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Posted to dev@taverna.apache.org by Edi KARADUMI <ed...@gmail.com> on 2016/04/18 14:09:14 UTC
Adding geospatial services to Taverna
Greetings,
My name is Edi Karadumi. I am pursuing a Master Degree in Software
Engineering at the University of Manchester.
The aim of my dissertation project is to add geospatial services based on
The Open Geospatial Consortium (OGC) standards to Taverna. Firstly, a
plugin that invokes and discovers OGC Web Processing Services (WPS) will be
implemented. Therefore, Taverna users will be able to discover WPS services
from a user specified wps server, configure it, and then execute it. The
project will be extended further to support OGC Web Map Servies and OGC
Sensor Observation Services.
A generic approach will be developed in order to support most of OGC
service standards. The plugin will be developed for Taverna 2.5, and after
that it will be migrated to the most recent development of Taverna 3.
If you are interested in this functionality, I welcome any
suggestions and, especially, offers to test my work
Kind Regards,
Edi Karadumi
Re: Adding geospatial services to Taverna
Posted by Stian Soiland-Reyes <st...@apache.org>.
Yes!
For Taverna 2:
http://dev.mygrid.org.uk/wiki/display/developer/1.+Create+project+from+archetype
For Taverna 3:
Documentation is missing :-(
but it should be something like
mvn archetype:generate -DarchetypeGroupId=org.apache.taverna.engine
-DarchetypeArtifactId=taverna-activity-archetype
-DarchetypeVersion=3.1.0-incubating-SNAPSHOT
-DarchetypeRepository=http://repository.apache.org/snapshots
On 30 April 2016 at 04:13, Edi Karadumi <ed...@gmail.com> wrote:
> Hi,
>
> Is there any maven archetype that creates the structure of the project like
> the samples illustrated in Taverna plugin tutorials?
>
>
>
> On Wed, Apr 27, 2016 at 9:58 AM, Stian Soiland-Reyes <st...@apache.org>
> wrote:
>
>> Edi,
>>
>> A new Git repository now ready for your pull requests:
>>
>> https://github.com/apache/incubator-taverna-plugin-gis/
>>
>> Feel free to suggest other modules and replace their poms.
>>
>> On 25 April 2016 at 18:18, Stian Soiland-Reyes <st...@apache.org> wrote:
>> > I've requested new git repository incubator-taverna-plugin-gis
>> >
>> > https://issues.apache.org/jira/servicedesk/agent/INFRA/issue/INFRA-11740
>> > https://issues.apache.org/jira/servicedesk/agent/INFRA/issue/INFRA-11741
>> >
>> >
>> > On 22 April 2016 at 16:09, Edi KARADUMI <ed...@gmail.com> wrote:
>> >> I would go for taverna-plugin-gis as it gives more information to the
>> >> users.Whereas ogc are the standards that will be supported by the plugin
>> >> (which different users might not now).
>> >>
>> >> On Fri, Apr 22, 2016 at 3:51 PM, Stian Soiland-Reyes <st...@apache.org>
>> >> wrote:
>> >>
>> >>> OK.. so what do you think would be a good plugin name then?
>> >>> taverna-plugin-ogc or taverna-plugin-gis ?
>> >>>
>> >>> On 22 April 2016 at 15:13, Edi KARADUMI <ed...@gmail.com> wrote:
>> >>> >>
>> >>> >>
>> >>> >> Are OGC services pretty common/generic, or is it something more
>> domain
>> >>> >> specific (e.g. warranting a incubator-taverna-plugin-geo ) ?
>> >>> >>
>> >>> >>
>> >>> > OGC services are used to build Geographical Information Systems.
>> There
>> >>> > might be an exception with Web Processing Services (WPS) which
>> provide
>> >>> > rules for standardizing input and output for geospatial processing
>> >>> > services, but can also be used in a generic way
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> 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
>>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Adding geospatial services to Taverna
Posted by Edi Karadumi <ed...@gmail.com>.
Hi,
Is there any maven archetype that creates the structure of the project like
the samples illustrated in Taverna plugin tutorials?
On Wed, Apr 27, 2016 at 9:58 AM, Stian Soiland-Reyes <st...@apache.org>
wrote:
> Edi,
>
> A new Git repository now ready for your pull requests:
>
> https://github.com/apache/incubator-taverna-plugin-gis/
>
> Feel free to suggest other modules and replace their poms.
