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Posted to users@taverna.apache.org by Ahmad Aburomman <ah...@rai.usc.es> on 2015/04/06 12:37:06 UTC

RE: A few questions before choosing Taverna for our project

Hello,
I modify the project of Vitor, here is the function: 
https://github.com/AhmadUsc/Java/blob/197819f798184721260789644f883221d166bb78/javaClient#L66

Okay I didn't touch Baclava, I added Enable Provenance function
I got the zip bundle but it was empty.

Can you Vitor regenerate the code with provenance data enabling ?
Here is Vitor project:
https://github.com/pgcc/taverna-java-client

Thanks in advance.

-----Original Message-----
From: Stian Soiland-Reyes [mailto:stain@apache.org] 
Sent: Tuesday, March 31, 2015 1:05 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project

No, you should not need to touch Baclava at all :)

You will need to retrieve the provenance bundle separately once the run has finished. It should be available at .../run-bundle in the REST
API:

http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/run-bundle

On 31 March 2015 at 11:34, Ahmad Aburomman <ah...@rai.usc.es> wrote:
> Thanks a lot for your indeed reply, actually I'm using this project 
> https://github.com/pgcc/taverna-java-client
>
> I have implemented the Provenance function in TavernaClient.java, it 
> is okay now and enabled but still can't get the provenance data with the output You mentioned that I have to do some function to Baclava, can you guide me please or give me the exact script to update my project.
>
> Regards
> Ahmad
>
> -----Original Message-----
> From: Stian Soiland-Reyes [mailto:stain@apache.org]
> Sent: Friday, March 27, 2015 2:24 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> Not sure where you found that code, as I found they were implemented here:
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org
> /taverna/server/client/Run.java#L344
>
>
> but in either case, the baclava input/output should NOT be used if you want the workflow run bundle back.
>
>
> Unfortunately the Taverna Server client code for Java has not been updated for the run bundle, which was new in 2.5 I think.
>
> It would be great if you could have a quick go - I think it should be quite doable, we've just not got around to it yet...
>
> Use the 'next' branch from https://github.com/myGrid/t2-server-jar/
>
>
> By
> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource
> :/runs/{id}/generate-provenance you need to send a PUT with "true" to 
> /runs/{id}/generate-provenance
>
> so perhaps something like this could work?
>
>
> package uk.org.taverna.server.client.Run add two new methods, e.g.:
>
> similar to isBaclavaOutput and requestBaclavaOutput
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org
> /taverna/server/client/Run.java#L404
>
> but with "generate-provenance" added to the run URL.
>
>
> Similarly add  getRunBundle() similar to getOutputZip()
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org
> /taverna/server/client/Run.java#L1140
>
> .. but requesting "run-bundle" added to the URL.
>
>
> To do it "proper REST-like" this can be generalized to find those two URI fragments from the runDescription as you see with getLink() in other bits of the code.
>
> On 27 March 2015 at 12:07, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>> Yes I see these code about baklava, but I don't know what to add exactly!
>>
>> @Override
>>     public String getBaclavaInput(String uuid) throws TavernaException {
>>         throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
>>     }
>>
>>     @Override
>>     public String setBaclavaInput(String uuid, String file) throws TavernaException {
>>         throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
>>     }
>>
>>
>>     @Override
>>     public void setBaclavaOutput(String uuid, String file) throws TavernaException {
>>         throw new UnsupportedOperationException("Not supported 
>> yet.");
>>
>>
>>
>> -----Original Message-----
>> From: Stian Soiland-Reyes [mailto:stain@apache.org]
>> Sent: Friday, March 27, 2015 12:28 PM
>> To: users@taverna.incubator.apache.org
>> Subject: Re: A few questions before choosing Taverna for our project
>>
>> I think it should suffice in the client - although you might have to add support for it in the java client as the generate-provenance option was added recently.. Would you be willing to have a go at that?
>>
>> On 27 March 2015 at 11:08, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>>> Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
>>> Please explain more
>>>
>>> Thanks
>>>
>>> -----Original Message-----
>>> From: alaninmcr [mailto:alaninmcr@googlemail.com]
>>> Sent: Thursday, March 26, 2015 9:03 PM
>>> To: users@taverna.incubator.apache.org
>>> Subject: Re: A few questions before choosing Taverna for our project
>>>
>>> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>>>> Dear Stian,
>>>>
>>>> I'm working on workflow and I ran it perfectly (tomcat6 and 
>>>> RESTful), I got the output without provenance bundle
>>>
>>> Before you started the run, did you set generate-provenance to true?
>>>
>>> Also, you need to make sure you are not sending the outputs to a Baclava file.
>>>
>>> See
>>> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resour
>>> c
>>> e
>>> :/runs/{id}/generate-provenance
>>>
>>>> I don't know how to configure Taverna server to enable provenance 
>>>> data, can you guide me please?
>>>
>>> It is not part of the server configuration. It is set for each run.
>>>
>>>> Kind regards
>>>>
>>>> Ahmad
>>>
>>> Alan
>>>
>>
>>
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>> http://orcid.org/0000-0001-9842-9718
>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>



