Re: Taverna Mobile play store release.

[alaninmcr]

On 28/07/2017 08:01, Sagar wrote:

Hi,


Hello


For generating Key Store certification, I need following details

- First and Last name
- Organizational unit
- Organization
- City or Locality
- State or Province
- Country Code

Please provide me with the details.


I assume that is for Apache. I think we may need to ask on
legal-disc...@apache.org . What do others think?

Alan

Taverna 2.5 SSL issue

[alaninmcr]

Hello everybody

I have been trying to find a workaround for a user's problem with the 
NCBI localworkers no longer working. Switching from HTTP to HTTPS was 
not sufficient as Taverna 2.5 would then complain about the "prime size 
must be multiple of 64".


Having gone down a rabbit hole of Java 8, I found a workaround for Java 
7, which is to remove the lines in taverna.bat and taverna.vmoptions 
that set


com.sun.net.ssl.enableECC to false

Removing those lines makes the localworkers work (after the change to 
HTTPS).


Does anyone see a problem with recommending this as a solution to the user?

Alan

Presentations on the Taverna website

[alaninmcr]

Hello everyone

Is there anywhere on the Taverna website to put links to presentations? 
There is an interesting talk I'd like to link to.


Alan

Secured services in Taverna 2.5 packs

[alaninmcr]

Hello Aleks and others

The secured workflows in the Taverna 2.5 starter packs no longer work 
(the services are no longer running).


Can you remove http://www.myexperiment.org/workflows/4216.html and 
http://www.myexperiment.org/workflows/4217.html from the packs?


Alan

Re: Taverna server and users

[alaninmcr]

On 02/12/2016 15:14, Ian Dunlop wrote:

Hello,

Well I guess my question is now "How do you authenticate against it". Is
it basic auth


Yes it is basic auth.


http://username:passw...@tavernaserver.com ?


That's not how I do the auth, but it looks right.


Cheers,

Ian


Alan

Re: Taverna server and users

[alaninmcr]

On 02/12/2016 12:55, Ian Dunlop wrote:

Hello,


Hello Ian


I've figured out how to secure it and admin it to add users but I
haven't managed to figure out how you tell the server that a run is for
a specific user. I guess it is something  around "Resource:
/runs/{id}/security" but I can't figure out what.


I'm not sure I understand the problem. Isn't the run "for" the user who 
authenticates and creates the run?



What is the "workflow"
for telling the server that a run is created for a specific user so that
no one else can see it? Is there a user guide rather than the API listing?

I think if we want Apache to set up a tavserv for us then we will need
this per user auth. Plus we will need it if we want to use it directly
from TavMob rather than via the player portal.

Cheers,

Ian


Alan

Re: Move taverna-perspective-biocatalogue to GitHub?

[alaninmcr]

On 21/09/2016 13:26, Stian Soiland-Reyes wrote:
[snip]


I don't know how much the Biocatalogue perspective is used in Taverna
2.5 - I know it can be very useful to find and use lots of web
services - so arguably it would be a bit of a loss. It also has lots
of code to replicate in Java Swing what is also on the
biocatalogue.org website - that is perhaps not as needed.


My long-standing opinion is that Taverna should not attempt to replicate 
a website, whether biocatalogue or myExperiment :)



What's your take?


I agree with moving it out to extras.

Alan

Re: taverna exit code

[alaninmcr]

On 16/09/2016 09:44, Stian Soiland-Reyes wrote:

[snip]


It's configurable to allow certain exit codes, but this is not exposed
in the UI.


It _is_ in the UI. It's under the "Command" tab in the field "Valid 
return codes". However, I think that Simone wants it to fail rather than 
be valid.


[snip]

Alan

Re: Taverna Player Portal JSON API queries ( Apache Taverna Mobile )

[alaninmcr]

On 08/09/2016 10:56, Sagar wrote:

Hi,


Hello Sagar


I was reading the readme and I found Taverna-language-API will only work
with JAVA 8 and newer.
We can't use in taverna-mobile because Android API 16 works with JAVA 6.

So, Now provide me with the schema of the .t2flow file.


There is a set of xsds in

/src/main/resources/org/apache/taverna/scufl2/translator/t2flow/xsd

within taverna-scufl2-t2flow in the incubator-taverna-language repository.


Thanks


Alan

Re: Removing (c) Manchester license headers - Copyright Cardiff?

[alaninmcr]

On 07/09/2016 12:49, Stian Soiland-Reyes wrote:

[snip]


// Copyright (C) 2008 The University of Manchester, University of Southampton
// and Cardiff University
package org.apache.taverna.ui.perspectives.myexperiment.model;

This is in various files in the myExperiment plugin, e.g.

https://github.com/apache/incubator-taverna-workbench/search?utf8=%E2%9C%93&q=Cardiff


Do anyone remember why this particular copyright? Did Southampton and
Cardiff even contribute here?


Not as far as I know. Southampton did work on myExperiment itself but 
not on the Taverna side.



Did they not sign the CLAs to
Manchester?


I have checked the CLAs that I have but they are all individual CLAs and 
so do not include Southampton and Cardiff universities (institutions).



What's odd is that the @author hints at Manchester folks, e.g.


* @author Jiten Bhagat, Sergejs Aleksejevs


Yes - Manchester folk :)

Alan

Re: change OperatingLimit and MaxRuns default values

[alaninmcr]

Hello Simone

Donal tells me that the values can be changed in the administration web 
GUI at https://some.host:8443/tavernaserver/admin/


Alan

Re: Docker Activity Plugin Enhancements

[alaninmcr]

Hello again Nadeesh

I noticed some problems with the messages in the health checker. It 
refers to REST activity, and also does not give a helpful message if the 
check fails. Can you fix those? Then I'll pull.


Alan

[GitHub] incubator-taverna-common-activities pull request #19: Docker activity health...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/19#discussion_r74689360
  
--- Diff: 
taverna-docker-activity/src/main/java/org/apache/taverna/activities/docker/DockerActivityHealthChecker.java
 ---
@@ -0,0 +1,48 @@
+package org.apache.taverna.activities.docker;
+
+import org.apache.taverna.visit.VisitReport;
+import org.apache.taverna.workflowmodel.health.HealthCheck;
+import org.apache.taverna.workflowmodel.health.HealthChecker;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class DockerActivityHealthChecker implements HealthChecker {
+
+@Override
+public boolean canVisit(Object o) {
+return o instanceof DockerActivity;
+}
+
+@Override
+public VisitReport visit(Object o, List list) {
+DockerActivity activity = (DockerActivity) o;
+DockerContainerConfiguration contCfg = 
activity.getContainerConfiguration();
+String containerName = contCfg.getName();
+boolean createValid = 
ValidationUtil.validateCreateContainer(contCfg, containerName);
+
+List reports = new ArrayList();
+
+if (createValid) {
+reports.add(new VisitReport(HealthCheck.getInstance(), 
activity,
+"Docker create container operation is healthy",
+HealthCheck.NO_PROBLEM, VisitReport.Status.OK));
+} else {
+reports.add(new VisitReport(HealthCheck.getInstance(), 
activity,
+"REST Activity - bad configuration",
+HealthCheck.INVALID_CONFIGURATION, 
VisitReport.Status.SEVERE));
+}
+
+// collection all reports together
+VisitReport.Status worstStatus = 
VisitReport.getWorstStatus(reports);
+VisitReport report = new VisitReport(HealthCheck.getInstance(), 
activity,
+"REST Activity Report", HealthCheck.NO_PROBLEM, 
worstStatus, reports);
--- End diff --

Why REST activity?


