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added -validate-sbml option #266

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merged 14 commits into from
Nov 15, 2023
Merged

added -validate-sbml option #266

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c69993f
initial attempt at a validate-sbml option for pynml.py
robertvi Oct 26, 2023
0b471e1
minor tweaks
robertvi Oct 26, 2023
ec6f9c4
added libsbml as an optional extra requirement
robertvi Oct 27, 2023
50d45e3
fix package name
robertvi Oct 27, 2023
375e4ee
pyneuroml/sbml/__init__.py now passing flake8 and black
robertvi Oct 30, 2023
883b2ca
pyneuroml/pynml.py changed by black
robertvi Oct 30, 2023
42a3912
converted my simple test into a pytest-able function, callable using …
robertvi Nov 8, 2023
1a078b9
improving error handling
robertvi Nov 9, 2023
056e762
tidied up error handling, corrected error code range
robertvi Nov 10, 2023
beb73ed
expanded the sbml test function
robertvi Nov 10, 2023
8b2ea3f
more accurate exception handling
robertvi Nov 13, 2023
a401d83
added a test for both unit inconsistency check modes
robertvi Nov 13, 2023
d30e57d
added two more test cases
robertvi Nov 13, 2023
c358b2f
added simple examples to test-ghactions.sh
robertvi Nov 13, 2023
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42 changes: 42 additions & 0 deletions examples/test_data/valid_doc.sbml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model substanceUnits="mole" timeUnits="second" extentUnits="mole">
<listOfUnitDefinitions>
<unitDefinition id="per_second">
<listOfUnits>
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="c1" spatialDimensions="3" size="1" units="litre" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1" compartment="c1" initialAmount="5" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S2" compartment="c1" initialAmount="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k" value="1" units="per_second" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r1" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="S1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k </ci>
<ci> S1 </ci>
<ci> c1 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
47 changes: 45 additions & 2 deletions pyneuroml/pynml.py
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Expand Up @@ -126,8 +126,8 @@ def parse_arguments():
"input_files",
type=str,
nargs="*",
metavar="<LEMS/NeuroML 2 file(s)>",
help="LEMS/NeuroML 2 file(s) to process",
metavar="<LEMS/NeuroML 2/SBML file(s)>",
help="LEMS/NeuroML 2/SBML file(s) to process",
)

mut_exc_opts_grp = parser.add_argument_group(
Expand Down Expand Up @@ -345,6 +345,16 @@ def parse_arguments():
action="store_true",
help=("(Via jNeuroML) Validate NeuroML file(s) against the\n" "v1.8.1 Schema"),
)
mut_exc_opts.add_argument(
"-validate-sbml",
action="store_true",
help=("Validate SBML file(s), unit consistency failure generates a warning"),
)
mut_exc_opts.add_argument(
"-validate-sbml-units",
action="store_true",
help=("Validate SBML file(s), unit consistency failure generates an error"),
)

return parser.parse_args()

Expand Down Expand Up @@ -2111,6 +2121,39 @@ def evaluate_arguments(args):
post_args = ""
exit_on_fail = True

# Deal with the SBML validation option which doesn't call run_jneuroml
if args.validate_sbml or args.validate_sbml_units:
try:
from pyneuroml.sbml import validate_sbml_files
except Exception:
logger.critical("Unable to import pyneuroml.sbml")
sys.exit(UNKNOWN_ERR)

if not len(args.input_files) >= 1:
logger.critical("No input files specified")
sys.exit(ARGUMENT_ERR)

if args.validate_sbml_units:
# A failed unit consistency check generates an error
strict_units = True
else:
# A failed unit consistency check generates only a warning
strict_units = False

try:
result = validate_sbml_files(args.input_files, strict_units)
except Exception as e:
logger.critical(f"validate_sbml_files failed with {str(e)}")
sys.exit(UNKNOWN_ERR)

if result:
# All files validated ok (with possible warnings but no errors)
sys.exit(0)

# Errors of some kind were found in one or more files
logger.error(f"one or more SBML files failed to validate")
sys.exit(UNKNOWN_ERR)

# These do not use the shared option where files are supplied
# They require the file name to be specified after
# TODO: handle these better
Expand Down
94 changes: 94 additions & 0 deletions pyneuroml/sbml/__init__.py
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"""
use libsbml.SBMLDocument.checkConsistency to check validaity of an SBML document
based on https://github.com/combine-org/combine-notebooks/blob/main/src/combine_notebooks/validation/validation_sbml.py
"""

import os
import errno
import libsbml
from libsbml import SBMLReader
from typing import List


def validate_sbml_files(input_files: List[str], strict_units: bool = False) -> bool:
"""
validate each input file using libsbml.SBMLDocument.checkConsistency
input_files is a list of one or more filepaths
strict_units converts unit consistency warnings into errors
"""

if not len(input_files) >= 1:
raise ValueError("No input files specified")

all_valid = True

for file_name in input_files:
# These checks are already implemented by SBMLReader
# But could just be logged along with the other error types rather than causing exceptions
if not os.path.isfile(file_name):
raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), file_name)

if not os.access(file_name, os.R_OK):
raise IOError(f"Could not read SBML file {file_name}")

try:
reader = SBMLReader()
doc = reader.readSBML(file_name)
except Exception:
# usually errors are logged within the doc object rather than being thrown
raise IOError(f"SBMLReader failed trying to open the file {file_name}")

