Re: [VOTE] Release Apache Taverna Server 3.1.0-incubating RC2

[Alan Williams]

On 08-Jan-18 17:31, Stian Soiland-Reyes wrote:


[ ] +1 Release this package
[ ]  0 I don't feel strongly about it, but don't object
[ ] -1 Do not release this package because...


A strong -1 Do not release from me.

This is because most of the package names are wrong. For example, 
taverna-server-port-description has the package 
org.taverna.server.port_description


taverna-server-client and taverna-server-usage have org.apache.taverna...

taverna-server-port-description, taverna-server-rmidaemon, 
taverna-server-runinterface, taverna-server-webapp and taverna-server-worker

all have org.taverna...


Anyone can participate in testing and voting, not just committers,
please feel free to try out the release candidate and provide your
votes!

How to review a release? https://s.apache.org/review-release


Sorry, but to repeat a *strong -1* from me

Alan


---
This email has been checked for viruses by Avast antivirus software.
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Re: Taverna Mobile play store release.

[Alan Williams]

On 08-Jul-17 13:14, Sagar wrote:

Hi All,

I think it time to release taverna mobile on play store.
What do you guys say?


Go for it.  I think the decision has to go to an official vote.

In the meantime, is everything set up to sign the app so it can go in 
the store?


Is there a release candidate?

Alan

Re: HI ALL

[Alan Williams]

On 08-Jul-17 10:44, Chalana Madusanka wrote:

Please can you help me how can be assigned to this issue.


Have you registered in the Jira at 
https://issues.apache.org/jira/secure/Signup!default.jspa ?


Once you have registered, e-mail your username and a Project Admin can 
add you to the Jira committers.


You can also start going down the route of becoming an official Apache 
Committer - see https://www.apache.org/dev/new-committers-guide.html 
That may seem very scary (it scares me) but it isn't that bad.


Alan


On Sat, Jul 8, 2017 at 2:19 PM, Alan Williams 
wrote:


On 08-Jul-17 09:39, Chalana Madusanka wrote:


Hi Alan,
Yeah sure. I already started to solve a problem that TAVERNA-977 Fix
Engine
build warnings. So please me kind enough to guide me.



Brilliant. I think the first thing to do is to register in Jira so you can
be assigned to the issue. That should stop anyone else working on it.

Depending on how you want to work on the issue, it may make it easier to
subdivide the issue into sub-issues. For example, "Fix Workflow Model impl
build issues" and "Fix unresolved package dependencies build issues".

Regards,

Chalana Madusanka.



Alan

Re: HI ALL

[Alan Williams]

On 08-Jul-17 09:39, Chalana Madusanka wrote:

Hi Alan,
Yeah sure. I already started to solve a problem that TAVERNA-977 Fix Engine
build warnings. So please me kind enough to guide me.


Brilliant. I think the first thing to do is to register in Jira so you 
can be assigned to the issue. That should stop anyone else working on it.


Depending on how you want to work on the issue, it may make it easier to 
subdivide the issue into sub-issues. For example, "Fix Workflow Model 
impl build issues" and "Fix unresolved package dependencies build issues".



Regards,
Chalana Madusanka.


Alan

Re: HI ALL

[Alan Williams]

On 06-Jul-17 09:11, Chalana Madusanka wrote:

Hi,


Hello


I am an undergraduate student of faculty of engineering university of
Peradeniya. I liked to involve in opensource software development. And I
have interested in involving with the apache taverna. I will be
contributing for the project from now on. Please be kind enough to guide me
through this journey.


I think the first thing to do is to decide on a specific problem to 
solve. Is there any area you are specifically interested in. It does not 
have to be code; documentation is very important. There is a list of 
known Taverna issues at

https://issues.apache.org/jira/browse/TAVERNA-1023?jql=project%20%3D%20TAVERNA

A filtered version with just TODO issues is at
https://tinyurl.com/y7b2z6sn


Thanks.
Chalana Madushanka


Alan

Re: TAVERNA-550

[Alan Williams]

On 07-Jul-17 19:46, Upeksha Iwanthi wrote:

Hi Thilina,


Hello Upeksha


Thank you for your reply. I went through the documentation that you

sent me. It as helpful and I hope some help further to work on this
issue. I already get the source code of taverna-workbench but I didn't
get the source code of taverna-common-activities. I thought that
building only source code of taverna-workbench is enough. I tried yo
build the project with maven but it not build successful and gave
errors. Actually I need some help for that.

Welcome to Taverna :)

When you have errors, you need to give enough information to try to 
solve the problem(s). A good way would be to include the errors that you 
get. It is OK to post that to this list; then everyone can help.


Welcome again


regards,
Upeksha.


Alan

Re: Running Taverna workflows via the REST API

[Alan Williams]

On 29-Mar-17 19:10, Paul Brack wrote:

Hi guys,



I’ve come across an issue running a Taverna workflow on Taverna Server.
Using the REST API, I can create a run, add input ports and start
workflows OK, but if I need a workflow with a tool that needs SSH
credentials to be run elsewhere, I don’t seem able to create the
credentials correctly. A very simple test workflow is attached


Yes. We have seen this very recently.

If you look in the log for the run, you should see something like:

No ConfirmTrustedCertificateSPI instances could could confirm or deny 
trusting of CN=...


The Taverna Server does not trust the site.

One way to check if this is the problem is to POST

xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/"; 
xmlns:t2s="http://ns.taverna.org.uk/2010/xml/server/";>


BYTES HERE



to  /runs/{id}/security/trusts

Where "BYTES HERE" is the byte-encoding of the site's certificate.

Previously I've got the certificate by visiting a site in Chrome :)

The longer term fix is to update the default truststore for the Java 
installation on the Taverna Server


I hope that helps.


Thanks,

Paul


Alan

Re: Graduation?

[Alan Williams]

On 26-Jan-17 11:33, Ian Dunlop wrote:

Hello,

This sounds like a horribly tangled web that we should just ignore for
the moment. Perhaps the biomoby-activity-ui can be moved to the
taverna-extras repo until we clear this up. To me it doesn't seem worth
expending  effort when most of the other apache taverna repos are almost
there regards licences.


+1


Cheers,

Ian


Alan

Re: Graduation?

[Alan Williams]

On 26-Jan-17 10:47, Stuart Owen wrote:

Martin Senger, along with several other contributors, contributed to
Taverna through work at the EBI, most likely through a grant. Rather
than them being personal contributions.


Although Martin Senger worked for the EBI, this code was part of the 
biomoby contribution, not the soaplab contribution. Very confusing I know.



regards,

Stuart Owen


Alan

Re: Graduation?

[Alan Williams]

On 25-Jan-17 16:59, Ian Dunlop wrote:

Hello,

Does anyone know who Martin Senger is so we can clear up the licence on
taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java


I believe he now works in Saudi Arabia at King Abdullah University of 
Science and Technology. Wouldn't Mark Wilkinson be a better person to 
contact about the license?



As it stands it's LGPL. Is CacheImpl.java used anywhere? A quick search
didn't reveal anything. Can we just delete it and worry about it later?

Cheers,

Ian


Alan

Re: Taverna mobile branch

[Alan Williams]

On 11-Jan-17 17:08, Ian Dunlop wrote:

Hello,

It's just an idea. An experiment at the moment. The branch doesn't do
anything more than start a run on a tavserver. No inputs or results yet.
That's the hard bit!


:) Should be very do-able.


Cheers,

Ian


Alan

Taverna mobile branch

[Alan Williams]

Mainly for Ian,

It looks as if you are switching the Taverna mobile to run directly off 
a Taverna Server. Is that correct?


Alan

Re: Presentations on the Taverna website

[Alan Williams]

On 10-Jan-17 14:09, Gale Naylor wrote:

OK! I added a Presentations page under the Publications and References
pages in the Community menu. If you would like anything changed (or want me
to add the link), just let me know!


Thanks.


Gale


Alan

Re: Presentations on the Taverna website

[Alan Williams]

On 09-Jan-17 21:03, Gale Naylor wrote:

Hi Alan,

I don't think we have a place to put presentations. I could put a
Presentations page under Community, where we have Publications and
References.

Anyone have a better idea?


No - your idea sounds good to me.


Gale


Alan

Re: Cannot run "Hello Anyone" workflow on BioVel via ipython.

[Alan Williams]

On 25-Nov-16 06:28, Kasikrit Damkliang wrote:

Dear All,


Hello Kasikrit


I try to run "Hello Anyone" workflow on BioVel via ipython but it is not
successful.

This is attached notebook

file.

I've tried with other workflows. The portal returned the same errors.


The problem is that the server for the portal specified in the notebook 
is not working, or at least not working correctly. You can register on 
the main portal.biovel.eu and use your login credentials on that machine.


Alternatively, we are putting a Taverna Player and Server on an Apache 
VM; I am not sure how long that will take.


Another alternative, and perhaps better for you, is to install your own 
Taverna Server and Portal.



Please suggest me.

Thanks,
Kasikrit D.


Alan

Re: Tav Server admin

[Alan Williams]

On 17-Nov-16 16:21, Stian Soiland-Reyes wrote:

The docker job adds this users.properties:

https://github.com/taverna-extras/taverna-server-docker/blob/master/users.properties

which claims to have admin/ADMIN - remember casing in the password!


Interesting! I checked the server code and that isn't the default there. 
I guess that's why it was changed :)


Is it in the documentation of the docker image, because otherwise it 
will be very confusing (as it was for Ian).



(See that repo for the rest of the Docker stuff)


Alan

Re: Tav Server admin

[Alan Williams]

On 17-Nov-16 14:55, Ian Dunlop wrote:

Hello,

That's the page I would like to see :) but it's not letting me. docker
logs doesn't reveal a whole lot beyond server startup. Nothing after:

"Nov 17, 2016 2:04:03 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 10757 ms"


Can you ssh into the docker using docker exec?


Cheers,

Ian


Alan

Re: Tav Server admin

[Alan Williams]

On 17-Nov-16 14:06, Ian Dunlop wrote:

Hello,

I get a 403 Access Denied with what the admin guide says are the default
username/password. Debugging this docker stuff is way harder than it
should be. I'm tempted to go back to bare metal Tomcat.


OK. Can you check in the docker what it receives and what it expects?

I have checked on the Taverna Server behind the BioVeL portal, and there 
is an admin page. Not sure if an attachment will come through so look at 
https://www.dropbox.com/s/i8dc6wmyrwzipwy/server.PNG?dl=0



Cheers,

Ian


Alan

Re: Tav Server admin

[Alan Williams]

On 17-Nov-16 12:27, Ian Dunlop wrote:

Hello,

I'm using the docker taverna/taverna-server image and want to add
users/change passwords etc.So.

