owlapi-version5/oboformat/src/main/java/org/obolibrary/oboformat/model/OBODoc.java
package org.obolibrary.oboformat.model;

import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;

import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.Map;
import java.util.Set;

import javax.annotation.Nullable;

import org.obolibrary.obo2owl.OboInOwlCardinalityTools;
import org.obolibrary.oboformat.model.Frame.FrameType;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;

/**
 * An OBODoc is a container for a header frame and zero or more entity frames.
 */
public class OBODoc {

    /**
     * The term frame map.
     */
    protected final Map<String, Frame> termFrameMap = new HashMap<>();
    /**
     * The typedef frame map.
     */
    protected final Map<String, Frame> typedefFrameMap = new HashMap<>();
    /**
     * The instance frame map.
     */
    protected final Map<String, Frame> instanceFrameMap = new HashMap<>();
    /**
     * The annotation frames.
     */
    protected final Collection<Frame> annotationFrames = new LinkedList<>();
    /**
     * The imported obo docs.
     */
    protected final Collection<OBODoc> importedOBODocs = new LinkedList<>();
    /**
     * The header frame.
     */
    @Nullable
    protected Frame headerFrame;

    private static void freezeFrameMap(Map<String, Frame> frameMap) {
        for (Frame frame : frameMap.values()) {
            frame.freeze();
        }
    }

    /**
     * Looks up the ID prefix to IRI prefix mapping. Header-Tag: idspace
     *
     * @param prefix prefix
     * @return IRI prefix as string
     */
    @Nullable
    public static String getIDSpace(String prefix) {
        // built-in
        if (prefix.equals("RO")) {
            return "http://purl.obolibrary.org/obo/RO_";
        }
        // TODO
        return null;
    }

    /**
     * @param prefix the prefix
     * @return true, if xref values should be treated as equivalent
     */
    public static boolean isTreatXrefsAsEquivalent(@Nullable String prefix) {
        if ("RO".equals(prefix)) {
            return true;
        }
        return false;
    }

    /**
     * @return the header frame
     */
    @Nullable
    public Frame getHeaderFrame() {
        return headerFrame;
    }

    /**
     * @param headerFrame the new header frame
     */
    public void setHeaderFrame(Frame headerFrame) {
        this.headerFrame = headerFrame;
    }

    /**
     * @return the term frames
     */
    public Collection<Frame> getTermFrames() {
        return termFrameMap.values();
    }

    /**
     * @return the typedef frames
     */
    public Collection<Frame> getTypedefFrames() {
        return typedefFrameMap.values();
    }

    /**
     * @return the instance frames
     */
    public Collection<Frame> getInstanceFrames() {
        return instanceFrameMap.values();
    }

    /**
     * Freezing an OBODoc signals that the document has become quiescent, and that the system may
     * optimize data structures for performance or space.
     */
    public void freezeFrames() {
        verifyNotNull(headerFrame,
            "headerFrame cannot be null at this stage. Setting the headr frame has been skipped")
                .freeze();
        freezeFrameMap(termFrameMap);
        freezeFrameMap(typedefFrameMap);
        freezeFrameMap(instanceFrameMap);
        for (Frame frame : annotationFrames) {
            frame.freeze();
        }
    }

    /**
     * @param id the id
     * @return the term frame
     */
    @Nullable
    public Frame getTermFrame(String id) {
        return getTermFrame(id, false);
    }

    /**
     * @param id the id
     * @param followImport the follow import
     * @return the term frame
     */
    @Nullable
    public Frame getTermFrame(String id, boolean followImport) {
        if (!followImport) {
            return termFrameMap.get(id);
        }
        // this set is used to check for cycles
        Set<String> visited = new HashSet<>();
        visited.add(getHeaderDescriptor());
        return getTermFrame(id, visited);
    }

    /**
     * @param id the id
     * @param visitedDocs the visited documents
     * @return the frame
     */
    @Nullable
    private Frame getTermFrame(String id, Set<String> visitedDocs) {
        Frame f = termFrameMap.get(id);
        if (f != null) {
            return f;
        }
        for (OBODoc doc : importedOBODocs) {
            String headerDescriptor = doc.getHeaderDescriptor();
            if (!visitedDocs.contains(headerDescriptor)) {
                visitedDocs.add(headerDescriptor);
                f = doc.getTermFrame(id, true);
            }
            if (f != null) {
                return f;
            }
        }
        return null;
    }

    /**
     * @param id the id
     * @return the typedef frame
     */
    @Nullable
    public Frame getTypedefFrame(String id) {
        return getTypedefFrame(id, false);
    }

    /**
     * @param id the id
     * @param followImports the follow imports
     * @return the typedef frame
     */
    @Nullable
    public Frame getTypedefFrame(String id, boolean followImports) {
        if (!followImports) {
            return typedefFrameMap.get(id);
        }
        // this set is used to check for cycles
        Set<String> visited = new HashSet<>();
        visited.add(getHeaderDescriptor());
        return getTypedefFrame(id, visited);
    }