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[GitHub] incubator-taverna-common-activities pull request #19: Docker activity health...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/19#discussion_r74689358
  
--- Diff: 
taverna-docker-activity/src/main/java/org/apache/taverna/activities/docker/DockerActivityHealthChecker.java
 ---
@@ -0,0 +1,48 @@
+package org.apache.taverna.activities.docker;
+
+import org.apache.taverna.visit.VisitReport;
+import org.apache.taverna.workflowmodel.health.HealthCheck;
+import org.apache.taverna.workflowmodel.health.HealthChecker;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class DockerActivityHealthChecker implements HealthChecker {
+
+@Override
+public boolean canVisit(Object o) {
+return o instanceof DockerActivity;
+}
+
+@Override
+public VisitReport visit(Object o, List list) {
+DockerActivity activity = (DockerActivity) o;
+DockerContainerConfiguration contCfg = 
activity.getContainerConfiguration();
+String containerName = contCfg.getName();
+boolean createValid = 
ValidationUtil.validateCreateContainer(contCfg, containerName);
+
+List reports = new ArrayList();
+
+if (createValid) {
+reports.add(new VisitReport(HealthCheck.getInstance(), 
activity,
+"Docker create container operation is healthy",
+HealthCheck.NO_PROBLEM, VisitReport.Status.OK));
+} else {
+reports.add(new VisitReport(HealthCheck.getInstance(), 
activity,
+"REST Activity - bad configuration",
--- End diff --

Why does it say REST activity? Also the message should be more meaningful.


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Re: Docker Activity Plugin Enhancements

[alaninmcr]

On 10/08/2016 02:34, Nadeesh Dilanga wrote:

Hi Alan, Hi Stian,
I send a pull request with the Health Check feature for Docker Activity
Plugin. Please review and let me know if I need to change anything.


Hello Nadeesh,

It looks good to me. I will do the pull today or tomorrow.

Have you looked at biobox and how to run a biobox?

Alan

[GitHub] incubator-taverna-common-activities pull request #19: Docker activity health...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/19#discussion_r74689262
  
--- Diff: 
taverna-docker-activity/src/main/java/org/apache/taverna/activities/docker/DockerActivityHealthChecker.java
 ---
@@ -0,0 +1,48 @@
+package org.apache.taverna.activities.docker;
+
+import org.apache.taverna.visit.VisitReport;
+import org.apache.taverna.workflowmodel.health.HealthCheck;
+import org.apache.taverna.workflowmodel.health.HealthChecker;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class DockerActivityHealthChecker implements HealthChecker {
+
+@Override
+public boolean canVisit(Object o) {
+return o instanceof DockerActivity;
+}
+
+@Override
+public VisitReport visit(Object o, List list) {
+DockerActivity activity = (DockerActivity) o;
+DockerContainerConfiguration contCfg = 
activity.getContainerConfiguration();
+String containerName = contCfg.getName();
+boolean createValid = 
ValidationUtil.validateCreateContainer(contCfg, containerName);
--- End diff --

Does validateCreateContainer also destroy the container after it has been 
created? If not, then repeated validation could create a lot of useless 
containers


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Re: Taverna Player integration ( Apache Taverna Mobile )

[alaninmcr]

On 12/08/2016 18:43, Sagar wrote:

I have created curl request to run workflow according
to Taverna-Player-Portal JSON API Documentation


curl -X POST -H "Accept: application/json" -H "Content-Type:
application/json" -H "Cache-Control: no-cache" -d '{
  "run" :
  {
"workflow_id" : 4201,
"name" : "My Run"
  }
}' "http://139.59.28.201:3000/runs";


I can only see workflow 1 on the site http://139.59.28.201:3000/workflows/1


I am getting some error .

if the server is not running  then you can find error HTML page in the
attachment.


Attachments are (I think) stripped out by the mailing list software. So, 
your attachment did not come through. Looking at the behaviour on the 
player, it does appear that it is unable to connect to a server. Is one 
running?



Sagar


Alan

Re: Taverna Gis Plugin new branch

[alaninmcr]

On 12/08/2016 14:21, Stian Soiland-Reyes wrote:

[snip]


As a "just for reference" branch I didn't do any checks on your
dependencies used here, or check for the Apache file headers.


The GIS plugin depends on packages from 52north.org - a very widely used 
open source community. They have listed the licenses applicable for the 
WPS client:



Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

This project includes:
  52North WPS Algorithm API under Apache License, Version 2.0
  52North WPS Algorithm Implementations under GNU GENERAL PUBLIC LICENSE 
Version 2, June 1991
  52North WPS Client Library under Apache License, Version 2.0
  52North WPS Commons under Apache License, Version 2.0
  52North WPS Input/Ouput Implementation under GNU GENERAL PUBLIC LICENSE 
Version 2, June 1991
  52North WPS Input/Output API under Apache License, Version 2.0
  Commons Codec under The Apache Software License, Version 2.0
  Commons IO under The Apache Software License, Version 2.0
  Guava: Google Core Libraries for Java under The Apache Software License, 
Version 2.0
  Hamcrest All under New BSD License
  Hamcrest Core under New BSD License
  HttpClient under Apache License
  Joda time under Apache 2
  JTS Topology Suite under Lesser General Public License (LGPL)
  JUnit under Common Public License Version 1.0
  Logging under The Apache Software License, Version 2.0
  mapscript under MapServer License (MIT license)
  OGC OWS schema (spec. v1.1.0) under The Apache Software License, Version 2.0
  OGC WPS schema (spec. v1.0.0) under The Apache Software License, Version 2.0
  SLF4J API Module under MIT License
  stax-utils under BSD
  Stax2 API under The BSD License
  W3C xlink schema (spec. v1.1.0) under The Apache Software License, Version 2.0
  Woodstox under The Apache Software License, Version 2.0
  WPS-Config under The Apache Software License, Version 2.0
  Xalan Java under The Apache Software License, Version 2.0
  Xalan Java Serializer under The Apache Software License, Version 2.0
  xercesImpl under The Apache Software License, Version 2.0
  XmlBeans under The Apache Software License, Version 2.0


52north are trying to move from GPL to Apache license, but as you can 
see some GPL licensed code is still there :(


Alan

Re: Taverna Player integration ( Apache Taverna Mobile )

[alaninmcr]

On 12/08/2016 14:10, Sagar wrote:

I have setup the taverna server and taverna player portal on DigitalOcean
and its URL is http://139.59.28.201:3000/.

To run a workflow I need workflow database.
Where can I find sample database to run and how to integrate it with the
server.


The server does not need a workflow database. You POST a workflow to the 
server.


You can find workflows on http://www.myexperiment.org . The best 
examples will probably be in the Taverna 2.5 sample pack 
http://www.myexperiment.org/packs/612.html



So that I can confirm that server is running correctly and proceed further.


The API is documented at 
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API


Alan

Re: Taverna Player integration ( Apache Taverna Mobile )

[alaninmcr]

On 10/08/2016 14:03, Ian Dunlop wrote:

Hello,

I no longer have access but @Stian or @Finn may be able to.


I have asked on a Manchester skype chat but had no response yet. I think 
it is best to assume that the player on heater is not available.



Cheers,

Ian


Alan

[GitHub] incubator-taverna-common-activities pull request #14: Docker activity readme...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/14#discussion_r70790253
  
--- Diff: 
taverna-docker-activity/src/test/java/org/apache/taverna/activities/docker/test/DockerActivityTest.java
 ---
@@ -85,4 +95,57 @@ public void testInspectImage() throws Exception {
 System.out.println(outputs.get(DockerActivity.RESPONSE_BODY_KEY));
 
Assert.assertNotNull(outputs.get(DockerActivity.RESPONSE_BODY_KEY));
}
+
+/**
+ * Tests a simple script (String output = input + "_returned") to 
ensure the script is invoked correctly.
+ * @throws Exception
+ */
+@Test
+public void testCreateContainer() throws Exception {
+RemoteClient remoteClient = new 
RemoteClient(containerConfiguration);
+Container container = 
getContainerFromName(remoteClient.listContainers(), CONTAINER_NAME);
+if( container != null){
+System.out.println(" Container already exists  \n" + 
container.toString());
+Assert.assertNotNull(container);
+return;
+}
+
+
containerConfiguration.getInternalPropertyMap().put(DockerContainerConfigurationImpl.IMAGE,IMAGE_NAME);
+
containerConfiguration.getInternalPropertyMap().put(DockerContainerConfigurationImpl.NAME,
 CONTAINER_NAME);
+DockerActivity activity = new 
DockerActivity(containerConfiguration);
+activity.configure(activityConfiguration);
+
+Map inputs = new HashMap();
+inputs.put(DockerActivity.ACTION, DockerActivity.CREATE_CONTAINER);
+
+Map> expectedOutputs = new HashMap>();
+expectedOutputs.put(DockerActivity.RESPONSE_BODY_KEY, 
String.class);
+
+Map outputs = 
ActivityInvoker.invokeAsyncActivity(activity, inputs, expectedOutputs);
+System.out.println(outputs.get(DockerActivity.RESPONSE_BODY_KEY));
+
Assert.assertNotNull(outputs.get(DockerActivity.RESPONSE_BODY_KEY));
+String id = new 
ObjectMapper().readTree((String)outputs.get(DockerActivity.RESPONSE_BODY_KEY)).get("container-id").textValue();
--- End diff --

