Improve missing imports resolution fixes #676

protege-editor-owl/src/main/java/org/protege/editor/owl/model/library/OntologyCatalogManager.java

@@ -7,8 +7,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.annotation.Nonnull;
 import java.io.File;
 import java.io.IOException;
+import java.net.MalformedURLException;
 import java.net.URI;
 import java.util.*;
 
@@ -175,6 +177,12 @@ public List<XMLCatalog> getAllCatalogs() {
     public XMLCatalog getActiveCatalog() {
     	return activeCatalog;
     }
+
+	public void changeActiveCatalog(@Nonnull File newCatalogFile) throws IOException {
+		File newCatalogDir = newCatalogFile.getParentFile();
+		localCatalogs.put(newCatalogDir, CatalogUtilities.parseDocument(newCatalogFile.toURI().toURL()));
+		activeCatalog = localCatalogs.get(newCatalogDir);
+	}
 
     public File getActiveCatalogFolder() {
 		return activeCatalogFolder;

protege-editor-owl/src/main/java/org/protege/editor/owl/ui/UIHelper.java

@@ -263,6 +263,14 @@ public File chooseOWLFile(String title) {
         return UIUtil.openFile(f, title, "OWL File", OWL_EXTENSIONS);
     }
 
+    public File chooseOWLOrCatalogFile(String title) {
+        JFrame f = (JFrame) SwingUtilities.getAncestorOfClass(JFrame.class, getParent());
+        if (f == null) {
+            f = new JFrame();
+        }
+        return UIUtil.openFile(f, title, "OWL or Catalog File", OWL_EXTENSIONS);
+    }
+
 
     public File saveOWLFile(String title) {
         return UIUtil.saveFile((JFrame) SwingUtilities.getAncestorOfClass(JFrame.class, getParent()),

protege-editor-owl/src/main/java/org/protege/editor/owl/ui/library/ChangeActiveOntologyLibraryAction.java

@@ -0,0 +1,65 @@
+package org.protege.editor.owl.ui.library;
+
+import org.protege.editor.core.ProtegeManager;
+import org.protege.editor.core.ui.util.UIUtil;
+import org.protege.editor.core.ui.workspace.WorkspaceFrame;
+import org.protege.editor.owl.model.library.OntologyCatalogManager;
+import org.protege.editor.owl.ui.action.ProtegeOWLAction;
+import org.protege.editor.owl.ui.ontology.imports.AddImportsStrategy;
+import org.protege.editor.owl.ui.ontology.imports.wizard.GetImportsVisitor;
+import org.protege.editor.owl.ui.ontology.imports.wizard.ImportInfo;
+import org.protege.xmlcatalog.XMLCatalog;
+import org.protege.xmlcatalog.entry.Entry;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.slf4j.LoggerFactory;
+
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.util.Collections;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+/**
+ * Created by vblagodarov on 24-07-17.
+ */
+public class ChangeActiveOntologyLibraryAction extends ProtegeOWLAction {
+    public void actionPerformed(ActionEvent e) {
+        try {
+            WorkspaceFrame frame = ProtegeManager.getInstance().getFrame(getOWLWorkspace());
+            File catalogFile = UIUtil.openFile(
+                    frame,
+                    "Choose catalog file containing ontology repository information",
+                    "Choose XML Catalog",
+                    Collections.singleton("xml"));
+            if (catalogFile != null) {
+                OntologyCatalogManager catalogManager = getOWLModelManager().getOntologyCatalogManager();
+                catalogManager.changeActiveCatalog(catalogFile);
+                XMLCatalog activeCatalog = catalogManager.getActiveCatalog();
+                GetImportsVisitor getter = new GetImportsVisitor();
+                for (Entry entry : activeCatalog.getEntries()) {
+                    entry.accept(getter);
+                }
+                OWLOntology activeOntology = getOWLModelManager().getActiveOntology();
+                XMLCatalogManager xmlCatalogManager = new XMLCatalogManager(activeCatalog);
+                Set<ImportInfo> importsToImport = xmlCatalogManager.getImports().stream().filter(
+                        importInfo -> activeOntology.getDirectImportsDocuments().contains(importInfo.getImportLocation())).collect(Collectors.toSet());
+
+                AddImportsStrategy ais = new AddImportsStrategy(getOWLEditorKit(), activeOntology, importsToImport);
+                ais.addImports();
+            }
+        } catch (Exception ex) {
+            LoggerFactory.getLogger(EditActiveOntologyLibraryAction.class)
+                    .error("An error occurred whilst attempting to change ontology catalog: {}", e);
+        }
+    }
+
+    @Override
+    public void initialise() throws Exception {
+
+    }
+
+    @Override
+    public void dispose() throws Exception {
+
+    }
+}

protege-editor-owl/src/main/java/org/protege/editor/owl/ui/library/XMLCatalogManager.java

