/**
* 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;
import java.util.Iterator;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.uima.jcas.JCas;
import org.apache.ctakes.core.fsm.output.DateToken;
import org.apache.ctakes.core.util.FSUtil;
import org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement;
import org.apache.ctakes.drugner.elements.ConfidenceScoreElement;
import org.apache.ctakes.drugner.elements.DosageElement;
import org.apache.ctakes.drugner.elements.DrugChangeStatusElement;
import org.apache.ctakes.drugner.elements.DurationElement;
import org.apache.ctakes.drugner.elements.FormElement;
import org.apache.ctakes.drugner.elements.FrequencyElement;
import org.apache.ctakes.drugner.elements.FrequencyUnitElement;
import org.apache.ctakes.drugner.elements.RouteElement;
import org.apache.ctakes.drugner.elements.StartDateElement;
import org.apache.ctakes.drugner.elements.StrengthElement;
import org.apache.ctakes.drugner.elements.StrengthUnitElement;
import org.apache.ctakes.drugner.elements.TextMentionElement;
import org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken;
import org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken;
import org.apache.ctakes.drugner.fsm.output.elements.RouteToken;
import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
import org.apache.ctakes.drugner.type.DosagesAnnotation;
import org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation;
import org.apache.ctakes.drugner.type.DurationAnnotation;
import org.apache.ctakes.drugner.type.FormAnnotation;
import org.apache.ctakes.drugner.type.FrequencyAnnotation;
import org.apache.ctakes.drugner.type.FrequencyUnitAnnotation;
import org.apache.ctakes.drugner.type.RouteAnnotation;
import org.apache.ctakes.drugner.type.StrengthAnnotation;
import org.apache.ctakes.drugner.type.StrengthUnitAnnotation;
/**
* Contains information from a single document - is not the result of data
* mining.
*/
public class DrugMention implements DrugModel {
/**
* The word(s) in the note that indicate the drug.
*/
public TextMentionElement drugMentionText;
public AssociatedPrimaryCodeElement associatedCodePrimary;
/**
* terminology unique identifier (e.g. RxNorm identifier). if not in the
* terminology, we will use the drug mention as the id.
*/
public AssociatedPrimaryCodeElement associatedCodeSecondary;
/**
* If there is a specific date in the note associated with the drug mention,
* the specific date. Also time might be capture by more general markers,
* e.g. "subsequently".
*/
public StartDateElement startDate;
public DateToken endDate;
/**
* e.g. 5 mg
*/
public DosageElement dosage;
/**
* e.g. twice daily
*/
public FrequencyElement frequency;
/**
* e.g. twice daily
*/
public FrequencyUnitElement frequencyUnit;
/**
* e.g. "for 2 weeks"
*/
public DurationElement duration;
/**
* e.g oral Topical Examples include medications applied onto the skin,
* asthma medications, enema, eye or ear drops, decongestants, vaginal
* creams. Enteral (oral) Most drugs taken by mouth such as tablets or
* capsules. Enteral (gastric) Examples include medications given through a
* gastric or duodenal tube. Enteral (rectal) Drugs in suppositories or
* enema form. Parenteral (intravenous) Parenteral (intra-arterial)
* Parenteral (intramuscular) Parenteral (intracardiac) Parenteral
* (subcutaneous) Medications such as insulin. Parenteral (intrathecal) Into
* the spinal canal. Parenteral (intraperitoneal) Parenteral (transdermal)
* Such as patches. Parenteral (transmucosal)
*/
public RouteElement route;
public StrengthElement strength;
/**
* Span the drug form, if available. The spanned mention needs to be mapped
* to the standard form available in the dropdown menu. In general don't
* infer. However, for a medication described in terms of cc or mL, the
* number of cc's or mL's is usually not a strength - for example "5 cc
* 0.5%" (or 5 mL 0.5%), indicates a strength of 0.5% -- for those, create a
* Form, with "cc" or "mL" spanned, and mapped to liquid, so that we capture
* the unit such as cc or mL.
*/
public StrengthUnitElement strengthUnit;
/**
* Span the drug form, if available. The spanned mention needs to be mapped
* to the standard form available in the dropdown menu. In general don't
* infer. However, for a medication described in terms of cc or mL, the
* number of cc's or mL's is usually not a strength - for example "5 cc
* 0.5%" (or 5 mL 0.5%), indicates a strength of 0.5% -- for those, create a
* Form, with "cc" or "mL" spanned, and mapped to liquid, so that we capture
* the unit such as cc or mL.
*/
public FormElement form;
/**
* aka change. - start: refers to an explicit mention of when the drug was
* started - stop: refers to an explicit mention of when the drug was
* stopped - increase and decrease: refer to explicit mentions of drug
* attribute changes - noChange: nothing is explicitly stated regarding
* changes. This will be the default case and does not need to be created.
* If there is some mention on the text such as "I told the patient to
* continue with his dosage of XXX 300 mg", then there would be textual
* evidence for noChange.
