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Exported SBML has errors

Steps to reproduce:

Go to https://minerva-dev.lcsb.uni.lu/minerva/index.xhtml?id=PD_150625_3&searchCoordinates=14828,8425,70,9&x=15225&y=8389&zoom=9&

Select the following area

Screenshot_2019-10-01_at_12.25.50

Export to SBML

file.xml

Then, in Python:

from libsbml import SBMLReader
reader = SBMLReader()
document = reader.readSBML('file.xml')
document.getNumErrors() # 21 Errors
document.printErrors()

This has been checked as well against http://sbml.org/Facilities/Documentation/Validator_Web_API

21 Errors
Error Line 625 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'boundaryCondition' is missing from the <species> with the id 'species_0'.
<species compartment="comp_0" id="species_0" multi:speciesType="minerva_species_type_GenericProtein" name="ULK1" sboTerm="SBO:0000252">
Error Line 625 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'species_0'.
<species compartment="comp_0" id="species_0" multi:speciesType="minerva_species_type_GenericProtein" name="ULK1" sboTerm="SBO:0000252">
Error Line 625 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'constant' is missing from the <species> with the id 'species_0'.
<species compartment="comp_0" id="species_0" multi:speciesType="minerva_species_type_GenericProtein" name="ULK1" sboTerm="SBO:0000252">
Error Line 678 Column 75: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'boundaryCondition' is missing from the <species> with the id 'species_1'.
<species compartment="comp_0" id="species_1" initialAmount="0" multi:speciesType="minerva_species_type_Complex" name="HSP90:CDC37:ULK1:ATG13" sboTerm="SBO:0000297">
Error Line 678 Column 75: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'species_1'.
<species compartment="comp_0" id="species_1" initialAmount="0" multi:speciesType="minerva_species_type_Complex" name="HSP90:CDC37:ULK1:ATG13" sboTerm="SBO:0000297">
Error Line 678 Column 75: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'constant' is missing from the <species> with the id 'species_1'.
<species compartment="comp_0" id="species_1" initialAmount="0" multi:speciesType="minerva_species_type_Complex" name="HSP90:CDC37:ULK1:ATG13" sboTerm="SBO:0000297">
Error Line 704 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'boundaryCondition' is missing from the <species> with the id 'species_2'.
<species compartment="comp_0" id="species_2" multi:speciesType="minerva_species_type_GenericProtein" name="ATG13" sboTerm="SBO:0000252">
Error Line 704 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'species_2'.
<species compartment="comp_0" id="species_2" multi:speciesType="minerva_species_type_GenericProtein" name="ATG13" sboTerm="SBO:0000252">
Error Line 704 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'constant' is missing from the <species> with the id 'species_2'.
<species compartment="comp_0" id="species_2" multi:speciesType="minerva_species_type_GenericProtein" name="ATG13" sboTerm="SBO:0000252">
Error Line 797 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'boundaryCondition' is missing from the <species> with the id 'species_3'.
<species compartment="comp_0" id="species_3" multi:speciesType="minerva_species_type_GenericProtein" name="HSP90AA1" sboTerm="SBO:0000252">
Error Line 797 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'species_3'.
<species compartment="comp_0" id="species_3" multi:speciesType="minerva_species_type_GenericProtein" name="HSP90AA1" sboTerm="SBO:0000252">
Error Line 797 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'constant' is missing from the <species> with the id 'species_3'.
<species compartment="comp_0" id="species_3" multi:speciesType="minerva_species_type_GenericProtein" name="HSP90AA1" sboTerm="SBO:0000252">
Error Line 823 Column 75: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'boundaryCondition' is missing from the <species> with the id 'species_4'.
<species compartment="comp_0" id="species_4" initialAmount="0" multi:speciesType="minerva_species_type_Complex" name="HSP90:CDC37:ULK1:ATG13" sboTerm="SBO:0000297">
Error Line 823 Column 75: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'species_4'.
<species compartment="comp_0" id="species_4" initialAmount="0" multi:speciesType="minerva_species_type_Complex" name="HSP90:CDC37:ULK1:ATG13" sboTerm="SBO:0000297">
Error Line 823 Column 75: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'constant' is missing from the <species> with the id 'species_4'.
<species compartment="comp_0" id="species_4" initialAmount="0" multi:speciesType="minerva_species_type_Complex" name="HSP90:CDC37:ULK1:ATG13" sboTerm="SBO:0000297">
Error Line 849 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'boundaryCondition' is missing from the <species> with the id 'species_5'.
<species compartment="comp_0" id="species_5" multi:speciesType="minerva_species_type_GenericProtein" name="CDC37" sboTerm="SBO:0000252">
Error Line 849 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'species_5'.
<species compartment="comp_0" id="species_5" multi:speciesType="minerva_species_type_GenericProtein" name="CDC37" sboTerm="SBO:0000252">
Error Line 849 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'constant' is missing from the <species> with the id 'species_5'.
<species compartment="comp_0" id="species_5" multi:speciesType="minerva_species_type_GenericProtein" name="CDC37" sboTerm="SBO:0000252">
Error Line 875 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'boundaryCondition' is missing from the <species> with the id 'species_6'.
<species compartment="comp_0" id="species_6" multi:speciesType="minerva_species_type_GenericProtein" name="ULK1" sboTerm="SBO:0000252">
Error Line 875 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'species_6'.
<species compartment="comp_0" id="species_6" multi:speciesType="minerva_species_type_GenericProtein" name="ULK1" sboTerm="SBO:0000252">
Error Line 875 Column 61: (SBML Validation Rule #20623) A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object. Reference: L3V2 Section 4.6 The required attribute 'constant' is missing from the <species> with the id 'species_6'.
<species compartment="comp_0" id="species_6" multi:speciesType="minerva_species_type_GenericProtein" name="ULK1" sboTerm="SBO:0000252">