|
libSBML C++ API
5.18.0
|
|
libSBML C++ API
5.18.0
|
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.
LibSBML can be configured to use any of a number of XML parsers; at the time of this writing, libSBML supports Xerces versions 2.4 through 3.1, Expat version 1.95.x and higher, and libxml2 version 2.6.16 and higher. These parsers each report different status codes for the various exceptions that can occur during XML processing. The XMLError object class abstracts away from the particular diagnostics reported by the different parsers and presents a single uniform interface and set of status codes, along with operations for manipulating the error objects.
When the libSBML XML parser layer encounters an error in the XML content being processed, or when there is something else wrong (such as an out-of-memory condition), the problems are reported as XMLError objects. Each XMLError object instance has an identification number that identifies the nature of the problem. This error identifier will be up to five digits long and drawn from the enumeration XMLErrorCode_t. Applications can use the error identifiers as a means of recognizing the error encountered and changing their behavior if desired.
Integer error codes are useful for software, but not so much for telling humans what happened. For this reason, XMLError also provides two text messages describing the nature of the error. These messages are accessible by means of the methods XMLError::getShortMessage() and XMLError::getMessage(). The method XMLError::getShortMessage() returns a very brief synopsis of the warning or error condition, whereas XMLError::getMessage() returns a longer explanation. These text strings are suitable for displaying to human users.
Each XMLError object also contains a category code; its value may be retrieved using the method XMLError::getCategory(). Category values are drawn from the enumeration XMLErrorCategory_t described below. Categories are used by libSBML to provide more information to calling programs about the nature of a given error.
In addition to category codes, each XMLError object also has a severity code; its value may be retrieved using the method XMLError::getSeverity(). Severity code values are drawn from the enumeration XMLErrorSeverity_t, described below. Severity levels range from informational (LIBSBML_SEV_INFO) to fatal errors (LIBSBML_SEV_FATAL).
Finally, XMLError objects record the line and column near where the problem occurred in the XML content. The values can be retrieved using the methods XMLError::getLine() and XMLError::getColumn(). We say "near
where the problem occurred", because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0 or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.
This is an enumeration of all the error and warning codes returned by the XML layer in libSBML. Each code is an integer with a 4-digit value less than 10000. The following table lists each possible value and a brief description of its meaning.
| Enumerator | Meaning | Category | Severity |
|---|---|---|---|
| XMLUnknownError | Unrecognized error encountered internally | INTERNAL | FATAL |
| XMLOutOfMemory | Out of memory | SYSTEM | FATAL |
| XMLFileUnreadable | File unreadable | SYSTEM | ERROR |
| XMLFileUnwritable | File unwritable | SYSTEM | ERROR |
| XMLFileOperationError | Error encountered while attempting file operation | SYSTEM | ERROR |
| XMLNetworkAccessError | Network access error | SYSTEM | ERROR |
| InternalXMLParserError | Internal XML parser state error | INTERNAL | FATAL |
| UnrecognizedXMLParserCode | XML parser returned an unrecognized error code | INTERNAL | FATAL |
| XMLTranscoderError | Character transcoder error | INTERNAL | FATAL |
| MissingXMLDecl | Missing XML declaration at beginning of XML input | XML | ERROR |
| MissingXMLEncoding | Missing encoding attribute in XML declaration | XML | ERROR |
| BadXMLDecl | Invalid or unrecognized XML declaration or XML encoding | XML | ERROR |