*/
public DrugChangeStatusElement changeStatus;
public ConfidenceScoreElement confidence;
public boolean findMaxValue = true;
/**
* regex pattern to look for, in this case alpha upper and lower characters
*/
private static final Pattern lookForAlpha = Pattern.compile("[a-zA-Z]+");
/**
* regex pattern to look for, in this case alpha upper and lower characters
*/
private static final Pattern lookForPercent = Pattern.compile("[%]");
public DrugMention(JCas jcas, int beginPos, int endPos) {
Iterator drugStatusTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, DrugChangeStatusAnnotation.type, beginPos, endPos);
while (drugStatusTokenItr.hasNext()){
DrugChangeStatusAnnotation focusToken = (DrugChangeStatusAnnotation) drugStatusTokenItr.next();
String localStatus = null;
if ((localStatus = findDrugChangeStatusElement(jcas, focusToken
.getBegin(), focusToken.getEnd())) == null) {
changeStatus = new DrugChangeStatusElement(focusToken
.getCoveredText(), focusToken.getBegin(),
focusToken.getEnd());
} else {
setDrugChangeStatusElement(localStatus, focusToken
.getBegin(), focusToken.getEnd());
}
}
if (changeStatus != null
&& (changeStatus.getDrugChangeStatus().equals(DrugChangeStatusToken.INCREASEFROM)
|| changeStatus.getDrugChangeStatus().equals(DrugChangeStatusToken.DECREASE))) {
findMaxValue = false;
}
Iterator dateTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
DateAnnotation.type, beginPos, endPos);
while (dateTokenItr.hasNext()){
DateAnnotation focusToken = (DateAnnotation) dateTokenItr.next();
String localDate = null;
if ((localDate = findStartDateElement(jcas, focusToken.getBegin(),
focusToken.getEnd())) == null) {
startDate = new StartDateElement(focusToken.getCoveredText(),
focusToken.getBegin(), focusToken.getEnd());
} else {
setStartDateElement(localDate, focusToken.getBegin(),
focusToken.getEnd());
}
}
Iterator doseTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
DosagesAnnotation.type, beginPos, endPos);
while (doseTokenItr.hasNext()){
DosagesAnnotation focusToken = (DosagesAnnotation) doseTokenItr.next();
String localDose = null;
if ((localDose = findDosageElement(jcas, focusToken.getBegin(),
focusToken.getEnd())) == null) {
dosage = new DosageElement(focusToken.getCoveredText(),
focusToken.getBegin(), focusToken.getEnd());
} else {
setDosageElement(localDose, focusToken.getBegin(),
focusToken.getEnd());
}
}
Iterator frequencyTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
FrequencyAnnotation.type, beginPos, endPos);
while (frequencyTokenItr.hasNext()){
FrequencyAnnotation focusToken = (FrequencyAnnotation) frequencyTokenItr.next();
String localFreq = null;
if ((localFreq = findFrequencyElement(jcas, focusToken
.getBegin(), focusToken.getEnd())) == null) {
frequency = new FrequencyElement(focusToken
.getCoveredText(), focusToken.getBegin(),
focusToken.getEnd());
} else if ((frequency != null && localFreq != null)
&& (frequency.getFrequencyMention().compareTo("") != 0)
&& (localFreq.compareTo("") != 0)
&& (parseIntValue(localFreq) > parseIntValue(frequency
.getFrequencyMention()) && findMaxValue == true)) {
// Need a way to find the largest frequency and/or convert
// it to factor daily dosage
setFrequencyElement(localFreq, focusToken.getBegin(),
focusToken.getEnd());
} else {
setFrequencyElement(localFreq, focusToken.getBegin(),
focusToken.getEnd());
}
}
Iterator frequencyUnitTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
FrequencyUnitAnnotation.type, beginPos, endPos);
while (frequencyUnitTokenItr.hasNext()){
FrequencyUnitAnnotation focusToken = (FrequencyUnitAnnotation) frequencyUnitTokenItr.next();
String localFreq = null;
if ((localFreq = findFrequencyUnitElement(jcas,
focusToken.getBegin(), focusToken.getEnd())) == null) {
frequencyUnit = new FrequencyUnitElement(focusToken
.getCoveredText(), focusToken.getBegin(),
focusToken.getEnd());
} else if (frequencyUnit == null
&& findMaxValue == true) {
// Need a way to find the largest frequency and/or convert
// it to factor daily dosage
setFrequencyUnitElement(localFreq, focusToken.getBegin(),
focusToken.getEnd());
}
}
Iterator strengthUnitTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, StrengthUnitAnnotation.type, beginPos, endPos);
while (strengthUnitTokenItr.hasNext()){
StrengthUnitAnnotation focusToken = (StrengthUnitAnnotation) strengthUnitTokenItr.next();
setStrengthUnitElement(focusToken.getCoveredText(),
focusToken.getBegin(), focusToken.getEnd());
}
Iterator strengthTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, StrengthAnnotation.type, beginPos, endPos);
while (strengthTokenItr.hasNext()){
StrengthAnnotation focusToken = (StrengthAnnotation) strengthTokenItr.next();
String localStrength = null;
if ((localStrength = findStrengthElement(jcas, focusToken
.getBegin(), focusToken.getEnd())) == null) {
strength = new StrengthElement(focusToken.getCoveredText(),
focusToken.getBegin(), focusToken.getEnd());
