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Posted to commits@airavata.apache.org by di...@apache.org on 2020/01/03 19:36:56 UTC
[airavata] branch airavata-3276 created (now 3cdfc19)
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dimuthuupe pushed a change to branch airavata-3276
in repository https://gitbox.apache.org/repos/asf/airavata.git.
at 3cdfc19 Fixing airavata-3276: Ignoring non-required empty input files adding into groovy script
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new 3cdfc19 Fixing airavata-3276: Ignoring non-required empty input files adding into groovy script
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[airavata] 01/01: Fixing airavata-3276: Ignoring non-required empty
input files adding into groovy script
Posted by di...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
dimuthuupe pushed a commit to branch airavata-3276
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 3cdfc19a8c1f75c67fadb4c7801559ea6915b23f
Author: Dimuthu Wannipurage <di...@gmail.com>
AuthorDate: Fri Jan 3 14:36:41 2020 -0500
Fixing airavata-3276: Ignoring non-required empty input files adding into groovy script
---
.../airavata/helix/impl/task/staging/InputDataStagingTask.java | 4 +---
.../helix/impl/task/submission/config/GroovyMapBuilder.java | 8 ++++++++
2 files changed, 9 insertions(+), 3 deletions(-)
diff --git a/modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java b/modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java
index 6ba0c24..e7e9010 100644
--- a/modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java
+++ b/modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java
@@ -20,7 +20,6 @@
package org.apache.airavata.helix.impl.task.staging;
import org.apache.airavata.agents.api.AgentAdaptor;
-import org.apache.airavata.agents.api.AgentException;
import org.apache.airavata.agents.api.StorageResourceAdaptor;
import org.apache.airavata.helix.impl.task.TaskContext;
import org.apache.airavata.helix.impl.task.TaskOnFailException;
@@ -34,7 +33,6 @@ import org.apache.helix.task.TaskResult;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import java.io.File;
import java.net.URI;
import java.net.URISyntaxException;
@@ -70,7 +68,7 @@ public class InputDataStagingTask extends DataStagingTask {
try {
- String sourceUrls[];
+ String[] sourceUrls;
if (dataStagingTaskModel.getProcessInput().getType() == DataType.URI_COLLECTION) {
logger.info("Found a URI collection so splitting by comma for path " + dataStagingTaskModel.getSource());
diff --git a/modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java b/modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java
index 0944b86..4332645 100644
--- a/modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java
+++ b/modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java
@@ -251,6 +251,14 @@ public class GroovyMapBuilder {
if (commandLineOnly && !inputDataObjectType.isRequiredToAddedToCommandLine()) {
continue;
}
+
+ if (!inputDataObjectType.isIsRequired() &&
+ (inputDataObjectType.getValue() == null || "".equals(inputDataObjectType.getValue())) &&
+ (inputDataObjectType.getType() == DataType.URI || inputDataObjectType.getType() == DataType.URI_COLLECTION)) {
+ // For URI/ Collection non required inputs, if the value is empty, ignore it. Fix for airavata-3276
+ continue;
+ }
+
if (inputDataObjectType.getApplicationArgument() != null
&& !inputDataObjectType.getApplicationArgument().equals("")) {
inputValues.add(inputDataObjectType.getApplicationArgument());