1) Is it possible to admin a Taverna Server instance through a web
interface? Is "Component: Taverna/Server/Users" in the admin guide
(http://dev.mygrid.org.uk/wiki/display/tav250/Administration+Guide)
referring to Java code or a web app?


There is definitely an admin web page. It is normally at 
/tavernaserver/admin . I am not sure what can be administered from there.



2) How do you access the WEB-INF/user.properties file in a docker image
so that you can change it? How can you persist it between container
restarts?


I think (but am not completely certain) that the changes done in the 
admin pane are saved in the server's database. That is read in 
preference to the user.properties file. user.properties specifies the 
properties to be used initially (when there are no values in the database).



Cheers,

Ian


Alan

Re: Create 'develop' branch for tavmob

[Alan Williams]

On 07-Nov-16 13:45, Gale Naylor wrote:

I was thinking the master was the latest release, too, but I have no strong
feelings either way.


I think the releases are tagged on the master branch, and the master 
branch is the main development one, with "side" branches for new 
features. That is how it is done in, for example, 
incubator-taverna-commandline. That is also how other open source 
projects I use work.


It does have the drawback that you cannot easily be preparing a release 
and continuing to develop at the same time. I don't think we have a 
large enough community to worry about that though.


Alan

Re: Fwd: Re: ASF for Google Code-In

[Alan Williams]

Hello everyone,

I am very much in favour of this. My concern is that the deadline for 
organizations to apply is 3rd November, which is very soon.


Alan

Re: Welcome to Sagar and Rajan

[Alan Williams]

On 01-Nov-16 09:12, Stian Soiland-Reyes wrote:

Congratulations!


Welcome, welcome!

Alan

Re: Taverna License review wiki page

[Alan Williams]

On 02-Sep-16 22:33, Gale Naylor wrote:

I downloaded a zip of incubator-taverna-server from GitHub and ran the RAT
check from the command line on each of the main and sub folders. It looks
like almost all the files need a header.

One if the files is the .opf.yml file, which contains references to
mygrid.org.uk and taverna.org.uk.:

name: Taverna Server
vendor: The University of Manchester
maintainer:
name: Donal Fellows
email: donal.k.fellows( AT )manchester.ac.uk
platform: "Java 6+, Tomcat 6, POSIX"
download: http://www.taverna.org.uk/download/server/
# Really the documentation page as the overall home page is shared with the
workbench but will do for now
homepage: http://dev.mygrid.org.uk/wiki/display/taverna/Taverna+Server+2.4
issues: http://dev.mygrid.org.uk/issues/browse/TAVSERV
# Note, no anti-spam armouring required for this one
support-contact: supp...@mygrid.org.uk

I'm guessing this information needs to be updated, too?


It's possible that the opf.yml can be deleted. It contains (as far as I 
know) information that is recommended by the Open Preservation 
Foundation as useful metadata. I think this was done because one the 
projects that Donal worked on, and developed Taverna Server for, was 
called SCAPE and that project was associated with the OPF.



Gale


Alan

Re: change OperatingLimit and MaxRuns default values

[Alan Williams]

Hello Simone

Looking at 
http://dev.mygrid.org.uk/wiki/display/tav250/Administration+Guide it 
suggests that you need to change context.xml


I will check with Donal Fellows tomorrow.

Alan

Re: Docker Activity Plugin Enhancements

[Alan Williams]

On 08-Aug-16 03:12, Nadeesh Dilanga wrote:

Hi Alan,
Thanks for the input.
Yes you are very correct. Activity configuration has the information of the
container. But what I meant more like is, what to do ? start/stop  etc. For
Health check, the interface taverna already given apparently does not
expect to check those individual entities separately. But more like check
whether create/start/inspect (all possible activities) potentially healthy
to execute as a whole. Is that correct ?


Yes.

An alternative would be to have sub-classes of DockerActivity, such as 
StartDockerActivity, and to have corresponding sub-classes of 
DockerConfiguration. I think for the GSOC work that this would be 
"overkill" and can be left for a future version 2 :)


Alan

Re: Docker Activity Plugin Enhancements

[Alan Williams]

On 05-Aug-16 04:29, Nadeesh Dilanga wrote:

Hi,
With the health check I hit on a road block and spent time to figure out
how. But could not get through. Hence asking for some help.

In my activity plugin, in  executeAsynch(), I am reading action parameters
from map (Map map). (Not from JsonNode set from
Activity.configure()). I thought that is the correct way(correct me if I am
wrong)


No. I think that is the right thing to do, at least for the first 
version of the activity.



ex: action=start-container  and name=myTestContainer1
action=inspect-image and image-id=img123



From HealthCheck visit() interface, how can I get hold to this input
parameter map similar to what I get in Activity#executeAsynch() .


You cannot. There is enough information in the DockerConfiguration to so 
some checks.


Alan

Re: Docker Activity Plugin Enhancements

[Alan Williams]

On 07-Aug-16 16:10, Nadeesh Dilanga wrote:

Shall I change the Activity plugin to read the action prams from
JSONode(Activity Configuration) instead of hash map I am using now?


I don't think you should do that. It is sensible to keep a strong split 
between the configuration of what to run (the 
DockerContainerConfiguration) and the values to run it with (the JSONNode).


There are still things you can check with just the 
DockerContainerConfiguration, such as checking the host name.


Alan

Re: CWL code questions

[Alan Williams]

On 05-Aug-16 18:42, Gale Naylor wrote:

Hello Gale


In CwlContextualView.java (I used the wrong filename in my previous email)
I'm also curious about the two private, final (but not static) constants
(?): configurationBean and activity.

I'm not sure this StackOverflow answer is 100% relevant because
configurationBean and activity do not have initial values, but this is all
I've been able to find online:
http://stackoverflow.com/questions/1415955/private-final-static-attribute-vs-private-final-attribute


If an attribute is not static then each instance of the class has its 
own attribute. So,


private final CwlActivityConfigurationBean configurationBean;

means that each CwlContextualView has its own configurationBean value.

If an attribute is declared as static, then all instances of the class 
share the same attribute value.


The private means that the value of the configurationBean cannot be 
accessed (directly) outside of the CwlContextualView. So


fred = myCwlContextualView.configurationBean // will not work

The final means that once the attribute has a value it cannot be 
changed. Even stronger, the value must be specified either in the 
declaration of the attribute, or when you construct an instance of 
CwlContextualView. (There are weird exceptions to the last sentence that 
are best ignored and never mentioned in polite company.)


If you look at

public CwlContextualView(CwlDumyActivity activity)

which makes a CwlContextualView, it contains the line:

this.configurationBean = activity.getConfiguration();

So once you have made a CwlConfigurationView, it has a configurationBean 
attribute, that nothing else can see, and that has a fixed value.



Can anyone point me to information that would help me understand this
nomenclature?


I think 
http://stackoverflow.com/questions/13772827/difference-between-static-and-final 
explains static and final well.



Thanks,

Gale


Alan

Re: Apache Taverna Commandline

[Alan Williams]

On 03-Aug-16 03:50, Chamini Prashakthi Jayasinghe wrote:

Hi all,
can someone explain me how to run the test case in Apache Taverna
Commandline common module.it is all commented and after remove comment mark
it shows errors.


What errors are you getting?


regards chamini


Alan

Re: Docker Activity Plugin Enhancements

[Alan Williams]

On 31-Jul-16 08:47, Nadeesh Dilanga wrote:

Hi,
Related to the validation piece, forgot to mention that Activity plugin
already checks those validations before it runs even now. ex: if I try to
start an already started container, it gives me a json response mentioning
the container already started.


I think that is reasonable. An alternative approach would be to take the 
running container. That, though, could lead to problems. What will 
happen if I try to run two instances of the activity at the same time 
i.e. same container. We will need to ensure that any conflict is prevented.


Alan

Re: Docker Activity Plugin Enhancements

[Alan Williams]

On 31-Jul-16 07:36, Nadeesh Dilanga wrote:

Hi Alan,

I added validation Utility class(also sent a pull request).


Thanks. I have seen it.


Also about this validation done (where the stage before workflow runs),
given I already added a utility class to do that, who suppose to call this
and do the validation ? Is it part of the activity plugin ?(some extension
point to add a custom validator which get executed by the workflow)


There would normally be:

public class DockerActivityHealthChecker

see 
incubator-taverna-common-activities/taverna-wsdl-activity/src/main/java/org/apache/taverna/activities/wsdl/WSDLActivityHealthChecker.java


and

incubator-taverna-common-activities/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthChecker.java

I would not worry if you do not have time to do this, as it can be done 
calling your utility class.



Hi Stian,
Can you please explain  what Alan meant "Capture docker metadata and add to
workflow run provenance", so that I can provide that capability.


If Stian does not answer, then you can ignore that _optional_ work, and 
just try the bioboxe support.



In addition, right now docker plugin not capable of pulling the actual
image in to the registry. But installing an existing image in the registry.
Do we need that capability as well ?


No. That is beyond the scope of Taverna.


What we have is "inspect image" where
you can get meta data of existing images in registry.


That is enough.


I am also in the process of getting familiar with "biobox" and how it fits
docker plugin.


Great.


On Tue, Jul 26, 2016 at 12:26 PM, Alan Williams 
wrote:


On 25-Jul-16 05:43, Nadeesh Dilanga wrote:


Hi Alan,
Thank you very much for the guidance. Is it safe to assume the priority
order is as same as the order you defined the tasks.



No. There is no order of the optional tasks. They are specified in
https://issues.apache.org/jira/browse/TAVERNA-901

Please find my

comments inline.

In addition, I will add class/methods/variable comments to make the code
more readable.

On Sun, Jul 24, 2016 at 5:52 AM, Alan Williams 
wrote:

On 24-Jul-16 10:18, Nadeesh Dilanga wrote:


Hi Alan, Hi Stian,




Thanks Nadeesh.

If the code needs any improvements/changes, please let me know. And given


the code is fine, can you please advice me on my next steps ?



There are four optional tasks:

* Validate Docker activity config, e.g. can the docker image be pulled?



Docker image metadata can be pulled? Right now it only shows you image id.
I will enhance it to give a comprehensive response with all relevant image
metadata. And on top of that, can you please explain the relation between
validating docker activity config with docker image. Can you please give
an
example.



There is a stage before a workflow is run. The activities in the workflow
are validated to check that they can be run. For example, a WSDL activity
might check that the operation is online - see


incubator-taverna-common-activities/taverna-wsdl-activity/src/main/java/org/apache/taverna/activities/wsdl/WSDLActivityHealthChecker.java

* Capture docker metadata and add to workflow run provenance (e.g. which

docker image ID was pulled)



Did you mean container metadata ? Sorry that I did not get the context.
Can
you please give an example from a Activity Plugin point of view.



