I am not sure I understand the question, so a problem to further explore. xpath
reports:
$ xpath -e "/sbml/model/notes/body/p/text()" sbml/WP5113.sbml
not well-formed (invalid token) at line 1, column 0, byte 0:
{"reason":"lcsb.mapviewer.model.map.InconsistentModelException: [StateTransitionReaction iddc9a88f6]\tProblem with exporting bioEntity","error":"Internal server error."}
^
at /usr/lib/x86_64-linux-gnu/perl5/5.32/XML/Parser.pm line 187.
With the SBML webserver reply which should have been SBML but it instead:
{"reason":"lcsb.mapviewer.model.map.InconsistentModelException: [StateTransitionReaction iddc9a88f6]\tProblem with exporting bioEntity","error":"Internal server error."}
Just going to report this here. I think it's really a GPML error, but it could be nice if the duplicate rdf:ID
would be reported as error, instead of cause the SBML generation to cause an Internal Server Error.
xpath
reports:
$ xpath -e "/sbml/model/notes/body/p/text()" sbml/WP4969.sbml
not well-formed (invalid token) at line 1, column 0, byte 0:
{"reason":"Biopax publication with d5e already exists.","error":"Internal server error."}
^
at /usr/lib/x86_64-linux-gnu/perl5/5.32/XML/Parser.pm line 187.
The SBML content returned is (which is indeed not SBML):
{"reason":"Biopax publication with d5e already exists.","error":"Internal server error."}
The SBML generates fine with the webservice, but the resulting XML is not. xmllint
reports:
$ xmllint --noout sbml/WP5039.sbml
sbml/WP5039.sbml:13083: parser error : Input is not proper UTF-8, indicate encoding !
Bytes: 0xDF 0x20 0x70 0x72
<p>High levels of viral load stimulate TGF� production, which is locally secrete
^
And xpath
reports:
$ xpath -e "/sbml/model/notes/body/p/text()" sbml/WP5039.sbml
not well-formed (invalid token) at line 13083, column 42, byte 824587:
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>High levels of viral load stimulate TGFß production, which is locally secreted.
=========================================^
</p>
at /usr/lib/x86_64-linux-gnu/perl5/5.32/XML/Parser.pm line 187.