| BadXMLDOCTYPE | Invalid, malformed or unrecognized XML DOCTYPE declaration | XML | ERROR |
| InvalidCharInXML | Invalid character in XML content | XML | ERROR |
| BadlyFormedXML | XML content is not well-formed | XML | ERROR |
| UnclosedXMLToken | Unclosed XML token | XML | ERROR |
| InvalidXMLConstruct | XML construct is invalid or not permitted | XML | ERROR |
| XMLTagMismatch | Element tag mismatch or missing tag | XML | ERROR |
| DuplicateXMLAttribute | Duplicate XML attribute | XML | ERROR |
| UndefinedXMLEntity | Undefined XML entity | XML | ERROR |
| BadProcessingInstruction | Invalid, malformed or unrecognized XML processing instruction | XML | ERROR |
| BadXMLPrefix | Invalid or undefined XML namespace prefix | XML | ERROR |
| BadXMLPrefixValue | Invalid XML namespace prefix value | XML | ERROR |
| MissingXMLRequiredAttribute | Missing a required XML attribute | XML | ERROR |
| XMLAttributeTypeMismatch | Data type mismatch for the value of an attribute | XML | ERROR |
| XMLBadUTF8Content | Invalid UTF8 content | XML | ERROR |
| MissingXMLAttributeValue | Missing or improperly formed attribute value | XML | ERROR |
| BadXMLAttributeValue | Invalid or unrecognizable attribute value | XML | ERROR |
| BadXMLAttribute | Invalid, unrecognized or malformed attribute | XML | ERROR |
| UnrecognizedXMLElement | Element either not recognized or not permitted | XML | ERROR |
| BadXMLComment | Badly formed XML comment | XML | ERROR |
| BadXMLDeclLocation | XML declaration not permitted in this location | XML | ERROR |
| XMLUnexpectedEOF | Reached end of input unexpectedly | XML | ERROR |
| BadXMLIDValue | Value is invalid for XML ID, or has already been used | XML | ERROR |
| BadXMLIDRef | XML ID value was never declared | XML | ERROR |
| UninterpretableXMLContent | Unable to interpret content | XML | ERROR |
| BadXMLDocumentStructure | Bad XML document structure | XML | ERROR |
| InvalidAfterXMLContent | Encountered invalid content after expected content | XML | ERROR |
| XMLExpectedQuotedString | Expected to find a quoted string | XML | ERROR |
| XMLEmptyValueNotPermitted | An empty value is not permitted in this context | XML | ERROR |
| XMLBadNumber | Invalid or unrecognized number | XML | ERROR |
| XMLBadColon | Colon characters are invalid in this context | XML | ERROR |
| MissingXMLElements | One or more expected elements are missing | XML | ERROR |
| XMLContentEmpty | Main XML content is empty | XML | ERROR |
As discussed above, each XMLError object contains a value for a category identifier, describing the type of issue that the XMLError object represents. The category can be retrieved from an XMLError object using the method XMLError::getCategory(). The value is chosen from the enumeration of category codes XMLErrorCategory_t. The following table lists each possible value and a brief description of its meaning.
| Enumerator | Meaning |
|---|---|
| LIBSBML_CAT_INTERNAL | A problem involving the libSBML software itself or the underlying XML parser. This almost certainly indicates a software defect (i.e., bug) in libSBML. Please report instances of this to the libSBML developers. |
| LIBSBML_CAT_SYSTEM | A problem reported by the operating system, such as an inability to read or write a file. This indicates something that is not a program error but is outside of the control of libSBML. |
| LIBSBML_CAT_XML | A problem in the XML content itself. This usually arises from malformed XML or the use of constructs not permitted in SBML. |
As described above, each XMLError object contains a value for a severity code, describing how critical is the issue that the XMLError object represents. The severity can be retrieved from an XMLError object using the method XMLError::getSeverity(). The value is chosen from the enumeration of category codes XMLErrorSeverity_t. The following table lists each possible value and a brief description of its meaning.
