Cannot install RightField

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Cartik Saravana

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Aug 1, 2017, 11:03:58 AM8/1/17
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Hello

I have been trying to install RightField on my MacBook. I downloaded the "rightfield-0.23.tar.gz" package from the "http://www.rightfield.org.uk/download" page. When I unzip this, I cannot find the "RightField icon" to install the software. What am I doing wrong here?

Regards

Cartik


ranis...@gmail.com

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Sep 16, 2017, 2:42:23 AM9/16/17
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Hi All,

Same here on Linux machine I tried the same and could not install.
Downloaded from here
https://bitbucket.org/fairdom/rightfield/downloads/rightfield-0.23.tar.gz

I had tried to install using sh file but no luck

>chmod +x rightfield.sh
>./rightfield.sh bash: ./rightfield.sh: /bin/sh^M: bad interpreter: No such file or directory >sudo ./rightfield.sh sudo: unable to execute ./rightfield.sh: No such file or directory Hangup >sudo bash rightfield.sh rightfield.sh: line 2: $'\r': command not found

list of file after untar ...
4.0K Sep  7 14:29 lib
1.6K Apr 12 15:36 LICENSE
145 May  4 17:38 rightfield.bat
658K May  4 18:03 rightfield-bin.jar
-rwxr-xr-x   268 Apr  7 16:28 rightfield.sh
rightfield.sh has execute permission

Stuart Owen

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Sep 18, 2017, 5:41:30 AM9/18/17
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Hi,

I'm currently looking into this and should hopefully have a fixed version soon.

regards,

Stuart.

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Stuart Owen

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Sep 18, 2017, 6:33:27 AM9/18/17
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Hi,

I've uploaded a new 0.23.1 version that should fix the problem you were having. There was a problem with the jar file that was including in the linux version and it needed rebuilding. The new linux version is now at https://bitbucket.org/fairdom/rightfield/downloads/rightfield-0.23.1.tar.gz and includes an executable rightfield.sh. You should be able to run this with just

./rightfield.sh

or

sh ./rightfield.sh

Apologies for the problem you were having.

Stuart.

ranis...@gmail.com

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Sep 25, 2017, 7:12:36 AM9/25/17
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Hi Stuart,
Thank you for the package update, I installed on to the linux machine and it did installed. But when I tried to open url from Bioportal (File-> open url from Bioportal) I get this error "An Unexpected SocketTimeoutException error occurred: connect timed out"
details of error
"These are technical details that can be sent to the RightField developers to help diagnose an unexpected problem

The version of RightField is: 0.23.1

java.net.SocketTimeoutException: connect timed out
"
But when I tried accessing https://bioportal.bioontology.org/ website, I noticed that its down

I tried to open ontology (File-> open onotology from a URL) and I tried this URL <http://amigo.geneontology.org/amigo/term/GO:0020015> again the same error.

There was a network related error trying to open the ontology for http://amigo.geneontology.org/amigo/term/GO:0020015, the resource you are trying to connect to may not be available or accessible

1.Is it  that I should set something in my system which is causing this problem?
2. Should I try installing in Windows system?
3. should I try some other URL?
4. Or its something with RightField itself?

Let me know what should I do.

Thank you

ranis...@gmail.com

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Sep 25, 2017, 7:39:27 AM9/25/17
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Stuart Owen

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Sep 26, 2017, 6:33:30 AM9/26/17
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Hi,

I've tried this out myself, and had no problem connecting to bioportal. The url https://bioportal.bioontology.org/ works fine, as does their API. Is it possible there was simply a problem with Bioportal or you network at the time? Are you able to contact https://bioportal.bioontology.org/ now?

Regarding opening an Ontology with a URL, the URL needs to point to an ontology file, usually OWL - for example: http://www.mygrid.org.uk/ontology/JERMOntology

regards,

Stuart

ranis...@gmail.com

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Sep 26, 2017, 2:32:19 PM9/26/17
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Hi Stuart,
Thank you for the reply,
At the time when I wrote a email, the bioportal url was down, so I was unsure if the problem is because  of the bioportal or rightfiled, but even after bioportal revived it still persisted with problem.

But now its working, I am not sure if its something to do with our institute network, as of now I am able to connect to bioportal and http://www.mygrid.org.uk/ontology/JERMOntology from the rightfield from my home connection.

Once again thank you, as this will helped us to start going.
regards
rani
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