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test.py
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test.py
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###
# This script validates the local NeuroML2 definitions as LEMS
# files and the NeuroML examples as NeuroML files. If any of these
# is not valid, it will report a test failure.
#
# It will also check for the consistency of the NeuroML and LEMS
# files in this repo with the copies that are supposed to be
# present in other local directories. Finally, it will check
# whether the local jnml executable can validate the NeuroML
# examples in the examples/ directory. It will report (though not
# by throwing a full test failure, as this shouldn't really concern
# this repo as long as the tests above pass) if any of these
# conditions is not met.
#
# Subject to change without notice.
###
import os
import sys
from lxml import etree
import subprocess
import filecmp
verbose = False
vverbose = False
if len(sys.argv) == 2 and sys.argv[1]=="-v":
verbose = True
if len(sys.argv) == 2 and sys.argv[1]=="-vv":
vverbose = True
lems_def_dir="NeuroML2CoreTypes"
lems_def_list=os.listdir(lems_def_dir)
lems_exs_dir="LEMSexamples"
lems_exs_list=os.listdir(lems_exs_dir)
lems_schema = "../LEMS/Schemas/LEMS/LEMS_v0.7.6.xsd"
lems_schema_file = open(lems_schema)
lems_xmlschema_doc = etree.parse(lems_schema_file)
lems_xmlschema = etree.XMLSchema(lems_xmlschema_doc)
lems_master_ex_dir="../LEMS/examples"
lems_master_ex_list=os.listdir(lems_master_ex_dir)
nml2_schema_name = "NeuroML_v2.3.1.xsd"
nml2_schema = "Schemas/NeuroML2/%s"%nml2_schema_name
nml2_schema_file = open(nml2_schema)
nml2_xmlschema_doc = etree.parse(nml2_schema_file)
nml2_xmlschema = etree.XMLSchema(nml2_xmlschema_doc)
nml2_ex_dir="examples"
nml2_ex_list=os.listdir(nml2_ex_dir)
template_src_dir="../git/som-codegen"
template_java_dir="../org.neuroml.export/src/main/resources"
##template_python_dir="../pylems/lems/"
template_list=['cvode/cvode.vm', 'cvode/Makefile', 'matlab/matlab_ode.vm', 'modelica/main_class.vm', 'modelica/run.vm', 'xpp/xpp.vm']
def check_same_file(fileA, fileB):
same = filecmp.cmp(fileA, fileB)
if vverbose: print(" -- Comparing files {} and {}...".format(fileA, fileB))
if not same and verbose: print(" -- Files {} and {} are different!".format(fileA, fileB))
return same
def check_valid_lems(schema, document):
tree = etree.parse(lems_def_dir + "/" + document)
assert lems_xmlschema.validate(tree), "{} is not valid LEMS!".format(document)
def check_valid_neuroml(document):
tree = etree.parse(nml2_ex_dir + "/" + document)
assert nml2_xmlschema.validate(tree)
def check_jnml_validates_neuroml(document):
p = subprocess.Popen(["jnml -validate "+ nml2_ex_dir+"/"+document], shell=True, stdout=subprocess.PIPE)
p.communicate()
return not bool(p.returncode), "{} is not valid NeuroML!".format(document)
def test_validate_lems_files():
print("Validating LEMS files against: {}".format(lems_schema))
for document in lems_def_list:
if document.endswith("xml") and not document.startswith("LEMS") and not document.startswith("Ex"):
yield check_valid_lems, lems_schema, document
def test_validate_neuroml_files():
print("Validating NeuroML 2 files against: {}".format(nml2_schema))
for document in nml2_ex_list:
if document.endswith("nml"):
yield check_valid_neuroml, document
if __name__ == '__main__':
import nose
print("--------------------------------------------------")
print(" Checking local copies of NeuroML schemas")
if not check_same_file('Schemas/NeuroML2/%s'%nml2_schema_name, '../libNeuroML/neuroml/nml/%s'%nml2_schema_name):
print("FAIL: NeuroML schemas in libNeuroML not in sync!")
