org.sbolstandard.core2

Class SBOLValidate

java.lang.Object

org.sbolstandard.core2.SBOLValidate

public class SBOLValidate
extends Object

Provides functionality for validating SBOL data models.

Version:

2.1

Author:

Zhen Zhang, Chris Myers

Constructor Summary

Constructors

Constructor and Description
SBOLValidate()

Method Summary

Modifier and Type	Method and Description
static void	clearErrors() Empties the error list that is used to store SBOL validation exceptions.
static void	compareDocuments(String file1, SBOLDocument doc1, String file2, SBOLDocument doc2) Compares the given two SBOL documents and outputs the difference into the list of errors.
static List<String>	getErrors() Returns the error list used to store SBOL validation exceptions.
static int	getNumErrors() Returns the number of errors in the error list.
static void	main(String[] args) Command line method for reading an input file and producing an output file.
static SBOLDocument	validate(PrintStream outputStream, PrintStream errorStream, String fileName, String URIPrefix, boolean complete, boolean compliant, boolean bestPractice, boolean typesInURI, String version, boolean keepGoing, String compareFile, String compareFileName, String mainFileName, String topLevelURIStr, boolean genBankOut, boolean sbolV1out, boolean fastaOut, boolean snapGeneOut, String outputFile, boolean showDetail, boolean noOutput, boolean changeURIPrefix) Deprecated.
static SBOLDocument	validate(PrintStream outputStream, PrintStream errorStream, String fileName, String URIPrefix, boolean complete, boolean compliant, boolean bestPractice, boolean typesInURI, String version, boolean keepGoing, String compareFile, String compareFileName, String mainFileName, String topLevelURIStr, boolean genBankOut, boolean sbolV1out, boolean fastaOut, String outputFile, boolean showDetail, boolean noOutput, boolean changeURIPrefix) Deprecated.
static SBOLDocument	validate(PrintStream outputStream, PrintStream errorStream, String fileName, String URIPrefix, String defaultDisplayId, boolean complete, boolean compliant, boolean bestPractice, boolean typesInURI, String version, boolean keepGoing, String compareFile, String compareFileName, String mainFileName, String topLevelURIStr, boolean genBankOut, boolean sbolV1out, boolean fastaOut, boolean snapGeneOut, String outputFile, boolean showDetail, boolean noOutput, boolean changeURIPrefix) The validate function will: - perform validation on the given input SBOL file - perform comparison between 2 SBOL files - perform interconversion between SBOL1 and SBOL2 - convert from SBOL to GenBank - convert from SBOL to FASTA
static void	validateSBOL(SBOLDocument sbolDocument, boolean complete, boolean compliant, boolean bestPractice) Validates the given SBOL document.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SBOLValidate

public SBOLValidate()

Method Detail

clearErrors

public static void clearErrors()

Empties the error list that is used to store SBOL validation exceptions.

getErrors

public static List<String> getErrors()

Returns the error list used to store SBOL validation exceptions.

Returns:

the error list used to store SBOL validation exceptions

getNumErrors

public static int getNumErrors()

Returns the number of errors in the error list.

Returns:

the number of errors in the error list

validateSBOL

public static void validateSBOL(SBOLDocument sbolDocument,
                                boolean complete,
                                boolean compliant,
                                boolean bestPractice)

Validates the given SBOL document. Errors encountered either throw exceptions or, if not fatal, are added to the list of errors that can be accessed using the getErrors() method. Interpretations of the complete, compliant, and bestPractice parameters are as follows:

• complete: A true value means that all identity URI references in the given SBOL document can dereference to objects in the same document; a false value means otherwise.
• compliant: A true value means that all URIs in the given SBOL document are compliant; a false value means otherwise.
• best practice: A true value means that validation rules with the RECOMMENDED condition in the SBOL specification are checked against the given SBOLDocuemnt object; a false value means otherwise.

Parameters:

sbolDocument - the given SBOLDocument object

complete - the given complete flag

compliant - the given compliant flag

bestPractice - the given bestPractice flag

compareDocuments

public static void compareDocuments(String file1,
                                    SBOLDocument doc1,
                                    String file2,
                                    SBOLDocument doc2)

Compares the given two SBOL documents and outputs the difference into the list of errors.

