Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Menaka,

Thanks for updating your blog! I have some additional feedback in the
form of two blog posts. One has a detailed description (as I
understand it) of the convert command and one has several examples,
building on the examples in your blog. I hope these will help the
discussion of the command structure. Here are the links:

https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-command-line-convert-command/

https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-command-line-convert-examples/

Some things to note:

(1) l basically used your June 18th post, but a few things (like the
validate command) are from earlier posts/emails.

(2) I showed the output-format without brackets to indicate it is
required and not optional because it appears to be always necessary.

(3) The way I understand the overall command structure, it seemed that
all options (e.g., the output file directory) should come before the
input-file-list, so that's what I assumed.

(4) I left the -json output file type as having a single dash, but all
the other output types have double-dashes. Should I change the json
output argument to --json?

Please let me know if anything is incorrect and I will change it. I
realize the command structure is fluid, and I'm happy to make any
changes as things evolve.

(Wordpress is driving me crazy because it is showing the double-dashes
as long single dashes, even when I use the monospace font-family. Any
suggestions?)

Thanks,

Gale

On Fri, Jun 19, 2015 at 10:11 AM, Menaka Madushanka
menaka12...@gmail.com wrote:
 Hi Gale,

 Thank you very much.

 . Can you help me
 understand what you mean when you say the files will get saved to the
 C directory?

 That was a mistake :-). I updated the blog. That should be corrected as
 *$tavlang convert –json -r -i /home/usrname/toConvert/  – *Convert the
 files and save them in the …/toConvert/converted/ directory.

 I would appreciate more feedback, modifications etc. So with the help of
 the community we could come up with a much better structure.
 Cheers
 Menaka

 On 19 June 2015 at 22:32, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 I am very happy to help, and I understand the command structure is a
 little fluid right now. Thank you for the blog post; it was very
 helpful.

 I am a little confused about your recursive example. Can you help me
 understand what you mean when you say the files will get saved to the
 C directory? Because you show the output being saved to:
 /home/usrname/toConvert/converted/somefile1.json

 This is the example:
 $tavlang convert –json -r -i /home/usrname/toConvert/  – Convert the
 files and save them in the C directory.

 Thank you!

 Gale

 B

 On Fri, Jun 19, 2015 at 2:15 AM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Hi Gale,
  I extremely appreciate your help. Thank you very much. :-)
 
  1) Is this still the basic structure of the command: tavlang convert
  [options] output format input files? Am I wrong in thinking that the
  output formats are handled as options?
 
 
  Yes there is a little difference in the structure of commands now and
 then.
  So for the moment the command structure is like this.
 
  $tavlang convert [--out-put format] [options] [arguments]
 
 
  2) Are -r and -i ever used independently? If so, under what
 circumstances?
 
  No. In recursive case the input will be a directory containing .t2flow of
  .wfbundle files. The output dir is optional for both recursive and non
  recursive cases.
 
  I created a blog about the conversion command.
 
 https://menakamadushanka.wordpress.com/2015/06/18/apache-taverna-language-command-line-conversion-documentation/
 
  If you have some suggestions, please inform.
 
  Thank you very much!
 
  Regards
  Menaka
 
  --
  Menaka Madushanka Jayawardena
  Faculty of Engineering, http://www.pdn.ac.lk/eng
  University of Peradeniyaya.
  LinkedIn http://lk.linkedin.com/in/menakajayawardena




 --
 Menaka Madushanka Jayawardena
 Faculty of Engineering, http://www.pdn.ac.lk/eng
 University of Peradeniyaya.
 LinkedIn http://lk.linkedin.com/in/menakajayawardena

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Thank you for the Wordpress tip, Menaka! I have changed the two blog
posts to use the pre tag, and it looks great. I also made a few
refinements.

Thanks,
Gale

On Fri, Jun 19, 2015 at 11:54 PM, Menaka Madushanka
menaka12...@gmail.com wrote:
 Thank you very much Gale,

 I showed the output-format without brackets to indicate it is
 required and not optional because it appears to be always necessary


 That would be more accurate I think. I'm very new for documentation. Thank
 you very much.

  I left the -json output file type as having a single dash, but all
 the other output types have double-dashes. Should I change the json
 output argument to --json?

 -json should be --json. In my email that was a mistake. So you can use --.

 (Wordpress is driving me crazy because it is showing the double-dashes
 as long single dashes, even when I use the monospace font-family. Any
 suggestions?)


 Yes, wordpress does what it wants, but not us. :-) Use preformatted. Not
 paragraph. Then it would be ok. I updated my blog.
 https://menakamadushanka.wordpress.com/2015/06/18/apache-taverna-language-command-line-conversion-documentation/

 Thank you very much.
 Menaka

 I'll go through your documentations.


 On 20 June 2015 at 03:43, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 Thanks for updating your blog! I have some additional feedback in the
 form of two blog posts. One has a detailed description (as I
 understand it) of the convert command and one has several examples,
 building on the examples in your blog. I hope these will help the
 discussion of the command structure. Here are the links:


 https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-command-line-convert-command/


 https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-command-line-convert-examples/

 Some things to note:

 (1) l basically used your June 18th post, but a few things (like the
 validate command) are from earlier posts/emails.

 (2) I showed the output-format without brackets to indicate it is
 required and not optional because it appears to be always necessary.

 (3) The way I understand the overall command structure, it seemed that
 all options (e.g., the output file directory) should come before the
 input-file-list, so that's what I assumed.

 (4) I left the -json output file type as having a single dash, but all
 the other output types have double-dashes. Should I change the json
 output argument to --json?

 Please let me know if anything is incorrect and I will change it. I
 realize the command structure is fluid, and I'm happy to make any
 changes as things evolve.

 (Wordpress is driving me crazy because it is showing the double-dashes
 as long single dashes, even when I use the monospace font-family. Any
 suggestions?)

 Thanks,

 Gale

 On Fri, Jun 19, 2015 at 10:11 AM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Hi Gale,
 
  Thank you very much.
 
  . Can you help me
  understand what you mean when you say the files will get saved to the
  C directory?
 
  That was a mistake :-). I updated the blog. That should be corrected as
  *$tavlang convert –json -r -i /home/usrname/toConvert/  – *Convert the
  files and save them in the …/toConvert/converted/ directory.
 
  I would appreciate more feedback, modifications etc. So with the help of
  the community we could come up with a much better structure.
  Cheers
  Menaka
 
  On 19 June 2015 at 22:32, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
  I am very happy to help, and I understand the command structure is a
  little fluid right now. Thank you for the blog post; it was very
  helpful.
 
  I am a little confused about your recursive example. Can you help me
  understand what you mean when you say the files will get saved to the
  C directory? Because you show the output being saved to:
  /home/usrname/toConvert/converted/somefile1.json
 
  This is the example:
  $tavlang convert –json -r -i /home/usrname/toConvert/  – Convert the
  files and save them in the C directory.
 
  Thank you!
 
  Gale
 
  B
 
  On Fri, Jun 19, 2015 at 2:15 AM, Menaka Madushanka
  menaka12...@gmail.com wrote:
   Hi Gale,
   I extremely appreciate your help. Thank you very much. :-)
  
   1) Is this still the basic structure of the command: tavlang convert
   [options] output format input files? Am I wrong in thinking that
 the
   output formats are handled as options?
  
  
   Yes there is a little difference in the structure of commands now and
  then.
   So for the moment the command structure is like this.
  
   $tavlang convert [--out-put format] [options] [arguments]
  
  
   2) Are -r and -i ever used independently? If so, under what
  circumstances?
  
   No. In recursive case the input will be a directory containing
 .t2flow of
   .wfbundle files. The output dir is optional for both recursive and non
   recursive cases.
  
   I created a blog about the conversion command.
  
 
 https://menakamadushanka.wordpress.com/2015

RE: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Menaka,

Thank you for the feedback and clarifying information. Sorry not to respond
sooner. I am learning about bundles, etc. and reading the link you sent.

One thing, I'm having trouble getting to the example in the Examples of Use
Section: Example in full is at org.apache.taverna.robundle.TestExample

Can you help me? This is what I've done so far:

- Clicking on the link gets me the This is not the web page you are looking
for page. (This is the actual link address:
https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/purl/wf4ever/robundle/TestExample.java)

- Entering org.apache.taverna.robundle.TestExample also doesn't work for
me. I didn't think it would, but I tried anyway.

- Searching for taverna robundle TestExample on the main Apache.com page
yields no results.

I will continue to read and understand the RO Bundle API page, but I would
like to see the full Test Example, if possible.

Thanks!

Gale


-Original Message-
From: Menaka Madushanka [mailto:menaka12...@gmail.com]
Sent: Saturday, June 20, 2015 11:09 AM
To: dev@taverna.incubator.apache.org
Subject: Re: Taverna Language Command Line tool - convert command doc

That's cool.!! :-)
Correction:
https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-command-line-convert-examples/

 Example 2: Simple conversion, multiple input files, no options

 $tavlang convert –-robundle /someFile1.wfbundle /someFile2.wfbundle

 Converts */someFile1.wfbundle* and */someFile2.wfbundle* into
 *.robundle* format and saves the output files to the */converted*
 folder in the current working directory.

Taverna language *cannot* convert .wfbundles/.t2flow into robundle format.
Its only for some specific bundle formats. Go through this doc for more
info.

https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle

cheers.

On 20 June 2015 at 22:43, Gale Naylor ga...@noventussolutions.com wrote:

 Thank you for the Wordpress tip, Menaka! I have changed the two blog
 posts to use the pre tag, and it looks great. I also made a few
 refinements.

 Thanks,
 Gale

 On Fri, Jun 19, 2015 at 11:54 PM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Thank you very much Gale,
 
  I showed the output-format without brackets to indicate it is
  required and not optional because it appears to be always necessary
 
 
  That would be more accurate I think. I'm very new for documentation.
 Thank
  you very much.
 
   I left the -json output file type as having a single dash, but all
  the other output types have double-dashes. Should I change the json
  output argument to --json?
 
  -json should be --json. In my email that was a mistake. So you can
  use
 --.
 
  (Wordpress is driving me crazy because it is showing the
  double-dashes
  as long single dashes, even when I use the monospace font-family.
  Any
  suggestions?)
 
 
  Yes, wordpress does what it wants, but not us. :-) Use preformatted.
  Not paragraph. Then it would be ok. I updated my blog.
 
 https://menakamadushanka.wordpress.com/2015/06/18/apache-taverna-langu
 age-command-line-conversion-documentation/
 
  Thank you very much.
  Menaka
 
  I'll go through your documentations.
 
 
  On 20 June 2015 at 03:43, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
  Thanks for updating your blog! I have some additional feedback in
  the form of two blog posts. One has a detailed description (as I
  understand it) of the convert command and one has several examples,
  building on the examples in your blog. I hope these will help the
  discussion of the command structure. Here are the links:
 
 
 
 https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-co
 mmand-line-convert-command/
 
 
 
 https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-co
 mmand-line-convert-examples/
 
  Some things to note:
 
  (1) l basically used your June 18th post, but a few things (like
  the validate command) are from earlier posts/emails.
 
  (2) I showed the output-format without brackets to indicate it is
  required and not optional because it appears to be always necessary.
 
  (3) The way I understand the overall command structure, it seemed
  that all options (e.g., the output file directory) should come
  before the input-file-list, so that's what I assumed.
 
  (4) I left the -json output file type as having a single dash, but
  all the other output types have double-dashes. Should I change the
  json output argument to --json?
 
  Please let me know if anything is incorrect and I will change it. I
  realize the command structure is fluid, and I'm happy to make any
  changes as things evolve.
 
  (Wordpress is driving me crazy because it is showing the
  double-dashes as long single dashes, even when I use the monospace
  font-family. Any
  suggestions?)
 
  Thanks,
 
  Gale
 
  On Fri, Jun 19, 2015 at 10:11 AM, Menaka Madushanka
  menaka12...@gmail.com wrote:
   Hi Gale,
  
   Thank you very

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Menaka,

I am very happy to help, and I understand the command structure is a
little fluid right now. Thank you for the blog post; it was very
helpful.

I am a little confused about your recursive example. Can you help me
understand what you mean when you say the files will get saved to the
C directory? Because you show the output being saved to:
/home/usrname/toConvert/converted/somefile1.json

This is the example:
$tavlang convert –json -r -i /home/usrname/toConvert/  – Convert the
files and save them in the C directory.

Thank you!

Gale

B

On Fri, Jun 19, 2015 at 2:15 AM, Menaka Madushanka
menaka12...@gmail.com wrote:
 Hi Gale,
 I extremely appreciate your help. Thank you very much. :-)

 1) Is this still the basic structure of the command: tavlang convert
 [options] output format input files? Am I wrong in thinking that the
 output formats are handled as options?


 Yes there is a little difference in the structure of commands now and then.
 So for the moment the command structure is like this.

 $tavlang convert [--out-put format] [options] [arguments]


 2) Are -r and -i ever used independently? If so, under what circumstances?

 No. In recursive case the input will be a directory containing .t2flow of
 .wfbundle files. The output dir is optional for both recursive and non
 recursive cases.

 I created a blog about the conversion command.
 https://menakamadushanka.wordpress.com/2015/06/18/apache-taverna-language-command-line-conversion-documentation/

 If you have some suggestions, please inform.

 Thank you very much!

 Regards
 Menaka

 --
 Menaka Madushanka Jayawardena
 Faculty of Engineering, http://www.pdn.ac.lk/eng
 University of Peradeniyaya.
 LinkedIn http://lk.linkedin.com/in/menakajayawardena

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Menaka,

 According to the documentations provided, SCUFL is an experimental module.
 So It has not added to the tool yet.

Okay, I see now. That makes sense. FYI, because I am a visual person,
I took the Taverna
Language Module information and created a diagram:
https://galenaylor.wordpress.com/2015/06/27/apache-taverna-language-modules-diagram/

 The taverna language is capable of converting .t2flow workflows into
 .wfbundle and other formats, and .wfbundles into formats except .t2flow.

So, .wfbundles can be converted to .json and .iwir formats as well as
.structure?
If so, I will update my table.

 (.t2flow is the format of Taverna 2 and .wfbundle is the format of Taverna
 3)

Is it true that .wfbundle is the *bundle* format of Taverna 3
(taverna-sculf2-wfbundle)
and scufl2 is the *workflow* format of Taverna 3 (taverna-scufl2-api)?

 Input file type detection was done to avoid any exceptions when reading the
 wokflow file. ...
 In new_features2, I removed it because I have entered the wrong logic. I
 restored it.

Okay, understood.

Thank you!

Gale

On Fri, Jun 26, 2015 at 1:48 PM, Menaka Madushanka
menaka12...@gmail.com wrote:
 Hi Gale,
 According to the documentations provided, SCUFL is an experimental module.
 So It has not added to the tool yet.

 I presumed that.scufl2 workflows could be converted to the same
 formats as .t2flow workflows, but if that's not correct, let me know
 and I'll fix it.

 The taverna language is capable of converting .t2flow workflows into
 .wfbundle and other formats, and .wfbundles into formats except .t2flow.
 (.t2flow is the format of Taverna 2 and .wfbundle is the format of Taverna
 3)

 Also, I was wondering about something you said in one of your June
 25th emails ([GitHub] incubator-taverna-language pull request: New
 features2).
 You said File type detection removed.

 Which file type detection is this? Is this related to Stain's June 4th
 email, in which he said the input format is auto-guessed by
 WorkflowBundleIO? Just wondering, because in my blog I included this
 comment and I wanted to make sure it is still accurate.


 Input file type detection was done to avoid any exceptions when reading the
 wokflow file. The WorkflowBundleIO can guess the media type and read the
 bundle but, the input format could be wrongly entered by the user. We can't
 promise that the user could always do the correct thing. Also in recursive
 conversion, there could be other files also.

 In new_features2, I removed it because I have entered the wrong logic. I
 restored it.

 Thank you
 Menaka



 On 27 June 2015 at 01:54, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 A couple more things.

 I am trying to organize my understanding of how the conversions work,
 so I wrote a new blog post with a conversion table:

 https://galenaylor.wordpress.com/2015/06/26/apache-taverna-language-command-line-conversion-file-type-mapping/

 I presumed that.scufl2 workflows could be converted to the same
 formats as .t2flow workflows, but if that's not correct, let me know
 and I'll fix it. Should .scufl (Taverna 1) formats also be listed? The
 table is my best guess from reading all of the emails, so please let
 me know if anything is wrong, or if I missed something.

 Also, I was wondering about something you said in one of your June
 25th emails ([GitHub] incubator-taverna-language pull request: New
 features2).
 You said File type detection removed.

 Which file type detection is this? Is this related to Stain's June 4th
 email, in which he said the input format is auto-guessed by
 WorkflowBundleIO? Just wondering, because in my blog I included this
 comment and I wanted to make sure it is still accurate.

 Thanks!

 Gale

 On Fri, Jun 26, 2015 at 11:55 AM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Have a nice weekend too.!!! :-)
 
  On 27 June 2015 at 00:24, Menaka Madushanka menaka12...@gmail.com
 wrote:
 
  Hi Gale,
  I'm really appreciate your feedback on my blogs. I'm very new and there
  could be some flows. Thank you very much for showing them. :-)
 
  1) Yes, the types of bundle formats that can be converted are listed in
  this blog.
 
 
 https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
  The bundles are not workflows.
 
  2) No. It seems like the way I have wrote it somewhat misleading.
  Actually scufl2 workflows are not Bundles. Those are two different APIs.
  I'll update the blog. :-)
 
  3).Yes, my mistake. Neither .t2flow nor wfbundle could be converted into
  robundle.
 
  4). Yes Gale. That modification should be done. Other wise it looks like
  any format could be converted into Robundle. I'll update my blog too.
 
  Are there any more facts that need clarification about the blogs please
  ask me. :)
 
  Thank you very much Gale.
  Menaka
 
  On 27 June 2015 at 00:00, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
  I've been reading

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Menaka,

A couple more things.

I am trying to organize my understanding of how the conversions work,
so I wrote a new blog post with a conversion table:
https://galenaylor.wordpress.com/2015/06/26/apache-taverna-language-command-line-conversion-file-type-mapping/

I presumed that.scufl2 workflows could be converted to the same
formats as .t2flow workflows, but if that's not correct, let me know
and I'll fix it. Should .scufl (Taverna 1) formats also be listed? The
table is my best guess from reading all of the emails, so please let
me know if anything is wrong, or if I missed something.

Also, I was wondering about something you said in one of your June
25th emails ([GitHub] incubator-taverna-language pull request: New
features2).
You said File type detection removed.

Which file type detection is this? Is this related to Stain's June 4th
email, in which he said the input format is auto-guessed by
WorkflowBundleIO? Just wondering, because in my blog I included this
comment and I wanted to make sure it is still accurate.

Thanks!

Gale

On Fri, Jun 26, 2015 at 11:55 AM, Menaka Madushanka
menaka12...@gmail.com wrote:
 Have a nice weekend too.!!! :-)

 On 27 June 2015 at 00:24, Menaka Madushanka menaka12...@gmail.com wrote:

 Hi Gale,
 I'm really appreciate your feedback on my blogs. I'm very new and there
 could be some flows. Thank you very much for showing them. :-)

 1) Yes, the types of bundle formats that can be converted are listed in
 this blog.

 https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
 The bundles are not workflows.

 2) No. It seems like the way I have wrote it somewhat misleading.
 Actually scufl2 workflows are not Bundles. Those are two different APIs.
 I'll update the blog. :-)

 3).Yes, my mistake. Neither .t2flow nor wfbundle could be converted into
 robundle.

 4). Yes Gale. That modification should be done. Other wise it looks like
 any format could be converted into Robundle. I'll update my blog too.

 Are there any more facts that need clarification about the blogs please
 ask me. :)

 Thank you very much Gale.
 Menaka

 On 27 June 2015 at 00:00, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 I've been reading and learning more about research objects, and I
 think I understand better what is going on, but I still have some
 questions.

 1) I am curious as to which file types *can* be converted to .robundle
 format? (I must have missed something because I thought .t2flow and
 .wfbundle were the only allowed input file types.)

 2) In rereading your June 18th blog post, I see you say that the
 command line tool is for converting and managing workflow bundles as
 well as research object bundles. Are t2flow files workflow bundles
 or just workflows? Or is there not a practical difference?

 3) I understand now that not all file format conversions are valid.
 I'm trying to understand this better. In your June 18th blog post you
 say:

 The conversion function supports converting .t2flow and .wfbundle
 formats into following formats:

 .structure

 .json

 .iwir

 .wfbundle

 .wfdesc.ttl – (development in progress)

 .robundle – (development in progress)

 To me, reading this looks like all combinations are valid.

 I'm wondering, can both .t2flow and .wfbundle files be converted to
 all file types *except* robundle?


 4) I fixed the examples in my blog post.  Should I also change the
 --robundle option description to say Output bundle as .robundle
 instead of Output workflow as .robundle ? (Same for .wfbundle
 option.)

 Thanks for the feedback and the correct link to the example!

 Have a nice weekend.

 Gale



 On Wed, Jun 24, 2015 at 10:52 PM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Hi Gale,
  Use this link
 
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
 
  Cheers
  Menaka
 
  On 25 June 2015 at 05:34, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
  Thank you for the feedback and clarifying information. Sorry not to
 respond
  sooner. I am learning about bundles, etc. and reading the link you
 sent.
 
  One thing, I'm having trouble getting to the example in the Examples
 of Use
  Section: Example in full is at
 org.apache.taverna.robundle.TestExample
 
  Can you help me? This is what I've done so far:
 
  - Clicking on the link gets me the This is not the web page you are
  looking
  for page. (This is the actual link address:
 
 
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/purl/wf4ever/robundle/TestExample.java
  )
 
  - Entering org.apache.taverna.robundle.TestExample also doesn't work
 for
  me. I didn't think it would, but I tried anyway.
 
  - Searching for taverna robundle TestExample on the main Apache.com
 page
  yields no results.
 
  I will continue to read

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Menaka,

I found this doc in
http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API

Thanks for the link. I also found this mygrid link:
http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle,
which is very clear about the .wfbundle file extension.

I did notice the mygrid pages said the information was out of date.
So, I also looked at the taverna incubator documentation, and the
incubator SCUFL API page pointed me to a github page for the latest
information. I found the github SCUFL examples to be helpful:
https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-examples.
In the readme file, the t2flowtowfbundle tool describes the conversion
of a .t2flow file to a SCUFL2 .wfbundle.

Although I did find one example of a .scufl2 bundle
(http://dev.mygrid.org.uk/wiki/display/developer/2011-02+Scufl2+status
), most of the references indicate the correct file extension is
.wfbundle. So, I removed the .scufl2 references from my mapping table.
Please let me know if I missed something here.

I also updated the table to reflect the .wfbundle -- .json and
.wfbundle -- .iwir mappings.

Thanks!

Gale

On Sat, Jun 27, 2015 at 1:38 PM, Menaka Madushanka
menaka12...@gmail.com wrote:
 Hi Gale,

 So, .wfbundles can be converted to .json and .iwir formats as well as
 .structure?


 Yes.

 Is it true that .wfbundle is the *bundle* format of Taverna 3
 (taverna-sculf2-wfbundle)
 and scufl2 is the *workflow* format of Taverna 3 (taverna-scufl2-api)?


 I found this doc in
 http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API

  Cheers
 Menaka

 On 27 June 2015 at 22:46, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

  According to the documentations provided, SCUFL is an experimental
 module.
  So It has not added to the tool yet.

 Okay, I see now. That makes sense. FYI, because I am a visual person,
 I took the Taverna
 Language Module information and created a diagram:

 https://galenaylor.wordpress.com/2015/06/27/apache-taverna-language-modules-diagram/

  The taverna language is capable of converting .t2flow workflows into
  .wfbundle and other formats, and .wfbundles into formats except .t2flow.

 So, .wfbundles can be converted to .json and .iwir formats as well as
 .structure?
 If so, I will update my table.

  (.t2flow is the format of Taverna 2 and .wfbundle is the format of
 Taverna
  3)

 Is it true that .wfbundle is the *bundle* format of Taverna 3
 (taverna-sculf2-wfbundle)
 and scufl2 is the *workflow* format of Taverna 3 (taverna-scufl2-api)?

  Input file type detection was done to avoid any exceptions when reading
 the
  wokflow file. ...
  In new_features2, I removed it because I have entered the wrong logic. I
  restored it.

 Okay, understood.

 Thank you!

 Gale

 On Fri, Jun 26, 2015 at 1:48 PM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Hi Gale,
  According to the documentations provided, SCUFL is an experimental
 module.
  So It has not added to the tool yet.
 
  I presumed that.scufl2 workflows could be converted to the same
  formats as .t2flow workflows, but if that's not correct, let me know
  and I'll fix it.
 
  The taverna language is capable of converting .t2flow workflows into
  .wfbundle and other formats, and .wfbundles into formats except .t2flow.
  (.t2flow is the format of Taverna 2 and .wfbundle is the format of
 Taverna
  3)
 
  Also, I was wondering about something you said in one of your June
  25th emails ([GitHub] incubator-taverna-language pull request: New
  features2).
  You said File type detection removed.
 
  Which file type detection is this? Is this related to Stain's June 4th
  email, in which he said the input format is auto-guessed by
  WorkflowBundleIO? Just wondering, because in my blog I included this
  comment and I wanted to make sure it is still accurate.
 
 
  Input file type detection was done to avoid any exceptions when reading
 the
  wokflow file. The WorkflowBundleIO can guess the media type and read the
  bundle but, the input format could be wrongly entered by the user. We
 can't
  promise that the user could always do the correct thing. Also in
 recursive
  conversion, there could be other files also.
 
  In new_features2, I removed it because I have entered the wrong logic. I
  restored it.
 
  Thank you
  Menaka
 
 
 
  On 27 June 2015 at 01:54, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
  A couple more things.
 
  I am trying to organize my understanding of how the conversions work,
  so I wrote a new blog post with a conversion table:
 
 
 https://galenaylor.wordpress.com/2015/06/26/apache-taverna-language-command-line-conversion-file-type-mapping/
 
  I presumed that.scufl2 workflows could be converted to the same
  formats as .t2flow workflows, but if that's not correct, let me know
  and I'll fix it. Should .scufl (Taverna 1) formats also be listed? The
  table is my best guess from reading all of the emails, so please let
  me know if anything is wrong

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Stian,

Absolutely, I would be happy to contribute this diagram to Apache.  I have
never done that before. Can you point me to a link that describes the steps
I need to follow?

Thank you,

Gale
On Jul 2, 2015 4:54 PM, Stian Soiland-Reyes st...@apache.org wrote:

 This is brilliant diagram.. do you think you would consider
 contributing it to Apache so we can include it on our website?

 On 27 June 2015 at 18:16, Gale Naylor ga...@noventussolutions.com wrote:
  Hi Menaka,
 
  According to the documentations provided, SCUFL is an experimental
 module.
  So It has not added to the tool yet.
 
  Okay, I see now. That makes sense. FYI, because I am a visual person,
  I took the Taverna
  Language Module information and created a diagram:
 
 https://galenaylor.wordpress.com/2015/06/27/apache-taverna-language-modules-diagram/
 
  The taverna language is capable of converting .t2flow workflows into
  .wfbundle and other formats, and .wfbundles into formats except .t2flow.
 
  So, .wfbundles can be converted to .json and .iwir formats as well as
  .structure?
  If so, I will update my table.
 
  (.t2flow is the format of Taverna 2 and .wfbundle is the format of
 Taverna
  3)
 
  Is it true that .wfbundle is the *bundle* format of Taverna 3
  (taverna-sculf2-wfbundle)
  and scufl2 is the *workflow* format of Taverna 3 (taverna-scufl2-api)?
 
  Input file type detection was done to avoid any exceptions when reading
 the
  wokflow file. ...
  In new_features2, I removed it because I have entered the wrong logic. I
  restored it.
 
  Okay, understood.
 
  Thank you!
 
  Gale
 
  On Fri, Jun 26, 2015 at 1:48 PM, Menaka Madushanka
  menaka12...@gmail.com wrote:
  Hi Gale,
  According to the documentations provided, SCUFL is an experimental
 module.
  So It has not added to the tool yet.
 
  I presumed that.scufl2 workflows could be converted to the same
  formats as .t2flow workflows, but if that's not correct, let me know
  and I'll fix it.
 
  The taverna language is capable of converting .t2flow workflows into
  .wfbundle and other formats, and .wfbundles into formats except .t2flow.
  (.t2flow is the format of Taverna 2 and .wfbundle is the format of
 Taverna
  3)
 
  Also, I was wondering about something you said in one of your June
  25th emails ([GitHub] incubator-taverna-language pull request: New
  features2).
  You said File type detection removed.
 
  Which file type detection is this? Is this related to Stain's June 4th
  email, in which he said the input format is auto-guessed by
  WorkflowBundleIO? Just wondering, because in my blog I included this
  comment and I wanted to make sure it is still accurate.
 
 
  Input file type detection was done to avoid any exceptions when reading
 the
  wokflow file. The WorkflowBundleIO can guess the media type and read the
  bundle but, the input format could be wrongly entered by the user. We
 can't
  promise that the user could always do the correct thing. Also in
 recursive
  conversion, there could be other files also.
 
  In new_features2, I removed it because I have entered the wrong logic. I
  restored it.
 
  Thank you
  Menaka
 
 
 
  On 27 June 2015 at 01:54, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
  A couple more things.
 
  I am trying to organize my understanding of how the conversions work,
  so I wrote a new blog post with a conversion table:
 
 
 https://galenaylor.wordpress.com/2015/06/26/apache-taverna-language-command-line-conversion-file-type-mapping/
 
  I presumed that.scufl2 workflows could be converted to the same
  formats as .t2flow workflows, but if that's not correct, let me know
  and I'll fix it. Should .scufl (Taverna 1) formats also be listed? The
  table is my best guess from reading all of the emails, so please let
  me know if anything is wrong, or if I missed something.
 
  Also, I was wondering about something you said in one of your June
  25th emails ([GitHub] incubator-taverna-language pull request: New
  features2).
  You said File type detection removed.
 
  Which file type detection is this? Is this related to Stain's June 4th
  email, in which he said the input format is auto-guessed by
  WorkflowBundleIO? Just wondering, because in my blog I included this
  comment and I wanted to make sure it is still accurate.
 
  Thanks!
 
  Gale
 
  On Fri, Jun 26, 2015 at 11:55 AM, Menaka Madushanka
  menaka12...@gmail.com wrote:
   Have a nice weekend too.!!! :-)
  
   On 27 June 2015 at 00:24, Menaka Madushanka menaka12...@gmail.com
  wrote:
  
   Hi Gale,
   I'm really appreciate your feedback on my blogs. I'm very new and
 there
   could be some flows. Thank you very much for showing them. :-)
  
   1) Yes, the types of bundle formats that can be converted are
 listed in
   this blog.
  
  
 
 https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
   The bundles are not workflows.
  
   2) No. It seems like the way I have wrote

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hello Menaka,

I'm glad I was able to help! You are very welcome.

Gale
On Jul 1, 2015 11:24 PM, Menaka Madushanka menaka12...@gmail.com wrote:

 Hello Gale,
 I really appreciate your grate support.
 I learnt a lot from you. Also I edited my blogs.
 These are not for any submission but to track the progress and for future
 use (completing the full documentation).
 But I noticed there were so many errors as I'm new to documentation and
 blogging. :-)
 However by now I was able to correct those errors with your kind support.
 Thank you very much Gale. :-)
 I hope that I could write the final documentation more successfully with
 the support that you have given me

 Thank you very much for the effort, time and every thing that you spent for
 me.
 Have a very nice vacation. :-)

 Cheers
 Menaka Madushanka

 On 1 July 2015 at 07:25, Gale Naylor ga...@noventussolutions.com wrote:

  Hi Menaka,
 
  You are doing an excellent job on the documentation. I'm sorry for
  bombarding you with feedback, but I wanted to help as much as possible
  before I go on vacation.
 
  As I was reviewing your blog posts, I noticed that not all of the
  words in the titles are capitalized as they should be.
 
  Also, is your initial post part of your deliverable documentation, or
  has it been replaced by your later blog posts?
 
  Just a couple of things in the research object post:
 
  Taverna Language Command line tool – Conversion Documentation – Research
  objects
 
  -- Use the in front of following bundle formats and use into
  instead of in to: The Apache Taverna Language is capable of
  converting the following bundle formats into Research Object bundles.
  -- Use development: instead of development process: The
  conversion capability for other formats is still in development.
  -- Use is instead of in: ***The support for recursive
  conversion or selecting the output file directory is not yet
  included.
 
  Thanks!
 
  Gale
 
 
  On Tue, Jun 30, 2015 at 6:08 PM, Gale Naylor
  ga...@noventussolutions.com wrote:
   Hi Menaka,
  
   I looked at your validation documentation and I realized I have a
   question: If the validate command is run with no options, what
   happens? In other words, if you choose not to write the validation
   results to a log file, what does the command do? Write the results to
   the terminal? Does this need to be explained. (I guess I have the same
   question about the stats command.)
  
   Same comment as with stats documentation about adding sections with
   larger, and bold fonts to help with readability.
  