I think Stian can address this better than me.

* Add Bioboxes support




* Integrate with CWL support (TAVERNA-900)


Personally, I would look at bioboxes http://bioboxes.org/ - but others
may disagree.

There are existing bioboxes docker images - search for bioboxes at
https://hub.docker.com.

So, I think you should try to run a biobox docker image. Then create a
small workflow that includes the running of the image. There are also
examples on the bioboxes.org website that show how different bioboxes
can
be connected to perform a scientific task. You may (if you have time) be
able to encode some of these as workflows.



I am already using ActivityInvoker.invokeAsyncActivity. Shall I give it a
try to create a dedicated test case for biobox(Assume these images
available in public registry) to do a start container with a given
container and docker json from Docker Activity Plugin.



Yes - that is a good first step.


Please don't forget that this is all optional and do not feel under

pressure to do it all :)





Alan




Alan

CFP: 11th Workflows in Support of Large-Scale Science (WORKS) Workshop

[Alan Williams]

 WORKS 2016 Workshop 
Workflows in Support of Large-Scale Science
Monday, 14 November 2016, Salt Lake City, Utah.
Held in conjunction with SC16 The International Conference for High
Performance Computing, Networking, Storage and Analysis
http://works.cs.cardiff.ac.uk/


Call For Papers

Data-Intensive Workflows (a.k.a. scientific workflows) are routinely 
used in most scientific disciplines today, especially in the context of
parallel and distributed computing. Workflows provide a systematic way 
of describing the analysis, and rely on workflow management systems to

execute the complex analyses on a variety of distributed resources. They
are at the interface of end-users and computing infrastructures. With 
the drastic increase of raw data volume in every domain, they play an 
even more critical role to assist scientists in organizing and 
processing their data and to leverage HPC or HTC resources.


This workshop focuses on the many facets of data-intensive workflow
management systems, ranging from job execution to service management and
the coordination of data, service, and job dependencies. The workshop
therefore covers a broad range of issues in the scientific workflow
lifecycle that include: data-intensive workflows representation and
enactment; designing workflow composition interfaces; workflow mapping
techniques that may optimize the execution of the workflow; workflow
enactment engines that need to deal with failures in the application and
execution environment; and a number of computer science problems related
to scientific workflows such as semantic technologies, compiler methods,
fault detection, and tolerance.

The topics of the workshop include but are not limited to:

Big Data analytics workflows
Data-driven workflow processing
Workflow composition, tools, and languages
Workflow execution in distributed environments
Workflows on the cloud
Dynamic data dependent workflow systems solutions
Exascale computing with workflows
Workflow refinement tools that can manage the workflow mappingprocess
Workflow fault-tolerance and recovery techniques
Workflow user environments, including portals
Workflow applications and their requirements
Adaptive workflows
Workflow monitoring
Workflow optimizations (including scheduling and energy efficiency)
Performance analysis of workflows
Workflow debugging
Workflow provenance
Interactive workflows
Workflow interoperability
Reproducible computational research using workflows


Paper Submission

Important Dates
Papers Due: August 31, 2016
Notifications of Acceptance: September 20, 2016
Final Papers Due: October 9, 2016

The paper must be at most 10 pages long. The proceedings should be
formatted according to
http://www.acm.org/publications/proceedings-templateand the proceedings
will be published in http://ceur-ws.org. Extended versions will be 
invited to a special issue in a high-ranked journal. Negotiations with 
Future Generation Computer Systems are underway.



WORKS 2016 Organizing Committee

- PC Chairs
Sandra Gesing, University of Notre Dame, USA
Rizos Sakellariou, University of Manchester, UK

- General Chairs
Johan Montagnat, French National Center for Scientific Research (CNRS),
Sophia Antipolis, France
Ian Taylor, Cardiff University, UK and University of Notre Dame, USA

- Steering Committee
David Abramson, University of Queensland, Australia
Malcolm Atkinson, University of Edinburgh, UK
Ewa Deelman, USC, USA
Michela Taufer, University of Delaware, USA

- Publicity Chairs
Rafael Ferreira da Silva, USC, USA
Ilia Pietri, University of Athens, Greece


WORKS 2016 Program Committee

Ilkay Altintas, UCSD, USA
Khalid Belhajjame, Paris-Dauphine University, France
Adam Belloum, University of Amsterdam, the Netherlands
Ivona Brandic, Vienna University of Technology, Austria
Marian Bubak, AGH Krakow, Poland
Raj Buyya, University of Melbourne, Australia
Ann Chervenak, USC Information Sciences Institute, USA
Daniel de Oliveira, Fluminense Federal University (UFF), Brazil
Ewa Deelman, USC Information Sciences Institute, USA
Rafael Ferreira Da Silva, USC Information Sciences Institute, USA
Daniel Garijo, USC Information Sciences Institute, USA
Sandra Gesing, University of Notre Dame, USA
Tristan Glatard, CNRS, France
Peter Kacsuk, MTA SZTAKI, Hungary
Daniel S. Katz, NCSA, USA
Tamas Kiss, University of Westminster, UK
Dagmar Krefting, University of Applied Sciences Berlin, Germany
Maciej Malawski, AGH University of Science and Technology, Poland
Anirban Mandal, UNC Chapel Hill, USA
Andrew Stephen McGough, Newcastle University, UK
Paolo Missier, Newcastle University, UK
Jarek Nabrzyski, University of Notre Dame, USA
Ilia Pietri, University of Athens, Greece
Radu Prodan, University of Innsbruck, Austria
Chase Qi

Re: Docker Activity Plugin Enhancements

[Alan Williams]

On 25-Jul-16 05:43, Nadeesh Dilanga wrote:

Hi Alan,
Thank you very much for the guidance. Is it safe to assume the priority
order is as same as the order you defined the tasks.


No. There is no order of the optional tasks. They are specified in 
https://issues.apache.org/jira/browse/TAVERNA-901



Please find my
comments inline.

In addition, I will add class/methods/variable comments to make the code
more readable.

On Sun, Jul 24, 2016 at 5:52 AM, Alan Williams 
wrote:


On 24-Jul-16 10:18, Nadeesh Dilanga wrote:


Hi Alan, Hi Stian,



Thanks Nadeesh.

If the code needs any improvements/changes, please let me know. And given

the code is fine, can you please advice me on my next steps ?



There are four optional tasks:

* Validate Docker activity config, e.g. can the docker image be pulled?



Docker image metadata can be pulled? Right now it only shows you image id.
I will enhance it to give a comprehensive response with all relevant image
metadata. And on top of that, can you please explain the relation between
validating docker activity config with docker image. Can you please give an
example.


There is a stage before a workflow is run. The activities in the 
workflow are validated to check that they can be run. For example, a 
WSDL activity might check that the operation is online - see


incubator-taverna-common-activities/taverna-wsdl-activity/src/main/java/org/apache/taverna/activities/wsdl/WSDLActivityHealthChecker.java


* Capture docker metadata and add to workflow run provenance (e.g. which
docker image ID was pulled)


Did you mean container metadata ? Sorry that I did not get the context. Can
you please give an example from a Activity Plugin point of view.


I think Stian can address this better than me.


* Add Bioboxes support




* Integrate with CWL support (TAVERNA-900)

Personally, I would look at bioboxes http://bioboxes.org/ - but others
may disagree.

There are existing bioboxes docker images - search for bioboxes at
https://hub.docker.com.

So, I think you should try to run a biobox docker image. Then create a
small workflow that includes the running of the image. There are also
examples on the bioboxes.org website that show how different bioboxes can
be connected to perform a scientific task. You may (if you have time) be
able to encode some of these as workflows.



I am already using ActivityInvoker.invokeAsyncActivity. Shall I give it a
try to create a dedicated test case for biobox(Assume these images
available in public registry) to do a start container with a given
container and docker json from Docker Activity Plugin.


Yes - that is a good first step.


Please don't forget that this is all optional and do not feel under
pressure to do it all :)





Alan


Alan

Re: Docker Activity Plugin Enhancements

[Alan Williams]

On 24-Jul-16 10:18, Nadeesh Dilanga wrote:

Hi Alan, Hi Stian,


Thanks Nadeesh.


If the code needs any improvements/changes, please let me know. And given
the code is fine, can you please advice me on my next steps ?


There are four optional tasks:

* Validate Docker activity config, e.g. can the docker image be pulled?

* Capture docker metadata and add to workflow run provenance (e.g. which 
docker image ID was pulled)


* Add Bioboxes support

* Integrate with CWL support (TAVERNA-900)

Personally, I would look at bioboxes http://bioboxes.org/ - but others 
may disagree.


There are existing bioboxes docker images - search for bioboxes at 
https://hub.docker.com.


So, I think you should try to run a biobox docker image. Then create a 
small workflow that includes the running of the image. There are also 
examples on the bioboxes.org website that show how different bioboxes 
can be connected to perform a scientific task. You may (if you have 
time) be able to encode some of these as workflows.


Please don't forget that this is all optional and do not feel under 
pressure to do it all :)


Alan

GitHub issue raised on Taverna Server

[Alan Williams]

When a workflow with a jsonpath activity is run, server throws an
error, which is visible in the workflow's detail.log:

WARN 2016-07-20 17:58:32,316
(net.sf.taverna.t2.workflowmodel.serialization.xml.AbstractXMLDeserializer:167)
- Can't discover artifact for
net.sf.taverna.t2.activities:jsonpath-activity

Re: [jira] [Commented] (TAVERNA-998) Fix compile errors in taverna-workbench-impl

[Alan Williams]

On 14-Jul-16 16:03, Gale Naylor wrote:

Just wondering: Are users required to register somewhere else?


Elsewhere in Taverna - no. Registration was always optional in the 
workbench, so most users did not register :-)


There is a "notice" capability in the Taverna 2.* workbench that pops up 
a message if we had anything important to announce. I am not sure if 
that is still in Taverna 3 workbench. We would have to decide where it 
read the notice from.


Alan

Re: [Docker Activity Plugin]Added README and pull request fixes

[Alan Williams]

On 14-Jul-16 03:12, Nadeesh Dilanga wrote:

Hi Alan, Hi Stian,


Hello


I have sent out a latest pull request which has a README on how to run the
unit tests and also added the feedback given by Stian.

Please let me know if anything else needs to be fixed.


The main issue I see is that you are using methods in 
DockerContainerConfigurationImpl. In my opinion anything that you need 
should be visible in DockerContainerConfiguration and accessed from that.