Better split into several statements? Difficult to see what it is doing


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[GitHub] incubator-taverna-common-activities pull request #14: Docker activity readme...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/14#discussion_r70790094
  
--- Diff: 
taverna-docker-activity/src/test/java/org/apache/taverna/activities/docker/test/DockerActivityTest.java
 ---
@@ -71,7 +80,8 @@ public void setup() throws Exception {
 */
@Test
public void testInspectImage() throws Exception {
-   DockerActivity activity = new 
DockerActivity(containerConfiguration);
+
containerConfiguration.getInternalPropertyMap().put(DockerContainerConfigurationImpl.IMAGE,IMAGE_NAME);
--- End diff --

Should not access implementation


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[GitHub] incubator-taverna-common-activities pull request #14: Docker activity readme...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/14#discussion_r70790039
  
--- Diff: 
taverna-docker-activity/src/test/java/org/apache/taverna/activities/docker/test/DockerActivityTest.java
 ---
@@ -44,13 +49,17 @@
 private DockerContainerConfigurationImpl containerConfiguration;
--- End diff --

Should be a DockerContainerConfiguration


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[GitHub] incubator-taverna-common-activities pull request #14: Docker activity readme...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/14#discussion_r70789901
  
--- Diff: 
taverna-docker-activity/src/test/java/org/apache/taverna/activities/docker/test/DockerActivityTest.java
 ---
@@ -52,6 +43,7 @@
 
 private DockerContainerConfigurationImpl containerConfiguration;
--- End diff --

Should be a DockerContainerConfiguration


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[GitHub] incubator-taverna-common-activities pull request #14: Docker activity readme...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/14#discussion_r70789844
  
--- Diff: 
taverna-docker-activity/src/test/java/org/apache/taverna/activities/docker/test/TestDockerCommands.java
 ---
@@ -40,7 +40,7 @@
 
 private static final String DOCKER_LOGIN_SUCCESS = "Login Succeeded";
 
-public TestDockerCommands(){
+public TestDockerCommands() {
 DockerContainerConfigurationImpl containerConfiguration = new 
DockerContainerConfigurationImpl(new TestConfigurationManager());
 
containerConfiguration.getInternalPropertyMap().put(DockerContainerConfigurationImpl.NAME,CONTAINER_NAME);
--- End diff --

containerConfiguration should be a DockerContainerConfiguration. Any code 
specific to the implementation should not be visible


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[GitHub] incubator-taverna-common-activities pull request #14: Docker activity readme...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/14#discussion_r70787704
  
--- Diff: taverna-docker-activity/README.txt ---
@@ -0,0 +1,30 @@
+## Docker Activity Plugin 

+
+This module implements the taverna activity plugin for Docker. The plugin 
capable of following functionality.
+
+1. Inspect Image
+2. Create Container
+3. Start Container
+4. List Containers
+5. Stop Container  - TODO
+6. Delete Container - TODO
+
+Test module src/test/java/ covers each and every capability. 
org.apache.taverna.activities.docker.RemoteClient
+capable of executing docker commands over TCP on the actual remote docker 
host using the docker-java api.
--- End diff --

is


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[GitHub] incubator-taverna-common-activities pull request #14: Docker activity readme...

[alaninmcr]

Github user alaninmcr commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/14#discussion_r70787675
  
--- Diff: taverna-docker-activity/README.txt ---
@@ -0,0 +1,30 @@
+## Docker Activity Plugin 

+
+This module implements the taverna activity plugin for Docker. The plugin 
capable of following functionality.
--- End diff --

plugin is


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Re: New Apache list archives

[alaninmcr]

On 13/05/2016 16:21, Stian Soiland-Reyes wrote:

https://lists.apache.org/list.html?taverna.apache.org

Looks pretty nice!

perhaps we should link to them from our web page instead of (or in
addition to) markmail?


I vote for "instead". Two ways will be confusing and I found the Apache 
one easy to use.


Alan

Re: News pages was Re: Draft download pages

[alaninmcr]

On 10/05/2016 14:09, Ian Dunlop wrote:

Hello,

I guess its the G+ feed that needs updated. Who controls it? Looks like
some GSoC 2016 news/tweets are needed. No point having the social media
feeds if they are not used :(


It's strange as some posts have been made e.g. BioVeL = SEEK and Taverna 
addressing climate change.



Cheers,

Ian


Alan

News pages was Re: Draft download pages

[alaninmcr]

Hello everyone,

I noticed the News https://taverna.incubator.apache.org/community/news 
is very out of date compared with the Tweets.


I think it would be better to hide out of date "News". Any ideas / comments?

Alan

Re: Draft download pages

[alaninmcr]

On 09/05/2016 18:58, Stian Soiland-Reyes wrote:

OK, great if you could put it live!

I think now with the Command Line relesse is a good time to force old users
through the Apache Taverna pages, even if it might mean they go back to the
archive page to download the 2.5 Workbench.


It should be live now.

Alan

Re: Release of Taverna Command Line?

[alaninmcr]

On 06/05/2016 10:19, Ian Dunlop wrote:

Hello,

JAVA_HOME set to 1.8 and everything builds successfully :)


Good to know.


Cheers,

Ian


Alan

Re: Release of Taverna Command Line?

[alaninmcr]

On 05/05/2016 16:23, Ian Dunlop wrote:

Hello,

Just doing some build checks in advance of this potential release and got a
failure for engine  :(

[INFO] Apache Taverna Reference Manager API ... FAILURE [
 0.583 s]

[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-compiler-plugin:3.2:compile
(default-compile) on project taverna-reference-api: Fatal error compiling:
invalid target release: 1.8 -> [Help 1]

Does that 1.8 refer to Java 8? What version are we targeting now?


1.8 see


1.8
1.8

in 
https://github.com/apache/incubator-taverna-maven-parent/blob/master/pom.xml



Cheer,

Ian


Alan

Re: atom feeds

[alaninmcr]

On 28/04/2016 16:44, Simone Bnà wrote:

Dear all,

I read the following sentences in the documentation:

The server also supports an overall Atom feed per user that allows you to find 
out when your workflows terminate without having to poll each one separately. 
This feed is at https://«SERVER:PORT»/taverna-server/feed (with the default 
web-application name). The feed is not available to anonymous users, and will 
only accept updates from the internal notification mechanism.

My question is:

Which tool can I use to parse the ATOM feeds?

I tried the feedparser python library without success.

#!/usr/bin/python
import feedparser
d = feedparser.parse('https://user:pssw@host:port/taverna-server/feed')
print d


What happens if you just try to open that URL in a browser?


Any suggestions are welcome.

Best regards,

Simone.


Alan

Re: Adding geospatial services to Taverna

[alaninmcr]

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: Enquiry about the features of Taverna 2.5

[alaninmcr]

On 11/04/2016 16:30, Stian Soiland-Reyes wrote:

Hi!


[snip]


4-Is there anything that has been done in relation to initiatives such as
iPython?



I think Alan might know about iPython and Jupyter..   Not sure if
anything was done since this:

http://www.taverna.org.uk/2014/05/20/calling-taverna-workflows-from-ipython-notebook/

Does the Taverna Player still support iPython in such a way?


That is really IPython calling Taverna workflows. It should still work.

Alan

Re: GSOC Taverna call today or tomorrow ?

[alaninmcr]

On 10/04/2016 22:09, Thilina Manamgoda wrote:

hi,


Hello


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  )


Do not worry - Stian filled in the necessary information without the 
audio/video chat.


I think it would still be a good thing to have the hangout or skype 
call. When is a good time for you?



regards ,
Thilina.


