/* Copyright (C) 2004 Univ. of Pennsylvania
This software is provided under the terms of the Common Public License,
version 1.0, as published by http://www.opensource.org. For further
information, see the file `LICENSE' included with this distribution. */
package edu.upenn.cis.taggers.frontend;
import java.util.*;
import java.io.*;
import edu.upenn.cis.taggers.*;
/**
* An article is a collection of field names and values, in the order they were received.
* Methods exist to tag fields and output in MEDLINE and HTML formats.
* @author Ryan McDonald <a href="mailto:ryantm@cis.upenn.edu">ryantm@cis.upenn.edu</a>
* @author Kevin Lerman <a href="mailto:klerman@seas.upenn.edu">Kevin Lerman</a>
* */
public class Article {
public final static boolean MEDLINE=true;
public final static boolean HTML=false;
private Tagger tagger;
private ArrayList fields=new ArrayList(), values = new ArrayList();
private ArrayList oldFields = new ArrayList(), oldValues = new ArrayList();
public Article(Tagger t){
tagger = t;
}
/**
* Add a field-value pair. Duplicates allowed.
* @param f The field
* @param v The value
* */
public void add(String f, String v){
oldFields.add(f);
oldValues.add(v);
fields.add(f);
values.add(v);
}
/**
* Tag the value associated with that field.
* Uses find() to get the value, so it only tags the first entry for that field
* if multiple exist. This is fine, so long as articles only have one title
* field and one abstract field. The old string will be retained for output
* to MEDLINE files.
* @param f The field whose value will be tagged
* */
public void tag(String f) throws IOException{
String old = getValue(f);
if(old!=null){
values.set(find(f),tagger.tag(old));
}
}
/**
* Returns this article in either MEDLINE or HTML format
* MEDLINE will use all the original strings, with additional tags
* (specified by the tagger) for the data. HTML will use XML and
* additional tags (usually font colors, as specified by the individual tagger)
* to show the tagger's work. Some formatting information
* is drawn from the tagger object.
* @param b Article.MEDLINE or Article.HTML depending which output you want
* @return This article, as either a MEDLINE entry or HTML
* */
public String toString(boolean b){
String toReturn="";
if(b==MEDLINE){
String toProcess="";
for(int x=0;x<values.size();x++){
String thisLine="";
thisLine=getField(x);
while(thisLine.length()<4) thisLine+=' ';
//Get tagging info from title and abstract to append them to the original MEDLINE entry
if(getField(x).equals("TI") || getField(x).equals("AB")){
toProcess+=getValue(x);
thisLine+="- "+getForMedline(getField(x)).trim()+'\n';
}
else{
thisLine+="- "+getValue(x).trim()+'\n';
}
toReturn+=thisLine;
}
toReturn+=xmlToMedline(toProcess);
if(xmlToMedline(toProcess).length()>0) toReturn+='\n';
}
else{
toReturn+="<HR>";
String[] tags = {"PMID","TI","AB","AU","DP","PT","SO"};
String[] label = {"PMID: ","","","Author: ","Published: ","Type: ","Reference: "};
boolean[] bold = {false,true,false,false,false,false,false};
boolean[] process = {false,true,true,false,false,false,false};
//Loop through the field-value pairs and tag anybody that should be tagged
for(int x=0;x<tags.length;x++){
String val = getValue(tags[x]);
if(val!=null){
if(process[x]) val = xmlToHTML(val);
if(bold[x]) toReturn+="<b>";
toReturn+=label[x]+val;
if(bold[x]) toReturn+="</b>";
toReturn+="<BR>";
}
}
}
return toReturn;
}
/**
* Return the value associated with a field, or null if there isn't one
* If it's been tagged or modified in any way, gets the modified one.