Alan

Re: Docker Activity Create/Start/List Container support

[Alan Williams]

On 11-Jul-16 06:39, Nadeesh Dilanga wrote:

Hi,
I worked this week on implementing this. I have sent 3 more new pull
requests.


Great. I will have a look.


Here I have added Docker Activity support for Create/Start and List
containers. This also came with pre defined port bindings capability also.
I have tested this with a docker sample python application and was able to
browse the application(hello world) form web browser. I took screen shots
on those.


Where are the screen shots kept?


I will probably create a user guide end of this project with
screen shots on how to run a container from scratch.

Right now everything is part if JUnit tests which is self descriptive. Can
you please review the pull requests(I saw four pull request to be merged at
the moment) and also any feedback of improvement.

I will implement stop/delete container support for Activity Plugin also and
send a another pull request.

One other thing to note is, output from the docker activity plugin is
always a JSON.


OK

Alan

Re: Contribute to taverna command line

[Alan Williams]

On 10-Jul-16 04:18, Chamini Prashakthi Jayasinghe wrote:

Hi ,


Hello


I would like to know that https://issues.apache.org/jira/browse/TAVERNA-871
is a good start for a begginer or not?


I think it is a very hard issue to work on - so no.

You could start with a simple issue, for example, 
https://issues.apache.org/jira/browse/TAVERNA-982


Alan

Re: draft release notes for Taverna cmd line 3.1.0

[Alan Williams]

On 04-Jul-16 10:23, Ian Dunlop wrote:

Hello,

Who can add the release to the google plus feed? If it's not being used
then there is not much point having it.


Good point Ian. I have added a Google+ post which should appear in the feed.


Cheers,

Ian


Alan

Re: draft release notes for Taverna cmd line 3.1.0

[Alan Williams]

On 01-Jul-16 14:21, Gale Naylor wrote:

Hi Alan,

You should have access to editing (and everything else) now.


Thanks Gale. I've added some comments.


Gale


Alan

Re: draft release notes for Taverna cmd line 3.1.0

[Alan Williams]

On 01-Jul-16 12:51, Stian Soiland-Reyes wrote:

I have made live the download pages for 3.1.0 and friends:
https://taverna.incubator.apache.org/download/commandline/

(You may spot that I've re-arranged the items in the Download menu and
/download/ front page)


And drafted release email:

https://cwiki.apache.org/confluence/display/TAVERNADEV/Taverna+Command+Line+3.1.0


What is the easiest way to comment / edit the draft? I can log into the 
cwiki but do not seem to have access to the page.



I'll clean up/remove the TBD bits.


Any edits/comments for the release notes? I'll post it in a couple of hours. :)

Thanks everyone!


Alan

Re: Issue in reusing ActivityInvoker#invokeAsyncActivity for unit tests

[Alan Williams]

On 30-Jun-16 04:19, Nadeesh Dilanga wrote:

Hi,
All variables are Strings. After a series of troubleshoot sessions, was
able to figure out the issue I was facing.
I had to do following;

 referenceService.renderIdentifier(inputs.get(KEY), String.class, context);

instead of just inputs.get(KEY).getLocalPart(). where inputs is a
Map. Now I could use the ActivityInvoker ;-).

One other problem facing(I am doing my testings in my Java Project and
running the tests through a Main method). But when removed and try to add
them to JUnit and run through mvn install in runtime it again fails with
that jackson method not found error. Working on finding that out. There
should be some other module or transient sub module that packs old jackson.



Will send a new pull request from a new feature branch with that fixed soon.


Brilliant! Well done.

Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 24-Jun-16 06:58, Nadeesh Dilanga wrote:

Hi all,


Hello


Yes, SSL issue also went away. When I point cert path in docker-java it
picks it up without any concern.


Great.

At the moment the cert-path in TestDockerCommands is hard-coded with 
values like "/Users/Nadeesh/Documents/docker/"  . In order for other 
people to run it, you need to change these.



I sent a pull request with latest code changes. And now the
RemoteClient(Utility client for docker commands) supports
- Inspect an Image
- Search Images
- List all Containers
- Create Container
- Start Container
- Stop Container


Pulling an Image is also supported, not implemented yet. Will do that also.
And obviously we can keep adding more capability. And in the activity
plugin execute, I am expecting an input "action" and based on it's value I
am executing the docker commands and putting a JSON String as output. For
errors, It is a error message.


OK. We can look at the execution once we are able to do the container 
and image :)



Please let me know your feedback on how I can further improve the code
base/structure. I will be keep adding remaining docker command support for
RemoteClient as well as Activity.


Good work.

Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 18-Jun-16 08:12, Nadeesh Dilanga wrote:

Hi Alan, Hi Stian,
Please refer my latest commit @
https://github.com/NadeeshDilanga/incubator-taverna-common-activities/commits/docker/taverna-docker-activity

where I have implemented reading a injected configuration. Can you please
review this and let me know what I am missing here. But one thing I would
like to know is, who is responsible of creating(populating) the
DockerContainerConfiguration ?


In the workbench, users are able to change such configurations. That is 
normally done under the File -> Preferences. I think for GSOC it is 
enough to specify what needs to be in the configuration.



We have to allow user to give a docker.conf
and from which some one construct the DockerContainerConfiguration and
inject it to the activity plugin.


Yes, long term we do. However, for GSOC it is enough to take a 
hand-written docker.conf


Your DockerContainerConfigurationImpl certainly looks to have the 
correct type of information.



Then I went through the taverna-engine repo code base looking for the clue
Stian gave, where I have to implement Configurable interface, and use
ConfigurationManager. And Configuration manager interface had
store/populate methods to override, but I found it bit unclear to figure
out how exactly I can use that to my use case/how it works/relation ship
between Configurable interface and ConfigurationManager. Do we have any
documentation on that ?


I am not sure. Stian and Gale may know.


For SSL issue, I am calling the container as
https://192.168.99.100:2376/containers/create  where 192.168.99.100 is my
container host. I assume that is the target you meant ?


Yes.

Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 20-Jun-16 06:47, Nadeesh Dilanga wrote:

Hi all, one more thing to add.
Create container is the most heavy API call(payload/parameter size). But
how about things like start/stop/search/info/delete/ like methods. Should
be think on accepting them as as activity plugin configs ?


docker-java has these, so I think it would be best to try to use that.

What extra information is needed to start the container?

Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 21-Jun-16 08:21, Nadeesh Dilanga wrote:

Hi Stain, Hi Alan,
Can you please review the code with my latest commit @
https://github.com/NadeeshDilanga/incubator-taverna-common-activities/commits/docker
where I came up with a Configuration Manager and also implemented
"Configurable".


I think you need a separate interface called 
DockerContainerConfiguration as well as the class 
DockerContainerConfigurationImpl. DockerActivity should then take a 
DockerContainerConfiguration not a DockerContainerConfigurationImpl.



I would like to add a unit test case for this by creating a
DockerContainerConfigurationImpl and inject a ConfigurationManager. Can you
please point me to such example. I tried, but could not find anything yet.
i.e I was not able to find a usage of "DatabaseConfigurationImpl" in
taverna-engine/taverna-osgi/taverna-common-activities repos.


DatabaseConfiguration and DatabaseConfigurationImpl are in the Taverna 
engine not in the common activities. For the unit test, I think it is OK 
to create an explicit DockerContainerConfigurationImpl and insert that 
into the DockerActivity.



Because I am planning to have a proper test case before the mid term
evaluation deadline. Also appreciate if you can provide your
feedback/expectations on this project's mid point


I will be satisfied if you can retrieve the metadata about an image and, 
if possible, talk to a container.



and if it has any
required TODOs I can complete them ASAP before the mid term evaluation
deadline.


Rather than implement your own REST calls to talk to a container, have 
you looked at https://github.com/docker-java/docker-java ? If it is too 
difficult to switch, then I think your REST utils are OK for the moment,


Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 17-Jun-16 05:32, Nadeesh Dilanga wrote:

Still got stuck further on the SSL issue[1]. May be something to do with my
setup. So I also implemented invoking simple HTTP(without SSL) in
additional to HTTP SSL.



Meanwhile I already started getting configuration thru that spring
inject-able framework. Will commit those changes also(without just blocking
on Http  SSL issue) to my private repo from which I am planning to send
pull request.


Great. Can you please do that as soon as possible?


[1]:

avax.net.ssl.SSLHandshakeException:
sun.security.validator.ValidatorException: PKIX path building failed:
sun.security.provider.certpath.SunCertPathBuilderException: unable to find
valid certification path to requested target


What is the target? Are you sure there is actually a certification path 
to the target?


Alan

Re: Fwd: Corrupted jar file on mygrid repository

[Alan Williams]

Hello evrybody

I have looked at what is in the "jar" and it is a HTML document

src="http://mcc.godaddy.com/park/oaSbLJ4gMzWmM2chMKVhLzI0"; 
style="visibility: visible;height: 100%; position:absolute" 
allowtransparency="true" marginheight="0" marginwidth="0" 
frameborder="0" width="100%">


Alan

Fwd: Corrupted jar file on mygrid repository

[Alan Williams]

 Forwarded Message 
Subject:Corrupted jar file on mygrid repository
Date:   Wed, 15 Jun 2016 12:45:29 +
From:   Choesang Tenzin 
To: supp...@mygrid.org.uk 



Hi!


We are using an instance of taverna and depend heavily on your 
repository for building the project.


I realized that there was an update to some jars on 13th June 06:56 am, 
which are corrupted.



http://repository.mygrid.org.uk/artifactory/mygrid-all/org/codehaus/plexus/plexus-utils/3.0/


regards,

Choesang Tenzin

Re: Being linked for Tav mobile gsoc report

[Alan Williams]

On 15-Jun-16 13:07, Ian Dunlop wrote:

Hello

I got a request for mid term evaluation for the tavmob gsoc proposal. I
thought that rajan decided to do a different one. I wonder why the admin
hasn't caught up because I remember us telling the Apache gsoc lists.


Was the evaluation request from Google ? Have you checked on the GSOC 
website to see what it thinks the status is?



Cheers

Ian


Alan

Re: Restructuring Taverna Mobile Dashboard

[Alan Williams]

On 15-Jun-16 13:01, Ian Dunlop wrote:

Hello

Can you confirm the uk time. I might be able to join.


Hello Ian

1500 IST was 1030 BST. I've suggested that a set of specific questions 
is circulated for the wireframes. Also that we rearrange for later this 
week. I know I'm not able to comment usefully on the UI design :)



Cheers

Ian


Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 15-Jun-16 09:02, Nadeesh Dilanga wrote:

Hi Alan,
Thank you very much for the pointer. I went through and understood how
works.
1. Implement docker factory class to return an activity configuration.
2. Accept the configuration in the DockerActivity constructor.

