SBML conversion not possible if errors exist

[fbergmann]

Currently if a JSON file (without level, or without units on measurements) is converted to SBML, that will fail with exception. It would be better, if that could be caught:

• a vessel could be automatically created and used
• unit should only be a warning in any case.

[JR-1991]

If I understand correctly, we should revert raising exceptions when there are missing vessel objects and references. Additionally, the requirement for units in measurements should not raise exceptions?

Could you provide an example that I can use to test this and integrate into the test suite?

[fbergmann]

The file from yesterdays course would do:

�[36mSBML�[0m	validation	�[31m�[1mERROR�[0m: Species 's1' of type 'SmallMolecule' does not have a vessel id.
  �[36mSBML�[0m	validation	�[31m�[1mERROR�[0m: Species 's2' of type 'SmallMolecule' does not have a vessel id.
  �[36mSBML�[0m	validation	�[31m�[1mERROR�[0m: Object of type 'MeasurementData' with id 's1' does not have a unit defined.
  �[36mSBML�[0m	validation	�[31m�[1mERROR�[0m: Object of type 'MeasurementData' with id 's2' does not have a unit defined.
  �[36mSBML�[0m	validation	�[31m�[1mERROR�[0m: Object of type 'MeasurementData' with id 's1' does not have a unit defined.
  �[36mSBML�[0m	validation	�[31m�[1mERROR�[0m: Object of type 'MeasurementData' with id 's2' does not have a unit defined.
  �[36mSBML�[0m	validation	�[31m�[1mERROR�[0m: Object of type 'MeasurementData' with id 's1' does not have a unit defined.
  �[36mSBML�[0m	validation	�[31m�[1mERROR�[0m: Object of type 'MeasurementData' with id 's2' does not have a unit defined.
  �[36mSBML�[0m	validation	�[33m�[1mWARNING�[0m: Parameter with id 'k_cat' should ideally have a unit defined.
  �[36mSBML�[0m	validation	�[33m�[1mWARNING�[0m: Parameter with id 'K_s' should ideally have a unit defined.

mystery_dataset_1_t.json

[fbergmann]

As for how to fix it, I would probably just create a default compartment (of size 1), and place the species in there upon import.

[JR-1991]

@fbergmann, I’ve made the requested changes:

• If there’s no vessel, a placeholder compartment is added to the document, and a warning is displayed to the logger to inform about the vessel’s addition.
• I’ve relaxed the requirement of measurement units and added a warning here as well, instead of an error.

However, I’m still encountering issues when trying to save the result as an OMEX file. The document is generated successfully, and libSBML validation doesn’t indicate any severe issues, except for warnings regarding the units. However, the resulting SBML doc in the OMEX file is empty. I suspect pymetadata uses libCombine internally, and there might be warnings or errors that aren’t being printed.

Could you review the document to identify any potential errors? If not, I’ll have to delve deeper into this, and it might be a technical issue rather than a problem with the document itself.

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns:enzymeml="https://www.enzymeml.org/v2" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
  <model name="Document Title" volumeUnits="u1">
    <annotation>
      <data xmlns="https://www.enzymeml.org/v2" file="./data.tsv">
        <measurement id="m0" name="m0">
          <speciesData species="s1" value="100.0" type="concentration"/>
          <speciesData species="s2" value="0.0" type="concentration"/>
        </measurement>
        <measurement id="m1" name="m1">
          <speciesData species="s1" value="34.0" type="concentration"/>
          <speciesData species="s2" value="0.0" type="concentration"/>
        </measurement>
        <measurement id="m2" name="m2">
          <speciesData species="s1" value="200.0" type="concentration"/>
          <speciesData species="s2" value="0.0" type="concentration"/>
        </measurement>
      </data>
    </annotation>
    <listOfUnitDefinitions>
      <unitDefinition id="u1" name="ml">
        <listOfUnits>
          <unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <listOfCompartments>
      <compartment id="v1" name="Placeholder Vessel" spatialDimensions="3" size="1" units="u1" constant="true">
        <annotation>
          <rdf:RDF xmlns:OBO="http://purl.obolibrary.org/obo/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
            <rdf:Description rdf:about="http://www.enzymeml.org/v2/Vessel/1674a7ae-b9bc-48bf-9f47-3d783aed968c">
              <schema:name>Placeholder Vessel</schema:name>
              <OBO:OBI_0002139 rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</OBO:OBI_0002139>
              <rdf:type rdf:resource="http://www.enzymeml.org/v2/Vessel"/>
              <rdf:type rdf:resource="http://purl.obolibrary.org/obo/OBI_0400081"/>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
      </compartment>
    </listOfCompartments>
    <listOfSpecies>
      <species sboTerm="SBO:0000247" id="s1" name="s1" compartment="v1" initialConcentration="100" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
            <rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/50c36c9c-5197-41e5-aac2-122d259dae1b">
              <schema:name>s1</schema:name>
              <rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
      </species>
      <species sboTerm="SBO:0000247" id="s2" name="s2" compartment="v1" initialConcentration="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
            <rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/1538277f-0e7d-4875-8011-4cae61460f2d">
              <schema:name>s2</schema:name>
              <rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
      </species>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k_cat" name="k_cat" constant="true">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
            <rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/c2c469d8-f22a-4c78-a9d8-844b9ef7bcba">
              <rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
      </parameter>
      <parameter id="K_s" name="K_s" constant="true">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
            <rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/395e7a5f-b568-49b8-bcbd-3ea790ed5be5">
              <rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
      </parameter>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" name="r1" reversible="false">
        <listOfReactants>
          <speciesReference species="s1" stoichiometry="1" constant="false"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="s2" stoichiometry="1" constant="false"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> k_cat </ci>
                <ci> s1 </ci>
              </apply>
              <apply>
                <plus/>
                <ci> K_s </ci>
                <ci> s1 </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>

[fbergmann]

However, I’m still encountering issues when trying to save the result as an OMEX file. The document is generated successfully, and libSBML validation doesn’t indicate any severe issues, except for warnings regarding the units. However, the resulting SBML doc in the OMEX file is empty. I suspect pymetadata

actually pymetadata is not using lib combine at all. What are the error messages that you are getting? The SBML file looks ok

[JR-1991]

Okay, thanks for the quick feedback and heads-up on pymetadata not using lib combine. Therefore, the error must be somewhere else.

The issue is that I’m not receiving any error messages, so I’m unsure about the exact problem. The resulting SBML file in the OMEX is empty. I’ve encountered similar problems in the past, and most of the time, it was malformed or invalid SBML. However, I suppose this is different here.

What makes this even more challenging is that the SBML content I’m attempting to add to the OMEX is not empty. The doc I have posted earlier is from a debug statement before adding to the OMEX, but as soon as I check the written archive, the model.xml is empty. PyMetadata expects the SBML file to be passed as a path, and I’m achieving this by writing it to a temporary file. Perhaps there’s an issue here or a synchronization problem.