayList;
import java.util.HashSet;
@@ -106,7 +107,11 @@
public Bundle registerInputs(Map<String, InputWorkflowPort> portMap,
CommandLineOptions options, InvocationContext context) throws InvalidOptionException,
ReadInputException, IOException {
- Bundle inputDataBundle = DataBundles.createBundle();
+ Bundle inputDataBundle;
+ inputDataBundle = DataBundles.createBundle();
+ inputDataBundle.setDeleteOnClose(false);
+ System.out.println("Bundle: " + inputDataBundle.getSource());
+
Path inputs = DataBundles.getInputs(inputDataBundle);
URL url;