# Always check for unit consistency
doc.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, True)
doc.checkConsistency()

# Get errors/warnings arising from the file reading or consistency checking calls above
n_errors: int = doc.getNumErrors()
errors: List[libsbml.SBMLError] = list()
warnings: List[libsbml.SBMLError] = list()

for k in range(n_errors):
error: libsbml.SBMLError = doc.getError(k)
severity = error.getSeverity()
if (severity == libsbml.LIBSBML_SEV_ERROR) or (
severity == libsbml.LIBSBML_SEV_FATAL
):
errors.append(error)
elif (
(strict_units is True)
# For error code definitions see
# https://github.com/sbmlteam/libsbml/blob/fee56c943ea39b9ac1f8491cac2fc9b3665e368f/src/sbml/SBMLError.h#L528
# and sbml.level-3.version-2.core.release-2.pdf page 159
and (error.getErrorId() >= 10500)
and (error.getErrorId() <= 10599)
):
# Treat unit consistency warnings as errors
errors.append(error)
else:
warnings.append(error)

# print results
print("-" * 80)
print(f"{'validation error(s)':<25}: {len(errors)}")
print(f"{'validation warning(s)':<25}: {len(warnings)}")

if len(errors) > 0:
all_valid = False
print("--- errors ---")
for kerr in enumerate(errors):
print(f"E{kerr}: {error.getCategoryAsString()} L{error.getLine()}")
print(
f"[{error.getSeverityAsString()}] {error.getShortMessage()} | {error.getMessage()}"
)

if len(warnings) > 0:
print("--- warnings ---")
for kwarn in enumerate(warnings):
print(f"E{kwarn}: {error.getCategoryAsString()} L{error.getLine()}")
print(
f"[{error.getSeverityAsString()}] {error.getShortMessage()} | {error.getMessage()}"
)

print("-" * 80)

return all_valid
4 changes: 4 additions & 0 deletions setup.cfg
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Expand Up @@ -101,6 +101,9 @@ plotly =
nsg =
pynsgr

sbml =
python-libsbml

all =
pyNeuroML[neuron]
pyNeuroML[brian]
Expand All @@ -113,6 +116,7 @@ all =
pyNeuroML[vispy]
pyNeuroML[plotly]
pyNeuroML[nsg]
pyNeuroML[sbml]

dev =
pyNeuroML[all]
Expand Down
7 changes: 7 additions & 0 deletions test-ghactions.sh
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Expand Up @@ -70,6 +70,13 @@ pynml LEMS_NML2_Ex9_FN.xml -spineml
pynml LEMS_NML2_Ex9_FN.xml -sbml


echo
echo "################################################"
echo "## Simple SBML validation example"

pynml -validate-sbml test_data/valid_doc.sbml
pynml -validate-sbml-units test_data/valid_doc.sbml


echo
echo "################################################"
Expand Down
42 changes: 42 additions & 0 deletions tests/sbml/test_data/inconsistent_units_doc.sbml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model substanceUnits="mole" timeUnits="second" extentUnits="mole">
<listOfUnitDefinitions>
<unitDefinition id="per_second">
<listOfUnits>
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="c1" spatialDimensions="3" size="1" units="litre" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1" compartment="c1" initialAmount="5" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S2" compartment="c1" initialAmount="0" substanceUnits="gram" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k" value="1" units="per_second" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r1" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="S1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k </ci>
<ci> S1 </ci>
<ci> S2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
2 changes: 2 additions & 0 deletions tests/sbml/test_data/invalid_doc00.sbml
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@@ -0,0 +1,2 @@
10 PRINT "HELLO"
20 GOTO 10
42 changes: 42 additions & 0 deletions tests/sbml/test_data/invalid_doc01.sbml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model substanceUnits="molerat" timeUnits="second" extentUnits="mole">
<listOfUnitDefinitions>
<unitDefinition id="per_second">
<listOfUnits>
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="c1" spatialDimensions="3" size="1" units="litre" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1" compartment="c1" initialAmount="5" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S2" compartment="c1" initialAmount="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k" value="1" units="per_second" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r1" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="S1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k </ci>
<ci> S1 </ci>
<ci> c1 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
42 changes: 42 additions & 0 deletions tests/sbml/test_data/invalid_doc02.sbml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model substanceUnits="mole" timeUnits="second" extentUnits="mole">
<listOfUnitDefinitions>
<unitDefinition id="per_second">
<listOfUnits>
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="c1" spatialDimensions="3" size="1" units="litre" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1" compartment="c1" initialAmount="5" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S2" compartment="c1" initialAmount="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k" value="1" units="per_second" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r1" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="S1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k </ci>
<ci> S1 </ci>
<ci> c1 </ci>
</math>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
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