   Here are some additional comments:
  
   Apache Taverna Language Command line documentation – Validation
  
   -- Use examining rather than examine: The validation is done
   by examining the following factors/ problems.
   -- Use API instead of api, and use consisting instead of
   consist: The API returns a validation report consisting of problems
   that exist in the workflow.
   -- Instead of type of the problem use either problem category
   or category of problem and I suggest using listed instead of the
   first shown: If there are problems, those problems are listed under
   the problem category shown above.
   -- After The command line tool can execute this validation
   process how about saying  and tell the user if the workflow has
   errors/ problems and what they are. So the complete sentence would
   be: The command line tool can execute this validation process and
   tell the user if the workflow has errors/ problems and what they are.
   -- Even though you only have one option, I would still put the
   option on the next line, like you did in the Stats documentation.
   -- Also, if it's possible it would be good to standardize the
   documentation to say either Supported options or Options. You can
   use option(s) -- with the s in parentheses -- to mean it could be
   one option or more than one option.
   -- In the Usage section, you use [args]: $tavlang validate
   [options][args] input_files. In the convert and research objects
   posts you use [arguments], and in stats you didn't list arguments at
   all, yet it looks to me like the command structure is similar. It
   would be good to be consistent and use either [args] or [arguments].
   -- In the stats post you say Supported file formats: .t2flow and
   .wfbundle using and and in the validate post you say Supported
   input file formats:- .t2flow/ .wfbundle using /. Would it be
   possible to make these the same?
   -- At the end of your example with options, how about this
   instead: The output file contains the detailed report, including a
   list of the workflow problems.
  
   Good job on all the documentation!
  
   Gale
  
   On Tue, Jun 30, 2015 at 5:25 PM, Gale Naylor
   ga...@noventussolutions.com wrote:
   Hi Menaka,
  
   I read your stats blog post; it looks good.  I am not very familiar
   with workflows, so I'm not sure I can comment a lot

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Menaka,

Thank you. I appreciate your feedback, and I'd like to help however I can.

When do you expect to finish your project and documentation?

I'll be on vacation from July 1 through July 10, but I'll try to stay in touch.

Thanks,

Gale

On Mon, Jun 29, 2015 at 11:23 AM, Menaka Madushanka
menaka12...@gmail.com wrote:
 Hello Gale,
 Great work. :-)

 I did notice the mygrid pages said the information was out of date.

 Yes. I also faced the same condition when I was starting the project. The
 documentation will be updated very soon as the project releases. :-)

 I am to write the full complete documentation for the command line tool.
 I'll appreciate your support for it. :-)

 Cheers.
 Menaka

 On 29 June 2015 at 22:10, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 I found this doc in
 http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API

 Thanks for the link. I also found this mygrid link:
 http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle,
 which is very clear about the .wfbundle file extension.

 I did notice the mygrid pages said the information was out of date.
 So, I also looked at the taverna incubator documentation, and the
 incubator SCUFL API page pointed me to a github page for the latest
 information. I found the github SCUFL examples to be helpful:

 https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-examples
 .
 In the readme file, the t2flowtowfbundle tool describes the conversion
 of a .t2flow file to a SCUFL2 .wfbundle.

 Although I did find one example of a .scufl2 bundle
 (http://dev.mygrid.org.uk/wiki/display/developer/2011-02+Scufl2+status
 ), most of the references indicate the correct file extension is
 .wfbundle. So, I removed the .scufl2 references from my mapping table.
 Please let me know if I missed something here.

 I also updated the table to reflect the .wfbundle -- .json and
 .wfbundle -- .iwir mappings.

 Thanks!

 Gale

 On Sat, Jun 27, 2015 at 1:38 PM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Hi Gale,
 
  So, .wfbundles can be converted to .json and .iwir formats as well as
  .structure?
 
 
  Yes.
 
  Is it true that .wfbundle is the *bundle* format of Taverna 3
  (taverna-sculf2-wfbundle)
  and scufl2 is the *workflow* format of Taverna 3 (taverna-scufl2-api)?
 
 
  I found this doc in
  http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API
 
   Cheers
  Menaka
 
  On 27 June 2015 at 22:46, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
   According to the documentations provided, SCUFL is an experimental
  module.
   So It has not added to the tool yet.
 
  Okay, I see now. That makes sense. FYI, because I am a visual person,
  I took the Taverna
  Language Module information and created a diagram:
 
 
 https://galenaylor.wordpress.com/2015/06/27/apache-taverna-language-modules-diagram/
 
   The taverna language is capable of converting .t2flow workflows into
   .wfbundle and other formats, and .wfbundles into formats except
 .t2flow.
 
  So, .wfbundles can be converted to .json and .iwir formats as well as
  .structure?
  If so, I will update my table.
 
   (.t2flow is the format of Taverna 2 and .wfbundle is the format of
  Taverna
   3)
 
  Is it true that .wfbundle is the *bundle* format of Taverna 3
  (taverna-sculf2-wfbundle)
  and scufl2 is the *workflow* format of Taverna 3 (taverna-scufl2-api)?
 
   Input file type detection was done to avoid any exceptions when
 reading
  the
   wokflow file. ...
   In new_features2, I removed it because I have entered the wrong
 logic. I
   restored it.
 
  Okay, understood.
 
  Thank you!
 
  Gale
 
  On Fri, Jun 26, 2015 at 1:48 PM, Menaka Madushanka
  menaka12...@gmail.com wrote:
   Hi Gale,
   According to the documentations provided, SCUFL is an experimental
  module.
   So It has not added to the tool yet.
  
   I presumed that.scufl2 workflows could be converted to the same
   formats as .t2flow workflows, but if that's not correct, let me know
   and I'll fix it.
  
   The taverna language is capable of converting .t2flow workflows into
   .wfbundle and other formats, and .wfbundles into formats except
 .t2flow.
   (.t2flow is the format of Taverna 2 and .wfbundle is the format of
  Taverna
   3)
  
   Also, I was wondering about something you said in one of your June
   25th emails ([GitHub] incubator-taverna-language pull request: New
   features2).
   You said File type detection removed.
  
   Which file type detection is this? Is this related to Stain's June
 4th
   email, in which he said the input format is auto-guessed by
   WorkflowBundleIO? Just wondering, because in my blog I included this
   comment and I wanted to make sure it is still accurate.
  
  
   Input file type detection was done to avoid any exceptions when
 reading
  the
   wokflow file. The WorkflowBundleIO can guess the media type and read
 the
   bundle but, the input format could be wrongly entered by the user. We
  can't

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Menaka,

I'm so glad I could help. You've done a nice job on your blog posts.
If you don't mind, I can suggest some slight wording changes that I
believe will make your meanings more clear. For example:

Apache Taverna Language Command Line Tool – Supported functions and file types
Paragraph 1
  --  Capitalize Taverna and Language: The Apache Taverna
Language is still …
  --  Use Currently instead of By now: Currently the tool
supports…
Paragraph 2
  --  Add The to the beginning of the sentence: The
following file types are supported...
  -- I noticed you use .scufl2 in this blogpost, but .t2flow
in the next blogpost.

Please let me know if this kind of feedback would be helpful.

Thanks,

Gale

On Tue, Jun 30, 2015 at 7:43 AM, Menaka Madushanka
menaka12...@gmail.com wrote:
 Yes Gale,
 I'm thinking on taking them as a reference. For the best, I have some much
 better doc from you. :-) :-)

 Thank you very much.
 Menaka

 On 30 June 2015 at 20:09, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 Sounds great! Do you plan to use your blog to prepare the documentation?

 Feel free to use anything I've prepared if it helps. And if I can do
 any more before I go on vacation, I will let you know.

 Thanks,

 Gale

 On Tue, Jun 30, 2015 at 7:32 AM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Hi Gale,
 
  The tool is almost done I think. The functionalities,
  conversion,
  validation,
  inspection and
  statistics
 
  are done.
 
  So what remaining is, completing the documentation.
  I'll be able to finish it before 10 July hopefully. :-)
 
 
 
  On 30 June 2015 at 19:43, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
  Thank you. I appreciate your feedback, and I'd like to help however I
 can.
 
  When do you expect to finish your project and documentation?
 
  I'll be on vacation from July 1 through July 10, but I'll try to stay in
  touch.
 
  Thanks,
 
  Gale
 
  On Mon, Jun 29, 2015 at 11:23 AM, Menaka Madushanka
  menaka12...@gmail.com wrote:
   Hello Gale,
   Great work. :-)
  
   I did notice the mygrid pages said the information was out of date.
  
   Yes. I also faced the same condition when I was starting the project.
 The
   documentation will be updated very soon as the project releases. :-)
  
   I am to write the full complete documentation for the command line
 tool.
   I'll appreciate your support for it. :-)
  
   Cheers.
   Menaka
  
   On 29 June 2015 at 22:10, Gale Naylor ga...@noventussolutions.com
  wrote:
  
   Hi Menaka,
  
   I found this doc in
   http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API
  
   Thanks for the link. I also found this mygrid link:
  
 http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle
  ,
   which is very clear about the .wfbundle file extension.
  
   I did notice the mygrid pages said the information was out of date.
   So, I also looked at the taverna incubator documentation, and the
   incubator SCUFL API page pointed me to a github page for the latest
   information. I found the github SCUFL examples to be helpful:
  
  
 
 https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-examples
   .
   In the readme file, the t2flowtowfbundle tool describes the
 conversion
   of a .t2flow file to a SCUFL2 .wfbundle.
  
   Although I did find one example of a .scufl2 bundle
   (
 http://dev.mygrid.org.uk/wiki/display/developer/2011-02+Scufl2+status
   ), most of the references indicate the correct file extension is
   .wfbundle. So, I removed the .scufl2 references from my mapping
 table.
   Please let me know if I missed something here.
  
   I also updated the table to reflect the .wfbundle -- .json and
   .wfbundle -- .iwir mappings.
  
   Thanks!
  
   Gale
  
   On Sat, Jun 27, 2015 at 1:38 PM, Menaka Madushanka
   menaka12...@gmail.com wrote:
Hi Gale,
   
So, .wfbundles can be converted to .json and .iwir formats as well
 as
.structure?
   
   
Yes.
   
Is it true that .wfbundle is the *bundle* format of Taverna 3
(taverna-sculf2-wfbundle)
and scufl2 is the *workflow* format of Taverna 3
  (taverna-scufl2-api)?
   
   
I found this doc in
http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API
   
 Cheers
Menaka
   
On 27 June 2015 at 22:46, Gale Naylor ga...@noventussolutions.com
 
   wrote:
   
Hi Menaka,
   
 According to the documentations provided, SCUFL is an
 experimental
module.
 So It has not added to the tool yet.
   
Okay, I see now. That makes sense. FYI, because I am a visual
 person,
I took the Taverna
Language Module information and created a diagram:
   
   
  
 
 https://galenaylor.wordpress.com/2015/06/27/apache-taverna-language-modules-diagram/
   
 The taverna language is capable of converting .t2flow workflows
  into
 .wfbundle and other formats, and .wfbundles into formats except
   .t2flow.
   
So

Re: [GitHub] incubator-taverna-language pull request: Readme

[Gale Naylor]

Hi Menaka,

I've reviewed your readme file and I have a question and some minor
suggestions:

Is there a reason you have two Contribute sections? Would it be possible to
combine these? (Also, your second Contribute section is at the same level
as your title; I'm not sure you want that.)

Specific suggested changes (and questions):

Line 20: It seems like run should be plural
(inputs/outputs/runs instead of inputs/outputs/run).

Line 25: Add commas around therefore
(…from Taverna 2 and Taverna 1, and, therefore, can be also used
independently).

Line 40: Use contains instead of contain (The file NOTICE contains
any additional attributes…).

Line 46: Use sending and discussing instead of send and discuss
(… contribute by submitting …, sending ..., or discussing …).

Line 53: Replace the spaces in the dev@taverna link with %20 so the link
will be active.
(http://taverna.incubator.apache.org/community/lists#dev%20mailing%20list)

Line 57: Replace feature plannings with planned features
(Bugs and planned features…).

Line 79: Hyphenate decision-making (… and decision-making process).

Lines 90-105: (Module lists) I think these would easier to understand
if you used loads and saves (for example) instead of load/save
and have the grammar match throughout. So, you would end up with:

taverna-robundle loads, saves, and manages Research Object Bundles
(ZIP-based containers) (Note containers instead of container.)

taverna-databundle loads and saves RO bundles with workflow inputs,
outputs, and workflow run provenance
(Is this a correct interpretation of what databundle does? Would ... and
provides workflow provenance make more sense?)

For schemas and examples, I guess you would use a verb like lists
or provides? (I'm not entirely sure of the function of these two
modules.) So the schemas link might read, taverna-scufl2-schemas provides
SCUFL2 XML schemas and OWL ontologies.

Line 140: Hyphenate time-consuming (these can be time-consuming).

Line 192: Remove space between Apache Taverna Language downloads
link text and the URL, so the link will be active.

In lines 198 and 199, it looks like you don't need the second add.
Would You can alternatively copy and add these JARs from the build
to your classpath be accurate?

Lines 214-216: Did you want these links to be a bulleted list like
the ones above it? You might need a carriage return after line 213.

Hope this helps! Let me know if I've misunderstood anything, or if I've
been unclear.

Thanks,

Gale

On Sat, Jul 25, 2015 at 9:08 AM, menaka121 g...@git.apache.org wrote:
 GitHub user menaka121 opened a pull request:

 https://github.com/apache/incubator-taverna-language/pull/21

 Readme

 documentation

 You can merge this pull request into a Git repository by running:

 $ git pull https://github.com/menaka121/incubator-taverna-language Readme

 Alternatively you can review and apply these changes as the patch at:

 https://github.com/apache/incubator-taverna-language/pull/21.patch

 To close this pull request, make a commit to your master/trunk branch
 with (at least) the following in the commit message:

 This closes #21

 
 commit 95087e7d6899e574cec6b90f9783af67c812bf48
 Author: Menaka Madushanka menaka12...@gmail.com
 Date:   2015-07-25T16:06:32Z

 Readme

 


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Re: [jira] [Created] (TAVERNA-843) Link to Apache's Jira on Taverna Website(s)

[Gale Naylor]

I just opened a pull request. Let me know how it looks and if it is
doing everything you want.

Thanks,

Gale

On Tue, Jul 28, 2015 at 2:45 AM, Ian Dunlop ian.dun...@manchester.ac.uk wrote:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA256

 Hello,

 Please go ahead Gale :) Look forward to seeing the changes.

 Cheers,

 Ian

 On 28/07/2015 01:39, Gale Naylor wrote:
 I will take a shot at this, unless someone else has already
 started.

 Gale

 On Mon, Jul 13, 2015 at 6:07 AM, Stian Soiland-Reyes (JIRA)
 j...@apache.org wrote:
 Stian Soiland-Reyes created TAVERNA-843:
 ---

 Summary: Link to Apache's Jira on Taverna Website(s) Key:
 TAVERNA-843 URL:
 https://issues.apache.org/jira/browse/TAVERNA-843 Project: Apache
 Taverna Issue Type: Bug Components: Website Reporter: Stian
 Soiland-Reyes Priority: Critical


 The website should link prominently to the Issue tracker, e.g.
 from:

 http://taverna.incubator.apache.org/community/#contribute

 http://taverna.incubator.apache.org/download/code/#contribute-to-apac
 he-taverna



 and probably the main Community menu.

 The issue tracker is at:
 https://issues.apache.org/jira/browse/TAVERNA but it is not too
 good as a landing page as it does not say how to create an issue
 (anyone can make an account), etc.  The components are shown,
 that is at least good.


 Relevant source for website:

 https://github.com/apache/incubator-taverna-site/tree/trunk/content/c
 ommunity


 https://github.com/apache/incubator-taverna-site/tree/trunk/content/down
 load/code
 https://github.com/apache/incubator-taverna-site/blob/trunk/templates
 /default_navbar.html



 Any volunteers..? :-)



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Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Stian,

Does it make sense to turn this into a JIRA issue?

Gale

On Thu, Jul 2, 2015 at 7:51 AM, Stian Soiland-Reyes st...@apache.org wrote:
 Hi, Gale, thanks for your effort on documenting tavlang - as it's
 being developed!

 Do you think you could have a go at adding this to the website in
 MarkDown/HTML format..? See

 https://github.com/apache/incubator-taverna-site/tree/trunk/content/documentation/scufl2
 which is the source for
 http://taverna.incubator.apache.org/documentation/scufl2/

 (perhaps /scufl2  in the URL should be renamed to /language ?)





 .wfbundle workflows is a kind of earlier form of RO Bundle, but
 predates their formal specification and does not use the
 taverna-robundle API. So they were meant to be updated to also be full
 RO Bundles - basically having a JSON manifest instead/in addition to
 the XML one.  So it should at some point be possible to convert them.
 Perhaps a prototype converter could just copy over the files
 internally between the UCFPackage and the Bundle and thus update the
 new manifest?



 The code that does the wfbundle writing:
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLWriter.java
 and reading:
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLReader.java

 So this relies on the UCF support from:
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
 .. which is basically a proxy for manipulating a ZIP file and its manifest.


 But this should ideally be updated to use the RO Bundle API from:
 https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle


 and thus have proper support for linking the annotation/ files to
 their corresponding workflow elements, rather than having to parse
 them all to find the right one.

 as the UCFPackage types are used throughout the wfbundle writer
 changing this would take a bit of effort.. or just wrapping it from
 UCFPackage. Here's an earlier attempt:

 https://github.com/apache/incubator-taverna-language/blob/ucfpackage-robundle/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java

 (Note: That branch has test errors)


 As you see it calls the writeAsODFManifest(); which writes out the
 classic META-INF/manifest.xml for backwards compatibility. This is
 permitted by our spec - but violating a NOT RECOMMENDED (e.g. Know
 what you are doing):
 https://w3id.org/bundle#manifest-xml

 On 26 June 2015 at 19:54, Menaka Madushanka menaka12...@gmail.com wrote:
 Hi Gale,
 I'm really appreciate your feedback on my blogs. I'm very new and there
 could be some flows. Thank you very much for showing them. :-)

 1) Yes, the types of bundle formats that can be converted are listed in
 this blog.
 https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
 The bundles are not workflows.

 2) No. It seems like the way I have wrote it somewhat misleading.
 Actually scufl2 workflows are not Bundles. Those are two different APIs.
 I'll update the blog. :-)

 3).Yes, my mistake. Neither .t2flow nor wfbundle could be converted into
 robundle.

 4). Yes Gale. That modification should be done. Other wise it looks like
 any format could be converted into Robundle. I'll update my blog too.

 Are there any more facts that need clarification about the blogs please ask
 me. :)

 Thank you very much Gale.
 Menaka

 On 27 June 2015 at 00:00, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 I've been reading and learning more about research objects, and I
 think I understand better what is going on, but I still have some
 questions.

 1) I am curious as to which file types *can* be converted to .robundle
 format? (I must have missed something because I thought .t2flow and
 .wfbundle were the only allowed input file types.)

 2) In rereading your June 18th blog post, I see you say that the
 command line tool is for converting and managing workflow bundles as
 well as research object bundles. Are t2flow files workflow bundles
 or just workflows? Or is there not a practical difference?

 3) I understand now that not all file format conversions are valid.
 I'm trying to understand this better. In your June 18th blog post you
 say:

 The conversion function supports converting .t2flow and .wfbundle
 formats into following formats:

 .structure

 .json

 .iwir

 .wfbundle

 .wfdesc.ttl – (development in progress)

 .robundle – (development in progress)

 To me, reading this looks like all combinations are valid.

 I'm wondering, can both .t2flow and .wfbundle files be converted to
 all file types *except* robundle?


 4) I fixed the examples in my blog post.  Should I also change

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

I would do it, but I need clarification as to what exactly you are looking for.

Gale

On Tue, Jul 28, 2015 at 12:25 PM, Gale Naylor
ga...@noventussolutions.com wrote:
 Hi Stian,

 Does it make sense to turn this into a JIRA issue?

 Gale

 On Thu, Jul 2, 2015 at 7:51 AM, Stian Soiland-Reyes st...@apache.org wrote:
 Hi, Gale, thanks for your effort on documenting tavlang - as it's
 being developed!

 Do you think you could have a go at adding this to the website in
 MarkDown/HTML format..? See

 https://github.com/apache/incubator-taverna-site/tree/trunk/content/documentation/scufl2
 which is the source for
 http://taverna.incubator.apache.org/documentation/scufl2/

 (perhaps /scufl2  in the URL should be renamed to /language ?)





 .wfbundle workflows is a kind of earlier form of RO Bundle, but
 predates their formal specification and does not use the
 taverna-robundle API. So they were meant to be updated to also be full
 RO Bundles - basically having a JSON manifest instead/in addition to
 the XML one.  So it should at some point be possible to convert them.
 Perhaps a prototype converter could just copy over the files
 internally between the UCFPackage and the Bundle and thus update the
 new manifest?



 The code that does the wfbundle writing:
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLWriter.java
 and reading:
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLReader.java

 So this relies on the UCF support from:
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
 .. which is basically a proxy for manipulating a ZIP file and its manifest.


 But this should ideally be updated to use the RO Bundle API from:
 https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle


 and thus have proper support for linking the annotation/ files to
 their corresponding workflow elements, rather than having to parse
 them all to find the right one.

 as the UCFPackage types are used throughout the wfbundle writer
 changing this would take a bit of effort.. or just wrapping it from
 UCFPackage. Here's an earlier attempt:

 https://github.com/apache/incubator-taverna-language/blob/ucfpackage-robundle/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java

 (Note: That branch has test errors)


 As you see it calls the writeAsODFManifest(); which writes out the
 classic META-INF/manifest.xml for backwards compatibility. This is
 permitted by our spec - but violating a NOT RECOMMENDED (e.g. Know
 what you are doing):
 https://w3id.org/bundle#manifest-xml

 On 26 June 2015 at 19:54, Menaka Madushanka menaka12...@gmail.com wrote:
 Hi Gale,
 I'm really appreciate your feedback on my blogs. I'm very new and there
 could be some flows. Thank you very much for showing them. :-)

 1) Yes, the types of bundle formats that can be converted are listed in
 this blog.
 https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
 The bundles are not workflows.

 2) No. It seems like the way I have wrote it somewhat misleading.
 Actually scufl2 workflows are not Bundles. Those are two different APIs.
 I'll update the blog. :-)

 3).Yes, my mistake. Neither .t2flow nor wfbundle could be converted into
 robundle.

 4). Yes Gale. That modification should be done. Other wise it looks like
 any format could be converted into Robundle. I'll update my blog too.

 Are there any more facts that need clarification about the blogs please ask
 me. :)

 Thank you very much Gale.
 Menaka

 On 27 June 2015 at 00:00, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 I've been reading and learning more about research objects, and I
 think I understand better what is going on, but I still have some
 questions.

 1) I am curious as to which file types *can* be converted to .robundle
 format? (I must have missed something because I thought .t2flow and
 .wfbundle were the only allowed input file types.)

 2) In rereading your June 18th blog post, I see you say that the
 command line tool is for converting and managing workflow bundles as
 well as research object bundles. Are t2flow files workflow bundles
 or just workflows? Or is there not a practical difference?

 3) I understand now that not all file format conversions are valid.
 I'm trying to understand this better. In your June 18th blog post you
 say:

 The conversion function supports converting .t2flow and .wfbundle
 formats into following formats:

 .structure

 .json

 .iwir

 .wfbundle

 .wfdesc.ttl – (development in progress)

 .robundle – (development in progress)

 To me, reading this looks like all combinations are valid

Re: [GitHub] incubator-taverna-language pull request: Readme

[Gale Naylor]

You are very welcome, Menaka! Glad I could help.

Gale
On Aug 5, 2015 9:53 AM, Menaka Madushanka menaka12...@gmail.com wrote:

 Hi Gale,

 That was very impressive.

 I did the modifications you mentioned.

 I greatly appreciate the support you gave me throughout the project. I was
 able to complete the work more accurately because of you. Thank you very
 much.

 Menaka

 On 5 August 2015 at 21:59, asfgit g...@git.apache.org wrote:

  Github user asfgit closed the pull request at:
 
  https://github.com/apache/incubator-taverna-language/pull/21
 
 
  ---
  If your project is set up for it, you can reply to this email and have
 your
  reply appear on GitHub as well. If your project does not have this
 feature
  enabled and wishes so, or if the feature is enabled but not working,
 please
  contact infrastructure at infrastruct...@apache.org or file a JIRA
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  with INFRA.
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 --
 Menaka Madushanka Jayawardena
 Faculty of Engineering, http://www.pdn.ac.lk/eng
 University of Peradeniyaya.
 LinkedIn http://lk.linkedin.com/in/menakajayawardena

Re: [GitHub] incubator-taverna-language pull request: Readme

[Gale Naylor]

Okay.  Thanks for the link.  I will take a look at it and get back to you.

Gale
On Aug 3, 2015 10:43 AM, Menaka Madushanka menaka12...@gmail.com wrote:

 Hello Gale,

 Thank you very much for reviewing. :-)
 But, I think you have reviewed the wrong file.
 The Readme.md which you have reviewed is the main project Readme file. The
 readme for the command line tool is in the taverna-language-commandline
 module and it is not merged yet.
 Here is the link for that file.

 https://github.com/menaka121/incubator-taverna-language/tree/Readme/taverna-language-commandline

 If you could please review it and give me some feedback. I used the content
 from my blogs which were reviewed by you. :-)
 So the structure is almost same.

 Thank you very much
 Menaka

 On 31 July 2015 at 02:12, Gale Naylor ga...@noventussolutions.com wrote:

  Hi Menaka,
 
  I've reviewed your readme file and I have a question and some minor
  suggestions:
 
  Is there a reason you have two Contribute sections? Would it be possible
 to
  combine these? (Also, your second Contribute section is at the same level
  as your title; I'm not sure you want that.)
 
  Specific suggested changes (and questions):
 
  Line 20: It seems like run should be plural
  (inputs/outputs/runs instead of inputs/outputs/run).
 
  Line 25: Add commas around therefore
  (…from Taverna 2 and Taverna 1, and, therefore, can be also used
  independently).
 
  Line 40: Use contains instead of contain (The file NOTICE contains
  any additional attributes…).
 
  Line 46: Use sending and discussing instead of send and discuss
  (… contribute by submitting …, sending ..., or discussing …).
 
  Line 53: Replace the spaces in the dev@taverna link with %20 so the link
  will be active.
  (
 http://taverna.incubator.apache.org/community/lists#dev%20mailing%20list)
 
  Line 57: Replace feature plannings with planned features
  (Bugs and planned features…).
 
  Line 79: Hyphenate decision-making (… and decision-making process).
 
  Lines 90-105: (Module lists) I think these would easier to understand
  if you used loads and saves (for example) instead of load/save
  and have the grammar match throughout. So, you would end up with:
 
  taverna-robundle loads, saves, and manages Research Object Bundles
  (ZIP-based containers) (Note containers instead of container.)
 
  taverna-databundle loads and saves RO bundles with workflow inputs,
  outputs, and workflow run provenance
  (Is this a correct interpretation of what databundle does? Would ... and
  provides workflow provenance make more sense?)
 
  For schemas and examples, I guess you would use a verb like lists
  or provides? (I'm not entirely sure of the function of these two
  modules.) So the schemas link might read, taverna-scufl2-schemas
 provides
  SCUFL2 XML schemas and OWL ontologies.
 
  Line 140: Hyphenate time-consuming (these can be time-consuming).
 
  Line 192: Remove space between Apache Taverna Language downloads
  link text and the URL, so the link will be active.
 
  In lines 198 and 199, it looks like you don't need the second add.
  Would You can alternatively copy and add these JARs from the build
  to your classpath be accurate?
 
  Lines 214-216: Did you want these links to be a bulleted list like
  the ones above it? You might need a carriage return after line 213.
 
  Hope this helps! Let me know if I've misunderstood anything, or if I've
  been unclear.
 
  Thanks,
 
  Gale
 
  On Sat, Jul 25, 2015 at 9:08 AM, menaka121 g...@git.apache.org wrote:
   GitHub user menaka121 opened a pull request:
  
   https://github.com/apache/incubator-taverna-language/pull/21
  
   Readme
  
   documentation
  
   You can merge this pull request into a Git repository by running:
  
   $ git pull https://github.com/menaka121/incubator-taverna-language
  Readme
  
   Alternatively you can review and apply these changes as the patch at:
  
   https://github.com/apache/incubator-taverna-language/pull/21.patch
  
   To close this pull request, make a commit to your master/trunk branch
   with (at least) the following in the commit message:
  
   This closes #21
  
   
   commit 95087e7d6899e574cec6b90f9783af67c812bf48
   Author: Menaka Madushanka menaka12...@gmail.com
   Date:   2015-07-25T16:06:32Z
  
   Readme
  
   
  
  
   ---
   If your project is set up for it, you can reply to this email and have
  your
   reply appear on GitHub as well. If your project does not have this
  feature
   enabled and wishes so, or if the feature is enabled but not working,
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 --
 Menaka Madushanka Jayawardena
 Faculty of Engineering, http://www.pdn.ac.lk/eng
 University of Peradeniyaya.
 LinkedIn http://lk.linkedin.com/in/menakajayawardena

Re: Draft: Taverna Language download page

[Gale Naylor]

@Stian One other minor thing: In the second paragraph, I think there
should be a semi-color between -section.jar and however, and a
comma after however. So, like this: ...artifacts include -javadoc.jar
and  -section.jar; however, you might prefer ...

Cheers!

Gale

On Mon, Aug 10, 2015 at 7:57 AM, Stian Soiland-Reyes st...@apache.org wrote:
 How about like this with split sections?

 http://taverna.staging.apache.org/download/language/

 On 10 August 2015 at 15:46, Stian Soiland-Reyes st...@apache.org wrote:
 Here means the 0.15.0-incubating headline right below.. so I'll
 change it to Below?



 On 10 August 2015 at 15:01, Gale Naylor ga...@noventussolutions.com wrote:
 Hi Stain,

 Is there supposed to be a link in the sentence (under Source Code) where it
 says, Here you can find all Taverna Language source releases.?

 Thanks,

 Gale

 -Original Message-
 From: Stian Soiland-Reyes [mailto:st...@apache.org]
 Sent: Monday, August 10, 2015 6:44 AM
 To: dev@taverna.incubator.apache.org
 Subject: Draft: Taverna Language download page

 I have drafted a download page for Taverna Language here:

 http://taverna.staging.apache.org/download/language/

 Note that the download and Maven links don't work yet, as Ian has push the
 right buttons and then we have to wait 24h for the mirrors.

 I included the taverna-parent download here, as I think it would be a bit
 silly on a page by itself. You wouldn't normally need it as it would be
 downloaded from Central if you just tried to build Language.


 Comments? Feel free to edit!



 Should we rename the file downloads to apache-taverna-* ?

 The checksums should stay the same, but Ian might have to regenerate the
 .asc signature. Mentors, is that permitted given that we voted on a sha1
 sum?

 Obviously for the future we should need to modify the Maven build so the
 release files always get the apache- prefix directly:



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



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



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

Re: Draft: Taverna Language download page

[Gale Naylor]

Yes! I think that looks better.

On Mon, Aug 10, 2015 at 7:57 AM, Stian Soiland-Reyes st...@apache.org wrote:
 How about like this with split sections?

 http://taverna.staging.apache.org/download/language/

 On 10 August 2015 at 15:46, Stian Soiland-Reyes st...@apache.org wrote:
 Here means the 0.15.0-incubating headline right below.. so I'll
 change it to Below?



 On 10 August 2015 at 15:01, Gale Naylor ga...@noventussolutions.com wrote:
 Hi Stain,

 Is there supposed to be a link in the sentence (under Source Code) where it
 says, Here you can find all Taverna Language source releases.?

 Thanks,

 Gale

 -Original Message-
 From: Stian Soiland-Reyes [mailto:st...@apache.org]
 Sent: Monday, August 10, 2015 6:44 AM
 To: dev@taverna.incubator.apache.org
 Subject: Draft: Taverna Language download page

 I have drafted a download page for Taverna Language here:

 http://taverna.staging.apache.org/download/language/

 Note that the download and Maven links don't work yet, as Ian has push the
 right buttons and then we have to wait 24h for the mirrors.

 I included the taverna-parent download here, as I think it would be a bit
 silly on a page by itself. You wouldn't normally need it as it would be
 downloaded from Central if you just tried to build Language.


 Comments? Feel free to edit!



 Should we rename the file downloads to apache-taverna-* ?

 The checksums should stay the same, but Ian might have to regenerate the
 .asc signature. Mentors, is that permitted given that we voted on a sha1
 sum?

 Obviously for the future we should need to modify the Maven build so the
 release files always get the apache- prefix directly:



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



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



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

RE: Draft: Taverna Language download page

[Gale Naylor]

Hi Stain,

Is there supposed to be a link in the sentence (under Source Code) where it
says, Here you can find all Taverna Language source releases.?

Thanks,

Gale

-Original Message-
From: Stian Soiland-Reyes [mailto:st...@apache.org]
Sent: Monday, August 10, 2015 6:44 AM
To: dev@taverna.incubator.apache.org
Subject: Draft: Taverna Language download page

I have drafted a download page for Taverna Language here:

http://taverna.staging.apache.org/download/language/

Note that the download and Maven links don't work yet, as Ian has push the
right buttons and then we have to wait 24h for the mirrors.

I included the taverna-parent download here, as I think it would be a bit
silly on a page by itself. You wouldn't normally need it as it would be
downloaded from Central if you just tried to build Language.


Comments? Feel free to edit!



Should we rename the file downloads to apache-taverna-* ?

The checksums should stay the same, but Ian might have to regenerate the
.asc signature. Mentors, is that permitted given that we voted on a sha1
sum?

