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 3EDED18E5C for ; Mon, 6 Jul 2015 17:20:36 +0000 (UTC) Received: (qmail 65294 invoked by uid 500); 6 Jul 2015 17:20:36 -0000 Delivered-To: apmail-taverna-users-archive@taverna.apache.org Received: (qmail 65258 invoked by uid 500); 6 Jul 2015 17:20:36 -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 65248 invoked by uid 99); 6 Jul 2015 17:20:36 -0000 Received: from Unknown (HELO spamd2-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 06 Jul 2015 17:20:36 +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 A708E1A6825 for ; Mon, 6 Jul 2015 17:20:35 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd2-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: 0.991 X-Spam-Level: X-Spam-Status: No, score=0.991 tagged_above=-999 required=6.31 tests=[KAM_LAZY_DOMAIN_SECURITY=1, T_RP_MATCHES_RCVD=-0.01, URIBL_BLOCKED=0.001] autolearn=disabled Received: from mx1-us-east.apache.org ([10.40.0.8]) by localhost (spamd2-us-west.apache.org [10.40.0.9]) (amavisd-new, port 10024) with ESMTP id SEWYMoMOTqUI for ; Mon, 6 Jul 2015 17:20:20 +0000 (UTC) Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by mx1-us-east.apache.org (ASF Mail Server at mx1-us-east.apache.org) with SMTP id 699B9428CC for ; Mon, 6 Jul 2015 17:20:20 +0000 (UTC) Received: (qmail 65142 invoked by uid 99); 6 Jul 2015 17:20:19 -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, 06 Jul 2015 17:20:19 +0000 Received: from mail-wi0-f174.google.com (mail-wi0-f174.google.com [209.85.212.174]) by mail-relay.apache.org (ASF Mail Server at mail-relay.apache.org) with ESMTPSA id 6E4E61A0347 for ; Mon, 6 Jul 2015 17:20:19 +0000 (UTC) Received: by wifm2 with SMTP id m2so36290404wif.1 for ; Mon, 06 Jul 2015 10:20:17 -0700 (PDT) X-Gm-Message-State: ALoCoQnELIjOgoBncU8iS+XSmZH9vTr74nVAFTRklN6yJXOxUP9Gcna7Gnq44or4rRn5E1Rucxoj X-Received: by 10.194.77.211 with SMTP id u19mr90799279wjw.19.1436203217876; Mon, 06 Jul 2015 10:20:17 -0700 (PDT) MIME-Version: 1.0 Received: by 10.28.101.5 with HTTP; Mon, 6 Jul 2015 10:19:58 -0700 (PDT) X-Originating-IP: [84.92.48.26] In-Reply-To: <55957475.5050608@manchester.ac.uk> References: <55957475.5050608@manchester.ac.uk> From: Stian Soiland-Reyes Date: Mon, 6 Jul 2015 18:19:58 +0100 Message-ID: Subject: Re: Taverna player usage To: Finn Bacall Cc: users@taverna.incubator.apache.org Content-Type: text/plain; charset=UTF-8 (Forwarding to list on behalf of Finn) On 2 July 2015 at 18:27, Finn Bacall wrote: > Hi all, > > It seems this issue is caused by a missing dependency: "ghostscript" > > Installing this via apt-get, or using the latest docker image (when it has > finished building [1]) should fix this issue. > > Cheers, > > Finn > > [1] > https://registry.hub.docker.com/u/fbacall/taverna-player-portal/builds_history/226759/ > > > > On 02/07/2015 17:18, Stian Soiland-Reyes wrote: >> >> Thanks for describing what you did to start the Taverna Player. I have >> copied Finn Bacall who has been maintaining it. >> >> Just to have a try, you could also use these two Docker images: >> >> >> docker run --name taverna -p 8080:8080 -d stain/taverna-server >> docker run --name taverna-portal --link taverna:taverna -p 3000:3000 >> -d fbacall/taverna-player-portal >> >> That will start up this portal on http://localhost:3000/ - linked to >> http://localhost:8080/ >> >> ... however it gives the same NotIdentifiedByImageMagickError. >> >> In the log I get: >> >> I, [2015-07-02T16:07:50.952952 #1] INFO -- : Command :: file -b >> --mime '/tmp/image_35283445860253326820150702-1-go20s8' >> I, [2015-07-02T16:07:50.965587 #1] INFO -- : Command :: identify >> -format '%wx%h,%[exif:orientation]' >> '/tmp/2c3f3120c2ed474472b4efe085057bd820150702-1-1quss2a[0]' >> 