Model class cannot be created or serialized

[cjmyers]

I’m getting an error trying to use Model: Attribute Error:  module ‘sbol2’ has no attribute ‘Model’
It looks like Model is not exported.

Further issue:
            model = sbol2.model.Model(display_id)
            model.source = sbml_file.filename
            model.language = “http://identifiers.org/edam/format_2585”
            model.framework = “http://identifiers.org/biomodels.sbo/SBO:0000062”
            doc.addModel(model)
Results in this serialization:
  <abc_sbml_xml rdf:about=“https://sbolcanvas.org/example/1”>
    <sbol:source rdf:resource=“abc_sbml.xml”/>
    sbol:displayIdexample</sbol:displayId>
    sbol:version1</sbol:version>
    <sbol:persistentIdentity rdf:resource=“https://sbolcanvas.org/example”/>
    <sbol:language rdf:resource=“http://identifiers.org/edam/format_2585”/>
    <sbol:framework rdf:resource=“http://identifiers.org/biomodels.sbo/SBO:0000062”/>
  </abc_sbml_xml>

[tcmitchell]

Thanks for submitting an issue. I agree that Model is not exported from the sbol2 package and should be. That's a straightforward fix and we should add a unit test to prevent regression.

Can you please explain what you think is wrong with the serialization? I see the serialization, but I don't know what you expected to see. Your code example is a snippet and not runnable as is, and the XML you provided appears to be damaged. Some of the tags lack their brackets, and what you've pasted is an incomplete document.

To get us started I have written a program that loosely attempts to recreate your issue:

"""This is an attempt to recreate https://github.com/SynBioDex/pySBOL2/issues/448"""
import sbol2

doc = sbol2.Document()
display_id = "idexample"
filename = "abc_sbml.xml"
model = sbol2.model.Model(display_id)
model.source = filename
model.language = "http://identifiers.org/edam/format_2585"
model.framework = "http://identifiers.org/biomodels.sbo/SBO:0000062"
doc.addModel(model)
print(doc.writeString())

That program has the following output:

<rdf:RDF xmlns:brick="https://brickschema.org/schema/Brick#" xmlns:csvw="http://www.w3.org/ns/csvw#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:dcmitype="http://purl.org/dc/dcmitype/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dcam="http://purl.org/dc/dcam/" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:geo="http://www.opengis.net/ont/geosparql#" xmlns:odrl="http://www.w3.org/ns/odrl/2/" xmlns:org="http://www.w3.org/ns/org#" xmlns:prof="http://www.w3.org/ns/dx/prof/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:qb="http://purl.org/linked-data/cube#" xmlns:schema="https://schema.org/" xmlns:sh="http://www.w3.org/ns/shacl#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:sosa="http://www.w3.org/ns/sosa/" xmlns:ssn="http://www.w3.org/ns/ssn/" xmlns:time="http://www.w3.org/2006/time#" xmlns:vann="http://purl.org/vocab/vann/" xmlns:void="http://rdfs.org/ns/void#" xmlns:wgs="https://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">
  <idexample rdf:about="http://examples.org/idexample/example/1">
    <sbol:source rdf:resource="abc_sbml.xml"/>
    <sbol:version>1</sbol:version>
    <sbol:persistentIdentity rdf:resource="http://examples.org/idexample/example"/>
    <sbol:framework rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000062"/>
    <sbol:language rdf:resource="http://identifiers.org/edam/format_2585"/>
    <sbol:displayId>example</sbol:displayId>
  </idexample>
</rdf:RDF>

[tcmitchell]

Oh, I think I see what one of the issues is. You have called the Model constructor with a display_id, but the first parameter to the constructor is the type URI, so your code is overwriting the type URI for the Model. Here is an updated program and output where the display_id is passed as the object URI instead of the type URI:

"""This is an attempt to recreate https://github.com/SynBioDex/pySBOL2/issues/448"""
import sbol2

doc = sbol2.Document()
display_id = "abc_sbml_xml"
filename = "abc_sbml.xml"
model = sbol2.model.Model(uri=display_id)
model.source = filename
model.language = "http://identifiers.org/edam/format_2585"
model.framework = "http://identifiers.org/biomodels.sbo/SBO:0000062"
doc.addModel(model)
print(doc.writeString())

<rdf:RDF xmlns:brick="https://brickschema.org/schema/Brick#" xmlns:csvw="http://www.w3.org/ns/csvw#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:dcmitype="http://purl.org/dc/dcmitype/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dcam="http://purl.org/dc/dcam/" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:geo="http://www.opengis.net/ont/geosparql#" xmlns:odrl="http://www.w3.org/ns/odrl/2/" xmlns:org="http://www.w3.org/ns/org#" xmlns:prof="http://www.w3.org/ns/dx/prof/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:qb="http://purl.org/linked-data/cube#" xmlns:schema="https://schema.org/" xmlns:sh="http://www.w3.org/ns/shacl#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:sosa="http://www.w3.org/ns/sosa/" xmlns:ssn="http://www.w3.org/ns/ssn/" xmlns:time="http://www.w3.org/2006/time#" xmlns:vann="http://purl.org/vocab/vann/" xmlns:void="http://rdfs.org/ns/void#" xmlns:wgs="https://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">
  <sbol:Model rdf:about="http://examples.org/Model/abc_sbml_xml/1">
    <sbol:framework rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000062"/>
    <sbol:language rdf:resource="http://identifiers.org/edam/format_2585"/>
    <sbol:persistentIdentity rdf:resource="http://examples.org/Model/abc_sbml_xml"/>
    <sbol:source rdf:resource="abc_sbml.xml"/>
    <sbol:version>1</sbol:version>
    <sbol:displayId>abc_sbml_xml</sbol:displayId>
  </sbol:Model>
</rdf:RDF>

Are there additional problems with the serialization of Model, or did I guess correctly that overwriting the type URI was the problem?

[cjmyers]

This looks good to me. Will you also release a patch that exports Model?

[tcmitchell]

This looks good to me. Will you also release a patch that exports Model?

Yes, but...

The unit tests were passing when they were last run in August 2025. Since then, enough seems to have changed that many are no longer passing. A bunch of errors are related to a change to the packaging package and I have filed an issue to inquire about that. There are also a lot of HTTP errors related to SynBioHub that I'll need to look into. Perhaps something has changed in the last year with respect to searching such that we are now getting 401 (unauthorized) and 403 (forbidden) errors. It will take time to work through these issues. Fortunately, you have a workaround until we are able to make a new release.

The current state of the testing is available to view at https://github.com/SynBioDex/pySBOL2/actions for anyone who wants to poke around.

[cjmyers]

We had to put synbiohub.org behind CloudFlare due to bots. If you want to connect to the API, you should use https://api.synbiohub.org. Also, we change synbiohub.org to require login to do anything, so you will need to login before running any test that uses SynBioHub.