Obviously for the future we should need to modify the Maven build so the
release files always get the apache- prefix directly:



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

Re: [GitHub] incubator-taverna-language pull request: Readme

[Gale Naylor]

Hi Menaka,

Okay, so I finally reviewed the *correct* file. ;-)  I'm not sure how I
managed to review the wrong file, but oh, well.

Your readme file looks very professional! It's a big file, and I did notice
a few typos and minor things, so here are my suggestions:

Line 26: Add a before work in progress (a *work in progress*).

Line 41: Use contains instead of contain (The file NOTICE contains
any additional …).

Line 47: Replace the spaces in the dev@taverna link with %20 so the
link will be active.
(http://taverna.incubator.apache.org/community/lists#dev%20mailing%20list)

Line 52: Replace feature plannings with planned features
(Bugs and planned features…).

Line 67: Is there a reason you chose Requisites instead of Prerequisites?
I could be wrong, but it seems to me that Prerequisites is the correct word. See
http://www.differencebetween.com/difference-between-prerequisite-and-vs-requisite/

Line 87: Misspelled Taverna in Usage/help section.

Line 89: To be consistent, you should capitalize the word validate in the
description section (Validate the given workflow).

Line 96: Consider starting the sentence with the (The Taverna language
command line tool…) and it should be accessing rather than access
(… for accessing the features…).

Line 97: Add a second the after has and end with a colon. Also,
in the spirit of using plain English, functions is probably better
than functionalities. Consider: The tool provides the following
functions:

Line 108: (This is a very common mistake.) Use its instead of it's.
(Each command has its own set of options.)

Line 111: Add a second the after has and end with a colon. Consider
using accepts instead of has. So, The tool accepts the following
major commands:

Line 122: Misspelled workflow.

Line 126: I'm curious what the 's mean. You have them around both
`--output_format` and options. Is `--output_format` optional?
Also, am I correct that [arguments] refers to the arguments for the options?
What about the filenames? (See Line 214 where you have
workflow bundles to be inspected. Or later on, you use input_files,
which is very self-explanatory.

Line 138: Since on the next few lines you are labeling the two ways of using
the conversion command as methods, consider saying something like
There are two methods for using the conversion command.

Line 154: You might want to mention that storing the converted files in the
/converted directory is the default behavior. Also, since you are using full
sentences, I would use the and say, … in the /converted directory.

Line 189: In this line it says … store them in
/home/user/workflows_to_convert/converted directory. But in line 187,
it says the directory is /home/workflows.
Are these supposed to be the same directory?
Also, it's okay to say … store them in /home/user/workflows (without
the word directory) but if you add the word directory you should
really use the and say the /home/user/workflows directory.

Line 210: Use supported instead of support and use and between
formats because there are only two.
(Supported workflow bundle formats: .wfbundle and .t2flow.)

Line 218: Misspelled service in servicetypes.

Lines 227 and 235: You have a number and nothing else. You might want
to say 1. Service Types and 2. Processor Names as headers here.

Line 255: Use gives instead of give (… file or files and gives the
validation report.)
Line 255: Capitalize validate (Validate tool checks for …)

Line 260: Hyphenate Non Absolute (Non-Absolute URI Problem)

Line 283: The code sample is rendering as regular test. There are a couple
of ways to fix this. If you delete the asterisk and space (* ), and make
Line 281 a regular line, the code that follows (in Line 283) will render
like the rest of the code samples.  Alternatively, if you add more spaces
to line 283, it will render correctly.  (Same issue in lines 295 – 304.)

Line 309: Do you mean to say here that this report contains more explanation?
If so, you could say, This report is more explanatory.

Line 361: Misspelled resources.

I know a lot of these are picky, but it will make your readme file
stand out in a good way! Nice job.

Gale

On Mon, Aug 3, 2015 at 11:27 AM, Gale Naylor
ga...@noventussolutions.com wrote:
 Okay.  Thanks for the link.  I will take a look at it and get back to you.

 Gale

 On Aug 3, 2015 10:43 AM, Menaka Madushanka menaka12...@gmail.com wrote:

 Hello Gale,

 Thank you very much for reviewing. :-)
 But, I think you have reviewed the wrong file.
 The Readme.md which you have reviewed is the main project Readme file. The
 readme for the command line tool is in the taverna-language-commandline
 module and it is not merged yet.
 Here is the link for that file.

 https://github.com/menaka121/incubator-taverna-language/tree/Readme/taverna-language-commandline

 If you could please review it and give me some feedback. I used the
 content
 from my blogs which were reviewed by you. :-)
 So the structure is almost same.

 Thank you very much
 Menaka

 On 31 July

Re: [jira] [Created] (TAVERNA-843) Link to Apache's Jira on Taverna Website(s)

[Gale Naylor]

I will take a shot at this, unless someone else has already started.

Gale

On Mon, Jul 13, 2015 at 6:07 AM, Stian Soiland-Reyes (JIRA)
j...@apache.org wrote:
 Stian Soiland-Reyes created TAVERNA-843:
 ---

  Summary: Link to Apache's Jira on Taverna Website(s)
  Key: TAVERNA-843
  URL: https://issues.apache.org/jira/browse/TAVERNA-843
  Project: Apache Taverna
   Issue Type: Bug
   Components: Website
 Reporter: Stian Soiland-Reyes
 Priority: Critical


 The website should link prominently to the Issue tracker, e.g. from:

 http://taverna.incubator.apache.org/community/#contribute

 http://taverna.incubator.apache.org/download/code/#contribute-to-apache-taverna

 and probably the main Community menu.

 The issue tracker is at:
 https://issues.apache.org/jira/browse/TAVERNA
 but it is not too good as a landing page as it does not say how to create an 
 issue (anyone can make an account), etc.  The components are shown, that is 
 at least good.


 Relevant source for website:

 https://github.com/apache/incubator-taverna-site/tree/trunk/content/community
 https://github.com/apache/incubator-taverna-site/tree/trunk/content/download/code
 https://github.com/apache/incubator-taverna-site/blob/trunk/templates/default_navbar.html

 Any volunteers..? :-)



 --
 This message was sent by Atlassian JIRA
 (v6.3.4#6332)

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Ian,

The last 3 pull requests I made (update index.md, merge pull request
#1, and update index.md) I did not intend to make. I didn't realize
they were going out. Sorry if it was confusing.

I tried to fix the broken links in the
https://github.com/apache/incubator-taverna-site pages, but now I
understand the links only work in the
http://taverna.incubator.apache.org/documentation/scufl2/ pages. I
thought I was trying something in a local copy.

Is there a process for rejecting them, or can I just delete my github
repository and fork a new one?


Gale

On Tue, Jul 21, 2015 at 7:35 AM, Ian Dunlop ian.dun...@manchester.ac.uk wrote:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA256

 Hello,

 Hi Gale. I can see the pull request here
 https://github.com/apache/incubator-taverna-site/pull/1
 Thanks very much :)
 We'll have a look and get it merged soon (or feedback in case any
 changes etc are needed).

 Cheers,

 Ian

 On 21/07/2015 15:04, Gale Naylor wrote:
 Hi Stian,

 I have submitted a pull request regarding adding the Taverna
 Language Modules diagram. This is my first time, so I'm not sure if
 I did it correctly or if there is anything else I need to do now.

 Thank you,

 Gale

 On Mon, Jul 13, 2015 at 8:33 AM, Stian Soiland-Reyes
 st...@apache.org wrote:
 Thanks!

 We have a general contributor guide for the website here:

 http://taverna.incubator.apache.org/community/edit


 Editing the website itself in a fork can be done in the GitHub
 web interface, but to add the diagram to a GitHub pull request
 (e.g. ) would probably require you to check out from your fork
 of https://github.com/apache/incubator-taverna-site --

 you could also contribute it as an attachment to a Jira bug
 report:
 https://issues.apache.org/jira/browse/TAVERNA/component/12326819


 I don't think a single diagram would require a CLA with ASF -
 your contribution should be automatically covered by the #5 in
 http://www.apache.org/licenses/LICENSE-2.0 - but we might need
 you to sign a CLA - http://www.apache.org/licenses/#clas - before
 we can accept larger contributions.





 On 3 July 2015 at 05:29, Gale Naylor
 ga...@noventussolutions.com wrote:
 Hi Stian,

 Yes, when I get home from vacation (July 10-11), I will look at
 this information more carefully and have a go at adding it to
 the website. I will let you know if I have any questions.

 Thank you,

 Gale On Jul 2, 2015 4:52 PM, Stian Soiland-Reyes
 st...@apache.org wrote:

 Hi, Gale, thanks for your effort on documenting tavlang - as
 it's being developed!

 Do you think you could have a go at adding this to the
 website in MarkDown/HTML format..? See


 https://github.com/apache/incubator-taverna-site/tree/trunk/content
 /documentation/scufl2


 which is the source for
 http://taverna.incubator.apache.org/documentation/scufl2/

 (perhaps /scufl2  in the URL should be renamed to /language
 ?)





 .wfbundle workflows is a kind of earlier form of RO Bundle,
 but predates their formal specification and does not use the
 taverna-robundle API. So they were meant to be updated to
 also be full RO Bundles - basically having a JSON manifest
 instead/in addition to the XML one.  So it should at some
 point be possible to convert them. Perhaps a prototype
 converter could just copy over the files internally between
 the UCFPackage and the Bundle and thus update the new
 manifest?



 The code that does the wfbundle writing:

 https://github.com/apache/incubator-taverna-language/blob/master/ta
 verna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDF
 XMLWriter.java


 and reading:

 https://github.com/apache/incubator-taverna-language/blob/master/ta
 verna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDF
 XMLReader.java



 So this relies on the UCF support from:

 https://github.com/apache/incubator-taverna-language/blob/master/ta
 verna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpacka
 ge/UCFPackage.java


 .. which is basically a proxy for manipulating a ZIP file and its manife
 st.


 But this should ideally be updated to use the RO Bundle API
 from:

 https://github.com/apache/incubator-taverna-language/tree/master/ta
 verna-robundle




 and thus have proper support for linking the annotation/ files to
 their corresponding workflow elements, rather than having to
 parse them all to find the right one.

 as the UCFPackage types are used throughout the wfbundle
 writer changing this would take a bit of effort.. or just
 wrapping it from UCFPackage. Here's an earlier attempt:


 https://github.com/apache/incubator-taverna-language/blob/ucfpackag
 e-robundle/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/sc
 ufl2/ucfpackage/UCFPackage.java



 (Note: That branch has test errors)


 As you see it calls the writeAsODFManifest(); which writes
 out the classic META-INF/manifest.xml for backwards
 compatibility. This is permitted by our spec - but violating
 a NOT RECOMMENDED (e.g. Know what you are doing

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Stian,

 Do you think you could have a go at adding this to the website in
 MarkDown/HTML format..? See

I'd be happy to. Are you referring to adding the Taverna Language
Module diagram to the website, or the command line documentation in my
blog posts? I created a pull request to add the diagram to the img
folder in the incubator-taverna-site/content folder.

 (perhaps /scufl2  in the URL should be renamed to /language ?)

I'm not sure. I just realized there is are two repositories:
incubator-taverna-site and incubator-taverna-language. Can you help me
understand the difference/relationship between these two repositories?

Also, I'm not sure what you wanted me to do with the rest of the
information you included:

 .wfbundle workflows is a kind of earlier form of RO Bundle, but
 predates their formal specification and does not use the
 taverna-robundle API. ...
...
 But this should ideally be updated to use the RO Bundle API from:
 https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle

etc.

But I'm not really a programmer. This would be outside my area of expertise.

Thanks,

Gale







 On 26 June 2015 at 19:54, Menaka Madushanka menaka12...@gmail.com wrote:
 Hi Gale,
 I'm really appreciate your feedback on my blogs. I'm very new and there
 could be some flows. Thank you very much for showing them. :-)

 1) Yes, the types of bundle formats that can be converted are listed in
 this blog.
 https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
 The bundles are not workflows.

 2) No. It seems like the way I have wrote it somewhat misleading.
 Actually scufl2 workflows are not Bundles. Those are two different APIs.
 I'll update the blog. :-)

 3).Yes, my mistake. Neither .t2flow nor wfbundle could be converted into
 robundle.

 4). Yes Gale. That modification should be done. Other wise it looks like
 any format could be converted into Robundle. I'll update my blog too.

 Are there any more facts that need clarification about the blogs please ask
 me. :)

 Thank you very much Gale.
 Menaka

 On 27 June 2015 at 00:00, Gale Naylor ga...@noventussolutions.com wrote:

 Hi Menaka,

 I've been reading and learning more about research objects, and I
 think I understand better what is going on, but I still have some
 questions.

 1) I am curious as to which file types *can* be converted to .robundle
 format? (I must have missed something because I thought .t2flow and
 .wfbundle were the only allowed input file types.)

 2) In rereading your June 18th blog post, I see you say that the
 command line tool is for converting and managing workflow bundles as
 well as research object bundles. Are t2flow files workflow bundles
 or just workflows? Or is there not a practical difference?

 3) I understand now that not all file format conversions are valid.
 I'm trying to understand this better. In your June 18th blog post you
 say:

 The conversion function supports converting .t2flow and .wfbundle
 formats into following formats:

 .structure

 .json

 .iwir

 .wfbundle

 .wfdesc.ttl – (development in progress)

 .robundle – (development in progress)

 To me, reading this looks like all combinations are valid.

 I'm wondering, can both .t2flow and .wfbundle files be converted to
 all file types *except* robundle?


 4) I fixed the examples in my blog post.  Should I also change the
 --robundle option description to say Output bundle as .robundle
 instead of Output workflow as .robundle ? (Same for .wfbundle
 option.)

 Thanks for the feedback and the correct link to the example!

 Have a nice weekend.

 Gale



 On Wed, Jun 24, 2015 at 10:52 PM, Menaka Madushanka
 menaka12...@gmail.com wrote:
  Hi Gale,
  Use this link
 
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
 
  Cheers
  Menaka
 
  On 25 June 2015 at 05:34, Gale Naylor ga...@noventussolutions.com
 wrote:
 
  Hi Menaka,
 
  Thank you for the feedback and clarifying information. Sorry not to
 respond
  sooner. I am learning about bundles, etc. and reading the link you sent.
 
  One thing, I'm having trouble getting to the example in the Examples of
 Use
  Section: Example in full is at org.apache.taverna.robundle.TestExample
 
  Can you help me? This is what I've done so far:
 
  - Clicking on the link gets me the This is not the web page you are
  looking
  for page. (This is the actual link address:
 
 
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/purl/wf4ever/robundle/TestExample.java
  )
 
  - Entering org.apache.taverna.robundle.TestExample also doesn't work
 for
  me. I didn't think it would, but I tried anyway.
 
  - Searching for taverna robundle TestExample on the main Apache.com
 page
  yields no results.
 
  I will continue to read and understand the RO Bundle API page, but I

RE: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Thank you, Ian!

-Original Message-
From: Ian Dunlop [mailto:ian.dun...@manchester.ac.uk]
Sent: Tuesday, July 21, 2015 7:36 AM
To: dev@taverna.incubator.apache.org
Subject: Re: Taverna Language Command Line tool - convert command doc

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Hello,

Hi Gale. I can see the pull request here
https://github.com/apache/incubator-taverna-site/pull/1
Thanks very much :)
We'll have a look and get it merged soon (or feedback in case any changes
etc are needed).

Cheers,

Ian

On 21/07/2015 15:04, Gale Naylor wrote:
 Hi Stian,

 I have submitted a pull request regarding adding the Taverna Language
 Modules diagram. This is my first time, so I'm not sure if I did it
 correctly or if there is anything else I need to do now.

 Thank you,

 Gale

 On Mon, Jul 13, 2015 at 8:33 AM, Stian Soiland-Reyes
 st...@apache.org wrote:
 Thanks!

 We have a general contributor guide for the website here:

 http://taverna.incubator.apache.org/community/edit


 Editing the website itself in a fork can be done in the GitHub web
 interface, but to add the diagram to a GitHub pull request (e.g. )
 would probably require you to check out from your fork of
 https://github.com/apache/incubator-taverna-site --

 you could also contribute it as an attachment to a Jira bug
 report:
 https://issues.apache.org/jira/browse/TAVERNA/component/12326819


 I don't think a single diagram would require a CLA with ASF - your
 contribution should be automatically covered by the #5 in
 http://www.apache.org/licenses/LICENSE-2.0 - but we might need you to
 sign a CLA - http://www.apache.org/licenses/#clas - before we can
 accept larger contributions.





 On 3 July 2015 at 05:29, Gale Naylor
 ga...@noventussolutions.com wrote:
 Hi Stian,

 Yes, when I get home from vacation (July 10-11), I will look at this
 information more carefully and have a go at adding it to the
 website. I will let you know if I have any questions.

 Thank you,

 Gale On Jul 2, 2015 4:52 PM, Stian Soiland-Reyes
 st...@apache.org wrote:

 Hi, Gale, thanks for your effort on documenting tavlang - as it's
 being developed!

 Do you think you could have a go at adding this to the website in
 MarkDown/HTML format..? See


 https://github.com/apache/incubator-taverna-site/tree/trunk/content
/documentation/scufl2


which is the source for
 http://taverna.incubator.apache.org/documentation/scufl2/

 (perhaps /scufl2  in the URL should be renamed to /language
 ?)





 .wfbundle workflows is a kind of earlier form of RO Bundle, but
 predates their formal specification and does not use the
 taverna-robundle API. So they were meant to be updated to also be
 full RO Bundles - basically having a JSON manifest instead/in
 addition to the XML one.  So it should at some point be possible to
 convert them. Perhaps a prototype converter could just copy over
 the files internally between the UCFPackage and the Bundle and thus
 update the new manifest?



 The code that does the wfbundle writing:

 https://github.com/apache/incubator-taverna-language/blob/master/ta
verna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDF
XMLWriter.java


and reading:

 https://github.com/apache/incubator-taverna-language/blob/master/ta
verna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDF
XMLReader.java



So this relies on the UCF support from:

 https://github.com/apache/incubator-taverna-language/blob/master/ta
verna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpacka
ge/UCFPackage.java


.. which is basically a proxy for manipulating a ZIP file and its manife st.


 But this should ideally be updated to use the RO Bundle API
 from:

 https://github.com/apache/incubator-taverna-language/tree/master/ta
verna-robundle




and thus have proper support for linking the annotation/ files to
 their corresponding workflow elements, rather than having to parse
 them all to find the right one.

 as the UCFPackage types are used throughout the wfbundle writer
 changing this would take a bit of effort.. or just wrapping it from
 UCFPackage. Here's an earlier attempt:


 https://github.com/apache/incubator-taverna-language/blob/ucfpackag
e-robundle/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/sc
ufl2/ucfpackage/UCFPackage.java



(Note: That branch has test errors)


 As you see it calls the writeAsODFManifest(); which writes out the
 classic META-INF/manifest.xml for backwards compatibility. This is
 permitted by our spec - but violating a NOT RECOMMENDED (e.g. Know
 what you are doing):
 https://w3id.org/bundle#manifest-xml

 On 26 June 2015 at 19:54, Menaka Madushanka menaka12...@gmail.com
 wrote:
 Hi Gale, I'm really appreciate your feedback on my blogs.
 I'm very new and there could be some flows. Thank you very much
 for showing them. :-)

 1) Yes, the types of bundle formats that can be converted are
 listed in this blog.

 https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-
command-line

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor]

Hi Stian,

Thank you for the information!  I will take a look at it and see if I have
any questions.

Gale
On Jul 13, 2015 8:34 AM, Stian Soiland-Reyes st...@apache.org wrote:

 Thanks!

 We have a general contributor guide for the website here:

 http://taverna.incubator.apache.org/community/edit


 Editing the website itself in a fork can be done in the GitHub web
 interface, but to add the diagram to a GitHub pull request (e.g. )
 would probably require you to check out from your fork of
 https://github.com/apache/incubator-taverna-site --

 you could also contribute it as an attachment to a Jira bug report:
 https://issues.apache.org/jira/browse/TAVERNA/component/12326819


 I don't think a single diagram would require a CLA with ASF - your
 contribution should be automatically covered by the #5 in
 http://www.apache.org/licenses/LICENSE-2.0
 - but we might need you to sign a CLA -
 http://www.apache.org/licenses/#clas - before we can accept larger
 contributions.





 On 3 July 2015 at 05:29, Gale Naylor ga...@noventussolutions.com wrote:
  Hi Stian,
 
  Yes, when I get home from vacation (July 10-11), I will look at this
  information more carefully and have a go at adding it to the website. I
  will let you know if I have any questions.
 
  Thank you,
 
  Gale
  On Jul 2, 2015 4:52 PM, Stian Soiland-Reyes st...@apache.org wrote:
 
  Hi, Gale, thanks for your effort on documenting tavlang - as it's
  being developed!
 
  Do you think you could have a go at adding this to the website in
  MarkDown/HTML format..? See
 
 
 
 https://github.com/apache/incubator-taverna-site/tree/trunk/content/documentation/scufl2
  which is the source for
  http://taverna.incubator.apache.org/documentation/scufl2/
 
  (perhaps /scufl2  in the URL should be renamed to /language ?)
 
 
 
 
 
  .wfbundle workflows is a kind of earlier form of RO Bundle, but
  predates their formal specification and does not use the
  taverna-robundle API. So they were meant to be updated to also be full
  RO Bundles - basically having a JSON manifest instead/in addition to
  the XML one.  So it should at some point be possible to convert them.
  Perhaps a prototype converter could just copy over the files
  internally between the UCFPackage and the Bundle and thus update the
  new manifest?
 
 
 
  The code that does the wfbundle writing:
 
 
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLWriter.java
  and reading:
 
 
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLReader.java
 
  So this relies on the UCF support from:
 
 
 https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
  .. which is basically a proxy for manipulating a ZIP file and its
 manifest.
 
 
  But this should ideally be updated to use the RO Bundle API from:
 
 
 https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle
 
 
  and thus have proper support for linking the annotation/ files to
  their corresponding workflow elements, rather than having to parse
  them all to find the right one.
 
  as the UCFPackage types are used throughout the wfbundle writer
  changing this would take a bit of effort.. or just wrapping it from
  UCFPackage. Here's an earlier attempt:
 
 
 
 https://github.com/apache/incubator-taverna-language/blob/ucfpackage-robundle/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
 
  (Note: That branch has test errors)
 
 
  As you see it calls the writeAsODFManifest(); which writes out the
  classic META-INF/manifest.xml for backwards compatibility. This is
  permitted by our spec - but violating a NOT RECOMMENDED (e.g. Know
  what you are doing):
  https://w3id.org/bundle#manifest-xml
 
  On 26 June 2015 at 19:54, Menaka Madushanka menaka12...@gmail.com
 wrote:
   Hi Gale,
   I'm really appreciate your feedback on my blogs. I'm very new and
 there
   could be some flows. Thank you very much for showing them. :-)
  
   1) Yes, the types of bundle formats that can be converted are listed
 in
   this blog.
  
 
 https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
   The bundles are not workflows.
  
   2) No. It seems like the way I have wrote it somewhat misleading.
   Actually scufl2 workflows are not Bundles. Those are two different
 APIs.
   I'll update the blog. :-)
  
   3).Yes, my mistake. Neither .t2flow nor wfbundle could be converted
 into
   robundle.
  
   4). Yes Gale. That modification should be done. Other wise it looks
 like
   any format could be converted into Robundle. I'll update my blog too.
  
   Are there any more facts that need clarification about the blogs
 please
  ask
   me. :)
  
   Thank

Re: Trouble setting up SSH

[Gale Naylor]

@Andy - I was able to connect using PuTTY, but still cannot connect via the
command line.
FYI, I am using GitBash on Windows, but can still do ssh -v. I can append
the whole session transcript, but it seems that the relevant section is:

>debug1: Authentications that can continue: publickey
>debug1: Next authentication method: publickey
>debug1: Trying private key: /c/Users/Gale/.ssh/id_rsa
>debug1: Trying private key: /c/Users/Gale/.ssh/id_dsa
>debug1: Trying private key: /c/Users/Gale/.ssh/id_ecdsa
>debug1: Trying private key: /c/Users/Gale/.ssh/id_ed25519
>debug1: No more authentication methods to try.
>Permission denied (publickey).

I think I figured out that I don't have my private key saved in the right
place. I tried a couple of things, but neither worked yet, so I'll have to
try again tomorrow.

@Ian - so, you haven't needed an SSH key? I just created and uploaded a PGP
key. I'll have to try tomorrow (PST) to see if I can make any commits.

Thanks!

Gale



On Tue, Dec 8, 2015 at 7:35 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hello,
>
> I don't think I added an ssh key and I haven't seemed to need one so
> far. At least I can't see one listed in my account details at
> id.apache.org. I have added my PGP public fingerprint.
>
> Cheers,
>
> Ian
>
> On 08/12/15 09:04, Andy Seaborne wrote:
> > On 08/12/15 00:49, Gale Naylor wrote:
> >> I've been following the instructions at:
> >> http://www.apache.org/dev/new-committers-guide.html#ssh-setup
> >> and
> >> ftp://ftp.meisei-u.ac.jp/mirror/content/dev/.svn/text-base/user-ssh-w
> indows.html.svn-base#overview
> >>
> >>
> >>
> and
> >> using the information at
> >> https://blogs.apache.org/infra/entry/committer_shell_access_to_people
> ,
> >>
> >>
> but
> >> I am still having trouble connecting to people.apache.org.
> >>
> >> I have generated keys and copied the public key to my LDAP data
> >> at https://id.apache.org. I waited more than 10 minutes, but got
> >> a Permission Denied (publickey) error. I ran ssh-add and tried
> >> again, but got the same message.
> >>
> >> Does anyone have any suggestions, or can you point me at more
> >> resources? I've also been searching Stack Overflow and other
> >> generic Internet resources, but have not found anything to help.
> >> Is it possible that my account has yet to be created?
> >>
> >> I am an SSH newbie, so maybe there is something else I am
> >> missing. Any help is appreciated.
> >>
> >> Thanks,
> >>
> >> Gale
> >>
> >
> > (if you are using linux or OS/X):
> >
> > What does "ssh -v" say?
> >
> > It will show which keys it is trying.
> >
> > Andy
> >
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1
>
> iQEcBAEBAgAGBQJWZvidAAoJEPK45GBX+Cy5JuwIAKjj61nynBtH71S1/Qt5aOqR
> bqgYllVhf0mp8gsNGpKbnjAuLggkSD1K3b18oWgP0ocCp4vBPyMPPUJvMU4pNuXg
> 3EQUkJgFJwWdFVtgB7B7c2rImLb6gH/hfBe0yRweb9dEPpg0lqHOxX54bndlpO6q
> v8MaC+AIjDU8NcOjEKqEWHoLEsKcRX15VXS0FDS0vmBSUvSFqVP26AUXF2n0SNXI
> LdVJsNO09Kq81+eJ+znUpvm12aMkCf8OmEIJYCHYh7oce4/RGjhfBmba+hV4pQ3q
> GoJFEgm9L6hFaiO0wgX6/WD49Ttj44jY5xx3GbIj49eTqqUf4Nh+67+ET2l9Yvg=
> =u/g8
> -END PGP SIGNATURE-
>

First commit

[Gale Naylor]

I was able to add myself to the committer list at
http://incubator.apache.org/projects/taverna.html, but my name shows up at
the end of the list, instead of where I added it. I looked online, but have
yet to find anything to explain this, or how to fix it.

Thanks,
Gale

Re: First commit

[Gale Naylor]

Thank you, Ian. That was the issue. I see how it works now. Thanks!

Gale

On Tue, Dec 15, 2015 at 12:14 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hello,
>
> In the CMS page you may have to click 'Update' first (at the top
> left). This tells SVN to update your 'local' (ie your apache account)
> copy of the repository. It's usually a good idea to update before
> doing any changes to a page.
>
> Cheers,
>
> Ian
>
> On 14/12/15 19:12, Gale Naylor wrote:
> > Hmm. https://svn.apache.org/repos/a
> > sf/incubator/public/trunk/content/projects/taverna.xml was NOT the
> > file I edited. (See next paragraph.) Am I supposed to be able to go
> > the svn site using the above link and edit the XML in the CMS from
> > there? When I try to edit that link (using the *Edit in CMS
> > *bookmarklet) I get an error: *The requested URL /redirect was not
> > found on this server.*
> >
> > This is the URL of the page I was trying to edit:
> > http://incubator.apache.org/projects/taverna.html. I followed the
> > instructions on http://taverna.incubator.apache.org/community/edit,
> > which say you can use the *Edit in CMS *bookmarklet from any Apache
> > page. It did work on the *About *page from the Taverna website,
> > where I added my name to the committer list.
> >
> > Part of my earlier problem was I did not fully understand the
> > editing process and didn't publish my changes. But, the weird thing
> > about taverna.html is that in the production page I see my name at
> > the bottom of the table, but when I attempt to edit it (using the
> > bookmarklet) I don't see my name listed at all. Very strange.
> >
> > I think I'll just let it be for now. But ultimately I'd like to
> > understand what's going on. At least I tested that I can make a
> > commit.
> >
> > Gale
> >
> >
> >
> >
> > On Fri, Dec 11, 2015 at 10:01 AM Andy Seaborne <a...@apache.org>
> > wrote:
> >
> >> On 11/12/15 16:39, Gale Naylor wrote:
> >>> I was able to add myself to the committer list at
> >>> http://incubator.apache.org/projects/taverna.html, but my name
> >>> shows up
> >> at
> >>> the end of the list, instead of where I added it. I looked
> >>> online, but
> >> have
> >>> yet to find anything to explain this, or how to fix it.
> >>>
> >>> Thanks, Gale
> >>>
> >>
> >> Hi Gale,
> >>
> >> It is driven off file:
> >>
> >>
> >> https://svn.apache.org/repos/asf/incubator/public/trunk/content/proje
> cts/taverna.xml
> <https://svn.apache.org/repos/asf/incubator/public/trunk/content/projects/taverna.xml>
> >>
> >>
> >>
> Is that file you editted?
> >>
> >> I added you this week (at the end) and I don't see your name
> >> except at the end.
> >>
> >> And it only gets to the HTML when the site is published by
> >> someone. Either you can drive that at the time of editing or just
> >> leave until someone sweeps the site up with some bigger change.
> >> I usually do the latter - it get published quite regularly
> >> anyway.
> >>
> >> Andy
> >>
> >> (And I just fixed some layout)
> >>
> >>
> >
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1
>
> iQEcBAEBAgAGBQJWb8vOAAoJEPK45GBX+Cy542AIAKOsVSowl0xPm+lMvQKv8pyE
> 5MOg9rkGC1kTfKh5KcHZL1beHxbF07y4h8MBHdeaF46/UhOh8FWOMAUxexANsP3Z
> C9tiThdOfXjchSFO0i33ulAHfEbRwejVPhqwPJ5jGYeGedQ92hSbRgiynQ4WU4Pm
> MY6xCF+KkweFcr3v9yRBaGRNicamcA8GlYwyovqmYSEyRtniALZ3qBSIN+kjF7tC
> Ep4pFrDD4X1aMhYON8oVRLXhnl8VunkaXK6BWNhC2PbN878xBsHWIwVSPd3U10zw
> +RdTaD3zDjUOASsHxKY6RNvtbJvPwebOBmtfJUoQZvYPah+2dGBDMXFoJdvmOeU=
> =fL2e
> -END PGP SIGNATURE-
>

Fwd: Taverna Site :- Documentation menu

[Gale Naylor]

Menaka has suggested a good edit to the Taverna website Documentation menu
(change command-line to Command Line), but I can't find the correct file to
change.

I've been through what feels like every file on the website.The closest
file I can find is templates/default_navbar.html, but it looks like an
earlier version and doesn't match the current navigation menus.

I'm happy to make the change if someone can help me find the correct file.

Thanks!

Gale

-- Forwarded message -
From: Menaka Madushanka <menaka12...@gmail.com>
Date: Sun, Dec 13, 2015 at 1:33 AM
Subject: Taverna Site :- Documentation menu
To: Gale Naylor <ga...@noventussolutions.com>, Andy Seaborne <
a...@apache.org>, Alan Williams <alanin...@googlemail.com>, Stian
Soiland-Reyes <st...@apache.org>


Hi everybody,

When I looked at the Taverna site, I spotted this menu item.

*command-line*

I don't know is this ok but I thought it should be corrected as *Command
Line*

Cheers...!!

Regards
Menka Madushanka

-- 
Menaka Madushanka Jayawardena
Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of Peradeniyaya.
LinkedIn <http://lk.linkedin.com/in/menakajayawardena>

Re: Apache Taverna site

[Gale Naylor]

Hi Menaka,

I'm sorry, but I still don't see an image. I have had this problem before
on dev list emails. I ended up putting the image in a blog and posting the
link.

