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<?php
include("libSBML.php");
function printUsageAndExit() {
echo "usage: validateSBML [-u] filename\n";
echo " -u : disable unit consistency check\n";
exit(1);
}
function validateSBML($file, $enableUnitCheck) {
echo "validating: $file\n";
$reader = new SBMLReader();
$doc = $reader->readSBMLFromFile($file);
$log = $doc->getErrorLog();
$numFatals = $log->getNumFailsWithSeverity(LIBSBML_SEV_FATAL);
$numErrors = $log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR);
if ($numFatals + $numErrors > 0) {
$doc->printErrors();
echo "Further consistency checking and validation aborted.\n";
return FALSE;
}
$doc->setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, $enableUnitCheck);
$failures = $doc->checkConsistency();
$numFatals = $log->getNumFailsWithSeverity(LIBSBML_SEV_FATAL);
$numErrors = $log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR);
if ($failures > 0) {
echo "\n*** consistency check ***\n";
$doc->printErrors();
}
if ($numFatals + $numErrors > 0) {
return FALSE;
}
return True;
}
echo "\n\nValidateSBML\n";
if ($argc < 2) {
printUsageAndExit();
}
$index = 1;
$file = $argv[1];
$enableUnitCheck = FALSE;
if ($file == "-u") {
$enableUnitCheck = TRUE;
$file = $argv[2];
$index = 2;
}
if ($file == "") {
printUsageAndExit();
}
$numInvalid = 0;
$numFiles = 0;
for ($i = $index; $i < $argc; $i++) {
$file = $argv[$index];
$numFiles = $numFiles +1;
if (!validateSBML($file, $enableUnitCheck))
$numInvalid = $numInvalid + 1;
}
$numValid = $numFiles - $numInvalid;
echo "\nValidated $numFiles file(s), $numValid valid file(s), ";
echo "$numInvalid invalid file(s)\n";
if (!$enableUnitCheck) {
echo " (Unit consistency checks skipped)\n";
}
echo "\n";
?>
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