Please correct me if I missed something.


I need a picture of what is being proposed :)


Also I am working on the implementation and commiting my code to my forked
repo at [1]. I will send pull requests once following TODOs finishes.
 1. Test HTTPS invocation(right now I am having a SSL handshake issue and
working on it)

I am using SSLContext.getDefault() and gives me
javax.net.ssl.SSLHandshakeException:
sun.security.validator.ValidatorException: PKIX path building failed:
sun.security.provider.certpath.SunCertPathBuilderException: unable to find
valid certification path to requested target

I have a unit test to test this. I also tried setting system properties
javax.net.ssl.keyStore, javax.net.ssl.trustStore,
javax.net.ssl.keyStorePassword. But no luck.


What is the target of the HTTPS ? Does it have a valid certificate?


 2. Enhance the activity class to read configuration injected by Spring.


[1] -
https://github.com/NadeeshDilanga/incubator-taverna-common-activities/commits/docker


Great.

Alan

Re: Restructuring Taverna Mobile Dashboard

[Alan Williams]

On 15-Jun-16 05:47, Rajan Maurya wrote:

Hi All,

We have hangout call on 15:00 IST. Please Let me know that if there is any
problem.


Who else is joining?

Alan

Re: Restructuring Taverna Mobile Dashboard

[Alan Williams]

On 14-Jun-16 11:44, Rajan Maurya wrote:

Can you send links to the wireframes?

Here is the link of the WireFrames :
https://drive.google.com/open?id=0B5wnE0S3WxbsOU9VUlQtazc4cEE .

Ok Tomorrow  is good at 15:00 GMT +5:30.


I'm confused by the "+5:30." Are you suggesting 1500 UTC? If so, that's 
OK with me, but you should wait for more people :)


Alan

Re: Restructuring Taverna Mobile Dashboard

[Alan Williams]

On 13-Jun-16 19:04, Rajan Maurya wrote:

Hi folks,

Now the Taverna Mobile code is stable and future PR will not break the code
standard after Code Analysis tools implementation.
So, Now we should go one step ahead and I want to fix first "WorkFlows
List" we can say Dashboard of App.
As the Taverna mobile, REST API designed. The dashboard is not properly
designed as accordingly and the data loading is not consistent. So, I want
to redesign this  according to REST API as I mentioned in my GSOC proposal.

I think we can discuss this whole on the hangout and can make changes
accordingly. I have already made the Wireframes of the Dashboard.


Can you send links to the wireframes?


Tomorrow will be fine for me others days also. Reply, When we can talk.


I am available Wednesday, Thursday and Friday from about 9:00 UTC to 
20:00 UTC


Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 14-Jun-16 05:04, Nadeesh Dilanga wrote:

Hi Alan,
Do you have an example link where we have used such Spring Configuration ?


Firstly, just to check are you targeting Taverna 2 or Taverna 3?

The Spring Configuration is for Taverna 3. You can see an example in 
/taverna-rest-activity/src/main/resources/META-INF/spring/rest-activity-context-osgi.xml 
where the credentialManager is "pulled in" by


interface="org.apache.taverna.security.credentialmanager.CredentialManager" 
/>


The credentialManager was "pushed" by the Taverna engine in

taverna-credential-manager-impl/src/main/resources/META-INF/spring/credential-manager-impl-context.xml

Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 10-Jun-16 02:49, Nadeesh Dilanga wrote:

Hi Stian,

Following API can be used to attach to a remote Docker. Refer  "Attach to a
container" for more details.

POST /containers/(id or name)/attach

Ok, it make sense to read it from some sort of a configuration instead from
the input JSON for the activity plugin. Inside an activity plugin, how can
I access this configuration ?


The activity plugin has a DockerContainerConfiguration injected by the 
Spring configuration. You would need a setDockerContainerConfigfuration 
method. For simplicity, you can have the dockerContainerConfiguration 
field as static.


@Stian - does that sound reasonable ?

Alan

Re: Design and Implementation of Docker Activity Plugin

[Alan Williams]

On 09-Jun-16 12:22, Nadeesh Dilanga wrote:

Hi Stian, Hi Alan,
Do you think we shouldn't use REST invocations to start Docker, but better
to use something else ?


Do you mean invocations of the REST activity? I think it would be better 
to use the Apache HttpClient directly. That will make it easier to debug 
and to maintain.


If you are asking if it is best to talk to docker using the Docker 
Remote API or by executing command line calls, I think that the API is 
the better way to proceed.



(Java API/use Taverna Command Line tool to execute
direct docker commands/anything else).


Alan

Re: [DISCUSS] The third RC of Taverna Command Line 3.1.0

[Alan Williams]

It all builds OK on my Maven 3.3.3

Alan

Re: [DISCUSS] The third RC of Taverna Command Line 3.1.0

[Alan Williams]

To answer Thilina's question on the VOTE thread,

what version of Maven are you running?

Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 04-Jun-16 05:10, Nadeesh Dilanga wrote:

Hi all,
I am starting this thread to discuss and finalize the docker commands we
need to expose for client side(Taverna).

Latest stable docker remote API is version 1.23[1]. And it has several APIs
that can be useful.


Yes. Where do you intend to run the docker containers? That would be 
similar to how you can specify where to run tool services - although I 
dislike how that is done.



The original JIRA [2] mentioned about the JSON format to a docker run. I
hope it meant about the docker config.json ?


That would be a lot of configuration. I am not sure that it is sensible 
to have it all specified in the workflow.



Because, given we use remote APIs, I would like to know what are the
expectations are ?

1. Do we assume that Images are created and published to the registry.


Yes, certainly for running you will know the registry and the image.


2. Do we assume that docker container is created


I don't think you can, as that would mean there are steps needed to be 
done before the workflow can be run.



Given #1 and #2 done, then we are talking about starting the
container(~docker run). If that is the case, when we use remote APIs we
only need following, and no need of a JSON:

Request: POST /containers/(id or name)/start
Response: HTTP/1.1 204 No Content

There are other responses too:

Status Codes:

   - *204* – no error
   - *304* – container already started
   - *404* – no such container
   - *500* – server error


You will need to look at how the input data is read and the results 
returned. It is not sufficient to just start the container if it expects 
input data to be sent to stdin, or to be in specific locations.



[1] - https://docs.docker.com/engine/reference/api/docker_remote_api_v1.23/


Alan

Re: Finalize Docker Invoke JSON format

[Alan Williams]

On 04-Jun-16 11:39, Stian Soiland-Reyes wrote:

Hi!



[snip]


What is the Docker API for setting up a container? Do you need to pull the
images first?


That is in the REST API referenced by Nadeesh - 
https://docs.docker.com/engine/reference/api/docker_remote_api_v1.23/



It would be cool if we can pull at the beginning of a
workflow run (e.g. asynchronously when an Activity is configured) so that
does not need to delay execution at a later step.


It may be worth checking with the Insigneo people from Sheffield who do 
something analogous for VMs created to run services for workflows.



We will probably need a volume mount of a temporary directory, so that
input and output files can be provided to the command, but if you prefer it
might be easier to start with stdin and stdout support; similar to the Tool
Activity.


Alan

Re: Direct-editing by Committers

[Alan Williams]

On 04-Jun-16 17:33, Gale Naylor wrote:

 I was going to add the license headers to the 2 taverna-engine README
files
(taverna-prov/reADME.md and taverna-reference-types/reADME.md),
but I wasn't sure of the procedure for editing directly.

I found the link, but wasn't sure how to edit without effecting what someone
else is doing.


It will just show up as a commit to the branch. If there are conflicts 
then anyone who has also made edits will need to do an update and merge 
first.



Do you want me to edit in the master branch or ??


I have no problem with edits such as this. Changing code would be more 
problematic.



Gale


Alan

Re: [VOTE] Release Apache Taverna Command-line Tool 3.1.0-incubating RC2

[Alan Williams]

On 02-Jun-16 17:01, Gale Naylor wrote:

Hello,

I am finding University of Manchester copyright notices on many of the
files in taverna-provenanceconnector. This is not allowed, right? (
http://www.apache.org/legal/src-headers.html#headers)

For example:
src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java

and all the java files in
/src/main/java/org/apache/taverna/provenance/lineageservice/types/


I can confirm that the files have the old Manchester license at the top 
with the Apache license later on. Github found several 
https://github.com/apache/incubator-taverna-engine/search?utf8=%E2%9C%93&q=University+of+Manchester


I checked the common activities and commandline and they seem OK.


Gale


Alan

Re: [DISCUSS] Release candidate 2 of Command-line Tool 3.1.0-incubating

[Alan Williams]

On 01-Jun-16 12:27, Alan Williams wrote:

Hello

I get a failure:

[INFO] [ERROR] Failed to execute goal
org.apache.maven.plugins:maven-surefire-plugin:2.19.1:test
(default-test) on project dummy-taverna-plugin-activity: Execution
default-test of goal
org.apache.maven.plugins:maven-surefire-plugin:2.19.1:t
est failed: The forked VM terminated without properly saying goodbye. VM
crash or System.exit called?
[INFO] [ERROR] Command was cmd.exe /X /C ""C:\Program
Files\Java\jdk1.8.0_51\jre\bin\java" -jar
C:\Users\alson\taverna\apache-taverna-engine-3.1.0-incubating-source-release\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefirebooter1896791380795738239.jar
C:\Us
ers\alson\taverna\apache-taverna-engine-3.1.0-incubating-source-release\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefire5943729575219558115tmp
C:\Users\alson\taverna\apache-taverna-engine-3.1.0-incubating-source-release\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefire_0317696432267187850tmp"


Is that the path length limit problem?


It built OK when I just had it under C:\engine instead of 
C:\Users\alson\taverna\apache-taverna-engine-3.1.0-incubating-source-release\apache-taverna-engine-3.1.0-incubating



Alan


Alan

Re: [DISCUSS] Release candidate 2 of Command-line Tool 3.1.0-incubating

[Alan Williams]

Hello

I get a failure:

[INFO] [ERROR] Failed to execute goal 
org.apache.maven.plugins:maven-surefire-plugin:2.19.1:test 
(default-test) on project dummy-taverna-plugin-activity: Execution 
default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.19.1:t
est failed: The forked VM terminated without properly saying goodbye. VM 
crash or System.exit called?
[INFO] [ERROR] Command was cmd.exe /X /C ""C:\Program 
Files\Java\jdk1.8.0_51\jre\bin\java" -jar 
C:\Users\alson\taverna\apache-taverna-engine-3.1.0-incubating-source-release\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefirebooter1896791380795738239.jar 
C:\Us
ers\alson\taverna\apache-taverna-engine-3.1.0-incubating-source-release\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefire5943729575219558115tmp 
C:\Users\alson\taverna\apache-taverna-engine-3.1.0-incubating-source-release\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefire_0317696432267187850tmp"


Is that the path length limit problem?

