David R Newman | 17 Nov 03:57 2014
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Re: Unauthorized when open workFlow API

Hi Jin,

 

You will only be able to use this method to download workflows if they are public or your user account is permitted to access them.  You can programmatically get a list of public workflows either by using the SPARQL query interface at http://rdf.myexperiment.org/sparql or requesting pages of workflow listings as follows:

 

http://www.myexperiment.org/workflows.xml?num=100

http://www.myexperiment.org/workflows.xml?num=100&page=2

http://www.myexperiment.org/workflows.xml?num=100&page=3

 

You can only request 100 at a time so you will have to increment the page number until you don’t get any more workflows back, if you want to make sure you have got every public workflow.

 

Regards


David Newman

 

 

From: myexperiment-discuss-bounces+drn=ecs.soton.ac.uk-qX2TKyscuCcdnm+yROfE0A@public.gmane.org [mailto:myexperiment-discuss-bounces+drn=ecs.soton.ac.uk-qX2TKyscuCcdnm+yROfE0A@public.gmane.org] On Behalf Of Jin Xi
Sent: 16 November 2014 23:53
To: myexperiment-discuss-qX2TKyscuCcdnm+yROfE0A@public.gmane.org
Cc: Jia Zhang; Jian Jiao; Qiwen Guo; wtan-r/Jw6+rmf7HQT0dZR+AlfA@public.gmane.org; Yu Gu; Ming Qi
Subject: [Myexperiment-discuss] Unauthorized when open workFlow API

 

Hi, officer, 

 

My name is Jin and I am from a team in professor Jia's Service Oriented Computing course in Carnegie Mellon University. We are doing a course project and want to use myExperiment's workFlows to be our data sets. however, when we tried to download workFlows using URl like http://www.myexperiment.org/workflow.xml?id=372. The web page sent the message that we were unauthorized. We tried to log in as the general user in myExperiment, but failed.

 

Is it possible that you can help us to solve the problem of authorization? we could speed up by building upon your workflows. Many thanks. 

 

Best regards,

Jin

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Jin Xi | 17 Nov 00:52 2014
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Unauthorized when open workFlow API

Hi, officer, 

My name is Jin and I am from a team in professor Jia's Service Oriented Computing course in Carnegie Mellon University. We are doing a course project and want to use myExperiment's workFlows to be our data sets. however, when we tried to download workFlows using URl like http://www.myexperiment.org/workflow.xml?id=372. The web page sent the message that we were unauthorized. We tried to log in as the general user in myExperiment, but failed.

Is it possible that you can help us to solve the problem of authorization? we could speed up by building upon your workflows. Many thanks. 

Best regards,
Jin
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Alan R Williams | 7 May 13:57 2013
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Changes to REST API for components

Hello everybody,

At the moment, components (and component profiles, families and 
versions) are implemented in myExperiment as packs, files, workflows and 
versions of them. When the REST API is used to talk to myExperiment, the 
components can only be dealt with as their myExperiment implementation.

This makes it hard for clients to talk to myExperiment about components. 
At the moment, the Java code in Taverna for talking to myExperiment is 
"hairy" and complicated. There is a need for Ruby applications to also 
be able to talk to myExperiment about components.

It would greatly help the BioVeL and SCAPE projects if the REST API 
dealt in components. There would then by one place for the mapping to 
the underlying implementation i.e. myExperiment side. This would allow 
later changes to the myExperiment implementation without the rewriting 
of the Ruby and Java Gems/packages.

What further information do the myExperiment development team need about 
the requirements?

Alan
Gmail | 10 Dec 21:56 2012
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Request for the provenance data from scientific workflow executions

Hi,

My name is Chalalai Chaihirunkarn, a Ph.D. student in the School of Computer Science at Carnegie Mellon University. I'm currently working on research that aims to enhance the usability of scientific software under the advisement of Professor James D. Herbsleb. 

We are interested in software co-occurrence inside scientific environments leveraged by scientific communities. We expect to identify the softwares that are used in collaboration and plan to suggest improvements of software tools present in such environments.

MyExperiment would be an effective environment for our studies. We have found that data source information, process definitions, dependencies among processes, and process execution periods, from the provenance of scientific workflows generated by Taverna, could massively benefit our research. 

