Return-Path: X-Original-To: archive-asf-public-internal@cust-asf2.ponee.io Delivered-To: archive-asf-public-internal@cust-asf2.ponee.io Received: from cust-asf.ponee.io (cust-asf.ponee.io [163.172.22.183]) by cust-asf2.ponee.io (Postfix) with ESMTP id BE76A200ACC for ; Mon, 2 May 2016 19:37:37 +0200 (CEST) Received: by cust-asf.ponee.io (Postfix) id BCDF81609B0; Mon, 2 May 2016 19:37:37 +0200 (CEST) Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by cust-asf.ponee.io (Postfix) with SMTP id B63991609A6 for ; Mon, 2 May 2016 19:37:36 +0200 (CEST) Received: (qmail 76182 invoked by uid 500); 2 May 2016 17:37:36 -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 76173 invoked by uid 99); 2 May 2016 17:37:35 -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, 02 May 2016 17:37:35 +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 7790D1A0776 for ; Mon, 2 May 2016 17:37:35 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd2-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: -2.02 X-Spam-Level: X-Spam-Status: No, score=-2.02 tagged_above=-999 required=6.31 tests=[HTML_MESSAGE=2, KAM_LAZY_DOMAIN_SECURITY=1, RCVD_IN_DNSWL_HI=-5, RCVD_IN_MSPIKE_H3=-0.01, RCVD_IN_MSPIKE_WL=-0.01, RP_MATCHES_RCVD=-0.001, WEIRD_PORT=0.001] autolearn=disabled Received: from mx1-lw-eu.apache.org ([10.40.0.8]) by localhost (spamd2-us-west.apache.org [10.40.0.9]) (amavisd-new, port 10024) with ESMTP id QMuLlsiWhVvk for ; Mon, 2 May 2016 17:37:32 +0000 (UTC) Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by mx1-lw-eu.apache.org (ASF Mail Server at mx1-lw-eu.apache.org) with SMTP id B69345F19A for ; Mon, 2 May 2016 17:37:30 +0000 (UTC) Received: (qmail 75771 invoked by uid 99); 2 May 2016 17:37:29 -0000 Received: from mail-relay.apache.org (HELO mail-relay.apache.org) (140.211.11.15) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 02 May 2016 17:37:29 +0000 Received: from mail-wm0-f46.google.com (mail-wm0-f46.google.com [74.125.82.46]) by mail-relay.apache.org (ASF Mail Server at mail-relay.apache.org) with ESMTPSA id 555A71A0046 for ; Mon, 2 May 2016 17:37:29 +0000 (UTC) Received: by mail-wm0-f46.google.com with SMTP id a17so154367241wme.0 for ; Mon, 02 May 2016 10:37:29 -0700 (PDT) X-Gm-Message-State: AOPr4FX2rHsX7bUNmCsHcqtVI7frg81NV+H8sAwFXyp2c4xV/Yga62XqPLNQPuK7sGOhHhcTSfUMPi90kHmEDQ== MIME-Version: 1.0 X-Received: by 10.28.17.211 with SMTP id 202mr19354071wmr.11.1462210648093; Mon, 02 May 2016 10:37:28 -0700 (PDT) Received: by 10.28.15.68 with HTTP; Mon, 2 May 2016 10:37:28 -0700 (PDT) X-Originating-IP: [84.92.48.26] Received: by 10.28.15.68 with HTTP; Mon, 2 May 2016 10:37:28 -0700 (PDT) In-Reply-To: References: Date: Mon, 2 May 2016 18:37:28 +0100 X-Gmail-Original-Message-ID: Message-ID: Subject: Re: Fwd: Taverna Server REST api provide input files From: Stian Soiland-Reyes To: users@taverna.incubator.apache.org Content-Type: multipart/alternative; boundary=001a1145b6ae444f5b0531df7236 archived-at: Mon, 02 May 2016 17:37:37 -0000 --001a1145b6ae444f5b0531df7236 Content-Type: text/plain; charset=UTF-8 This was also discussed on dev@taverna - we found it was a bug in the executeworkflow command line. > Tracked as https :// issues.apache.org / jira /browse/TAVERNA-964 It should not be too complicated to fix - perhaps you want to have a go on a pull request? :-) On 29 Apr 2016 11:26 a.m., "Daniele Tartarini" wrote: > Hi, > > I am using a Taverna server 2.5.4 to run a workflow based on Taverna tools > service. > > I can run execution correctly following the REST API here: > http://dev.mygrid.org.uk/wiki/display/tav250/Conceptual+Interface > > The workflow I'm using is very simple and takes a single input file. > > I noted that when I upload to Taverna server input file using: > POST to > https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/wd/IN > > and then associating the port to the file using: > > PUT to > https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/input/input/input_file_text > with data > > IN/myfile.txt > > execution is correct but input files are hard copied from the > /tmp/42d06756-b9c4-45ef-b69d-a141c69499be > to the Taverna Tool service working folder 'usecase....dir' > > I would like to avoid this copy because I would be dealing to substantial > inputs and on a parameter sweep can affect performance. > > In Taverna Workbench this issue is solved in a elegant way using the "Set > File Location" tab in the form input window. Files are not copied but > replaced by symbolic links. > > *How can I achieve the same result via Taverna server API or a baclava > file (I noted the Set file location information is not saved inside the > baclava)?* > > I tried to use the Taverna server API setting the input as reference as > documented in: > http://dev.mygrid.org.uk/wiki/display/tav250/Conceptual+Interface > section: "Using a File Already on the Taverna Server Installation" > > Using: > PUT > https://myserver.ac.uk:8444/taverna-server/rest/runs/88f79b84-6451-4aed-b151-6b051328d922 > /input/input/input_file_text > > with data ({'content-type': 'application/xml'}): > > > > > https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/ > wd/IN/myfile.txt > > > > > I get the following 403 error: filename may not be absolute > > *Any Idea how to solve both issues?* > > Many thanks in advance. > > Cheers > > Daniele > > > -- > -- > Daniele Tartarini > > Post-Doctoral Research Associate > Dept. Mechanical Engineering & > INSIGNEO, institute for *in silico* medicine, > University of Sheffield, Sheffield, UK > linkedIn > > > > > -- > -- > Daniele Tartarini > > Post-Doctoral Research Associate > Dept. Mechanical Engineering & > INSIGNEO, institute for *in silico* medicine, > University of Sheffield, Sheffield, UK > linkedIn > > --001a1145b6ae444f5b0531df7236 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