--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718

A few questions before choosing Taverna for our project

Posted by Ahmad Aburomman <ah...@rai.usc.es>.
So I have to build that, but it is very hard to build, I have no idea about it . 
I'm also trying with Taverna Command Line Tool, also it is seem that there is no provenance data can be generate!!

I need a solution to run my workflow and get the output with the provenance data. 

Regards

> Hello,

Hello

> I appreciate your time and cooperation, really thank you very much.
>
> But I got confused :(

Sorry about that.

> What I got that you want me to merge the client side from this project:
>      https://github.com/taverna/taverna-server/tree/2.5/server-client
>
> with the server side from the this project:
> https://github.com/taverna/taverna-server.git
>
> the problem it the last project (https://github.com/taverna/taverna-server.git) is the same of the first one, it load the same one.

Yes. The client code is in
https://github.com/taverna/taverna-server/tree/2.5/server-client . To build it, you will (currently) have to build the whole of the Taverna Server code - but you can then just use the server-client.

Alan

Re: A few questions before choosing Taverna for our project

Posted by alaninmcr <al...@googlemail.com>.
On 23/04/2015 22:25, Ahmad Aburomman wrote:
> Hello,

Hello

> I appreciate your time and cooperation, really thank you very much.
>
> But I got confused :(

Sorry about that.

> What I got that you want me to merge the client side from this project:
>      https://github.com/taverna/taverna-server/tree/2.5/server-client
>
> with the server side from the this project:
> https://github.com/taverna/taverna-server.git
>
> the problem it the last project (https://github.com/taverna/taverna-server.git) is the same of the first one, it load the same one.

Yes. The client code is in 
https://github.com/taverna/taverna-server/tree/2.5/server-client . To 
build it, you will (currently) have to build the whole of the Taverna 
Server code - but you can then just use the server-client.

Alan

Re: A few questions before choosing Taverna for our project

Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 23/04/2015 22:25, Ahmad Aburomman wrote:
> But I got confused:(

You're not experienced with building fairly large Maven projects with
lots of dependencies? Get the build from our Artifactory. :-)

http://repository.mygrid.org.uk/artifactory/libs-snapshot-local/uk/org/taverna/server/server-client/2.5.5-SNAPSHOT/server-client-2.5.5-20150425.104736-20.jar

That should be a largely self-contained JAR (85kB) with a few external 
dependencies (org.jvnet.ws.wadl:wadl-core:1.1.6, 
com.sun.jersey:jersey-client:1.8, commons-io:commons-io:2.4, 
org.apache.tika:tika-core:1.5, com.google.code.findbugs:jsr305:1.3.7) 
which we don't include since we don't normally repackage external 
libraries in the Open Source world. ;-)

The above URL is not persistent; it is to a version that may go away 
without warning (because we only keep a limited number of snapshot 
versions). I'm not sure how to generate a link to the directory in the 
Artifactory tree.