Alan

Re: GSOC Taverna call today or tomorrow ?

[alaninmcr]

On 08/04/2016 12:25, Michael Crusoe wrote:

On Fri, Apr 8, 2016 at 1:21 PM, Stian Soiland-Reyes 
wrote:

For the CWL related projects please include me; thanks!


Will do.

Alan

Fwd: add a plugin to a taverna server

[alaninmcr]

 Forwarded Message 
Subject: add a plugin to a taverna server
Date: Thu, 31 Mar 2016 15:37:38 +0200
From: Simone Bnà 
To: support 

Dear Taverna Team,

I have two questions for you:

1) How can I get the uuid of a workflow run in a Beanshell script?

2) How can I add new libraries to be used from a Beanshell script in 
taverna server?
Am I supposed to copy the *.jar libraries in 
.../apache-tomcat-x.x.x/webapps/taverna-server/WEB-INF/lib?


Best regards,

Simone.


--
Simone Bnà, PhD
C++ Software Developer, CINECA
Via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy
office:   +39-0516171938
email: s@scsitaly.com/s...@cineca.it

Advice on GSOC proposal submission

[alaninmcr]

Hello everybody,

Good advice for proposal submission:

Students can submit a Final PDF right now if they want to. The student 
can  upload new final pdf versions up until the deadline on March 25th 
at 19:00 UTC if they want to make changes to their final proposal. They 
shouldn't wait until the final moments (or even hours) to submit a Final 
PDF of their proposal- that is a very bad idea.


Alan

Re: Taverna Android App

[alaninmcr]

On 24/03/2016 13:09, RM wrote:

Hi All,

I want to know, What is the process to submitting the proposal, I
should submit it to Apache organisation or is there any other way.


You submit to GSOC with Apache Software Foundation as the Organization.
Give your proposal an obvious title so we can find it.



Thanks,

Rajan Maurya, Student.


Alan

Re: GSOC: Add CWL support to Taverna

[alaninmcr]

On 22/03/2016 11:46, Thilina Manamgoda wrote:

a)Please can you be more specific ?


Where will you get your CWL tool descriptions from? I think this is 
where engagement with CWL community will help.


You need two kinds of test data:
1) Data written to test specific functionality of your tool. So unit 
tests with associated input data and expected output data. Those tool 
descriptions do not need to "make sense" as real functional tools.


2) Real tool descriptions corresponding to real tools that would run in 
CWL. You need to test that your plugin works with these real examples.



b) No i will use examples in CWL git repositories


I think you need to check that the examples in CWL git repositories 
cover all the possibilities.



c) At the moment Tutorials for plugin creation are fo Taverna 2.So i have
to test it on Taverna 2 and then convert it to Taverna 3


You need to have a plan to test it. That does not need to be in the 
proposal, but you need to have a stage for deciding how you will test 
the plugin.


Alan

Re: GSOC: Add CWL support to Taverna

[alaninmcr]

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 proposal. So

(a) How will you choose which CWL tool providers to use?
(b) Will you create your own test tool descriptions?
(c) How will you know if your plugin is working correctly?

I think you should probably consider having engagement with the CWL 
community as well as Apache Taverna.



regards
Thilina.


Alan

Re: GSoC 2016 Docker support for Taverna

[alaninmcr]

On 17/03/2016 05:34, Nadeesh Dilanga wrote:

Hi team,
I am Nadeesh, a final year undergraduate in Computer Science from Sri
Lanka.


Hello Nadeesh


I found Docker as an excellent solution for scaling, easy deployment and
obviously a hot topic these days in enterprises who want to implement micro
services based architecture/deployment for low footprint servers/services.

I presume the idea behind Docker support for Taverna is NOT from a micro
service standpoint, but more like from a packaging and deployment
perspective. Please correct me if I am wrong.


There are two separate issues:

https://issues.apache.org/jira/browse/TAVERNA-901 is to allow Taverna 
workflows to include steps that are tools that inside docker containers. 
That would be deployment of an existing docker.


https://issues.apache.org/jira/browse/TAVERNA-879 is to create docker 
containers for Taverna workflows. That is packaging and (because the 
containers will be part of a CWL workflow) deployment.



If that is the case, can you please clarify what is the current packaging
deployment model ?


There is no current mechanism for packaging up something to run a 
specific Taverna workflow. You can run workflows from the command line 
tool or on a Taverna Server.



Like puppet for example. So that I can go through them
to understand how things works and then reuse or port those to docker.

Thanks

/nadeesh


Alan

Re: GSOC 2016

[alaninmcr]

On 11/03/2016 16:18, Ian Dunlop wrote:

Hello,

What is the mentor deadline? I need to have a think about it.


I've checked the e-mails and could not see when the mentor registration 
deadline was. It will have to be before 25th March (which is the student 
application deadline), but don't know when.



Cheers,

Ian


Alan

Re: Taverna Android App

[alaninmcr]

On 03/03/2016 11:12, RM wrote:

Sir,


Hello


I have looked your taverna Github project and I found that this app is for
your organisation people, that is very helpful for your organisation
people.I found many things that is being depreciated which will not work in
Above than 21 API SDK and App many times not working (Crashing many
times unexpected):



Here I am listing some of libraries and code staff that is messed up after
i go through your Github Project
 Code .


1. Apache HTTP standard library is used for handling the server request
that is not useable in above than API 21 SDK.

2. Xml parser self written bit of code.

3. No Material Design.

4. Crashing many times unexpected.

5. Images and Data is overlapping.


I also found many glitches in the current Android Application.


Can you submit those problems as Jira issues?


I want to work on this project as my GSOC project. I think it will be
beneficial for both the app and me as I will be able to build on my
existing knowledge.


Although there is no Taverna project proposed for 2016 in this area, as 
a potential GSOC student, you can submit your own GSOC proposal saying 
that you want to work on this. You then need someone to mentor your 
proposed project.


I think the first steps are to produce a draft proposal and then ask for 
potential mentors. The draft proposal does not have to be in detail, but 
enough to get interest of potential mentors.


[snip]


*Rajan Maurya*


Alan

Re: GSOC 2016 projects

[alaninmcr]

On 02/03/2016 17:56, Ian Dunlop wrote:

Hello


Hello


Would be nice to see some of the ogc discussion on the dev list so it can
be captured for any Apache taverna development. Nice for community
development as well.


Yes. I have asked the student to sign up and say "hello" :)


Cheers

Ian


Alan

GSOC 2016 projects

[alaninmcr]

Hello everybody

There are two GSOC2016 issues in the Jira:

https://issues.apache.org/jira/browse/TAVERNA-900 (Add Common Workflow 
Language support to Taverna) and


https://issues.apache.org/jira/browse/TAVERNA-901 (Run Docker from Taverna)

The first one has a set of tasks of which students are expected to do 
one or more. I am wondering if it should be split into the five tasks - 
so making issues TAVERNA-881, TAVERNA-877, TAVERNA-878, TAVERNA-880 and 
TAVERNA-879 into GSOC issues.


Also, having separate GSOC issues would allow different mentors. Also, 
Stian is down as mentor for both TAVERNA-900 and TAVERNA-901. I think 
the rules would mean we only have one GSOC project for Taverna.


Alan

Re: [DISCUSS] Release Candidate 5 of taverna-language-0.15.1 and taverna-osgi-0.2.1

[alaninmcr]

For dmitry mainly,

You probably have to put

+1

in the VOTE message. It's not enough to say it worked :)

Alan

Re: [VOTE] Release taverna-language-0.15.1-incubating-RC5 and taverna-osgi-0.2.1-incubating-RC5

[alaninmcr]

Hello everybody,

+1

All code builds on Windows 8, Oracle Java 8 (1.8.0_51), Maven 3.3.3.
MD5 and SHA1 Checksums match.
gpg key signing matches on all artifacts.

Alan

Re: [VOTE] Release taverna-language-0.15.1-incubating-RC5 and taverna-osgi-0.2.1-incubating-RC5

[alaninmcr]

Hello everybody,

+1

All code builds on Windows 8, Oracle Java 8 (1.8.0_51), Maven 3.3.3.
MD5 and SHA1 Checksums match.
gpg key signing matches on all artifacts.