Gale

On Sat, Dec 12, 2015 at 2:02 AM Menaka Madushanka <menaka12...@gmail.com>
wrote:

> Hello Ian and Gale,
>
> Sorry for it... :-)
> Here I have attached the image.
>
> Cheers
> Menaka
>
> On 11 December 2015 at 19:15, Ian Dunlop <ian.dun...@manchester.ac.uk>
> wrote:
>
>> Hello,
>>
>> I can't see the image either Menaka. Can ou resend or say what the
>> problem is please.
>>
>> Cheers,
>>
>> Ian
>>
>> On 10/12/2015 15:17, Gale Naylor wrote:
>> > I cannot see the image.
>> >
>> > On Thu, Dec 10, 2015 at 4:00 AM Menaka Madushanka <
>> menaka12...@gmail.com>
>> > wrote:
>> >
>> >> Hi everybody,
>> >>
>> >> When I looked at the Taverna site, I spotted this.
>> >>
>> >>
>> >> ​
>> >> *command-line is not as the others.*
>> >>
>> >> I don't know is this ok but I thought it should be corrected.
>> >>
>> >> Cheers...!!
>> >>
>> >> Regards
>> >> Menka Madushanka
>> >>
>> >>
>> >> --
>> >> Menaka Madushanka Jayawardena
>> >> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>> >> University of Peradeniyaya.
>> >> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>> >>
>> >
>>
>> --
>> Ian Dunlop, eScience Lab
>> School of Computer Science
>> The University of Manchester
>> http://orcid.org/-0001-7066-3350
>>
>
>
>
> --
> Menaka Madushanka Jayawardena
> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> University of Peradeniyaya.
> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>

Re: Fwd: Taverna Site :- Documentation menu

[Gale Naylor]

Hi Ian,

Thanks again! I thought I was working with an updated directory, but I
couldn't see navbar.html. That's the right file to change, and the website
is now updated.

Gale

On Thu, Dec 17, 2015 at 8:16 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA256
>
> Hello,
>
> I think it is in the /trunk/templates/ directory. There seems to be 2
> navbars - default_navbar.html and navbar.html, not sure why. Try
> changing navbar.html and see if that works.
>
> Cheers,
>
> Ian
>
> On 17/12/2015 03:29, Gale Naylor wrote:
> > Menaka has suggested a good edit to the Taverna website
> > Documentation menu (change command-line to Command Line), but I
> > can't find the correct file to change.
> >
> > I've been through what feels like every file on the website.The
> > closest file I can find is templates/default_navbar.html, but it
> > looks like an earlier version and doesn't match the current
> > navigation menus.
> >
> > I'm happy to make the change if someone can help me find the
> > correct file.
> >
> > Thanks!
> >
> > Gale
> >
> > -- Forwarded message - From: Menaka Madushanka
> > <menaka12...@gmail.com <mailto:menaka12...@gmail.com>> Date: Sun,
> > Dec 13, 2015 at 1:33 AM Subject: Taverna Site :- Documentation
> > menu To: Gale Naylor <ga...@noventussolutions.com
> > <mailto:ga...@noventussolutions.com>>, Andy Seaborne
> > <a...@apache.org <mailto:a...@apache.org>>, Alan Williams
> > <alanin...@googlemail.com <mailto:alanin...@googlemail.com>>, Stian
> > Soiland-Reyes <st...@apache.org <mailto:st...@apache.org>>
> >
> >
> > Hi everybody,
> >
> > When I looked at the Taverna site, I spotted this menu item. *
> > command-line*
> >
> > I don't know is this ok but I thought it should be corrected as
> > *Command Line*
> >
> > Cheers...!!
> >
> > Regards Menka Madushanka
> >
> > -- Menaka Madushanka Jayawardena Faculty of Engineering,
> > <http://www.pdn.ac.lk/eng> University of Peradeniyaya. LinkedIn
> > <http://lk.linkedin.com/in/menakajayawardena>
>
> - --
> Ian Dunlop, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/-0001-7066-3350
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v2
>
> iQEcBAEBCAAGBQJWct/cAAoJEPK45GBX+Cy5UhgIAIbsvN3gnXUFOG22j5MGefrI
> plMJoguH7VzzXNZqb+bKf3RyYSkSKL8T42Xxfz8WM3JCul0TFoTelf0mu7hT5T3U
> mMLhg3Dl0mOWZl1dYWkXMkU8P5ktTtrqoDQrC4KcqzG4nmRFANROe239Wphv/929
> z17qjyvCwMLUdeQyaSHx9EE4wbsEZ+iCcm3+vjeOHDXDjGj3WyZOEeC5lS6n0HRU
> Prnpgn+BibrKrJXnpc55g9/VyCf+UMY4b+wwpeZntX2UP9gUE4uy1B0sqT9bJeHP
> ck7nPD7lUk4WjiwIRZsLV/rvm+ST3K/cvgGj9JEH1l/feuM1OM5AyppK+1uiH0E=
> =0Kcj
> -END PGP SIGNATURE-
>

Re: Apache Taverna site

[Gale Naylor]

I cannot see the image.

On Thu, Dec 10, 2015 at 4:00 AM Menaka Madushanka 
wrote:

> Hi everybody,
>
> When I looked at the Taverna site, I spotted this.
>
>
> ​
> *command-line is not as the others.*
>
> I don't know is this ok but I thought it should be corrected.
>
> Cheers...!!
>
> Regards
> Menka Madushanka
>
>
> --
> Menaka Madushanka Jayawardena
> Faculty of Engineering, 
> University of Peradeniyaya.
> LinkedIn 
>

Re: First commit

[Gale Naylor]

Hmm. https://svn.apache.org/repos/a
sf/incubator/public/trunk/content/projects/taverna.xml was NOT the file I
edited. (See next paragraph.) Am I supposed to be able to go the svn site
using the above link and edit the XML in the CMS from there? When I try to
edit that link (using the *Edit in CMS *bookmarklet) I get an error: *The
requested URL /redirect was not found on this server.*

This is the URL of the page I was trying to edit:
http://incubator.apache.org/projects/taverna.html. I followed the
instructions on http://taverna.incubator.apache.org/community/edit, which
say you can use the *Edit in CMS *bookmarklet from any Apache page. It did
work on the *About *page from the Taverna website, where I added my name to
the committer list.

Part of my earlier problem was I did not fully understand the editing
process and didn't publish my changes. But, the weird thing about
taverna.html is that in the production page I see my name at the bottom of
the table, but when I attempt to edit it (using the bookmarklet) I don't
see my name listed at all. Very strange.

I think I'll just let it be for now. But ultimately I'd like to understand
what's going on. At least I tested that I can make a commit.

Gale




On Fri, Dec 11, 2015 at 10:01 AM Andy Seaborne <a...@apache.org> wrote:

> On 11/12/15 16:39, Gale Naylor wrote:
> > I was able to add myself to the committer list at
> > http://incubator.apache.org/projects/taverna.html, but my name shows up
> at
> > the end of the list, instead of where I added it. I looked online, but
> have
> > yet to find anything to explain this, or how to fix it.
> >
> > Thanks,
> > Gale
> >
>
> Hi Gale,
>
> It is driven off file:
>
>
> https://svn.apache.org/repos/asf/incubator/public/trunk/content/projects/taverna.xml
>
> Is that file you editted?
>
> I added you this week (at the end) and I don't see your name except at
> the end.
>
> And it only gets to the HTML when the site is published by someone.
> Either you can drive that at the time of editing or just leave until
> someone sweeps the site up with some bigger change.  I usually do the
> latter - it get published quite regularly anyway.
>
> Andy
>
> (And I just fixed some layout)
>
>

Re: Common workflow language

[Gale Naylor]

Creating JIRA issues makes sense to me. Unless we have another way to keep
track of proposed or potential actions.

Gale

On Fri, Dec 11, 2015 at 6:02 AM Ian Dunlop 
wrote:

> Hello,
>
> I know this is a crazy suggestion, but..are there some issues that
> we can add to JIRA around CWL or jbatch. Otherwise it will be lost in
> the email thread.
>
> eg
> * CWL reader for SCUFL2
> * Docker image for taverna activities (docker compose based?)
> * Integrate with CWL tool registries (which I guess means getting the
> workbench working!)
>
> Cheers,
>
> Ian
>
> On 10/12/2015 09:35, Stian Soiland-Reyes wrote:
> >  I've signed up for the CWL hackathon, but I hope others would join!
> >
> >
> > I find CWL interesting as it has focused on the tool descriptions, and
> > packaging them using Docker. This is a pragmatic approach that means
> > lots of issues on reproducibility, installation and repurposability is
> > pretty much solved.
> >
> > It does however means it is hard to use non-local tools like REST
> > services, as you would need an equivalent command line tool.  Message
> > parsing and shims are trickier, but on the plus side you could use
> > your favourite scripting language (as long as it works on Linux :)).
> >
> >
> > Docker is also an important part of http://bioboxes.org/
> >
> >
> > CWL Tool descriptions are annotated with the EDAM ontology, which
> > includes many ELIXIR folks. ELIXIR is building a tool registry.
> >
> > Now I think it would be nice if we could also use such a tool registry
> > and descriptions from Taverna.
> >
> >
> > CWL focuses on data as files, in a way that is very similar to the
> > current Tool service.
> >
> > I think we could update the Tool Service to handle "CWL tools" or at
> > least handle docker images.  Of course you could do this today with
> > just having a command line tool that is "docker run blablabla".
> >
> >
> > I would like to start work on a CWL reader for SCUFL2, which would
> > create such Tool instances in the first place.
> >
> >
> > Representing any SCUFL2/Taverna workflow in CWL can be tricky, as you
> > would need to extend the tool type to have REST, WSDL, etc/. This is
> > an extension point in CWL though - and so it would perhaps raise the
> > question of why use CWL with custom extensions if nobody else can run
> > such the Taverna services. Still, the workflow structure can be
> > repurposed, with a different activity inserted in other CWL engines.
> > There's a danger here of "standards mutation" - like we saw a decade
> > ago with WSDL being modified beyond recognition in Globus web services
> > and WSRF.
> >
> >
> > Another approach could be to create Docker images that can execute
> > Taverna activities (e.g. using the wsdl-generic command line). This
> > would be more of an interesting research angle, perhaps, as it means
> > we would be more freely able to try to run a Taverna workflow with an
> > alternate CWL workflow engine.
> >
> >
> > Taverna workflows allow various control mechanisms like Retry,
> > Failover, Parallelism, inplicit iterations, dot/cross product - which
> > could be tricky to represent in CWL. I think only a subset of Taverna
> > workflows could be run as CWL - without again adding customizations -
> > kind of like a CWL profile.
> >
> >
> > I think one aspect is that CWL is also a focus opportunity for Taverna
> > - coordinating command line tools is simpler than trying to integrate
> > "everything". I think also this is more of the growing space we find
> > Taverna in now, rather than 8 years ago when Taverna aimed to be
> > bioinformatician's best friend and we added lots of GUI and activity
> > plugins for various bioinformatics-centric services. (however
> > AstroTaverna is one landscape which is still open to be claimed in
> > such a way.).  CWL is a bit more on a "hacker level" - which I think
> > we can be more comfortable with catering for.
> >
> >
> > For CWL, Taverna is a valuable proposition as we know how to handle
> > workflow provenance, we can easily add preservation aspects (e.g.
> > packaging all the docker images used in a run).  The Taverna Workbench
> > has a pluggable way to add service descriptions, so we could connect
> > to CWL tool registries and turn Taverna into a "CWL editor".
> >
> >
> > On 4 December 2015 at 17:05, Alan Williams 
> wrote:
> >> On 04-Dec-15 15:28, Ian Dunlop wrote:
> >>>
> >>> -BEGIN PGP SIGNED MESSAGE-
> >>> Hash: SHA256
> >>>
> >>> Hello,
> >>>
> >>> Does anyone have views on how Apache Taverna fits into the goals of
> >>> the Common Workflow Language project
> >>> https://github.com/common-workflow-language/common-workflow-language ?
> >>> Should taverna adopt CWL instead of SCUFL2. Are there things that
> >>> SCUFL2 or the current taverna engine offers that CWL does not?
> >>
> >>
> >> Stian is probably the best person to answer this as he has been quite
> >> involved with CWL. To the best of my 

Re: Trouble setting up SSH

[Gale Naylor]

Thank you, Andy! That solved it!

On Wed, Dec 9, 2015 at 1:20 AM Andy Seaborne <a...@apache.org> wrote:

> Hi Gale - sorry, I'm not a Windows users.
>
> IIRC Putty private keys are different format from OpenSSL and that -v
> output looks like OpenSSL. option.
>
> Hmm - this maybe:
> There's some kind of "export to OpenSSL" according to
>
>
> http://serverfault.com/questions/194567/how-do-i-tell-git-for-windows-where-to-find-my-private-rsa-key
>
> Andy
>
> On 09/12/15 04:01, Gale Naylor wrote:
> > @Andy - I was able to connect using PuTTY, but still cannot connect via
> the
> > command line.
> > FYI, I am using GitBash on Windows, but can still do ssh -v. I can append
> > the whole session transcript, but it seems that the relevant section is:
> >
> >> debug1: Authentications that can continue: publickey
> >> debug1: Next authentication method: publickey
> >> debug1: Trying private key: /c/Users/Gale/.ssh/id_rsa
> >> debug1: Trying private key: /c/Users/Gale/.ssh/id_dsa
> >> debug1: Trying private key: /c/Users/Gale/.ssh/id_ecdsa
> >> debug1: Trying private key: /c/Users/Gale/.ssh/id_ed25519
> >> debug1: No more authentication methods to try.
> >> Permission denied (publickey).
> >
> > I think I figured out that I don't have my private key saved in the right
> > place. I tried a couple of things, but neither worked yet, so I'll have
> to
> > try again tomorrow.
> >
> > @Ian - so, you haven't needed an SSH key? I just created and uploaded a
> PGP
> > key. I'll have to try tomorrow (PST) to see if I can make any commits.
> >
> > Thanks!
> >
> > Gale
> >
> >
> >
> > On Tue, Dec 8, 2015 at 7:35 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
> > wrote:
> >
> >> -BEGIN PGP SIGNED MESSAGE-
> >> Hash: SHA1
> >>
> >> Hello,
> >>
> >> I don't think I added an ssh key and I haven't seemed to need one so
> >> far. At least I can't see one listed in my account details at
> >> id.apache.org. I have added my PGP public fingerprint.
> >>
> >> Cheers,
> >>
> >> Ian
> >>
> >> On 08/12/15 09:04, Andy Seaborne wrote:
> >>> On 08/12/15 00:49, Gale Naylor wrote:
> >>>> I've been following the instructions at:
> >>>> http://www.apache.org/dev/new-committers-guide.html#ssh-setup
> >>>> and
> >>>> ftp://ftp.meisei-u.ac.jp/mirror/content/dev/.svn/text-base/user-ssh-w
> >> indows.html.svn-base#overview
> >>>>
> >>>>
> >>>>
> >> and
> >>>> using the information at
> >>>> https://blogs.apache.org/infra/entry/committer_shell_access_to_people
> >> ,
> >>>>
> >>>>
> >> but
> >>>> I am still having trouble connecting to people.apache.org.
> >>>>
> >>>> I have generated keys and copied the public key to my LDAP data
> >>>> at https://id.apache.org. I waited more than 10 minutes, but got
> >>>> a Permission Denied (publickey) error. I ran ssh-add and tried
> >>>> again, but got the same message.
> >>>>
> >>>> Does anyone have any suggestions, or can you point me at more
> >>>> resources? I've also been searching Stack Overflow and other
> >>>> generic Internet resources, but have not found anything to help.
> >>>> Is it possible that my account has yet to be created?
> >>>>
> >>>> I am an SSH newbie, so maybe there is something else I am
> >>>> missing. Any help is appreciated.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Gale
> >>>>
> >>>
> >>> (if you are using linux or OS/X):
> >>>
> >>> What does "ssh -v" say?
> >>>
> >>> It will show which keys it is trying.
> >>>
> >>> Andy
> >>>
> >> -BEGIN PGP SIGNATURE-
> >> Version: GnuPG v1
> >>
> >> iQEcBAEBAgAGBQJWZvidAAoJEPK45GBX+Cy5JuwIAKjj61nynBtH71S1/Qt5aOqR
> >> bqgYllVhf0mp8gsNGpKbnjAuLggkSD1K3b18oWgP0ocCp4vBPyMPPUJvMU4pNuXg
> >> 3EQUkJgFJwWdFVtgB7B7c2rImLb6gH/hfBe0yRweb9dEPpg0lqHOxX54bndlpO6q
> >> v8MaC+AIjDU8NcOjEKqEWHoLEsKcRX15VXS0FDS0vmBSUvSFqVP26AUXF2n0SNXI
> >> LdVJsNO09Kq81+eJ+znUpvm12aMkCf8OmEIJYCHYh7oce4/RGjhfBmba+hV4pQ3q
> >> GoJFEgm9L6hFaiO0wgX6/WD49Ttj44jY5xx3GbIj49eTqqUf4Nh+67+ET2l9Yvg=
> >> =u/g8
> >> -END PGP SIGNATURE-
> >>
> >
>
>

Edit of Scufl2-Workflow Bundle

[Gale Naylor]

I reviewed the entire Scufl2-Workflow Bundle page (bundle.md) and made some
edits for clarity, consistency, grammar, and I also fixed some typos.

I'm not sure what to do about double-braces:

- one is in Bundle Path and Root Files: {{application/rdf+xml}). I'm
guessing the right parenthesis is supposed to be a second closing brace?

- in the very last line of the file:  {/workflowBundle.rdf}}  Is this
supposed to have two opening braces?

If someone can let me know what the corrections should be, I will take care
of it.

Thanks,

Gale

Re: Edit of Scufl2-Workflow Bundle

[Gale Naylor]

Excellent.  I will fix them.

On Thu, Jan 7, 2016, 3:00 AM Ian Dunlop <ian.dun...@manchester.ac.uk> wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA256
>
> Hello,
>
> I think {/workflowBundle.rdf}} is supposed to be the same as the one
> on the line above ie `/workflowBundle.rdf`.
> Also {{application/rdf+xml}) should be `application/rdf+xml`.
> I think it is because it was copied from the old website which used
> {{}} for formatting whereas in markdown (md) it uses backticks ``
>
> Cheers,
>
> Ian
>
> On 06/01/2016 23:07, Gale Naylor wrote:
> > I reviewed the entire Scufl2-Workflow Bundle page (bundle.md) and
> > made some edits for clarity, consistency, grammar, and I also fixed
> > some typos.
> >
> > I'm not sure what to do about double-braces:
> >
> > - one is in Bundle Path and Root Files: {{application/rdf+xml}).
> > I'm guessing the right parenthesis is supposed to be a second
> > closing brace?
> >
> > - in the very last line of the file:  {/workflowBundle.rdf}}  Is
> > this supposed to have two opening braces?
> >
> > If someone can let me know what the corrections should be, I will
> > take care of it.
> >
> > Thanks,
> >
> > Gale
> >
>
> - --
> Ian Dunlop, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/-0001-7066-3350
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v2
>
> iQEcBAEBCAAGBQJWjkU4AAoJEPK45GBX+Cy5pUQH/0MQ3UJeK3efuopAbIUNi4IV
> F8wMhukOu+t449BsYJrCwNCwV+8nOGYbUOqnBEvOG+fyk9fSVNpJKtUoacilPEW5
> py9TaNXBCUI0RcpgxXLDQXTvddAKa9SIeXKBB+ta5f4/jlpDfKuLY6w+kQEMkJpx
> UoLsCxOqmFeUsbyOsvA+ZYDxQTKqMLfBZIuL73mudwAQzjIHGVBu3KyqgzBSWPGj
> bmq4OPAvyQJDDwnKe22p0EjOagIJiq9R4isFXBexa8urK8BsJpgcljuwEEarCKxQ
> 7QVM96kdXckjd63K3z3ItVi0m1tP/3on9xAT+SxA6Lt4h4M9hc+dOhuqWtKl/JQ=
> =+TBv
> -END PGP SIGNATURE-
>

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

[Gale Naylor]

I mocked up a Publications page on my blog.
https://galenaylor.wordpress.com/2016/01/11/references-and-publications/
(Wordpress
did not like the 4th level headers (e.g., 2015), so I would fix that,
of course.)

It seems like this should be two pages: one for how to reference Taverna
and the website, and one to list relevant publications.

Also, I wasn't sure what to do about the reference to the latest canonical
citations.

Does this seem like a good start, or what should be changed?

(Sorry for the long emails with abstracts. I just now found the direct
links to the papers.)

Gale

On Mon, Jan 11, 2016 at 1:48 PM Gale Naylor <ga...@noventussolutions.com>
wrote:

> What about this paper from October 2014? Would you want to include this on
> a publications page?
>
> Title: BIFI: a Taverna plugin for a simplified and user-friendly workflow
> platform.
>
> Authors: Yildiz A; Dilaveroglu E; Visne I; Günay B; Sefer E; Weinhausel
> A; Rattay F; Goble CA; Pandey RV; Kriegner A (Health & Environment
> Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria.
> albert.krieg...@ait.ac.at.)
>
> Source: BMC Research Notes [BMC Res Notes] 2014 Oct 20; Vol. 7, pp. 740.
> Date of Electronic Publication: 2014 Oct 20.
>
> Journal Info: Publisher: Biomed Central Country of Publication: England
> NLM ID: 101462768 Publication Model: Electronic Cited Medium: Internet
> ISSN: 1756-0500 (Electronic) Linking ISSN: 17560500 NLM ISO Abbreviation:
> BMC Res Notes Subsets: MEDLINE
>
> Abstract: Background: Heterogeneity in the features, input-output
> behaviour and user interface for available bioinformatics tools and
> services is still a bottleneck for both expert and non-expert users.
> Advancement in providing common interfaces over such tools and services are
> gaining interest among researchers. However, the lack of (meta-)
> information about input-output data and parameter prevents to provide
> automated and standardized solutions, which can assist users in setting the
> appropriate parameters. These limitations must be resolved especially in
> the workflow-based solution in order to ease the integration of software.
>
> Findings: We report a Taverna Workbench plugin: the XworX BIFI (Beautiful
> Interfaces for Inputs) implemented as a solution for the aforementioned
> issues. BIFI provides a Graphical User Interface (GUI) definition language
> used to layout the user interface and to define parameter options for
> Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF)
> directly or discover appropriate instances from a configured repository. In
> the absence of a GDF, BIFI generates a default interface.
>
> Conclusion: The Taverna Workbench is an open source software providing the
> ability to combine various services within a workflow. Nevertheless, users
> can supply input data to the workflow via a simple user interface providing
> only a text area to enter the input in text form. The workflow may contain
> meta-information in human readable form such as description text for the
> port and an example value. However, not all workflow ports are documented
> so well or have all the required information.BIFI uses custom user
> interface components for ports which give users feedback on the parameter
> data type or structure to be used for service execution and enables
> client-side data validations. Moreover, BIFI offers user interfaces that
> allow users to interactively construct workflow views and share them with
> the community, thus significantly increasing usability of heterogeneous,
> distributed service consumption.
>
> DOI: 10.1186/1756-0500-7-740
>
>
> On Mon, Jan 11, 2016 at 1:01 PM Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
>> On the other hand, I found this September 2015 paper on EBSCOHost, and it
>> looks promising:
>>
>> Title: Scientific workflow optimization for improved peptide and protein
>> identification.
>> Authors: Holl, Sonja; Mohammed, Yassene; Zimmermann, Olav; Palmblad,
>> Magnus (n.m.palmb...@lumc.nl)
>>
>> Source: BMC Bioinformatics. 9/3/2015, Vol. 16 Issue 1, p1-13. 13p. 1
>> Color Photograph, 1 Diagram, 3 Charts, 4 Graphs.
>>
>> Author-Supplied Keywords: Optimization, Scientific workflow, Tandem mass
>> spectrometry, Taverna workbench, X!Tandem
>>
>> Abstract: Background: Peptide-spectrum matching is a common step in most
>> data processing workflows for mass spectrometry-based proteomics. Many
>> algorithms and software packages, both free and commercial, have been
>> developed to address this task. However, these algorithms typically require
>> the user to select instrument- and sample-dependent parameters, such as
>> mass meas

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

[Gale Naylor]

I looked at the links to the Google scholar searches above and mostly found
oblique references to Apache Taverna, along the lines of what Alan
mentioned. The only one that looked promising to me was this one:

Local Graph Patterns for Scientific Workflow Similarity Search

https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/teaching/studienDiplomArbeiten/running/expose_wiegandt_151116.pdf


But, it looked more like a detailed abstract and not a compete paper.


The other searches seemed only to return older references to Taverna (2013
and earlier).


I can make an Apache Taverna page for citations, but I will need help with
what publications you think are good to include.


Gale



On Mon, Jan 11, 2016 at 8:21 AM alaninmcr  wrote:

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

[Gale Naylor]

On the other hand, I found this September 2015 paper on EBSCOHost, and it
looks promising:

Title: Scientific workflow optimization for improved peptide and protein
identification.
Authors: Holl, Sonja; Mohammed, Yassene; Zimmermann, Olav; Palmblad, Magnus
(n.m.palmb...@lumc.nl)

Source: BMC Bioinformatics. 9/3/2015, Vol. 16 Issue 1, p1-13. 13p. 1 Color
Photograph, 1 Diagram, 3 Charts, 4 Graphs.

Author-Supplied Keywords: Optimization, Scientific workflow, Tandem mass
spectrometry, Taverna workbench, X!Tandem

Abstract: Background: Peptide-spectrum matching is a common step in most
data processing workflows for mass spectrometry-based proteomics. Many
algorithms and software packages, both free and commercial, have been
developed to address this task. However, these algorithms typically require
the user to select instrument- and sample-dependent parameters, such as
mass measurement error tolerances and number of missed enzymatic cleavages.
In order to select the best algorithm and parameter set for a particular
dataset, in-depth knowledge about the data as well as the algorithms
themselves is needed. Most researchers therefore tend to use default
parameters, which are not necessarily optimal. Results: *We have applied a
new optimization framework for the Taverna scientific workflow management
system* (http://ms-utils.org/Taverna_Optimization.pdf) to find the best
combination of parameters for a given scientific workflow to perform
peptide-spectrum matching. The optimizations themselves are non-trivial, as
demonstrated by several phenomena that can be observed when allowing for
larger mass measurement errors in sequence database searches. On-the-fly
parameter optimization embedded in scientific workflow management systems
enables experts and non-experts alike to extract the maximum amount of
information from the data. The same workflows could be used for exploring
the parameter space and compare algorithms, not only for peptide-spectrum
matching, but also for other tasks, such as retention time prediction.
Conclusion: Using the optimization framework, we were able to learn about
how the data was acquired as well as the explored algorithms. We observed a
phenomenon identifying many ammonia-loss b-ion spectra as peptides with
N-terminal pyroglutamate and a large precursor mass measurement error.
These insights could only be gained with the extension of the common range
for the mass measurement error tolerance parameters explored by the
optimization framework. [ABSTRACT FROM AUTHOR]

Copyright of BMC Bioinformatics is the property of BioMed Central and its
content may not be copied or emailed to multiple sites or posted to a
listserv without the copyright holder's express written permission.
However, users may print, download, or email articles for individual use.
This abstract may be abridged. No warranty is given about the accuracy of
the copy. Users should refer to the original published version of the
material for the full abstract. (Copyright applies to all Abstracts.)

DOI: 10.1186/s12859-015-0714-x


On Mon, Jan 11, 2016 at 12:42 PM Gale Naylor <ga...@noventussolutions.com>
wrote:

> I looked at the links to the Google scholar searches above and mostly
> found oblique references to Apache Taverna, along the lines of what Alan
> mentioned. The only one that looked promising to me was this one:
>
> Local Graph Patterns for Scientific Workflow Similarity Search
>
>
> https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/teaching/studienDiplomArbeiten/running/expose_wiegandt_151116.pdf
>
>
> But, it looked more like a detailed abstract and not a compete paper.
>
>
> The other searches seemed only to return older references to Taverna (2013
> and earlier).
>
>
> I can make an Apache Taverna page for citations, but I will need help with
> what publications you think are good to include.
>
>
> Gale
>
>
>
> On Mon, Jan 11, 2016 at 8:21 AM alaninmcr <alanin...@googlemail.com>
> wrote:
>
>> 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: [DISCUSS] Release candidate 2 of Command-line Tool 3.1.0-incubating

[Gale Naylor]

 dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.aop:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.beans:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.core:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.transaction:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Not an OSGi bundle : junit:junit:jar:4.4
[INFO] [INFO]
[INFO] [INFO] ---
taverna-maven-plugin:0.2.1-incubating:plugin-prepare-bundles
(default-plugin-prepare-bundles) @ dummy-taverna-plugin-plugin ---
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.context:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.aop:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.beans:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.core:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.transaction:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Not an OSGi bundle : junit:junit:jar:4.4

On Thu, Jun 2, 2016 at 11:50 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> I'm so sorry - I've been replying to the VOTE thread.
>
> I'll copy my comments here:
>
> --
> UP-FRONT CHECKS
> --
> The MD5 checksums in the [VOTE] email are the same as the SHA1 checksums.
> I'm using the downloaded MD5 and SHA-1.
>
> (Originally I missed the commit IDs in the Vote email - don't know how -
> but they are there.)
>
>
> --
> LICENSES - THIRD-PARTY.properties file
> --
>
> ---
> GNU License?
>
> The list of # Already used licenses in project : includes
>
> # - GNU Lesser General Public License, Version 2.1
> Isn't this a category-x license? (It doesn't show up in the
> "Please fill in the missing licenses" list at the bottom of the file.)
>
>
> ---
> Missing license information:
>
> # http://x-stream.github.io/license.html - this link says BSD (but not
> which type);
> should this copyright be included in our Notice file?
>
> org.aopalliance--com.springsource.org.aopalliance--1.0.0  - no license
> listed
>
> # https://github.com/hunterhacker/jdom/blob/jdom-1.1/core/LICENSE.txt  -
> this link has a copyright;
> include in Notice file? What do we use for "type" of license? "Copyright?"
> Or is this also a "JDOM License" like
> org.jdom--com.springsource.org.jdom--1.1.0?
>
> # http://www.xmlpull.org/  - no license listed
>
>
> ---
> Category B licenses?
>
> Aren't the following licenses listed under category-b, binary release
> only? Or do they meet the exception
> for allowing in a source release? ("For small amounts of source that is
> directly
> consumed by the ASF product at runtime in source form, and for which that
> source is unmodified and unlikely to be changed ...")
>
> javax.transaction--com.springsource.javax.transaction--1.1.0 - CDDL 1.0
>
> org.aspectj--com.springsource.org.aspectj.runtime--1.6.0 - Eclipse Public
> License 1.0
> org.aspectj--com.springsource.org.aspectj.weaver--1.6.0 - Eclipse Public
> License 1.0
>
>
> ---
> Source File Headers
> ---
>
> ---
> Non-ASF Copyrights
>
>
> 1) University of Manchester copyright in taverna-provenanceconnector
> files (see previous email).
>
> 2) taverna-execution-hadoop Crossproduct.java file contains copyrigh

Re: Taverna Mobile Application

[Gale Naylor]

Hi Rajan,

The dev@taverna mailing list is intended to collect all development work,
including things like your suggested fixes to the Taverna Mobile App!

Can you please include your suggestions in an email to the dev list? (A
reply to this email would make sense.)

Thanks!

Gale

On Thu, Jun 2, 2016 at 10:28 AM Rajan Maurya 
wrote:

> Hi Sagar,
>
> I have reviewed the PR.
> Please look and fix all of these that i have mentioned.
>
> Thanks
> On Jun 2, 2016 11:23 AM, "Rajan Maurya"  wrote:
>
> > Hi Sagar,
> >
> > Its looks good. I will review it today and update you if  there is any
> > need to change.
> >
> > Implement rest of  Announcement Details part
> >
> > Good :)
> >
> >
> > On Thu, Jun 2, 2016 at 10:58 AM, Sagar 
> wrote:
> >
> >> Hi All,
> >> My semester end exam gone well and I am starting my internship on
> this
> >> project as we talk earlier, Now I started working on Taverna Mobile
> >> Application.
> >>
> >> I go through Rajan Maurya's GsoC proposal and found he researched well
> and
> >> I am following it as accordingly.
> >>
> >>  I have sent  a pull request (PR no #14
> >> )  and I
> have
> >> added some libraries and start working on  Announcements features.
> >>
> >>- Added MVP architecture basic
> >>- Setup Retrofit
> >>- Setup Simple xml parser
> >>- Setup Rx-JAVA and Rx-Android
> >>- Setup ButterKnife
> >>- Design Announcement layout
> >>- Working ListView to show all Announcements
> >>- [WIP] Detail of clicked Announcement
> >>
> >> I am currently working on it.
> >>
> >> Rajan Maurya, Please reviews the #PR
> >>  till now
> >> and
> >> suggests me something if there is something needed to change .
> >>
> >> If anyone else wants to work on it or review my work, it'd be great.
> >>
> >> --
> >>
> >> *With warm regards  *
> >> *Sincerely yours*
> >> Sagar
> >>
> >>
> >> *Student ,(6th Semester )B.Tech IT and mathematical innovation*
> >> *Cluster Innovation Centre*
> >> *University of Delhi *
> >>
> >
> >
> >
> > --
> > *Thanks*
> > *Namaste*
> >
> > Rajan Maurya
> > Contact Number : +91 8010665248
> > Github : https://github.com/therajanmaurya
> > College : Cluster Innovation Centre, University of Delhi
> > Student : B.Tech. (Information Technology & Mathematical Innovations)
> >
> >
>

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

[Gale Naylor]

Fingers crossed for RC3!  I will be out of town for a couple of days, but
will review and build when I return.