} else {
if (strength != null) {
// check for range and compare
int spacePosition = strength.getStrengthMention()
.indexOf(" ");
int spacePos = localStrength
.indexOf(" ");
if (spacePosition > 0 && spacePos > 0
&& parseDoubleValue(strength
.getStrengthMention().substring(0,
spacePosition)) < parseDoubleValue(localStrength
.substring(0, localStrength
.indexOf(" ")))&& findMaxValue == true) {
setStrengthElement(localStrength, focusToken
.getBegin(), focusToken.getEnd());
} else {
String stringRange = strength.getStrengthMention();
int hyphPosition = 0;
if ((stringRange.length() > 0)
&& (stringRange.indexOf('-') > 0)) {
hyphPosition = stringRange.indexOf('-');
Double firstValue = new Double(
parseDoubleValue(stringRange
.subSequence(0, hyphPosition)));
Double secondValue = new Double(
parseDoubleValue(stringRange
.substring(hyphPosition + 2)));
if (firstValue.doubleValue() >= secondValue
.doubleValue() && findMaxValue == true) {
setStrengthElement(firstValue.toString(),
focusToken.getBegin(), focusToken
.getEnd());
} else {
setStrengthElement(firstValue.toString(),
focusToken.getBegin(), focusToken
.getEnd());
}
}
}
} else if ((localStrength.length() > 0)
&& (localStrength.indexOf('-') > 0)) {
int hyphPosition = 0;
hyphPosition = localStrength.indexOf('-');
Double firstValue = new Double(
parseDoubleValue(localStrength.subSequence(0,
hyphPosition)));
Double secondValue = new Double(
parseDoubleValue(localStrength
.substring(hyphPosition + 2)));
if (firstValue.doubleValue() >= secondValue
.doubleValue() && findMaxValue == true) {
setStrengthElement(firstValue.toString(),
focusToken.getBegin(), focusToken.getEnd());
} else {
setStrengthElement(firstValue.toString(),
focusToken.getBegin(), focusToken.getEnd());
}
setStrengthElement(localStrength,
focusToken.getBegin(), focusToken.getEnd());
} else {
setStrengthElement(localStrength,
focusToken.getBegin(), focusToken.getEnd());
}
}
}
Iterator formTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, FormAnnotation.type, beginPos, endPos);
while (formTokenItr.hasNext()){
FormAnnotation focusToken = (FormAnnotation) formTokenItr.next();
String localForm = null;
if ((localForm = findFormElement(jcas, focusToken.getBegin(),
focusToken.getEnd())) == null) {
form = new FormElement(focusToken.getCoveredText(),
focusToken.getBegin(), focusToken.getEnd());
} else {
setFormElement(localForm, focusToken.getBegin(), focusToken
.getEnd());
}
}
Iterator routeTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, RouteAnnotation.type, beginPos, endPos);
while (routeTokenItr.hasNext()){
RouteAnnotation focusToken = (RouteAnnotation) routeTokenItr.next();
String localRoute = null;
if ((localRoute = findRouteElement(jcas, focusToken.getBegin(),
focusToken.getEnd())) == null) {
route = new RouteElement(focusToken.getCoveredText(),
focusToken.getBegin(), focusToken.getEnd());
} else {
setRouteElement(localRoute, focusToken.getBegin(),
focusToken.getEnd());
}
}
Iterator durationTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, DurationAnnotation.type, beginPos, endPos);
while (durationTokenItr.hasNext()){
DurationAnnotation focusToken = (DurationAnnotation) durationTokenItr.next();
String localDuration = null;
if ((localDuration = findDurationElement(jcas, focusToken
.getBegin(), focusToken.getEnd())) == null) {
duration = new DurationElement(focusToken.getCoveredText(),
focusToken.getBegin(), focusToken.getEnd());
} else {
setDurationElement(localDuration, focusToken.getBegin(),
focusToken.getEnd());
}
}
}
public void setPrimaryAssociatedCodeElement(String name, int beginOffset,
int endOffset) {
// need a method to find most suitable primary cui here
associatedCodePrimary = new AssociatedPrimaryCodeElement(name, beginOffset,
endOffset);
}
public void setSecondaryAssociatedCodeElement(String name, int beginOffset,
int endOffset) {
// need a method to find most suitable secondary cui here
associatedCodeSecondary = new AssociatedPrimaryCodeElement(name, beginOffset,
endOffset);
}
public void setStartDateElement(String date, int beginOffset, int endOffset) {
startDate = new StartDateElement(date, beginOffset, endOffset);
}
public void setEndDateElement(String name, int beginOffset, int endOffset) {
}
public void setDosageElement(String dose, int beginOffset, int endOffset) {
dosage = new DosageElement(dose, beginOffset, endOffset);
}
public void setFrequencyElement(String name, int beginOffset, int endOffset) {
frequency = new FrequencyElement(name, beginOffset, endOffset);
}
public void setFrequencyUnitElement(String name, int beginOffset,
int endOffset) {
frequencyUnit = new FrequencyUnitElement(name, beginOffset, endOffset);
}
public void setFormElement(String name, int beginOffset, int endOffset) {
form = new FormElement(name, beginOffset, endOffset);
}
public void setDurationElement(String name, int beginOffset, int endOffset) {
duration = new DurationElement(name, beginOffset, endOffset);