Alan

Re: Fwd: [DISCUSS] Release Candidate 4 of taverna-language-0.15.1 and taverna-osgi-0.2.1

[alaninmcr]

On 23/02/2016 15:38, Ian Dunlop wrote:

Hello,

I add zip.close() to the validate code and it built ok. Code fragment
below. Shall I commit it to master and then we can start the release
process again? Or am I missing something?


If the declaration of the ZipFile is moved inside the try, Java 8 should 
(from my reading of the documentation) auto-close it. Perhaps the 
handling of autoclose is different according to the OS.



Cheers,

Ian


Alan

Re: Fwd: [DISCUSS] Release Candidate 4 of taverna-language-0.15.1 and taverna-osgi-0.2.1

[alaninmcr]

On 23/02/2016 14:49, Stian Soiland-Reyes wrote:

Hm, but that looks like https://issues.apache.org/jira/browse/TAVERNA-919

Somehow bugs don't really go away in Windows.. :-(


Did this happen also if you turned off Real-Time Protection? (See
Microsoft Defender or similar)


Yes :(

It made no difference if the real-time protection was on or off. This is 
on Windows 8, Java 1.8.0_51, Maven 3.3.3


If it is the defender trying to read the generated classes, can we try a 
two step. So install then go have a coffee then test? Does that make any 
sense?


Alan

Re: Fwd: [DISCUSS] Release Candidate 4 of taverna-language-0.15.1 and taverna-osgi-0.2.1

[alaninmcr]

Hello

I cannot get the RO bundle API in language to compile. I'm getting

---

Test set: org.apache.taverna.robundle.validator.ValidatorTest

---

Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.336 
sec <<< FAILURE! - in org.apache.taverna.robundle.validator.ValidatorTest
test(org.apache.taverna.robundle.validator.ValidatorTest)  Time elapsed: 
0.335 sec  <<< ERROR!


java.nio.file.FileSystemException: 
C:\Users\alanrw\AppData\Local\Temp\test5027612704020713570.bundle.zip: 
The process cannot access the file because it is being used by another 
process.



	at 
sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:86)
	at 
sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:97)
	at 
sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:102)
	at 
sun.nio.fs.WindowsFileSystemProvider.implDelete(WindowsFileSystemProvider.java:269)
	at 
sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)

at java.nio.file.Files.delete(Files.java:1126)
	at 
org.apache.taverna.robundle.validator.ValidatorTest.test(ValidatorTest.java:47)



Is this the issue you thought was with the real time protection? I got 
it even with the protection switched off.


Alan

Re: [DISCUSS] Release Candidate 3 of taverna-language-0.15.1 and taverna-osgi-0.2.1

[alaninmcr]

On 23/02/2016 10:32, alaninmcr wrote:

Hello Stian

The download links are not working for me. Have you taken them down?


It's OK. I see we are already on RC4 :)


Alan


Alan

Re: [DISCUSS] Release Candidate 3 of taverna-language-0.15.1 and taverna-osgi-0.2.1

[alaninmcr]

Hello Stian

The download links are not working for me. Have you taken them down?

Alan

Re: [DISCUSS] Release taverna-language-0.15.1-incubating-RC2 and taverna-osgi-0.2.1-incubating-RC2

[alaninmcr]

On 19/02/2016 15:38, Stian Soiland-Reyes wrote:

I can confirm this in Windows with both java 8u40 and 8u74.

https://issues.apache.org/jira/browse/TAVERNA-920

I think this means I'll cancel the vote. (But feel free to keep checing! ;-))


Is it normal to cancel a vote, or to let it run and fail? I'm slightly 
wary of you having the power to cancel the vote, even though you called 
it :D


Alan (being awkward)

Re: [VOTE] Release taverna-language-0.15.1-incubating-RC2 and taverna-osgi-0.2.1-incubating-RC2

[alaninmcr]

Hello everybody

I checked on Windows 8 with mvn 3.3.3 and Oracle Java 1.8.0_51

My votes are:

Apache Taverna Maven Parent 2-incubating
-1 not binding because of the rat check issue (TAVERNA-921)

Apache Taverna Language 0.15.1-incubating
-1 binding because of the ucf package issue (TAVERNA-920)

Apache Taverna OSGi plugin system 0.2.1-incubating
-1 not binding because of the rat check issue (TAVERNA-921)

Apache Taverna Maven Parent 2-incubating and Apache Taverna OSGi plugin 
system 0.2.1-incubating did install OK. It was just the rat check that 
causes problems.


Alan

Re: [DISCUSS] Release taverna-language-0.15.1-incubating-RC2 and taverna-osgi-0.2.1-incubating-RC2

[alaninmcr]

Hello again

The rat checks are failing (for me) for Apache Taverna Maven Parent 
2-incubating and Apache Taverna OSGi plugin system 0.2.1-incubating.


It complains about DEPENDENCIES :)

Alan

Re: [DISCUSS] Release taverna-language-0.15.1-incubating-RC2 and taverna-osgi-0.2.1-incubating-RC2

[alaninmcr]

Hello everybody

When I try to mvn clean install the Apache Taverna Language 
0.15.1-incubating, I get a test failure :(


I am running on Windows 8, Java 1.8.0.51 and mvn 3.3.3 Is this an Oracle 
Java v OpenJDK issue ?


Test set: org.apache.taverna.scufl2.ucfpackage.TestUCFPackage

---

Tests run: 34, Failures: 3, Errors: 0, Skipped: 0, Time elapsed: 2.623 
sec <<< FAILURE! - in org.apache.taverna.scufl2.ucfpackage.TestUCFPackage
setRootfileSaved(org.apache.taverna.scufl2.ucfpackage.TestUCFPackage) 
Time elapsed: 0.038 sec  <<< FAILURE!


org.junit.ComparisonFailure: expected:<[]> but was:<[ns3]>
at org.junit.Assert.assertEquals(Assert.java:115)
at org.junit.Assert.assertEquals(Assert.java:144)
	at 
org.apache.taverna.scufl2.ucfpackage.TestUCFPackage.setRootfileSaved(TestUCFPackage.java:656)



addResourceContainerXml(org.apache.taverna.scufl2.ucfpackage.TestUCFPackage) 
 Time elapsed: 0.119 sec  <<< FAILURE!


org.junit.ComparisonFailure: expected:<[]> but was:<[ns3]>
at org.junit.Assert.assertEquals(Assert.java:115)
at org.junit.Assert.assertEquals(Assert.java:144)
	at 
org.apache.taverna.scufl2.ucfpackage.TestUCFPackage.addResourceContainerXml(TestUCFPackage.java:708)



setRootfileExtendsContainerXml(org.apache.taverna.scufl2.ucfpackage.TestUCFPackage) 
 Time elapsed: 0.043 sec  <<< FAILURE!


org.junit.ComparisonFailure: expected:<[]> but was:<[ns3]>
at org.junit.Assert.assertEquals(Assert.java:115)
at org.junit.Assert.assertEquals(Assert.java:144)
	at 
org.apache.taverna.scufl2.ucfpackage.TestUCFPackage.setRootfileExtendsContainerXml(TestUCFPackage.java:787)

Re: [DISCUSS] Release taverna-language-0.15.1-incubating-RC2 and taverna-osgi-0.2.1-incubating-RC2

[alaninmcr]

On 18/02/2016 11:02, Stian Soiland-Reyes wrote:

Please us this discussion thread for any questions and comments
about the release candidates for RC2 of

   Apache Taverna Maven Parent 2-incubating
   Apache Taverna Language 0.15.1-incubating
   Apache Taverna OSGi plugin system 0.2.1-incubating

at
https://dist.apache.org/repos/dist/dev/incubator/taverna/source/


Use the [VOTE] thread to place your votes on the release candidate/


So it is three separate votes?

I'm asking because I think if the parent fails to pass, then the OSGI 
must(?) fail as it relies on the parent.



See also corresponding JIRA issue:
https://issues.apache.org/jira/browse/TAVERNA-902


Alan

Check consistency between baclava and t2flow

[alaninmcr]

Hi all,

I experienced a problem when running a workflow with an inconsistent 
baclava.