On Mon, Jun 6, 2016, 7:31 AM Stian Soiland-Reyes  wrote:

> This is the discussion thread for Command Line 3.1.0 RC3.
>
> You can place your votes in the corresponding [VOTE] thread:
>
>
> https://lists.apache.org/thread.html/03184f452898d3f8280301b93b40fce5902d45997ce03e341afaf3d1@%3Cdev.taverna.apache.org%3E
>
>
> and ask anything else here.
>
>
> Anyone can participate in testing and voting, not just
> committers, please feel free to try out the release candidate
> and provide your votes!
>
> How to review a release candidate? https://s.apache.org/review-release
>
>
> You may want to temporarily disable your anti-virus / "Windows
> Defender" software while testing this build.
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: Code Analysis Tools Implementation

[Gale Naylor]

You should be all set, Sagar!

On Thu, Jun 9, 2016 at 10:01 AM Sagar <kumarsagar15...@gmail.com> wrote:

> Hi Gale,
>
> I sign-up here : https://cwiki.apache.org/confluence/signup.action
>
> my username : sagar15795
>
> Thanks.
> Sagar
>
> On Thu, Jun 9, 2016 at 8:00 PM, Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
> > Hi Rajan,
> >
> > You should be able to add a wiki now. Please let me know if you have any
> > difficulties.
> >
> > Thanks,
> > Gale
> >
> > On Thu, Jun 9, 2016 at 4:08 AM Rajan Maurya <rajanmaurya...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > I sign-up here : https://cwiki.apache.org/confluence/signup.action
> > >
> > > my username : therajanmaurya
> > >
> > > Thanks.
> > >
> > >
> > > On Wed, Jun 8, 2016 at 9:40 PM, Stian Soiland-Reyes <st...@apache.org>
> > > wrote:
> > >
> > > > On 6 June 2016 at 06:02, Rajan Maurya <rajanmaurya...@gmail.com>
> > wrote:
> > > > > Hi Sagar,
> > > > >
> > > > > I have looked you #PR
> > > > > <https://github.com/apache/incubator-taverna-mobile/pull/14>. It's
> > now
> > > > > completed. You did a good job.
> > > >
> > > > Thanks for your good mentoring, Rajan! Pull request merged.
> > > >
> > >
> > >
> > >
> > > --
> > > *Thanks*
> > > *Namaste*
> > >
> > > Rajan Maurya
> > > Contact Number : +91 8010665248
> > > Github : https://github.com/therajanmaurya
> > > College : Cluster Innovation Centre, University of Delhi
> > > Student : B.Tech. (Information Technology & Mathematical Innovations)
> > >
> >
>
>
>
> --
>
> *With warm regards  *
> *Sincerely yours*
> Sagar
>
>
> *Student ,(6th Semester )B.Tech IT and mathematical innovation*
> *Cluster Innovation Centre*
> *University of Delhi *
>

Re: Code Analysis Tools Implementation

[Gale Naylor]

I created a GSOC 2016 Apache Taverna Mobile parent page. You can add wiki
page(s) as child pages. Let me know if you have any problems.

Gale

On Thu, Jun 9, 2016 at 10:27 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> You should be all set, Sagar!
>
> On Thu, Jun 9, 2016 at 10:01 AM Sagar <kumarsagar15...@gmail.com> wrote:
>
>> Hi Gale,
>>
>> I sign-up here : https://cwiki.apache.org/confluence/signup.action
>>
>> my username : sagar15795
>>
>> Thanks.
>> Sagar
>>
>> On Thu, Jun 9, 2016 at 8:00 PM, Gale Naylor <ga...@noventussolutions.com>
>> wrote:
>>
>> > Hi Rajan,
>> >
>> > You should be able to add a wiki now. Please let me know if you have any
>> > difficulties.
>> >
>> > Thanks,
>> > Gale
>> >
>> > On Thu, Jun 9, 2016 at 4:08 AM Rajan Maurya <rajanmaurya...@gmail.com>
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > I sign-up here : https://cwiki.apache.org/confluence/signup.action
>> > >
>> > > my username : therajanmaurya
>> > >
>> > > Thanks.
>> > >
>> > >
>> > > On Wed, Jun 8, 2016 at 9:40 PM, Stian Soiland-Reyes <st...@apache.org
>> >
>> > > wrote:
>> > >
>> > > > On 6 June 2016 at 06:02, Rajan Maurya <rajanmaurya...@gmail.com>
>> > wrote:
>> > > > > Hi Sagar,
>> > > > >
>> > > > > I have looked you #PR
>> > > > > <https://github.com/apache/incubator-taverna-mobile/pull/14>.
>> It's
>> > now
>> > > > > completed. You did a good job.
>> > > >
>> > > > Thanks for your good mentoring, Rajan! Pull request merged.
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > *Thanks*
>> > > *Namaste*
>> > >
>> > > Rajan Maurya
>> > > Contact Number : +91 8010665248
>> > > Github : https://github.com/therajanmaurya
>> > > College : Cluster Innovation Centre, University of Delhi
>> > > Student : B.Tech. (Information Technology & Mathematical Innovations)
>> > >
>> >
>>
>>
>>
>> --
>>
>> *With warm regards  *
>> *Sincerely yours*
>> Sagar
>>
>>
>> *Student ,(6th Semester )B.Tech IT and mathematical innovation*
>> *Cluster Innovation Centre*
>> *University of Delhi *
>>
>

Added Structure to Confluence Wiki Pages

[Gale Naylor]

I organized the wiki pages so that all the GSOC-related pages are under a
parent page called GSOC 2016, which serves as a table of contents.

I also added a parent page called Releases, which has all the
release-related pages, and acts as a table of contents.

Does this seem reasonable?

Gale

Re: [DISCUSS] Release candidate 2 of Command-line Tool 3.1.0-incubating

[Gale Naylor]

Yes, I think we can do the package.html file headers after the release.


On Mon, Jun 6, 2016 at 7:27 AM Stian Soiland-Reyes <st...@apache.org> wrote:

> On 4 June 2016 at 17:30, Gale Naylor <ga...@noventussolutions.com> wrote:
> > Thanks for the explanations, Stian. A vote-email script might not be a
> bad
> > idea! It certainly
> > seems to be a complicated thing to pull together.
> >
> > In response to Stian's email, I found some additional, related ASF
> > resources that support not
> > requiring license headers in files whose content cannot be copyrighted
> > (e.g., files that contain
> > "Hello"). Here is the link:
> > http://www.apache.org/legal/src-headers.html#faq-exceptions
> >
> > The exception also applies to "Test data for which the addition of a
> source
> > header would cause
> > the tests to fail."
> >
> > It seems that most of the files that currently do not have license
> headers,
> > including
> > files in the services sub-directories, meet the criteria of being exempt
> > from the license header
> > requirement.
>
> Ah, great. So we're generally good to go with those test files then,
> and can just list them in the apache-rat excludes - which I think is a
> good way to say "Yeah, we know about this file, 's fine".
>
>
> > However, it sounds like we SHOULD add license headers to the
> > package.html files.
> > Do we want to do that way now, and then later convert to
> > package-info.java files?
>
> Just convert them right away, I think.. it's generally just rename and
> add the ASF header and the Java "package " line.
>
> The only tricky thing about them is that you need to use the two
> different Java comment blocks carefully so that the ASF header does
> not become the JAvadoc, that is
>
> src/main/java/org/apache/taverna/foo/package-info.java
>
> /* ASF */
> /** javadoc for this package **/
> package org.apache.taverna.foo;
>
> And we should have such package info for all API-like packages at
> least.. like in all the *-api bits in taverna-engine.   (It might just
> have a one-liner with the description from README)
>
>
> Shall we do this after this release?
>
>
>
> > I also found an ASF link that confirms what Stian said about only BUNDLED
> > dependencies
> > needing to be included in NOTICE files. Good to know.
> > (http://www.apache.org/dev/licensing-howto.html#bundled-vs-non-bundled)
>
> Yes - so bundled would be when we make a binaries/ upload.
>
> Not sure if this also covers any bundling in Maven Central - e.g.
>
>
> http://central.maven.org/maven2/org/apache/taverna/language/taverna-tavlang-tool/0.15.1-incubating/taverna-tavlang-tool-0.15.1-incubating.jar
> includes bundled JARs, but the Maven plugins seem to have managed to
> combine the contained META-INF/NOTICE. (Thanks, Menaka)
>
>
>
> > Also, regarding 3rd party copyrighted works:  I found an ASF link that
> > explicitly states:
> > -- not to modify/remove copyright headers from 3rd party works;
> > -- not to add the standard ASF license header to 3rd party works.
> > http://www.apache.org/legal/src-headers.html#3party
>
> OK, so we'll leave those BSD copyrights in place in say the
> taverna-engine hadoop crossproduct.java
>
>
> > One remaining question about 3rd party license in
> > src/license/THIRD-PARTY.properties:
> >
> > javax.transaction--com.springsource.javax.transaction--1.1.0  (CDDL
> 1.0)
> >
> > Is this an exception to the category-b license "binary only" rule
> because
> > we use only
> > a small amount of source code?
>
> But it's not included - we don't distribute javax.transaction in the
> source archive; it's downloaded from Maven repositories.  You won't
> see it until you have built the commandline product:
>
>  Directory of
> D:\src\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating\lib\javax.transaction
>
> 2016-06-06  14:10  .
> 2016-06-06  14:10  ..
> 2016-05-31  16:2315,518
> com.springsource.javax.transaction-1.1.0.jar
>
> (or look in ~/.m2/repository/javax/transaction)
>
> > One observation about headers in JSON files
> > Most of the JSON files have the header you described (
> http://purl.org.
> > ..).
>
> Yeah.. some kind of JSON-LD-like workaround -- the key is unlikely to
> be used for anything but for licenses - and generally JSON consumers
> ignore extra keys.
>
>
> > Is it okay if the JSON fil

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

[Gale Naylor]

taverna-engine, taverna-common-activities, and taverna-commandline all build
successfully on my Windows 10 machine running Maven 3.3.9 and Java 1.8.0_91.

I do not have time to perform a detailed check of the source headers
for the common-activities or commandline files at this time, or check the
dependencies. (But Alan has done a GitHub search for copyrights and the
files are clean.)

These warnings in Activity archetype seem to be the most serious:

[INFO] [WARNING] Some problems were encountered while building the
effective model for com.example:dummy-taverna-plugin:pom:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for
org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 22,
column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for
org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 50,
column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for
org.apache.maven.plugins:maven-jar-plugin is missing. @ line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for
 org.apache.maven.plugins:maven-source-plugin is missing. @ line 29, column
12


Can we release with these warnings?


See a summary of the non-Javadoc warnings below, followed by
a summary of all warnings (including Javadoc warnings).

---
Warnings (other than Javadoc warnings):
---
  taverna-engine
- Workflow Model impl - private reference
- Reference Manager impl - unused package warning
- Activity archetype: missing plug-in warnings, empty jar warning,
  and unresolved package dependency warnings

  taverna-common-activities
- Common Activities: empty jar warning

  taverna-commandline
- Command-line tool: empty jar warning
- Command-line tool Product: missing POMs

---
Detailed summary (including Javadoc warnings)
---

taverna-engine
  - Engine and Platform: empty jar warning
  - Reference Manager API: Javadoc warnings
  - Observer pattern: Javadoc warnings
  - Workflow Model API: Javadoc warnings
  - Workflow Model Extension Points: Javadoc warnings
  - Workflow Model impl: Javadoc warnings; private reference warning
  [WARNING] Bundle org.apache.taverna.engine:taverna-workflowmodel-
  impl:bundle:3.1.0-incubating :
  Export org.apache.taverna.workflowmodel.impl,  has 1,  private
references
  [org.apache.taverna.workflowmodel.processor.dispatch.impl],

  - Reference Manager impl: Javadoc warnings; unused package warning
  [WARNING] Bundle org.apache.taverna.engine:taverna-reference-
  impl:bundle:3.1.0-incubating : Unused Import-Package instructions:
  [org.springframework.orm.*]

  - Activity archetype: missing plug-in warnings, empty jar warning,
and unresolved package dependency warnings
  EXAMPLE 1: [INFO] [WARNING] 'build.plugins.plugin.version' for
  org.apache.maven.plugins:maven-compiler-plugin is missing.
  @ com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
  ...\taverna-activity-archetype\target\test-classes\projects\
  dummyActivity\project\dummy-taverna-plugin\pom.xml, line 22, column 12

  EXAMPLE 2: [INFO] [WARNING] Bundle : org.springframework:
  org.springframework.context:jar:3.0.5.RELEASE has unresolved package
  dependencies: org.apache.commons.logging;version="[1.1.1,2.0.0)"

  - Platform Capability API: Javadoc warnings
  - Credential Manager API: Javadoc warnings
  - Credential Manager impl: Javadoc warnings
  - Platform Report Service: Javadoc warnings
  - Platform Execution Service API: Javadoc warnings
  - Platform Run Service API: Javadoc warnings

taverna-common-activities
   - Common Activities: empty jar warning
   - Beanshell Activity: Javadoc warnings
   - External Tool Activity: Javadoc warnings
   - REST Activity: Javadoc warnings
   - Spreadsheet Import Activity: Javadoc warnings
   - WSDL-generic Library: Javadoc warnings
   - WSDL Activity: Javadoc warnings

taverna-commandline
- Command-line tool: empty jar warning
- Command-line tool Common: a few Javadoc warnings
- Command-line tool Product: missing POMs
EXAMPLE: [WARNING] Missing POM for org.springframework:org.
springframework.aop:jar:3.0.0.RC1

Packages/modules (what is the correct term?) that are not listed
have no warnings.


Gale

On Wed, Jun 8, 2016 at 3:49 AM Stian Soiland-Reyes  wrote:

> Thilina Manamgoda wrote:
> > 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.
>
> Do you have any more details of this test error? It should look like a
> stack trace mentioning which tests fail.
>
> You can also look in the *.txt files in
> taverna-credential-manager-impl/target/surefire-reports/
>
> In case you built with -T1.5C, 

Re: Code Analysis Tools Implementation

[Gale Naylor]

Hi Rajan,

You should be able to add a wiki now. Please let me know if you have any
difficulties.

Thanks,
Gale

On Thu, Jun 9, 2016 at 4:08 AM Rajan Maurya 
wrote:

> Hi,
>
> I sign-up here : https://cwiki.apache.org/confluence/signup.action
>
> my username : therajanmaurya
>
> Thanks.
>
>
> On Wed, Jun 8, 2016 at 9:40 PM, Stian Soiland-Reyes 
> wrote:
>
> > On 6 June 2016 at 06:02, Rajan Maurya  wrote:
> > > Hi Sagar,
> > >
> > > I have looked you #PR
> > > . It's now
> > > completed. You did a good job.
> >
> > Thanks for your good mentoring, Rajan! Pull request merged.
> >
>
>
>
> --
> *Thanks*
> *Namaste*
>
> Rajan Maurya
> Contact Number : +91 8010665248
> Github : https://github.com/therajanmaurya
> College : Cluster Innovation Centre, University of Delhi
> Student : B.Tech. (Information Technology & Mathematical Innovations)
>

Re: Code Analysis Tools Implementation

[Gale Naylor]

If you only need one page, go ahead and use this one:

https://cwiki.apache.org/confluence/display/TAVERNADEV/GSOC+2016+Apache+Taverna+Mobile

If you need multiple pages, go ahead and create them - we can always sort
out the organization later.

On Thu, Jun 9, 2016 at 10:54 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> I created a GSOC 2016 Apache Taverna Mobile parent page. You can add wiki
> page(s) as child pages. Let me know if you have any problems.
>
> Gale
>
> On Thu, Jun 9, 2016 at 10:27 AM Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
>> You should be all set, Sagar!
>>
>> On Thu, Jun 9, 2016 at 10:01 AM Sagar <kumarsagar15...@gmail.com> wrote:
>>
>>> Hi Gale,
>>>
>>> I sign-up here : https://cwiki.apache.org/confluence/signup.action
>>>
>>> my username : sagar15795
>>>
>>> Thanks.
>>> Sagar
>>>
>>> On Thu, Jun 9, 2016 at 8:00 PM, Gale Naylor <ga...@noventussolutions.com
>>> >
>>> wrote:
>>>
>>> > Hi Rajan,
>>> >
>>> > You should be able to add a wiki now. Please let me know if you have
>>> any
>>> > difficulties.
>>> >
>>> > Thanks,
>>> > Gale
>>> >
>>> > On Thu, Jun 9, 2016 at 4:08 AM Rajan Maurya <rajanmaurya...@gmail.com>
>>> > wrote:
>>> >
>>> > > Hi,
>>> > >
>>> > > I sign-up here : https://cwiki.apache.org/confluence/signup.action
>>> > >
>>> > > my username : therajanmaurya
>>> > >
>>> > > Thanks.
>>> > >
>>> > >
>>> > > On Wed, Jun 8, 2016 at 9:40 PM, Stian Soiland-Reyes <
>>> st...@apache.org>
>>> > > wrote:
>>> > >
>>> > > > On 6 June 2016 at 06:02, Rajan Maurya <rajanmaurya...@gmail.com>
>>> > wrote:
>>> > > > > Hi Sagar,
>>> > > > >
>>> > > > > I have looked you #PR
>>> > > > > <https://github.com/apache/incubator-taverna-mobile/pull/14>.
>>> It's
>>> > now
>>> > > > > completed. You did a good job.
>>> > > >
>>> > > > Thanks for your good mentoring, Rajan! Pull request merged.
>>> > > >
>>> > >
>>> > >
>>> > >
>>> > > --
>>> > > *Thanks*
>>> > > *Namaste*
>>> > >
>>> > > Rajan Maurya
>>> > > Contact Number : +91 8010665248
>>> > > Github : https://github.com/therajanmaurya
>>> > > College : Cluster Innovation Centre, University of Delhi
>>> > > Student : B.Tech. (Information Technology & Mathematical Innovations)
>>> > >
>>> >
>>>
>>>
>>>
>>> --
>>>
>>> *With warm regards  *
>>> *Sincerely yours*
>>> Sagar
>>>
>>>
>>> *Student ,(6th Semester )B.Tech IT and mathematical innovation*
>>> *Cluster Innovation Centre*
>>> *University of Delhi *
>>>
>>

Re: Taverna Mobile Application

[Gale Naylor]

Thanks, Rajan!

On Thu, Jun 2, 2016, 8:15 PM Rajan Maurya <rajanmaurya...@gmail.com> wrote:

> Hi Gale,
>
> Ok, Actually I forget to mention the GitHub PR.
>
> Here is some point need to fix first to merge the PR
>
>1. Implement Parcelable in POJO for making faster HTTPS Calls
>2.
>
>Do not make multiple POJO class in single like you have done here
>
>  app/src/main/java/org/apache/taverna/mobile/data/model/Announcement.java.
>Made author POJO in Announcement POJO because author POJO will be used
>further in many places in future so make it separate.
>3.
>
>When you will make separate POJOs then you do not need the hierarchical
>initialization of List. It's not good practice.
>4.
>
>Naming convention mMainPresenter in AnnouncementFragment, make it
>mAnnouncementPresenter. It can be good. for future follow this
>
> https://github.com/ribot/android-guidelines/blob/master/project_and_code_guidelines.md#2-code-guidelines
> .
>5.
>
>You are using ConnectivityManager for checking internet connection two
>times in the same file bad practice.
>I suggest making a util/ConnectionInfo something class to use anywhere
>you need to check internet connection.
>6.
>
>What about if the loading data failed from the internet. Implement
>showResponseError.
>
>
> Thanks
>
>
>
>
> On Fri, Jun 3, 2016 at 3:37 AM, Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
> > Hi Rajan,
> >
> > The dev@taverna mailing list is intended to collect all development
> work,
> > including things like your suggested fixes to the Taverna Mobile App!
> >
> > Can you please include your suggestions in an email to the dev list? (A
> > reply to this email would make sense.)
> >
> > Thanks!
> >
> > Gale
> >
> > On Thu, Jun 2, 2016 at 10:28 AM Rajan Maurya <rajanmaurya...@gmail.com>
> > wrote:
> >
> > > Hi Sagar,
> > >
> > > I have reviewed the PR.
> > > Please look and fix all of these that i have mentioned.
> > >
> > > Thanks
> > > On Jun 2, 2016 11:23 AM, "Rajan Maurya" <rajanmaurya...@gmail.com>
> > wrote:
> > >
> > > > Hi Sagar,
> > > >
> > > > Its looks good. I will review it today and update you if  there is
> any
> > > > need to change.
> > > >
> > > > Implement rest of  Announcement Details part
> > > >
> > > > Good :)
> > > >
> > > >
> > > > On Thu, Jun 2, 2016 at 10:58 AM, Sagar <kumarsagar15...@gmail.com>
> > > wrote:
> > > >
> > > >> Hi All,
> > > >> My semester end exam gone well and I am starting my internship
> on
> > > this
> > > >> project as we talk earlier, Now I started working on Taverna Mobile
> > > >> Application.
> > > >>
> > > >> I go through Rajan Maurya's GsoC proposal and found he researched
> well
> > > and
> > > >> I am following it as accordingly.
> > > >>
> > > >>  I have sent  a pull request (PR no #14
> > > >> <https://github.com/apache/incubator-taverna-mobile/pull/14>)  and
> I
> > > have
> > > >> added some libraries and start working on  Announcements features.
> > > >>
> > > >>- Added MVP architecture basic
> > > >>- Setup Retrofit
> > > >>- Setup Simple xml parser
> > > >>- Setup Rx-JAVA and Rx-Android
> > > >>- Setup ButterKnife
> > > >>- Design Announcement layout
> > > >>- Working ListView to show all Announcements
> > > >>- [WIP] Detail of clicked Announcement
> > > >>
> > > >> I am currently working on it.
> > > >>
> > > >> Rajan Maurya, Please reviews the #PR
> > > >> <https://github.com/apache/incubator-taverna-mobile/pull/14> till
> now
> > > >> and
> > > >> suggests me something if there is something needed to change .
> > > >>
> > > >> If anyone else wants to work on it or review my work, it'd be great.
> > > >>
> > > >> --
> > > >>
> > > >> *With warm regards  *
> > > >> *Sincerely yours*
> > > >> Sagar
> > > >>
> > > >>
> > > >> *Student ,(6th Semester )B.Tech IT and mathematical innovation*
> > > >> *Cluster Innovation Centre*
> > > >> *University of Delhi *
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > *Thanks*
> > > > *Namaste*
> > > >
> > > > Rajan Maurya
> > > > Contact Number : +91 8010665248
> > > > Github : https://github.com/therajanmaurya
> > > > College : Cluster Innovation Centre, University of Delhi
> > > > Student : B.Tech. (Information Technology & Mathematical Innovations)
> > > >
> > > >
> > >
> >
>
>
>
> --
> *Thanks*
> *Namaste*
>
> Rajan Maurya
> Contact Number : +91 8010665248
> Github : https://github.com/therajanmaurya
> College : Cluster Innovation Centre, University of Delhi
> Student : B.Tech. (Information Technology & Mathematical Innovations)
>

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

[Gale Naylor]

I do not think any of the issues I raised should stop the release. I agree
to adding the non-Javadoc warnings individually to JIRA. There are a lot of
Javadoc warnings, can we have one JIRA issue for each component that
collects all of the Javadoc warnings?

I'm ready to [VOTE].

On Mon, Jun 13, 2016 at 9:17 AM Stian Soiland-Reyes 
wrote:

> Thanks, Alan.. would you feel ready to [VOTE]..?
>
> On 6 June 2016 at 17:31, Alan Williams  wrote:
> > It all builds OK on my Maven 3.3.3
> >
> > Alan
> >
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: [] Release Apache Taverna Command-line Tool 3.1.0-incubating RC3

[Gale Naylor]

+1

taverna-engine, taverna-common-activities, and taverna-commandline all build
successfully on my Windows 10 machine running Maven 3.3.9 and Java 1.8.0_91.

Add the following warnings to JIRA:

---
Warnings (other than Javadoc warnings) - Individual JIRA issues
---
  taverna-engine
- Workflow Model impl - private reference
- Reference Manager impl - unused package warning
- Activity archetype: missing plug-in warnings, empty jar warning,
  and unresolved package dependency warnings

  taverna-common-activities
- Common Activities: empty jar warning

  taverna-commandline
- Command-line tool: empty jar warning
- Command-line tool Product: missing POMs

---
Detailed summary (including Javadoc warnings)
---

taverna-engine
  - Engine and Platform: empty jar warning
  - Reference Manager API: Javadoc warnings
  - Observer pattern: Javadoc warnings
  - Workflow Model API: Javadoc warnings
  - Workflow Model Extension Points: Javadoc warnings
  - Workflow Model impl: Javadoc warnings; private reference warning
  [WARNING] Bundle org.apache.taverna.engine:taverna-workflowmodel-
  impl:bundle:3.1.0-incubating :
  Export org.apache.taverna.workflowmodel.impl,  has 1,  private
references
  [org.apache.taverna.workflowmodel.processor.dispatch.impl],

  - Reference Manager impl: Javadoc warnings; unused package warning
  [WARNING] Bundle org.apache.taverna.engine:taverna-reference-
  impl:bundle:3.1.0-incubating : Unused Import-Package instructions:
  [org.springframework.orm.*]

  - Activity archetype: missing plug-in warnings, empty jar warning,
and unresolved package dependency warnings
  EXAMPLE 1: [INFO] [WARNING] 'build.plugins.plugin.version' for
  org.apache.maven.plugins:maven-compiler-plugin is missing.
  @ com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
  ...\taverna-activity-archetype\target\test-classes\projects\
  dummyActivity\project\dummy-taverna-plugin\pom.xml, line 22, column 12

  EXAMPLE 2: [INFO] [WARNING] Bundle : org.springframework:
  org.springframework.context:jar:3.0.5.RELEASE has unresolved package
  dependencies: org.apache.commons.logging;version="[1.1.1,2.0.0)"

  - Platform Capability API: Javadoc warnings
  - Credential Manager API: Javadoc warnings
  - Credential Manager impl: Javadoc warnings
  - Platform Report Service: Javadoc warnings
  - Platform Execution Service API: Javadoc warnings
  - Platform Run Service API: Javadoc warnings

taverna-common-activities
   - Common Activities: empty jar warning
   - Beanshell Activity: Javadoc warnings
   - External Tool Activity: Javadoc warnings
   - REST Activity: Javadoc warnings
   - Spreadsheet Import Activity: Javadoc warnings
   - WSDL-generic Library: Javadoc warnings
   - WSDL Activity: Javadoc warnings

taverna-commandline
- Command-line tool: empty jar warning
- Command-line tool Common: a few Javadoc warnings
- Command-line tool Product: missing POMs
EXAMPLE: [WARNING] Missing POM for org.springframework:org.
springframework.aop:jar:3.0.0.RC1




On Mon, Jun 13, 2016 at 9:49 AM Stian Soiland-Reyes 
wrote:

> On 13 June 2016 at 10:04, Andy Seaborne  wrote:
> > One of the few issues that Taverna has before graduation is getting VOTEs
> > done.  When a TLP, the future-PMC is going to have to be able to muster
> the
> > necessary 3 votes for a releases.  The active PPMC of Taverna is looking
> > minimal.
> >
> > 1/ What about this vote?
>
> Thanks for raising this, Andy.
>
>
> I agree we need to be speedier on a VOTE - but I think it's fair that
> we have due review of the very first release of this particular code -
> e.g. we dropped a RC because of misleading copyright headers; which I
> think shows a functioning PMC.
>
>
> One thing I think is important is that we should not strive for code
> perfection, as a small project I am afraid we don't have that luxury.
> We should rather try to Release Early, Release Often.
>
>
> > 2/ How can the pool of active (P)PMC members be grown?
>
> We still need new members, but I think we also need to keep the
> existing PPMC members engaged.
>
> ASF processes come with.. well, some overhead. I guess that can be
> tiring sometimes.
>
>
> I know everyone is busy - perhaps the remaining part of the PPMC [1]
> could chip in on what we could do to get you to review/vote? :)
>
>
> Have we made the release process [2][3] too big?   Or is it too much
> to review 3 artifacts at once?
>
> Note that everyone don't have to test everything on the list!
>
>
> [1] https://taverna.incubator.apache.org/about/
> [2]
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+How+to+Review+a+Release+and+Vote
> [3]
> 

Direct-editing by Committers

[Gale Naylor]

 I was going to add the license headers to the 2 taverna-engine README
files
(taverna-prov/reADME.md and taverna-reference-types/reADME.md),
but I wasn't sure of the procedure for editing directly.

I found the link, but wasn't sure how to edit without effecting what someone
else is doing.

Do you want me to edit in the master branch or ??

Gale

Re: Podling Report Reminder - June 2016

[Gale Naylor]

Looks good! The only comment I have is that the mailing list stats are in
chronological order and the user stats are in reverse chronological order.
It may be easier to read if they are both the same, unless there is a
reason why they are reported this way.

Thank you! You answered the question I was just going to ask!

Fingers crossed!

Gale

On Mon, May 30, 2016, 3:24 PM Stian Soiland-Reyes  wrote:

> Sorry about the delay.. bank holiday weekend in the UK - for once with
> lovely weather!
>
> Draft report added to https://wiki.apache.org/incubator/June2016
> (not May2016)
>
>
> Comments welcome below, or as changes in the incubator wiki.
>
>
> Taverna
>
> Taverna is a domain-independent suite of tools used to design and execute
> data-driven workflows.
>
> Taverna has been incubating since 2014-10-20.
>
> Three most important issues to address in the move towards graduation:
>
>   1. Project maturity evaluation
>   2.
>   3.
>
> Any issues that the Incubator PMC (IPMC) or ASF Board wish/need to be
> aware of?
>
>   ASF guidance on US export ECCN cryptography registration
>   https://www.apache.org/dev/crypto.html
>   has not yet been updated for the 2010 rule changes, confusion
>   around this classification caused Taverna delays.
>
>   Many registrations on https://www.apache.org/licenses/exports/ are
>   outdated (e.g. graduated podlings and 404 source repos),
>   these need to be updated by each PMC - see
>   https://lists.apache.org/thread.html/Z6a17eutravbs96
>
>
> How has the community developed since the last report?
>
>   Two GSOC students now active. The third applicant accepted
>   with Apache Mifos instead - but is still in touch and willing
>   to help a fourth student who volunteered to contribute independently.
>   Another student willing to contribute a new plugin.
>
>   A total of four ICLAs registered - however these students need
>   further encouragement and guidance to submit regular pull requests.
>
>
>   dev@taverna mailing lists stats:
>
>   Mar 2016: 312
>   Apr 2016: 102
>   May 2015: 184
>
>
>   users@taverna:
>
>   Mar 2016: 12
>   Apr 2016: 6
>   May 2015: 1
>
>
>   JIRA issues over last 90 days:
>
>   49 created
>   25 resolved
>
>
> How has the project developed since the last report?
>
>   Preparations for release of the main workflow engine has had focus,
>   including build stability across platforms,
>   documentation update and US Export classifications of
>   encryption items (which caused some delays).
>
>   Taverna Engine/Command Line Release candidate now under vote.
>
>   Traffic on users@ show interest mainly on Taverna Server, so
>   this component should probably be the development
>   focus after GSOC.
>
>
> Date of last release:
>
>   2016-03-11 taverna-osgi-0.2.1-incubating
>   2016-03-11 taverna-language-0.15.1-incubating
>
>   Release Candidates under vote:
>   taverna-engine, taverna-common-activities, taverna-commandline
>
>
> When were the last committers or PMC members elected?
>
>   2015-12-04
>
>
> Signed-off-by:
>
>   [ ](taverna) Andy Seaborne
>   [ ](taverna) Daniel J Debrunner
>   [ ](taverna) Suresh Srinivas
>   [ ](taverna) Suresh Marru
>   [ ](taverna) Marlon Pierce
>
> Shepherd/Mentor notes:
>
> On 27 May 2016 at 01:40,   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 of time to
> > prepare your quarterly board report.
> >
> > The board meeting is scheduled for Wed, 15 June 2016, 10:30 am PDT.
> > The report for your podling will form a part of the Incubator PMC
> > report. The Incubator PMC requires your report to be submitted 2 weeks
> > before the board meeting, to allow sufficient time for review and
> > submission (Wed, June 1st).
> >
> > Please submit your report with sufficient time to allow the Incubator
> > PMC, and subsequently board members to review and digest. Again, the
> > very latest you should submit your report is 2 weeks prior to the board
> > meeting.
> >
> > Thanks,
> >
> > The Apache Incubator PMC
> >
> > Submitting your Report
> >
> > --
> >
> > Your report should contain the following:
> >
> > *   Your project name
> > *   A brief description of your project, which assumes no knowledge of
> > the project or necessarily of its field
> > *   A list of the three most important issues to address in the move
> > towards graduation.
> > *   Any issues that the Incubator PMC or ASF Board might wish/need to be
> > aware of
> > *   How has the community developed since the last report
> > *   How has the project developed since the last report.
> >
> > This should be appended to the Incubator Wiki page at:
> >
> > http://wiki.apache.org/incubator/May2016
> >
> > Note: This is manually populated. You may need to wait a little before
> > this page is created from a template.
> >
> > Mentors
> > ---
> >
> > Mentors should review reports for 

Re: Starting command line 3.1.0 release process

[Gale Naylor]

What about the 2nd taverna-engine build failure? Has that been resolved?

http://apache-taverna-dev.markmail.org/message/olyip2p5rioghodm?q=+from:%22Gale+Naylor%22=1

On Thu, May 26, 2016, 9:08 AM Stian Soiland-Reyes  wrote:

> OK, so now that the US export thingie has been sent off, I'm back from
> my travels, and the newly discovered TAVERNA-971 was fixed - I can try
> to start tomorrow with the release candidates of:
>
> taverna-engine 3.1.0-incubating
> taverna-common-activities 2.1.0-incubating
> taverna-commandline 3.1.0-incubating
>
> Fire in the hole!
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: Possible changes to groupId, etc?

