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Carole Goble | 10 Mar 2011 12:24
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Data Privacy Survey of Workflow Users/Builders

Sent on behalf of CMU:

Dear Colleagues,

We are researchers at Carnegie Mellon University who are conducting a 
survey of users who compose web services in their workflows to build 
applications. One of the goals of this survey is to better understand 
the privacy concerns of web service users (or lack thereof), and how 
well users are able to resolve these concerns. Even if you have no data 
privacy and security problems while using web services, we would still 
appreciate your feedback because that would give us a better perspective 
of the problem scenario.

Please take time to fill the following questionnaire:
https://www.surveymonkey.com/s/JT83KJJ

The survey consists of maximum 17 questions and can be completed in 
about 10-15 minutes. There are no correct or incorrect responses. This 
survey is approved by CMU Institutional Review Board (IRB), and would 
follow the appropriate safety protocols set by the IRB (Protocol Number: 
HS11-091). All responses would be treated confidentially and will not be 
traceable to individual respondents.

Thank you in advance for your assistance and time !!

Best Regards,

Vishal Dwivedi
Carnegie Mellon University,
Pittsburgh, USA.
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Olivier Hamon | 10 Mar 2011 15:47

Sharing experience about a myExperiment local installation

Hello everyone,

After spending some time on a myExperiment local installation, I would 
like to share the issues I encountered and the solutions I found to make 
myExperiment work. Some issues may be due to my misunderstanding about 
the instructions, and I guess there are certainly better solutions!

My software specifications are the following (a bit more up-to-date than 
in the instructions):
  * Debian squeeze
  * Apache 2.2.14
  * MySQL Version 14.14, Distribution 5.1.41
  * Java 1.6.0

I have used the instructions from 
http://wiki.myexperiment.org/index.php/Developer:UbuntuInstallation, as 
available on March 10.

Looking at the different instruction steps, here are the actions that I 
have had to add.

  - Before installing all the GEMs required by MyExperiment (gem install 
builder cgi_multipart_eof_fix daemons dsl_accessor fastthread gem_plugin 
hoe json mime-types mongrel mongrel_cluster needle net-sftp net-ssh 
openid_login_generator RedCloth ruby-yadis solr-ruby xml-simple 
libxml-ruby oauth ruby-hmac openurl --include-dependencies), the 
following command was required:

 >> gem update --system
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Olivier Hamon | 10 Mar 2011 17:21

local myExperiment usage

Hello again,

Now that my local myExperiment is installed, I'm trying to use it. And 
there too, some bugs disturbed me. could be my configuration not correct?

First, I got an error message when submitting a new workflow: "undefined 
local variable or method `workflow_types' for 
#<#<Class:0x7f1f8ba7f6a0>:0x7f1f8ba7f650>"

For the time being, I just deleted " + workflow_types" in the 
"app/views/workflows/_main_metadata_form.rhtml" file. And of course, it 
doesn't really please to me...

Second issue with "undefined method `length’ for Enumerable Enumerator 
on text_helper.rb:50:in `truncate’". To correct this, I did what is 
recommended there: 
http://blog.sviluppoweb.eu/2008/11/26/undefined-method-length-for-enumerableenumerator-on-text_helperrb50in-truncate/

Finally, "workflow_context_object" is not recognized in the 
"app/views/workflows/show.rhtml" file. I did not find anything else than 
deleting the line...

Any help would be most of welcome.

Best,
Olivier

--

-- 
---------------------------------------------------------------------------------------------------
Olivier HAMON                          hamon@...
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Jiten Bhagat | 10 Mar 2011 18:08
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Wf inputs and outputs info

Hi,

Is there an easier way of getting information about the inputs and 
outputs of a workflow via the API?

I know I can get the "components" of the workflow and then parse that, 
but this would be different per workflow type.

Also, is the content type info in the API? I couldn't see a way of 
getting the content type for a workflow, apart from "content-type", 
which gives me just the mime type (and not the myExp ContentType resource).

Thanks,
Jits
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Jiten Bhagat | 10 Mar 2011 18:10
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Re: Wf inputs and outputs info

> Also, is the content type info in the API? I couldn't see a way of 
> getting the content type for a workflow, apart from "content-type", 
> which gives me just the mime type (and not the myExp ContentType 
> resource). 

Ignore this. Just found the <type> element. D'oh!

Jits

On 10/03/11 17:08, Jiten Bhagat wrote:
> Hi,
>
> Is there an easier way of getting information about the inputs and 
> outputs of a workflow via the API?
>
> I know I can get the "components" of the workflow and then parse that, 
> but this would be different per workflow type.
>
> Also, is the content type info in the API? I couldn't see a way of 
> getting the content type for a workflow, apart from "content-type", 
> which gives me just the mime type (and not the myExp ContentType 
> resource).
>
> Thanks,
> Jits
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Don Cruickshank | 14 Mar 2011 10:38
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RE: local myExperiment usage

Hi Olivier,

All of those issues actually look like they're caused by the same issue - an error in early start up that's
causing the system to not fully initialise.  It's likely that there's either a missing or incompatible gem.

Would you send me the output from "gem list" please?

Many thanks,
Don.