Parameters:

file1 - the file name associated with doc1

doc1 - the first SBOL document

file2 - the file name associated with doc2

doc2 - the second SBOL document

validate

@Deprecated
public static SBOLDocument validate(PrintStream outputStream,
                                                PrintStream errorStream,
                                                String fileName,
                                                String URIPrefix,
                                                boolean complete,
                                                boolean compliant,
                                                boolean bestPractice,
                                                boolean typesInURI,
                                                String version,
                                                boolean keepGoing,
                                                String compareFile,
                                                String compareFileName,
                                                String mainFileName,
                                                String topLevelURIStr,
                                                boolean genBankOut,
                                                boolean sbolV1out,
                                                boolean fastaOut,
                                                String outputFile,
                                                boolean showDetail,
                                                boolean noOutput,
                                                boolean changeURIPrefix)

Deprecated.

The validate function will: - perform validation on the given input SBOL file - perform comparison between 2 SBOL files - perform interconversion between SBOL1 and SBOL2 - convert from SBOL to GenBank - convert from SBOL to FASTA

Parameters:

outputStream - - stream for the output messages

errorStream - - stream for the error messages

fileName - - Input SBOL file name

URIPrefix - - Default URI prefix to set the SBOL Document to be read in or to be created.

complete - - Set boolean variable to false to allow SBOL document to be incomplete. True otherwise.

compliant - - Set boolean variable to false to allow non-compliant URIs. True otherwise.

bestPractice - - Set boolean variable to true to check best practices. False otherwise.

typesInURI - - Set boolean variable to true to indicate that types are inserted into top-level identity URIs when they are created of the SBOL Document.

version - - Specify the version to use for converted SBOL objects.

keepGoing - - Set boolean variable to false to indicate fail on first error and stop program from continuing. True otherwise.

compareFile - - Second SBOL file to compare to the primary SBOL file.

compareFileName - - The name of the second SBOL file to compare to the primary SBOL file.

mainFileName - - Primary SBOL file to compare to the second SBOL file.

topLevelURIStr - - Specify the top level URI SBOL object contained within the given SBOL Document.

genBankOut - - Set boolean variable to true to convert input file to GenBank. False otherwise.

sbolV1out - - Set boolean variable to true to convert input file to SBOL1. False otherwise.

fastaOut - - Set boolean variable to true to convert input file to FASTA. False otherwise.

outputFile - - The specified output name to be generated if the validation must produce an output file.

showDetail - - Set boolean variable to true to display detailed error trace. False otherwise.

noOutput - - Set boolean variable to true to indicate no output file to be generated from validation

changeURIPrefix - - Change the URI prefix to the specified URI prefix.

Returns:

SBOLDocument generated by conversion

validate

@Deprecated
public static SBOLDocument validate(PrintStream outputStream,
                                                PrintStream errorStream,
                                                String fileName,
                                                String URIPrefix,
                                                boolean complete,
                                                boolean compliant,
                                                boolean bestPractice,
                                                boolean typesInURI,
                                                String version,
                                                boolean keepGoing,
                                                String compareFile,
                                                String compareFileName,
                                                String mainFileName,
                                                String topLevelURIStr,
                                                boolean genBankOut,
                                                boolean sbolV1out,
                                                boolean fastaOut,
                                                boolean snapGeneOut,
                                                String outputFile,
                                                boolean showDetail,
                                                boolean noOutput,
                                                boolean changeURIPrefix)

Deprecated.

The validate function will: - perform validation on the given input SBOL file - perform comparison between 2 SBOL files - perform interconversion between SBOL1 and SBOL2 - convert from SBOL to GenBank - convert from SBOL to FASTA

Parameters:

outputStream - - stream for the output messages

errorStream - - stream for the error messages

fileName - - Input SBOL file name

URIPrefix - - Default URI prefix to set the SBOL Document to be read in or to be created.

complete - - Set boolean variable to false to allow SBOL document to be incomplete. True otherwise.

compliant - - Set boolean variable to false to allow non-compliant URIs. True otherwise.

bestPractice - - Set boolean variable to true to check best practices. False otherwise.

typesInURI - - Set boolean variable to true to indicate that types are inserted into top-level identity URIs when they are created of the SBOL Document.

version - - Specify the version to use for converted SBOL objects.

keepGoing - - Set boolean variable to false to indicate fail on first error and stop program from continuing. True otherwise.

compareFile - - Second SBOL file to compare to the primary SBOL file.

compareFileName - - The name of the second SBOL file to compare to the primary SBOL file.

mainFileName - - Primary SBOL file to compare to the second SBOL file.

topLevelURIStr - - Specify the top level URI SBOL object contained within the given SBOL Document.