else:
print("NeuroML schemas in libNeuroML are in sync.")
if os.path.isdir('../neuroConstruct') and not check_same_file('Schemas/NeuroML2/NeuroML_v2alpha.xsd', '../neuroConstruct/NeuroML2/Schemas/NeuroML2/NeuroML_v2alpha.xsd'):
print("FAIL: NeuroML alpha schemas in neuroConstruct not in sync!")
else:
print("NeuroML alpha schemas in neuroConstruct are in sync.")
if os.path.isdir('../neuroConstruct') and not check_same_file('Schemas/NeuroML2/%s'%nml2_schema_name, '../neuroConstruct/NeuroML2/Schemas/NeuroML2/%s'%nml2_schema_name):
print("FAIL: NeuroML schemas in neuroConstruct not in sync!")
else:
print("NeuroML schemas in neuroConstruct are in sync.")
if os.path.isdir('../git/NeuroMLWebsite') and not check_same_file('Schemas/NeuroML2/%s'%nml2_schema_name, '../git/NeuroMLWebsite/public/schema/neuroml2/%s'%nml2_schema_name):
print("FAIL: NeuroML schemas in NeuroMLWebsite not in sync!")
else:
print("NeuroML schemas in NeuroMLWebsite are in sync.")
print("--------------------------------------------------")
print(" Checking local copies of examples")
are_files_identical_list = []
for filename in lems_master_ex_list:
if filename.endswith("xml"):
main_ex = lems_master_ex_dir+"/"+filename
copy_org_lems_ex = "../jLEMS/src/test/resources/"+filename
are_files_identical_list.append(check_same_file(main_ex, copy_org_lems_ex))
if not all(are_files_identical_list):
print("FAIL: LEMS examples in jLEMS are not in sync!")
else:
print("LEMS examples in jLEMS are in sync.")
are_files_identical_list = []
for filename in lems_master_ex_list:
if filename.endswith("xml"):
main_ex = lems_master_ex_dir+"/"+filename
copy_org_lems_ex = "../pylems/examples/"+filename
are_files_identical_list.append(check_same_file(main_ex, copy_org_lems_ex))
if not all(are_files_identical_list):
print("FAIL: LEMS examples in pylems are not in sync!")
else:
print("LEMS examples in pylems are in sync.")
are_files_identical_list = []
for filename in template_list:
src_template = template_src_dir+"/"+filename
java_template = template_java_dir+"/"+filename
are_files_identical_list.append(check_same_file(src_template, java_template))
if not all(are_files_identical_list):
print("FAIL: Templates for Java are not in sync!")
else:
print("LEMS Templates for Java are in sync.")
print("-------------------------------------------------------")
print(" Testing if jnml validates the NeuroML example files")
not_validated_by_jnml =[]
for document in nml2_ex_list:
if document.endswith("nml"):
if not check_jnml_validates_neuroml(document):
not_validated_by_jnml.append(document)
print("FAIL: jnml does not validate {}".format(document))
if not not_validated_by_jnml:
print("jnml validates all NeuroML example files.")
if '-r' in sys.argv:
print("--------------------------------------------------")
print(" Testing execution of LEMS files using jLEMS")
import subprocess
import os
lems_exs_list.sort()
to_ignore = ['LEMS_NML2_Ex13_Instances.xml']
for file in lems_exs_list:
if file.endswith("xml") and file.startswith("LEMS") and not file in to_ignore:
lems_file = '%s/%s'%(lems_exs_dir,file)
print("Testing %s..." %(lems_file))
#subprocess.call(['lems %s'%(lems_file)])
#os.system('~/jLEMS/lems %s'%(lems_file))
subprocess.call('jnml %s -nogui &'%(lems_file), shell=True)
print("-------------------------------------------------------")
print(" Validating NeuroML definitions and examples")
nose.main()