libSBML Python API
5.11.0
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This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
The error log is a list. Each SBMLDocument maintains its own SBMLErrorLog. When a libSBML operation on SBML content results in an error, or when there is something worth noting about the SBML content, the issue is reported as an SBMLError object stored in the SBMLErrorLog list.
SBMLErrorLog is derived from XMLErrorLog, an object class that serves exactly the same purpose but for the XML parsing layer. XMLErrorLog provides crucial methods such as getNumErrors() for determining how many SBMLError or XMLError objects are in the log. SBMLErrorLog inherits these methods.
The general approach to working with SBMLErrorLog in user programs involves first obtaining a pointer to a log from a libSBML object such as SBMLDocument. Callers should then use getNumErrors() to inquire how many objects there are in the list. (The answer may be 0.) If there is at least one SBMLError object in the SBMLErrorLog instance, callers can then iterate over the list using SBMLErrorLog.getError(), using methods provided by the SBMLError class to find out the error code and associated information such as the error severity, the message, and the line number in the input.
If you wish to simply print the error strings for a human to read, an easier and more direct way might be to use SBMLDocument.printErrors().
Public Member Functions | |
def | add (self, error) |
def | changeErrorSeverity (self, args) |
Changes the severity override for errors in the log that have a given severity. More... | |
def | clearLog (self) |
Deletes all errors from this log. More... | |
def | contains (self, errorId) |
Returns true if SBMLErrorLog contains an errorId. More... | |
def | getError (self, n) |
Log of diagnostics reported during processing. More... | |
def | getErrorWithSeverity (self, n, severity) |
Returns the nth SBMLError object with given severity in this log. More... | |
def | getNumErrors (self) |
Log of diagnostics reported during XML processing. More... | |
def | getNumFailsWithSeverity (self, args) |
Returns the number of errors that have been logged with the given severity code. More... | |
def | getSeverityOverride (self) |
Returns the current override. More... | |
def | isSeverityOverridden (self) |
Returns a boolean indicating whether or not the severity has been overridden. More... | |
def | printErrors (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | remove (self, errorId) |
Removes an error having errorId from the SBMLError list. More... | |
def | setSeverityOverride (self, severity) |
Set the severity override. More... | |
def | toString (self) |
Writes all errors contained in this log to a string and returns it. More... | |
def | unsetSeverityOverride (self) |
Usets an existing override. More... | |
def libsbml.SBMLErrorLog.add | ( | self, | |
error | |||
) |
add(SBMLError error)
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inherited |
Changes the severity override for errors in the log that have a given severity.
changeErrorSeverity(long originalSeverity, long targetSeverity, string package) changeErrorSeverity(long originalSeverity, long targetSeverity)
This method searches through the list of errors in the log, comparing each one's severity to the value of originalSeverity
. For each error encountered with that severity logged by the named package
, the severity of the error is reset to targetSeverity
.
originalSeverity | the severity code to match |
targetSeverity | the severity code to use as the new severity |
package | a string, the name of an SBML Level 3 package extension to use to narrow the search for errors. A value of 'all' signifies to match against errors logged from any package; a value of a package nickname such as 'comp' signifies to limit consideration to errors from just that package. If no value is provided, 'all' is the default. |
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inherited |
Deletes all errors from this log.
clearLog()
def libsbml.SBMLErrorLog.contains | ( | self, | |
errorId | |||
) |
Returns true if SBMLErrorLog contains an errorId.
errorId | the error identifier of the error to be found. |
contains(long errorId) bool
def libsbml.SBMLErrorLog.getErrorWithSeverity | ( | self, | |
n, | |||
severity | |||
) |
Returns the nth SBMLError object with given severity in this log.
getErrorWithSeverity(long n, long severity) SBMLError
Index n
is counted from 0. Callers should first inquire about the number of items in the log by using the getNumFailsWithSeverity() method. Attempts to use an error index number that exceeds the actual number of errors in the log will result in a None
being returned.
n | the index number of the error to retrieve (with 0 being the first error). |
severity | the severity of the error to retrieve |
None
if n
is greater than or equal to getNumFailsWithSeverity().def libsbml.SBMLErrorLog.getNumFailsWithSeverity | ( | self, | |
args | |||
) |
Returns the number of errors that have been logged with the given severity code.
getNumFailsWithSeverity(long severity) long
severity | a value from the set of LIBSBML_SEV_ constants defined by the interface class libsbml. |
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inherited |
Returns the current override.
getSeverityOverride() long
LIBSBML_OVERRIDE_
:
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inherited |
Returns a boolean indicating whether or not the severity has been overridden.
isSeverityOverridden() bool
True
if an error severity override has been set, False
otherwise.
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inherited |
This method has multiple variants; they differ in the arguments they accept.
printErrors(ostream stream) printErrors() printErrors(ostream stream, long severity)
Each variant is described separately below.
printErrors(std::ostream& stream = std::cerr)
Prints all the errors or warnings stored in this error log.
This method prints the text to the stream given by the optional parameter stream
. If no stream is given, the method prints the output to the standard error stream.
The format of the output is:
N error(s): line NNN: (id) message
If no errors have occurred, i.e., getNumErrors() == 0
, then no output will be produced.
stream | the ostream or ostringstream object indicating where the output should be printed. |
printErrors(std::ostream& stream, long severity)
Prints the errors or warnings with given severity stored in this error log.
This method prints the text to the stream given by the optional parameter stream
. If no stream is given, the method prints the output to the standard error stream.
The format of the output is:
N error(s): line NNN: (id) message
If no errors with that severity was found, then no output will be produced.
stream | the ostream or ostringstream object indicating where the output should be printed. |
severity | the severity of the errors sought. |
def libsbml.SBMLErrorLog.remove | ( | self, | |
errorId | |||
) |
Removes an error having errorId from the SBMLError list.
remove(long errorId)
Only the first item will be removed if there are multiple errors with the given errorId.
errorId | the error identifier of the error to be removed. |
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inherited |
Set the severity override.
setSeverityOverride(long severity)
severity | an override code indicating what to do. If the value is LIBSBML_OVERRIDE_DISABLED (the default setting) all errors logged will be given the severity specified in their usual definition. If the value is LIBSBML_OVERRIDE_WARNING, then all errors will be logged as warnings. If the value is LIBSBML_OVERRIDE_DONT_LOG, no error will be logged, regardless of their severity. |
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inherited |
Writes all errors contained in this log to a string and returns it.
toString() string
This method uses printErrors() to format the diagnostic messages. Please consult that method for information about the organization of the messages in the string returned by this method.
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inherited |
Usets an existing override.
unsetSeverityOverride()