Return-Path: X-Original-To: apmail-taverna-users-archive@minotaur.apache.org Delivered-To: apmail-taverna-users-archive@minotaur.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id EBA9E194E0 for ; Mon, 11 Apr 2016 15:58:19 +0000 (UTC) Received: (qmail 46045 invoked by uid 500); 11 Apr 2016 15:58:19 -0000 Delivered-To: apmail-taverna-users-archive@taverna.apache.org Received: (qmail 46015 invoked by uid 500); 11 Apr 2016 15:58:19 -0000 Mailing-List: contact users-help@taverna.incubator.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: users@taverna.incubator.apache.org Delivered-To: mailing list users@taverna.incubator.apache.org Received: (qmail 45995 invoked by uid 99); 11 Apr 2016 15:58:19 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd2-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 11 Apr 2016 15:58:19 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd2-us-west.apache.org (ASF Mail Server at spamd2-us-west.apache.org) with ESMTP id 5D8021A0665; Mon, 11 Apr 2016 15:58:19 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd2-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: 2.379 X-Spam-Level: ** X-Spam-Status: No, score=2.379 tagged_above=-999 required=6.31 tests=[DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, HTML_MESSAGE=2, KAM_EU=0.5, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H3=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_PASS=-0.001] autolearn=disabled Authentication-Results: spamd2-us-west.apache.org (amavisd-new); dkim=pass (2048-bit key) header.d=googlemail.com Received: from mx1-lw-us.apache.org ([10.40.0.8]) by localhost (spamd2-us-west.apache.org [10.40.0.9]) (amavisd-new, port 10024) with ESMTP id FKNvR8rkG7Ee; Mon, 11 Apr 2016 15:58:17 +0000 (UTC) Received: from mail-yw0-f179.google.com (mail-yw0-f179.google.com [209.85.161.179]) by mx1-lw-us.apache.org (ASF Mail Server at mx1-lw-us.apache.org) with ESMTPS id D093B5F1F7; Mon, 11 Apr 2016 15:58:16 +0000 (UTC) Received: by mail-yw0-f179.google.com with SMTP id i84so208629941ywc.2; Mon, 11 Apr 2016 08:58:16 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=googlemail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :cc; bh=jOGzN46jctIwLQHBrGoTOfgucKTfbgitOpX7WiHRhxA=; b=ugtJrsWPmbBmvMys8vQKZZbP6MM6kel2FRo7udni8cJnE9wHGmRjG+n6hgzWkub6La pZdUV6jf9ftEXe5/lrldr2AmfiZkR8b/+Kze7FuG+XZK08fw5Z7Di0CywS+4ng5d5Hw8 EAZiahtELf9iXsSty0d+xfKaOwwki+CmErMlhxTqNu056v20Bzy9kJ/IKn/c+c0x+J21 1ipwqe0ZDQM2M7DrA9siiGd5ZPKufGW0tf+AsqYBBsvgm/VTf1dAvk7ObePzhnBwY0QJ e9NAmsS/+sjdb/NVyRKziIlZUkxQXEpwzgNpWj6G1ktFBX92G/gN7kDpNERp/oKycHy2 dEvA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:in-reply-to:references:date :message-id:subject:from:to:cc; bh=jOGzN46jctIwLQHBrGoTOfgucKTfbgitOpX7WiHRhxA=; b=ZUMMeH5+BaQPZsFfpHrHci+9RDvyCJFYwrbJ18pgjcxmu5mReAHYkdKRIVh9NSeyaT YKIYqbCNkSqHloqDsoPxDxtOHh7tz/iGkJMqV24W6oHXMqoJiEL/tnTUdU1Yed2k0t5c Rcxzo15W1trSoV4yDZJWpiNmKqSGbiJ2xYc7OtDGuvDZdGby2DrQs+nypOFkLav3lQwW wACMxHdnIfn2AN/ag51HN75JnY9V3p9x5CphA6ydpHqTorSgNz4/B8W5c7f6euJtomEb 1ay6BMOsYYKa8wxLC4CNsnB860gl2lfn7DxihQ1LF3R/mmQ1FUCPV3scHtaA1aERCrdf K7Hw== X-Gm-Message-State: AD7BkJI0Wv1Npz8/SlBEvMjNg1/GTRfrvzypONdgH8xdwIp4J3aDjmcJZ/9wOUcs9ElPbb+qHNG00nXNF5zmDg== MIME-Version: 1.0 X-Received: by 10.129.124.87 with SMTP id x84mr11294437ywc.209.1460390296267; Mon, 11 Apr 2016 08:58:16 -0700 (PDT) Received: by 10.129.70.212 with HTTP; Mon, 11 Apr 2016 08:58:16 -0700 (PDT) In-Reply-To: References: Date: Mon, 11 Apr 2016 17:58:16 +0200 Message-ID: Subject: Re: Enquiry about the features of Taverna 2.5 From: Khalid Belhajjame To: users@taverna.incubator.apache.org Cc: dev@taverna.incubator.apache.org Content-Type: multipart/alternative; boundary=001a114942ccd7b2020530379c7b --001a114942ccd7b2020530379c7b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks alot