package org.biopax.paxtools.impl;

import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.util.BPCollections;
import org.hibernate.annotations.DynamicInsert;
import org.hibernate.annotations.DynamicUpdate;
import org.hibernate.annotations.Proxy;

import javax.persistence.*;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.Map;
@Entity
@Proxy(proxyClass= BioPAXElement.class)
@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@DiscriminatorColumn(length=40)
@DynamicUpdate
@DynamicInsert
@NamedQueries({
        @NamedQuery(name="org.biopax.paxtools.impl.BioPAXElementExists",
                                query="select 1 from BioPAXElementImpl where pk=:md5uri")
        })
public abstract class BioPAXElementImpl implements BioPAXElement
{
        // Full-text search field names (case sensitive!)
        public static final String FIELD_AVAILABILITY = "availability";
        public static final String FIELD_COMMENT = "comment"; // biopax comments
        public static final String FIELD_KEYWORD = "keyword"; //anything, e.g., names, terms, comments, incl. - from child elements 
        public static final String FIELD_NAME = "name"; // standardName, displayName, other names
        public static final String FIELD_TERM = "term"; // CV terms
        public static final String FIELD_XREFDB = "xrefdb"; //xref.db
        public static final String FIELD_XREFID = "xrefid"; //xref.id
        public static final String FIELD_ECNUMBER = "ecnumber";
        public static final String FIELD_SEQUENCE = "sequence";
        // Full-text search / Filter field names (case sensitive!) -
        public static final String FIELD_ORGANISM = "organism";
        public static final String FIELD_DATASOURCE = "dataSource"; //(case sensitive)
        public static final String FIELD_PATHWAY = "pathway";
        
        // Global search filter definitions in the (paxtools-core PhysicalEntityImpl, case sensitive!)
        public static final String FILTER_BY_ORGANISM = "organism";
        public static final String FILTER_BY_DATASOURCE = "datasource";
        
        private String uri;
        
        // anything extra can be stored in this map (not to persist in a DB usually)
        private Map<String, Object> annotations;

        private String _pk; // Primary Key

        @Version
        private long version;
        
        public BioPAXElementImpl() {
                this.annotations = BPCollections.I.createMap();
        }
        

        // Primary Key for persistence
        // could not use names like: 'key' (SQL conflict), 'id', 'idx' 
        // (conflicts with the property in sub-classes).
        // @GeneratedValue - did not work (for stateless sessions)      
    /**
     * Gets Primary Key.
     * 
     * This method may be useful within a
     * persistence context (Hibernate). This is not part of
     * Paxtools standard BioPAX API, it is implementation detail.
     * 
     * Normally, one should always use {@link #getRDFId()}
     * to get BioPAX element's URI and use it in 
     * data analysis.
     * 
     * @return primary key (for persistence)
     */
        @Id
        @Column(name="pk", length=32) // enough to save MD5 digest Hex.
        public String getPk() {
                return _pk;
        }

        
        /**
         * Primary Key setter (non-public method).
         * 
         * This is called only from {@link #setRDFId(String)} 
         * and Hibernate framework (optional). Primary Key is not required 
         * (can be ignored) if this BioPAX element (model, algorithm) 
         * is not persistent (i.e., when not using any persistence provider, 
         * database, etc. to handle the BioPAX model)
         * 
         * 
         * @param pk
         */
        @SuppressWarnings("unused")
        private void setPk(String pk) {
                this._pk = pk;
        }

        //private simple setter/getter, for persistence only
        //(use biopax element RDFId property instead)
        @Lob
        @Column(nullable=false)
    private String getUri() {
        return uri;
    }
    @SuppressWarnings("unused")
        private void setUri(String uri) {
        this.uri = uri;
    }   
        
        @Transient
    public boolean isEquivalent(BioPAXElement element)
    {
        return this.equals(element) || this.semanticallyEquivalent(element);
    }

    protected boolean semanticallyEquivalent(BioPAXElement element)
    {
        return false;
    }

    public int equivalenceCode()
    {
        return uri.hashCode();
    }


        // Beware PROBLEMs, do not use RDFId (URI) as primary key 
        // (e.g., Mysql 5.x PK/index is case-insensitive, only 64-chars long, by default;
    // and there're performance issues too)
    @Transient
    public String getRDFId()
    {
        return uri;
    }

    /**
     * Private setter for the biopax element RDFId 
     * (full URI). Using the URI string, this setter 
     * also sets or updates the primary key field, 
     * {@link #getPk()}
     * 
     * Normally, URI should never be modified 
     * after the object is created unless you know 
     * what you're doing (and can use Java Reflection).
     * 
     * @param uri
     */
    @SuppressWarnings("unused")
        private synchronized void setRDFId(String uri)
    {
        if(uri == null)
                throw new IllegalArgumentException();
        
        this.uri = uri;
        this._pk = md5hex(this.uri);
    }

    
    public String toString()
    {
        return uri;
    }

    
    @Transient
    public Map<String, Object> getAnnotations() {
                return annotations;
        }
    

        /**
         * Utility method that is called once per object
         * to generate the primary key {@link #getPk()}
         * from URI. URIs can be long and are case sensitive,
         * and therefore would make bad DB primary key.
         * 
         * @param id
         * @return
         */
        private static String md5hex(String id) {
                
                // MessageDigest is not thread-safe and cheap to build 
                // - so we create a instance every time here:
                MessageDigest md5; 
                try {
                        md5 = MessageDigest.getInstance("MD5");
                } catch (NoSuchAlgorithmException e) {
                        throw new RuntimeException("Cannot instantiate MD5 MessageDigest!", e);
                }
                
                byte[] digest = md5.digest(id.getBytes());
                
                StringBuffer sb = new StringBuffer();
                for (byte b : digest)
                        sb.append(Integer.toHexString((int) (b & 0xff) | 0x100).substring(1, 3));
                
                return sb.toString();
        }
    
        
        /**
         * true if and only if the other obj has the same biopax type 
         * (same {@link #getModelInterface()}, not a subclass) and 
         * same URI. Other properties are not considered.
         * 
         */
        @Override
        public boolean equals(Object obj) {
                return (obj instanceof BioPAXElement) 
                        && this.getModelInterface() == ((BioPAXElement) obj).getModelInterface()
                        && this.uri.equals(((BioPAXElement) obj).getRDFId());
        }
        
        
        /**
         * This method is consistent with the 
         * overridden {@link #equals(Object)} method
         * (biopax type and URI are what matters) 
         */
        @Override
        public int hashCode() {
                return (getModelInterface() + uri).hashCode();
        }

}