MAVEN INSTRUCTIONS
------------------
DO NOT USE THESE IF YOU AREN'T USING MAVEN FOR THE REST OF YOUR CLIENT. 
THESE ASSUME THAT YOU KNOW HOW MAVEN WORKS ALREADY; WE WON'T TEACH YOU THAT!

It has the following Maven coordinates:

   <dependency>
       <groupId>uk.org.taverna.server</groupId>
       <artifactId>server-client</artifactId>
       <version>2.5.5-SNAPSHOT</version>
   </dependency>

And that will depend on you having the myGrid repository set up:

   <repositories>
       <repository>
           <releases />
           <snapshots>
               <enabled>false</enabled>
           </snapshots>
           <id>mygrid-repository</id>
           <name>myGrid Respository</name>
           <url>http://www.mygrid.org.uk/maven/repository</url>
       </repository>
       <repository>
           <releases>
               <enabled>false</enabled>
           </releases>
           <snapshots>
               <enabled>true</enabled>
           </snapshots>
           <id>mygrid-snapshots</id>
           <name>myGrid Snapshot Respository</name>
           <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
       </repository>
   </repositories>

Donal.

RE: A few questions before choosing Taverna for our project

Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Hello, 
I appreciate your time and cooperation, really thank you very much.
 
But I got confused :(
What I got that you want me to merge the client side from this project: 
    https://github.com/taverna/taverna-server/tree/2.5/server-client

with the server side from the this project: 
https://github.com/taverna/taverna-server.git

the problem it the last project (https://github.com/taverna/taverna-server.git) is the same of the first one, it load the same one. 


_____________________________________________________
On 13/04/2015 13:27, alaninmcr wrote:
> I've started a hangout. If anyone else wants to join, the URL is
> https://plus.google.com/hangouts/_/gwg7xzlz4c6cyabi5popr6mohma

As was discussed, the code at:

    https://github.com/myGrid/t2-server-jar

is really quite old, and is missing critical features. The client in the 
server codebase:

    https://github.com/taverna/taverna-server/tree/2.5/server-client

is up to date (and is part of what we've contributed to Apache, so it 
will continue to be supported) though it is currently a bit awkward to 
build and isn't a finished release yet. To build the 2.5 version (NB: 
NOT Apache code, but equivalent to) check out the server code from github:

    https://github.com/taverna/taverna-server.git

and then use maven to build it. I recommend 'mvn install' for that. That 
will download the world a bit, but will eventually create the following 
artefact in your system-local maven repository.

    <dependency>
        <groupId>uk.org.taverna.server</groupId>
        <artifactId>server-client</artifactId>
        <version>2.5.5-SNAPSHOT</version>
    </dependency>

That should be quite fully featured enough to support generating 
provenance (as part of the run bundle) provided you ask for it; you're 
still expected to understand the general server usage patterns, which 
are documented online currently at:

    http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+Server+2.5

What we (well, probably I) will do next is to update the build so that a 
proper client artefact is produced that doesn't have explicit 
dependencies on other parts of the server build (currently it uses a 
supporting library for handling Resource Usage Records) and get 2.5.5 
released so that we can have an actual artefact that we can point to, 
rather than some sort of SNAPSHOT.

Oh, and you *might* be able to use the build in our Artifactory:

http://repository.mygrid.org.uk/artifactory/libs-snapshot-local/uk/org/taverna/server/server-client/2.5.5-SNAPSHOT/server-client-2.5.5-20150304.170355-11.jar

That's not a long-term guaranteed URL and I don't know if it has all the 
dependencies you need. But maybe it will work? :-)

Donal.