}
public void setRouteElement(String name, int beginOffset, int endOffset) {
route = new RouteElement(name, beginOffset, endOffset);
}
public void setDrugChangeStatusElement(String name, int beginOffset,
int endOffset) {
changeStatus = new DrugChangeStatusElement(name, beginOffset, endOffset);
}
public void setConfidenceScoreElement(double score, int beginOffset,
int endOffset) {
confidence = new ConfidenceScoreElement(score, beginOffset, endOffset);
}
public void setStrengthElement(String name, int beginOffset, int endOffset) {
strength = new StrengthElement(name, beginOffset, endOffset);
}
public String getStrengthUnitElement() {
// TODO Auto-generated method stub
if (strengthUnit != null)
return strengthUnit.getStrengthMention();
else
return null;
}
public void setStrengthUnitElement(String name, int beginOffset, int endOffset) {
// TODO Auto-generated method stub
strengthUnit = new StrengthUnitElement(name, beginOffset, endOffset);
}
public String getPrimaryAssociatedCodeElement() {
if (associatedCodePrimary != null)
return associatedCodePrimary.getCuiCode();
else
return null;
}
public String getSecondaryAssociatedCodeElement() {
if (associatedCodeSecondary != null)
return associatedCodeSecondary.getCuiCode();
else
return null;
}
public String getStartDateElement() {
if (startDate != null)
return startDate.getDate();
else return "";
}
public String getEndDateElement() {
return endDate.toString();
}
public String getDosageElement() {
if (dosage != null)
return dosage.getDosage();
else
return "1.0";
}
public String getFrequencyElement() {
if (frequency != null)
return frequency.getFrequencyMention();
else
return "1.0";
}
public String getFrequencyUnitElement() {
if (frequencyUnit != null)
return frequencyUnit.getFrequencyUnitMention();
else
return null;
}
public String getFormElement() {
if (form != null)
return form.getFormMention();
else
return null;
}
public String getDurationElement() {
if (duration != null)
return duration.getDuration();
else
return null;
}
public String getRouteElement() {
if (route != null)
return route.getRouteMention();
else
return null;
}
public String getDrugChangeStatusElement() {
if (changeStatus != null)
return changeStatus.getDrugChangeStatus();
else
return DrugChangeStatusElement.NOCHANGE_STATUS;
}
public String getStrengthElement() {
if (strength != null)
return strength.getStrengthMention();
else
return "";
}
public double getConfidenceScoreElement() {
if (confidence != null)
return confidence.getConfidenceScoreElement();
else
return 0;
}
private String findStartDateElement(JCas jcas, int beginOffset, int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
DateAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
DateAnnotation da = (DateAnnotation) firItr.next();
if (da.getBegin() == beginOffset)
return da.getCoveredText();
}
return null;
}
private String findEndDateElement(JCas jcas, int beginOffset, int endOffset) {
Iterator firItr = FSUtil.getAnnotationsInSpanIterator(jcas,
DateAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
DateAnnotation da = (DateAnnotation) firItr.next();
if (da.getBegin() == beginOffset)
return da.getCoveredText();
}
return null;
}
private String findDosageElement(JCas jcas, int beginOffset, int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
DosagesAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
DosagesAnnotation da = (DosagesAnnotation) firItr.next();
if (da.getBegin() == beginOffset) {
int posSpace = da.getCoveredText().lastIndexOf(' ');
int posHyph = da.getCoveredText().lastIndexOf('-');
String lastTerm = da.getCoveredText();
int ofSpace = da.getCoveredText().indexOf("of");
if (ofSpace > 0)
lastTerm = da.getCoveredText().substring(0, ofSpace).trim();
if ((lastTerm.compareToIgnoreCase("one-half-tablet") == 0)
|| (lastTerm.compareToIgnoreCase("one-half") == 0)
|| (lastTerm.compareToIgnoreCase("1/2") == 0)
|| (lastTerm.compareToIgnoreCase("half-tablet") == 0)) {
return "0.5";
} else if (lastTerm.compareToIgnoreCase("one-and-a-half") == 0) {
return "1.5";
} else if ((lastTerm.compareToIgnoreCase("one-quarter") == 0)
|| (lastTerm.compareToIgnoreCase("one-fourth") == 0)
|| (lastTerm.compareToIgnoreCase("1/4") == 0)
|| (lastTerm.compareToIgnoreCase("a-fourth") == 0)) {
return ".25";
} else if ((lastTerm.compareToIgnoreCase("one-third") == 0)
|| (lastTerm.compareToIgnoreCase("thirds") == 0)
|| (lastTerm.compareToIgnoreCase("1/3") == 0)
|| (lastTerm.compareToIgnoreCase("a-third") == 0)) {
return ".33";
} else {
if (posSpace > 0)
lastTerm = lastTerm.substring(posSpace + 1);
else if (posHyph > 0)
lastTerm = lastTerm.substring(posHyph + 1);
}
return convertFromTextToNum(lastTerm);
}
}
return null;
}
private String findFormElement(JCas jcas, int beginOffset, int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
FormAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
FormAnnotation da = (FormAnnotation) firItr.next();