Let me explain better:
If I submit a workflow to Taverna with a set of input ports which are 
different from the ones described in the baclava,

taverna does not complain but the run will never terminate.
Is there a way to check the consistency between a t2flow workflow and 
the baclava?


Best regards,

Simone.


--
Simone Bnà, PhD
C++ Software Developer, CINECA
Via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy
office:   +39-0516171938
email: s@scsitaly.com/s...@cineca.it

Re: Snapshot issue when releasing taverna language

[alaninmcr]

On 01/02/2016 12:35, Menaka Madushanka wrote:

Hello,
I get this error when building tavlang tool

[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs) on
project taverna-language-commandline: MavenReportException: Error while
creating archive:
[ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
[ERROR]
[ERROR] Command line was: /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
@options @packages


Is that option only available in Java 8?

Alan

Workflows in the language repository

[alaninmcr]

Hello everybody

Following the Google hangout, I have looked at the workflows in 
incubator-taverna-language and the coverage of activity types. The list 
is below.


There is duplication of workflows e.g.

taverna-language-commandline/src/test/resources/workflows/t2flow/as.t2flow

taverna-scufl2-examples/src/test/resources/workflows/t2flow/as.t2flow

taverna-scufl2-t2flow/src/test/resources/as.t2flow

except for a license formatting difference.

Suggestions are welcome on how to proceed.

Alan

=

./incubator-taverna-language/taverna-language-commandline/src/test/resources/workflows/t2flow/as.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-annotation/src/test/resources/helloanyone.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-annotation/src/test/resources/valid_component_imagemagickconvert.t2flow
ExternalTool

./incubator-taverna-language/taverna-scufl2-examples/examples/helloanyone.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-examples/examples/helloworld.t2flow
StringConstant

./incubator-taverna-language/taverna-scufl2-examples/src/test/resources/workflows/t2flow/as.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-examples/src/test/resources/workflows/t2flow/defaultActivitiesTaverna2.2.t2flow
ApiConsumer
Beanshell
Biomoby
BiomobyObject
Localworker
Rshell
Soaplab
StringConstant
WSDL
XMLSplitter

./incubator-taverna-language/taverna-scufl2-examples/src/test/resources/workflows/t2flow/helloanyone.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-integration-tests/src/test/resources/apiconsumer.t2flow
ApiConsumer

./incubator-taverna-language/taverna-scufl2-integration-tests/src/test/resources/rest.t2flow
REST
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/annotated2.2.t2flow
Beanshell

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/as.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/beanshell-deps.t2flow
Beanshell

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/dataflow_link_then_merge.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2.t2flow
ApiConsumer
Beanshell
Biomoby
BiomobyObject
Localworker
Rshell
Soaplab
StringConstant
WSDL
XMLSplitter

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/dispatchlayers.t2flow
Beanshell
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/fasta_and_pscan.t2flow
Localworker
Soaplab

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/fasta_pscan_and_dbfetch.t2flow
Localworker
REST
Soaplab
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/interaction-with-strange-loop.t2flow
Interaction
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/interaction_multiple_choice.t2flow
Interaction
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/interaction_simple_tell.t2flow
Interaction
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/iterationstrategies.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/merge_fun.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/merge_then_dataflow_link.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/missing_merge.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/random.t2flow
StringConstant
WSDL
XMLSplitter

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/rest-2-2.t2flow
REST

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/rshell-2-2.t2flow
Rshell

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse.t2flow
Localworker

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/simple_fasta.t2flow
Localworker

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/sleepers.t2flow
Beanshell

./incubator-taverna-language/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
ExternalTool
XPath

./incubator-taverna-language/taverna-scufl2-wfdesc/src/test/resources/allTypes.t2flow
Beanshell
ExternalTool
Localworker
REST
Rshell
StringConstant
WSDL
XPath

./incubator-taverna-language/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
Localworker
StringConstant

./incubator-taverna-language/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
StringConstant

./incubator-taverna-language/taverna-scufl2-wfdesc/src/test/resources/localdepe

Re: Trying to understand the big picture

[alaninmcr]

On 25/01/2016 20:04, Gale Naylor wrote:

Thanks, Ian. I've modified Stian's architecture drawing to take into
account the additional information (at least, as best I understand it.)

https://galenaylor.wordpress.com/2016/01/25/revised-apache-taverna-3-architecture-diagram/

Comments, anyone?


Looks good.

When you run a workflow in the workbench or the command line tool, then 
it can generate a data bundle as an output of the workflow run. The 
databundle contains information about the inputs and outputs of the run 
and also provenance information e.g. when part of the workflow ran and 
what intermediate inputs and outputs it took/produced. The databundle 
viewer allows you to explore a databundle.


The player and server can also produce a databundle, that they get 
indirectly from the command line tool they run.



Thanks,
Gale


Alan

Re: Proposed google hangout

[alaninmcr]

On 20/01/2016 15:20, Ian Dunlop wrote:

Hello,

We have arranged a google hangout. Hopefully the following link will
work -
https://plus.google.com/hangouts/_/talk.google.com/taverna-g?authuser=0&hceid=MDY3N2VlajQ5MWVtOHQzcjg1aDBpMTJzOGdAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.gqmf2415hk9gb7r7uo7bggvi7s


Hello Ian,

That link gives me an error. "Sorry, we've encountered a problem with 
joining this video call."


Does it work for other people?

Alan


Cheers,

Ian


Alan

Re: Proposed google hangout

[alaninmcr]

Sounds like Friday is best.

Alan

On 18/01/2016 22:49, Gale Naylor wrote:

+1 for Friday 15:00 GMT and for the agenda.

On Mon, Jan 18, 2016 at 8:25 AM Stian Soiland-Reyes 
wrote:


Both are good for myself, but +1 for Friday 15:00 GMT.

On 18 January 2016 at 15:44, Ian Dunlop 
wrote:

Hello,

So we have 2 times proposed: Wednesday 20th 16-18 GMT or Friday 22nd
15-16 GMT. We need to select one quickly. I vote for Friday (to give us
a couple of days prep).

Some proposed items for discussion:

* running the taverna command line - code/bug fixes required
* planned releases - taverna language
* Common Workflow Language - discussion of integration points
* publications page
* website refresh -streamlining the navbar

Cheers,

Ian

--
Ian Dunlop, eScience Lab
School of Computer Science
The University of Manchester
http://orcid.org/-0001-7066-3350




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

Re: Redirection from taverna.org.uk

[alaninmcr]

On 15/01/2016 18:22, Gale Naylor wrote:

I would like to join. I am available Wednesday 16-18 GMT and Friday 15-16
GMT.


Either of those times is OK for me, with a slight preference for Wednesday.

Alan

Re: Redirection from taverna.org.uk

[alaninmcr]

Hello

Can we have a Google hangout about this? I think it is more complicated 
e.g. the domain-specific versions of Taverna 2.5


Alan

Re: [jira] [Created] (TAVERNA-882) Publications page

[alaninmcr]

Just a warning that you need to be careful when doing a search. A lot of 
the citations will be unhelpful like "Popular workflow systems include 
X, Y, Taverna and Z" or "Our system is better than X, Y, Taverna and Z 
because ...".


Alan

Re: Taverna components

[alaninmcr]

Hello Yassene

When you create the component family on myExperiment, you are able to 
specify whether the family and its member components will be private or 
public. Did you choose public?


I've looked at the code and I do not understand, if I can see your 
components, that your colleagues cannot. Are there any messages in the 
log files? Can they see the component in a browser or in the myE 
perspective of Taverna?


At the moment there are no utilities for sharing private families. I 
think the best way would be to have a private family that you use for 
development and then publish (copy) a component into a public family.


Alan

Re: Taverna components

[alaninmcr]

On 03/12/2015 14:35, y.moham...@lumc.nl wrote:

Many thanks Alan for your emails.  Yes, I updated the component
permission individually yesterday.  I probably do not understand the
process very well: I have created a family and few components and
made the component pack open to everyone. I still however needed to
update the permission for each single workflow in the component pack
so everyone can see them. Nonetheless, people still cannot see the
pack and the component are not accessible in a workflow, for instance
try the attached one. Even when pressing on add new service ->
component -> myExperiment,  the component pack protein_network_2 is
not visible.


