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  • Sep 22 2016 11:39
    stain closed #1
  • Sep 22 2016 11:39
    stain closed #1
  • Sep 22 2016 11:39
    stain opened #1
  • Sep 22 2016 11:35
    stain commented #1
  • Sep 22 2016 11:34
    stain opened #1
Sagar
@sagar15795
@stain please
Hitesh Gautam
@Hiteshgautam01
Hey @sagar15795 @stain , I am currently writing the UI tests using espresso and mockito. Currently i am really facing some problems while writing the tests for the application :-( . You can see my PR's apache/incubator-taverna-mobile#89 , apache/incubator-taverna-mobile#90 opened 6 days ago and not yet resolved due to errors. I think i am going in some wrong direction. I request you to suggest some projects which uses similar type of approach in UI test with integration testing. Also please comment out in the PR the correct approach of doing the stuff or how to do something with a example this time. Please help.
Majdi Haouech
@haouech
Hi all, I am currently working on adding support for nested workflows in CWL and parse them into workflows in Taverna. I didn't find anything that let me create a nested relationship given a processor, a workflow and a profile. As I spoke with @stain, I know how to do it and we agreed to add a helper insinde Scufl2Tools. For more details on how it will be done, I will create an activity that has the same structure as the processor, create a configuration with a"nestedWorkflow": workflow.getName() to the same profile. Do you think this is the good way?
Sagar
@sagar15795
@Hiteshgautam01 Sorry for late response. You need to mock the dependency using dagger. And for sample project, we have followed the ribot's android boilerplate. I think you can follow that
Hitesh Gautam
@Hiteshgautam01
Hey @sagar15795, In my one of the PR the travis says connection timed out. I want to see if my PR is passing or not. So, for that it needs to be fixed. Please help.
Sagar
@sagar15795
@Hiteshgautam01 Could you mention the PR number?
Sagar
@sagar15795
I think you are talking about #apache/incubator-taverna-mobile#88
Hitesh Gautam
@Hiteshgautam01
Yes #88
Sagar
@sagar15795
ok I will review it manually .
Murad
@m-murad
Y
Sagar
@sagar15795
@Hiteshgautam01 I have reviewed your PR. Please change the requested changes.
And You build was passing. It was the travis issue.
Hitesh Gautam
@Hiteshgautam01
@sagar15795 i have done the requested changes. Please review.
Vimig Socrates
@vsocrates
Hi, I emailed the users mailing list, but following up here. Does anyone know how to get more specific updates from Taverna Server 2.5 beyond just Operating, or Finished. I want to know what step I am currently on.
Ian Dunlop
@ianwdunlop
Hi @vsocrates. Sorry no one replied yet. I think there are only a few states, detailed in https://taverna.incubator.apache.org/documentation/server/3.1/usage. Initial, initialized, operating, finished, destroyed & stopped.
You can also see all the various REST calls detailed on that page
Vimig Socrates
@vsocrates
@ianwdunlop thanks for the reply! I responded to the email in case this will help someone in the future.
Vimig Socrates
@vsocrates
@ianwdunlop I sent an email to the list, but was wondering how I would embed the image of the workflow (that I see on the Workbench) from the Taverna Server 2.5 into my Django app.
Ian Dunlop
@ianwdunlop
@vsocrates Most of the code around taverna is written in Java although there are also some Ruby libraries. One of which reads a t2flow and outputs a png image. This might give you some ideas about how to do it in Python. It also needs graphviz to do this. See https://rubygems.org/gems/taverna-t2flow plus https://github.com/myExperiment/workflow_parser-t2flow and https://github.com/myExperiment/workflow_parser-t2flow/blob/master/lib/t2flow/dot.rb
Dipak Agrawal
@DipakDA
Hey. I just joined the Taverna Community. I would like to contribute to it. Any suggestions on how do I start?
Ian Dunlop
@ianwdunlop
@DipakDA Welcome. A good place to start is https://taverna.incubator.apache.org/download/code/#contribute-to-apache-taverna. Plus say hello on the "dev" mailing list. Have a look at https://issues.apache.org/jira/projects/TAVERNA/issues/TAVERNA-1024?filter=allopenissues and see if there are any issues that look interesting. Have a chat on the dev list about it.
Stian Soiland-Reyes
@stain
@DipakDA hi! A good idea is to look at old GSOC ideas: for instance
https://issues.apache.org/jira/browse/TAVERNA-1037?jql=project%20%3D%20TAVERNA%20AND%20labels%20%3D%20gsoc2018 is a good one to start on
also that is in the Taverna Language project which has very few dependencies to worry about
AhlemRZ
@AhlemRZ
hi ,is it possible to use apache Taverna to monitor scientific workflow ! if yes ,then how ?
Ian Dunlop
@ianwdunlop
Hi @AhlemRZ . Taverna is mainly used a tool to run scientific workflows. You can monitor them by adding steps to output some information to, for example, a webservice or via email. I would ask the users list since they will likely have a lot of experience of doing this sort of thing. See https://taverna.incubator.apache.org/community/lists for mailing list details.
Nafti Najeh
@NaftiNajeh_twitter
is it possible to deploy Taverna inside an openstack instance ? if yes how can i do this ?
Ian Dunlop
@ianwdunlop
@NaftiNajeh_twitter Taverna is Java based so you should be able to deploy it on any VM infrastructure. I don't know if anyone has done this. It may be worth asking the Taverna mailing lists.
Abhijit Ramesh
@abhijitramesh
Hello I am Abhijit Ramesh , CSE undergrad student at Amirita School of engineering Amritapuri. I would like to start contributing to this project.I have subscribed to the development mailing list , Can Anyone help me on where to start?
Abhijit Ramesh
@abhijitramesh
I have built the application but I can't sign in through it even after registering myExperiment.
Ian Dunlop
@ianwdunlop
Hi @abhijitramesh what application have you built? I think you mean Taverna Mobile. If you could would you ask your question on the development list. There are probably more people monitoring the list than looking at gitter.
sararodreg
@sararodreg
hi, i downloaded the Taverna engine source code from the following link: https://github.com/apache/incubator-taverna-engine
I followed all the instructions described in this link and I managed to build the engine.
I want to know if it is possible to have an example of workflow (in the form of an XML file or other extension) to execute it on Taverna engine.
Ian Dunlop
@ianwdunlop
@sararodreg This is a good basic workflow to try http://www.myexperiment.org/workflows/824.html
sararodreg
@sararodreg
i want to know how can i run this example on cmd
Vimig Socrates
@vsocrates
Hi, following up from my email to the mailing list.

