Merge branch 'robertvi-feat/sedml-validator' into experimental

NeuroML · Dec 13, 2023 · 064744d · 064744d
2 parents 9a56b68 + 20c2991
commit 064744d
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Showing 10 changed files with 413 additions and 7 deletions.
diff --git a/pyneuroml/pynml.py b/pyneuroml/pynml.py
@@ -60,18 +60,18 @@
     # continue to work
     from pyneuroml.plot import generate_plot, generate_interactive_plot  # noqa
 else:
-    # Define a new method, which only gets called if a user explicitly tries to 
+    # Define a new method, which only gets called if a user explicitly tries to
     # run generate_plot (and so requires matplotlib). If it's never called, matplotlib
     # doesn't get imported
 
     def generate_plot(*args, **kwargs):
         try:
             import matplotlib
             from pyneuroml.plot import generate_plot as gp
+
             return gp(*args, **kwargs)
-        
+
         except Exception as e:
-
             logger.error("Matplotlib not found!")
             warnings.warn(
                 """
@@ -87,10 +87,10 @@ def generate_interactive_plot(*args, **kwargs):
         try:
             import matplotlib
             from pyneuroml.plot import generate_interactive_plot as gp
+
             return gp(*args, **kwargs)
-        
+
         except Exception as e:
-
             logger.error("Matplotlib not found!")
             warnings.warn(
                 """
@@ -102,6 +102,7 @@ def generate_interactive_plot(*args, **kwargs):
                 stacklevel=2,
             )
 
+
 DEFAULTS = {
     "v": False,
     "default_java_max_memory": "400M",
@@ -404,6 +405,11 @@ def parse_arguments():
         action="store_true",
         help=("Validate SBML file(s), unit consistency failure generates an error"),
     )
+    mut_exc_opts.add_argument(
+        "-validate-sedml",
+        action="store_true",
+        help=("Validate SEDML file(s)"),
+    )
 
     return parser.parse_args()
 
@@ -2213,6 +2219,32 @@ def evaluate_arguments(args):
         logger.error(f"one or more SBML files failed to validate")
         sys.exit(UNKNOWN_ERR)
 
+    # Deal with the SEDML validation option which doesn't call run_jneuroml
+    if args.validate_sedml:
+        try:
+            from pyneuroml.sedml import validate_sedml_files
+        except Exception:
+            logger.critical("Unable to import pyneuroml.sedml")
+            sys.exit(UNKNOWN_ERR)
+
+        if not len(args.input_files) >= 1:
+            logger.critical("No input files specified")
+            sys.exit(ARGUMENT_ERR)
+
+        try:
+            result = validate_sedml_files(args.input_files)
+        except Exception as e:
+            logger.critical(f"validate_sedml_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 SEDML 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

diff --git a/pyneuroml/sedml/__init__.py b/pyneuroml/sedml/__init__.py
@@ -0,0 +1,60 @@
+"""
+use libsedml getErrorLog().getNumFailsWithSeverity(libsedml.LIBSEDML_SEV_ERROR) to validate SEDML file(s)
+based on example here https://github.com/SED-ML/libSEDML/blob/master/examples/python/echo_sedml.py
+"""
+
+import os
+import errno
+import libsedml
+from typing import List
+
+
+def check_file(file_name):
+    """
+    check string path points to a file and that we have read access to it
+    """
+
+    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 file {file_name}")
+
+
+def validate_sedml_files(input_files: List[str]) -> bool:
+    """
+    validate SEDML file(s)
+    input_files is a list of one or more filepaths
+    """
+
+    if not len(input_files) >= 1:
+        raise ValueError("No input files specified")
+
+    all_valid = True
+
+    for file_name in input_files:
+        # check file exists and is readable
+        check_file(file_name)
+
+        try:
+            doc = libsedml.readSedML(file_name)
+        except Exception:
+            raise IOError(f"readSedML failed trying to open the file {file_name}")
+
+        # readSedML does not check existance of model source files, do it ourselves here
+        for model in doc.getListOfModels():
+            # treat file path as relative to SEDML file
+            dir_name = os.path.dirname(file_name)
+            source_file = os.path.join(dir_name, model.getSource())
+
+            try:
+                check_file(source_file)
+            except Exception:
+                all_valid = False
+                print("Cannot find or access model source file {source_file}")
+
+        if doc.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSEDML_SEV_ERROR) > 0:
+            all_valid = False
+            print(doc.getErrorLog().toString())
+
+    return all_valid
diff --git a/setup.cfg b/setup.cfg
@@ -100,8 +100,9 @@ plotly =
 nsg =
     pynsgr
 
