Skip to content
GitLab
Projects Groups Topics Snippets
  • /
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
  • Sign in
  • C core
  • Project information
    • Project information
    • Activity
    • Labels
    • Members
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributor statistics
    • Graph
    • Compare revisions
    • Locked files
  • Issues 93
    • Issues 93
    • List
    • Boards
    • Service Desk
    • Milestones
    • Iterations
    • Requirements
  • Merge requests 2
    • Merge requests 2
  • CI/CD
    • CI/CD
    • Pipelines
    • Jobs
    • Schedules
    • Test cases
  • Deployments
    • Deployments
    • Environments
    • Releases
  • Packages and registries
    • Packages and registries
    • Container Registry
  • Monitor
    • Monitor
    • Incidents
  • Analytics
    • Analytics
    • Value stream
    • CI/CD
    • Code review
    • Insights
    • Issue
    • Repository
  • External wiki
    • External wiki
  • Activity
  • Graph
  • Create a new issue
  • Jobs
  • Commits
  • Issue Boards
Collapse sidebar
  • minervaminerva
  • core
  • Issues
  • #1804
Closed
Open
Issue created Oct 24, 2022 by Marek Ostaszewski@marek.ostaszewskiOwner

global xml namespace definition causes MINERVA to fail on processing model notes

CellDesigner defines a number of namespaces locally (html, RDF etc).
When these xml definitions are moved to the header, CellDesigner still opens such a file correctly.
However, specifically for model notes, such definition:

<?xml version='1.0' encoding='UTF-8'?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:html="http://www.w3.org/1999/xhtml" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" level="2" version="4">
<model>
<notes><html:html><html:head><html:title /></html:head><html:body /></html:html></notes><annotation>

causes MINERVA to throw an error:

107605 Other ERROR Problem with uploading map: notes cannot contain <html> tag. More details can be found in log file.. Message: notes cannot contain <html> tag

even though empty notes in the following format are accepted:

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:html="http://www.w3.org/1999/xhtml" level="2" version="4">
<model metaid="CDMT00001">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</notes>
<annotation>
Assignee
Assign to
Time tracking