-----Original Message-----
From:
myexperiment-discuss-bounces+dgc=ecs.soton.ac.uk@...
[mailto:myexperiment-discuss-bounces+dgc=ecs.soton.ac.uk@...]
On Behalf Of Olivier Hamon
Sent: 10 March 2011 16:22
To: myexperiment-discuss@...
Subject: [Myexperiment-discuss] local myExperiment usage

Hello again,

Now that my local myExperiment is installed, I'm trying to use it. And there too, some bugs disturbed me.
could be my configuration not correct?

First, I got an error message when submitting a new workflow: "undefined local variable or method
`workflow_types' for #<#<Class:0x7f1f8ba7f6a0>:0x7f1f8ba7f650>"

For the time being, I just deleted " + workflow_types" in the
"app/views/workflows/_main_metadata_form.rhtml" file. And of course, it doesn't really please to me...
(Continue reading)

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Olivier Hamon | 14 Mar 2011 10:58

Re: local myExperiment usage

Hello Don,

Thanks for your reply.

You'll find below my gem list.

Best,
Olivier

*** LOCAL GEMS ***

abstract (1.0.0)
actionmailer (3.0.5, 1.3.6)
actionpack (3.0.5, 1.13.6)
actionwebservice (1.2.6)
activemodel (3.0.5)
activerecord (3.0.5, 1.15.6)
activeresource (3.0.5)
activesupport (3.0.5, 1.4.4)
addressable (2.2.4, 2.2.2)
arel (2.0.9)
builder (3.0.0, 2.1.2)
bundler (1.0.10)
cgi_multipart_eof_fix (2.5.0)
daemons (1.1.0)
dnsruby (1.51, 1.50)
dsl_accessor (0.4.0)
erubis (2.6.6)
fastthread (1.0.7)
gem_plugin (0.2.3)
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Don Cruickshank | 21 Mar 2011 12:27
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RE: local myExperiment usage

Hi Olivier,

Would you please install the "marc" and the "curb" gems and try again?  Looking at the latest install I have to
hand, they are dependencies of the "openurl" and "oauth" gems and the gem dependency metadata is clearly missing.

I shall add explicit instructions to install these since it's not the first time for either of these gems!

Regards,
Don.

-----Original Message-----
From: Olivier Hamon [mailto:hamon@...] 
Sent: 14 March 2011 09:59
To: Don Cruickshank
Cc: myexperiment-discuss@...
Subject: Re: [Myexperiment-discuss] local myExperiment usage

Hello Don,

Thanks for your reply.

You'll find below my gem list.

Best,
Olivier

*** LOCAL GEMS ***

abstract (1.0.0)
actionmailer (3.0.5, 1.3.6)
(Continue reading)

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Olivier Hamon | 21 Mar 2011 15:18

Re: local myExperiment usage

Hello Don,

Great, it seems to have fixed the issues! Thanks a lot! Notice that I 
had to do first "apt-get install libcurl4-openssl-dev" so as to make the 
gem install work.

BTW, the issue related to the database migration is still there when 
installing the application (see a previous post to this one), but I can 
still install it with the same handling.

Thanks again,
Olivier

On 21/03/2011 12:27, Don Cruickshank wrote:
> Hi Olivier,
>
> Would you please install the "marc" and the "curb" gems and try again?  Looking at the latest install I have
to hand, they are dependencies of the "openurl" and "oauth" gems and the gem dependency metadata is
clearly missing.
>
> I shall add explicit instructions to install these since it's not the first time for either of these gems!
>
> Regards,
> Don.
>
> -----Original Message-----
> From: Olivier Hamon [mailto:hamon@...]
> Sent: 14 March 2011 09:59
> To: Don Cruickshank
> Cc: myexperiment-discuss@...
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Peter Ansell | 22 Mar 2011 03:32
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MyExperiment SPARQL endpoint returns incorrect results

Hi,

The SPARQL endpoint at http://rdf.myexperiment.org/sparql isn't
working properly right now for queries with optional unbound items.

The query below should only return bindings for ?linkedRecordType
?label, ?title, or ?skoslabel when they actually exist.

CONSTRUCT {
?s ?p <http://www.myexperiment.org/workflows/72> .
?s a  ?linkedRecordType .
?s  <http://www.w3.org/2000/01/rdf-schema#label> ?label .
?s  <http://purl.org/dc/elements/1.1/title> ?title .
?s  <http://www.w3.org/2004/02/skos/core#prefLabel> ?skoslabel .
} WHERE {
?s ?p <http://www.myexperiment.org/workflows/72> .
OPTIONAL { ?s a ?linkedRecordType . }
OPTIONAL { ?s  <http://www.w3.org/2000/01/rdf-schema#label> ?label . }
OPTIONAL { ?s <http://purl.org/dc/elements/1.1/title> ?title . }
OPTIONAL { ?s <http://www.w3.org/2004/02/skos/core#prefLabel> ?skoslabel . }
} LIMIT 500 OFFSET 0

Right now the Garlik 4Store SPARQL engine is returning bindings that
don't actually exist as blank nodes with an rdf:nodeID="LL". This is
worse than it seems as it is inconsistent. It implies that all of the
resources that will be bound to ?s have labels/titles/prefLabel's, and
that they all point to the same blank node, although there is no other
information available about the blank node they reference.

You may want to try upgrading to the latest version of 4Store as you
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