>
> On 25 April 2016 at 18:18, Stian Soiland-Reyes <st...@apache.org> wrote:
> > I've requested new git repository incubator-taverna-plugin-gis
> >
> > https://issues.apache.org/jira/servicedesk/agent/INFRA/issue/INFRA-11740
> > https://issues.apache.org/jira/servicedesk/agent/INFRA/issue/INFRA-11741
> >
> >
> > On 22 April 2016 at 16:09, Edi KARADUMI <ed...@gmail.com> wrote:
> >> I would go for taverna-plugin-gis as it gives more information to the
> >> users.Whereas ogc are the standards that will be supported by the plugin
> >> (which different users might not now).
> >>
> >> On Fri, Apr 22, 2016 at 3:51 PM, Stian Soiland-Reyes <st...@apache.org>
> >> wrote:
> >>
> >>> OK.. so what do you think would be a good plugin name then?
> >>> taverna-plugin-ogc or taverna-plugin-gis ?
> >>>
> >>> On 22 April 2016 at 15:13, Edi KARADUMI <ed...@gmail.com> wrote:
> >>> >>
> >>> >>
> >>> >> Are OGC services pretty common/generic, or is it something more
> domain
> >>> >> specific (e.g. warranting a incubator-taverna-plugin-geo ) ?
> >>> >>
> >>> >>
> >>> > OGC services are used to build Geographical Information Systems.
> There
> >>> > might be an exception with Web Processing Services (WPS) which
> provide
> >>> > rules for standardizing input and output for geospatial processing
> >>> > services, but can also be used in a generic way
> >>>
> >>>
> >>>
> >>> --
> >>> 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
>
Re: Adding geospatial services to Taverna
Posted by Stian Soiland-Reyes <st...@apache.org>.
Edi,
A new Git repository now ready for your pull requests:
https://github.com/apache/incubator-taverna-plugin-gis/
Feel free to suggest other modules and replace their poms.
On 25 April 2016 at 18:18, Stian Soiland-Reyes <st...@apache.org> wrote:
> I've requested new git repository incubator-taverna-plugin-gis
>
> https://issues.apache.org/jira/servicedesk/agent/INFRA/issue/INFRA-11740
> https://issues.apache.org/jira/servicedesk/agent/INFRA/issue/INFRA-11741
>
>
> On 22 April 2016 at 16:09, Edi KARADUMI <ed...@gmail.com> wrote:
>> I would go for taverna-plugin-gis as it gives more information to the
>> users.Whereas ogc are the standards that will be supported by the plugin
>> (which different users might not now).
>>
>> On Fri, Apr 22, 2016 at 3:51 PM, Stian Soiland-Reyes <st...@apache.org>
>> wrote:
>>
>>> OK.. so what do you think would be a good plugin name then?
>>> taverna-plugin-ogc or taverna-plugin-gis ?
>>>
>>> On 22 April 2016 at 15:13, Edi KARADUMI <ed...@gmail.com> wrote:
>>> >>
>>> >>
>>> >> Are OGC services pretty common/generic, or is it something more domain
>>> >> specific (e.g. warranting a incubator-taverna-plugin-geo ) ?
>>> >>
>>> >>
>>> > OGC services are used to build Geographical Information Systems. There
>>> > might be an exception with Web Processing Services (WPS) which provide
>>> > rules for standardizing input and output for geospatial processing
>>> > services, but can also be used in a generic way
>>>
>>>
>>>
>>> --
>>> 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
Re: Adding geospatial services to Taverna
Posted by Stian Soiland-Reyes <st...@apache.org>.
I've requested new git repository incubator-taverna-plugin-gis
https://issues.apache.org/jira/servicedesk/agent/INFRA/issue/INFRA-11740
https://issues.apache.org/jira/servicedesk/agent/INFRA/issue/INFRA-11741
On 22 April 2016 at 16:09, Edi KARADUMI <ed...@gmail.com> wrote:
> I would go for taverna-plugin-gis as it gives more information to the
> users.Whereas ogc are the standards that will be supported by the plugin
> (which different users might not now).
>
> On Fri, Apr 22, 2016 at 3:51 PM, Stian Soiland-Reyes <st...@apache.org>
> wrote:
>
>> OK.. so what do you think would be a good plugin name then?
>> taverna-plugin-ogc or taverna-plugin-gis ?
