Re: Release Taverna Language?

Hi, I was able to build this repository using java 9 *without* *tests*. But with test build fails at *Apache Taverna RO Bundle API *module. I have attached the maven log for both builds. On Mon, Apr 23, 2018 at 11:49 PM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > Hi Stain,

Re: TAVERNA-550

Hi, This failure is caused by taverna-app-configuration-impl module where "taverna.app.startup" system property is not initialized at runtime. This is the implementation

Re: TAVERNA-550

welcome Upeksha !. Here you can find instructions regarding contributing https://taverna.incubator.apache.org/download/code/#contribute-to-apache-taverna In this case you have to build taverna-common-activities and taverna-workbench

CWL Pre Processing: $Import resolving

Hi all, I have been working on the $subject. Please review the PR . I think we should come up with a better architecture for this. All suggestions are welcome !. Also CWL import can be represented as a

Re: Welcome Thilina!

Hi Menaka, Thank you very much !! Regards, Thilina

Re: To pull or not to pull

HI, I think this is a good idea. There may be mistakes in my code because still i am not a expert thus code review is a good approach. Regards, Thilina On Thu, Nov 3, 2016 at 10:05 PM, Ian Dunlop wrote: > Hello, > > I think we need a policy decision on how to add new

Re: Welcome Thilina!

Hi, Thank you very much ! Regards, Thilina On Mon, Sep 26, 2016 at 5:31 AM, Gale Naylor <ga...@noventussolutions.com> wrote: > Welcome! > > On Sun, Sep 25, 2016, 4:59 PM Stian Soiland-Reyes <st...@apache.org> > wrote: > > > The Apache Taverna PPMC is pleased t

Re: incubator-taverna-workbench license issues

think it's any point in doing paperwork for. > > I think we might have to replace them. They were never particularly > intuitive anyway! > > Could we draw a 16x16 pixel of just a . and + perhaps? Leaf node can > just be a ">" ? Feel free to use a colour. > > > O

incubator-taverna-workbench license issues

ducticon.png 3. https://github.com/apache/incubator-taverna-workbench/blob/master/taverna-iteration-strategy-ui/src/main/resources/org/apache/taverna/workbench/iterationstrategy/icons/leafnodeicon.png If the initial committer can clarify copyrights of these files that would be great !. Tha

Re: Move taverna-perspective-biocatalogue to GitHub?

Hi, I think that's a good idea. We can fix those license issue seperatly and bring it back. Thanks, Thilina On Wed, Sep 21, 2016 at 8:21 PM, Ian Dunlop wrote: > Hello, > > They can still use the web services - just takes a little bit more effort > since they have to

Re: Replace the #taverna IRC channel with Gitter webchat?

Hi this is a really good idea ! On Fri, Sep 16, 2016 at 10:26 PM, Gale Naylor wrote: > I signed up and signed it. Looks interesting. > > On Fri, Sep 16, 2016 at 3:54 AM Stian Soiland-Reyes > wrote: > > > Hi, > > > > On

Re: No apache License headers in taverna-workbench module

HI, I can help with that. If you can guide me through the process :) thanks, Thilina. On Thu, Sep 8, 2016 at 5:27 AM, Gale Naylor wrote: > >>Any volunteers? We can add sections at the >>end of the wiki with the > >>rat output for each. > > Volunteers to manually

Re: CWL code questions

Hi, Thanks for pointing that out. I have fixed them https://github.com/apache/incubator-taverna-common-activities/pull/13 Thanks ! On Thu, Aug 4, 2016 at 12:18 AM, Gale Naylor wrote: > I have a couple of questions about the CWL code. > > (1) In

CWL contextual View class tests

Hi, i need to create this "*new CwlContextualView(activity,colourManager)*" but i can't set the configuration for the activity object. activity object is a instance of *org.apache.taverna.scufl2.api.activity.Activity.* regards, Thilina

Re: Wiki access?

HI, Thank you very much ! . Which one should i select for tutorial(Upgrading Taverna Ui plugin to Taverna version 3) ?. "Blank page" or "How-to article" ? regards, Thilina On Thu, Jul 21, 2016 at 10:42 PM, Gale Naylor wrote: > I just added user maanafunedu. > >

Re: [GitHub] incubator-taverna-maven-parent pull request #4: TAVERNA-1003 : fixed the dep...