This is _very_ strange. I can see the component pack and I can add the 
components to a workflow. I can also run the workflow that you attached.


Can the people see _any_ components?


Is there any step by step tutorial that I can follow. how do you guys
uploaded all the current components?


I will look this weekend.


Again any hint is very much appreciated.

Many thanks, Yassene


Alan

Re: Taverna components

[alaninmcr]

Yassene

I guess you have changed the visibility as I now see the component family.

Alan

Re: Taverna components

[alaninmcr]

Finn checked and

http://www.myexperiment.org/workflows/4773.html

and

http://www.myexperiment.org/files/1410.html

are not public.

Alan

Re: Taverna components

[alaninmcr]

Hello Yassene

On 02/12/2015 15:52, y.moham...@lumc.nl wrote:

Hi Alan,

I actually have the permission for that component pack as public and
every one can view and update (see attached screenshot).  I even
shared each workflow of each component openly with everyone. So I
wonder how can I let a new computer see these components and further
see that component pack in the drop down menu of Import new
services->component service.


Attached is what I see for the items. The profile and the 
single_double_flatten workflow are not public.  Finn is checking on myE.



Any hint is much appreciated.

Thanks,



Yassene


Alan

Re: Taverna components

[alaninmcr]

On 23/11/2015 11:17, Alan Williams wrote:

Dear Taverna team,

How do I make the component I put on MyExperiment available?  I tried
private and public, but I still cannot see them from a different
computer.


Hello Yassene.

How did you upload the component to myExperiment?


A related question that I have, where can I browse the available
components? how to download them, modify them, etc. ?


You can browse the components in Taverna. Alternatively, you can filter 
the workflows on myExperiment as they are tagged with "component". You 
can open the components in Taverna and (if you have sufficient 
privileges) modify them and save them again to myExperiment. This should 
be done, though, through the components menus _not_ through the normal 
myE access.


The UI of myE (sadly) has not been updated for components, although the 
API has.



Many thanks in advance,
Yassene


Alan

Fwd: Registry/CWL/Workbench integration Hackathon

[alaninmcr]

Hello everybody

Some of you may be interested in the ELIXIR / Galaxy / Taverna hackathon.

Alan

 Forwarded Message 
Subject: Registry/CWL/Workbench integration Hackathon
Date: Tue, 10 Nov 2015 17:17:58 +
From: Hervé Ménager 
To: common-workflow-langu...@googlegroups.com 



Good evening,
We are considering holding a joint event between the ELIXIR registry and
the CWL community (including people from the Galaxy and Taverna
communities), working on collaborating and integrating both systems. It
would take place in Paris in May. As a first step on the planning of the
event, I'd like to know if and when you would be available to attend in
May. Here's the link to the doodle poll:
http://doodle.com/poll/6fc8dw9arv68dht8.
Thank you for your answers, comments are welcome! Please forward to anyone
interested.
Cheers,
Hervé

Question about creating a register for components

[alaninmcr]

Subject: Question about creating a register for components
Date: Mon, 14 Sep 2015 10:49:07 +0100
From: Kewei Duan 
To: support 



To whom it may concern:

I am interested in creating an repository/registry for components that
has the function to provide an interface for Taverna just like the
myExperiment's corresponding function. The screenshot below shows where
we want to add our own repository. Do you think it is possible? I think
there are some APIs/rules to follow. Could you provide some information
about how to do that if it is possible?

Thanks,
Inline images 1

--
Kewei DUAN
/Senior Software Developer, INSIGNEO, University of Sheffield/

E09
INSIGNEO Institute for in silico Medicine
Pam Liversidge Building
Sir Frederick Mappin Building
Mappin Street
Sheffield
S1 3JD
UK

Re: Taverna Databundle Viewer - progress

[alaninmcr]

Hello Denis

I think the request is pulled into the Apache repository OK.

Alan

Re: Taverna Databundle Viewer - progress

[alaninmcr]

On 20/08/2015 16:00, Denis Karyakin wrote:

Hello,
I improved test coverage and code quality (by Code Climate metrics)

I didn't sent pull request, because github say that this pull request can’t
automatically merge
And in canceled pull request I saw my commits, content of which already
contained in original repository


Hello,

Do you have a pull request to the github repository? I'm confused :)

Alan

Re: Taverna Databundle Viewer - progress

[alaninmcr]

On 04/08/2015 23:31, Denis Karyakin wrote:

Hello,
What I need to do with different commits?


I am uncertain what you are asking. Were the merge conflicts sorted out?


Currently I work with new features in separate git branch. I processed all
workflow files from the Starter Pack and now work by show workflow run from
input to output step by step


Hello. I think we need to get user feedback. Do you have a server stood 
up or should I do it?


Alan

Re: Taverna poster

[alaninmcr]

On 04/08/2015 23:28, Denis Karyakin wrote:

Thank you very much for supporting and advices.
People are interested in poster, they asked many questions about Taverna
and some of them promised to try the Taverna Workbench.

I create pull request with poster in svg and pdf formats
https://github.com/apache/incubator-taverna-site/pull/3


Can you check the svg? On my machine it has no text in the space below 
INTRODUCTION and then almost all the rest of the text is invisible. I 
can see that it is there in the svg source though.


The PDF looks good to me.

Alan

Re: [DISCUSS] Release Apache Taverna Parent 1-incubating-RC4 & Apache Taverna Language 0.15.0-incubating RC4

[alaninmcr]

On 04/08/2015 14:06, Pierce, Marlon wrote:

The vote has been open at least 72 hours, and you have several +1s as well
a -0 from a mentor.  What is your next step?


Ian said the vote would "close at midnight GMT on 4 August 2015." So not 
long to go now :)



Marlon


Alan

Re: wsdl-generic (experimental) and SSL

[alaninmcr]

On 28/07/2015 16:25, Dmitry wrote:

If the server certificate is missing / wrong then you should detect it.

I am not sure how is this possible in Java. :-(
Browsers have a long list of trusted authorities.
On the other hand, Taverna uses its own KeyStrore.
I cannot ask the user trust the server certificate, neither I have all
trusted authorities in a java certificates.


You do not have all of them, but there is a default set.


For example, I have a transPLANT web services registry (based on BioSWR)
which is protected via SSL.
https://transplantdb.bsc.es/registry/rest/service/94259BD285E07E855382DD197BC61D62


But the WSDL location may be different from the service one.
So there are two things here:

1. https wsdl location
2. web service location (which by the way may be a usual http).


True, they may be different. However, I think you should flag any 
problems as soon as you know about them.



By the way, how Taverna's server execute https services?


Donal can probably answer that better.


Does it provide certificates as a part of the workflow?


No. Non-standard certificates must be sent to the server for the run. 
See the description for /runs/{id}/security/trusts on


http://dev.mygrid.org.uk/wiki/display/tav250/REST+API


Dmitry


Alan

Removal of hibernate dependency

[alaninmcr]

Hello everybody,

I have removed the hibernate dependency from taverna-reference-impl. 
There may be cascade effects that will need to be fixed as well.


Alan

Re: wsdl-generic (experimental) and SSL

[alaninmcr]

On 28/07/2015 10:25, Dmitry wrote:

Hello,


Hello


I am working to add https support to my experimental wsdl-generic code.

Currently, wsdl-generic doesn't support https directly.
Taverna's credential manager hooks into https requests.


You should probably be OK without the credential manager in there.

You can use the Java trust store.


Because I use wsdl-generic as a stand-alone package, I'd like to provide
https secured services support.

1. I just ignore server certificate while getting WSDL/Schema files.
 Is it OK?


Not really. If the server certificate is missing / wrong then you should 
detect it.


Also, from a user's point of view, the services normally are on the same 
site as a WSDL. So it will be better to identify a problem when the WSDL 
is read, rather than "down the line".



IMHO getting WSDL is not that critical issue...
2. Is it OK to do the same for the service execution?


Even less that for getting the WSDL.

I think HTTPS should be enforced as much as possible.


Any thoughts and comments are very appreciated :-).

Dmitry


Alan

Re: Taverna poster

[alaninmcr]

On 23/07/2015 22:50, Denis Karyakin wrote:

Hello,
I printed poster in Saturday, without mention and thanks to the GSOC. I'm
on the bioinformatics school now and here some troubles with internet
connection.


