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