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 <alanin...@googlemail.com>
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 <alanin...@googlemail.com>
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