if (da.getBegin() == beginOffset) {
if ((da.getCoveredText().compareToIgnoreCase(
FormElement.AEROSOL) == 0)
|| (da.getCoveredText().compareToIgnoreCase("aerosols") == 0))
return FormElement.AEROSOL;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.CREAM) == 0)
|| (da.getCoveredText().compareToIgnoreCase("creams") == 0))
return FormElement.CREAM;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.ELIXIR) == 0)
|| (da.getCoveredText().compareToIgnoreCase("elixirs") == 0))
return FormElement.ELIXIR;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.EMULSION) == 0)
|| (da.getCoveredText().compareToIgnoreCase(
"emulutions") == 0))
return FormElement.EMULSION;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.ENEMA) == 0)
|| (da.getCoveredText().compareToIgnoreCase("ememas") == 0))
return FormElement.ENEMA;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.GEL) == 0)
|| (da.getCoveredText().compareToIgnoreCase("gels") == 0))
return FormElement.GEL;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.IMPLANT) == 0)
|| (da.getCoveredText().compareToIgnoreCase("implants") == 0))
return FormElement.IMPLANT;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.INHALANT) == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("inhalants") == 0))
return FormElement.INHALANT;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.INJECTION) == 0)
|| (da.getCoveredText().compareToIgnoreCase(
"injections") == 0))
return FormElement.INJECTION;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.LIQUID) == 0)
|| (da.getCoveredText().compareToIgnoreCase("liquids") == 0))
return FormElement.LIQUID;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.LOTION) == 0)
|| (da.getCoveredText().compareToIgnoreCase("lotions") == 0))
return FormElement.LOTION;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.LOZENGE) == 0)
|| (da.getCoveredText().compareToIgnoreCase("lozenges") == 0))
return FormElement.LOZENGE;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.OINTMENT) == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("ointments") == 0))
return FormElement.OINTMENT;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.PATCH) == 0)
|| (da.getCoveredText().compareToIgnoreCase("patches") == 0))
return FormElement.PATCH;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.PILL) == 0)
|| (da.getCoveredText().compareToIgnoreCase("pills") == 0))
return FormElement.PILL;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.POWDER) == 0)
|| (da.getCoveredText().compareToIgnoreCase("powders") == 0))
return FormElement.POWDER;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.SHAMPOO) == 0)
|| (da.getCoveredText().compareToIgnoreCase("shampoos") == 0))
return FormElement.SHAMPOO;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.SOAP) == 0)
|| (da.getCoveredText().compareToIgnoreCase("soaps") == 0))
return FormElement.SOAP;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.SOLUTION) == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("solutions") == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("soln") == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("concentrate") == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("concentrat") == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("conc") == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("solu") == 0))
return FormElement.SOLUTION;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.SPRAY) == 0)
|| (da.getCoveredText().compareToIgnoreCase("sprays") == 0)
|| (da.getCoveredText().compareToIgnoreCase(
"nebulizers") == 0)
|| (da.getCoveredText()
.compareToIgnoreCase("nebulizer") == 0))
return FormElement.SPRAY;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.SUPPOSITORY) == 0)
|| (da.getCoveredText().compareToIgnoreCase(
"suppositories") == 0))
return FormElement.SUPPOSITORY;
else if ((da.getCoveredText().compareToIgnoreCase(FormElement.SYRINGE) == 0 )
|| (da.getCoveredText().compareToIgnoreCase("syrnge") == 0))
return FormElement.SYRINGE;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.SYRUP) == 0)
|| (da.getCoveredText().compareToIgnoreCase("syrups") == 0))
return FormElement.SYRUP;
else if ((da.getCoveredText().compareToIgnoreCase(
FormElement.TABLET) == 0)
|| (da.getCoveredText().compareToIgnoreCase("tablets") == 0)
// Capsule needs to be handled differently
// || (da.getCoveredText().compareToIgnoreCase("capsule") == 0)
// || (da.getCoveredText().compareToIgnoreCase("capsules") == 0)
// || (da.getCoveredText().compareToIgnoreCase("cap") == 0)
// || (da.getCoveredText().compareToIgnoreCase("caps") == 0)
|| (da.getCoveredText().compareToIgnoreCase("tab") == 0)
|| (da.getCoveredText().compareToIgnoreCase("tabs") == 0))
return FormElement.TABLET;
else if ((da.getCoveredText().compareToIgnoreCase(FormElement.CAPSULE) == 0)
|| (da.getCoveredText().compareToIgnoreCase("capsule") == 0)
|| (da.getCoveredText().compareToIgnoreCase("capsules") == 0)