genBankOut - - Set boolean variable to true to convert input file to GenBank. False otherwise.

sbolV1out - - Set boolean variable to true to convert input file to SBOL1. False otherwise.

fastaOut - - Set boolean variable to true to convert input file to FASTA. False otherwise.

snapGeneOut - - Set boolean variable to true to convert input file to SnapGene DNA. False otherwise.

outputFile - - The specified output name to be generated if the validation must produce an output file.

showDetail - - Set boolean variable to true to display detailed error trace. False otherwise.

noOutput - - Set boolean variable to true to indicate no output file to be generated from validation

changeURIPrefix - - Change the URI prefix to the specified URI prefix.

Returns:

SBOLDocument generated by conversion

validate

public static SBOLDocument validate(PrintStream outputStream,
                                    PrintStream errorStream,
                                    String fileName,
                                    String URIPrefix,
                                    String defaultDisplayId,
                                    boolean complete,
                                    boolean compliant,
                                    boolean bestPractice,
                                    boolean typesInURI,
                                    String version,
                                    boolean keepGoing,
                                    String compareFile,
                                    String compareFileName,
                                    String mainFileName,
                                    String topLevelURIStr,
                                    boolean genBankOut,
                                    boolean sbolV1out,
                                    boolean fastaOut,
                                    boolean snapGeneOut,
                                    String outputFile,
                                    boolean showDetail,
                                    boolean noOutput,
                                    boolean changeURIPrefix)

The validate function will: - perform validation on the given input SBOL file - perform comparison between 2 SBOL files - perform interconversion between SBOL1 and SBOL2 - convert from SBOL to GenBank - convert from SBOL to FASTA

Parameters:

outputStream - - stream for the output messages

errorStream - - stream for the error messages

fileName - - Input SBOL file name

URIPrefix - - Default URI prefix to set the SBOL Document to be read in or to be created.

defaultDisplayId - - Default displayId to set the SBOL Document to be read in or to be created.

complete - - Set boolean variable to false to allow SBOL document to be incomplete. True otherwise.

compliant - - Set boolean variable to false to allow non-compliant URIs. True otherwise.

bestPractice - - Set boolean variable to true to check best practices. False otherwise.

typesInURI - - Set boolean variable to true to indicate that types are inserted into top-level identity URIs when they are created of the SBOL Document.

version - - Specify the version to use for converted SBOL objects.

keepGoing - - Set boolean variable to false to indicate fail on first error and stop program from continuing. True otherwise.

compareFile - - Second SBOL file to compare to the primary SBOL file.

compareFileName - - The name of the second SBOL file to compare to the primary SBOL file.

mainFileName - - Primary SBOL file to compare to the second SBOL file.

topLevelURIStr - - Specify the top level URI SBOL object contained within the given SBOL Document.

genBankOut - - Set boolean variable to true to convert input file to GenBank. False otherwise.

sbolV1out - - Set boolean variable to true to convert input file to SBOL1. False otherwise.

fastaOut - - Set boolean variable to true to convert input file to FASTA. False otherwise.

snapGeneOut - - Set boolean variable to true to convert input file to SnapGene DNA. False otherwise.

outputFile - - The specified output name to be generated if the validation must produce an output file.

showDetail - - Set boolean variable to true to display detailed error trace. False otherwise.

noOutput - - Set boolean variable to true to indicate no output file to be generated from validation

changeURIPrefix - - Change the URI prefix to the specified URI prefix.

Returns:

SBOLDocument generated by conversion

main

public static void main(String[] args)

Command line method for reading an input file and producing an output file.

By default, validations on compliance and completeness are performed, and types for top-level objects are not used in URIs.

Options:

"-o" specifies an output filename

"-e" specifies a file to compare if equal to

"-l" indicates the language for output (default=SBOL2, other options SBOL1, GenBank, FASTA, SnapGene)

"-s" select only this topLevel object and those it references

"-p" specifies the default URI prefix for converted objects

"-c" change URI prefix to specified URIprefix

"-v" specifies version to use for converted objects

"-t" uses types in URIs

"-n" allow non-compliant URIs

"-i" allow SBOL document to be incomplete

"-b" check best practices

"-f" fail on first error

"-d" display detailed error trace

"-mf" main SBOL file if file diff. option is selected

"-cf" second SBOL file if file diff. option is selected

"-no" indicate no output file to be generated from validation

Parameters:

args - arguments supplied at command line