Stian, These are very helpful. best wishes, khalid On 11 April 2016 at 17:30, Stian Soiland-Reyes wrote: > Hi! > > (Folks, Khalid help do lots of work on research object, wfprov and > wfdesc which we use in taverna-language and > taverna-engine/taverna-prov) > > On 11 April 2016 at 15:17, Khalid Belhajjame > wrote: > > I would like to enquiry about some of the current features of Taverna. = I > > have an answer for most of the question, but I would like to know the > status > > with respect to the current version (2.5) of Taverna. I will be gratefu= l > if > > you could take the time to answer them. > > > > 1- In the current version of Taverna (2.5), I can see that the provenan= ce > > can be saved as PROV, but not as OPM. I am guessing that OPM export was > > deprecated. Let me know if I am wrong. Regarding the PROV export, you a= re > > using TavernaProv isn=E2=80=99t it? If so, do you have TavernaProv docu= mented > > somewhere? I would like to see how it compares to wfprov. > > > Yes, you are correct in that the OPM export was deprecated in 2.5 - it > was also less in match with what was happening in the workflow so it > was rather removed. > > TavernaProv became part of Taverna from 2.5. Documentation and example > here: > > https://github.com/apache/incubator-taverna-engine/tree/master/taverna-pr= ov > > (It's not yet fully integrated into Taverna 3) > > > TavernaProv is basically wfprov+prov+taverna - you will see that > everything is stated both with pure prov and in wfprov - which often > provides shortcuts. For details such as at which iteration something > happened you have to use the tavernaprov aspects - which also adds a > cnt:chars for embedding smaller values, and checksums like > tavernaprov:sha512. > > > > 2- Are there any utilities/means that help users to either deploy > workflows > > on the cloud or call services/use resource on the cloud? I remember the > work > > of Sonja with Unicore. Is there any other work that was conducted on th= is > > front? > > A bit related - we have a GSOC student working on Docker: > > https://issues.apache.org/jira/browse/TAVERNA-879 > > As for actually managing cloud instances or grid jobs I am not aware > of any current initiatives. Perhaps Dmitry or Vadim Surpin knows of > something? > > I think the http://www.vph-dare.eu/ project is using VPH Share and > local Grid infrastructure via Taverna Server - but I'm not sure of the > details. > > > > 3- is the CWL used somehow to allow for the exchange of workflow > > specifications between workflow systems? > > > In CWL we are discussing how we can use wfprov and some aspects of > tavernaprov. See > > https://github.com/common-workflow-language/common-workflow-language/issu= es/84 > > > We are working on CWL support in Apache Taverna this summer - we might > get three Google Summer Of Code students this year: > > https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+GSOC+2016 > > And I will pick up some work here as well for http://bioexcel.eu/ - my > use case is to use CWL and Docker with Open PHACTS and > Taverna/Galaxy/Knime - with deployment on the EGI grid/cloud: > > http://slides.com/soilandreyes/2016-02-11-bioexcel-use-case-open-phacts > > > > 4-Is there anything that has been done in relation to initiatives such = as > > iPython? > > > I think Alan might know about iPython and Jupyter.. Not sure if > anything was done since this: > > > http://www.taverna.org.uk/2014/05/20/calling-taverna-workflows-from-ipyth= on-notebook/ > > Does the Taverna Player still support iPython in such a way? > > > -- > Stian Soiland-Reyes > Apache Taverna (incubating), Apache Commons RDF (incubating) > http://orcid.org/0000-0001-9842-9718 > --001a114942ccd7b2020530379c7b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks alot Stian,=C2=A0
These are very helpful.
=