Alan

Re: [DISCUSS] Release candidate 2 of Command-line Tool 3.1.0-incubating

[Alan Williams]

On 01-Jun-16 12:03, Stian Soiland-Reyes wrote:

Use this thread to discuss the release candidate proposed in
https://lists.apache.org/thread.html/Z320lz77ps9xnov


Please reply on the corresponding [VOTE] thread to place votes.

Anyone can participate in testing and voting, not just committers,
please feel free to try out the release candidate and provide your
votes!

How to review a release? https://s.apache.org/review-release


Do they need to be built in a specific order e.g. engine, common 
activities, command line?


Alan

Re: [DISCUSS] Release candidate 1 of Command-line Tool 3.1.0-incubating

[Alan Williams]

On 31-May-16 17:15, Stian Soiland-Reyes wrote:

On 31 May 2016 at 17:01, Alan Williams  wrote:

I just hit this :)


Bah! Too quick! :)


I think it is best to do another RC. I'll continue with minimal testing of
this one.


All right.

I can have another go tomorrow - let me know if you find any other
pecularities!  :)


All three built.

I did have a problem with the command line the first time. It was unable 
to find 
https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpclient-osgi/4.5.2/httpclient-osgi-4.5.2.pom 
. That was probably an internet glitch though as it built the second 
time around.


Alan

Re: [DISCUSS] Release candidate 1 of Command-line Tool 3.1.0-incubating

[Alan Williams]

On 31-May-16 16:51, Stian Soiland-Reyes wrote:

First inconvenience:

https://issues.apache.org/jira/browse/TAVERNA-975

Sadly I only found this problem at the end of the day when testing the
RC on Windows.


I just hit this :)


To make sure taverna-engine builds, you have to use this workaround
the first time building:

  mvn clean install -Darchetype.test.skip=true

As mentioned in Jira, the workaround is only needed while this release
is not in Maven Central (e.g. during vote on dev@taverna and later on
general@incubator) - the fix should be trivial, so we can do another
release candidate if you prefer.


I think it is best to do another RC. I'll continue with minimal testing 
of this one.


Alan

Re: Release of Taverna Command Line?

[Alan Williams]

On 27-May-16 16:06, Gale Naylor wrote:

Okay. I'll test that. It makes sense. How about if we just add a notice in
the Readme? (Maybe even just suggest that Windows USERS install at their
top level directory?) Probably I'm the only one who buries their file so
deeply! :)


I think something in the README is a good idea as a quick workaround. I 
don't think though that the source directories that are failing are 
atypical. Mine are something like C:\Users\alson\taverna\commandline


http://stackoverflow.com/questions/27680647/does-max-path-issue-still-exists-in-windows-10 
suggests that the max length has been kept to ensure compatibility :O 
Also 
http://stackoverflow.com/questions/1880321/why-does-the-260-character-path-length-limit-exist-in-windows 
for "explanation"!


Alan


On Fri, May 27, 2016, 7:55 AM Stian Soiland-Reyes  wrote:


I managed to reproduce it as well - it's related to the folder length:

[INFO] Command was cmd.exe /X /C ""C:\Program
Files\Java\jdk1.8.0_92\jre\bin\java" -jar
"C:\Users\stain\ApacheTavernaBuilds\04 Try Engine

Again\incubator-taverna-engine\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefirebooter3609180204497295203.jar"
"C:\Users\stain\ApacheTavernaBuilds\04 Try Engine

Again\incubator-taverna-engine\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefire9169840870606093708tmp"
"C:\Users\stain\ApacheTavernaBuilds\04 Try Engine

Again\incubator-taverna-engine\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\surefire\surefire_05020064088761634944tmp""
[INFO]  at
org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:590)
[INFO]  at
org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:460)
[INFO]  at
org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:229)
[INFO]  at
org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:201)
[INFO]  at
org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeProvider(AbstractSurefireMojo.java:1026)
[INFO]  at
org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:862)
[INFO]  at
org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:755)
[INFO]  at
org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
[INFO]  ... 21 more

On 27 May 2016 at 15:39, Stian Soiland-Reyes  wrote:

Hm, this error seems different from the previous


[ERROR] Archetype IT 'dummyActivity' failed: Cannot run additions goals.


I was able to reproduce the above in Windows 10 by removing the
maven-invoker dependency from the pom.xml - and if I add it back in,
it works.

IS it because of the space in your folder name
C:\Users\Gale\ApacheTavernaBuilds\04 Try Engine again\ or possibly the
total length of the file path?

I built it from D:\incubator-taverna-engine without reproducing the
problem.  Could you try to say build it from C:\1\  ?

(BTW - to save time you can test this by running just mvn clean
install within the taverna-activity-archetype folder)


If I try to copy this folder to my
C:\Users\stain\ApacheTavernaBuilds\04 Try Engine Again I actually get
an error from Windows Explorer:


The filename(s) would be too long for the destination folder
DummyActivityFactory.java


so a big hint that the folder paths of the internal test project can
become a bit long for Windows. (It's OK as long as you are inside
Java, you are allowed to make and use "too long" paths - but it breaks
as soon as you then try to start a sub-process as the inner maven fork
would do)


Should we disable this test on Windows or just warn about this in the
README? I think it could affect other parts as well - which is why I
tend to put my source code straight on my D:\ while in Windows :)



On 23 May 2016 at 15:01, Gale Naylor 

wrote:

Sorry, BUILD FAILURE again. Actually, two: Dummy Taverna activity
and Apache Taverna Activity archetype.

[INFO] [INFO]

[INFO] [INFO] Reactor Summary:
[INFO] [INFO]
[INFO] [INFO] Dummy Taverna project ..

SUCCESS

[ 12.754 s]
[INFO] [INFO] Dummy Taverna activity .

FAILURE

[ 23.582 s]
[INFO] [INFO] Dummy Taverna plugin ...

SKIPPED

[INFO] [INFO]

[INFO] [INFO] BUILD FAILURE
[INFO] [INFO]

[INFO] [INFO] Total time: 38.075 s
[INFO] [INFO] Finished at: 2016-05-23T06:51:36-07:00
[INFO] [INFO] Final Memory: 26M/202M
[INFO] [INFO]

Re: "Potato Man" activity icon: What is the license?

[Alan Williams]

On 15-May-16 19:14, Stian Soiland-Reyes wrote:

Hi,


[snip]


But doing so, I just realized the archetype includes a dummy activity PNG

https://github.com/apache/incubator-taverna-engine/blob/master/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/exampleIcon.png

it's the "Potato man" - do anyone remember the origin of this? Did we
make it, or do we need to replace it?


I think it needs to be replaced as if you expand it, it is obviously Mr 
Potato Head which is copyrighted. We could just use a ? instead.


Alan

Re: Trying to invoke docker image

[Alan Williams]

On 15-May-16 15:30, Nadeesh Dilanga wrote:

Hi Stian,


Hello


I tried many things these days. Here I focused on core parts of the project.
First I successfully built and run a simple workflow using 'FASTA' service.
Here I used 'Taverna Workbench Core 2.5.0' IDE.
Then I run a existing docker image which is called 'hello-world' and got an
output like this 'Hello from Docker' etc.


Great.


My next aim is to invoke docker through the REST API.
I tried to enable REST API on Docker, but got an error.  Now I'm fixing it


Don't forget that you can ask for help on this mailing list - or look on 
stackoverflow :)



and hope to finish it ASAP. When it done I'm ready to use Chrome REST
client through the activity plugin with the help of curl commands.


I use the PostMan app.

So you plan to initially have a tool service that runs curl?


So then I can try these steps programmatically for the project.
By the way right now, I'm creating a docker container and a docker image
with the help of youtube videos. :)


Youtube is an excellent source of technical videos.

Have you considered using a blogging site to describe your progress?

Alan

Re: Release of Taverna Command Line?

[Alan Williams]

On 11-May-16 17:51, Stian Soiland-Reyes wrote:


I tried from an empty .m2/repository and built just the command line
product, and then I got

[INFO] BUILD SUCCESS


I tried from an empty repository and built the three in order.

No problems - and I run Windows :)

Alan

Re: Draft download pages

[Alan Williams]

On 09-May-16 17:48, Stian Soiland-Reyes wrote:

Hi,

I have drafted download pages for the upcoming release:

http://taverna.staging.apache.org/download/engine/
http://taverna.staging.apache.org/download/common-activities/
http://taverna.staging.apache.org/download/commandline/


And listed them on
http://taverna.staging.apache.org/download/

(Please, don't push the CMS publish button now!)


Please review and edit!


While the first two are new, and basically clones of the
/download/osgi/ page, the third page  include links to Taverna Command
Line 2.5, as I think 'normal' users should still generally download
2.5 before we know how well 3.1.0 works on 'real' workflows.


For 2.5, should we keep the links to the legacy site's
http://www.taverna.org.uk/download/command-line-tool/2-5/

(Alan - what happened about those legacy banners?)


I wondered that as well! They are still on prototype.taverna.org.uk 
though so I will do another copy tomorrow.



or just send them to the big list on
https://bitbucket.org/taverna/taverna-commandline-product/downloads/
?


I think it's OK to go to the legacy pages.

Alan

Re: Release of Taverna Command Line?

[Alan Williams]

On 06-May-16 12:14, Stian Soiland-Reyes wrote:

Thanks for checking Ian!

I think I updated all the READMEs to say we need Java 8 now.  We
agreed to that update in
https://issues.apache.org/jira/browse/TAVERNA-869


I'm going to do a pre-flight test in Windows 10 as well so we don't
need to do the dance on the RCs again..

I'll be brave and even have a go inside the new Ubuntu in Windows
subsystem... if it works there, then we have nothing to worry about :)


Perhaps Alan can have a go in his temperamental Windows 8?


Alan had a go :)

Windows 8.1
Java 1.8.0_51
Maven 3.3.3

Engine, Common Activities and CommandLine all installed with no problems.

Alan

Re: Release of Taverna Command Line?

[Alan Williams]

On 26-Apr-16 17:05, Stian Soiland-Reyes wrote:

We can do taverna-engine and taverna-common-activities separately if
that makes sense.. I was thinking that we don't really know they work
until used in the command line and the command line would be useful
for the GSOC students (e.g. particularly for the Docker activity) -
but I'm open to either. If we don't do the

I was thinking of preparing the release candidate this week - but I
think rather wait until early May so we get that US Export declaration
sorted first.


