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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
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
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
RabiaAhmad3
@RabiaAhmad3
Hi @ianwdunlop @stain Is there any way to execute .sh file through taverna workbench?
subesingh1981
@subesingh1981
How to read input from an Array
Array has multiple json
subesingh1981
@subesingh1981
hi there?
is anyone help to read the array as inputs.
subesingh1981
@subesingh1981
Could anyone help to find scripting language supported by Apache Taverna
Stian Soiland-Reyes
@stain
@RabiaAhmad3 @RabiaAhmad98_twitter yes, you can use the Tool service where it should fit into the Command screen. If it's a non-trivial shell script then you better add it as a File Input.
@subesingh1981 you can run Beanshell scripts inline, or Python etc. externally using the above.
subesingh1981
@subesingh1981
org.taverna.server.master.localworker.ForkRunFactory.getRemoteFactoryHandle
Caused by: java.rmi.NotBoundException: ForkRunFactory.b9ac9bb7-842c-4401-9b8b-6ef7191ebf27
at sun.rmi.registry.RegistryImpl.lookup(RegistryImpl.java:166)
at org.taverna.server.master.localworker.ForkRunFactory.getRemoteFactoryHandle(ForkRunFactory.java:204)
at org.taverna.server.master.localworker.ForkRunFactory.initFactory(ForkRunFactory.java:167)
at org.taverna.server.master.localworker.ForkRunFactory.getRealRun(ForkRunFactory.java:364)
at org.taverna.server.master.localworker.AbstractRemoteRunFactory.create(AbstractRemoteRunFactory.java:333)
... 96 more
I am getting this error while executing workflow on taverna server 2.5. i.e. running on local machine
subesingh1981
@subesingh1981
er ForkRunFactory - about to look up resource called ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4
20200120T190305.748 INFO Worker ForkRunFactory - resource "ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4" not yet registered...
20200120T190306.755 INFO Worker ForkRunFactory - about to look up resource called ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4
20200120T190306.756 INFO Worker ForkRunFactory - resource "ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4" not yet registered...
20200120T190307.757 INFO Worker ForkRunFactory - about to look up resource called ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4
20200120T190307.757 INFO Worker ForkRunFactory - resource "ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4" not yet registered...
20200120T190308.761 INFO Worker ForkRunFactory - about to look up resource called ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4
20200120T190308.762 INFO Worker ForkRunFactory - resource "ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4" not yet registered...
20200120T190309.763 INFO Worker ForkRunFactory - about to look up resource called ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4
20200120T190309.765 INFO Worker ForkRunFactory - resource "ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4" not yet registered...
20200120T190310.766 INFO Worker ForkRunFactory - about to look up resource called ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4
20200120T190310.767 INFO Worker ForkRunFactory - resource "ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4" not yet registered...
20200120T190311.768 INFO Worker ForkRunFactory - about to look up resource called ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4
20200120T190311.768 INFO Worker ForkRunFactory - resource "ForkRunFactory.1c7667b6-e9f9-4f1d-9e70-daff585ee6b4" not yet registered...
Kindly help to solve above given issue on Taverna server 2.5
subesingh1981
@subesingh1981
I am running Taverna Server on Windows 10 environment.
Stian Soiland-Reyes
@stain
Hi, @subesingh1981 - which Java version and Web container is it?
and how did you do your "runAs" config?
subesingh1981
@subesingh1981
jdk1.8
tomcat 9
apache taverna version 2.5
subesingh1981
@subesingh1981
Anyone could you please answer my queries.
subesingh1981
@subesingh1981
Hi guys are you there?
I am not able to run Apache Taverna 3.1.0 on my local machine.
I want to build and run it on local machine.
I want to eavaluate complete tool suite.
subesingh1981
@subesingh1981
@vsocrates have you follow all the instruction given in https://taverna.incubator.apache.org/documentation/server/3.1/usage
you need to pass user name and password tavera/taverna
I am able to run the workflow by not received any run id in response.
Get http response 200 ok
Following as output
subesingh1981
@subesingh1981

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>

<ts-rest:runList xmlns:ts-rest="http://ns.taverna.org.uk/2010/xml/server/rest/" xmlns:feed="http://ns.taverna.org.uk/2010/xml/server/feed/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:ts-soap="http://ns.taverna.org.uk/2010/xml/server/soap/" xmlns:admin="http://ns.taverna.org.uk/2010/xml/server/admin/" xmlns:port="http://ns.taverna.org.uk/2010/port/" xmlns:ts="http://ns.taverna.org.uk/2010/xml/server/"/>

I am not able to fetch RUN_ID
I check the response header as well. Nothing found
I tried it using postman as well as a java program.