| Enumerator | Meaning |
|---|---|
| LIBSBML_SEV_INFO | The error is actually informational and not necessarily a serious problem. |
| LIBSBML_SEV_WARNING | The error object represents a problem that is not serious enough to necessarily stop the problem, but applications should take note of the problem and evaluate what its implications may be. |
| LIBSBML_SEV_ERROR | The error object represents a serious error. The application may continue running but it is unlikely to be able to continue processing the same XML file or data stream. |
| LIBSBML_SEV_FATAL | A serious error occurred, such as an out-of-memory condition, and the software should terminate immediately. |
Public Member Functions | |
| unsigned int | getCategory () const |
| Returns the category of this error. More... | |
| const std::string & | getCategoryAsString () const |
| Returns a string describing the category of this error. More... | |
| unsigned int | getColumn () const |
| Returns the column number in the XML input near where the error, warning or other diagnostic occurred. More... | |
| unsigned int | getErrorId () const |
| Returns the identifier of this error. More... | |
| unsigned int | getErrorIdOffset () const |
| Returns libSBML's internal numerical offset for the error code associated with this error. More... | |
| unsigned int | getLine () const |
| Returns the line number in the XML input near where the error, warning or other diagnostic occurred. More... | |
| const std::string & | getMessage () const |
| Returns the message text of this error. More... | |
| const std::string & | getPackage () const |
| Returns the SBML Level 3 package extension (if any) that logged this error. More... | |
| unsigned int | getSeverity () const |
| Returns the severity of this error. More... | |
| const std::string & | getSeverityAsString () const |
| Returns a string describing the severity level of this error. More... | |
| const std::string & | getShortMessage () const |
| Returns a brief message for this error. More... | |
| bool | isError () const |
Predicate returning true or false depending on whether this error is a significant error. More... | |
| bool | isFatal () const |
Predicate returning true or false depending on whether this error is a fatal run-time error. More... | |
| bool | isInfo () const |
Predicate returning true or false depending on whether this error object is for information purposes only. More... | |
| bool | isInternal () const |
Predicate returning true or false depending on whether this error resulted from an internal program error. More... | |
| bool | isSystem () const |
Predicate returning true or false depending on whether this error was generated by the operating system. More... | |
| bool | isValid () const |
Predicate returning true or false depending on whether this error resulted from a problem or whether it was logged as an unknown error. More... | |
| bool | isWarning () const |
Predicate returning true or false depending on whether this error object is a warning. More... | |
| bool | isXML () const |
Predicate returning true or false depending on whether this error resulted from a problem in the XML input (e.g., an XML syntax error). More... | |
| XMLError & | operator= (const XMLError &rhs) |
| Assignment operator for XMLError. More... | |
| int | setColumn (unsigned int column) |
| Sets the column number where this error occurred. More... | |
| int | setLine (unsigned int line) |
| Sets the line number where this error occurred. More... | |
| XMLError (const int errorId=0, const std::string details="", const unsigned int line=0, const unsigned int column=0, const unsigned int severity=LIBSBML_SEV_FATAL, const unsigned int category=LIBSBML_CAT_INTERNAL) | |
| Creates a new XMLError to report that something occurred during XML processing. More... | |
| XMLError (const XMLError &orig) | |
| Copy constructor; creates a copy of this XMLError. More... | |
| virtual | ~XMLError () |
| Destroys this XMLError. More... | |
Static Public Member Functions | |
| static const std::string | getStandardMessage (const int code) |
| Returns a copy of the message string associated with the given predefined XMLError code. More... | |
| XMLError::XMLError | ( | const int | errorId = 0, |
| const std::string | details = "", |
||
| const unsigned int | line = 0, |
||
| const unsigned int | column = 0, |
||
| const unsigned int | severity = LIBSBML_SEV_FATAL, |
||
| const unsigned int | category = LIBSBML_CAT_INTERNAL |
||
| ) |
Creates a new XMLError to report that something occurred during XML processing.
XMLError objects have identification numbers to indicate the nature of the exception. These numbers are drawn from the enumeration XMLErrorCode_t. The argument errorId to this constructor can be (but does not have to be) a value from this enumeration. If it is a value from XMLErrorCode_t, the XMLError class assumes the error is a low-level system or XML layer error and prepends a built-in, predefined error message to any string passed in the argument details to this constructor. In addition, all XMLErrorCode_t errors have associated values for the severity and category codes, and these fields are filled-in as well from the enumerations XMLErrorSeverity_t and XMLErrorCategory_t, respectively.
If the error identifier errorId is a number greater than 9999, this constructor assumes that the error was generated from another part of the software, and does not do additional filling in of values beyond the defaults in the constructor itself. This allows XMLError to serve as a base class for other errors (and is used in this way elsewhere in libSBML). Callers should fill in all the parameters with suitable values if generating errors with codes greater than 9999 to make maximum use of the XMLError facilities.