[Gale Naylor]

Excellent! Thanks, Stian. I am working on the Web pages.

On Thu, May 26, 2016, 9:15 AM Stian Soiland-Reyes  wrote:

> Done:
>
>
> https://github.com/apache/incubator-taverna-commandline/commit/b096abbe15ee90dbd5f9c28bb56a3ed64f6b91e6
>
> [INFO] Apache Taverna Command-line Tool ... SUCCESS [
> 0.150 s]
> [INFO] Apache Taverna Command-line Tool API ... SUCCESS [
> 0.007 s]
> [INFO] Apache Taverna Command-line Tool Common  SUCCESS [
> 0.007 s]
> [INFO] Apache Taverna Command-line Tool Launcher .. SUCCESS [
> 0.013 s]
> [INFO] Apache Taverna Command-line Tool Product ... SUCCESS [
> 0.100 s]
>
>
> https://github.com/apache/incubator-taverna-commandline#apache-taverna-command-line-tool
>
>
>
> On 26 May 2016 at 17:09, Stian Soiland-Reyes  wrote:
> > On 26 May 2016 at 17:07, Stian Soiland-Reyes  wrote:
> >> We didn't reach a conclusion - perhaps to enable the Release Candidate
> >> now, can we perhaps try:
> >>
> >> a) Stick with the repository names, groupId and package names as-is
> >> b) Update documentation and READMEs to consistently use "Command Line
> >> Tool" in English
> >
> > Now I got it wrong.. we agreed:
> >
> >  "Taverna Command-line Tool" in English.
> >
> >
> > --
> > Stian Soiland-Reyes
> > Apache Taverna (incubating), Apache Commons
> > http://orcid.org/-0001-9842-9718
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: Release of Taverna Command Line?

[Gale Naylor]

I also got several JavaDoc warnings. I'll try to slog through them and add
them to JIRA in the next week or so.

Gale

On Fri, May 27, 2016 at 8:42 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> Thanks for the links, Alan!
>
> I'm happy to say the entire engine project now builds successfully.
>
> However, I got a few warnings that look serious ("...Maven versions might
> no longer support building such malformed projects.") and ("...using
> platform encoding Cp1252, i.e. build is platform dependent!") -- SEE BELOW
>
> Plus several org.springframework:org. jars have unresolved dependencies
> and org.apache.taverna.workflowmodel.impl has a private reference. -- SEE
> BELOW
>
> [INFO] [WARNING]
> [INFO] [WARNING] Some problems were encountered while building the
> effective model for
> com.example:dummy-taverna-plugin-plugin:taverna-plugin:0.1.0-SNAPSHOT
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-compiler-plugin is missing. @
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
> C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
> line 20, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-surefire-plugin is missing. @
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
> C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
> line 48, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-jar-plugin is missing. @
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
> C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
> line 38, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-source-plugin is missing. @
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
> C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
> line 27, column 12
> [INFO] [WARNING]
> [INFO] [WARNING] Some problems were encountered while building the
> effective model for
> com.example:dummy-taverna-plugin-activity:bundle:0.1.0-SNAPSHOT
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-compiler-plugin is missing. @
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
> C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
> line 20, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-surefire-plugin is missing. @
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
> C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
> line 48, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-jar-plugin is missing. @
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
> C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
> line 38, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-source-plugin is missing. @
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
> C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
> line 27, column 12
> [INFO] [WARNING]
> [INFO] [WARNING] Some problems were encountered while building the
> effective model for com.example:dummy-taverna-plugin:pom:0.1.0-SNAPSHOT
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 20,
> column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 48,
> column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-jar-plugin is missing. @ line 38, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for
> org.apache.maven.plugins:maven-source-plugin is missing. @ line 27, column
> 12
> [INFO] [WARNING]
> [INFO] [WARNING] It is highly recommended to fix these problems because
> they threaten the stability of your build.
> [INFO] [WARNING]
> [INFO] [WARNING] For this reason, future Maven versions might no longer
> support building such malformed projects.
> [INFO] [WARNING]
>
>
> [I

Re: Release of Taverna Command Line?

[Gale Naylor]

G] File encoding has not been set, using platform encoding
Cp1252, i.e. build is platform dependent!
[INFO] [INFO] Compiling 3 source files to
C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\target\classes
[INFO] [INFO]
[INFO] [INFO] --- maven-resources-plugin:3.0.0:testResources
(default-testResources) @ dummy-taverna-plugin-activity ---
[INFO] [WARNING] Using platform encoding (Cp1252 actually) to copy filtered
resources, i.e. build is platform dependent!
[INFO] [INFO] skip non existing resourceDirectory
C:\incubator-taverna-engine-master\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\dummy-taverna-plugin-activity\src\test\resources
[INFO] [INFO]
[INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile
(default-testCompile) @ dummy-taverna-plugin-activity ---
[INFO] [INFO] Changes detected - recompiling the module!
[INFO] [WARNING] File encoding has not been set, using platform encoding
Cp1252, i.e. build is platform dependent!

AND AGAIN IN THE TEST SECTION:
[INFO] [INFO] --- maven-resources-plugin:3.0.0:resources
(default-resources) @ dummy-taverna-plugin-activity ---
[INFO] [WARNING] Using platform encoding (Cp1252 actually) to copy filtered
resources, i.e. build is platform dependent!



[INFO] [INFO]

[INFO] [INFO] Building Dummy Taverna plugin 0.1.0-SNAPSHOT
[INFO] [INFO]

[INFO] [INFO]
[INFO] [INFO] --- taverna-maven-plugin:0.2.1-incubating:plugin-generate
(default-plugin-generate) @ dummy-taverna-plugin-plugin ---
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.context:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.aop:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.beans:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.core:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.transaction:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Not an OSGi bundle : junit:junit:jar:4.4
[INFO] [INFO]
[INFO] [INFO] ---
taverna-maven-plugin:0.2.1-incubating:plugin-prepare-bundles
(default-plugin-prepare-bundles) @ dummy-taverna-plugin-plugin ---
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.context:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.aop:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.beans:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.core:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Bundle :
org.springframework:org.springframework.transaction:jar:3.0.5.RELEASE has
unresolved package dependencies:
[INFO] [WARNING] org.apache.commons.logging;version="[1.1.1,2.0.0)"
[INFO] [WARNING] Not an OSGi bundle : junit:junit:jar:4.4


[INFO] --- maven-bundle-plugin:2.5.4:bundle (default-bundle) @
taverna-workflowmodel-impl ---
[WARNING] Bundle
org.apache.taverna.engine:taverna-workflowmodel-impl:bundle:3.1.0-incubating-SNAPSHOT
: Export org.apache.taverna.workflowmodel.impl,  has 1,  private references
[org.apache.taverna.workflowmodel.processor.dispatch.impl],


On Fri, May 27, 2016 at 8:20 AM Alan Williams <alanin...@googlemail.com>
wrote:

> On 27-May-16 16:06, Gale Naylor wrote:
> > Okay. I'll test that. It makes sense. How about if we just add a notice
> in
> > the Readme? (Maybe even just suggest that Windows USERS install at their
> > top level directory?) Probably I'm the only one who buries their file so
> > deeply! :)
>
> I think something in the README is a good idea as a quick workaround. I
> don't think though that the sour

Re: [VOTE] Release Apache Taverna Command-line Tool 3.1.0-incubating RC2

[Gale Naylor]

I finished reviewing all the file headers. Here is what I found:

---
Non-ASF Copyrights
---

1) University of Manchester copyright in taverna-provenanceconnector
files (see previous email).

2) taverna-execution-hadoop Crossproduct.java file contains copyright
by Adam Pingel and no ASF license.

 I know this is copyright is included in the top level NOTICE
 file, but doesn't it have to be removed from the Java file?

---
Missing ASF licenses?
---

1) Two README files without license headers:

/taverna-engine-rc2/taverna-prov/README.md
/taverna-engine-rc2/taverna-reference-types/README.md


2) One JSON file without license header

/taverna-engine-rc2/taverna-run-impl/src/test/resources/workflowrun.json


4) Miscellaneous text and html files don't have a license header.
(Also spring.handlers and spring.schemas.)
Are these not considered "code?"

Examples:
taverna-activity-archetype...goal.txt,
taverna-credential-manager...text.html,
taverna-prov...3a/3a82e39d-a537-40cf-91a0-2c89d4a2e62b.txt
taverna-prov...greeting.txt
taverna-prov...mimetype
taverna-workflowmodel-impl...package.html
taverna-reference-impl...spring.handlers (and spring.schemas)


5) Files in services subdirectories also do not have a license headers. Are
they exempt?

Examples:
taverna-credential-manager...services/
org.apache.taverna.security.credentialmanager.CredentialProviderSPI
taverna-dataflow-activity.../services/
net.sf.taverna.t2.workflowmodel.health.HealthChecker


Well. That was mind-numbing. Whew! Glad I'm done with that part.

Gale

On Thu, Jun 2, 2016 at 9:30 AM Alan Williams <alanin...@googlemail.com>
wrote:

> On 02-Jun-16 17:01, Gale Naylor wrote:
> > Hello,
> >
> > I am finding University of Manchester copyright notices on many of the
> > files in taverna-provenanceconnector. This is not allowed, right? (
> > http://www.apache.org/legal/src-headers.html#headers)
> >
> > For example:
> > src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java
> >
> > and all the java files in
> > /src/main/java/org/apache/taverna/provenance/lineageservice/types/
>
> I can confirm that the files have the old Manchester license at the top
> with the Apache license later on. Github found several
>
> https://github.com/apache/incubator-taverna-engine/search?utf8=%E2%9C%93=University+of+Manchester
>
> I checked the common activities and commandline and they seem OK.
>
> > Gale
>
> Alan
>

Re: [VOTE] Release Apache Taverna Command-line Tool 3.1.0-incubating RC2

[Gale Naylor]

There is no #3. I just forgot to adjust the numbers.

On Thu, Jun 2, 2016 at 10:56 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> I finished reviewing all the file headers. Here is what I found:
>
> ---
> Non-ASF Copyrights
> ---
>
> 1) University of Manchester copyright in taverna-provenanceconnector
> files (see previous email).
>
> 2) taverna-execution-hadoop Crossproduct.java file contains copyright
> by Adam Pingel and no ASF license.
>
>  I know this is copyright is included in the top level NOTICE
>  file, but doesn't it have to be removed from the Java file?
>
> ---
> Missing ASF licenses?
> ---
>
> 1) Two README files without license headers:
>
> /taverna-engine-rc2/taverna-prov/README.md
> /taverna-engine-rc2/taverna-reference-types/README.md
>
>
> 2) One JSON file without license header
>
> /taverna-engine-rc2/taverna-run-impl/src/test/resources/workflowrun.json
>
>
> 4) Miscellaneous text and html files don't have a license header.
> (Also spring.handlers and spring.schemas.)
> Are these not considered "code?"
>
> Examples:
> taverna-activity-archetype...goal.txt,
> taverna-credential-manager...text.html,
> taverna-prov...3a/3a82e39d-a537-40cf-91a0-2c89d4a2e62b.txt
> taverna-prov...greeting.txt
> taverna-prov...mimetype
> taverna-workflowmodel-impl...package.html
> taverna-reference-impl...spring.handlers (and spring.schemas)
>
>
> 5) Files in services subdirectories also do not have a license headers.
> Are they exempt?
>
> Examples:
> taverna-credential-manager...services/
> org.apache.taverna.security.credentialmanager.CredentialProviderSPI
> taverna-dataflow-activity.../services/
> net.sf.taverna.t2.workflowmodel.health.HealthChecker
>
>
> Well. That was mind-numbing. Whew! Glad I'm done with that part.
>
> Gale
>
> On Thu, Jun 2, 2016 at 9:30 AM Alan Williams <alanin...@googlemail.com>
> wrote:
>
>> On 02-Jun-16 17:01, Gale Naylor wrote:
>> > Hello,
>> >
>> > I am finding University of Manchester copyright notices on many of the
>> > files in taverna-provenanceconnector. This is not allowed, right? (
>> > http://www.apache.org/legal/src-headers.html#headers)
>> >
>> > For example:
>> > src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java
>> >
>> > and all the java files in
>> > /src/main/java/org/apache/taverna/provenance/lineageservice/types/
>>
>> I can confirm that the files have the old Manchester license at the top
>> with the Apache license later on. Github found several
>>
>> https://github.com/apache/incubator-taverna-engine/search?utf8=%E2%9C%93=University+of+Manchester
>>
>> I checked the common activities and commandline and they seem OK.
>>
>> > Gale
>>
>> Alan
>>
>

Re: [VOTE] Release Apache Taverna Command-line Tool 3.1.0-incubating RC2

[Gale Naylor]

Hello,

I am finding University of Manchester copyright notices on many of the
files in taverna-provenanceconnector. This is not allowed, right? (
http://www.apache.org/legal/src-headers.html#headers)

For example:
src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java

and all the java files in
/src/main/java/org/apache/taverna/provenance/lineageservice/types/

Gale

On Wed, Jun 1, 2016 at 6:16 PM Gale Naylor <ga...@noventussolutions.com>
wrote:

> Starting the review process...
>
> --
> UP-FRONT CHECKS
> --
> The MD5 checksums in the [VOTE] email are the same as the SHA1 checksums.
> I'm using the downloaded MD5 and SHA-1.
>
> (Question) I'm curious what r13865 means:
>   https://dist.apache.org/repos/dist/dev/incubator/taverna/source/rc2/
> (r13865)
>
> I didn't see the commit ID in the [VOTE] email. Did I miss it?
>
> --
> LICENSES - THIRD-PARTY.properties file
> --
>
> The list of # Already used licenses in project : includes
>
> # - GNU Lesser General Public License, Version 2.1
> Isn't this a category-x license? (It doesn't show up in the
> "Please fill in the missing licenses" list.)
>
>
> Missing licenses:
> # http://x-stream.github.io/license.html - this link says BSD (but not
> which type);
> should this copyright be included in our Notice file?
>
> org.aopalliance--com.springsource.org.aopalliance--1.0.0  - no license
> listed
>
> # https://github.com/hunterhacker/jdom/blob/jdom-1.1/core/LICENSE.txt  -
> this link has a copyright;
> include in Notice file? What do we use for "type" of license? "Copyright?"
> Or is this also a "JDOM License" like
> org.jdom--com.springsource.org.jdom--1.1.0?
>
> # http://www.xmlpull.org/  - no license listed
>
> Category B licenses?
> Aren't these listed under category-b, binary release only? Or do they meet
> the exception
> for allowing in a source release? ("For small amounts of source that is
> directly
> consumed by the ASF product at runtime in source form, and for which that
> source is unmodified and unlikely to be changed ...")
>
> javax.transaction--com.springsource.javax.transaction--1.1.0 - CDDL 1.0
>
> org.aspectj--com.springsource.org.aspectj.runtime--1.6.0 - Eclipse Public
> License 1.0
> org.aspectj--com.springsource.org.aspectj.weaver--1.6.0 - Eclipse Public
> License 1.0
>
> That's as far as I can get today. Will do the rest of the review tomorrow.
>
> Gale
>
> On Wed, Jun 1, 2016 at 7:18 AM Stian Soiland-Reyes <st...@apache.org>
> wrote:
>
>> On 1 June 2016 at 12:01, Stian Soiland-Reyes <st...@apache.org> wrote:
>> > I am pleased to be calling this vote for the source release of
>> >
>> >   Apache Taverna Engine 3.1.0-incubating
>> >   Apache Taverna Common Activities 2.1.0-incubating
>> >   Apache Taverna Command-line Tool 3.1.0-incubating
>> > ..
>> > Build the release candidate *in the above order*, using:
>>
>> Sorry I mixed up the order in the checksums which were immediately
>> above in this vote email - to clarify the build order is:
>>
>> taverna-engine
>> taverna-common-activities
>> taverna-commandline
>>
>> The reason is that command line depends on common-activities, which
>> depend on taverna-engine, all in the same version as being released.
>>
>>
>> Perhaps for the next vote emails I will include the full URIs to the
>> folders rather than just ../rc2/
>>
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons
>> http://orcid.org/-0001-9842-9718
>>
>

Re: [DISCUSS] Release candidate 2 of Command-line Tool 3.1.0-incubating

[Gale Naylor]

I'm so sorry - I've been replying to the VOTE thread.

I'll copy my comments here:

--
UP-FRONT CHECKS
--
The MD5 checksums in the [VOTE] email are the same as the SHA1 checksums.
I'm using the downloaded MD5 and SHA-1.

(Originally I missed the commit IDs in the Vote email - don't know how -
but they are there.)


--
LICENSES - THIRD-PARTY.properties file
--

---
GNU License?

The list of # Already used licenses in project : includes

# - GNU Lesser General Public License, Version 2.1
Isn't this a category-x license? (It doesn't show up in the
"Please fill in the missing licenses" list at the bottom of the file.)


---
Missing license information:

# http://x-stream.github.io/license.html - this link says BSD (but not
which type);
should this copyright be included in our Notice file?

org.aopalliance--com.springsource.org.aopalliance--1.0.0  - no license
listed

# https://github.com/hunterhacker/jdom/blob/jdom-1.1/core/LICENSE.txt  -
this link has a copyright;
include in Notice file? What do we use for "type" of license? "Copyright?"
Or is this also a "JDOM License" like
org.jdom--com.springsource.org.jdom--1.1.0?

# http://www.xmlpull.org/  - no license listed


---
Category B licenses?

Aren't the following licenses listed under category-b, binary release only?
Or do they meet the exception
for allowing in a source release? ("For small amounts of source that is
directly
consumed by the ASF product at runtime in source form, and for which that
source is unmodified and unlikely to be changed ...")

javax.transaction--com.springsource.javax.transaction--1.1.0 - CDDL 1.0

org.aspectj--com.springsource.org.aspectj.runtime--1.6.0 - Eclipse Public
License 1.0
org.aspectj--com.springsource.org.aspectj.weaver--1.6.0 - Eclipse Public
License 1.0


---
Source File Headers
---

---
Non-ASF Copyrights


1) University of Manchester copyright in taverna-provenanceconnector
files (see previous email).

2) taverna-execution-hadoop Crossproduct.java file contains copyright
by Adam Pingel and no ASF license.

 I know this is copyright is included in the top level NOTICE
 file, but doesn't it have to be removed from the Java file?


---
Missing ASF licenses?


1) Two README files without license headers:

/taverna-engine-rc2/taverna-prov/README.md
/taverna-engine-rc2/taverna-reference-types/README.md


2) One JSON file without license header

/taverna-engine-rc2/taverna-run-impl/src/test/resources/workflowrun.json


3) Miscellaneous text and html files don't have a license header.
(Also spring.handlers and spring.schemas.)
Are these not considered "code?"

Examples:
taverna-activity-archetype...goal.txt,
taverna-credential-manager...text.html,
taverna-prov...3a/3a82e39d-a537-40cf-91a0-2c89d4a2e62b.txt
taverna-prov...greeting.txt
taverna-prov...mimetype
taverna-workflowmodel-impl...package.html
taverna-reference-impl...spring.handlers (and spring.schemas)


4) Files in services subdirectories also do not have a license headers. Are
they exempt?

Examples:
taverna-credential-manager...services/
org.apache.taverna.security.credentialmanager.CredentialProviderSPI
taverna-dataflow-activity.../services/
net.sf.taverna.t2.workflowmodel.health.HealthChecker


 Gale


On Wed, Jun 1, 2016 at 7:21 AM Stian Soiland-Reyes  wrote:

> Great! Yes, the long one sounds like trouble..
>
> The README says:
>
> https://github.com/apache/incubator-taverna-engine/#building-on-windows
>
> > If you are building on Windows, ensure you unpack this source code to a
> folder with a short path name lenght, e.g. C:\src - as Windows has a
> limitation on the total path length which might otherwise prevent this code
> from building successfully.
>
> I tested mine as D:\apache-taverna-engine-3.1.0-incubating\ which just
> about worked.
>
> I am not sure if Maven could detect this in advance somehow, perhaps
> something to ask on dev@maven.. (I'll ask)
>
>
> On 1 June 2016 at 13:18, Alan Williams  wrote:
> > On 01-Jun-16 12:27, Alan Williams wrote:
> >>
> >> Hello
> >>
> >> I get a failure:
> >>
> >> [INFO] [ERROR] Failed to execute goal
> >> org.apache.maven.plugins:maven-surefire-plugin:2.19.1:test
> >> (default-test) on project dummy-taverna-plugin-activity: Execution
> >> default-test of goal
> >> org.apache.maven.plugins:maven-surefire-plugin:2.19.1:t
> >> est failed: The forked VM terminated without properly saying goodbye. VM
> >> crash or System.exit called?
> >> [INFO] [ERROR] Command was cmd.exe /X /C ""C:\Program
> >> Files\Java\jdk1.8.0_51\jre\bin\java" -jar
> >>
> >>
> 

Edited Command-line Tool Web Pages

[Gale Naylor]

Hello, all.

I edited the Command-line Tool web pages (to fix the tool name, etc.) and
they are staged in the CMS.
Please review:
(A) Download page: http://taverna.staging.apache.org/download/commandline/
(B) Documentation page:
http://taverna.staging.apache.org/documentation/command-line/

I added sections to the documentation page and did some significant editing
for grammar and style. I also have a few questions/issues on the
documentation page. In particular:

(1) "Important: The database name in the jdbcuri property must be
T2Provenance, as this database name is hard-coded into the MySQL provenance
SQL queries." (I presume this is different now?)

(2) Part of the section on creating lists is confusing: "If a list of
greater depth is required (i.e., a list or lists or deeper)" I presume this
is referring to the indentation level of the list, but I don't understand
"a list or lists or deeper." Can someone give me an example of what a lists
might look like, and what a wrapped list would look like?

(3) Is "extended version" relevant for 3.x? - this link goes to
http://dev.mygrid.org.uk/wiki/display/tav250/Extended+version

(4) Is everything on this page current for Taverna 3? There are a few
references to taverna-cmdline-2.x.x or T2.

Thanks!

Gale

Re: [VOTE] Release Apache Taverna Command-line Tool 3.1.0-incubating RC2

[Gale Naylor]

Starting the review process...

--
UP-FRONT CHECKS
--
The MD5 checksums in the [VOTE] email are the same as the SHA1 checksums.
I'm using the downloaded MD5 and SHA-1.

(Question) I'm curious what r13865 means:
  https://dist.apache.org/repos/dist/dev/incubator/taverna/source/rc2/
(r13865)

I didn't see the commit ID in the [VOTE] email. Did I miss it?

--
LICENSES - THIRD-PARTY.properties file
--

The list of # Already used licenses in project : includes

# - GNU Lesser General Public License, Version 2.1
Isn't this a category-x license? (It doesn't show up in the
"Please fill in the missing licenses" list.)


Missing licenses:
# http://x-stream.github.io/license.html - this link says BSD (but not
which type);
should this copyright be included in our Notice file?

org.aopalliance--com.springsource.org.aopalliance--1.0.0  - no license
listed

# https://github.com/hunterhacker/jdom/blob/jdom-1.1/core/LICENSE.txt  -
this link has a copyright;
include in Notice file? What do we use for "type" of license? "Copyright?"
Or is this also a "JDOM License" like
org.jdom--com.springsource.org.jdom--1.1.0?

# http://www.xmlpull.org/  - no license listed

Category B licenses?
Aren't these listed under category-b, binary release only? Or do they meet
the exception
for allowing in a source release? ("For small amounts of source that is
directly
consumed by the ASF product at runtime in source form, and for which that
source is unmodified and unlikely to be changed ...")

javax.transaction--com.springsource.javax.transaction--1.1.0 - CDDL 1.0

org.aspectj--com.springsource.org.aspectj.runtime--1.6.0 - Eclipse Public
License 1.0
org.aspectj--com.springsource.org.aspectj.weaver--1.6.0 - Eclipse Public
License 1.0

That's as far as I can get today. Will do the rest of the review tomorrow.

Gale

On Wed, Jun 1, 2016 at 7:18 AM Stian Soiland-Reyes  wrote:

> On 1 June 2016 at 12:01, Stian Soiland-Reyes  wrote:
> > I am pleased to be calling this vote for the source release of
> >
> >   Apache Taverna Engine 3.1.0-incubating
> >   Apache Taverna Common Activities 2.1.0-incubating
> >   Apache Taverna Command-line Tool 3.1.0-incubating
> > ..
> > Build the release candidate *in the above order*, using:
>
> Sorry I mixed up the order in the checksums which were immediately
> above in this vote email - to clarify the build order is:
>
> taverna-engine
> taverna-common-activities
> taverna-commandline
>
> The reason is that command line depends on common-activities, which
> depend on taverna-engine, all in the same version as being released.
>
>
> Perhaps for the next vote emails I will include the full URIs to the
> folders rather than just ../rc2/
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: Starting command line 3.1.0 release process

[Gale Naylor]

Thanks for taking care of all this. I like the wiki page.

On Mon, May 30, 2016, 4:40 PM Stian Soiland-Reyes  wrote:

> On 27 May 2016 at 10:05, Stian Soiland-Reyes  wrote:
> > No, I see that compile problem was not fixed.. sorry. I'll have a go
> > in Windows if I can find out what's going on.
>
> As that Windows bug was now resolved
>
> https://lists.apache.org/thread.html/Zt3r3adq46msey9
>
> (and I added the README notes)
>
> so I will proceed with the release candidates. As mentioned I think I
> would rather do a wiki page to keep notes about the release procedure
> progress rather than 30 JIRA subtasks which spams the list!
>
>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-06+Command+Line+3.1.0+Release
>
>
> Apologies for not getting started on this last week - it was a special
> week in many ways.
>

Re: Checkstyle/Findbugs LGPL - does it matter

[Gale Naylor]

If they are not part of the distribution, where are they? Are they in the
repositories?

On Wed, Jun 15, 2016 at 11:04 AM Donal Fellows <
donal.k.fell...@manchester.ac.uk> wrote:

> The plugins should be fine. They are not required to build anything (if
> anyone is super-worried, they can be put in a maven profile; it can be
> enabled by default for our convenience) and there is a lot of precedent for
> allowing LGPL tools to work with Apache products.
>
> Donal.
>
> Ian Dunlop  wrote:
>
> >Hello,
> >
> >I noticed that the checkstyle and findbugs code analysis tools are LGPL
> >licensed. I don't think that matters as long as they are not part of the
> >distribution. Any thoughts?
> >
> >Cheers,
> >
> >Ian
>

Re: Redirection from taverna.org.uk

[Gale Naylor]

Hi Stian,

I'm curious about redirecting the top level pages. If each page has the
Deprecated banner, isn't that good enough? What am I missing?

Gale

On Mon, Jan 11, 2016 at 8:41 AM alaninmcr  wrote:

> 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: Redirection from taverna.org.uk

[Gale Naylor]

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

On Fri, Jan 15, 2016 at 8:05 AM Stian Soiland-Reyes 
wrote:

> I'll delay changing www.taverna.org.uk pending the outcome of that
> hangout.
>
> On 15 January 2016 at 16:04, Stian Soiland-Reyes  wrote:
> > OK, let's do a Hangout next week - it could be good to catch up in
> > voice. We'll summarize on the list what we agree to look at.
> >
> > What time works well with yourself? Gale - would you be able to join..?
> >
> >
> > I'm good most of Wednesday 9-15 and 16-18 GMT, and Friday 13-16 GMT -
> > but I can also try late in the evenings (e.g. 21-23 GMT) if that suits
> > Gale's timezone more.
> >
> >
> > On 11 January 2016 at 16:46, alaninmcr  wrote:
> >> 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
> >
> >
> >
> > --
> > Stian Soiland-Reyes
> > Apache Taverna (incubating), Apache Commons RDF (incubating)
> > http://orcid.org/-0001-9842-9718
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/-0001-9842-9718
>

Re: Proposed google hangout

[Gale Naylor]

+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: Functionality in next release?

[Gale Naylor]

Here is a draft of the release notes based mostly on @stain's list:
https://galenaylor.wordpress.com/2016/02/01/draft-taverna-language-release-notes-2/

@Stian, I'm a little confused because some of the information seems to
apply to more than Taverna Language. (See comments and questions in
document.)

I also noticed in that Menaka's readme refers to the tavlang tool (or
whatever we end up calling it) as a "planned" part of Taverna Language and
as a GSOC "work in progress." These probably need to be changed to reflect
that is is finished and being released?

"This is planned as a command line for the Apache Taverna Language, an API
for the Apache Taverna workflows.
This module is a work in progress as part of Google Summer of Code 2015."

Thanks,
Gale
On Mon, Feb 1, 2016 at 3:23 AM Stian Soiland-Reyes <st...@apache.org> wrote:

> Right - we will need proper release notes, won't we. Let's see..
> (sorry, this is not formatted as release notes)
>
>
> The taverna-language release would be an update that fixes some bugs
> (TAVERNA-874) and adds the tavlang command line, which we should say
> was contributed by Menaka Madushanka, sponsored by Google Summer of
> Code 2015. Mentors - would that be appropriate attribution?
>
>
> The release of taverna-osgi, taverna-engine, taverna-common-activities
> and taverna-commandline would give you a Taverna 3.1.0 command line -
> which functionally is a follow-up from an earlier alpha-release before
> we went to Apache - see
> http://www.taverna.org.uk/developers/work-in-progress/taverna-3/ -- so
> in principle it is the same functionality, but now released by Apache,
> with a new license.
>
>
> Package names have changed to org.apache.taverna.* and the OSGi
> support has been stabilized. Source code has been reorganized - see
> http://taverna.incubator.apache.org/code/
>
>
> One new functionality of the taverna-commandline is the ability to
> save the workflow run provenance as a workflow run bundle - see
>
> https://github.com/apache/incubator-taverna-engine/tree/master/taverna-prov#structure-of-exported-provenance
> (TODO: Move this doc to the website)
>
>
>
> The new release would add Dmitris improved WSDL support using Apache
> Woden - Dmitri, is this change also giving WSDL2 support? What are the
> improvements here?
>
>
>
> I think it is fair to mention the functionality that is
> disabled/missing compared to earlier, I think these activities are NO
> LONGER supported (they were part of 3.0.a2)
>
> RShell
> Soaplab
> Biomart
>
>
> They are now maintained (??) separately as part of the
> https://github.com/apache/incubator-taverna-plugin-bioinformatics/
> and https://github.com/taverna-extras/
>
>
> (I just moved RShell activity to taverna-extras and updated it, it
> seems we had forgotten it on https://github.com/taverna/ !)
>
>
>
> These plugins *ARE* included in the 3.1.0 release:
>
> Beanshell scripts
> External Tool
> Interaction service
> REST service
> Spreadsheet
> XML splitters
> WSDL services
> XPath
>
> (Which Alan is looking at workflows to test them all)
>
>
> On 23 January 2016 at 00:57, Gale Naylor <ga...@noventussolutions.com>
> wrote:
> > Is there a description of what functionality will be available for
> Taverna
> > 3 users as a result of the upcoming release?
> >
> > Gale
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/-0001-9842-9718
>

Re: TAVERNA-867 doclint javadoc and Java 7 (was: Snapshot issue when releasing taverna language)

[Gale Naylor]

I'm looking at the readme files for Java 7 references. I found several in
taverna-databundle/readme.md, but they are not simple find-and-replace. For
example, "This API is built on the Java 7 NIO Files and the RO Bundle API,
which uses the Java 7 ZIP file provider to generate the Data Bundle." There
is also a Java 7 code sample. In addition, the file contains several broken
links, along with references to myGrid, which seemed out-of-place to me,
but maybe they are okay. If you give me some direction and help (e.g., for
the Java 7 code sample) I can make the changes. I'm including a list of all
the questionable (to me) items in order:

taverna-databundle/readme.md

(1) Says "build failing"? at top of readme

***
INTRODUCTORY PARAGRAPHS
***

(1) myGRID REFERENCE
Refers to myGrid data bundle requirements (
http://dev.mygrid.org.uk/wiki/display/TAVOSGI/2013-02+Data+bundle+requirements
)

(2) BROKEN LINK
"TestDataBundles.java" (
https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/test/java/uk/org/taverna/databundle/TestDataBundles.java
)

(3) JAVA 7
"This API is built on the Java 7 NIO Files and the RO Bundle API, which
uses the Java 7 ZIP file provider to generate the Data Bundle."

(4) JAVA 7
"The class org.apache.taverna.databundle.DataBundles complements the Java 7
java.nio.Files API with more specific helper methods to work with Data
Bundles."

(5) BROKEN LINK
Broken "org.apache.taverna.databundle.DataBundles" link (
https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/main/java/uk/org/taverna/databundle/DataBundles.java
)


Building SECTION


(5) JAVA 7
"should normally work, given a recent version of Maven 3 and Java 7 SDK."

