Issue 5 namespace errors need a libsedml based fix

[robertvi]

The namespace related errors in this issue are likely due to a missing namespace attribute near the top of the sedml file https://github.com/robertvi/SBMLShowcase/issues/5

We manually fixed this error in a single sedml file by adding the following missing attribute: xmlns:sbml="http://www.sbml.org/sbml/level2/version2" see here.

It would probably make sense to be able to programmatically add the missing attribute using libsedml if there is a suitable library function available

[stellaprins]

to do:

• [x] check out BioSimulators utils library for reading, writing, validating and executing SED-ML documents. A tutorial for the command-line interface is available here.
• [x] create fix_sedml helper function for create_omex if sedml namespace is invalid

In the future: fix_sedml functionality to pynml. This is the current implementation of the "get model files" to which the fix_sedml and create_omex could be eventually added.

libraries and tools working with SED-ML can be found here

[stellaprins]

Can the currently set namespaces be fetched from a SED-ML file?

The BioSimulators utils library for reading, writing, validating and executing SED-ML documents could be helpful. A tutorial for the command-line interface is available here.

Relevant libSEDML issues:

• Can't figure out how to add namespace in python #158
• [SEDBase::getNamespaces only returns the namespaces declared on the root element

  77](https://github.com/fbergmann/libSEDML/issues/77)

Check functions getElementNamespaces getNamespaces and setNamespaces mentioned in libSEDML issue #158

• • [x] sedml_file.getElementNamespaces() <libcombine.XMLNamespaces; proxy of <Swig Object of type 'XMLNamespaces *' at 0x000001F438A8E370> >
• • [x] sedml_file.getNamespaces() <libcombine.XMLNamespaces; proxy of <Swig Object of type 'XMLNamespaces *' at 0x000001F438A8EC40> >
• • [x] sedml_file.setNamespaces() TypeError: SedBase.setNamespaces() missing 1 required positional argument: 'xmlns'

[stellaprins]

To do

• [x] treat the SED-ML file as text and do a detect replace approach
• [x] create temporary SED-ML files that are fixed (i.e. xmlns:sbmlattribute added), and are deleted after they have been used to create an OMEX file which has been tested