I am thinking about switching to Taverna 3.1.0. Are there other major changes, apart from those listed on this blog post?

https://cwiki.apache.org/confluence/display/TAVERNADEV/2018/01/17/Apache+Taverna+Server+3.1.0-incubating+released

If so, please point me in the right direction to the release notes. Thanks!

Vimig Socrates
@vsocrates
Hi, I tried to install taverna-server-3.1.0-incubating using Tomcat 8 and Ubuntu 16.04 and upload a t2flow workflow. I keep getting a 503 error with "failed to build workflow run worker". Where are the logs so I can see more information and debug this problem?
Ian Dunlop
@ianwdunlop
Hi @vsocrates. Sorry no one has got back to you about this. I'm not sure what the answer is to your original T3 question. I haven't tried the T3 server recently. Maybe I'll spin one up and see what happens. What steps did it take to get the 503 error. the logs should be somewhere inside Tomcat though maybe not in the logs directory but inside the T3 war directory instead.
Ian Dunlop
@ianwdunlop
@vsocrates The log file seems to be in tomcat/logs/tavserv.out. I have the same issue as you. In fact it has been reported in this channel before but there has never been a satisfactory solution. It seems to me that the server is not parsing the xml in the expected way and appears to ignore the namespace declaration for t2flow. This needs to be raised as a serious bug. I would stick to the t2 server until this is fixed.
Ian Dunlop
@ianwdunlop
Vimig Socrates
@vsocrates
sounds good, thanks! I'll keep an eye out for a fix. If I get a chance I'll pick up the issue and see if I can help out!
AhlemRZ
@AhlemRZ
hi, I can't tell the difference between processor, activity and job in Taverna
Ian Dunlop
@ianwdunlop
@AhlemRZ I can't remember the exact distinctions between these things now (it's been a while!) but here is a page explaining how to move from T2 to T3 https://cwiki.apache.org/confluence/display/TAVERNADEV/Tutorial%3A+Move+a+plugin+from+Taverna+2+to+Taverna+3 which might help a bit. This is definitely a question to send to the mailing lists. There is bound to be someone lurking on there who can remember what all this stuff means. I think the Activity is basically what does all the processing - the thing inside the box in a workflow diagram. I think Processor is what it was called in T1.
Rabia Ahmad
@RabiaAhmad98_twitter
Hi @stain. how can i use rest service to use an api in a taverna workflow which requires authentication?
Rabia Ahmad
@RabiaAhmad98_twitter
Authentication of api
Stian Soiland-Reyes
@stain
hi, @RabiaAhmad98_twitter - I think that should work with the REST service http://dev.mygrid.org.uk/wiki/display/tav250/REST if it requires Basic Auth. In the workbench it would pop up a credential manager dialogue for the username password. If it requires some other authentication header (e.g. OAuth) it's a bit more complicated and you would have to configure it as a custom HTTP header and get it into the workflow inputs
RabiaAhmad3
@RabiaAhmad3
Hi @stain. Is it possible to run a service without running a complete workflow? and output of that service can be use as a input for the remaining workflow?
RabiaAhmad3
@RabiaAhmad3
Hi, I want to create a workflow which takes requirements from user and create a machine on cloud. Is there any service for this purpose or I have to create on my own?
nbit3m
@nbit3m
hi, I want to create a workflow engine for monitoring the assets. Is this taverna self-hosted tool ?
Stian Soiland-Reyes
@stain
@nbit3m hi, I am not sure if that makes sense - Taverna is targeted for data analysis workflows. You can install locally on the desktop or on your own server