As mentioned above, there are two other enumerations, XMLErrorSeverity_t and XMLErrorCategory_t, used for indicating the severity and category of error for the predefined XMLError codes. The values passed in severity and category override the defaults assigned based on the error code. If the value of errorId is a value from XMLErrorCode_t, callers do not need to fill in severity and category. Conversely, if errorId is not a value from XMLErrorCode_t, callers can use other values (not just those from XMLErrorSeverity_t and XMLErrorCategory_t, but their own special values) for severity and category.
| errorId | an unsigned int, the identification number of the error. |
| details | a string containing additional details about the error. If the error code in errorId is one that is recognized by XMLError, the given message is appended to a predefined message associated with the given code. If the error code is not recognized, the message is stored as-is as the text of the error. |
| line | an unsigned int, the line number at which the error occured. |
| column | an unsigned int, the column number at which the error occured. |
| severity | an integer indicating severity of the error. |
| category | an integer indicating the category to which the error belongs. |
| XMLError::XMLError | ( | const XMLError & | orig | ) |
|
virtual |
Destroys this XMLError.
| unsigned int XMLError::getCategory | ( | ) | const |
Returns the category of this error.
XMLError defines an enumeration of category codes for the XML layer. Applications that build on XMLError by subclassing it may add their own categories with numbers higher than those in the predefined set of category codes.
Categories can be used to partition errors into distinct groups. Among other things, this can be used to prevent id conflicts by uniquely identifying an XMLError by both id and category.
| const std::string & XMLError::getCategoryAsString | ( | ) | const |
Returns a string describing the category of this error.
XMLError defines an enumeration of category codes for the XML layer. Applications that build on XMLError by subclassing it may add their own categories with numbers higher than those in the predefined set of category codes.
Categories can be used to partition errors into distinct groups. Among other things, this can be used to prevent id conflicts by uniquely identifying an XMLError by both id and category.
| unsigned int XMLError::getColumn | ( | ) | const |
Returns the column number in the XML input near where the error, warning or other diagnostic occurred.
We say "near where the problem occurred", because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0 or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.
| unsigned int XMLError::getErrorId | ( | ) | const |
Returns the identifier of this error.
| unsigned int XMLError::getErrorIdOffset | ( | ) | const |
Returns libSBML's internal numerical offset for the error code associated with this error.
In the SBML Level 3 package specifications, package validation rules are identified by 5-digit numbers prefixed with the nickname of the package itself—e.g., “comp-10101”, “fbc-20301”, etc. Historically, libSBML reported error codes as pure integers, and some application software systems make decisions based on the numerical values of the error codes. To permit these applications to continue to function in this fashion, libSBML internally continues to maintain error identifiers as pure integers. To handle the possibility that errors may come from package extensions, libSBML uses numerical offsets added to the internal error codes. These offsets add two leading digits to the regular 5-digit error codes; for example, “comp” error codes are stored as 1010101, 1020102, etc. The offset in this case is 1000000. Another package will have the offset 2000000, yet another will have 3000000, etc.
This method returns the integer offset in this error's error code. Calling applications can get the 5-digit package-specific number for a given error code by subtracting the offset from the value reported by getErrorId():
getErrorId() - getErrorIdOffset()
When libSBML produces error messages, it combines the text string returned by getPackage() with the subtracted value of the error code, to produce a text string of the form “comp-10101”.
| unsigned int XMLError::getLine | ( | ) | const |
Returns the line number in the XML input near where the error, warning or other diagnostic occurred.
We say "near where the problem occurred", because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0 or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.
| const string & XMLError::getMessage | ( | ) | const |
Returns the message text of this error.
The message associated with an error object describes the nature of the problem. The message returned by this method is generally longer and clearer than the message returned by XMLError::getShortMessage(), but not in all cases.
Callers may use XMLError::getCategory() and XMLError::getSeverity() to obtain additional information about the nature and severity of the problem.
| const std::string & XMLError::getPackage | ( | ) | const |
Returns the SBML Level 3 package extension (if any) that logged this error.
Each error logged by an libSBML extension for SBML Level 3 packages includes a record of the package that logged it. The field is a simple text string. If the string is empty or has the value "core", then the error came from libSBML core; otherwise, the string will be the short-form name of the package (e.g., "comp" for the Hierarchical Model Composition package).
