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Atomizer errors on level 3 SBML #7

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Open
Atomizer errors on level 3 SBML#7

Description

@alubbock
alubbock
opened on Oct 23, 2019

Atomizer fails with the following error when I try to run it on a small SBML level 3 model:

Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)

Here's the SBML model:

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

Here's the same model encoded as SBML level 2, which works on atomizer without error:

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

Both models were exported from Python LibSBML.

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Atomizer errors on level 3 SBML · Issue #7 · RuleWorld/atomizer · GitHub
      Skip to content
      Atomizer errors on level 3 SBML #7
      Open
      Open
      Atomizer errors on level 3 SBML#7
      Description
      @alubbock
      alubbock
      opened on Oct 23, 2019
      Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
      Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)

      Here's the SBML model:
      <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

      Here's the same model encoded as SBML level 2, which works on atomizer without error:
      <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

      Both models were exported from Python LibSBML.
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Atomizer errors on level 3 SBML · Issue #7 · RuleWorld/atomizer · GitHub
          Skip to content
          Atomizer errors on level 3 SBML #7
          Open
          Open
          Atomizer errors on level 3 SBML#7
          Description
          @alubbock
          alubbock
          opened on Oct 23, 2019
          Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
          Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)

          Here's the SBML model:
          <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

          Here's the same model encoded as SBML level 2, which works on atomizer without error:
          <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

          Both models were exported from Python LibSBML.
          Metadata
          Metadata
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          No one assigned
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            No labels
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              None yet
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              No branches or pull requests
              Issue actions
              
, 'i');
if (__m === '*' || __re.test(location.href)) {
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var ref = document.referrer;
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Atomizer errors on level 3 SBML · Issue #7 · RuleWorld/atomizer · GitHub
              Skip to content
              Atomizer errors on level 3 SBML #7
              Open
              Open
              Atomizer errors on level 3 SBML#7
              Description
              @alubbock
              alubbock
              opened on Oct 23, 2019
              Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
              Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)

              Here's the SBML model:
              <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

              Here's the same model encoded as SBML level 2, which works on atomizer without error:
              <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

              Both models were exported from Python LibSBML.
              Metadata
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                No labels
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
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var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Atomizer errors on level 3 SBML · Issue #7 · RuleWorld/atomizer · GitHub
                  Skip to content
                  Atomizer errors on level 3 SBML #7
                  Open
                  Open
                  Atomizer errors on level 3 SBML#7
                  Description
                  @alubbock
                  alubbock
                  opened on Oct 23, 2019
                  Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
                  Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)

                  Here's the SBML model:
                  <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

                  Here's the same model encoded as SBML level 2, which works on atomizer without error:
                  <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

                  Both models were exported from Python LibSBML.
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
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                    No labels
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                    No type
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                    No projects
                      Milestone
                      No milestone
                      Relationships
                      None yet
                      Development
                      No branches or pull requests
                      Issue actions
                      
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Atomizer errors on level 3 SBML · Issue #7 · RuleWorld/atomizer · GitHub
                      Skip to content
                      Atomizer errors on level 3 SBML #7
                      Open
                      Open
                      Atomizer errors on level 3 SBML#7
                      Description
                      @alubbock
                      alubbock
                      opened on Oct 23, 2019
                      Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
                      Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)

                      Here's the SBML model:
                      <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

                      Here's the same model encoded as SBML level 2, which works on atomizer without error:
                      <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

                      Both models were exported from Python LibSBML.
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Atomizer errors on level 3 SBML · Issue #7 · RuleWorld/atomizer · GitHub
                          Skip to content
                          Atomizer errors on level 3 SBML #7
                          Open
                          Open
                          Atomizer errors on level 3 SBML#7
                          Description
                          @alubbock
                          alubbock
                          opened on Oct 23, 2019
                          Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
                          Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)

                          Here's the SBML model:
                          <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

                          Here's the same model encoded as SBML level 2, which works on atomizer without error:
                          <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

                          Both models were exported from Python LibSBML.
                          Metadata
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                          No one assigned
                            Labels
                            No labels
                            No labels
                            Type
                            No type
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                            No projects
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                              No milestone
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                              None yet
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                              No branches or pull requests
                              Issue actions
                              
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Atomizer errors on level 3 SBML · Issue #7 · RuleWorld/atomizer · GitHub
                              Skip to content
                              Atomizer errors on level 3 SBML #7
                              Open
                              Open
                              Atomizer errors on level 3 SBML#7
                              Description
                              @alubbock
                              alubbock
                              opened on Oct 23, 2019
                              Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
                              Traceback (most recent call last):
File "<string>", line 68, in <module>
File "<string>", line 58, in main
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 542, in analyzeFile
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/libsbml2bngl", line 673, in analyzeHelper
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 903, in getReactions
File "/Users/travis/build/rhclark/atomizer/build/sbmlTranslator/out00-PYZ.pyz/sbml2bngl", line 699, in reduceComponentSymmetryFactors
TypeError: append() takes exactly one argument (2 given)

                              Here's the SBML model:
                              <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="export-test">
<listOfCompartments>
<compartment id="default" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false">
<listOfProducts>
<speciesReference species="__s0" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

                              Here's the same model encoded as SBML level 2, which works on atomizer without error:
                              <?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model name="export-test">
<listOfCompartments>
<compartment id="default" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="__s0" name="A()" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="kf" name="kf" value="100"/>
<parameter id="parameterId_0" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="r0" name="r1" reversible="false" fast="false">
<listOfProducts>
<speciesReference species="__s0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> parameterId_0 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> kf </ci>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

                              Both models were exported from Python LibSBML.
                              Metadata
                              Metadata
                              Assignees
                              No one assigned
                                Labels
                                No labels
                                No labels
                                Type
                                No type
                                Projects
                                No projects
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                                  None yet
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                                  Issue actions