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