>>
>> On 22 April 2016 at 15:13, Edi KARADUMI <ed...@gmail.com> wrote:
>> >>
>> >>
>> >> Are OGC services pretty common/generic, or is it something more domain
>> >> specific (e.g. warranting a incubator-taverna-plugin-geo ) ?
>> >>
>> >>
>> > OGC services are used to build Geographical Information Systems. There
>> > might be an exception with Web Processing Services (WPS) which provide
>> > rules for standardizing input and output for geospatial processing
>> > services, but can also be used in a generic way
>>
>>
>>
>> --
>> 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
Re: Adding geospatial services to Taverna
Posted by Edi KARADUMI <ed...@gmail.com>.
I would go for taverna-plugin-gis as it gives more information to the
users.Whereas ogc are the standards that will be supported by the plugin
(which different users might not now).
On Fri, Apr 22, 2016 at 3:51 PM, Stian Soiland-Reyes <st...@apache.org>
wrote:
> OK.. so what do you think would be a good plugin name then?
> taverna-plugin-ogc or taverna-plugin-gis ?
>
> On 22 April 2016 at 15:13, Edi KARADUMI <ed...@gmail.com> wrote:
> >>
> >>
> >> Are OGC services pretty common/generic, or is it something more domain
> >> specific (e.g. warranting a incubator-taverna-plugin-geo ) ?
> >>
> >>
> > OGC services are used to build Geographical Information Systems. There
> > might be an exception with Web Processing Services (WPS) which provide
> > rules for standardizing input and output for geospatial processing
> > services, but can also be used in a generic way
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
Re: Adding geospatial services to Taverna
Posted by Stian Soiland-Reyes <st...@apache.org>.
OK.. so what do you think would be a good plugin name then?
taverna-plugin-ogc or taverna-plugin-gis ?
On 22 April 2016 at 15:13, Edi KARADUMI <ed...@gmail.com> wrote:
>>
>>
>> Are OGC services pretty common/generic, or is it something more domain
>> specific (e.g. warranting a incubator-taverna-plugin-geo ) ?
>>
>>
> OGC services are used to build Geographical Information Systems. There
> might be an exception with Web Processing Services (WPS) which provide
> rules for standardizing input and output for geospatial processing
> services, but can also be used in a generic way
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Adding geospatial services to Taverna
Posted by Edi KARADUMI <ed...@gmail.com>.
>
>
> Are OGC services pretty common/generic, or is it something more domain
> specific (e.g. warranting a incubator-taverna-plugin-geo ) ?
>
>
OGC services are used to build Geographical Information Systems. There
might be an exception with Web Processing Services (WPS) which provide
rules for standardizing input and output for geospatial processing
services, but can also be used in a generic way
Re: Adding geospatial services to Taverna
Posted by Stian Soiland-Reyes <st...@apache.org>.
On 22 April 2016 at 14:28, alaninmcr <al...@googlemail.com> wrote:
> I think you now just start issuing pull requests :)
Alan - do you think we should make an OGC branch on
https://github.com/apache/incubator-taverna-common-activities or make
a new git repository?
Are OGC services pretty common/generic, or is it something more domain
specific (e.g. warranting a incubator-taverna-plugin-geo ) ?
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Adding geospatial services to Taverna
Posted by alaninmcr <al...@googlemail.com>.
On 22/04/2016 13:48, Edi KARADUMI wrote:
> Hi,
>
> I sent the icla electronically and got the following reply:
>
> This message acknowledges receipt of your ICLA, which has been filed in the
> Apache Software Foundation records.
Yes and you are listed on
https://people.apache.org/unlistedclas.html
> If you have been invited as a committer, please advise the project PMC that
> your ICLA has been filed.
>
> Should I do anything else?
I think you now just start issuing pull requests :)
> Regards,
> Edi
Alan
Re: Adding geospatial services to Taverna
Posted by Edi KARADUMI <ed...@gmail.com>.
Hi,
I sent the icla electronically and got the following reply:
This message acknowledges receipt of your ICLA, which has been filed in the
Apache Software Foundation records.
If you have been invited as a committer, please advise the project PMC that
your ICLA has been filed.
Should I do anything else?
Regards,
Edi
On Tue, Apr 19, 2016 at 12:14 AM, Stian Soiland-Reyes <st...@apache.org>
wrote:
> On 18 April 2016 at 17:11, Edi KARADUMI <ed...@gmail.com> wrote:
>
> >> https://www.apache.org/licenses/icla.txt
> >> (You would need to send it to secretary@apache.org )
> > I am very happy to contribute to Apache Taverna.