Hi, sorry for the late response. I have modified this also https://github.com/apache/incubator-taverna-osgi/pull/1. regards, Thilina On Fri, Jul 15, 2016 at 9:55 PM, Stian Soiland-Reyes wrote: > Thanks! > > You seem to have added an extra pom.xml~ > > It's good to check

Configurable Service Provider

Hi stain, ConfigurableServiceProvider interface cannot have static methods unless the JRE is 1.8. If it is 1.8 then what should be the Configuration ? regards, Thilina

Re: [jira] [Commented] (TAVERNA-990) Fix compile errors in taverna-configuration-impl

Hi, This error occurs due to the nullpointer in the package org.apache.taverna.configuration.app.impl ApplicationConfigurationImpl class. System.getProperty(APP_STARTUP) line is returning null since there is no system property called "taverna.app.home" listed. Before calling this function,

Re: [GSOC] Bumped taverna-common-activities version

=0B86Wyi6fP3OBN0xMclgtOHlXLXc regards, Thilina. On Fri, Jul 1, 2016 at 2:39 AM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > Hi, > > when " mvn -U clean install" executed : > > [ERROR] Failed to execute goal on project taverna-cwl-activity: Could not >

Re: [jira] [Assigned] (TAVERNA-989) Fix compile errors in taverna-activity-palette-impl

Hi, I have fixed the bug in ServiceDescriptionRegistryImpl class. i found this bug when i try to build, Compilation failure: [ERROR]

Re: CWL Browser: File vs Path when parsing *.cwl

. Although workbench runs it doesn't recognize CWL Ui plugin. Import service doesn't contain CWL Service ? regards,, Thilina. On Mon, Jun 27, 2016 at 11:01 PM, Stian Soiland-Reyes <st...@apache.org> wrote: > On 27 June 2016 at 18:26, Thilina Manamgoda <maanafun...@gmail.com> wrote: >

Re: CWL port name

cates. (the final name is returned) > > > https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/common/NamedSet.html > > On 26 June 2016 at 15:34, Thilina Manamgoda <maanafun...@gmail.com> wrote: > > Hi, > > > > > > Any su

CWL port name

Hi, Any suggestions on how can i make a good port names in Taverna workbench. Because if the port name in CWL tool is too long it's going to be a problem. 1.What is the suitable number of characters that port name can have. 2. Removing space is one approach can anyone suggest more ? regards,

Re: CWL Browser: File vs Path when parsing *.cwl

her workbench ? How can i use log4j in my implementation ? regards, Thilina. On Fri, Jun 24, 2016 at 7:40 PM, Stian Soiland-Reyes <st...@apache.org> wrote: > On 24 June 2016 at 01:25, Thilina Manamgoda <maanafun...@gmail.com> wrote: > > Can you provide me the instruct

Re: CWL Browser: File vs Path when parsing *.cwl

Hi, i have tried this and this is the implementation https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/tree/stream . Any comments on how can i improve it more or change ?. Can you provide me the instruction to run this plugin inside the Taverna workbench. At the moment i

Re: CWL Service detail panel

Hi, i will rename "Utility" to "CWLUtil". For coming week i will do testing the plugin using these cwl tools as test subjects . Also make port name more suitable for taverna workbench and adding

CWL "format" tag

Hi stain, This is an example of how format is defined in cwl tool. $namespaces: dct: http://purl.org/dc/terms/ foaf: http://xmlns.com/foaf/0.1/ doap: http://usefulinc.com/ns/doap# adms: http://www.w3.org/ns/adms# dcat: http://www.w3.org/ns/dcat# edam: http://edamontology.org/ inputs: - id:

CWL Service detail panel

Hi, So last week i have been working on the cwl service panel. Here you can have a peek how it's going to be shown in the workbench. link These are the problems that i ran into : 1. I have changed the CWL

Taverna service decription

Hi, where can i set the description of a service in the workbench . for example service - "description" in the service panel ? regards , Thilina.

Re: [DISCUSS] The third RC of Taverna Command Line 3.1.0

i have updated the maven to 3.3.9 and i got this failure Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.18.1:test (default-test) on project taverna-credential-manager-impl: There are test failures. On Mon, Jun 6, 2016 at 10:01 PM, Alan Williams

Re: [DISCUSS] The third RC of Taverna Command Line 3.1.0

version is 3.0.5 On Mon, Jun 6, 2016 at 8:47 PM, Alan Williams wrote: > To answer Thilina's question on the VOTE thread, > > what version of Maven are you running? > > Alan > >

