org.obolibrary.robot

Class ReportOperation

java.lang.Object

org.obolibrary.robot.ReportOperation

public class ReportOperation
extends Object

Report issues with an ontology using a series of QC SPARQL queries.

Author:

Becky Tauber, James A. Overton

Constructor Summary

Constructors

Constructor and Description
ReportOperation()

Method Summary

Modifier and Type	Method and Description
static Map<String,String>	getDefaultOptions() Return a map from option name to default option value, for all the available report options.
static Report	getReport(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options) Given an ontology, an IOHelper, and a map of options, create a Report object and run the report queries specified in a profile (from options, or default).
static Report	getTDBReport(org.apache.jena.query.Dataset dataset, Map<String,String> options) Given a dataset and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default).
static Report	getTDBReport(IOHelper ioHelper, org.apache.jena.query.Dataset dataset, Map<String,String> options) Given a dataset and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default).
static Report	getTDBReport(String inputPath, Map<String,String> options) Given an input path to an ontology and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default).
static boolean	processReport(Report report, String outputPath, Map<String,String> options) Given a Report, an output path, and a map of report options, process the Report results and save the report to the output path.
static void	report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper) Report on the ontology using the rules within the profile and print results.
static void	report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options) Report on the ontology using the rules within the profile and print results.
static boolean	report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, String outputPath, Map<String,String> options) Given an ontology, an IOHelper, an output path (or null), and a map of options (or null), report on the ontology using the rules within the profile specified by the options and write results to the output path.
static boolean	report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, String profilePath, String outputPath, String format, String failOn) Given an ontology, an IOHelper, a profile path (or null), an output path (or null), a report format (or null), and a level to fail on, report on the ontology using the rules within the profile and write results to the output path.
static boolean	report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, String profilePath, String outputPath, String format, String failOn, boolean useLabels) Given an ontology, an IOHelper, a profile path (or null), an output path (or null), a report format (or null), a level to fail on, and a boolean indicating to use labels, report on the ontology using the rules within the profile and write results to the output path.
static boolean	report(org.semanticweb.owlapi.model.OWLOntology ontology, String profilePath, String outputPath, String format, String failOn) Given an ontology, a profile path (or null), an output path (or null), and a report format (or null) report on the ontology using the rules within the profile and write results to the output path.
static boolean	tdbReport(String inputPath, String outputPath, Map<String,String> options) Given an input path, an output path (or null), and a map of options, report on the ontology using the rules within the profile specified by the options and write results to the output path.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReportOperation

public ReportOperation()

Method Detail

getDefaultOptions

public static Map<String,String> getDefaultOptions()

Return a map from option name to default option value, for all the available report options.

Returns:

a map with default values for all available options

report

public static void report(org.semanticweb.owlapi.model.OWLOntology ontology,
                          IOHelper ioHelper)
                   throws Exception

Report on the ontology using the rules within the profile and print results. Prefer report(OWLOntology ontology, String profilePath, String outputPath, String format, String failOn).

Parameters:

ontology - the OWLOntology to report

ioHelper - IOHelper to work with ontology

Throws:

Exception - on any reporting error

report

public static boolean report(org.semanticweb.owlapi.model.OWLOntology ontology,
                             String profilePath,
                             String outputPath,
                             String format,
                             String failOn)
                      throws Exception

Given an ontology, a profile path (or null), an output path (or null), and a report format (or null) report on the ontology using the rules within the profile and write results to the output path. If profile is null, use the default profile in resources. If the output path is null, write results to console. If the format is null, write results in TSV format.

Parameters:

ontology - OWLOntology to report on

profilePath - user profile file path to use, or null

outputPath - string path to write report file to, or null

format - string format for the output report (TSV or YAML), or null

failOn - logging level to fail execution

Returns:

true if successful, false if failed

Throws:

Exception - on any error

report

public static boolean report(org.semanticweb.owlapi.model.OWLOntology ontology,
                             IOHelper ioHelper,
                             String profilePath,
                             String outputPath,
                             String format,
                             String failOn)
                      throws Exception

Given an ontology, an IOHelper, a profile path (or null), an output path (or null), a report format (or null), and a level to fail on, report on the ontology using the rules within the profile and write results to the output path. If profile is null, use the default profile in resources. If the output path is null, write results to console. If the format is null, write results in TSV format. Exit with status 1 if any violations of fail-on level are found.

Parameters:

ontology - OWLOntology to report on

ioHelper - IOHelper to use

profilePath - user profile file path to use, or null

outputPath - string path to write report file to, or null

format - string format for the output report (TSV or YAML), or null

failOn - logging level to fail execution

Returns:

true if successful, false if failed

Throws:

Exception - on any error

report

public static void report(org.semanticweb.owlapi.model.OWLOntology ontology,
                          IOHelper ioHelper,
                          Map<String,String> options)
                   throws Exception

Report on the ontology using the rules within the profile and print results. Prefer report(OWLOntology ontology, IOHelper ioHelper, String outputPath, Map<String,String> options).

