/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
* under the License.
*/
package org.apache.ctakes.drugner.fsm.machines.util;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.ctakes.core.fsm.condition.WordSetCondition;
import org.apache.ctakes.core.fsm.state.NamedState;
import org.apache.ctakes.core.fsm.token.BaseToken;
import org.apache.ctakes.drugner.fsm.output.util.HyphenatedDrugToken;
import net.openai.util.fsm.AnyCondition;
import net.openai.util.fsm.Condition;
import net.openai.util.fsm.Machine;
import net.openai.util.fsm.State;
/**
* Uses one or more finite state machines to detect hyphenated drug information
* adjoined to dosage data in the given input of tokens.
*
* @author Mayo Clinic
*/
public class HyphenatedDrugFSM {
// text fractions
Set iv_hyphenDrugSet = new HashSet();
// contains the finite state machines
private Set iv_machineSet = new HashSet();
/**
*
* Constructor
*
*/
public HyphenatedDrugFSM() {
iv_hyphenDrugSet.add("alka-seltzer");
iv_hyphenDrugSet.add("abilify");
iv_hyphenDrugSet.add("actiq");
iv_hyphenDrugSet.add("ambi-1000");
iv_hyphenDrugSet.add("almacone-2");
iv_hyphenDrugSet.add("alexan-100");
iv_hyphenDrugSet.add("azo-100");
iv_hyphenDrugSet.add("allerhist-1");
iv_hyphenDrugSet.add("acne-5");
iv_hyphenDrugSet.add("andriod-10");
iv_hyphenDrugSet.add("andriod-25");
iv_hyphenDrugSet.add("andriod-50");
iv_hyphenDrugSet.add("acys-5");
iv_hyphenDrugSet.add("aldoclor-250");
iv_hyphenDrugSet.add("aerolin-400");
iv_hyphenDrugSet.add("alka-seltzer plus");
iv_hyphenDrugSet.add("allegra-d");
iv_hyphenDrugSet.add("b-complex");
iv_hyphenDrugSet.add("bactroban");
iv_hyphenDrugSet.add("chlor-trimeton");
iv_hyphenDrugSet.add("claritin-d");
iv_hyphenDrugSet.add("cleocin-t");
iv_hyphenDrugSet.add("daranide");
iv_hyphenDrugSet.add("depo-medrol");
iv_hyphenDrugSet.add("depo-provera");
iv_hyphenDrugSet.add("effexor-xr");
iv_hyphenDrugSet.add("glucosamine-chondroitin");
iv_hyphenDrugSet.add("fml-s");
iv_hyphenDrugSet.add("hep-lock");
iv_hyphenDrugSet.add("l-arginine");
iv_hyphenDrugSet.add("l-thyroxine");
iv_hyphenDrugSet.add("lupron-depot");
iv_hyphenDrugSet.add("metro cream");
iv_hyphenDrugSet.add("micro-k");
iv_hyphenDrugSet.add("multi-vitamin");
iv_hyphenDrugSet.add("muro-128");
iv_hyphenDrugSet.add("naphcon-a");
iv_hyphenDrugSet.add("neo-synephrine");
iv_hyphenDrugSet.add("no-doz");
iv_hyphenDrugSet.add("noctec");
iv_hyphenDrugSet.add("nor-qd");
iv_hyphenDrugSet.add("ocuflox");
iv_hyphenDrugSet.add("ortho tri-cyclen");
iv_hyphenDrugSet.add("ortho tri-cyclen lo");
iv_hyphenDrugSet.add("ortho-cept");
iv_hyphenDrugSet.add("ortho-novum");
iv_hyphenDrugSet.add("os-cal D");
iv_hyphenDrugSet.add("os-cal 500");
iv_hyphenDrugSet.add("os-cal");
iv_hyphenDrugSet.add("peg-intron");
iv_hyphenDrugSet.add("phospho-soda");
iv_hyphenDrugSet.add("pred-g");
iv_hyphenDrugSet.add("retin-a");
iv_hyphenDrugSet.add("robitussin-dm");
iv_hyphenDrugSet.add("senokot-s");
iv_hyphenDrugSet.add("serentil");
iv_hyphenDrugSet.add("sleep-eze");
iv_hyphenDrugSet.add("tegretol-xr");
iv_hyphenDrugSet.add("theo-dur");
iv_hyphenDrugSet.add("tilade");
iv_hyphenDrugSet.add("tri-sprintec");
iv_hyphenDrugSet.add("vasocon-a");
iv_hyphenDrugSet.add("vivelle-dot");
iv_hyphenDrugSet.add("vira-a");
iv_hyphenDrugSet.add("vitamin-a");
iv_hyphenDrugSet.add("vitamin-b6");
iv_hyphenDrugSet.add("vitamin-b complex");
iv_hyphenDrugSet.add("vitamin-b");
iv_hyphenDrugSet.add("vitamin-b1");
iv_hyphenDrugSet.add("vitamin-c");
iv_hyphenDrugSet.add("vitamin-d");
iv_hyphenDrugSet.add("vitamin-d2");
iv_hyphenDrugSet.add("vitamin-e");
iv_machineSet.add(getDashMachine());
}
/**
* Gets a finite state machine that detects the following:
* <ol>
* <li>zyrtec-d</li>
* <li>alka-seltzer plus</li>
* </ol>
*
* @return
*/
private Machine getDashMachine() {
State startState = new NamedState("START");
State endState = new NamedState("END");
endState.setEndStateFlag(true);
Machine m = new Machine(startState);
State hyphenatedDrugState = new NamedState("HYPH_DRUG");
Condition hyphenatedDrugCondition = new WordSetCondition(
iv_hyphenDrugSet, false);
startState.addTransition(hyphenatedDrugCondition, endState);//hyphenatedDrugState);
startState.addTransition(new AnyCondition(), startState);
hyphenatedDrugState.addTransition(new AnyCondition(), startState);
endState.addTransition(new AnyCondition(), startState);
return m;
}
/**
* Executes the finite state machines.
*
* @param tokens
* @return Set of FractionToken objects.
* @throws Exception
*/
public Set execute(List tokens) throws Exception {
Set fractionSet = new HashSet();
// maps a fsm to a token start index
// key = fsm , value = token start index
Map tokenStartMap = new HashMap();
for (int i = 0; i < tokens.size(); i++) {
BaseToken token = (BaseToken) tokens.get(i);
Iterator machineItr = iv_machineSet.iterator();
while (machineItr.hasNext()) {
Machine fsm = (Machine) machineItr.next();
fsm.input(token);
State currentState = fsm.getCurrentState();
if (currentState.getStartStateFlag()) {
tokenStartMap.put(fsm, new Integer(i));
}
if (currentState.getEndStateFlag()) {
Object o = tokenStartMap.get(fsm);
int tokenStartIndex;
if (o == null) {
// By default, all machines start with
// token zero.
tokenStartIndex = 0;
} else {
tokenStartIndex = ((Integer) o).intValue();
// skip ahead over single token we don't want
tokenStartIndex++;
}
BaseToken startToken = (BaseToken) tokens
.get(tokenStartIndex);
BaseToken endToken = token;
HyphenatedDrugToken fractionToken = new HyphenatedDrugToken(
startToken.getStartOffset(), endToken
.getEndOffset());
fractionSet.add(fractionToken);
fsm.reset();
}
}
}
// cleanup
tokenStartMap.clear();
// reset machines
Iterator itr = iv_machineSet.iterator();
while (itr.hasNext()) {
Machine fsm = (Machine) itr.next();
fsm.reset();
}
return fractionSet;
}
}