Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Restriction visitor rewrite supports most complex restrictions. Change most lists to sets. Some mapper updates to deal with those changes #180

Draft
wants to merge 10 commits into
base: master
Choose a base branch
from
Draft

Restriction visitor rewrite supports most complex restrictions. Change most lists to sets. Some mapper updates to deal with those changes #180

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
604bc8d
clean up spacing and indents for RestrictionVisitor
cweedall May 9, 2024
ea17501
more spacing
cweedall May 9, 2024
15884de
lists to sets; min/max for certain types
cweedall May 17, 2024
ef214d4
lists to sets
cweedall May 17, 2024
156a4d7
lists to sets; anyOf/allOf/enum fixes; composedSchema cardinality
cweedall May 18, 2024
8e0d1d6
pass first ontology of set
cweedall May 18, 2024
8ba263d
list to set; remove unnecessary args
cweedall May 18, 2024
01c7150
rewrite visitor class; list to set; fix affected tests
cweedall May 18, 2024
efff892
list to set; update affected areas from restriction visitor rewrite
cweedall May 18, 2024
c926bde
bump to new minor version instead of patch version
cweedall May 18, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<packaging>jar</packaging>
<groupId>edu.isi.oba</groupId>
<artifactId>oba</artifactId>
<version>3.9.1</version>
<version>3.10.0</version>
<name>core</name>
<url>https://github.com/KnowledgeCaptureAndDiscovery/OBA</url>

Expand Down
150 changes: 73 additions & 77 deletions src/main/java/edu/isi/oba/Mapper.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,20 +29,19 @@ class Mapper {
public final Map<IRI, String> schemaDescriptions = new HashMap<>(); //URI-description of the schemas
public Map<String, Schema> schemas = new HashMap<>();
final Paths paths = new Paths();
List<String> selected_paths;
List<OWLOntology> ontologies;
List<OWLClass> selected_classes;
List<OWLClass> mappedClasses;
Set<String> selected_paths = new HashSet<>();
Set<OWLOntology> ontologies = new HashSet<>();
List<OWLClass> selected_classes = new ArrayList<>();
List<OWLClass> mappedClasses = new ArrayList<>();
YamlConfig config_data;

public OWLOntologyManager manager = OWLManager.createOWLOntologyManager();

public Mapper(YamlConfig config_data) throws OWLOntologyCreationException, IOException {
this.config_data = config_data;
this.selected_paths = config_data.getPaths();
this.mappedClasses = new ArrayList<>();

List<String> config_ontologies = config_data.getOntologies();
Set<String> config_ontologies = config_data.getOntologies();
String destination_dir = config_data.getOutput_dir() + File.separator + config_data.getName();
File outputDir = new File(destination_dir);
if (!outputDir.exists()) {
Expand All @@ -51,28 +50,28 @@ public Mapper(YamlConfig config_data) throws OWLOntologyCreationException, IOExc

//Load the ontology into the manager
int i = 0;
List<String> ontologyPaths = new ArrayList<>();
Set<String> ontologyPaths = new HashSet<>();
this.download_ontologies(config_ontologies, destination_dir, i, ontologyPaths);
//set ontology paths in YAML to the ones we have downloaded (for later reference by owl2jsonld)
this.config_data.setOntologies(ontologyPaths);
ontologies = this.manager.ontologies().collect(Collectors.toList());
ontologies = this.manager.ontologies().collect(Collectors.toSet());

//Create a temporal Map<IRI, String> schemaNames with the classes
for (OWLOntology ontology : ontologies) {
Set<OWLClass> classes = ontology.getClassesInSignature();
this.setSchemaNames(classes);
this.setSchemaDrescriptions(classes,ontology);
this.setSchemaDescriptions(classes, ontology);
}

if (config_data.getClasses() != null) {
this.selected_classes = this.filter_classes();
this.selected_classes.addAll(this.filter_classes());
}
}

private void download_ontologies(List<String> config_ontologies, String destination_dir, int i, List<String> ontologyPaths) throws OWLOntologyCreationException, IOException {
private void download_ontologies(Set<String> config_ontologies, String destination_dir, int i, Set<String> ontologyPaths) throws OWLOntologyCreationException, IOException {
for (String ontologyPath : config_ontologies) {
//copy the ontologies used in the destination folder
String destinationPath = destination_dir + File.separator +"ontology"+i+".owl";
String destinationPath = destination_dir + File.separator + "ontology" + i + ".owl";
File ontologyFile = new File (destinationPath);
//content negotiation + download in case a URI is added
if(ontologyPath.startsWith("http://") || ontologyPath.startsWith("https://")){
Expand All @@ -84,7 +83,7 @@ private void download_ontologies(List<String> config_ontologies, String destinat
//copy to the right folder
Files.copy(new File(ontologyPath).toPath(), ontologyFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
} catch (IOException ex) {
Logger.getLogger(Mapper.class.getName()).log(Level.SEVERE, "ERROR while loading file: "+ontologyPath, ex);
Logger.getLogger(Mapper.class.getName()).log(Level.SEVERE, "ERROR while loading file: " + ontologyPath, ex);
throw ex;
}
}
Expand Down Expand Up @@ -119,17 +118,20 @@ public void createSchemas(String destination_dir) {
for (OWLOntology ontology : this.ontologies) {

