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PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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Invalid characters in output owl #298

Closed ozgunbabur closed 6 years ago

ozgunbabur commented 6 years ago

I am getting an owl file with the following graph query.

http://beta.pathwaycommons.org/pc2/graph?source=CDK4&source=CDKN2A&kind=commonstream&direction=DOWNSTREAM

But Paxtools cannot load it because an author name in the file has invalid (or non-ascii, or whatever) characters in it. I am not sure if that is a data import problem or a BioPAX generation problem.

IgorRodchenkov commented 6 years ago

Have you got that biopax with curl or wget or programmatically?

Otherwise, sounds like a re-occurrence of the old paxtools bug...

IR

On Jun 14, 2018, at 12:32 PM, Özgün Babur notifications@github.com wrote:

I am getting an owl file with the following graph query.

http://beta.pathwaycommons.org/pc2/graph?source=CDK4&source=CDKN2A&kind=commonstream&direction=DOWNSTREAM

But Paxtools cannot load it because an author name in the file has invalid (or non-ascii, or whatever) characters in it. I am not sure if that is a data import problem or a BioPAX generation problem.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or mute the thread.

ozgunbabur commented 6 years ago

I am just clicking on the link and Chrome downloads the owl. I try to open the owl with ChiBE, but the Paxtools inside throws the error. I also tried outside of ChiBE, using Main in paxtools-console. I got:

Exception in thread "main" org.biopax.paxtools.util.BioPaxIOException: XMLStreamException ParseError at [row,col]:[8747,74] Message: Invalid byte 2 of 3-byte UTF-8 sequence.; Line number = 8747 Column number = 74 System Id = null Public Id = null Location Uri= null CharacterOffset = 743620

at org.biopax.paxtools.io.SimpleIOHandler.createAndBind(SimpleIOHandler.java:314)
IgorRodchenkov commented 6 years ago

Confirmed

IgorRodchenkov commented 6 years ago

Fixed!

IgorRodchenkov commented 6 years ago

Fixed.

On Thu, Jun 14, 2018 at 1:28 PM, Özgün Babur notifications@github.com wrote:

I am just clicking on the link and Chrome downloads the owl. I try to open the owl with ChiBE, but the Paxtools inside throws the error. I also tried outside of ChiBE, using Main in paxtools-console. I got:

Exception in thread "main" org.biopax.paxtools.util.BioPaxIOException: XMLStreamException ParseError at [row,col]:[8747,74] Message: Invalid byte 2 of 3-byte UTF-8 sequence.; Line number = 8747 Column number = 74 System Id = null Public Id = null Location Uri= null CharacterOffset = 743620

at org.biopax.paxtools.io.SimpleIOHandler.createAndBind(SimpleIOHandler.java:314)

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/cpath2/issues/298#issuecomment-397375215, or mute the thread https://github.com/notifications/unsubscribe-auth/AA8fwRI6IndOcvn4mNfVW4GQh46V-Symks5t8p1HgaJpZM4UoSH9 .