>
> Hurray!
>
> > Do they need a hard copy of the Contributor License Agreement?
>
> If you have PGP/GPG, then you can do it fully electronically:
>
> 1) Make sure you have made a GPG key with your full name, and it has
> been published (gpg --send-key)
> 2) Fill in icla.txt in a text editor
> 3) Sign it with gpg --sign --armor --detach icla.txt
> 4) pre-flight check: gpg --verify icla.txt.asc
> 5) email both icla.txt and icla.txt.asc to secretary@apache.org
>
> See http://www.apache.org/dev/openpgp.html for details on gpg.
>
>
> or go old skool (probably faster, but more boring):
>
> 1) Fill in icla.txt in a text editor
> 2) Print and sign by hand
> 3a) scan and email to secretary@apache.org
> or
> 3b) send by fax (!)
>
> I can help you with fax/scan if you want; as I have the necessary
> training. :)
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
Re: Adding geospatial services to Taverna
Posted by Stian Soiland-Reyes <st...@apache.org>.
On 18 April 2016 at 17:11, Edi KARADUMI <ed...@gmail.com> wrote:
>> https://www.apache.org/licenses/icla.txt
>> (You would need to send it to secretary@apache.org )
> I am very happy to contribute to Apache Taverna.
Hurray!
> Do they need a hard copy of the Contributor License Agreement?
If you have PGP/GPG, then you can do it fully electronically:
1) Make sure you have made a GPG key with your full name, and it has
been published (gpg --send-key)
2) Fill in icla.txt in a text editor
3) Sign it with gpg --sign --armor --detach icla.txt
4) pre-flight check: gpg --verify icla.txt.asc
5) email both icla.txt and icla.txt.asc to secretary@apache.org
See http://www.apache.org/dev/openpgp.html for details on gpg.
or go old skool (probably faster, but more boring):
1) Fill in icla.txt in a text editor
2) Print and sign by hand
3a) scan and email to secretary@apache.org
or
3b) send by fax (!)
I can help you with fax/scan if you want; as I have the necessary training. :)
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Adding geospatial services to Taverna
Posted by Edi KARADUMI <ed...@gmail.com>.
On Mon, Apr 18, 2016 at 2:11 PM, Stian Soiland-Reyes <st...@apache.org>
wrote:
> Thank you for explaining your project!
>
> (BTW: Edi has already talked to me and Alan in person in Manchester
> about this work)
>
>
> I think it makes sense to start with 2.5 plugin as you say, and then
> adapt it for Taverna 3. This means you can try it out in a full
> workbench right away - as we have not yet release Apache Taverna 3
> workbench. Then you can update the code for 3.0 - the changes are
> mainly different package names and that it will run under OSGi rather
> than our own plugin system.
>
>
> Feel free to ask this list any questions during development of your
> plugin - I'm sure the other folk will also be able to help you.
>
Thank you
>
> You might also find it useful to follow this list as there are three
> potential Google Summer of Code students this year who would be
> developing Taverna and Taverna plugins as well (but for Common
> Workflow Language, Docker and Taverna Mobile)
>
>
I'm aware of that and I have been following your discussions.
>
> You'll probably find this tutorial useful for the Taverna 2.5 plugin:
>
>
> http://dev.mygrid.org.uk/wiki/display/developer/Creating+plugins+for+Taverna+2
I have already completed the plugin invocation and discovery tutorials. In
addition, I read the Development, releases and testing procedures tutorial.
Please feel free to suggest any other tutorials that might help.
> There is unfortunately not an updated plugin tutorial for 3.0 - which
> changes slightly how you do Activity configuration. If you keep your
> plugin using a Jackson JSONObject as a configuration bean - then it
> should be straight forwards to later update it for Taverna 3.
>
>
Ok. I will use JSONObject.
>
> Are you considering contributing your plugin to Apache Taverna? We
> would be very happy if you consider this - in which case I hope you
> would be OK to sign and send in a Contributor License Agreement to
> ASF:
>
> https://www.apache.org/licenses/icla.txt
>
> (You would need to send it to secretary@apache.org )
>
I am very happy to contribute to Apache Taverna.
Do they need a hard copy of the Contributor License Agreement?
