Update configuration and docker commands

[nyu-zeeshan]

No description provided.

[sagar15795]

@nyu-zeeshan
have you verified that taverna player is working with latest taverna server?

[nyu-zeeshan]

@sagar15795
Yes, its working.

[ianwdunlop]

I tried running a couple of t2flow workflows and got a similar error with each from taverna-server-3. @stain I imagine this must be a known bug:

Hello-abcd:

Caused by: javax.xml.bind.UnmarshalException: unexpected element (uri:"http://ns.taverna.org.uk/2010/xml/server/", local:"workflow"). Expected elements are <{http://taverna.sf.net/2008/xml/t2flow}abstractConfigBean>,<{}net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean>,<{}net.sf.taverna.t2.component.ComponentActivityConfigurationBean>,<{http://taverna.sf.net/2008/xml/t2flow}workflow>

Fetch xkcd:

Caused by: javax.xml.bind.UnmarshalException: unexpected element (uri:"http://ns.taverna.org.uk/2010/xml/server/", local:"workflow"). Expected elements are <{http://taverna.sf.net/2008/xml/t2flow}abstractConfigBean>,<{}net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean>,<{}net.sf.taverna.t2.component.ComponentActivityConfigurationBean>,<{http://taverna.sf.net/2008/xml/t2flow}workflow>

[stain]

Exactly how did you submit how? It seems to do with wrapping XML element or not.. Donal, did something change in the XML requirements for workflow upload in T3? It might be easier to try to do it as a application/vnd.taverna.t2flow+xml upload (Sending binary file as-is) than wrapp it in a <server:workflow> as application/xml.

…

On 7 February 2018 at 10:49, Ian Dunlop ***@***.***> wrote: I tried running a couple of t2flow workflows and got a similar error with each from taverna-server-3. @stain <https://github.com/stain> I imagine this must be a known bug: Hello-abcd: Caused by: javax.xml.bind.UnmarshalException: unexpected element (uri:" http://ns.taverna.org.uk/2010/xml/server/", local:"workflow"). Expected elements are <{http://taverna.sf.net/2008/xml/t2flow}abstractConfigBean> ,<{}net.sf.taverna.t2.activities.externaltool. ExternalToolActivityConfigurationBean>,<{}net.sf.taverna.t2. activities.interaction.InteractionActivityConfigurati onBean>,<{}net.sf.taverna.t2.activities.rest. RESTActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.usecase. UseCaseActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.xpath. XPathActivityConfigurationBean>,<{}net.sf.taverna.t2.component. ComponentActivityConfigurationBean>,<{http://taverna.sf.net/ 2008/xml/t2flow}workflow> Fetch xkcd: Caused by: javax.xml.bind.UnmarshalException: unexpected element (uri:" http://ns.taverna.org.uk/2010/xml/server/", local:"workflow"). Expected elements are <{http://taverna.sf.net/2008/xml/t2flow}abstractConfigBean> ,<{}net.sf.taverna.t2.activities.externaltool. ExternalToolActivityConfigurationBean>,<{}net.sf.taverna.t2. activities.interaction.InteractionActivityConfigurati onBean>,<{}net.sf.taverna.t2.activities.rest. RESTActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.usecase. UseCaseActivityConfigurationBean>,<{}net.sf.taverna.t2.activities.xpath. XPathActivityConfigurationBean>,<{}net.sf.taverna.t2.component. ComponentActivityConfigurationBean>,<{http://taverna.sf.net/ 2008/xml/t2flow}workflow> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#45 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAPd5aZugZHkk-Oa8umhAasr5jPjtr8zks5tSX-cgaJpZM4R3qPE> .

-- Stian Soiland-Reyes http://orcid.org/0000-0001-9842-9718

[ianwdunlop]

I sent it via taverna-player-portal. I was testing whether they could both be started vis docker and play nicely with each other. I haven't tried sending from mobile to portal to server.

[ianwdunlop]

Anyone tried TavServ 3 with TavMob recently? I couldn't get it to work which is probably why this pull request never got merged.

[ianwdunlop]

Not sure we should really be telling people to change the strings.xml code inside the app before they run it. Doesn't seem very user friendly. I need to double check the ports that you recommend changing. I guess we need them all to be the defaults for each app which is what I think you are driving for here.

[ianwdunlop]

It might be easier to try to do it as a application/vnd.taverna.t2flow+xml upload (Sending binary file as-is) than wrapp it in a server:workflow as application/xml.

Well if you know where in the many layered stack of taverna-player-portal>taverna-player>t2-server-gem it is doing this then please let me know ;)
I think it might be in https://github.com/myGrid/t2-server-gem/blob/master/lib/t2-server/server.rb#L261 but if you look at the call sequence it seems to be sending as Post with type "application/vnd.taverna.t2flow+xml".

[ianwdunlop]

I actually managed to recreate the issue by using the t2-server-gem directly in irb. T2Server::Run.create() seems to be where the issue occurs. Doesn't mean it is to blame though. It could be the server that is wrong. Would need to run directly against TavServ3 using curl or similar to find out. Now where did I put those notes......