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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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Cannot "get" a Pathway via URL/ID #57

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Not sure if I have done this exactly right, but here are the steps.

First, I did a full text search:

http://awabi.cbio.mskcc.org/cpath2/xml/search?q=DNA%20Repair&type=Pathway

The first fit looks like this:

<uri>
HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PATHWAY855_1_9606
</uri>
<biopaxClass>Pathway</biopaxClass>
<name>DNA Repair</name>
<dataSource>urn:miriam:reactome</dataSource>
</searchHit>

I then tried to get this Pathway via GET, e.g.

http://awabi.cbio.mskcc.org/cpath2/get?uri=HTTP://WWW.REACTOME.ORG/BIOPAX/48887#
PATHWAY855_1_9606

I just get back a blank screen.

Original issue reported on code.google.com by cer...@gmail.com on 26 May 2011 at 7:53

GoogleCodeExporter commented 9 years ago 
It is briefly explained at the bottom of 
http://code.google.com/p/pathway-commons/wiki/cPathSquaredWebService#Test_Links

Unlike cPath (where IDs were simple and short), in cPath2 we do our best to 
keep original provider's IDs unchanged (except for some utility class elements, 
where we have to normalize in order to merge pathway data from different 
sources).  

URI (actually everything that is used as url parameter) must be properly 
encoded. Some browser are "smart" enough to replace spaces with %20 at least, 
but not all that has to be. This is normal. However, there is no such problem 
when the webservice used via a standard client API, which usually does 
encoding/decoding transparently for you.

Original comment by rod...@gmail.com on 26 May 2011 at 8:47

GoogleCodeExporter commented 9 years ago

Original comment by rod...@gmail.com on 5 Jan 2013 at 12:06