Can you give a brief summary of the "US Export declaration" issue?

Alan

Re: add a plugin to a taverna server

[Alan Williams]

On 21-Apr-16 08:27, Stian Soiland-Reyes wrote:

Yes, as $TAVERNA_RUN_ID

Here's the output from running env on my server:

INTERACTION_WEBDAV=/rest/runs/1addd0f3-8ad9-4d82-8ffa-350b809374fd/wd/interactions
INTERACTION_PORT=32768
HOSTNAME=e4e7a0a0908c
HOME=/root
RAVEN_APPHOME=/tmp/1addd0f3-8ad9-4d82-8ffa-350b809374fd
WAR_MD5=20d27405b27a3418b783777171734514
CATALINA_HOME=/usr/local/tomcat
TOMCAT_MAJOR=7
JAVA_VERSION=7u79
JAVA_DEBIAN_VERSION=7u79-2.5.5-1~deb8u1
PATH=/usr/lib/jvm/java-7-openjdk-amd64/jre/bin:/usr/local/tomcat/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
TOMCAT_TGZ_URL=https://www.apache.org/dist/tomcat/tomcat-7/v7.0.63/bin/apache-tomcat-7.0.63.tar.gz
TAVERNA_VERSION=2.5.4
LANG=C.UTF-8
TOMCAT_VERSION=7.0.63
INTERACTION_FEED=/rest/runs/1addd0f3-8ad9-4d82-8ffa-350b809374fd/interaction
TAVERNA_RUN_ID=1addd0f3-8ad9-4d82-8ffa-350b809374fd
PWD=/tmp/usecase4814808815707856724dir
INTERACTION_HOST=http://localhost

As mentioned earlier, from within the workflow you can use the
taverna.runid system property, fetched with Get_environment and XPath
/property-list/property[@name="taverna.runid"]/@value


I think the run id will need to be passed into the activity as an 
additional parameter. I would not expect the run id to be in the 
environment of a tool running, for example, on a different machine.


Alan

Re: add a plugin to a taverna server

[Alan Williams]

On 16-Apr-16 13:21, Stian Soiland-Reyes wrote:

Ah.. but then I'm not sure if my UUIDs will help you, as those
identify the command line engine's run ID - while I guess you want to
match the UUIDs used in the REST interface of the Taverna Server.

I am not sure if the Taverna Server can be told to inject the external
run UUID into the workflow.. Donal?


I think the Taverna Server's run UUID may be used as part of the 
environment variables for running the command line tool in? That (along 
with lots of other environment variables) is made visible by the 
Get_Environment_Variables_as_XML service. If so, it can be pulled out 
and fed into the beanshell.


For example, that XML contains (for my test run):

value="%2Ftserver%2Frest%2Fruns%2Fff2bc479-8260-427b-ac1b-004055d65e02%2Finteraction"/>


So, I think the run ID might be 2Fff2bc479-8260-427b-ac1b-004055d65e02

I think it's worth trying :)

Alan

Re: [GSoC 2016] Hi!!

[Alan Williams]

On 15-Mar-16 19:35, Stian Soiland-Reyes wrote:

OK, I've updated the wiki to say you prefer 900 :)

Task TAVERNA-900 includes all of the 5 (now 6!) CWL sub-tasks - or a
selection of those. We never intended for the GSOC student to complete
all of those, but completing more than one task would be brilliant!

You can work on your project proposal and detail what work you are
considering to focus on, in which order. Of course with more tasks you
will need to think a bit more about milestones, and declare which
tasks would be optional if you have enough time (and likewise what
could be skipped if you run short!).

GSOC students - your proposal and tasks does not have to match the
Jira description - it is better if it doesn't and show what you have
already investigated and planned!  But it's OK if the first part of
the project is to investigate different solutions/libraries and try
out some quick manual prototypes.


Also, (to repeat myself) when writing your proposal, do not forget to 
consider:


(a) how you will become involved in the developer community,
(b) how you will involve any interested users in evaluation of your work,
(c) how you will test the work
(d) the schedule, if possible with milestones
(e) any time(s) you will not be available.

Alan

Re: Fwd: TAVERNA-901- GSOC 2016 : Add Docker support to Taverna

[Alan Williams]

On 13-Mar-16 05:15, Kandauda Amila De Zoysa Karunathilaka wrote:

Hi Stian,


Hello


I'm Amila Karunathilaka 3rd year undergraduate student in Computer Science
& Engineering from University of Moratuwa Sri Lanka.
I'm interested about this project idea. I have knowledge and experience
about Java, Docker and Kuberneties.
I followed your references.
I would like to know more about this project. Please give me some tips to
getting started.


As you already know Docker and Java, the main issue will be 
understanding how Taverna describes activities. I think the best thing 
would be to follow Stian's advice in his comment to 901 on 29th February.



Thank you.
Regards,
*Amila Karunathilaka*


Alan

Re: [GSoC 2016] Hi!!

[Alan Williams]

On 13-Mar-16 15:23, Willy Aguirre wrote:

could you give me some steps? I'm reading about CWL


I think the easiest thing may be to look at a very simple CWL workflow 
and compare it to a simple workflow in SCUFL2.


A workflow for echoing the input parameter is at

https://github.com/common-workflow-language/workflows/blob/master/workflows/hello/hello-param.cwl

A similar SCUFL2 workflow is in

https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.wfbundle

or the JSON may be easier to understand:

https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.json

Alan

Re: [GSoC 2016] Hi!!

[Alan Williams]

On 13-Mar-16 15:23, Willy Aguirre wrote:

Thanks for answer! So I prefer to implement CWL

https://github.com/common-workflow-language


Do you mean 881 https://issues.apache.org/jira/browse/TAVERNA-881 ?

Before the four sub-tasks, there is an essential first step - 
understanding CWL and Taverna as much as possible, or at least to the 
depth where you know which parts you do not know :)


Because 881 links to other issues, 877 and 879, you will need to think 
about how your work will relate to them. For example, can you use a 
dummy configuration until 877 is done.


When writing your proposal, do not forget to consider:

(a) how you will become involved in the developer community,
(b) how you will involve any interested users in evaluation of your work,
(c) how you will test the work
(d) the schedule, if possible with milestoones
(e) any time(s) you will not be available.

Good luck

Alan

Re: [GSoC 2016] Hi!!

[Alan Williams]

On 07-Mar-16 18:48, Willy Aguirre wrote:

Hi!


Hello Willy

Thank you for your interest in the Taverna GSOC issues.


I'm Willy Aguirre from Lima Peru Actually I'm studing at UPC(
http://epe.upc.edu.pe/)

I don't have experience in Workflow System but I used BPMN (Bisagi) I think
is new experience for me.

I'm working as a java developer and also I used Play Framework 1.* it uses
yaml

https://pe.linkedin.com/in/willyaguirre

I passed GSoC 2015 for Apache Aurora
https://issues.apache.org/jira/browse/AURORA-1164

I'm interesting in these ideas

https://issues.apache.org/jira/browse/TAVERNA-881

https://issues.apache.org/jira/browse/TAVERNA-879


These two issues (881 and 879) are part of a group 
https://issues.apache.org/jira/browse/TAVERNA-900 for adding support for 
the Common Workflow Language to Taverna. For information about CWL, 
please follow the links in the description of 900. GSOC students are 
only expected to do one, or maybe two, of the issues - so do not panic :)


I think 879 consists of four sub-tasks.

(a) creating small workflows corresponding to the calling of a single 
Taverna activity,


(b) putting a Taverna Command Line Tool that calls a Taverna workflow 
into a docker image


(c) creating a CWL configuration for the docker so that the Taverna 
workflow can be run as part of a CWL workflow.


The fourth task

(d) extend the CWL reader so that it recognizes CWL processes that wrap 
Taverna workflows and re-instate the Taverna workflow (or activity if a 
single activity)


depends on someone doing 877 and so obviously may not be done (if no one 
does 877) or will require co-ordination.


For 879, I think your proposal would be relatively easy to write as the 
issue is well-organized.


881 (saving Taverna workflows as CWL) is less straight-forward and you 
would need to put more work into how you would go about achieving the 
task, especially how to have testable parts.


For me (and other people will have different opinions), 879 is primarily 
a programming issue, but 881 is more "software engineering". Which one 
you choose to do will depend on what you would like to get out of GSOC. 
As you have already done a programming GSOC, perhaps 879 would be a good 
challenge.


The members of the dev mailing list will be able to help advise on any 
questions / suggestions you have.




Cheers!
Willy


Thanks again for your interest.





Alan

GSOC 2016

[Alan Williams]

Hello everybody

Just to let you know that I am "in" as a GSOC 2016 mentor :)

@Stian - you are the only person down as a potential mentor for the 
issues in Jira. Do you want me to be an alternative?


Alan

Re: Taverna Android App

[Alan Williams]

On 03-Mar-16 21:46, Larry Akah wrote:

Good observation there Rajan. However, the app does crash because the
server used during development was down. You can't really evaluate all
features as you would need to deploy taverna on a local server and
configuring the app with the new parameters before fetching workflow data.


Although it shouldn't "crash" if it can't talk to the server. It should 
give an error message.


Alan

Re: Taverna Android App

[Alan Williams]

On 03-Mar-16 19:07, RM wrote:

Thanks Alan,
   I am ready for this draft proposal but I have a
Question "How can I find a potential mentors" in Taverna
  developer list.


I'd suggest putting the draft proposal into a Google doc and asking 
people to look at it, comment and volunteer as a mentor.


Alan

Re: GSOC 2016 projects

[Alan Williams]

On 02-Mar-16 15:59, Stian Soiland-Reyes wrote:

Yeah, why I mentioned T2 was because you can run the developer
tutorial there and get started right away..  and the only thing that I
think has changed in that API for Taverna 3 is that you return the
activity by URI rather than by instance, and that you return the
configuration as a JSON object rather than a bean.

So if the configuration is a JSON object anyway, then you are 95%
compatible with Taverna 3 Workbench.


Yes. That is what is being done by an MSc student we have in Manchester 
looking at OGC services.


The main work of discovering what building blocks are available, what 
inputs and outputs they have, the cardinality of the data on the 
inputs/outputs, invoking the "block", dealing with results or errors, 
all that is basically the same.



I think the Taverna 3 workbench can run from SNAPSHOT builds, but it
might need some updates, e.g. it refers to
net.sf.taverna.t2.maven.plugins:taverna-maven-plugin:0.3.1-SNAPSHOT
rather than the org.apache.taverna.osgi version that is under a VOTE
right now.