Re: A few questions before choosing Taverna for our project

Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 13/04/2015 13:27, alaninmcr wrote:
> I've started a hangout. If anyone else wants to join, the URL is
> https://plus.google.com/hangouts/_/gwg7xzlz4c6cyabi5popr6mohma

As was discussed, the code at:

    https://github.com/myGrid/t2-server-jar

is really quite old, and is missing critical features. The client in the 
server codebase:

    https://github.com/taverna/taverna-server/tree/2.5/server-client

is up to date (and is part of what we've contributed to Apache, so it 
will continue to be supported) though it is currently a bit awkward to 
build and isn't a finished release yet. To build the 2.5 version (NB: 
NOT Apache code, but equivalent to) check out the server code from github:

    https://github.com/taverna/taverna-server.git

and then use maven to build it. I recommend 'mvn install' for that. That 
will download the world a bit, but will eventually create the following 
artefact in your system-local maven repository.

    <dependency>
        <groupId>uk.org.taverna.server</groupId>
        <artifactId>server-client</artifactId>
        <version>2.5.5-SNAPSHOT</version>
    </dependency>

That should be quite fully featured enough to support generating 
provenance (as part of the run bundle) provided you ask for it; you're 
still expected to understand the general server usage patterns, which 
are documented online currently at:

    http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+Server+2.5

What we (well, probably I) will do next is to update the build so that a 
proper client artefact is produced that doesn't have explicit 
dependencies on other parts of the server build (currently it uses a 
supporting library for handling Resource Usage Records) and get 2.5.5 
released so that we can have an actual artefact that we can point to, 
rather than some sort of SNAPSHOT.

Oh, and you *might* be able to use the build in our Artifactory:

http://repository.mygrid.org.uk/artifactory/libs-snapshot-local/uk/org/taverna/server/server-client/2.5.5-SNAPSHOT/server-client-2.5.5-20150304.170355-11.jar

That's not a long-term guaranteed URL and I don't know if it has all the 
dependencies you need. But maybe it will work? :-)

Donal.

Re: A few questions before choosing Taverna for our project

Posted by alaninmcr <al...@googlemail.com>.
I've started a hangout. If anyone else wants to join, the URL is 
https://plus.google.com/hangouts/_/gwg7xzlz4c6cyabi5popr6mohma

Alan

RE: A few questions before choosing Taverna for our project

Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Can we start hangout ? 

-----Original Message-----
From: Donal K. Fellows [mailto:donal.k.fellows@manchester.ac.uk] 
Sent: Friday, April 10, 2015 3:21 PM
To: Ahmad Aburomman
Cc: users@taverna.incubator.apache.org; Alan Williams
Subject: Re: A few questions before choosing Taverna for our project

On 06/04/2015 11:37, Ahmad Aburomman wrote:
> I modify the project of Vitor, here is the function:
> https://github.com/AhmadUsc/Java/blob/197819f798184721260789644f883221
> d166bb78/javaClient#L66
>
> Okay I didn't touch Baclava, I added Enable Provenance function I got 
> the zip bundle but it was empty.
>
> Can you Vitor regenerate the code with provenance data enabling ?
> Here is Vitor project:
> https://github.com/pgcc/taverna-java-client

We were wondering whether you want a Google hangout so that you can discuss this with us. Perhaps sometime on Monday? That is, on 13/04/2015, some time between 0900 GMT and 1500 GMT, at least for preference. We can do other times by arrangement too (in which case we'll set up a doodle poll to arrange things) but they're the ones we can do with minimum fuss. :-)

Donal.

Re: A few questions before choosing Taverna for our project

Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 06/04/2015 11:37, Ahmad Aburomman wrote:
> I modify the project of Vitor, here is the function:
> https://github.com/AhmadUsc/Java/blob/197819f798184721260789644f883221d166bb78/javaClient#L66
>
> Okay I didn't touch Baclava, I added Enable Provenance function
> I got the zip bundle but it was empty.
>
> Can you Vitor regenerate the code with provenance data enabling ?
> Here is Vitor project:
> https://github.com/pgcc/taverna-java-client

We were wondering whether you want a Google hangout so that you can 
discuss this with us. Perhaps sometime on Monday? That is, on 
13/04/2015, some time between 0900 GMT and 1500 GMT, at least for 
preference. We can do other times by arrangement too (in which case 
we'll set up a doodle poll to arrange things) but they're the ones we 
can do with minimum fuss. :-)

Donal.