|| (da.getCoveredText().compareToIgnoreCase("cap") == 0)
|| (da.getCoveredText().compareToIgnoreCase("caps") == 0))
return FormElement.CAPSULE;
return null;
}
}
return null;
}
private String findFrequencyElement(JCas jcas, int beginOffset, int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
FrequencyAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
FrequencyAnnotation da = (FrequencyAnnotation) firItr.next();
if (da.getBegin() == beginOffset) {
int posSpace = da.getCoveredText().indexOf(' ');
int posHyph = da.getCoveredText().indexOf('-');
int lastPosHyph = da.getCoveredText().lastIndexOf('-');
String firstTerm = da.getCoveredText();
String lastTerm = da.getCoveredText();
if (posSpace > 0)
firstTerm = da.getCoveredText().substring(0, posSpace);
else if (posHyph > 0)
firstTerm = firstTerm.substring(0, posHyph);
if (lastPosHyph > 0){
lastTerm = lastTerm.substring(lastPosHyph+1, lastTerm.length());
//this.setFrequencyUnitElement(lastTerm, beginOffset+lastPosHyph+1, endOffset);
}
int lastSpace = lastTerm.lastIndexOf(' ');
if (lastSpace > 0)
lastTerm = lastTerm.substring(0, lastSpace);
while ((lastSpace = lastTerm.lastIndexOf(' ')) > 1)
lastTerm = lastTerm.substring(lastSpace+1);
String returnFirstValue = convertFromTextToNum(firstTerm);
String returnLastValue = convertFromTextToNum(lastTerm);
try {
if (new Double(returnFirstValue).intValue()
< new Double(returnLastValue).intValue() && findMaxValue){
return returnLastValue;
}
else
return returnFirstValue;
}
catch (NumberFormatException nfe){
return returnFirstValue;
}
}
}
return null;
}
private String findFrequencyUnitElement(JCas jcas, int beginOffset,
int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
FrequencyUnitAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
FrequencyUnitAnnotation da = (FrequencyUnitAnnotation) firItr
.next();
if (da.getBegin() == beginOffset && da.getPeriod() > holdLargestPeriod) {
holdLargestPeriod = da.getPeriod();
int posHyph = da.getCoveredText().lastIndexOf('-');
String lastTerm = da.getCoveredText();
int szString = lastTerm.toString().length();
if (posHyph > 0) {
lastTerm = lastTerm.substring(posHyph + 1, szString);
}
if (da.getPeriod() == FrequencyUnitToken.QUANTITY_ONE) {
return FrequencyUnitElement.DAILY;
} else if (da.getPeriod() == FrequencyUnitToken.QUANTITY_TWO) {
if (frequency != null
&& (frequency.getBeginOffset() != beginOffset && frequency
.getEndOffset() != endOffset)) {
if ((dosage == null
|| (dosage != null
&& convertFromTextToNum(
dosage.getDosage()).compareTo(
"1") == 0 && (dosage
.getBeginOffset() != beginOffset && dosage
.getEndOffset() != endOffset)))
&& (changeStatus != null && (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.OTHER) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASEFROM) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASEFROM) != 0))) {
setFrequencyElement(
frequency.getFrequencyMention(), frequency
.getBeginOffset(), frequency
.getEndOffset());
} else {
double updateFreq = new Double(frequency
.getFrequencyMention()).doubleValue() * 2.0;
setFrequencyElement(String.valueOf(updateFreq), beginOffset,
endOffset);
}
} else {
setFrequencyElement("2.0", beginOffset, endOffset);
}
return FrequencyUnitElement.DAILY;
} else if (da.getPeriod() == FrequencyUnitToken.QUANTITY_THREE) {
if (frequency != null
&& (frequency.getBeginOffset() != beginOffset && frequency
.getEndOffset() != endOffset)) {
if ((dosage == null
|| (dosage != null
&& convertFromTextToNum(
dosage.getDosage()).compareTo(
"1") == 0 && (dosage
.getBeginOffset() != beginOffset && dosage
.getEndOffset() != endOffset)))
&& (changeStatus != null && (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.OTHER) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASEFROM) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASEFROM) != 0))){
setFrequencyElement(
frequency.getFrequencyMention(), frequency
.getBeginOffset(), frequency
.getEndOffset());
} else {
double updateFreq = new Double(frequency
.getFrequencyMention()).doubleValue() * 3.0;
setFrequencyElement(String.valueOf(updateFreq), beginOffset,
endOffset);
}
} else {
setFrequencyElement("3.0", beginOffset, endOffset);
}
return FrequencyUnitElement.DAILY;
} else if (da.getPeriod() == FrequencyUnitToken.QUANTITY_FOUR) {
if (frequency != null
&& (frequency.getBeginOffset() != beginOffset && frequency
.getEndOffset() != endOffset)) {
if ((dosage == null
|| (dosage != null
&& convertFromTextToNum(
dosage.getDosage()).compareTo(
"1") == 0 && (dosage
.getBeginOffset() != beginOffset && dosage
.getEndOffset() != endOffset)))
&& (changeStatus != null && (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.OTHER) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASEFROM) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASEFROM) != 0))) {
setFrequencyElement(
frequency.getFrequencyMention(), frequency
.getBeginOffset(), frequency
.getEndOffset());
} else {