>
> If you do this earlier, it makes it easier for us to accept your code
> early rather than requiring an additional Intellectual Property
> clearance process at the end of your project. (BTW - this is the
> pattern we have used for Google Summer of Code students)
>
>
> If contributed, your plugin would need to use dependencies that are
> compatible with the Apache license -
> http://www.apache.org/legal/resolved.html - in short GPL and LGPL are
> not allowed, but pretty much anything open source is OK as a pom.xml
> dependency. Inclusion of third-party work in the source code is much
> trickier area - avoid this if possible.
>
>
>
>
> On 18 April 2016 at 13:09, Edi KARADUMI <ed...@gmail.com> wrote:
> > Greetings,
> >
> > My name is Edi Karadumi. I am pursuing a Master Degree in Software
> > Engineering at the University of Manchester.
> >
> > The aim of my dissertation project is to add geospatial services based on
> > The Open Geospatial Consortium (OGC) standards to Taverna. Firstly, a
> > plugin that invokes and discovers OGC Web Processing Services (WPS) will
> be
> > implemented. Therefore, Taverna users will be able to discover WPS
> services
> > from a user specified wps server, configure it, and then execute it. The
> > project will be extended further to support OGC Web Map Servies and OGC
> > Sensor Observation Services.
> >
> > A generic approach will be developed in order to support most of OGC
> > service standards. The plugin will be developed for Taverna 2.5, and
> after
> > that it will be migrated to the most recent development of Taverna 3.
> >
> > If you are interested in this functionality, I welcome any
> > suggestions and, especially, offers to test my work
> >
> > Kind Regards,
> > Edi Karadumi
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
Re: Adding geospatial services to Taverna
Posted by Stian Soiland-Reyes <st...@apache.org>.
Thank you for explaining your project!
(BTW: Edi has already talked to me and Alan in person in Manchester
about this work)
I think it makes sense to start with 2.5 plugin as you say, and then
adapt it for Taverna 3. This means you can try it out in a full
workbench right away - as we have not yet release Apache Taverna 3
workbench. Then you can update the code for 3.0 - the changes are
mainly different package names and that it will run under OSGi rather
than our own plugin system.
Feel free to ask this list any questions during development of your
plugin - I'm sure the other folk will also be able to help you.
You might also find it useful to follow this list as there are three
potential Google Summer of Code students this year who would be
developing Taverna and Taverna plugins as well (but for Common
Workflow Language, Docker and Taverna Mobile)
You'll probably find this tutorial useful for the Taverna 2.5 plugin:
http://dev.mygrid.org.uk/wiki/display/developer/Creating+plugins+for+Taverna+2
There is unfortunately not an updated plugin tutorial for 3.0 - which
changes slightly how you do Activity configuration. If you keep your
plugin using a Jackson JSONObject as a configuration bean - then it
should be straight forwards to later update it for Taverna 3.
Are you considering contributing your plugin to Apache Taverna? We
would be very happy if you consider this - in which case I hope you
would be OK to sign and send in a Contributor License Agreement to
ASF:
https://www.apache.org/licenses/icla.txt
(You would need to send it to secretary@apache.org )
If you do this earlier, it makes it easier for us to accept your code
early rather than requiring an additional Intellectual Property
clearance process at the end of your project. (BTW - this is the
pattern we have used for Google Summer of Code students)
If contributed, your plugin would need to use dependencies that are
compatible with the Apache license -
http://www.apache.org/legal/resolved.html - in short GPL and LGPL are
not allowed, but pretty much anything open source is OK as a pom.xml
dependency. Inclusion of third-party work in the source code is much
trickier area - avoid this if possible.
On 18 April 2016 at 13:09, Edi KARADUMI <ed...@gmail.com> wrote:
> Greetings,
>
> My name is Edi Karadumi. I am pursuing a Master Degree in Software
> Engineering at the University of Manchester.
>
> The aim of my dissertation project is to add geospatial services based on
> The Open Geospatial Consortium (OGC) standards to Taverna. Firstly, a
> plugin that invokes and discovers OGC Web Processing Services (WPS) will be
> implemented. Therefore, Taverna users will be able to discover WPS services
> from a user specified wps server, configure it, and then execute it. The
> project will be extended further to support OGC Web Map Servies and OGC
> Sensor Observation Services.
>
> A generic approach will be developed in order to support most of OGC
> service standards. The plugin will be developed for Taverna 2.5, and after
> that it will be migrated to the most recent development of Taverna 3.
>
> If you are interested in this functionality, I welcome any
> suggestions and, especially, offers to test my work
>
> Kind Regards,
> Edi Karadumi
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718