Menu
▾
▴
#378 comp flattening converter bugs
The comp package flattening converter fails with the following sbml test suite cases:
Notice: Running Test: 1128
Notice: flattening model /Users/andy/src/sbml_test/cases/semantic/01128/01128-sbml-l3v1.xml
Warning: Errors durring model flattening, model MIGHT contain errors:
SBMLError(0): Errors arose during the attempt to flatten the model. The subsequent errors are from this attempt.
SBMLError(1): If one element replaces another, whether it is the target of a <replacedBy> element, or whether it has a child <replacedElement>, if the replaced element has the 'metaid' attribute set, the replacement element must also have the 'metaid' attribute set.
Reference: L3V1 Comp V1 Section 3.6.5
Unable to transform IDs in ReplacedBy::updateIDs during replacement: the replacement of the element with metaid 'p2_meta' does not have a metaid.
Warning: Global parameter, 'param2' missing value and missing init assignment and assignment rule!, defaulting value to 0.0.
Warning: This probably is NOT what you want with global parameter 'param2'.
=============== Test 1128 failed =============
Notice: Running Test: 1135
Notice: flattening model /Users/andy/src/sbml_test/cases/semantic/01135/01135-sbml-l3v1.xml
Warning: Errors durring model flattening, model MIGHT contain errors:
SBMLError(0): Errors arose during the attempt to flatten the model. The subsequent errors are from this attempt.
SBMLError(1): Any one SBML object may only be referenced in one of the following ways: referenced by a single <port> object; referenced by a single <deletion> object; referenced by a single <replacedElement>; be the parent of a single <replacedBy> child; be referenced by one or more <replacedBy> objects; or be referenced by one or more <replacedElement> objects all using the 'deletion' attribute. Essentially, once an object has been referenced in one of these ways it cannot be referenced again.
Reference: L3V1 Comp V1 Section 3.7.1
Error discovered in CompModelPlugin::saveAllReferencedElements when checking the model 'moddef2': a <parameter> with the id 'p4' has a <replacedBy> child and is also pointed to by a <port>, <deletion>, <replacedElement>, or one or more <replacedBy> objects.
=============== Test 1135 failed =============
Notice: Running Test: 1136
Notice: flattening model /Users/andy/src/sbml_test/cases/semantic/01136/01136-sbml-l3v1.xml
Warning: Errors durring model flattening, model MIGHT contain errors:
SBMLError(0): Errors arose during the attempt to flatten the model. The subsequent errors are from this attempt.
SBMLError(1): Any one SBML object may only be referenced in one of the following ways: referenced by a single <port> object; referenced by a single <deletion> object; referenced by a single <replacedElement>; be the parent of a single <replacedBy> child; be referenced by one or more <replacedBy> objects; or be referenced by one or more <replacedElement> objects all using the 'deletion' attribute. Essentially, once an object has been referenced in one of these ways it cannot be referenced again.
Reference: L3V1 Comp V1 Section 3.7.1
Error discovered in CompModelPlugin::saveAllReferencedElements when checking the model 'moddef2': a <parameter> with the id 'p4' has a <replacedBy> child and is also pointed to by a <port>, <deletion>, <replacedElement>, or one or more <replacedBy> objects.
=============== Test 1136 failed =============
Notice: Running Test: 1153
Notice: flattening model /Users/andy/src/sbml_test/cases/semantic/01153/01153-sbml-l3v1.xml
Warning: Errors durring model flattening, model MIGHT contain errors:
SBMLError(0): Errors arose during the attempt to flatten the model. The subsequent errors are from this attempt.
SBMLError(1): Any one SBML object may only be referenced in one of the following ways: referenced by a single <port> object; referenced by a single <deletion> object; referenced by a single <replacedElement>; be the parent of a single <replacedBy> child; be referenced by one or more <replacedBy> objects; or be referenced by one or more <replacedElement> objects all using the 'deletion' attribute. Essentially, once an object has been referenced in one of these ways it cannot be referenced again.
Reference: L3V1 Comp V1 Section 3.7.1
Error discovered in CompModelPlugin::saveAllReferencedElements when checking the model 'bar': multiple <deletion>, <replacedElement>, and/or <port> elements point directly to the <parameter> with the id 'y'.
Error: Failed simulate in test 1153, error: RoadRunner exception: No sbml element exists for symbol 'AAQ'
Case 1153: Exception: Failed running simulation
Notice: Running Test: 1166
Notice: flattening model /Users/andy/src/sbml_test/cases/semantic/01166/01166-sbml-l3v1.xml
Warning: Errors durring model flattening, model MIGHT contain errors:
SBMLError(0): The value of attribute 'comp:required' on the SBML object must be set to 'true'.
Reference: L3V1 Comp V1 Section 3.1
SBMLError(1): Errors arose during the attempt to flatten the model. The subsequent errors are from this attempt.
SBMLError(2): Any one SBML object may only be referenced in one of the following ways: referenced by a single <port> object; referenced by a single <deletion> object; referenced by a single <replacedElement>; be the parent of a single <replacedBy> child; be referenced by one or more <replacedBy> objects; or be referenced by one or more <replacedElement> objects all using the 'deletion' attribute. Essentially, once an object has been referenced in one of these ways it cannot be referenced again.
Reference: L3V1 Comp V1 Section 3.7.1
Error discovered in CompModelPlugin::saveAllReferencedElements when checking the model 'enzyme': multiple <deletion>, <replacedElement>, and/or <port> elements point directly to the <compartment> with the id 'comp'.
Warning: Warning, errors found in sbml document: line 167: (comp-20212 [Error]) The value of attribute 'comp:required' on the SBML object must be set to 'true'.
Reference: L3V1 Comp V1 Section 3.1
Notice: Running Test: 1169
Notice: flattening model /Users/andy/src/sbml_test/cases/semantic/01169/01169-sbml-l3v1.xml
Warning: Errors durring model flattening, model MIGHT contain errors:
SBMLError(0): Errors arose during the attempt to flatten the model. The subsequent errors are from this attempt.
SBMLError(1): Any one SBML object may only be referenced in one of the following ways: referenced by a single <port> object; referenced by a single <deletion> object; referenced by a single <replacedElement>; be the parent of a single <replacedBy> child; be referenced by one or more <replacedBy> objects; or be referenced by one or more <replacedElement> objects all using the 'deletion' attribute. Essentially, once an object has been referenced in one of these ways it cannot be referenced again.
Reference: L3V1 Comp V1 Section 3.7.1
Error discovered in CompModelPlugin::saveAllReferencedElements when checking the model 'submod': multiple <deletion>, <replacedElement>, and/or <port> elements point directly to the <parameter> with the id 'q'.
Warning: Global parameter, 'Q' missing value and missing init assignment and assignment rule!, defaulting value to 0.0.
Warning: This probably is NOT what you want with global parameter 'Q'.
Error: Failed simulate in test 1169, error: RoadRunner exception: No sbml element exists for symbol 'A__S1'
Case 1169: Exception: Failed running simulation
NOTICE NOTICE NOTICE
The comments associated with this ticket were lost in late 2014.
The SBML Team manually recovered the comments. The text is appended below.
NOTICE NOTICE NOTICE
Comment By: Andy Somogyi (asomogyi)
Date: 2014-08-26 03:50
Nevermind, these seem to be fixed with a new test suite files.
Comment By: Frank Bergmann (fbergmann)
Date: 2014-08-26 06:25
thanks for letting us know
Frank