(6) myGRID REFERENCE
Refers to "myGrid's Jenkins installation" (http://build.mygrid.org.uk/ci/)

(7) BROKEN LINK
Broken "databundles" link(http://build.mygrid.org.uk/ci/job/databundles/)

(8) BROKEN LINK
Broken "robundles" link(http://build.mygrid.org.uk/ci/job/robundle/)

(9) myGRID REFERENCE
Refers to "myGrid's snapshot repository" (
http://build.mygrid.org.uk/maven/snapshot-repository/uk/org/taverna/databundle/databundle/
)

(10) wf4ever LINK
"robundle" links to https://github.com/wf4ever/robundle, which says "Move
to Apache Taverna"

(11) myGRID REFERENCE
Says to download "robundle" from "myGrid's snapshot repository" (
http://build.mygrid.org.uk/maven/snapshot-repository/org/purl/wf4ever/robundle/robundle/
)

**
Example of use SECTION
**

(12) BROKEN LINK
Broken "org.apache.taverna.databundle.TestExample" link (
https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/test/java/uk/org/taverna/databundle/TestExample.java
)

(13) JAVA 7
Code sample using "Java 7 style"

---

Gale

On Mon, Feb 1, 2016 at 9:47 AM Andy Seaborne  wrote:

> Jena has to turn off Java8 doclint because it fails builds for imperfect
> javadoc.
>
>  
>
>doclint-java8-disable
>
>  [1.8,)
>
>
>
>  
>
>  org.apache.maven.plugins
>  maven-javadoc-plugin
>  
>-Xdoclint:none
>  
>
>  
>
>  
>
> We also have the problem with false warnings
>
> [WARNING]
>
> /home/jenkins/jenkins-slave/workspace/Jena_Development_Deploy/jena-core/src/main/java/org/apache/jena/ontology/OntProperty.java:497:
> warning - @propertyDescription is an unknown tag.
>
> except there is no @propertyDescription in the source!
>
> @propertyDescription can only be used in JavaFX properties getters and
> setters.
> [WARNING]
>
> /home/jenkins/jenkins-slave/workspace/Jena_Development_Deploy/jena-core/src/main/java/org/apache/jena/ontology/OntProperty.java:490:
> warning - Tags @propertyGetter, @propertySetter and @propertyDescription
> can only be used in JavaFX properties getters and setters.
>
> JavaFX ???
>
> Andy
>
> On 01/02/16 17:01, Stian Soiland-Reyes wrote:
> > Yes, I think ironically we need it to ignore some errors from Java 8's
> > javadoc - this came up as we were doing the 0.15.0 release of
> > taverna-language.
> >
> > See also:
> > https://issues.apache.org/jira/browse/MJAVADOC-387
> >
> >
> > You can also enable it conditionally with  based on the JDK
> > version like here:
> >
> > https://github.com/jai-imageio/jai-imageio-core/blob/master/pom.xml#L195
> >
> > If we do that we can keep 1.7 support - I mean if we really want to. :)
> >
> >
> >
> > Alternatively I guess we can go through and fix the Javadoc warnings..
> >
> > Some examples:
> >
> >
> > [ERROR]
> /home/stain/src/taverna/incubator-taverna-language/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/impl/odfdom/pkg/OdfPackage.java:910:
> > warning: no description for @throws
> > [ERROR] * @throws Exception
> > [ERROR] ^
> >
> > [ERROR]
> 

Re: TAVERNA-867 doclint javadoc and Java 7 (was: Snapshot issue when releasing taverna language)

[Gale Naylor]

In hindsight, I probably should keep all of the readme reviews as part of
this thread. (Sorry for the duplicate email.)

taverna-language-commandline/readme.md

***
INTRODUCTORY PARAGRAPHS
***

(1) "planned" and "work in progress" should change to reflect code is
complete. (Mentioned in "functionality in next release" email.)

***
License SECTION
***

(2) BROKEN LINK -- have fix for this
Broken "NOTICE" link (
https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/resources/NOTICE
)
- SHOULD BE:
https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/resources/META-INF/NOTICE

***
Building and install requirements SECTION
***

(3) JAVA 7
"Java 1.7 or newer" -- change to "Java 1.8" ?

***
Commands: inspect  SECTION
***

(4) BROKEN LINK
Broken "http://ns.taverna.org.uk/2010/activity/constant; link (Service
types used in helloworld.wfbundle)



On Tue, Feb 2, 2016 at 7:55 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> I'm looking at the readme files for Java 7 references. I found several in
> taverna-databundle/readme.md, but they are not simple find-and-replace.
> For example, "This API is built on the Java 7 NIO Files and the RO Bundle
> API, which uses the Java 7 ZIP file provider to generate the Data Bundle."
> There is also a Java 7 code sample. In addition, the file contains several
> broken links, along with references to myGrid, which seemed out-of-place to
> me, but maybe they are okay. If you give me some direction and help (e.g.,
> for the Java 7 code sample) I can make the changes. I'm including a list of
> all the questionable (to me) items in order:
>
> taverna-databundle/readme.md
>
> (1) Says "build failing"? at top of readme
>
> ***
> INTRODUCTORY PARAGRAPHS
> ***
>
> (1) myGRID REFERENCE
> Refers to myGrid data bundle requirements (
> http://dev.mygrid.org.uk/wiki/display/TAVOSGI/2013-02+Data+bundle+requirements
> )
>
> (2) BROKEN LINK
> "TestDataBundles.java" (
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/test/java/uk/org/taverna/databundle/TestDataBundles.java
> )
>
> (3) JAVA 7
> "This API is built on the Java 7 NIO Files and the RO Bundle API, which
> uses the Java 7 ZIP file provider to generate the Data Bundle."
>
> (4) JAVA 7
> "The class org.apache.taverna.databundle.DataBundles complements the Java
> 7 java.nio.Files API with more specific helper methods to work with Data
> Bundles."
>
> (5) BROKEN LINK
> Broken "org.apache.taverna.databundle.DataBundles" link (
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/main/java/uk/org/taverna/databundle/DataBundles.java
> )
>
> 
> Building SECTION
> 
>
> (5) JAVA 7
> "should normally work, given a recent version of Maven 3 and Java 7 SDK."
>
> (6) myGRID REFERENCE
> Refers to "myGrid's Jenkins installation" (http://build.mygrid.org.uk/ci/)
>
> (7) BROKEN LINK
> Broken "databundles" link(http://build.mygrid.org.uk/ci/job/databundles/)
>
> (8) BROKEN LINK
> Broken "robundles" link(http://build.mygrid.org.uk/ci/job/robundle/)
>
> (9) myGRID REFERENCE
> Refers to "myGrid's snapshot repository" (
> http://build.mygrid.org.uk/maven/snapshot-repository/uk/org/taverna/databundle/databundle/
> )
>
> (10) wf4ever LINK
> "robundle" links to https://github.com/wf4ever/robundle, which says "Move
> to Apache Taverna"
>
> (11) myGRID REFERENCE
> Says to download "robundle" from "myGrid's snapshot repository" (
> http://build.mygrid.org.uk/maven/snapshot-repository/org/purl/wf4ever/robundle/robundle/
> )
>
> **
> Example of use SECTION
> **
>
> (12) BROKEN LINK
> Broken "org.apache.taverna.databundle.TestExample" link (
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/test/java/uk/org/taverna/databundle/TestExample.java
> )
>
> (13) JAVA 7
> Code sample using "Java 7 style"
>
> ---
>
> Gale
>
> On Mon, Feb 1, 2016 at 9:47 AM Andy Seaborne <a...@apache.org> wrote:
>
>> Jena has to turn off Java8 doclint because it fails builds for imperfect
>> javadoc.
>>
>>  
>>
>>doclint-java8-di

Re: Snapshot issue when releasing taverna language

[Gale Naylor]

I created a couple of pull requests to make minor changes to the tavlang
readme file and to CommandLineTool.java. In the Java file, line 197 says
"List of files to be converted.\n " I'm not sure what the ".\n" means. Is
this correct? The rest of the descriptions all look good to me. @stain, I
can't check the help files directly at this time.

Also, is iwir support still in the tavlang tool? (Sorry, if I missed this
somewhere else. I've been, and still am, pretty sick.)

Gale



On Mon, Feb 1, 2016 at 6:48 AM alaninmcr  wrote:

> 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
>

Re: TAVERNA-867 doclint javadoc and Java 7 (was: Snapshot issue when releasing taverna language)

[Gale Naylor]

Java 7 references, broken links, and other notes on taverna-robundle/
readme.md:

***
INTRODUCTORY PARAGRAPHS
***

(1) Java 7
"This API is built on the Java 7 NIO Files and uses the Java 7 ZIP file
provider to generate the RO Bundle.
The class org.apache.taverna.robundle.Bundles complements the Java 7
java.nio.Files API with more specific helper methods to work with RO
Bundles."

(2) BROKEN LINK
Broken "org.apache.taverna.robundle.Bundles" links to
https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/main/java/org/purl/wf4ever/robundle/Bundles.java

(3) WRONG LINK?
"Taverna Data Bundles API" links to non-Apache repo, which says "Moved to
Apache Taverna."
(https://github.com/taverna/taverna-databundle)

***
Usage SECTION
***

(4) myGRID REFERENCE
pom.xml code sample says to add "mygrid-repository" and points to
http://www.mygrid.org.uk/maven/repository

(5) wf4ever REFERENCE
"robundle releases" links to https://github.com/wf4ever/robundle/releases

(6) myGRID REFERENCE
"myGrid's Maven repository" links to
http://repository.mygrid.org.uk/artifactory/mygrid-all/org/purl/wf4ever/robundle/robundle/

***
Building SECTION
***

(7) JAVA 7
"should normally work, given a recent version of Maven 3 and Java 7 SDK."

(8) myGRID REFERENCE
"myGrid's Jenkins installation" links to http://build.mygrid.org.uk/ci/

(9) BROKEN LINK
Broken "robundle" link to http://build.mygrid.org.uk/ci/job/robundle/

(10) myGRID REFERENCE
"myGrid's snapshot Maven repository" links to
http://www.mygrid.org.uk/maven/snapshot-repository/org/purl/wf4ever/robundle/robundle/

(11) myGRID REFERENCE
pom.xml code sample says to add "mygrid-snapshot-repository" and points to
http://www.mygrid.org.uk/maven/snapshot-repository

***
Supported bundle formats SECTION
***

(12) Question: Is Adobe UFC still relevant?
The readme link is redirected from "
https://wikidocs.adobe.com/wiki/display/PDFNAV/UCF+overview; to a general
support site: https://helpx.adobe.com/support.html#/top_products, and I
couldn't find anything when I searched for UFC..

***
Example of use SECTION
***

(13) BROKEN LINK
Broken "org.apache.taverna.robundle.TestExample" link to
https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/purl/wf4ever/robundle/TestExample.java

(14) JAVA 7
Code sample includes Java 7 style ("// Or Java 7 style" + code)

-- 
Gale


On Tue, Feb 2, 2016 at 8:18 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> In hindsight, I probably should keep all of the readme reviews as part of
> this thread. (Sorry for the duplicate email.)
>
> taverna-language-commandline/readme.md
>
> ***
> INTRODUCTORY PARAGRAPHS
> ***
>
> (1) "planned" and "work in progress" should change to reflect code is
> complete. (Mentioned in "functionality in next release" email.)
>
> ***
> License SECTION
> ***
>
> (2) BROKEN LINK -- have fix for this
> Broken "NOTICE" link (
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/resources/NOTICE
> )
> - SHOULD BE:
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/resources/META-INF/NOTICE
>
> ***
> Building and install requirements SECTION
> ***
>
> (3) JAVA 7
> "Java 1.7 or newer" -- change to "Java 1.8" ?
>
> ***
> Commands: inspect  SECTION
> ***
>
> (4) BROKEN LINK
> Broken "http://ns.taverna.org.uk/2010/activity/constant; link (Service
> types used in helloworld.wfbundle)
>
>
>
> On Tue, Feb 2, 2016 at 7:55 AM Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
>> I'm looking at the readme files for Java 7 references. I found several in
>> taverna-databundle/readme.md, but they are not simple find-and-replace.
>> For example, "This API is built on the Java 7 NIO Files and the RO Bundle
>> API, which uses the Java 7 ZIP file provider to generate the Data Bundle."
>> There is also a Java 7 code sample. In addition, the file contains several
>> broken links, along with references to myGrid, which seemed out-of-place to
>> me, but maybe they are okay. If you give me some direction and help (e.g.,
>> for the Java 7 code sample) I can make the changes. I'm including a list of
>> all t

Review readme for taverna-language-commandline

[Gale Naylor]

(Ref TAVERNA-867)

Here is what I noticed in the taverna-language-commandline readme file:

***
INTRODUCTORY PARAGRAPHS
***

(1) "planned" and "work in progress" should change to reflect code is
complete? (Already mentioned in "functionality in next release" email.)

***
License SECTION
***

(2) BROKEN LINK -- have fix for this
Broken "NOTICE" link (
https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/resources/NOTICE
)
- SHOULD BE:
https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/resources/META-INF/NOTICE

***
Building and install requirements SECTION
***

(3) JAVA 7
"Java 1.7 or newer" -- change to "Java 1.8" ?

***
Commands: inspect  SECTION
***

(4) BROKEN LINK
Broken "http://ns.taverna.org.uk/2010/activity/constant; link (Service
types used in helloworld.wfbundle)

Re: Snapshot issue when releasing taverna language

[Gale Naylor]

I removed the instances of iwir in the tavlang tool readme (and created a
pull request), but I don't want to touch the actual java code. There are
several instances of iwir in tavlang/CommandLineTool.java:

REMOVE iwir INSTANCES?

(1) Line 98 - @Option(name = "--iwir", ...)

(2) Line 116/117 - else if (isIwir) / return"iwir";

(3) Line 232 - } else if(Filetype.isIwir || ...



On Tue, Feb 2, 2016 at 4:47 PM Stian Soiland-Reyes <st...@apache.org> wrote:

> I just disabled the iwir-dependency and the myGrid repository from
> tavlang.. as I found out that the LGPL iwirTool dependency it uses
> does not exist in Maven Central either, so there was not much point in
> releasing scufl2-iwir to Central.
>
>
> I guess some kind of feature request for tavlang would be to be able
> to "drop in" such libraries? I guess this doesn't work too well with a
> shaded JAR though (modifying -classpath).
>
> On 1 February 2016 at 18:31, Gale Naylor <ga...@noventussolutions.com>
> wrote:
> > I created a couple of pull requests to make minor changes to the tavlang
> > readme file and to CommandLineTool.java. In the Java file, line 197 says
> > "List of files to be converted.\n " I'm not sure what the ".\n" means. Is
> > this correct? The rest of the descriptions all look good to me. @stain, I
> > can't check the help files directly at this time.
> >
> > Also, is iwir support still in the tavlang tool? (Sorry, if I missed this
> > somewhere else. I've been, and still am, pretty sick.)
> >
> > Gale
> >
> >
> >
> > On Mon, Feb 1, 2016 at 6:48 AM alaninmcr <alanin...@googlemail.com>
> wrote:
> >
> >> 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
> >>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/-0001-9842-9718
>

Re: TAVERNA-867 doclint javadoc and Java 7 (was: Snapshot issue when releasing taverna language)

[Gale Naylor]

@stian, so, at some point, taverna-wfbundle should be changed to use
robundle instead of taverna-scufl2-ucfpackage?

On Tue, Feb 2, 2016 at 4:41 PM Stian Soiland-Reyes <st...@apache.org> wrote:

> The UCF documentation even disappeared from adobe.com.. so it's good
> we are deprecating it.  But still the taverna-scufl2-ucfpackage is
> used by taverna-wfbundle (which should use robundle instead) - so it's
> needed as an internal dependency.
>
>
>
> On 2 February 2016 at 18:43, Gale Naylor <ga...@noventussolutions.com>
> wrote:
> > taverna-robundle, item (12) should be Adobe UCF, not UFC. I see in the
> > taverna-language readme that the module for Adobe UCF ZIP files is
> > deprecated. So should we just eliminate the link in the robundle readme?
> >
> > On Tue, Feb 2, 2016 at 9:26 AM Gale Naylor <ga...@noventussolutions.com>
> > wrote:
> >
> >>
> >> Java 7 references, broken links, and other notes on taverna-robundle/
> >> readme.md:
> >>
> >> ***
> >> INTRODUCTORY PARAGRAPHS
> >> ***
> >>
> >> (1) Java 7
> >> "This API is built on the Java 7 NIO Files and uses the Java 7 ZIP file
> >> provider to generate the RO Bundle.
> >> The class org.apache.taverna.robundle.Bundles complements the Java 7
> >> java.nio.Files API with more specific helper methods to work with RO
> >> Bundles."
> >>
> >> (2) BROKEN LINK
> >> Broken "org.apache.taverna.robundle.Bundles" links to
> >>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/main/java/org/purl/wf4ever/robundle/Bundles.java
> >>
> >> (3) WRONG LINK?
> >> "Taverna Data Bundles API" links to non-Apache repo, which says "Moved
> to
> >> Apache Taverna."
> >> (https://github.com/taverna/taverna-databundle)
> >>
> >> ***
> >> Usage SECTION
> >> ***
> >>
> >> (4) myGRID REFERENCE
> >> pom.xml code sample says to add "mygrid-repository" and points to
> >> http://www.mygrid.org.uk/maven/repository
> >>
> >> (5) wf4ever REFERENCE
> >> "robundle releases" links to
> https://github.com/wf4ever/robundle/releases
> >>
> >> (6) myGRID REFERENCE
> >> "myGrid's Maven repository" links to
> >>
> http://repository.mygrid.org.uk/artifactory/mygrid-all/org/purl/wf4ever/robundle/robundle/
> >>
> >> ***
> >> Building SECTION
> >> ***
> >>
> >> (7) JAVA 7
> >> "should normally work, given a recent version of Maven 3 and Java 7
> SDK."
> >>
> >> (8) myGRID REFERENCE
> >> "myGrid's Jenkins installation" links to http://build.mygrid.org.uk/ci/
> >>
> >> (9) BROKEN LINK
> >> Broken "robundle" link to http://build.mygrid.org.uk/ci/job/robundle/
> >>
> >> (10) myGRID REFERENCE
> >> "myGrid's snapshot Maven repository" links to
> >>
> http://www.mygrid.org.uk/maven/snapshot-repository/org/purl/wf4ever/robundle/robundle/
> >>
> >> (11) myGRID REFERENCE
> >> pom.xml code sample says to add "mygrid-snapshot-repository" and points
> to
> >> http://www.mygrid.org.uk/maven/snapshot-repository
> >>
> >> ***
> >> Supported bundle formats SECTION
> >> ***
> >>
> >> (12) Question: Is Adobe UFC still relevant?
> >> The readme link is redirected from "
> >> https://wikidocs.adobe.com/wiki/display/PDFNAV/UCF+overview; to a
> general
> >> support site: https://helpx.adobe.com/support.html#/top_products, and I
> >> couldn't find anything when I searched for UFC..
> >>
> >> ***
> >> Example of use SECTION
> >> ***
> >>
> >> (13) BROKEN LINK
> >> Broken "org.apache.taverna.robundle.TestExample" link to
> >>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/purl/wf4ever/robundle/TestExample.java
> >>
> >> (14) JAVA 7
> >> Code sample includes Java 7 style ("// Or Java 7 style" + code)
> >>
> >> --
> >> Gale
> >>
> >>
> >> On Tue, Feb 2, 2016 at 8:18 AM Gale Naylor <ga...@noventussolutions.com
> >
> &

Re: TAVERNA-867 doclint javadoc and Java 7 (was: Snapshot issue when releasing taverna language)

[Gale Naylor]

A couple of still-broken links and one code sample Java 7 reference:

taverna-tavlang-tool/readme.md

(1) BROKEN LINK
"http://ns.taverna.org.uk/2010/activity/constant;
which links to
http://ns.taverna.org.uk/2010/activity/constant
redirects to
http://taverna.incubator.apache.org/ns/2010/activity/constant
and gives a 404 File Not found error.


taverna-robundle/readme.md

(1) BROKEN LINK
"org.apache.taverna.robundle.TestExample"
IS (periods): java/org/apache.taverna.robundle/TestExample.java
SHOULD BE (fwd slashes): java/org/apache/taverna/robundle/TestExample.java

(2) CODE SAMPLE CONTAINS JAVA 7 REFERENCE
 // Or Java 7 style
Path localFile = Files.createTempFile("", ".txt");
Files.copy(in1, localFile, StandardCopyOption.REPLACE_EXISTING);
System.out.println("Written to: " + localFile);


On Wed, Feb 3, 2016 at 11:07 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> Broken/old links in taverna-scufl2-wfdesc/readme.md:
>
> 
> Extracted annotations SECTION
> 
>
> (1) myGRID LINK
> "Taverna Components"
> http://dev.mygrid.org.uk/wiki/display/taverna/Components
>
> (2) BROKEN LINK
> "valid_component_imagemagickconvert_wfdesc_ttl"
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.wfdesc.ttl
>
>
>
> On Wed, Feb 3, 2016 at 10:53 AM Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
>> Broken/old links and questions in taverna-scufl2-examples/readme.md:
>>
>> 
>> INTRODUCTORY PARAGRAPHS
>> 
>>
>> (1) CORRECT LINK?
>> "SCUFL2 API" links to Download Taverna Language - is this correct? (
>> http://taverna.incubator.apache.org/download/language/)
>>
>> 
>> Build SECTION
>> 
>>
>> (2) BROKEN LINK "Maven" http://maven.apache.org/download
>>
>> 
>> workflowmaker SECTION
>> 
>>
>> (3) myGRID LINK
>> "SCUFL2 wfbundle"
>> http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle
>> ---> should be?:
>> http://taverna.incubator.apache.org/documentation/scufl2/bundle
>>
>> 
>> t2flowtowfbundle SECTION
>> 
>>
>> (4) BROKEN LINK
>> "helloworld.wfbundle"
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.wfbundle?raw=true
>> -->should be?:
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.wfbundle
>>
>> (5) BROKEN LINK
>> "helloanyone.wfbundle"
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.wfbundle?raw=true
>> --should be?:
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.wfbundle
>>
>> (6) BROKEN LINK
>> "helloworld.t2flow"
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.t2flow?raw=true
>> --> should be?:
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.t2flow
>>
>> (7) BROKEN LINK
>> "helloanyone.t2flow"
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.t2flow?raw=true
>> --> should be?:
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.t2flow
>>
>> 
>> jsonexport SECTION
>> 
>>
>> (8) BROKEN LINK
>> "examples/helloworld.json"
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.json
>> --> should be?:
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.json
>>
>> (9) BROKEN LINK
>> "examples/helloanyone.json"
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.json
>> --> should be?:
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.json
>>
>>
>>
>> On Wed, Feb 3, 2016 at 10:27 AM Gale Naylor <ga...@noventussolutions.com>
>> wrote

Re: TAVERNA-867 doclint javadoc and Java 7 (was: Snapshot issue when releasing taverna language)

[Gale Naylor]

Broken/old links in taverna-scufl2-wfdesc/readme.md:


Extracted annotations SECTION


(1) myGRID LINK
"Taverna Components"
http://dev.mygrid.org.uk/wiki/display/taverna/Components

(2) BROKEN LINK
"valid_component_imagemagickconvert_wfdesc_ttl"
https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.wfdesc.ttl



On Wed, Feb 3, 2016 at 10:53 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> Broken/old links and questions in taverna-scufl2-examples/readme.md:
>
> 
> INTRODUCTORY PARAGRAPHS
> 
>
> (1) CORRECT LINK?
> "SCUFL2 API" links to Download Taverna Language - is this correct? (
> http://taverna.incubator.apache.org/download/language/)
>
> 
> Build SECTION
> 
>
> (2) BROKEN LINK "Maven" http://maven.apache.org/download
>
> 
> workflowmaker SECTION
> 
>
> (3) myGRID LINK
> "SCUFL2 wfbundle"
> http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle
> ---> should be?:
> http://taverna.incubator.apache.org/documentation/scufl2/bundle
>
> 
> t2flowtowfbundle SECTION
> 
>
> (4) BROKEN LINK
> "helloworld.wfbundle"
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.wfbundle?raw=true
> -->should be?:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.wfbundle
>
> (5) BROKEN LINK
> "helloanyone.wfbundle"
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.wfbundle?raw=true
> --should be?:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.wfbundle
>
> (6) BROKEN LINK
> "helloworld.t2flow"
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.t2flow?raw=true
> --> should be?:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.t2flow
>
> (7) BROKEN LINK
> "helloanyone.t2flow"
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.t2flow?raw=true
> --> should be?:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.t2flow
>
> 
> jsonexport SECTION
> 
>
> (8) BROKEN LINK
> "examples/helloworld.json"
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.json
> --> should be?:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.json
>
> (9) BROKEN LINK
> "examples/helloanyone.json"
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.json
> --> should be?:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.json
>
>
>
> On Wed, Feb 3, 2016 at 10:27 AM Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
>> Or change tavtool to tavlang (link) tool, to be consistent with other
>> instances
>>
>> On Wed, Feb 3, 2016 at 10:21 AM Gale Naylor <ga...@noventussolutions.com>
>> wrote:
>>
>>> Questions and broken links in taverna-scufl2-api/readme.md.
>>>
>>> 
>>> INTRODUCTORY PARAGRAPHS
>>> 
>>>
>>> (1) LINK ERROR?
>>> Looks like it should be a link ... [SCUFL2][9] "For more information,
>>> see the
>>> [SCUFL2 API][9] pages..."
>>>
>>> 
>>> Usage
>>> 
>>>
>>> (2) BROKEN LINK - fix?
>>> "Apache Taverna Language"
>>> https://github.com/apache/incubator-taverna-language/blob/master
>>> ---> SHOULD BE?:
>>> https://github.com/apache/incubator-taverna-language/blob/master/README.md
>>>
>>> (3) BROKEN LINK
>>> In table of supported file formats, "RDF Turtle" link gives 403 error
>>> http://www.w3.org/TR/turtle/%22
>>>
>>> (4) iwir REFERENCE
>>> In table of supported file formats, "scufl2-iwir"
>>>
>>> (5) Change tavtool to tavlang-tool?
>>> "You can use

Re: TAVERNA-867 doclint javadoc and Java 7 (was: Snapshot issue when releasing taverna language)

[Gale Naylor]

Or change tavtool to tavlang (link) tool, to be consistent with other
instances

On Wed, Feb 3, 2016 at 10:21 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> Questions and broken links in taverna-scufl2-api/readme.md.
>
> 
> INTRODUCTORY PARAGRAPHS
> 
>
> (1) LINK ERROR?
> Looks like it should be a link ... [SCUFL2][9] "For more information, see
> the
> [SCUFL2 API][9] pages..."
>
> 
> Usage
> 
>
> (2) BROKEN LINK - fix?
> "Apache Taverna Language"
> https://github.com/apache/incubator-taverna-language/blob/master
> ---> SHOULD BE?:
> https://github.com/apache/incubator-taverna-language/blob/master/README.md
>
> (3) BROKEN LINK
> In table of supported file formats, "RDF Turtle" link gives 403 error
> http://www.w3.org/TR/turtle/%22
>
> (4) iwir REFERENCE
> In table of supported file formats, "scufl2-iwir"
>
> (5) Change tavtool to tavlang-tool?
> "You can use the tavtool command line to perform..."
>
>
> On Wed, Feb 3, 2016 at 9:43 AM Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
>> @stian, so, at some point, taverna-wfbundle should be changed to use
>> robundle instead of taverna-scufl2-ucfpackage?
>>
>> On Tue, Feb 2, 2016 at 4:41 PM Stian Soiland-Reyes <st...@apache.org>
>> wrote:
>>
>>> The UCF documentation even disappeared from adobe.com.. so it's good
>>> we are deprecating it.  But still the taverna-scufl2-ucfpackage is
>>> used by taverna-wfbundle (which should use robundle instead) - so it's
>>> needed as an internal dependency.
>>>
>>>
>>>
>>> On 2 February 2016 at 18:43, Gale Naylor <ga...@noventussolutions.com>
>>> wrote:
>>> > taverna-robundle, item (12) should be Adobe UCF, not UFC. I see in the
>>> > taverna-language readme that the module for Adobe UCF ZIP files is
>>> > deprecated. So should we just eliminate the link in the robundle
>>> readme?
>>> >
>>> > On Tue, Feb 2, 2016 at 9:26 AM Gale Naylor <
>>> ga...@noventussolutions.com>
>>> > wrote:
>>> >
>>> >>
>>> >> Java 7 references, broken links, and other notes on taverna-robundle/
>>> >> readme.md:
>>> >>
>>> >> ***
>>> >> INTRODUCTORY PARAGRAPHS
>>> >> ***
>>> >>
>>> >> (1) Java 7
>>> >> "This API is built on the Java 7 NIO Files and uses the Java 7 ZIP
>>> file
>>> >> provider to generate the RO Bundle.
>>> >> The class org.apache.taverna.robundle.Bundles complements the Java 7
>>> >> java.nio.Files API with more specific helper methods to work with RO
>>> >> Bundles."
>>> >>
>>> >> (2) BROKEN LINK
>>> >> Broken "org.apache.taverna.robundle.Bundles" links to
>>> >>
>>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/main/java/org/purl/wf4ever/robundle/Bundles.java
>>> >>
>>> >> (3) WRONG LINK?
>>> >> "Taverna Data Bundles API" links to non-Apache repo, which says
>>> "Moved to
>>> >> Apache Taverna."
>>> >> (https://github.com/taverna/taverna-databundle)
>>> >>
>>> >> ***
>>> >> Usage SECTION
>>> >> ***
>>> >>
>>> >> (4) myGRID REFERENCE
>>> >> pom.xml code sample says to add "mygrid-repository" and points to
>>> >> http://www.mygrid.org.uk/maven/repository
>>> >>
>>> >> (5) wf4ever REFERENCE
>>> >> "robundle releases" links to
>>> https://github.com/wf4ever/robundle/releases
>>> >>
>>> >> (6) myGRID REFERENCE
>>> >> "myGrid's Maven repository" links to
>>> >>
>>> http://repository.mygrid.org.uk/artifactory/mygrid-all/org/purl/wf4ever/robundle/robundle/
>>> >>
>>> >> ***
>>> >> Building SECTION
>>> >> ***
>>> >>
>>> >> (7) JAVA 7
>>> >> "should normally work, given a recent version of Maven 3 and Java 7
>>> SDK."
>>> >>
>>> >> (8) myGRID REFERENCE
>>> >> &

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

[Gale Naylor]

FYI: The sha512sum got cut off for taverna-maven-parent.

On Sat, Feb 27, 2016 at 4:03 PM Dmitry  wrote:

> Master.
>
> Going to try RC5.
>
> Dmitry
>
> On 2/28/2016 12:56 AM, Stian Soiland-Reyes wrote:
> > Thanks! Do you mean the tag 0.15.1-incubating-RC5 (0.15.1-incubating)
> > or master (which is 0.15.1-incubating-SNAPSHOT)?
> >
> > Could you try the RC5 release candidate download? (or verify it
> > matches the commit you tested)
> >
> >
> > On 27 February 2016 at 23:47, Dmitry  wrote:
> >> I was able to compile the fresh taverna-language-0.15.1 from git (with
> empty
> >> local maven repo).
> >> Win 7 64x, Java 8u73, Netbeans 8.1.
> >>
> >> Dmitry
> >>
> >>
> >> On 2/28/2016 12:33 AM, Stian Soiland-Reyes wrote:
> >>> Use this thread to discuss any issues with RC5 which is currently
> >>> under VOTE. If needed we'll also make Jira issues.
> >>>
> >>> Under the corresponding [VOTE] thread - only reply with your vote,
> >>> e.g. "+1". It is a single vote for releasing all three artifacts at
> >>> once.
> >>>
> >>>
> >>>
> >>>
> >>> Vote thread:
> >>> http://apache-taverna-dev.markmail.org/thread/vfwbtfdpie4t24ng
> >>>
> >>>
> >
> >
>
>

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

[Gale Naylor]

Thank you very much for the details, Andy. I'm doing my best to come up to
speed on all this.

A question:
In looking at the LICENSE files, and the Apache documentation (
http://www.apache.org/legal/src-headers.html#notice), I'm wondering about
the Taverna Language License, which contains several copyright notices. The
documentation I referenced says: "Use the NOTICE file to collect copyright
notices and required attributions." Am I misinterpreting this? Should these
copyright notices be in the NOTICE file? (Profuse apologies if this was
already discussed when I was less up-to-speed.)

Gale

On Sun, Feb 28, 2016 at 2:19 AM Andy Seaborne  wrote:

> On 27/02/16 23:33, Stian Soiland-Reyes wrote:
> > Use this thread to discuss any issues with RC5 which is currently
> > under VOTE. If needed we'll also make Jira issues.
> >
> > Under the corresponding [VOTE] thread - only reply with your vote,
> > e.g. "+1". It is a single vote for releasing all three artifacts at
> > once.
> >
>
> Releases are the high point a project.
>
> PPMC members - feel morally obliged to vote!
>
> Everyone else - help out - it's not "devs and users" - it's "community".
>
> Don't forget what really matters when you vote +1 is that the release
> meets the Apache requirements and then any additional local community
> norms.
>
> A quick and not complete summary of what a VOTE entails:
>
> ** Source
>
> The source artifact is the thing being released.
> Binaries and git are secondary.
>
> People voting must download the source artifact and check it.
>
> do the signatures on the source archive check out?
> does the commit id lead to the same sources?
>
> ** ASF licensing policy
>
> Much of this code being is released for the first time so LICENSE and
> NOTICE are mostly new.
>
> does the NOTICE file contain all necessary attributions?
> is there a correct LICENSE and NOTICE file in each artifact (both source
> and binary artifacts)?
>
> ** Build
>
> does the build of the source artifact actually produce the binaries?
> check the dependencies.
>
> ** Process
>
> Support the release manager!
>
> The minimum is 3 +1 votes with a majority in favour.
> The RM decides about what to do about comments.
>
> Does the quality level meet the group norms?
>("can we live with it?" and not "is it perfect?")
>
>
> https://www.apache.org/dev/release.html
>
> Andy
>
>

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

[Gale Naylor]

RE: LICENSES
Now I've come across this set of statements: "These third party notices
vary from license to license. Apache releases should contain a copy of each
license, usually contained in the LICENSE document." (
http://apache.org/legal/resolved.html#required-third-party-notices.) But
maybe this is saying: Apache releases should contain a copy of each (3rd
party) license, which is usually contained in the *3rd party* LICENSE
document? (Rather than saying the notice should be in the Apache LICENSE
document, which is what I thought at first. Can anyone shed light on this?