Re: [GitHub] incubator-taverna-common-activities issue #4: Cwl browse

Hi, So what is next step ? . i little confused about what do next . regards, Thilina. On Mon, Jun 6, 2016 at 7:12 PM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > are cropping,resizing considered as modifying > > On Mon, Jun 6, 2016 at 7:11 PM, Thilina Manamgoda <maa

Re: [GitHub] incubator-taverna-common-activities issue #4: Cwl browse

i just removed it and pushed it again On Mon, Jun 6, 2016 at 7:09 PM, stain wrote: > Github user stain commented on the issue: > > https://github.com/apache/incubator-taverna-common-activities/pull/4 > > Ah now, the CC SA for unmodifiable binaries, so OK as long

Re: [GitHub] incubator-taverna-common-activities issue #4: Cwl browse

are cropping,resizing considered as modifying On Mon, Jun 6, 2016 at 7:11 PM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > i just removed it and pushed it again > > > On Mon, Jun 6, 2016 at 7:09 PM, stain <g...@git.apache.org> wrote: > >> Github

Re: CWL Tool Description

Hi, how can i resolve the conflict. i can't see any conflict in my git account ? On Sat, Jun 4, 2016 at 5:25 PM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > Hi, > > No those are cwl files are not mine. but i can write few of them for > testing.The "Testing&

Re: CWL Tool Description

hich > case you can also add ASF headers to those (using "# " comments). If > they come from elsewhere we have to be more careful - so it's better > if they are your own. :) > > On 4 June 2016 at 11:54, Thilina Manamgoda <maanafun...@gmail.com> wrote: > > Hi, > >

CWL Tool Description

Hi, I have made the pull request on github .please tell me am i doing it correct or not. regards, thilina

apache-taverna-engine-3.1.0-incubating build failure

Hi , when i execute mvn clean install it give build failure.This is the log file . regards, Thilina.

Re: Taverna -CWL tool description 880

Hi , i have made a pull request and current progress on this blog <http://maanadevgsoc2016.blogspot.com/> . regards, Thilina On Tue, May 24, 2016 at 11:10 AM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > Hi, > There is way to parse cwl using Snakeyaml. i have to map t

Re: Podling Report Reminder - June 2016

Hi, i am 2016 GSOC student .Do i need to submit this report ? regards, Thilina. On Tue, May 31, 2016 at 10:27 PM, wrote: > Dear podling, > > This email was sent by an automated system on behalf of the Apache > Incubator PMC. It is an initial reminder to give you plenty

Re: Taverna-cwl tool description

On Sun, May 29, 2016 at 12:35 AM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > Hi , > > addInput(IN_FIRST_INPUT, 0, true, null, String.class); > > when addInput method is called i should pass the class which is, the > inputs are going to be rendered. In the tu

Re: Taverna-cwl tool description

work requires proxy settings, in which case you have to > configure Java/Maven about those. > On 25 May 2016 11:40 p.m., "Thilina Manamgoda" <maanafun...@gmail.com> > wrote: > > > Hi, > > > > I ran into this problem when i

Re: Taverna-cwl tool description

Hi, This a try to get CWL services into the workbench. https://github.com/ThilinaManamgoda/exampletool. regards, Thilina On Thu, May 26, 2016 at 3:27 AM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > Hi, > > I ran into this problem when i execute "mvn install"

Taverna CWL plugin 880

Hi , So tutorial ( http://dev.mygrid.org.uk/wiki/display/developer/3.+Configuring+the+service+instance) show example of how to configure an Activity. Does configuring Input and Output ports enough for CWL Activity to work ?. regards, Thilina.

Taverna -CWL tool description 880

Hi, Michael has proposed a new approach to read cwl tool description using cwl in build preprocessing tool ( https://github.com/common-workflow-language/cwljava/issues/13) . In this way we can read JSON description of a cwl tool. Any comments ? regards, Thilina.

Re: GSOC git branches

Hi , This is my blog for this Gsoc project ( http://maanadevgsoc2016.blogspot.com/). every thing i do will be updated there . Thanks. On Sat, Apr 30, 2016 at 9:25 AM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > Hi stian, > > my ICLA has been filed. > > > On We

Re: GSOC git branches

nything more) > > >> > > >> > > >> Some links: > > >> > > >> http://swcarpentry.github.io/git-novice/ > > >> https://guides.github.com/activities/hello-world/ > > >> https://guides.github.com/activities/contributi

Re: GSOC Taverna call today or tomorrow ?

hi, Sorry for the late . is it now late to do that or can i still be part of that process ?. if so please let me know when should i join .(Please be specific about the TIMEZONE when your saying the time ) regards , Thilina. On Fri, Apr 8, 2016 at 5:56 PM, alaninmcr