Parameters:

ontology - the OWLOntology to report

ioHelper - IOHelper to work with ontology

options - map of report options

Throws:

Exception - on any reporting error

report

public static boolean report(org.semanticweb.owlapi.model.OWLOntology ontology,
                             IOHelper ioHelper,
                             String profilePath,
                             String outputPath,
                             String format,
                             String failOn,
                             boolean useLabels)
                      throws Exception

Given an ontology, an IOHelper, a profile path (or null), an output path (or null), a report format (or null), a level to fail on, and a boolean indicating to use labels, report on the ontology using the rules within the profile and write results to the output path. If profile is null, use the default profile in resources. If the output path is null, write results to console. If the format is null, write results in TSV format. Exit with status 1 if any violations of fail-on level are found.

Parameters:

ontology - OWLOntology to report on

ioHelper - IOHelper to use

profilePath - user profile file path to use, or null

outputPath - string path to write report file to, or null

format - string format for the output report (TSV or YAML), or null

failOn - logging level to fail execution

useLabels - if true, use labels for output

Returns:

true if successful, false if failed

Throws:

Exception - on any error

report

public static boolean report(org.semanticweb.owlapi.model.OWLOntology ontology,
                             IOHelper ioHelper,
                             String outputPath,
                             Map<String,String> options)
                      throws Exception

Given an ontology, an IOHelper, an output path (or null), and a map of options (or null), report on the ontology using the rules within the profile specified by the options and write results to the output path. If profile is null, use the default profile in resources. If the output path is null, write results to console. If the format is null, write results in TSV format.

Parameters:

ontology - the OWLOntology to report

ioHelper - IOHelper to work with ontology

outputPath - string path to write report file to, or null

options - map of report options

Returns:

false if there are violations at or above the fail-on level, true otherwise

Throws:

Exception - on any reporting error

getReport

public static Report getReport(org.semanticweb.owlapi.model.OWLOntology ontology,
                               IOHelper ioHelper,
                               Map<String,String> options)
                        throws Exception

Given an ontology, an IOHelper, and a map of options, create a Report object and run the report queries specified in a profile (from options, or default). Return the completed Report object.

Parameters:

ontology - OWLOntology to report on

ioHelper - IOHelper to resolve labels

options - Map of report options

Returns:

Report object with violation details

Throws:

Exception - on any reporting error

tdbReport

public static boolean tdbReport(String inputPath,
                                String outputPath,
                                Map<String,String> options)
                         throws Exception

Given an input path, an output path (or null), and a map of options, report on the ontology using the rules within the profile specified by the options and write results to the output path. Ontology is loaded to dataset backed on disk. The labels option is not supported with TDB.

Parameters:

inputPath - String path of ontology to load

outputPath - String path to write report file to, or null

options - map of report options

Returns:

false if there are violations at or above the fail-on level, true otherwise

Throws:

Exception - on any reporting error

getTDBReport

public static Report getTDBReport(String inputPath,
                                  Map<String,String> options)
                           throws Exception

Given an input path to an ontology and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default). Return the completed Report object. The labels option is not supported with TDB.

Parameters:

inputPath - path to load triples to TDB

options - map of report options

Returns:

Report object with violation details

Throws:

Exception - on any loading, query, or reporting error

getTDBReport

public static Report getTDBReport(org.apache.jena.query.Dataset dataset,
                                  Map<String,String> options)
                           throws Exception

Given a dataset and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default). Return the completed Report object. The labels option is not supported with TDB.

Parameters:

dataset - TDB Dataset to perform Report operation on

options - Map of report options

Returns:

Report object with violation details

Throws:

Exception - on any reporting error

getTDBReport

public static Report getTDBReport(IOHelper ioHelper,
                                  org.apache.jena.query.Dataset dataset,
                                  Map<String,String> options)
                           throws Exception

Given a dataset and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default). Return the completed Report object. The labels option is not supported with TDB.

Parameters:

ioHelper - IOHelper to resolve IRIs

dataset - TDB Dataset to perform Report operation on

options - Map of report options

Returns:

Report object with violation details

Throws:

Exception - on any reporting error

processReport

public static boolean processReport(Report report,
                                    String outputPath,
                                    Map<String,String> options)
                             throws IOException

Given a Report, an output path, and a map of report options, process the Report results and save the report to the output path.

Parameters:

report - completed Report object

outputPath - path to save report to

options - Map of report options

Returns:

true if report passed, false if it failed

Throws:

IOException - on issue writing to file