On Sun, Feb 28, 2016 at 2:54 PM Gale Naylor <ga...@noventussolutions.com>
wrote:

> Thank you very much for the details, Andy. I'm doing my best to come up to
> speed on all this.
>
> A question:
> In looking at the LICENSE files, and the Apache documentation (
> http://www.apache.org/legal/src-headers.html#notice), I'm wondering about
> the Taverna Language License, which contains several copyright notices. The
> documentation I referenced says: "Use the NOTICE file to collect copyright
> notices and required attributions." Am I misinterpreting this? Should these
> copyright notices be in the NOTICE file? (Profuse apologies if this was
> already discussed when I was less up-to-speed.)
>
> Gale
>
> On Sun, Feb 28, 2016 at 2:19 AM Andy Seaborne <a...@apache.org> wrote:
>
>> On 27/02/16 23:33, Stian Soiland-Reyes wrote:
>> > Use this thread to discuss any issues with RC5 which is currently
>> > under VOTE. If needed we'll also make Jira issues.
>> >
>> > Under the corresponding [VOTE] thread - only reply with your vote,
>> > e.g. "+1". It is a single vote for releasing all three artifacts at
>> > once.
>> >
>>
>> Releases are the high point a project.
>>
>> PPMC members - feel morally obliged to vote!
>>
>> Everyone else - help out - it's not "devs and users" - it's "community".
>>
>> Don't forget what really matters when you vote +1 is that the release
>> meets the Apache requirements and then any additional local community
>> norms.
>>
>> A quick and not complete summary of what a VOTE entails:
>>
>> ** Source
>>
>> The source artifact is the thing being released.
>> Binaries and git are secondary.
>>
>> People voting must download the source artifact and check it.
>>
>> do the signatures on the source archive check out?
>> does the commit id lead to the same sources?
>>
>> ** ASF licensing policy
>>
>> Much of this code being is released for the first time so LICENSE and
>> NOTICE are mostly new.
>>
>> does the NOTICE file contain all necessary attributions?
>> is there a correct LICENSE and NOTICE file in each artifact (both source
>> and binary artifacts)?
>>
>> ** Build
>>
>> does the build of the source artifact actually produce the binaries?
>> check the dependencies.
>>
>> ** Process
>>
>> Support the release manager!
>>
>> The minimum is 3 +1 votes with a majority in favour.
>> The RM decides about what to do about comments.
>>
>> Does the quality level meet the group norms?
>>("can we live with it?" and not "is it perfect?")
>>
>>
>> https://www.apache.org/dev/release.html
>>
>> Andy
>>
>>

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

[Gale Naylor]

More on LICENSES
Apache includes Creative Commons Attribution licenses in their "weak
copyleft" list and (though I don't understand why) Apache suggests
attaching "an appropriate and prominent label to the distribution ... for
example in a README." (http://www.apache.org/legal/resolved.html). Should
we have some kind of notice in the scufl2-wfdesc and robundle (etc.) README
files that flags the embedded CCA licenses?

Also, I have yet to independently verify this, but I presume it was
determined earlier that the oa.rdf (robundle) W3C CCLA license is okay, as
well as the Open-document (robundle) OASIS license/notification.

Thanks,

Gale

On Sun, Feb 28, 2016 at 3:02 PM Gale Naylor <ga...@noventussolutions.com>
wrote:

> RE: LICENSES
> Now I've come across this set of statements: "These third party notices
> vary from license to license. Apache releases should contain a copy of each
> license, usually contained in the LICENSE document." (
> http://apache.org/legal/resolved.html#required-third-party-notices.) But
> maybe this is saying: Apache releases should contain a copy of each (3rd
> party) license, which is usually contained in the *3rd party* LICENSE
> document? (Rather than saying the notice should be in the Apache LICENSE
> document, which is what I thought at first. Can anyone shed light on this?
>
> On Sun, Feb 28, 2016 at 2:54 PM Gale Naylor <ga...@noventussolutions.com>
> wrote:
>
>> Thank you very much for the details, Andy. I'm doing my best to come up
>> to speed on all this.
>>
>> A question:
>> In looking at the LICENSE files, and the Apache documentation (
>> http://www.apache.org/legal/src-headers.html#notice), I'm wondering
>> about the Taverna Language License, which contains several copyright
>> notices. The documentation I referenced says: "Use the NOTICE file to
>> collect copyright notices and required attributions." Am I misinterpreting
>> this? Should these copyright notices be in the NOTICE file? (Profuse
>> apologies if this was already discussed when I was less up-to-speed.)
>>
>> Gale
>>
>> On Sun, Feb 28, 2016 at 2:19 AM Andy Seaborne <a...@apache.org> wrote:
>>
>>> On 27/02/16 23:33, Stian Soiland-Reyes wrote:
>>> > Use this thread to discuss any issues with RC5 which is currently
>>> > under VOTE. If needed we'll also make Jira issues.
>>> >
>>> > Under the corresponding [VOTE] thread - only reply with your vote,
>>> > e.g. "+1". It is a single vote for releasing all three artifacts at
>>> > once.
>>> >
>>>
>>> Releases are the high point a project.
>>>
>>> PPMC members - feel morally obliged to vote!
>>>
>>> Everyone else - help out - it's not "devs and users" - it's "community".
>>>
>>> Don't forget what really matters when you vote +1 is that the release
>>> meets the Apache requirements and then any additional local community
>>> norms.
>>>
>>> A quick and not complete summary of what a VOTE entails:
>>>
>>> ** Source
>>>
>>> The source artifact is the thing being released.
>>> Binaries and git are secondary.
>>>
>>> People voting must download the source artifact and check it.
>>>
>>> do the signatures on the source archive check out?
>>> does the commit id lead to the same sources?
>>>
>>> ** ASF licensing policy
>>>
>>> Much of this code being is released for the first time so LICENSE and
>>> NOTICE are mostly new.
>>>
>>> does the NOTICE file contain all necessary attributions?
>>> is there a correct LICENSE and NOTICE file in each artifact (both source
>>> and binary artifacts)?
>>>
>>> ** Build
>>>
>>> does the build of the source artifact actually produce the binaries?
>>> check the dependencies.
>>>
>>> ** Process
>>>
>>> Support the release manager!
>>>
>>> The minimum is 3 +1 votes with a majority in favour.
>>> The RM decides about what to do about comments.
>>>
>>> Does the quality level meet the group norms?
>>>("can we live with it?" and not "is it perfect?")
>>>
>>>
>>> https://www.apache.org/dev/release.html
>>>
>>> Andy
>>>
>>>

Re: [CANCELLED] [VOTE] Release taverna-language-0.15.1-incubating-RC4 and taverna-osgi-0.2.1-incubating-RC4

[Gale Naylor]

I hope I'll be up-to-speed in time to participate in the next release!

On Wed, Feb 24, 2016, 11:15 PM Stian Soiland-Reyes  wrote:

> Thanks to all who tested this release candidate and provided feedback in
> the DISCUSS thread?!
>
> I'm sorry to be CANCELLING this vote, as TAVERNA-918 still prevented build
> on Windows. Thanks to Ian, Menaka, Dmitry and Andy for quickly figuring out
> a solution, so I'll start immediately to prepare a RC5.
>

Re: Draft March 2016 incubator report for Taverna

[Gale Naylor]

Looks good to me.

On Mon, Feb 29, 2016 at 4:07 AM Stian Soiland-Reyes 
wrote:

> Thanks, Ian!
>
> I've added them (and my draft) to
> https://wiki.apache.org/incubator/March2016
>
>
> I don't think we need to comment on the copyright review thread, that
> is just part of normal project development.
>
>
> On 29 February 2016 at 11:54, Ian Dunlop 
> wrote:
> > Hello,
> >
> > Looks good Stian. Do we need to add the copyright sign off bit - I can't
> > see where that should go. Do we need a bit about mailing list traffic.
> > Dev has been very active:
> >
> > Dec 2015: 42
> > Jan 2016: 128
> > Feb 2016: 325
> >
> > Users not so active:
> >
> > Dec 2015: 2
> > Jan 2016: 0
> > Feb 2016: 2
> >
> > (Nice summaries via http://apache-taverna-users.markmail.org/search/?q=
> > and http://apache-taverna-dev.markmail.org/search/?q=)
> >
> > JIRA issues over last 90 days:
> >
> > 50 created
> > 32 resolved
> >
> > Cheers,
> >
> > Ian
> >
> > On 29/02/2016 08:26, Stian Soiland-Reyes wrote:
> >> Please help review/edit this report for the incubator, due this
> >> Wednesdasy 2016-03-02
> >> https://wiki.apache.org/incubator/March2016
> >>
> >>
> >>
> >> Taverna
> >>
> >> Taverna is a domain-independent suite of tools used to design and
> execute
> >> data-driven workflows.
> >>
> >> Taverna has been incubating since 2014-10-20.
> >>
> >> Three most important issues to address in the move towards graduation:
> >>
> >>   1. Community growth
> >>   2. Release more of the imported code to create engagement
> >>   3. Move to a sustainable development pattern
> >>
> >>
> >>
> >> Any issues that the Incubator PMC (IPMC) or ASF Board wish/need to be
> >> aware of?
> >>
> >> Several mentors have reported they have little or no time available as
> >> Taverna's project pace is picking up again.
> >>
> >> We have started recruiting new mentors on the incubator list:
> >>
> http://mail-archives.apache.org/mod_mbox/incubator-general/201602.mbox/%3CCAMBJEmW6ezFS7Dtsxo2FwSV7dXj1MPQ_%3DEfuiQmkcVsqCJ73aA%40mail.gmail.com%3E
> >>
> >>
> >>
> >>
> >> How has the community developed since the last report?
> >>
> >> Welcomed new PPMC member.
> >> GSOC 2016 project ideas are already getting interest.
> >>
> >>
> >> How has the project developed since the last report?
> >>
> >> Good buzz around release preparation, release candidate currently
> >> under vote.
> >>
> >>
> >>
> >> Date of last release:
> >>
> >>
> >> 2015-08-11 taverna-language-0.15.0-incubating
> >>
> >> (new release currently under vote)
> >>
> >>
> >> When were the last committers or PMC members elected?
> >>
> >> 2015-12-04
> >>
> >>
> >> Signed-off-by:
> >>
> >>   [ ](taverna) Andy Seaborne
> >>   [ ](taverna) Chris Mattmann
> >>   [ ](taverna) Suresh Srinivas
> >>   [ ](taverna) Suresh Marru
> >>   [ ](taverna) Marlon Pierce
> >>
> >> Shepherd/Mentor notes:
> >>
> >>
> >>
> >
> > --
> > 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: [DISCUSS] Release Candidate 5 of taverna-language-0.15.1 and taverna-osgi-0.2.1

[Gale Naylor]

I have successfully built the files, but I'm not ready to vote because I
have a few questions.

I am following Andy's "quick and not complete summary of what a VOTE
entails":

(1) How do I verify that the commit id in the downloaded files matches that
in the VOTE email? (I've looked on the internet, but have yet to find
anything helpful.)

(2) Are the "binary artifacts" in the target folders? Which files are
considered "binary artifacts?"

(3) How do I verify that the build produces the binaries? By visual
inspection? What am I looking for?

(4) How do I check the dependencies?

Regarding the build output: Since this is the first time I've done this, I
don't know what's okay to ignore. Here is a summary of the warning messages
I received when I ran mvn clean install. I sent the output to two different
files using the following command (Windows 10/ GitBash): mvn clean install
> output1.txt 2> output2.txt. I appreciate any insight.

** taverna-parent-2: Build successful. The errors file was empty and the
console file had one warning about an empty jar.

** taverna language: Build successful. Warnings, some with multiple
occurrences.
-
language output1 file
-
(1) Empty jar warning

(2) Lots of JavaDoc warnings -- @return tag has no arguments, illegal
characters, can't find configurationsFor(Activity,Profile) etc.

(3) Private references -- Export org.apache.taverna.scufl2.ucfpackage,  has
1,  private references
[org.apache.taverna.scufl2.ucfpackage.impl.odfdom.pkg.manifest],

(4) Program names are deprecated -- e.g., The usage of program name
(workflowmaker) is deprecated. Please use program.id instead.

(5) Private packages -- Unused Private-Package instructions, no such
package(s) on the class path: [!*]

(6) Relative URIs -- Relative URIs are not permitted in RDF: specifically


(7) Overlapping classes -- for example, xpp3_min-1.1.4c.jar,
xmlpull-1.1.3.1.jar define 2 overlapping classes:
 - org.xmlpull.v1.XmlPullParserException
 - org.xmlpull.v1.XmlPullParser
-
language output2 file
-
(1) Unexpected failure of setLastModifiedTime on root --
java.nio.file.oSuchFileException:

(2) Unexpected exception-- java.nio.file.NoSuchFileException: test.txt
at com.sun.nio.zipfs.ZipFileSystem.newFileChannel
(ZipFileSystem.java:709)
[and about 30 more in list]

(3) log4j - no appenders could be found for logger ... Please initialize
the log4j system properly.
log4j

(4) Expected literal  -- Expected literal. not -183cb345:1532e6bc46e:-7ffe

(5) Skipping aggregation -- Skipping aggregation without URI:
266e243ce4d408285e522380c4484af0

(6) Ignoring unsupported PropertyResource -- (from wfbundle 0.2.0 or older)
for Configuration "Hello" [beanshell:script: null]

(7) Could not translate link -- for example, ... More than one link to
non-merged port InputProcessorPort "inputlist"

(8) Unknown T2 activity or dispatch layer  --
http://ns.taverna.org.uk/2010/xml/t2flow/raven/undefined/net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize,
install supporting T2Parser

(9) Invalid output port binding -- unknown processor port: value->value in
Processor "alternates"

(10) Ambiguous owl:versionInfo -- there is more than one owl:Ontology
element.

** taverna osgi: Build successful. Warnings.
-
osgi output1 file
-
(1) Deprecated @component -- for example, Deprecated @component for project
field in org.apache.taverna.mavenplugin.TavernaProfileDeployMojo.: replace
with @parameter name="${project}" @readonly

(2) Several sets of JavaDoc errors.
-
osgi output2 file
-
(1) log4j warning -- no appenders could be found for logger... Please
initialize the log4j system properly.
log4j
---

Thank you.

On Mon, Feb 29, 2016 at 3:16 AM Stian Soiland-Reyes <st...@apache.org>
wrote:

> Looking back at OASIS license I am not sure now.
>
> I've made
> https://issues.apache.org/jira/browse/TAVERNA-925
> to clarify.
>
> As far as I can see why are fine legally to distribute the ODF spec
> files as we have not modified them, however it would seem to be
> against ASF policy:
>
> _ Errors file



> http://www.apache.org/legal/resolved.html#no-modification
>
>
> I believe that as we are legally OK against OASIS, and we are still an
> incubating project with DISCLAIMER, this policy breach should not be a
> blocker for this release - but it would have to be sorted before the
> first proper ASF release of Taverna Language.
>
> Other views? Mentors?
>
> On 29 February 2016 at 01:18, Gale Naylor <ga...@noventussolutions.com>
> wrote:
> > More on LICENSES
> > Apache includes Creative Commons Attribution licenses in their "weak
>

Trying to understand the big picture

[Gale Naylor]

Hi, all. I'm trying to map the release items (
http://taverna.incubator.apache.org/download/code/ - Source code
repositories section) with the overall architecture of Taverna 3 so I can
understand the big picture. I'm using the diagram from Stian's 2014-10-31
presentation (
http://www.slideshare.net/soilandreyes/20141031taverna3architecture) .

I have a couple of general questions:
1) Is this the right architecture diagram to use?
2) Does it make sense to map the git repos to the architecture elements?

If it makes sense to proceed, are these mappings correct?:
taverna maven parent -- Taverna Core?
taverna language -- Taverna Core?
taverna osgi -- Taverna Platform API (OSGI)
taverna engine -- Taverna Engine
taverna common activities -- part of Taverna Engine?
taverna commandline -- Taverna Command Line Tools (part of?)
taverna server -- Taverna Server
taverna workbench -- Taverna Workbench
taverna workbench common activities -- part of Taverna Workbench
taverna workbench product -- part of Taverna workbench
taverna plugin component -- part of Core: Activity Plugins?
taverna plugin bioinformatics -- part of Core: Activity Plugins?
taverna databundle viewer -- ??
taverna mobile -- ??

What about Taverna Player and Taverna Lite?

Thanks!

Gale

Re: schema.org metadata

[Gale Naylor]

So I can see how you chose to tag it.

On Fri, Jan 22, 2016 at 3:55 PM Gale Naylor <ga...@noventussolutions.com>
wrote:

> @Stian, when you get a chance, could you give me an example of a webpage
> you have already tagged with the schema.org metadata so I can see what it
> looks like?
>
> Thanks,
>
> Gale
>

Re: Trying to understand the big picture

[Gale Naylor]

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?

Thanks,
Gale

On Mon, Jan 25, 2016 at 5:46 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
wrote:

> Hello,
>
> I think taverna-language is part of the taverna-platform in this diagram.
> taverna-mobile sits to the right of taverna-player.
> I think taverna-common-activities is part of core since the engine works
> without them (just doesn't have anything to run).
> I don't think Taverna Player (or the Taverna Player Portal(?)) have been
> moved to Apache (probably still part of mygrid
> https://github.com/myGrid/taverna-player-portal) but they are still part
> of the taverna ecosystem - we need to think about this. Not sure about
> Taverna Lite and whether that is a 'real' product any more.
> I think the diagram is useful as an introduction to all the components
> and yes, it does make sense to map the repos to the diagram. One of the
> hardest parts is trying to figure out how it all fits together.
>
> Cheers,
>
> Ian
>
> On 22/01/2016 20:57, Gale Naylor wrote:
> > Hi, all. I'm trying to map the release items (
> > http://taverna.incubator.apache.org/download/code/ - Source code
> > repositories section) with the overall architecture of Taverna 3 so I can
> > understand the big picture. I'm using the diagram from Stian's 2014-10-31
> > presentation (
> > http://www.slideshare.net/soilandreyes/20141031taverna3architecture) .
> >
> > I have a couple of general questions:
> > 1) Is this the right architecture diagram to use?
> > 2) Does it make sense to map the git repos to the architecture elements?
> >
> > If it makes sense to proceed, are these mappings correct?:
> > taverna maven parent -- Taverna Core?
> > taverna language -- Taverna Core?
> > taverna osgi -- Taverna Platform API (OSGI)
> > taverna engine -- Taverna Engine
> > taverna common activities -- part of Taverna Engine?
> > taverna commandline -- Taverna Command Line Tools (part of?)
> > taverna server -- Taverna Server
> > taverna workbench -- Taverna Workbench
> > taverna workbench common activities -- part of Taverna Workbench
> > taverna workbench product -- part of Taverna workbench
> > taverna plugin component -- part of Core: Activity Plugins?
> > taverna plugin bioinformatics -- part of Core: Activity Plugins?
> > taverna databundle viewer -- ??
> > taverna mobile -- ??
> >
> > What about Taverna Player and Taverna Lite?
> >
> > Thanks!
> >
> > Gale
> >
>
> --
> Ian Dunlop, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/-0001-7066-3350
>

Re: Proposed google hangout

[Gale Naylor]

@Ian - No problem! I didn't realize we had a Twitter account, but I just
looked it up!

On Wed, Jan 20, 2016 at 7:47 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
wrote:

> Hello,
>
> "tweet-vertise" advertise via twitter!! Or maybe a tweetvert?
> (I just made it up. Apologies!)
>
> Cheers,
>
> Ian
>
> On 20/01/2016 15:29, Gale Naylor wrote:
> > It looks like that link will work for me. If not, I also have the Hangout
> > app on my phone. But since this is my first time, maybe monitoring the
> IRC
> > channel (at least, at the beginning) would be a good idea?
> >
> > @Ian, what is "tweet-vertise?"
> >
> > Thanks!
> >
> > Gale
> >
> >
> > On Wed, Jan 20, 2016 at 7:20 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
> > 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=MDY3N2VlajQ5MWVtOHQzcjg1aDBpMTJzOGdAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.gqmf2415hk9gb7r7uo7bggvi7s
> >>
> >> Cheers,
> >>
> >> Ian
> >>
> >> On 20/01/2016 14:58, Stian Soiland-Reyes wrote:
> >>> Yeah, I think you can tick a button once you have started to record it
> >>> to Youtube, which I guess we should do for mailing list purposes. That
> >>> would give you also a corresponding Youtube live stream - but we
> >>> shouldn't be looking at that as then you can't talk.  (That is more
> >>> for like 10.000 followers kind of scenario)
> >>>
> >>> If you are using Google Hangout for the first time in your browser you
> >>> will probably need to install a plugin. See
> >>> https://www.google.com/tools/dlpage/hangoutplugin
> >>>
> >>> (From a phone/tablet it should be enough with the Hangout app)
> >>>
> >>> You will also need a Google account to log in.
> >>>
> >>>
> >>> I understand if someone might have reservations (I certainly don't
> >>> like installing plugins), in which case you could resort to watching
> >>> the Youtube stream and text back on the #taverna IRC channel -
> >>> http://taverna.incubator.apache.org/community/irc  -- if anyone
> >>> prefers that, please say so in this thread so we know to watch the IRC
> >>> and can send the URL.
> >>>
> >>>
> >>> On 20 January 2016 at 14:35, Ian Dunlop <ian.dun...@manchester.ac.uk>
> >> wrote:
> >>>> Hello,
> >>>>
> >>>> Consensus is Friday 1500-1600 GMT. I guess we will use google hangout.
> >>>> What is the best way to set this up. Do we use a "hangout on air" so
> >>>> that we can broadcast it? @Stian - can you remember what you did for
> the
> >>>> last taverna hangout?
> >>>> Anyway, details to follow soon. Hope to see you all there. Should we
> >>>> tweet-vertise etc?
> >>>>
> >>>> Cheers,
> >>>>
> >>>> Ian
> >>>>
> >>>> On 19/01/2016 13:07, alaninmcr wrote:
> >>>>> 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 <
> st...@apache.org
> >>>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> Both are good for myself, but +1 for Friday 15:00 GMT.
> >>>>>>>
> >>>>>>> On 18 January 2016 at 15:44, Ian Dunlop <
> ian.dun...@manchester.ac.uk
> >>>
> >>>>>>> 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
> >>>>>>>
> >>>>>>
> >>>>
> >>>> --
> >>>> Ian Dunlop, eScience Lab
> >>>> School of Computer Science
> >>>> The University of Manchester
> >>>> http://orcid.org/-0001-7066-3350
> >>>
> >>>
> >>>
> >>
> >> --
> >> Ian Dunlop, eScience Lab
> >> School of Computer Science
> >> The University of Manchester
> >> http://orcid.org/-0001-7066-3350
> >>
> >
>
> --
> Ian Dunlop, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/-0001-7066-3350
>

Re: Proposed google hangout

[Gale Naylor]

It looks like that link will work for me. If not, I also have the Hangout
app on my phone. But since this is my first time, maybe monitoring the IRC
channel (at least, at the beginning) would be a good idea?

@Ian, what is "tweet-vertise?"

Thanks!

Gale


On Wed, Jan 20, 2016 at 7:20 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
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=MDY3N2VlajQ5MWVtOHQzcjg1aDBpMTJzOGdAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.gqmf2415hk9gb7r7uo7bggvi7s
>
> Cheers,
>
> Ian
>
> On 20/01/2016 14:58, Stian Soiland-Reyes wrote:
> > Yeah, I think you can tick a button once you have started to record it
> > to Youtube, which I guess we should do for mailing list purposes. That
> > would give you also a corresponding Youtube live stream - but we
> > shouldn't be looking at that as then you can't talk.  (That is more
> > for like 10.000 followers kind of scenario)
> >
> > If you are using Google Hangout for the first time in your browser you
> > will probably need to install a plugin. See
> > https://www.google.com/tools/dlpage/hangoutplugin
> >
> > (From a phone/tablet it should be enough with the Hangout app)
> >
> > You will also need a Google account to log in.
> >
> >
> > I understand if someone might have reservations (I certainly don't
> > like installing plugins), in which case you could resort to watching
> > the Youtube stream and text back on the #taverna IRC channel -
> > http://taverna.incubator.apache.org/community/irc  -- if anyone
> > prefers that, please say so in this thread so we know to watch the IRC
> > and can send the URL.
> >
> >
> > On 20 January 2016 at 14:35, Ian Dunlop <ian.dun...@manchester.ac.uk>
> wrote:
> >> Hello,
> >>
> >> Consensus is Friday 1500-1600 GMT. I guess we will use google hangout.
> >> What is the best way to set this up. Do we use a "hangout on air" so
> >> that we can broadcast it? @Stian - can you remember what you did for the
> >> last taverna hangout?
> >> Anyway, details to follow soon. Hope to see you all there. Should we
> >> tweet-vertise etc?
> >>
> >> Cheers,
> >>
> >> Ian
> >>
> >> On 19/01/2016 13:07, alaninmcr wrote:
> >>> 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 <st...@apache.org
> >
> >>>> wrote:
> >>>>
> >>>>> Both are good for myself, but +1 for Friday 15:00 GMT.
> >>>>>
> >>>>> On 18 January 2016 at 15:44, Ian Dunlop <ian.dun...@manchester.ac.uk
> >
> >>>>> 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
> >>>>>
> >>>>
> >>
> >> --
> >> Ian Dunlop, eScience Lab
> >> School of Computer Science
> >> The University of Manchester
> >> http://orcid.org/-0001-7066-3350
> >
> >
> >
>
> --
> Ian Dunlop, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/-0001-7066-3350
>

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

[Gale Naylor]

Will do. I'm working on it, and gathering online links to doi, etc where I
can. I also like the style you described. Should be done before Friday.

On Tue, Jan 19, 2016, 6:59 AM Stian Soiland-Reyes (JIRA) 
wrote:

>
> [
> https://issues.apache.org/jira/browse/TAVERNA-882?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15106834#comment-15106834
> ]
>
> Stian Soiland-Reyes commented on TAVERNA-882:
> -
>
> +1 to what Ian says, just do it and get things done :)  If anyone
> disagrees, they can change it again or raise another issue.
>
> (it's only on releases we have to be more careful)
>
> For reference style, personally I prefer the style with all full names
> (space is cheap on the web), bold on title, and italics on journal/venue. I
> always try to include DOI and/or preprint. I must admit I don't remember if
> this is Harvard style or what.. but it's quite readable on the web.
>
> {code}
> Jun Zhao, Jose Manuel Gomez-Perezy, Khalid Belhajjame, Graham Klyne,
> Esteban Garcia-Cuestay, Aleix Garridoy, Kristina Hettne, Marco Roos, David
> De Roure, Carole Goble (2012):
> **Why Workflows Break - Understanding and Combating Decay in Taverna
> Workflows**, _eScience 2012_, Chicago, October 2012.
> [[preprint]](http://users.ox.ac.uk/~oerc0033/preprints/why-decay.pdf)
> {code}
>
> > Publications page
> > -
> >
> > Key: TAVERNA-882
> > URL: https://issues.apache.org/jira/browse/TAVERNA-882
> > Project: Apache Taverna
> >  Issue Type: New Feature
> >  Components: Website
> >Reporter: Stian Soiland-Reyes
> >Priority: Minor
> >
> > It would be good to have a Publications page with academic publications
> that are about Taverna or use Taverna.
> > The older http://www.taverna.org.uk/cite/ refers to the latest
> canonical citations about Taverna, http://dx.doi.org/10.1093/nar/gkt328
> > but even after moving to Apache we have gathered new citations:
> >
> https://scholar.google.co.uk/scholar?hl=en=%22Apache+Taverna%22=_sdt=1%2C5_sdtp=
> > Some searches (must be filtered further):
> >
> https://scholar.google.co.uk/scholar?q=Taverna+workflow==en_sdt=0%2C5
> >
> https://scholar.google.co.uk/scholar?q=Taverna+workbench==en_sdt=0%2C5
> > Also anything with Taverna on
> http://dev.mygrid.org.uk/wiki/display/about/myGrid+Publications
> > In addition to listing the master citation
> http://dx.doi.org/10.1093/nar/gkt328 I would propose a single
> chronological text page along the style we have used on
> http://www.esciencelab.org.uk/publications/ with links to the DOI and a
> preprint if it's not Open Access. (I guess those links can be tricky for
> older papers).
>
>
>
> --
> This message was sent by Atlassian JIRA
> (v6.3.4#6332)
>

Re: Proposed google hangout

[Gale Naylor]

@Ian - never mind!

On Fri, Jan 22, 2016 at 8:12 AM Gale Naylor <ga...@noventussolutions.com>
wrote:

> @Ian, do you typically
> copy the IRC "minutes" to the email list?
>
> Thanks,
> Gale
>
> On Fri, Jan 22, 2016 at 7:10 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
> wrote:
>
>> Hello,
>>
>> The classic tech support answer :)
>> "Have you tried turning it on and off again?"
>>
>> Cheers,
>>
>> Ian
>>
>> On 22/01/2016 15:01, Gale Naylor wrote:
>> > I'm rebooting. Will try in a sec.
>> >
>> > On Fri, Jan 22, 2016, 6:55 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
>> > wrote:
>> >
>> >> Hello,
>> >>
>> >> try this hangout on air
>> >>
>> >> https://plus.google.com/events/cg8d6fl9786orgjb8ms7tvddo80
>> >>
>> >> Cheers,
>> >>
>> >> Ian
>> >>
>> >> On 22/01/2016 14:45, alaninmcr wrote:
>> >>> 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=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
>> >>
>> >> --
>> >> Ian Dunlop, eScience Lab
>> >> School of Computer Science
>> >> The University of Manchester
>> >> http://orcid.org/-0001-7066-3350
>> >>
>> >
>>
>> --
>> Ian Dunlop, eScience Lab
>> School of Computer Science
>> The University of Manchester
>> http://orcid.org/-0001-7066-3350
>>
>

Re: Proposed google hangout

[Gale Naylor]

@Ian, do you typically
copy the IRC "minutes" to the email list?

Thanks,
Gale

On Fri, Jan 22, 2016 at 7:10 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
wrote:

> Hello,
>
> The classic tech support answer :)
> "Have you tried turning it on and off again?"
>
> Cheers,
>
> Ian
>
> On 22/01/2016 15:01, Gale Naylor wrote:
> > I'm rebooting. Will try in a sec.
> >
> > On Fri, Jan 22, 2016, 6:55 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
> > wrote:
> >
> >> Hello,
> >>
> >> try this hangout on air
> >>
> >> https://plus.google.com/events/cg8d6fl9786orgjb8ms7tvddo80
> >>
> >> Cheers,
> >>
> >> Ian
> >>
> >> On 22/01/2016 14:45, alaninmcr wrote:
> >>> 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=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
> >>
> >> --
> >> Ian Dunlop, eScience Lab
> >> School of Computer Science
> >> The University of Manchester
> >> http://orcid.org/-0001-7066-3350
> >>
> >
>
> --
> Ian Dunlop, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/-0001-7066-3350
>

Re: Proposed google hangout

[Gale Naylor]

I'm rebooting. Will try in a sec.

On Fri, Jan 22, 2016, 6:55 AM Ian Dunlop 
wrote:

> Hello,
>
> try this hangout on air
>
> https://plus.google.com/events/cg8d6fl9786orgjb8ms7tvddo80
>
> Cheers,
>
> Ian
>
> On 22/01/2016 14:45, alaninmcr wrote:
> > 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=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
>
> --
> Ian Dunlop, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/-0001-7066-3350
>

Re: Proposed google hangout

[Gale Naylor]

ga...@noventussolutions.com

On Fri, Jan 22, 2016 at 7:05 AM Stian Soiland-Reyes <st...@apache.org>
wrote:

> Sorry, the Plus event was one-way only.. we're trying
> https://hangouts.google.com/call/rtzb5xdxxf7fv7aueii2kpxhnya  but it
> seems even though it's shared to "anyone with the link" I need to
> invite specifically.
>
> On 22 January 2016 at 15:01, Gale Naylor <ga...@noventussolutions.com>
> wrote:
> > I'm rebooting. Will try in a sec.
> >
> > On Fri, Jan 22, 2016, 6:55 AM Ian Dunlop <ian.dun...@manchester.ac.uk>
> > wrote:
> >
> >> Hello,
> >>
> >> try this hangout on air
> >>
> >> https://plus.google.com/events/cg8d6fl9786orgjb8ms7tvddo80
> >>
> >> Cheers,
> >>
> >> Ian
> >>
> >> On 22/01/2016 14:45, alaninmcr wrote:
> >> > 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=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
> >>
> >> --
> >> 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
>

schema.org metadata

[Gale Naylor]

@Stian, when you get a chance, could you give me an example of a webpage
you have already tagged with the schema.org metadata so I can see what it
looks like?

Thanks,

Gale