Re: GSOC: Add CWL support to Taverna

edule for exams - I assume this also > includes time to prepare for those exams? > > > On 22 March 2016 at 11:03, Thilina Manamgoda <maanafun...@gmail.com> > wrote: > > Hi, > > > > Do i need to add working hours per week in the proposal ? > > >

Re: GSOC: Add CWL support to Taverna

with CWL community when creating YAML parser is that okay ? 4) Don't i need to change proposal and put these details in.Also about Time management ,can you tell me whether i did write or wrong On Tue, Mar 22, 2016 at 5:27 PM, alaninmcr <alanin...@googlemail.com> wrote: > On 22/03/2016 11:46

Re: GSOC: Add CWL support to Taverna

wrote: > On 21/03/2016 19:44, Thilina Manamgoda wrote: > >> Hi, >> Did you get my proposal ?.Can you comment what improvements are needed or >> my approach is correct or wrong ? >> > > Good proposal. > > I think testing should have a greater profile in the pr

Re: GSOC: Add CWL support to Taverna

Hi, Do i need to add working hours per week in the proposal ? regards Thilina. On Tue, Mar 22, 2016 at 1:15 AM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > > -- Forwarded message ------ > From: Thilina Manamgoda <maanafun...@gmail.com> > Date: Tue,

Project Proposal GSOC 2016 - TAVERNA-880 Browse+use CWL tool descriptions - Invitation to edit

I've shared an item with you: Project Proposal GSOC 2016 - TAVERNA-880 Browse+use CWL tool descriptions https://docs.google.com/document/d/1knZSoKN-2oW7ljYwz5UFkcwjtd0tYRBs_zGsYBupx6U/edit?usp=sharing=CKLT24YO=56f04eaf It's not an attachment -- it's stored online. To open this item, just click

Fwd: GSOC: Add CWL support to Taverna

-- Forwarded message -- From: Thilina Manamgoda <maanafun...@gmail.com> Date: Tue, Mar 22, 2016 at 1:14 AM Subject: Re: GSOC: Add CWL support to Taverna To: dev@taverna.incubator.apache.org Hi, Did you get my proposal ?.Can you comment what improvements are needed or my ap

Re: GSOC: Add CWL support to Taverna

es, and the types of its parameters. This for a collection of CWL tools > the annotations can also be used to search or categorize the tools. > > CWL folks area also looking at using DOAP and schema.org for generic > metadata like project info. I'll try to dig out some examples.

Re: GSOC: Add CWL support to Taverna

> to cover any of 878 that would a real bonus. Don't get distracted by it > though. Aim for the achievable, not the impossible. > > Cheers > > Ian > On 16 Mar 2016 5:47 pm, "Thilina Manamgoda" <maanafun...@gmail.com> wrote: > > > Hi, > > >

Re: GSOC: Add CWL support to Taverna

? regards , Thilina. On Tue, Mar 15, 2016 at 8:24 PM, Thilina Manamgoda <maanafun...@gmail.com> wrote: > Hi, > > > On Tue, Mar 15, 2016 at 8:00 PM, Stian Soiland-Reyes <st...@apache.org> > wrote: > >> On 15 March 2016 at 08:07, Thilina Manamgoda <maanafun...@g

Re: GSOC: Add CWL support to Taverna

Hi, On Tue, Mar 15, 2016 at 8:00 PM, Stian Soiland-Reyes <st...@apache.org> wrote: > On 15 March 2016 at 08:07, Thilina Manamgoda <maanafun...@gmail.com> > wrote: > > > I have gone through the tutorials Service invocation plugin > > < > http://dev.mygrid

Re: GSOC: Add CWL support to Taverna

Hi , I have gone through the tutorials Service invocation plugin and Service discovery plugin . So in order to bring CWL

Re: GSOC: Add CWL support to Taverna

HI , Thanks for quick response.I am Thilina Manamgoda third year undergraduate of Computer Engineering ,University of Peradeniya.I live in town called Matale in Sri Lanka.This our faculty web site :http://www.ce.pdn.ac.lk/ .I have done IOT backend server project in my short semester and several

Re: GSOC: Add CWL support to Taverna

On 27-Feb-16 09:05, Thilina Manamgoda wrote: > >> HI, >> > > Hello > > Source: https://issues.apache.org/jira/browse/TAVERNA-900 >> >> I am Thilina Manamgoda undergraduate from University of Perandeniya. I >> would like to contribute this project for