In v2.8.1, if it's installed, then the core BioPAX plugin does not work
(File->Import->Network (Multiple...) fails), but you can open a BioPAX file
via Plugins->BiNoM I/O menu; when this plugin is removed, the core BioPAX
works again
(Paxtools parser conflicts with this plugin for some reason...)

IR.

Igor,

I've tried to load a BioPAX 3 file with cytoscape 2.8.2, without the BiNoM
plugin installed, and it fails with an error message like this:

 cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed:
org.biopax.paxtools.util.BioPaxIOException: XMLStreamException ParseError
at [row,col]:[11929,70]
Message: Invalid byte 2 of 2-byte UTF-8 sequence.; Line number = 11929
Column number = 70
System Id = null
Public Id = null
Location Uri= null
CharacterOffset = 920909

When the BiNoM plugin is loaded, it also fails to a BioPAX 3 file.

Not sure why and where there would be a conflict...

Eric
Le jeudi 3 mai 2012 22:51:57 UTC+2, IgorRodchenkov a écrit :

I'm the current maintainer of the BiNoM plugin.

I tried with Cytoscape 2.8.2 to import a BioPAX3 file, without the
BiNoM plugin installed,  but it fails with the error:

cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed:
org.biopax.paxtools.util.BioPaxIOException: XMLStreamException
ParseError at [row,col]:[11929,70] Message: Invalid byte 2 of 2-byte
UTF-8 sequence.; Line number = 11929 Column number = 70 System Id =
null Public Id = null Location Uri= null CharacterOffset = 920909

It also fails when the BiNoM plugin is loaded, with a different error
message though.

Eric

On 3 mai, 22:51, IgorRodchenkov <rod...@gmail.com> wrote:

Hi Eric,

This is a different issue; - can be another bug, wrong file, or char
encoding problem (must be "UTF-8", and if it's not your system default,
try setting the Java option: -Dfile.encoding=UTF8 within the cytoscape
script).

Anyway, please try using one of simple examples
at http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Lev...
 (e.g.,
http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/raw-file/1356d2b...)
first.

Let me know how's going.

Regards,
Igor R.

Hi Igor,

Thanks for your indications. I've modified the cytoscape startup as you
indicated (via the Cytoscape.vmoptions file; I'm using a Linux Debian box).
Now I can import the "canonical" files you've mentionned in your previous
email. But it still fails on a biopax3 file exported from Reactome with the
following message:

 cytoscape[WARN]: Could not find RVC:
cytoscape.visual.mappings.rangecalculators.StringRangeValueCalculator@b92a8 48

------------------------------
  1  cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed:
java.lang.NullPointerException  
------------------------------
  2  cytoscape.Cytoscape[WARN]: Network reader didn't return any nodes  
------------------------------
  3  cytoscape.Cytoscape[WARN]: Network reader didn't return any edges  
------------------------------
  4  cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed:
org.biopax.paxtools.util.BioPaxIOException: XMLStreamException ParseError
at [row,col]:[11929,70]
Message: Invalid byte 2 of 2-byte UTF-8 sequence.; Line number = 11929
Column number = 70
System Id = null
Public Id = null
Location Uri= null
CharacterOffset = 920909
  ------------------------------
  5  cytoscape.Cytoscape[WARN]: Network reader didn't return any nodes  
------------------------------
  6  cytoscape.Cytoscape[WARN]: Network reader didn't return any edges  
------------------------------
  7  cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed:
org.biopax.paxtools.util.BioPaxIOException: XMLStreamException ParseError
at [row,col]:[11929,70]
Message: Invalid byte 2 of 2-byte UTF-8 sequence.; Line number = 11929
Column number = 70
System Id = null
Public Id = null
Location Uri= null
CharacterOffset = 920909
  ------------------------------
  8  cytoscape.Cytoscape[WARN]: Network reader didn't return any nodes  
------------------------------
  9  cytoscape.Cytoscape[WARN]: Network reader didn't return any edges

 Looks like there is some string formatting error ...

Now if I load the BiNoM plugin and re-try to load one of the "canonical"
files, it indeed fails with this error message:
 cytoscape[WARN]: Could not find RVC:
cytoscape.visual.mappings.rangecalculators.StringRangeValueCalculator@1629c e8c

------------------------------
  1  cytoscape[WARN]: Could not find RVC:
cytoscape.visual.mappings.rangecalculators.StringRangeValueCalculator@1629c e8c

------------------------------
  2  cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed:
org.biopax.paxtools.util.BioPaxIOException: Unexpected element at start: 6  
------------------------------
  3  cytoscape.Cytoscape[WARN]: Network reader didn't return any nodes  
------------------------------
  4  cytoscape.Cytoscape[WARN]: Network reader didn't return any edges

 So as you said there seems to be some sort of conflict. I'm willing to
help but have no clue where this conflict might originate from. Maybe some
library that both modules are using??

All the best,

Eric

Le jeudi 26 avril 2012 21:41:22 UTC+2, B. Arman Aksoy a écrit :

Hi Eric,

Let's move our discussion in private (I'll reply to you), because there is
nothing do discuss here (not BioPAX issue but rather Cytoscape app's one);
so we'll just have to create a ticket and find a solution/fix to this
technical issue.

Anyone interested, please email me or Eric directly or use Cytoscape issue
trackers: http://cbio.mskcc.org/cytoscape/bugs/ (for versions 2.8.x)
or http://code.cytoscape.org/redmine/projects/cytoscape3/issues (new v.3.x)

Igor R.