[jira] [Commented] (TAVERNA-1018) newlines are stripped out from embedded scripts (e.g., python) in the t2flow, when executing in taverna server

["Stian Soiland-Reyes (JIRA)" <ji...@apache.org>]

    [ https://issues.apache.org/jira/browse/TAVERNA-1018?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15949178#comment-15949178 ] 

Stian Soiland-Reyes commented on TAVERNA-1018:
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Donal - would you know why this happens? 

When retrieving back the uploaded workflow in the REST interface, and running and inspecting the .t2flow file on disk, all newlines are stripped and it's on a single line. That means constants like embeded file content in the Tool Service gets their newlines removed as well.

I suspect it's because of JAXB marshalling/unmarshalling in Workflow.java:

https://github.com/apache/incubator-taverna-server/blob/old/2.5.4/server-webapp/src/main/java/org/taverna/server/master/common/Workflow.java#L93

and it has

{code}
			marshaller.setProperty(JAXB_FORMATTED_OUTPUT, false);
{code}

is it sufficient to set this to true?

> newlines are stripped out from embedded scripts (e.g., python) in the t2flow, when executing in taverna server 
> ---------------------------------------------------------------------------------------------------------------
>
>                 Key: TAVERNA-1018
>                 URL: https://issues.apache.org/jira/browse/TAVERNA-1018
>             Project: Apache Taverna
>          Issue Type: Bug
>          Components: Taverna Server
>            Reporter: Raul Palma
>
> This problem only occur with taverna server. Taverna workbench seems to be ok.
> Try for instance the simple example t2flow from: http://www.myexperiment.org/workflows/4218.html



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