Alan

Re: GSOC: Add CWL support to Taverna

[Alan Williams]

On 27-Feb-16 09:05, Thilina Manamgoda wrote:

HI,


Hello


Source: https://issues.apache.org/jira/browse/TAVERNA-900

I am Thilina Manamgoda undergraduate from University of Perandeniya. I
would like to contribute this project for GSOC 2016.


That is great.


In order to add CWL support to Taverna  following steps should be taken.

1.Save Taverna workflows as CWL
2.Read CWL workflows
3.Execute CWL tool descriptions
4.Browse and use CWL tool descriptions from the workbench
5.Create a Docker tool for executing Taverna activities

So for Gsoc 2016 i need to get better idea about the project ,am i supposed
to do one of above task or all of them ?.


As the issue says, "the GSOC student can ... choose to pursue one or two 
of these tasks in detail"


So, if you are interested in (for example) Docker, you might want to 
concentrate on #5.


As part of a submission to become a GSOC student, you do a proposal of 
what you plan to do. That proposal will depend on which task(s) you are 
interested in working on. The content of a proposal from someone 
interested in #1 would be very different to that for someone working on #4.


Which task(s) are you interested in?

Feel free to ask as many questions as you want.


Regards,
Thilina.


Alan

Re: Problem on Taverna Plugin Installation

[Alan Williams]

 Forwarded Message 
Subject: Re: Problem on Taverna Plugin Installation
Date: Tue, 09 Feb 2016 21:46:13 +0200
From: PARASKEVOPOULOU MARIA 
To: alaninmcr 

Hi Ian,

For Taverna v2.5. in order to install the plugin, the following plugin
site should be added :
http://192.185.115.65/~diana/DIANA_plugin_updated/test-plugins/. You
can also see the relevant information on our site
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=site/help&topic=taverna.

Thank you in advance for your support.

Best regards,
Maria

Quoting alaninmcr :


 Forwarded Message 
Subject: Re: Problem on Taverna Plugin Installation
Date: Tue, 9 Feb 2016 13:57:08 +
From: Ian Dunlop 
Reply-To: dev@taverna.incubator.apache.org
To: dev@taverna.incubator.apache.org

Hello,

What does the plugins.xml say eg
/home/johndoe/.taverna-core-2.5.0/plugins.xml. Maybe taverna can't find
your server for some reason.

Where is your plugin deployed ie the info you put in when adding a new
plugin site? We could then try and install it and see if we get the same
result.

Cheers,

Ian

On 08/02/2016 18:52, PARASKEVOPOULOU MARIA wrote:

Dear Taverna team,

We have implemented a Taverna plugin incorporating services and
algorithms implemented in the DIANA LAB (www.microrna.gr).
The plugin initially worked for Taverna 2.3, while several months ago we
have updated the plugin and had it functional for both Taverna 2.3 and
2.5 versions.

However, the last month DIANA users complain that they cannot add the
DIANA Taverna plugin in their Taverna workbench.

The installation has been performed several times in the past with success.
We uninstalled the plugin from our server and also observed a failure in
the reinstallation.
We redeployed the plugin but the error remains.

The logs produced in Taverna, report a failure in fetching a Pom file.


"WARN  2015-07-22 19:34:34,036
(net.sf.taverna.raven.repository.impl.LocalRepository:85) - Could not
read com.example:DIANA_Services-activity-ui:1.2-SNAPSHOT from
http://www.mygrid.org.uk/maven/biomoby/biomoby.org/m2repo/
java.io.IOException: Server returned HTTP response code: 409 for URL:
http://repository.mygrid.org.uk/artifactory/biomoby/com/example/DIANA_Services-activity-ui/1.2-SNAPSHOT/DIANA_Services-activity-ui-1.2-SNAPSHOT.pom

"
We assume that this failure is due to the fact that Taverna is not
trying to install/download the DIANA plugin from our server,defined in
the plugin's project pom.xml, but from http://repository.mygrid.org.uk.

Did something change concerning the format of the project pom.xml that
is utilized for the plugin deployment?
Will the error be fixed, if we change the pom.xml? For the the pom.xml
design we followed a similar format as in the following pom file
https://github.com/taverna/taverna-prov/blob/master/pom.xml.

It would be grateful if we could have your feedback on how to
troubleshoot the issue.

Thank you in advance,

DIANA Team



--
Ian Dunlop, eScience Lab
School of Computer Science
The University of Manchester
http://orcid.org/-0001-7066-3350

Re: Apache Taverna site

[Alan Williams]

On 12-Dec-15 16:22, Gale Naylor wrote:

Hi Menaka,

I'm sorry, but I still don't see an image. I have had this problem before
on dev list emails. I ended up putting the image in a blog and posting the
link.


I think you're right Gale and the mailing system strips out attachments 
- probably to prevent spamming.



Gale


Alan

Re: Common workflow language

[Alan Williams]

On 10-Dec-15 09:35, Stian Soiland-Reyes wrote:

  I've signed up for the CWL hackathon, but I hope others would join!


I will go - I just didn't care what date it is :)

Alan

Re: Common workflow language

[Alan Williams]

On 04-Dec-15 15:28, Ian Dunlop wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Hello,

Does anyone have views on how Apache Taverna fits into the goals of
the Common Workflow Language project
https://github.com/common-workflow-language/common-workflow-language ?
Should taverna adopt CWL instead of SCUFL2. Are there things that
SCUFL2 or the current taverna engine offers that CWL does not?


Stian is probably the best person to answer this as he has been quite 
involved with CWL. To the best of my knowledge, CWL started off very 
similar to SCUFL2 but diverged.


There is a CWL/Taverna/Galaxy hackathon planned for May 2016 in Paris. I 
think (hope) I sent around the Doodle poll for it.



Cheers,

Ian


Alan

Re: Taverna components

[Alan Williams]

Hello Yassene

When I view the component family on myE, I see "You are not authorised 
to view the item this entry points to." for all four items. I wonder if 
this is the problem.


Alan

Taverna components

[Alan Williams]

Dear Taverna team,

How do I make the component I put on MyExperiment available?  I tried private 
and public, but I still cannot see them from a different computer.
A related question that I have, where can I browse the available components? 
how to download them, modify them, etc. ?

Many thanks in advance,
Yassene

Re: Cannot register list at depth 0

[Alan Williams]

On 20-Sep-15 20:41, Stian Soiland-Reyes wrote:

Probably irrelevant - but [ and ] are not valid URL characters in path and
should be %-escaped.


I tried the escaped versions and they also would not work. Using a WSDL 
version and some crafty XPath I managed to get the PNGs out. I think the 
WSDL (and SoapLab) do not match what is actually returned.


Alan

Re: Cannot register list at depth 0

[Alan Williams]

On 19-Sep-15 19:38, Kasikrit Damkliang wrote:

Yes, it cannot access at SIB server.
BTW, I use Decode_Base_64_to_byte_Array service to save it as PNG file.


Even doing that, it is weird as Taverna thinks the XML returned from the 
getResults does not to match the WSDL.


I resorted to using an XPath to extract the PNGs from the data it 
actually does return.


It now seems to work.


Kasikrit.


Alan

Re: Cannot register list at depth 0

[Alan Williams]

Having done in in WSDL, the URL for the PNG is (for an example):

http://wsembnet.vital-it.ch:8080/soaplab2/results/[display.pepnet]_62088d16.14fda3eb41c._7f7d_Graphics_in_PNG.001.png

which appears not to work.

The PNG (supposedly) in the results is also not recognized as an image.

I can generate a postscript though (although the URL still does not 
work). Will that help? I'm sending it you offlist.


Alan

Re: Cannot register list at depth 0

[Alan Williams]

I can reproduce the error.

Looking in the log it has:

INFO  2015-09-19 18:21:22,291 
(net.sf.taverna.t2.activities.soaplab.SoaplabActivity:328) - Soaplab 
input type 'long' unknown for input 'sbegin_sequence' in 
http://wsembnet.vital-it.ch/soaplab2-axis/services/protein_2d_structure.pepnet, 
will attempt to add as String depth 0
INFO  2015-09-19 18:21:22,292 
(net.sf.taverna.t2.activities.soaplab.SoaplabActivity:328) - Soaplab 
input type 'long' unknown for input 'send_sequence' in 
http://wsembnet.vital-it.ch/soaplab2-axis/services/protein_2d_structure.pepnet, 
will attempt to add as String depth 0
INFO  2015-09-19 18:21:22,292 
(net.sf.taverna.t2.activities.soaplab.SoaplabActivity:328) - Soaplab 
input type 'boolean' unknown for input 'sprotein_sequence' in 
http://wsembnet.vital-it.ch/soaplab2-axis/services/protein_2d_structure.pepnet, 
will attempt to add as String depth 0
INFO  2015-09-19 18:21:22,292 
(net.sf.taverna.t2.activities.soaplab.SoaplabActivity:328) - Soaplab 
input type 'boolean' unknown for input 'snucleotide_sequence' in 
http://wsembnet.vital-it.ch/soaplab2-axis/services/protein_2d_structure.pepnet, 
will attempt to add as String depth 0
INFO  2015-09-19 18:21:22,292 
(net.sf.taverna.t2.activities.soaplab.SoaplabActivity:328) - Soaplab 
input type 'boolean' unknown for input 'sreverse_sequence' in 
http://wsembnet.vital-it.ch/soaplab2-axis/services/protein_2d_structure.pepnet, 
will attempt to add as String depth 0
INFO  2015-09-19 18:21:22,292 
(net.sf.taverna.t2.activities.soaplab.SoaplabActivity:328) - Soaplab 
input type 'boolean' unknown for input 'slower_sequence' in 
http://wsembnet.vital-it.ch/soaplab2-axis/services/protein_2d_structure.pepnet, 
will attempt to add as String depth 0
INFO  2015-09-19 18:21:22,292 
(net.sf.taverna.t2.activities.soaplab.SoaplabActivity:328) - Soaplab 
input type 'boolean' unknown for input 'supper_sequence' in 
http://wsembnet.vital-it.ch/soaplab2-axis/services/protein_2d_structure.pepnet, 
will attempt to add as String depth 0
INFO  2015-09-19 18:21:22,292 
(net.sf.taverna.t2.activities.soaplab.SoaplabActivity:328) - Soaplab 
input type 'boolean' unknown for input 'amphipathic' in 
http://wsembnet.vital-it.ch/soaplab2-axis/services/protein_2d_structure.pepnet, 
will attempt to add as String depth 0


I think those may be something to do with the error. I'll look further.

Alan

Re: Cannot register list at depth 0

[Alan Williams]

Got it now

Alan