OWLDocumentFormat format = ontology.getFormat();
String defaultOntologyPrefixIRI = format.asPrefixOWLDocumentFormat().getDefaultPrefix();
if (defaultOntologyPrefixIRI == null) {
logger.severe("Unable to find the default prefix for the ontology");
if (format == null) {
logger.severe("No ontology format found. Unable to proceed.");
System.exit(1);
}
} else {
String defaultOntologyPrefixIRI = format.asPrefixOWLDocumentFormat().getDefaultPrefix();
if (defaultOntologyPrefixIRI == null) {
logger.severe("Unable to find the default prefix for the ontology. Unable to proceed.");
System.exit(1);
}

Set<OWLClass> classes = ontology.getClassesInSignature();
for (OWLClass cls : classes) {
//filter if the class prefix does not have the default ontology prefix
if (cls.getIRI() != null) {
if (this.selected_classes == null || this.selected_classes.contains(cls)) {
Set<OWLClass> classes = ontology.getClassesInSignature();
for (OWLClass cls : classes) {
//filter if the class prefix does not have the default ontology prefix
if (cls.getIRI() != null) {
this.add_owlclass_to_openapi(query, pathGenerator, ontology, defaultOntologyPrefixIRI, cls, true);
}
}
Expand Down Expand Up @@ -162,59 +164,61 @@ private List<OWLClass> add_owlclass_to_openapi(Query query, PathGenerator pathGe
String defaultOntologyPrefixIRI, OWLClass cls, Boolean topLevel) {
List<OWLClass> ref = new ArrayList<>();
String classPrefixIRI = cls.getIRI().getNamespace();
if (defaultOntologyPrefixIRI.equals(classPrefixIRI)) {
try{
MapperSchema mapperSchema = getMapperSchema(query, ontology, cls, this.schemaDescriptions.get(cls.getIRI()));

// add references to schemas in class restrictions (check selected classes to avoid conflicts)
for (String classToCheck : mapperSchema.getPropertiesFromObjectRestrictions_ranges()) {
OWLClass clsToCheck = manager.getOWLDataFactory().getOWLClass(IRI.create(classPrefixIRI + classToCheck));
if (this.mappedClasses.contains(clsToCheck) || (this.selected_classes != null && this.selected_classes.contains(clsToCheck))){
logger.info("The class " + clsToCheck + " exists ");
} else {
//rare cases have instances, so we filter them out and recheck that the target is a class.
if(ontology.containsClassInSignature(clsToCheck.getIRI())) {
System.out.println("ADD "+ clsToCheck);
for (OWLOntology temp_ontology : this.ontologies) {
if (this.config_data.getConfigFlagValue(CONFIG_FLAG.FOLLOW_REFERENCES)) {
this.mappedClasses.add(clsToCheck);
this.getMapperSchema(query, temp_ontology, clsToCheck, this.schemaDescriptions.get(clsToCheck.getIRI()));
this.add_owlclass_to_openapi(query, pathGenerator, temp_ontology, classPrefixIRI, clsToCheck, false);
}
}
}
}
}
try{
MapperSchema mapperSchema = this.getMapperSchema(query, cls, this.schemaDescriptions.get(cls.getIRI()));

// add references to schemas in property ranges
for (OWLClass ref_class : mapperSchema.getProperties_range()) {
if (this.mappedClasses.contains(ref_class)){
logger.info("The class " + ref_class + " exists ");
} else {
// add references to schemas in class restrictions (check selected classes to avoid conflicts)
for (String classToCheck : mapperSchema.getPropertiesFromObjectRestrictions_ranges()) {
final var classIRI = IRI.create(classPrefixIRI + classToCheck);
OWLClass clsToCheck = manager.getOWLDataFactory().getOWLClass(classIRI);
if (this.mappedClasses.contains(clsToCheck) || this.selected_classes.contains(clsToCheck)){
logger.info("The class " + clsToCheck + " exists ");
} else {
//rare cases have instances, so we filter them out and recheck that the target is a class.
if(ontology.containsClassInSignature(classIRI)) {
System.out.println("ADD "+ clsToCheck);
for (OWLOntology temp_ontology : this.ontologies) {
if (this.config_data.getConfigFlagValue(CONFIG_FLAG.FOLLOW_REFERENCES)) {
this.mappedClasses.add(ref_class);
this.getMapperSchema(query, temp_ontology, ref_class,this.schemaDescriptions.get(ref_class.getIRI()));
this.add_owlclass_to_openapi(query, pathGenerator, temp_ontology, classPrefixIRI, ref_class, false);
this.mappedClasses.add(clsToCheck);
this.getMapperSchema(query, clsToCheck, this.schemaDescriptions.get(classIRI));
this.selected_classes.addAll(this.add_owlclass_to_openapi(query, pathGenerator, temp_ontology, classPrefixIRI, clsToCheck, false));
}
}
}
}