Have a great time at the bioinformatics school and enjoy Moscow. The 
poster looks really nice.


Alan

Re: [DISCUSS] Release Apache Taverna Parent 1-incubating-RC3 Apache Taverna Language 0.15.0-incubating RC3

[alaninmcr]

On 15/07/2015 14:18, Stian Soiland-Reyes wrote:

I don't think we should need to wait for GSOC to end as it would loose
the momentum now.. it would also be great to include all the fixes
Martin Scharm also has included.


I am not clear what you are suggesting.

Alan

Re: Taverna Databundle Viewer - progress

[alaninmcr]

On 14/07/2015 23:11, Denis Karyakin wrote:

Hello,
This is my report for almost two weeks.


It is OK to do more frequent commits - hint :)


I send last commits with new feature
1) User can upload databundle file
2) User can navigates to inputs and outputs of databundle file
3) Store uploaded files to Amazon S3


So does someone need an Amazon account to view databundles?


4) Updated routes.rb with licence and removing unused staff
5) Display errors on log in

I will run all workflows from the Starter Pack of the myExperiment for see
diffrent types of inputs and outputs.
Temporarily pages with show databundles contain ugly UI, I search good way
for show workflow run


There are lots of people here who can help with styling and presentation 
issues.



How this commits will be merge?
In original repository presented commits, which not presented in my
repository. Would I need to do pull from original?


That would be the best way. I think it is just the NOTICE, LICENSE and 
README.md that have been changed.


Alan

Re: Taverna poster

[alaninmcr]

On 14/07/2015 23:13, Denis Karyakin wrote:

Hello,
I completed the Apache Taverna poster.

10 July was deadline for approval participate in poster session.
Deadline for send poster - 19 July.

I used Inkscape for create poster.
This is links to download
https://dl.dropboxusercontent.com/u/71489000/Taverna%20Poster.pdf (PDF -
for view in browser)
https://dl.dropboxusercontent.com/u/71489000/Poster_Taverna.svg (SVG -
source file)

Please, review it


Looks good.

Some suggestions:

INTRODUCTION

Workflow Management System -> A Workflow Management System

the WMS provide -> the WMS provides

Can you add Taverna Player into the list of tools in the suite?

DESIGN AND CONSTRUCTION

SOAP/WSDL/WSRF/REST -> SOAP or REST

Invoke any command line tools -> Invoke any command line tool or script

I think you need a line break before Pluggable components of reusable 
workflows


EXECUTION

shows graphical progress -> shows the progress of a workflow run

Command line execution allows Workflows can also -> Command line 
execution allows Workflows to also


",integrating with otherRemote" - some text has gone missing

I think something has gone wrong with the text. There should probably be 
a line break before Remote workflow execution


"appsProgrammatic execution..." does not make sense

SHARING AND DISCOVERY

Probably should mention myExperiment

---

Do not be afraid to reduce the font size

In INTRODUCTION you use bold but not elsewhere. I think it is good, so 
pick important things such as BioCatalogue


It is a very good idea to make sure boxes are the same size e.g. the 
INTRODUCTION and EXECUTION boxes.


Try to align things

I think some of the paragraphs are justified (so the ends line up). I 
think this looks strange. However, it is your choice


Alan

Re: GSOC Taverna Mobile: Uploading workflows to the Taverna player

[alaninmcr]

On 06/07/2015 12:03, Ian Dunlop wrote:

Hello,

I just sent workflow 16 to the taverna player by base64 encoding it
on the command line and using curl and it all worked ok. Here is the
base64 version
https://dl.dropboxusercontent.com/u/4958764/wf16.base64 Maybe you
need to ensure it is UTF-8 character set.


Also that it is not broken into lines. That file correctly keeps the 
base64 all in one line. Some base64 methods will, by default, break it 
into human-friendly lines which can be confusing for the reading system.



Cheers,

Ian


Alan

Re: GSOC Taverna Mobile: Uploading workflows to the Taverna player

[alaninmcr]

On 03/07/2015 16:27, Larry Akah wrote:

Could you guide me more, because according to documentation here:
http://wiki.myexperiment.org/index.php/Developer:WorkflowsResource i don't
see what i need to specify to get only t2 workflows.


You can certainly check if they are t2 workflows by looking at the 
content type of an individual workflow. It should have


application/vnd.taverna.t2flow+xml

and not

application/vnd.taverna.scufl+xml

So, you can get all the workflows and then filter out all of them except 
t2 ones. I think there is a better way but cannot remember it (Friday 
afternoon).



Cheers


Alan

Re: GSOC Taverna Mobile: Uploading workflows to the Taverna player

[alaninmcr]

On 03/07/2015 16:15, Larry Akah wrote:

am using workflows ending with .xml but they are t1 workflows.


Use t2 workflows. (You can get myExperiment to only return t2 workflows.)

Alan

Re: GSOC Taverna Mobile: Uploading workflows to the Taverna player

[alaninmcr]

Larry,

It is worth using a tool like http://jsonlint.com/ to validate the 
format of the JSON you are sending.


Alan

Re: GSOC Taverna Mobile: Uploading workflows to the Taverna player

[alaninmcr]

On 03/07/2015 14:28, Ian Dunlop wrote:

Hello,

Pretty much except the keys need quotes around them. Something like this:
String post = "{\"workflow\": 
{\"document\":\"data:application/octet-stream;base64,\""+Base64.encodeToString(sb.toString().getBytes(),


You should not call getBytes on a String without specifying the 
character set you want to use. It will default to the platform's 
character set; this causes difficult to debug errors.


Alan

Re: GSoC taverna mobile - how is the workflow upload

[alaninmcr]

Hello Larry,

Can you reproduce this with a small workflow and send the postJson ?

Alan

Re: [VOTE] Release Apache Taverna Language 0.15.0-incubating RC2

[alaninmcr]

On 01/07/2015 14:13, Ian Dunlop wrote:

Hello,

A release with the build issues fixed but with the documentation issues added 
to JIRA.


So a RC3. Sounds OK to me.


Cheers,

Ian


Alan

Re: [VOTE] Release Apache Taverna Language 0.15.0-incubating RC2

[alaninmcr]

On 01/07/2015 13:24, Ian Dunlop wrote:

Hello,

It's been a few days since we discussed the possible release of
Apache Taverna Language incubator. Since then we have corrected many
build issues and identified areas where documentation (NOTICE,
LICENSE and README) can be improved. I don't think that any of the
documentation issues are enough to stop us going ahead with the
release and the fact that we identified build issues and corrected
them shows that the release process is working. I believe that we
should go ahead with the release while adding the documentation
issues to JIRA so that we can fix them when we have time to do so.


I'm confused as to if you are suggesting going ahead with the 
0.15.0-incubating RC2 with the known build issues (and documentation 
issues), or a release with the build issues fixed but still with the 
documentation issues.



Cheers,

Ian


Alan

Re: Taverna Databundle Viewer - progress

[alaninmcr]

On 25/06/2015 23:47, Denis Karyakin wrote:

Yes, I missed restful url, sorry)

I didn't find how to set provenance parameter because t2-server gem version
1.0.0 didn't use provenance. After upgrade t2-server to 1.3.0 I find how to
set up provenance. This upgrade I sent in pull request to
taverna-player-portal.

After creating workflow run in taverna server I have sent put request by
using T2Server::Run#generate_provenance. In wireshark I see this request:
PUT
/taverna-2.5.4/rest/runs/f844a875-e1c5-42c4-96ea-9e58073b9994/generate-provenance
HTTP/1.1\r\n
with true parameter.

But taverna server returned again zip archive with only outputs..


I am a bit confused. On heater, I created a run, set generate provenance 
to true, set the run to Operating, waited and then fetched the run bundle.


Can you try with a very simple workflow such as that from 
http://www.myexperiment.org/workflows/2648.html ?


Alan

Re: gsoc taverna mobile progress so far

[alaninmcr]

On 25/06/2015 09:48, Larry Akah wrote:

Ooops, i think my connection was a little unstable. Its ok now i think.


How well does the App cope with an unstable connection?

Alan