-sbml =
+combine =
     python-libsbml
+    python-libsedml
 
 all =
     pyNeuroML[neuron]
@@ -115,7 +116,7 @@ all =
     pyNeuroML[vispy]
     pyNeuroML[plotly]
     pyNeuroML[nsg]
-    pyNeuroML[sbml]
+    pyNeuroML[combine]
 
 dev =
     pyNeuroML[all]

diff --git a/tests/sedml/test_data/invalid_doc01.sedml b/tests/sedml/test_data/invalid_doc01.sedml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by phraSED-ML version v0.5beta on 2015-12-01 15:44 with libSBML version 5.11.9. -->
+<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
+  <listOfSimulations>
+    <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfPoints="10">
+      <algorithm kisaoID="KISAO:0000019"/>
+    </uniformTimeCourse>
+  </listOfSimulationz>
+  <listOfModels>
+    <model id="mod1" language="urn:sedml:language:sbml.level-3.version-1" source="00001-sbml.xml"/>
+  </listOfModels>
+  <listOfTasks>
+    <task id="task1" modelReference="mod1" simulationReference="sim1"/>
+  </listOfTasks>
+  <listOfDataGenerators>
+    <dataGenerator id="report_0_0_0" name="time">
+      <listOfVariables>
+        <variable id="time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> time </ci>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="report_0_0_1" name="a">
+      <listOfVariables>
+        <variable id="a" target="/sbml:sbml/sbml:model/descendant::*[@id='a']" taskReference="task1" modelReference="mod1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> a </ci>
+      </math>
+    </dataGenerator>
+  </listOfDataGenerators>
+  <listOfOutputs>
+    <report id="report_0">
+      <listOfDataSets>
+        <dataSet id="report_0_0_0_dataset" label="time" dataReference="report_0_0_0"/>
+        <dataSet id="report_0_0_1_dataset" label="a" dataReference="report_0_0_1"/>
+      </listOfDataSets>
+    </report>
+  </listOfOutputs>
+</sedML>
diff --git a/tests/sedml/test_data/invalid_doc02.sedml b/tests/sedml/test_data/invalid_doc02.sedml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by phraSED-ML version v0.5beta on 2015-12-01 15:44 with libSBML version 5.11.9. -->
+<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
+  <listOfSimulations>
+    <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfPoints="10">
+      <algorithm kisaoID="KISAO:0000019"/>
+    </uniformTimeCourse>
+  </listOfSimulations>
+  <listOfNoodles>
+    <model id="mod1" language="urn:sedml:language:sbml.level-3.version-1" source="00001-sbml.xml"/>
+  </listOfNoodles>
+  <listOfTasks>
+    <task id="task1" modelReference="mod1" simulationReference="sim1"/>
+  </listOfTasks>
+  <listOfDataGenerators>
+    <dataGenerator id="report_0_0_0" name="time">
+      <listOfVariables>
+        <variable id="time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> time </ci>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="report_0_0_1" name="a">
+      <listOfVariables>
+        <variable id="a" target="/sbml:sbml/sbml:model/descendant::*[@id='a']" taskReference="task1" modelReference="mod1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> a </ci>
+      </math>
+    </dataGenerator>
+  </listOfDataGenerators>
+  <listOfOutputs>
+    <report id="report_0">
+      <listOfDataSets>
+        <dataSet id="report_0_0_0_dataset" label="time" dataReference="report_0_0_0"/>
+        <dataSet id="report_0_0_1_dataset" label="a" dataReference="report_0_0_1"/>
+      </listOfDataSets>
+    </report>
+  </listOfOutputs>
+</sedML>
diff --git a/tests/sedml/test_data/missing_model_source.sedml b/tests/sedml/test_data/missing_model_source.sedml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by phraSED-ML version v0.5beta on 2015-12-01 15:44 with libSBML version 5.11.9. -->
+<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
+  <listOfSimulations>
+    <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfPoints="10">
+      <algorithm kisaoID="KISAO:0000019"/>
+    </uniformTimeCourse>
+  </listOfSimulations>
+  <listOfModels>
+    <model id="mod1" language="urn:sedml:language:sbml.level-3.version-1" source="nonexistant.sbml"/>
+  </listOfModels>
+  <listOfTasks>
+    <task id="task1" modelReference="mod1" simulationReference="sim1"/>
+  </listOfTasks>
+  <listOfDataGenerators>
+    <dataGenerator id="report_0_0_0" name="time">
+      <listOfVariables>