* @param f The field whose value will be retrieved
* @return The first value associated with that field
* */
public String getValue(String f){
if(find(f)!=-1)
return (String)(values.get(find(f)));
else return null;
}
/**
* Return the n'th value, or null if there isn't one
* @param n The number value to return
* @return The n'th value, or null if there isn't one
* */
private String getValue(int n){
if(n<values.size()) return (String)(values.get(n));
else return null;
}
/**
* Return the n'th field, or null if there isn't one
* @param n The number field to return
* @return The n'th field, or null if there isn't one
* */
private String getField(int f){
if(f<fields.size()) return (String)(fields.get(f));
else return null;
}
/**
* Find the (first) index of a field, or return -1 if it's not there
* @param f The field
* @return The first index of that field, or -1 if there isn't one
* */
private int find(String f){
for(int x=0;x<fields.size();x++)
if(((String)(fields.get(x))).equals(f)) return x;
return -1;
}
/**
* Search the input string for XML tags, and return them in MEDLINE format
* @param in The string to search
* @return A String consisting of the MEDLINE tags generated by the Tagger
* */
private String xmlToMedline(String in){
String[] open = tagger.xmlTags();
String[] close = tagger.xmlTags();
String[] tags = tagger.medlineTags();
for(int x=0;x<close.length;x++){
close[x]="</"+open[x].substring(1,open[x].length());
while (tags[x].length()<4)
tags[x]+=' ';
tags[x]=tags[x]+"- ";
}
ArrayList[] list = {new ArrayList(), new ArrayList(), new ArrayList(), new ArrayList()};
int found=0;
//Do a search-and-destroy sequence until we run out of things to destroy
do{
found=0;
for(int x=0;x<open.length;x++){
//Look for the open and close tags, then extract the stuff between them. Destroy the set, then increment found
int start = in.indexOf(open[x]);
int end = in.indexOf(close[x]);
if(start!=-1 && end!=-1){
found++;
String value = (in.substring(start+open[x].length(),end)).trim().toLowerCase();
boolean canI=true;
for(int y=0;y<list[x].size() && canI;y++){
if(((String)(list[x].get(y))).equals(value)) canI=false;
}
if(canI) list[x].add(value);
found++;
if(end+close[x].length()<in.length())
in = in.substring(0,start)+in.substring(end+close[x].length(),in.length());
else
in = in.substring(0,start);
}
}
} while(found>0);
String toReturn="";
for(int x=0;x<list.length;x++){
for(int n=0;n<list[x].size();n++){
toReturn+=tags[x]+((String)(list[x].get(n)))+'\n';
}
}
if(toReturn.length()>0)
return toReturn.substring(0,toReturn.length()-1);
else return "";
}
/**
* Insert <font> tags as specified by the tagger object into the input string
* wherever XML tags are found. Return the new string.
* @param in The input string
* @return The input string, with HTML tags inserted as dictated by the Tagger
* */
private String xmlToHTML(String in){
String[] open = tagger.xmlTags();
String[] close = tagger.xmlTags();
String[] openFont = tagger.htmlOpenTags();
String[] closeFont = tagger.htmlCloseTags();
for(int x=0;x<close.length;x++){
close[x]="</"+open[x].substring(1,open[x].length());
closeFont[x]=closeFont[x]+' ';
}
String toReturn="";
boolean found=false;
do{
found=false;
int o = in.length()+1;
int t = -1;
for(int x=0;x<open.length;x++){
if(in.indexOf(open[x])!=-1 && in.indexOf(open[x])<o){
o = in.indexOf(open[x]);
t = x;
found=true;
}
}
if(found){
//Now o is where the tag opens, and t is the type of tag we're looking for
int c = in.indexOf(close[t]);
String value = (in.substring(o+open[t].length(),c));
if(o!=0) toReturn+=in.substring(0,o);
toReturn+=open[t]+openFont[t]+value+closeFont[t]+close[t];
if(c+close[t].length()<in.length())
in = in.substring(c+close[t].length(),in.length());
else
in = "";
}
}while(found);
//If there's anything leftover, transfer it.
return toReturn+in;
}
/**
* Return the value associated with a field. If the value's since been modified,
* this will return the old version. Returns null if not found.
* @param f The field to search for.
* @return The unmodified value associated with that field / null if there isn't one
* */
private String getForMedline(String f){
for(int x=0;x<oldFields.size();x++){
if(((String)(oldFields.get(x))).equals(f)){return (String)(oldValues.get(x));}
}
return null;
}
}