    /**
     * @param id the id
     * @param visitedDocs the visited documents
     * @return the frame
     */
    @Nullable
    private Frame getTypedefFrame(String id, Set<String> visitedDocs) {
        Frame f = typedefFrameMap.get(id);
        if (f != null) {
            return f;
        }
        for (OBODoc doc : importedOBODocs) {
            String headerDescriptor = doc.getHeaderDescriptor();
            if (!visitedDocs.contains(headerDescriptor)) {
                visitedDocs.add(headerDescriptor);
                f = doc.getTypedefFrame(id, true);
            }
            if (f != null) {
                return f;
            }
        }
        return null;
    }

    /**
     * @param id the id
     * @return the instance frame
     */
    public Frame getInstanceFrame(String id) {
        return instanceFrameMap.get(id);
    }

    /**
     * @return the imported obo documents
     */
    public Collection<OBODoc> getImportedOBODocs() {
        return importedOBODocs;
    }

    /**
     * @param importedOBODocs the new imported obo documents
     */
    public void setImportedOBODocs(Collection<OBODoc> importedOBODocs) {
        this.importedOBODocs.clear();
        this.importedOBODocs.addAll(importedOBODocs);
    }

    /**
     * Adds the imported obo doc.
     *
     * @param doc the doc
     */
    public void addImportedOBODoc(OBODoc doc) {
        importedOBODocs.add(doc);
    }

    /**
     * Adds the frame.
     *
     * @param f the frame
     * @throws FrameMergeException the frame merge exception
     */
    public void addFrame(Frame f) throws FrameMergeException {
        if (f.getType() == FrameType.TERM) {
            addTermFrame(f);
        } else if (f.getType() == FrameType.TYPEDEF) {
            addTypedefFrame(f);
        } else if (f.getType() == FrameType.INSTANCE) {
            addInstanceFrame(f);
        }
    }

    /**
     * Adds the term frame.
     *
     * @param f the frame
     * @throws FrameMergeException the frame merge exception
     */
    public void addTermFrame(Frame f) throws FrameMergeException {
        String id = f.getId();
        if (termFrameMap.containsKey(id)) {
            termFrameMap.get(id).merge(f);
        } else {
            termFrameMap.put(id, f);
        }
    }

    /**
     * Adds the typedef frame.
     *
     * @param f the frame
     * @throws FrameMergeException the frame merge exception
     */
    public void addTypedefFrame(Frame f) throws FrameMergeException {
        String id = f.getId();
        if (typedefFrameMap.containsKey(id)) {
            typedefFrameMap.get(id).merge(f);
        } else {
            typedefFrameMap.put(id, f);
        }
    }

    /**
     * Adds the instance frame.
     *
     * @param f the frame
     * @throws FrameMergeException the frame merge exception
     */
    public void addInstanceFrame(Frame f) throws FrameMergeException {
        String id = f.getId();
        if (instanceFrameMap.containsKey(id)) {
            instanceFrameMap.get(id).merge(f);
        } else {
            instanceFrameMap.put(id, f);
        }
    }

    /**
     * Merge contents.
     *
     * @param extDoc the external doc
     * @throws FrameMergeException the frame merge exception
     */
    public void mergeContents(OBODoc extDoc) throws FrameMergeException {
        for (Frame f : extDoc.getTermFrames()) {
            addTermFrame(f);
        }
        for (Frame f : extDoc.getTypedefFrames()) {
            addTypedefFrame(f);
        }
        for (Frame f : extDoc.getInstanceFrames()) {
            addInstanceFrame(f);
        }
    }

    /**
     * Adds the default ontology header.
     *
     * @param defaultOnt the default ontology
     */
    public void addDefaultOntologyHeader(String defaultOnt) {
        Frame hf = verifyNotNull(getHeaderFrame());
        Clause ontClause = hf.getClause(OboFormatTag.TAG_ONTOLOGY);
        if (ontClause == null) {
            ontClause = new Clause(OboFormatTag.TAG_ONTOLOGY, defaultOnt);
            hf.addClause(ontClause);
        }
    }

    /**
     * Check this document for violations, i.e. cardinality constraint violations.
     *
     * @see OboInOwlCardinalityTools for equivalent checks in OWL
     */
    public void check() {
        verifyNotNull(headerFrame).check();
        for (Frame f : getTermFrames()) {
            f.check();
        }
        for (Frame f : getTypedefFrames()) {
            f.check();
        }
        for (Frame f : getInstanceFrames()) {
            f.check();
        }
    }

    @Override
    public String toString() {
        return getHeaderDescriptor();
    }

    /**
     * @return the header descriptor
     */
    private String getHeaderDescriptor() {
        return "OBODoc(" + headerFrame + ')';
    }
}