+        <variable id="time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> time </ci>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="report_0_0_1" name="a">
+      <listOfVariables>
+        <variable id="a" target="/sbml:sbml/sbml:model/descendant::*[@id='a']" taskReference="task1" modelReference="mod1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> a </ci>
+      </math>
+    </dataGenerator>
+  </listOfDataGenerators>
+  <listOfOutputs>
+    <report id="report_0">
+      <listOfDataSets>
+        <dataSet id="report_0_0_0_dataset" label="time" dataReference="report_0_0_0"/>
+        <dataSet id="report_0_0_1_dataset" label="a" dataReference="report_0_0_1"/>
+      </listOfDataSets>
+    </report>
+  </listOfOutputs>
+</sedML>
diff --git a/tests/sedml/test_data/no_read_access.sedml b/tests/sedml/test_data/no_read_access.sedml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by phraSED-ML version v0.5beta on 2015-12-01 15:44 with libSBML version 5.11.9. -->
+<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
+  <listOfSimulations>
+    <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfPoints="10">
+      <algorithm kisaoID="KISAO:0000019"/>
+    </uniformTimeCourse>
+  </listOfSimulations>
+  <listOfModels>
+    <model id="mod1" language="urn:sedml:language:sbml.level-3.version-1" source="00001-sbml.xml"/>
+  </listOfModels>
+  <listOfTasks>
+    <task id="task1" modelReference="mod1" simulationReference="sim1"/>
+  </listOfTasks>
+  <listOfDataGenerators>
+    <dataGenerator id="report_0_0_0" name="time">
+      <listOfVariables>
+        <variable id="time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> time </ci>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="report_0_0_1" name="a">
+      <listOfVariables>
+        <variable id="a" target="/sbml:sbml/sbml:model/descendant::*[@id='a']" taskReference="task1" modelReference="mod1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> a </ci>
+      </math>
+    </dataGenerator>
+  </listOfDataGenerators>
+  <listOfOutputs>
+    <report id="report_0">
+      <listOfDataSets>
+        <dataSet id="report_0_0_0_dataset" label="time" dataReference="report_0_0_0"/>
+        <dataSet id="report_0_0_1_dataset" label="a" dataReference="report_0_0_1"/>
+      </listOfDataSets>
+    </report>
+  </listOfOutputs>
+</sedML>
diff --git a/tests/sedml/test_data/valid_doc.sbml b/tests/sedml/test_data/valid_doc.sbml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.8.1 on 2015-12-02 12:55 with libSBML version 5.11.9. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+  <model id="__main" name="__main">
+    <listOfParameters>
+      <parameter id="a" value="3" constant="true"/>
+    </listOfParameters>
+  </model>
+</sbml>
diff --git a/tests/sedml/test_data/valid_doc.sedml b/tests/sedml/test_data/valid_doc.sedml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by phraSED-ML version v0.5beta on 2015-12-01 15:44 with libSBML version 5.11.9. -->
+<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
+  <listOfSimulations>
+    <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfPoints="10">
+      <algorithm kisaoID="KISAO:0000019"/>
+    </uniformTimeCourse>
+  </listOfSimulations>
+  <listOfModels>
+    <model id="mod1" language="urn:sedml:language:sbml.level-3.version-1" source="valid_doc.sbml"/>
+  </listOfModels>
+  <listOfTasks>
+    <task id="task1" modelReference="mod1" simulationReference="sim1"/>
+  </listOfTasks>
+  <listOfDataGenerators>
+    <dataGenerator id="report_0_0_0" name="time">
+      <listOfVariables>
+        <variable id="time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> time </ci>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="report_0_0_1" name="a">
+      <listOfVariables>
+        <variable id="a" target="/sbml:sbml/sbml:model/descendant::*[@id='a']" taskReference="task1" modelReference="mod1"/>
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> a </ci>
+      </math>
+    </dataGenerator>
+  </listOfDataGenerators>
+  <listOfOutputs>
+    <report id="report_0">
+      <listOfDataSets>
+        <dataSet id="report_0_0_0_dataset" label="time" dataReference="report_0_0_0"/>
+        <dataSet id="report_0_0_1_dataset" label="a" dataReference="report_0_0_1"/>
+      </listOfDataSets>
+    </report>
+  </listOfOutputs>
+</sedML>