We would like to request assistance from anyone who could send us provenance data from workflow executions, or could suggest how to access those data. The data could be in any format such as XML files, spreadsheets, or database scripts. The data would remain private and used only for research purposes. 

If you have any questions regarding our research and the use of the provenance data, please feel free to contact me at chalalai-AD0acThlWL4@public.gmane.orgu.

We would really appreciate your interest and participation. 


Thank you,

Chalalai Chaihirunkarn
PhD. student in Computation, Organizations, and Society
School of Computer Science, Carnegie Mellon University
500 Forbes Ave. Pittsburgh, PA, 15213. USA

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Alan R Williams | 7 Nov 09:52 2012
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Profiles for how to share

Hello everybody,

I have requested before that there is the ability for a group 
administrator to set up profiles for how objects should be shared 
(including which layout to use). Having to do everything by hand has 
just caused problems for the BioVeL project. Can this be increased in 
priority?

Alan
Alan R Williams | 2 Nov 17:43 2012
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Doodle poll for meeting to discuss contextualization of menus

Hello everybody,

The top-level menus on myExperiment do not do what many users expect. 
For example, when visiting a Group page, users think that the Workflows 
tab will then show the Workflows _for that group_. However, it currently 
shows all the workflows on myExperiment and the group's workflows are 
under the Shared Items tab of the groups' page mixed up with the group's 
other items.

It is proposed to

(1) hold a one hour skype call to discuss what functionality users want (*)

(2) allow a gap of several days for myExperiment coders to eliminate 
some suggestions as impossible

(3) a second one hour skype call to agree on a solution to be implemented

I have created a Doodle poll for the first one hour call. We hope to 
have it sometime in the next two weeks.

The poll is at http://doodle.com/zreqhbs26k74s5f4

If you cannot make the skype call but have suggestions then please 
e-mail me or myexperiment-discuss@...  Also, if you are
satisfied 
with the current functionality and do not want it changed, please e-mail 
or join the call.

Thanks in advance,

Alan

(*) Because it is only a one hour call, discussion should be focused on 
this topic and should be limited to what users want, not how coders 
can/cannot achieve it.
Mark Thompson | 20 Sep 12:48 2012
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change or bug in the read-workflow rest API?

Hi,

I'm maintaining an application (t2-web) that depends on the
MyExperiment REST-API. It was working fine until recently. In the XML
output of "read workflow" it looks for an element <components> should
contain information about the inputs and outputs of a workflow as
<source> and <sink> elements.

However, if I look at the output of:
  http://www.myexperiment.org/workflow.xml?id=74&all_elements=yes
then the <components> element is empty. Actually, I tried a few
different Taverna workflows, and <components> is always empty.

Is this a bug in the rest-api XML output, or has the API changed recently?

Regards,
Mark Thompson
Alan R Williams | 12 Sep 16:06 2012
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Social side of myExperiment

Hello everybody,

In BioVeL we are developing workflows in several related biovdiversity 
domains. The BioVeL workflows are being kept on myExperiment.

Some of the domains have related resources such as facebook groups and 
youtube videos. So, the workflow is part of a dynamic social world. I 
was wondering if there is a presentation or roadmap about how it is 
intended for myExperiment to deal with this (assuming it is).

Alan
Danius Michaelides | 12 Sep 12:25 2012
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myExperiment down

Hi,

Regrettably myExperiment went down earlier today and we are working on
resolving the problem and bringing the service back online. Please except
our apologies.

Regards,
Danius
--
myExperiment team
Julien Wollbrett | 10 Sep 11:46 2012
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problem to update a workflow

Hello,

I have a problem to update a workflow named : Oryza Sativa QTLs and genes retrieval from TropGene, Gramene and Ensembl
I try to "upload new version" but  I have a problem with main metadata.
When I try to infer metadata I have this message :
we are sorry but something went wrong

And when I enter custom metadata I have this message :
There were problems with the following fields:
  • Title can't be blank

even if my title is not blank.

Julien Wollbrett

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Katy Wolstencroft | 28 Aug 11:41 2012
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problems with myExperiment

Hi all,

I'm having trouble logging into myExperiment today and performing 
searches. I just get the "We're sorry, but something went wrong" message.

Cheers,

Katy

--

-- 
Dr. Katy Wolstencroft
Research Fellow
School of Computer Science
1.17 Kilburn Building
University of Manchester
Manchester
M13 9PL

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