"core". | unsigned int XMLError::getSeverity | ( | ) | const |
Returns the severity of this error.
XMLError defines an enumeration of severity codes for the XML layer. Applications that build on XMLError by subclassing it may add their own severity codes with numbers higher than those in the predefined set of severity codes.
| const std::string & XMLError::getSeverityAsString | ( | ) | const |
Returns a string describing the severity level of this error.
XMLError defines an enumeration of severity codes for the XML layer. Applications that build on XMLError by subclassing it may add their own severity codes with numbers higher than those in the predefined set of severity codes.
| const string & XMLError::getShortMessage | ( | ) | const |
Returns a brief message for this error.
This is an alternative error message that, in general, is as short as the authors could make it. However, brevity is often inversely proportional to clarity, so this short message may not be sufficiently informative to understand the nature of the error. Calling applications may wish to check XMLError::getMessage() in addition or instead.
|
static |
Returns a copy of the message string associated with the given predefined XMLError code.
| code | the error code whose message is sought; it must be a predefined value from XMLErrorCode_t. |
| bool XMLError::isError | ( | ) | const |
Predicate returning true or false depending on whether this error is a significant error.
This is equivalent to obtaining the severity code from an XMLError object (via XMLError::getSeverity()) and then comparing it to the value LIBSBML_SEV_ERROR from the enumeration XMLErrorSeverity_t.
true if this error is an error, false otherwise.| bool XMLError::isFatal | ( | ) | const |
Predicate returning true or false depending on whether this error is a fatal run-time error.
This is equivalent to obtaining the severity code from an XMLError object (via XMLError::getSeverity()) and then comparing it to the value LIBSBML_SEV_FATAL from the enumeration XMLErrorSeverity_t.
true if this error is a fatal error, false otherwise.| bool XMLError::isInfo | ( | ) | const |
Predicate returning true or false depending on whether this error object is for information purposes only.
This is equivalent to obtaining the severity code from an XMLError object (via XMLError::getSeverity()) and then comparing it to the value LIBSBML_SEV_INFO from the enumeration XMLErrorSeverity_t.
true if this XMLError is for informational purposes only, false otherwise.| bool XMLError::isInternal | ( | ) | const |
Predicate returning true or false depending on whether this error resulted from an internal program error.
This is equivalent to obtaining the category identifier from an XMLError object (via XMLError::getCategory()) and then comparing it to the value LIBSBML_CAT_INTERNAL from the enumeration XMLErrorCategory_t.
| bool XMLError::isSystem | ( | ) | const |
Predicate returning true or false depending on whether this error was generated by the operating system.
This is equivalent to obtaining the category identifier from an XMLError object (via XMLError::getCategory()) and then comparing it to the value LIBSBML_CAT_SYSTEM from the enumeration XMLErrorCategory_t.
| bool XMLError::isValid | ( | ) | const |
Predicate returning true or false depending on whether this error resulted from a problem or whether it was logged as an unknown error.
This is equivalent to obtaining the error identifier from an XMLError object (via XMLError::getErrorId()) and then comparing it to the value XMLUnknownError or UnknownError from the enumeration XMLErrorCode_t.
true) or whether it is unknown (false). | bool XMLError::isWarning | ( | ) | const |
Predicate returning true or false depending on whether this error object is a warning.
This is equivalent to obtaining the severity code from an XMLError object (via XMLError::getSeverity()) and then comparing it to the value LIBSBML_SEV_WARNING from the enumeration XMLErrorSeverity_t.
true if this error is a warning, false otherwise.| bool XMLError::isXML | ( | ) | const |
Predicate returning true or false depending on whether this error resulted from a problem in the XML input (e.g., an XML syntax error).
This is equivalent to obtaining the category identifier from an XMLError object (via XMLError::getCategory()) and then comparing it to the value LIBSBML_CAT_XML from the enumeration XMLErrorCategory_t.
| int XMLError::setColumn | ( | unsigned int | column | ) |
Sets the column number where this error occurred.
| column | an unsigned int, the column number to set. |
| int XMLError::setLine | ( | unsigned int | line | ) |
Sets the line number where this error occurred.
| line | an unsigned int, the line number to set. |