Hi Alan, I added validation Utility class(also sent a pull request). 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)
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. 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 ? What we have is "inspect image" where you can get meta data of existing images in registry. I am also in the process of getting familiar with "biobox" and how it fits docker plugin. On Tue, Jul 26, 2016 at 12:26 PM, Alan Williams <[email protected]> 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 <[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 > >