@@ -0,0 +1,179 @@
+package org.protege.editor.owl.ui.library;
+
+import com.google.common.base.Optional;
+import org.protege.editor.owl.model.repository.MasterOntologyIDExtractor;
+import org.protege.editor.owl.ui.ontology.imports.wizard.GetImportsVisitor;
+import org.protege.editor.owl.ui.ontology.imports.wizard.ImportInfo;
+import org.protege.xmlcatalog.EntryVisitor;
+import org.protege.xmlcatalog.XMLCatalog;
+import org.protege.xmlcatalog.entry.*;
+import org.protege.xmlcatalog.owlapi.XMLCatalogIRIMapper;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntologyID;
+import org.slf4j.LoggerFactory;
+
+import javax.annotation.Nonnull;
+import java.io.IOException;
+import java.net.URI;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Created by vblagodarov on 01-08-17.
+ */
+public class XMLCatalogManager {
+
+    XMLCatalogIRIMapper iriMapper;
+    XMLCatalogEntriesVisitor entriesVisitor;
+    MasterOntologyIDExtractor extractor = new MasterOntologyIDExtractor();
+    XMLCatalog catalog;
+
+    public XMLCatalogManager(XMLCatalog xmlCatalog) {
+        catalog = xmlCatalog;
+        iriMapper = new XMLCatalogIRIMapper(xmlCatalog);
+        entriesVisitor = new XMLCatalogEntriesVisitor();
+        for (Entry entry : xmlCatalog.getEntries()) {
+            entry.accept(entriesVisitor);
+        }
+    }
+
+    public XMLCatalog getCatalog() {
+        return catalog;
+    }
+
+    public Collection<ImportInfo> getImports() {
+        Set<ImportInfo> imports = new HashSet<>();
+        for (XMLCatalogUriEntry entry : getAllUriEntries()) {
+            ImportInfo myImport = new ImportInfo();
+            myImport.setImportLocation(IRI.create(entry.getEntry().getName()));
+            myImport.setPhysicalLocation(entry.getPhysicalLocation());
+
+            Optional<OWLOntologyID> id = extractor.getOntologyId(entry.getPhysicalLocation());
+            //If ID is not set, the import will be ignored
+            if (id.isPresent()) {
+                myImport.setOntologyID(id.get());
+            }
+            imports.add(myImport);
+        }
+        return imports;
+    }
+
+    public boolean containsUri(URI physicalLocation) {
+        if (physicalLocation == null) {
+            return false;
+        }
+        return getAllUriEntries().stream().filter(
+                entry -> entry.getPhysicalLocation().equals(physicalLocation)).findAny().isPresent();
+    }
+
+    public Collection<XMLCatalogUriEntry> getAllUriEntries() {
+        Set<XMLCatalogUriEntry> entries = new HashSet<>();
+        for (UriEntry uriEntry : entriesVisitor.getAllUriEntries()) {
+            IRI ontologyIRI = IRI.create(uriEntry.getName());
+            URI redirect = iriMapper.getDocumentIRI(ontologyIRI).toURI();
+            entries.add(redirect == null ? new XMLCatalogUriEntry(ontologyIRI, uriEntry) :
+                    new XMLCatalogUriEntry(ontologyIRI, uriEntry, redirect));
+        }
+
+        return entries;
+    }
+
+    public class XMLCatalogUriEntry {
+        private UriEntry entry;
+        private URI location;
+        private IRI ontologyIRI;
+
+        public XMLCatalogUriEntry(@Nonnull IRI ontologyIRI, @Nonnull UriEntry uriEntry) {
+            this(ontologyIRI, uriEntry, uriEntry.getAbsoluteURI());
+        }
+
+        public XMLCatalogUriEntry(@Nonnull IRI ontologyIRI, @Nonnull UriEntry uriEntry, @Nonnull URI physicalLocation) {
+            this.ontologyIRI = ontologyIRI;
+            entry = uriEntry;
+            location = physicalLocation;
+        }
+
+        public UriEntry getEntry() {
+            return entry;
+        }
+
+        public IRI getOntologyIRI() {
+            return ontologyIRI;
+        }
+
+        public URI getPhysicalLocation() {
+            return location;
+        }
+    }
+
+    private class XMLCatalogEntriesVisitor implements EntryVisitor {
+
+        private Set<UriEntry> uriEntries = new HashSet<>();
+
+        public Set<UriEntry> getAllUriEntries() {
+            return uriEntries;
+        }
+
+        @Override
+        public void visit(UriEntry entry) {
+            uriEntries.add(entry);
+        }
+
+        @Override
+        public void visit(GroupEntry entry) {
+            for (Entry subEntry : entry.getEntries()) {
+                subEntry.accept(this);
+            }
+        }
+
+        @Override
+        public void visit(PublicEntry entry) {
+
+        }
+
+        @Override
+        public void visit(SystemEntry entry) {
+
+        }
+
+        @Override
+        public void visit(RewriteSystemEntry entry) {
+
+        }
+
+        @Override
+        public void visit(DelegatePublicEntry entry) {
+
+        }
+
+        @Override
+        public void visit(DelegateSystemEntry entry) {
+
+        }
+
+        @Override
+        public void visit(RewriteUriEntry entry) {
+
+        }
+
+        @Override
+        public void visit(DelegateUriEntry entry) {
+
+        }
+
+        @Override
+        public void visit(NextCatalogEntry entry) {
+
+            try {
+                XMLCatalog catalog = entry.getParsedCatalog();
+                for (Entry subEntry : catalog.getEntries()) {
+                    subEntry.accept(this);
+                }
+            } catch (IOException e) {
+                LoggerFactory.getLogger(GetImportsVisitor.class)
+                        .error("Ad error occurred whilst attempting to process the XMLCatalog file: {}", e);
+            }
+        }
+    }
+}