//Add the OpenAPI paths
if (topLevel) {
addOpenAPIPaths(pathGenerator, mapperSchema, cls);
}

// add references to schemas in property ranges
for (OWLClass ref_class : mapperSchema.getProperties_range()) {
if (this.mappedClasses.contains(ref_class)){
logger.info("The class " + ref_class + " exists ");
} else {
for (OWLOntology temp_ontology : this.ontologies) {
if (this.config_data.getConfigFlagValue(CONFIG_FLAG.FOLLOW_REFERENCES)) {
this.mappedClasses.add(ref_class);
this.getMapperSchema(query, ref_class, this.schemaDescriptions.get(ref_class.getIRI()));
this.selected_classes.addAll(this.add_owlclass_to_openapi(query, pathGenerator, temp_ontology, classPrefixIRI, ref_class, false));
}
}
}
}catch(Exception e){
logger.log(Level.SEVERE,"Could not parse class "+cls.getIRI().toString());
}

//Add the OpenAPI paths
if (topLevel) {
this.add_path(pathGenerator, mapperSchema);
}
}catch(Exception e){
logger.log(Level.SEVERE,"Could not parse class " + cls.getIRI().toString());
logger.log(Level.SEVERE,"\n\tdetails:\n" + e);
}

return ref;
}

private MapperSchema getMapperSchema(Query query, OWLOntology ontology, OWLClass cls, String cls_description) {
private MapperSchema getMapperSchema(Query query, OWLClass cls, String cls_description) {
//Convert from OWL Class to OpenAPI Schema.
MapperSchema mapperSchema = new MapperSchema(this.ontologies, cls, cls_description, schemaNames, ontology, this.config_data.getConfigFlags());
MapperSchema mapperSchema = new MapperSchema(this.ontologies, cls, cls_description, schemaNames, this.config_data.getConfigFlags());
//Write queries
query.write_readme(mapperSchema.name);
//Create the OpenAPI schema
Expand All @@ -223,16 +227,8 @@ private MapperSchema getMapperSchema(Query query, OWLOntology ontology, OWLClass
return mapperSchema;
}

private void addOpenAPIPaths(PathGenerator pathGenerator, MapperSchema mapperSchema, OWLClass cls) {
if (this.selected_classes != null && !this.selected_classes.contains(cls)) {
logger.info("Ignoring class " + cls.toString());
} else {
this.add_path(pathGenerator, mapperSchema);
}
}

private void setSchemaNames(Set<OWLClass> classes) {
for (OWLClass cls : classes) {
for (OWLClass cls: classes) {
this.schemaNames.put(cls.getIRI(), cls.getIRI().getShortForm());
}
}
Expand All @@ -243,10 +239,10 @@ private void setSchemaNames(Set<OWLClass> classes) {
* @param classes the classes you want the description for
* @param ontology the ontology from where we will extract the descriptions
*/
private void setSchemaDrescriptions(Set<OWLClass> classes, OWLOntology ontology){
private void setSchemaDescriptions(Set<OWLClass> classes, OWLOntology ontology) {
for (OWLClass cls: classes) {
System.out.println(cls);
schemaDescriptions.put(cls.getIRI(), ObaUtils.getDescription(cls, ontology, this.config_data.getConfigFlagValue(CONFIG_FLAG.DEFAULT_DESCRIPTIONS)));
this.schemaDescriptions.put(cls.getIRI(), ObaUtils.getDescription(cls, ontology, this.config_data.getConfigFlagValue(CONFIG_FLAG.DEFAULT_DESCRIPTIONS)));
}
}

Expand All @@ -266,17 +262,17 @@ private void add_path(PathGenerator pathGenerator, MapperSchema mapperSchema) {
mapperSchema.getCls().getIRI().getIRIString()));
}


public List<OWLClass> filter_classes() {
List<String> selected_classes_iri = this.config_data.getClasses();
ArrayList<OWLClass> filtered_classes = new ArrayList();
for (OWLOntology ontology : this.ontologies) {
for (OWLClass cls : ontology.getClassesInSignature()) {
public Set<OWLClass> filter_classes() {
Set<String> selected_classes_iri = this.config_data.getClasses();
Set<OWLClass> filtered_classes = new HashSet<>();
for (OWLOntology ontology: this.ontologies) {
for (OWLClass cls: ontology.getClassesInSignature()) {
if (selected_classes_iri.contains(cls.getIRI().toString())) {
filtered_classes.add(cls);
}
}
}

return filtered_classes;
}
}
Loading
Loading