2>/dev/null >> I, [2015-07-02T16:07:51.036714 #1] INFO -- : [paperclip] An error was >> received while processing: >> #> Paperclip::Errors::NotIdentifiedByImageMagickError> >> I, [2015-07-02T16:07:51.036971 #1] INFO -- : Command :: identify >> -format '%wx%h,%[exif:orientation]' >> '/tmp/2c3f3120c2ed474472b4efe085057bd820150702-1-1quss2a[0]' >> 2>/dev/null >> I, [2015-07-02T16:07:51.094239 #1] INFO -- : [paperclip] An error was >> received while processing: >> #> Paperclip::Errors::NotIdentifiedByImageMagickError> >> >> >> yet identify works in the shell: >> >> >> root@da925ce1ee9b:/taverna-player-portal/log# identify -format >> '%wx%h,%[exif:orientation]' >> '/tmp/2c3f3120c2ed474472b4efe085057bd820150702-1-1quss2a[0]' >> 2>/dev/null ; echo >> 1890x301, >> >> >> 2c3f3120c2ed474472b4efe085057bd820150702 is a dot file of the t2flow. >> >> >> >> Any idea, Finn? >> >> On 2 July 2015 at 14:27, divzee Chandrashakher >> wrote: >>> >>> Hi Denis, >>> >>> Thank you for your step-wise instructions. I installed ruby 2.1.6 and >>> followed the steps. But still I couldn't succeed (see below from A to F). >>> I >>> am thinking of writing simple web page that uses restful api of taverna >>> server to execute workflows. Its a pity that there is no easy/simple >>> guide >>> for taverna beginners to install server and portal. I believe this might >>> slow down user's adoption of taverna. >>> >>> A. "rake setup" did not work. >>> [admin@localhost taverna-player-portal-master]$ rake setup >>> rake aborted! >>> Don't know how to build task 'setup' >>> >>> (See full trace by running task with --trace) >>> >>> B. So I simply invoked "rake". But it threw error which is something to >>> do >>> with paperclip (Diagram >>> Paperclip::Errors::NotIdentifiedByImageMagickError) >>> [admin@localhost taverna-player-portal-master]$ rake >>> [Coveralls] Set up the SimpleCov formatter. >>> [Coveralls] Using SimpleCov's 'rails' settings. >>> DEPRECATION WARNING: superclass_delegating_accessor is deprecated and >>> will >>> be removed from Rails 5.0 (use class_attribute instead). (called from >>> >> (required)> at >>> >>> /home/admin/01_Installations/taverna-player-portal-master/test/performance/authorization_test.rb:4) >>> Run options: --seed 3155 >>> >>> # Running: >>> >>> ....EEE.EEEEEEEEE.EEEEE.EFEEEEEEEEFEE... >>> >>> Finished in 4.373955s, 9.1450 runs/s, 3.8866 assertions/s. >>> >>> 1) Error: >>> TavernaPlayer::RunsControllerTest#test_should_get_edit_form_if_admin: >>> ActiveRecord::RecordInvalid: Validation failed: Diagram >>> Paperclip::Errors::NotIdentifiedByImageMagickError, Diagram >>> Paperclip::Errors::NotIdentifiedByImageMagickError >>> test/controllers/taverna_player/runs_controller_test.rb:43:in `block >>> in >>> ' >>> >>> (output cut) >>> >>> 30) Error: >>> WorkflowsTest#test_filters_out_non-visible_workflows: >>> ActiveRecord::RecordInvalid: Validation failed: Diagram >>> Paperclip::Errors::NotIdentifiedByImageMagickError, Diagram >>> Paperclip::Errors::NotIdentifiedByImageMagickError >>> test/models/workflows_test.rb:22:in `block in ' >>> >>> 40 runs, 17 assertions, 2 failures, 28 errors, 0 skips >>> [Coveralls] Outside the CI environment, not sending data. >>> [admin@localhost taverna-player-portal-master]$ >>> >>> >>> C. accessing portal via http://localhost:3000 asked me to run the >>> following >>> command. so I executed it >>> [admin@localhost taverna-player-portal-master]$ bin/rake db:migrate >>> RAILS_ENV=development >>> >>> D. Started server again >>> [admin@localhost taverna-player-portal-master]$ bin/rails s >>> => Booting WEBrick >>> => Rails 4.2.1 application starting in development on >>> http://localhost:3000 >>> => Run `rails server -h` for more startup