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 <[email protected]>
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