best wishes,
khalid

On 11 April 2016 at 17:30, Stia= n Soiland-Reyes <stain@apache.org> wrote:
Hi!

(Folks, Khalid help do lots of work on research object, wfprov and
wfdesc which we use in taverna-language and
taverna-engine/taverna-prov)

On 11 April 2016 at 15:17, Khalid Belhajjame <kbelhajj@googlemail.com> wrote:
> I would like to enquiry about some of the current features of Taverna.= I
> have an answer for most of the question, but I would like to know the = status
> with respect to the current version (2.5) of Taverna. I will be gratef= ul if
> you could take the time to answer them.
>
> 1- In the current version of Taverna (2.5), I can see that the provena= nce
> can be saved as PROV, but not as OPM. I am guessing that OPM export wa= s
> deprecated. Let me know if I am wrong. Regarding the PROV export, you = are
> using TavernaProv isn=E2=80=99t it? If so, do you have TavernaProv doc= umented
> somewhere? I would like to see how it compares to wfprov.


Yes, you are correct in that the OPM export was deprecated in 2.5 - = it
was also less in match with what was happening in the workflow so it
was rather removed.

TavernaProv became part of Taverna from 2.5.=C2=A0 Documentation and exampl= e here:

https://github.com/apache= /incubator-taverna-engine/tree/master/taverna-prov

(It's not yet fully integrated into Taverna 3)


TavernaProv is basically wfprov+prov+taverna - you will see that
everything is stated both with pure prov and in wfprov - which often
provides shortcuts.=C2=A0 For details such as at which iteration something<= br> happened you have to use the tavernaprov aspects - which also adds a
cnt:chars for embedding smaller values, and checksums like
tavernaprov:sha512.


> 2- Are there any utilities/means that help users to either deploy work= flows
> on the cloud or call services/use resource on the cloud? I remember th= e work
> of Sonja with Unicore. Is there any other work that was conducted on t= his
> front?

A bit related - we have a GSOC student working on Docker:

https://issues.apache.org/jira/browse/TAVERNA-879

As for actually managing cloud instances or grid jobs I am not aware
of any current initiatives. Perhaps Dmitry or Vadim Surpin knows of
something?

I think the http://www.vph-dare.eu/ project is using VPH Share and
local Grid infrastructure via Taverna Server - but I'm not sure of the<= br> details.


> 3- is the CWL used somehow to allow for the exchange of workflow
> specifications between workflow systems?


In CWL we are discussing how we can use wfprov and some aspects of tavernaprov. See
https://github.com/com= mon-workflow-language/common-workflow-language/issues/84


We are working on CWL support in Apache Taverna this summer - we might
get three Google Summer Of Code students this year:

https://cwiki.apache.org/con= fluence/display/TAVERNADEV/2016-03+GSOC+2016

And I will pick up some work here as well for http://bioexcel.eu/ - my
use case is to use CWL and Docker with Open PHACTS and
Taverna/Galaxy/Knime - with deployment on the EGI grid/cloud:

http://slides.com/soilandreye= s/2016-02-11-bioexcel-use-case-open-phacts


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


I think Alan might know about iPython and Jupyter..=C2=A0 =C2=A0Not = sure if
anything was done since this:

http://www.tave= rna.org.uk/2014/05/20/calling-taverna-workflows-from-ipython-notebook/<= br>
Does the Taverna Player still support iPython in such a way?


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

--001a114942ccd7b2020530379c7b--