options >>> => Ctrl-C to shutdown server >>> [2015-07-01 23:26:46] INFO WEBrick 1.3.1 >>> [2015-07-01 23:26:46] INFO ruby 2.1.6 (2015-04-13) [x86_64-linux] >>> [2015-07-01 23:26:46] INFO WEBrick::HTTPServer#start: pid=12947 >>> port=3000 >>> >>> E. from another console started job worker >>> [admin@localhost taverna-player-portal-master]$ bin/rake jobs:work >>> [Worker(host:localhost.localdomain pid:13058)] Starting job worker >>> >>> F. I could see the portal home page. Registered and logged in to upload >>> taverna workflow. But this step failed with the following error >>> >>> 2 errors prohibited this workflow from being saved: >>> >>> Diagram Paperclip::Errors::NotIdentifiedByImageMagickError >>> Diagram Paperclip::Errors::NotIdentifiedByImageMagickError >>> >>> Thanks >>> Rakesh >>> >>> On Sun, Jun 28, 2015 at 11:42 AM, Denis Karyakin >>> wrote: >>>> >>>> Hello, >>>> Taverna-player - only middleware for run workflows in Taverna Server. I >>>> am >>>> not so long ago work with taverna, so more experienced members can >>>> correct >>>> me. >>>> >>>> For run workflows you can use taverna-player-portal. For get this >>>> application go to https://github.com/myGrid/taverna-player-portal and >>>> download zip archive or clone git repository. >>>> You should have installed ruby 2.1.6 version. >>>> >>>> Copy file >>>> `taverna-player-portal/config/initializers/taverna_server.rb.example` to >>>> `taverna-player-portal/config/initializers/taverna_server.rb` and modify >>>> server_address to your server url. >>>> >>>> After this go to folder taverna-player-portal and run following >>>> commands: >>>> rake setup - for install dependencies and create database >>>> rails s - for start rails server with UI >>>> rake jobs:work - for start queues server, that will be control run >>>> workflow in Taverna Server. >>>> >>>> Now you can go to url localhost:3000 for upload and run workflows >>>> >>>> >>>> 2015-06-28 1:23 GMT+03:00 divzee Chandrashakher : >>>>> >>>>> Hi, >>>>> >>>>> I am newbie to Taverna. I could install Taverna Server (v 2.5.4) and >>>>> Taverna player (v 0.11.0) in CentOS Virtual machine. For player >>>>> installation, I followed the tutorial at >>>>> >>>>> http://mygrid.github.io/taverna-player/0.11.0/ >>>>> >>>>> 1. In the above link, under "Essential (required) configuration", I am >>>>> not able to understand the following snippet to be included in >>>>> taverna_player.rb >>>>> >>>>> config.workflow_model_proxy("Workflow") do |proxy| >>>>> proxy.file_method_name = :file_name >>>>> end >>>>> >>>>> Shall i simply copy the above lines to taverna_player.rb file? I don't >>>>> know ruby much. >>>>> >>>>> 2. I am using the 'dummy' rails application that is available within >>>>> the >>>>> taverna_player gem installtion folder to test the server & player >>>>> installation. I configured the taverna_server.rb to point to my server >>>>> installation. >>>>> >>>>> Server >>>>> http://localhost:8080/ts254/ >>>>> --- works fine. prints the taverna help page >>>>> >>>>> Player (started the rails server) >>>>> http://localhost:3000/ >>>>> >>>>> The above url displays the following error: >>>>> Couldn't find TavernaPlayer::Workflow with id=3 >>>>> >>>>> I'm have no clue how id gets the value 3. I am not able to understand >>>>> where the workflows are stored and how the taverna player can request >>>>> the >>>>> server to execute a particular workflow from the pool of workflows. >>>>> Please >>>>> help me. >>>>> >>>>> Thanks in advance >>>>> Rakesh >>>>> >>>>> >>>>> >>> >>> >>> -- >>> Divya C >>> www.dealbitte.com >>> Ideas for smart shopping >> >> >> > -- Stian Soiland-Reyes Apache Taverna (incubating), Apache Commons RDF (incubating) http://orcid.org/0000-0001-9842-9718