This was also discussed on dev@taverna - we found it was a b= ug in the executeworkflow command line.

> Tracked as=C2=A0https://issues.apache.org/jira/browse/TAVERNA-964

It should not be too complicated to fix - perhaps you want t= o have a go on a pull request? :-)

On 29 Apr 2016 11:26 a.m., "Daniele Tartari= ni" <d.tartarini@she= ffield.ac.uk> wrote:
Hi,

I am using a Taverna server 2.5.4 to run a workflow based on Tave= rna tools service.

I can run execution correctly following the REST = API here:
http://dev.mygrid.org.uk/wiki/display/tav= 250/Conceptual+Interface

The workflow I&= #39;m using is very simple and takes a single input file.

I n= oted that when I upload to Taverna server input file using:
POST =C2=A0to https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-4= 5ef-b69d-a141c69499be/wd/IN

and then associating the port= to the file using:

PUT to https://myse= rver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/in= put/input/input_file_text
with data
<t2sr:runInput xmlns:t2sr=3D"http://ns.taverna.org= .uk/2010/xml/server/rest/"> <t2sr:file>IN/myfile.txt</= t2sr:file> </t2sr:runInput>

execution is correct but input files are hard copied from the=C2= =A0/tmp/42d06756-b9c4-45ef-b69d-= a141c69499be
to the Taverna Tool service working folder=C2= =A0'usecase....dir'

I would like to avoid = this copy because I would be dealing to substantial inputs and on a paramet= er sweep can affect performance.

In Taverna Workbench this issue is solved in a elegant way usi= ng the "Set File Location" tab in the form input window. Files ar= e not copied but replaced by symbolic links.

How can I ach= ieve the same result via Taverna server API or a baclava file (I noted the = Set file location information is not saved inside the baclava)?<= /div>

I tried to use the Taverna server API setting the input as reference a= s documented =C2=A0in:
http://dev.mygrid.org.uk/wiki/display/tav250/Conceptual+Interface = section: "Using a File Already on the Taverna Server Installation"= ;

Using:
PUT https://myserver.ac.uk:8444/taverna-s= erver/rest/runs/88f79b84-6451-4aed-b151-6b051328d922 /input/input/input= _file_text

with data ({'= content-type': <= /span>'application/xml&= #39;}):

<t2sr:runInput xmlns:t2sr=3D"http://ns.taverna.org.uk/2010/xml= /server/rest/">
=C2=A0 =C2=A0 <t2sr:reference>
=C2= =A0 =C2=A0 =C2=A0 =C2=A0=C2=A0https://myserver.ac.uk/t= averna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/wd/IN/myfile.txt
=C2=A0 =C2=A0 </t2s= r:reference>
</t2sr:runInput>


I get the following 403 error:=C2=A0filen= ame may not be absolute

Any Idea how to solve both issues?

Many thanks in advance.

Che= ers

Daniele


--=C2=A0
--
Daniele Tartarini
Post-Doctoral Research Associate=
Dept. Mechanical Engineering &= ;
INSIGNEO, institute for in si= lico medicine,
University of S= heffield, Sheffield, UK



--
--
Daniele Tartarini

Post-Doctoral Research Ass= ociate
Dept. Mechanical Engineerin= g &
INSIGNEO, institute for in silico medicine,
Universit= y of Sheffield, Sheffield, UK
--001a1145b6ae444f5b0531df7236--