double updateFreq = new Double(frequency
.getFrequencyMention()).doubleValue() * 4.0;
setFrequencyElement(String.valueOf(updateFreq), beginOffset,
endOffset);
}
} else {
setFrequencyElement("4.0", beginOffset, endOffset);
}
return FrequencyUnitElement.DAILY;
} else if (da.getPeriod() == FrequencyUnitToken.QUANTITY_FIVE) {
if (frequency != null
&& (frequency.getBeginOffset() != beginOffset && frequency
.getEndOffset() != endOffset)) {
if ((dosage == null
|| (dosage != null
&& convertFromTextToNum(
dosage.getDosage()).compareTo(
"1") == 0 && (dosage
.getBeginOffset() != beginOffset && dosage
.getEndOffset() != endOffset)))
&& (changeStatus != null && (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.OTHER) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASEFROM) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASEFROM) != 0))){
setFrequencyElement(
frequency.getFrequencyMention(), frequency
.getBeginOffset(), frequency
.getEndOffset());
} else {
double updateFreq = new Double(frequency
.getFrequencyMention()).doubleValue() * 5.0;
setFrequencyElement(String.valueOf(updateFreq), beginOffset,
endOffset);
}
} else {
setFrequencyElement("5.0", beginOffset, endOffset);
}
return FrequencyUnitElement.DAILY;
} else if (da.getPeriod() == FrequencyUnitToken.QUANTITY_SIX) {
if (frequency != null
&& (frequency.getBeginOffset() != beginOffset && frequency
.getEndOffset() != endOffset)) {
if ((dosage == null
|| (dosage != null
&& convertFromTextToNum(
dosage.getDosage()).compareTo(
"1") == 0 && (dosage
.getBeginOffset() != beginOffset && dosage
.getEndOffset() != endOffset)))
&& (changeStatus != null && (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.OTHER) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASEFROM) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASEFROM) != 0))) {
setFrequencyElement(
frequency.getFrequencyMention(), frequency
.getBeginOffset(), frequency
.getEndOffset());
} else {
double updateFreq = new Double(frequency
.getFrequencyMention()).doubleValue() * 6.0;
setFrequencyElement(String.valueOf(updateFreq), beginOffset,
endOffset);
}
} else {
setFrequencyElement("6.0", beginOffset, endOffset);
}
return FrequencyUnitElement.DAILY;
} else if (da.getPeriod() == FrequencyUnitToken.QUANTITY_SEVEN) {
if (frequency != null
&& (frequency.getBeginOffset() != beginOffset && frequency
.getEndOffset() != endOffset)) {
if ((dosage == null
|| (dosage != null
&& convertFromTextToNum(
dosage.getDosage()).compareTo(
"1") == 0 && (dosage
.getBeginOffset() != beginOffset && dosage
.getEndOffset() != endOffset)))
&& (changeStatus != null && (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.OTHER) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASEFROM) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASEFROM) != 0))){
setFrequencyElement(
frequency.getFrequencyMention(), frequency
.getBeginOffset(), frequency
.getEndOffset());
} else {
double updateFreq = new Double(frequency
.getFrequencyMention()).doubleValue() * 7.0;
setFrequencyElement(String.valueOf(updateFreq), beginOffset,
endOffset);
}
} else {
setFrequencyElement("7.0", beginOffset, endOffset);
}
return FrequencyUnitElement.DAILY;
} else if (da.getPeriod() == FrequencyUnitToken.QUANTITY_EIGHT) {
if (frequency != null
&& (frequency.getBeginOffset() != beginOffset && frequency
.getEndOffset() != endOffset)) {
if ((dosage == null
|| (dosage != null
&& convertFromTextToNum(
dosage.getDosage()).compareTo(
"1") == 0 && (dosage
.getBeginOffset() != beginOffset && dosage
.getEndOffset() != endOffset)))
&& (changeStatus != null && (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.OTHER) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.DECREASEFROM) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASE) != 0)
&& (changeStatus.getDrugChangeStatus().compareTo(DrugChangeStatusToken.INCREASEFROM) != 0))) {
setFrequencyElement(
frequency.getFrequencyMention(), frequency
.getBeginOffset(), frequency
.getEndOffset());
} else {
double updateFreq = new Double(frequency
.getFrequencyMention()).doubleValue() * 8.0;
setFrequencyElement(String.valueOf(updateFreq), beginOffset,
endOffset);
}
} else {
setFrequencyElement("8.0", beginOffset, endOffset);
}
return FrequencyUnitElement.DAILY;
} else if (da.getPeriod() == new Float(
FrequencyUnitToken.QUANTITY_EVERY_OTHER_DAY)
.floatValue()) {
return FrequencyUnitElement.EVERYOTHERDAY;
} else if (da.getPeriod() == new Float(
FrequencyUnitToken.QUANTITY_WEEKLY).floatValue()) {
return FrequencyUnitElement.WEEKLY;
} else if (da.getPeriod() == new Float(
FrequencyUnitToken.QUANTITY_MONTHLY).floatValue()) {
return FrequencyUnitElement.MONTHLY;
} else if (da.getPeriod() == FrequencyUnitToken.QUANTITY_PRN) {
return FrequencyUnitElement.ASNEEDED;
}
return lastTerm;
}
}
return null;
}
private String findDurationElement(JCas jcas, int beginOffset, int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
DurationAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
DurationAnnotation da = (DurationAnnotation) firItr.next();
if (da.getBegin() == beginOffset)
return da.getCoveredText();
}
return null;
}
private String findRouteElement(JCas jcas, int beginOffset, int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
RouteAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
RouteAnnotation ra = (RouteAnnotation) firItr.next();
if (ra.getBegin() == beginOffset) {
if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.GASTRIC)
return RouteElement.GASTRIC;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.ORAL)
return RouteElement.ORAL;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.INTRAARTERIAL)
return RouteElement.INTRAARTERIAL;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.INTRACARDIAC)
return RouteElement.INTRACARDIAC;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.INTRAMUSCULAR)
return RouteElement.INTRAMUSCULAR;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.INTRAPERITONEAL)
return RouteElement.INTRAPERITONEAL;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.INTRATHECAL)
return RouteElement.INTRATHECAL;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.INTRAVENOUS)
return RouteElement.INTRAVENOUS;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.RECTAL)
return RouteElement.RECTAL;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.SUBCUTANEOUS)
return RouteElement.SUBCUTANEOUS;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.TOPICAL)
return RouteElement.TOPICAL;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.TRANSDERMAL)
return RouteElement.TRANSDERMAL;
else if (new Integer(ra.getIntakeMethod()).intValue() == RouteToken.TRANSMUCOSAL)
return RouteElement.TRANSMUCOSAL;
return ra.getCoveredText();
}
}
return null;
}
private String findDrugChangeStatusElement(JCas jcas, int beginOffset,
int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
DrugChangeStatusAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
DrugChangeStatusAnnotation dcsa = (DrugChangeStatusAnnotation) firItr
.next();
if (dcsa.getBegin() == beginOffset) {
int posSpace = dcsa.getCoveredText().indexOf(' ');
int posHyph = dcsa.getCoveredText().indexOf('-');
String firstTerm = dcsa.getCoveredText();
if (posSpace > 0)
firstTerm = dcsa.getCoveredText().substring(0, posSpace);
if (posHyph > 0)
firstTerm = firstTerm.substring(0, posHyph);
return dcsa.getChangeStatus();//convertToChangeStatus(firstTerm);
}
}
return null;
}
private String findStrengthElement(JCas jcas, int beginOffset, int endOffset) {
Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
StrengthAnnotation.type, beginOffset, endOffset + 1);
while (firItr.hasNext()) {
StrengthAnnotation dcsa = (StrengthAnnotation) firItr.next();
String strength = dcsa.getCoveredText();
int findHyph = strength.indexOf('-');
if (findHyph > 0){
// large value in the range
strength = strength.substring(findHyph+1);
}
if (dcsa.getBegin() == beginOffset) {
return parseRegex(strength);
}
}
return null;
}
private String parseRegex(String stringGlob) {
if (stringGlob.matches("[0-9]*[\\.]*[0-9]+\\s[a-zA-Z]+")) {
// do nothing for now
} else if (stringGlob.matches("[0-9]*[\\.]*[0-9]+[-]+[a-zA-Z]+")) {
stringGlob = stringGlob.replaceAll("-", " ");
} else if (stringGlob.matches("[0-9]*[\\.]*[0-9]+[a-zA-Z]+")) {
int intRegex = indexOfRegex(stringGlob, lookForAlpha);
stringGlob = stringGlob.substring(0, intRegex) + " "
+ stringGlob.substring(intRegex);
} else if (stringGlob.matches("[0-9]*[\\.]*[0-9]+[\\%]")) {
int intRegex = indexOfRegex(stringGlob, lookForPercent);
stringGlob = stringGlob.substring(0, intRegex) + " "
+ stringGlob.substring(intRegex);
} else if (stringGlob.matches("[0-9]*[\\.]*[0-9]+[\\s][\\%]")) {
// do nothing for now
} else if (stringGlob.matches("[0-9]*[\\.]*[0-9]+[-]\\%")) {
stringGlob = stringGlob.replaceAll("-", "");
}
return stringGlob.trim().replace('\n', ' ').replaceAll(",", "").replaceAll("-", "");
}
public int parseIntValue(Object strength) {
String text = (String) strength;
String strengthNumText = "";
String subText = "";
boolean containsNums = false;
boolean doneHere = false;
int textSize = text.length();
int pos = 0;
Integer posInt = null;
while (!doneHere && (textSize > pos) && (textSize >= 1)) {
try {
String numString = text.substring(pos, pos + 1);
/*
* if (numString.compareTo(".") == 0) { subText =
* text.substring(pos + 1, textSize); pos++; }
*/
Integer posNum = Integer.decode(numString);
int checkInt = posNum.intValue();
if ((checkInt >= 0) && (checkInt <= 9)) {
containsNums = true;
subText = text.substring(pos + 1, textSize);
pos++;
strengthNumText = strengthNumText + numString;
} else
return 0;
}
catch (NullPointerException npe) {
return 0;
} catch (NumberFormatException nfe) {
if (!containsNums)
return 0;
else
doneHere = true;
}
}
return new Integer(strengthNumText).intValue();
}
public double parseDoubleValue(Object strength) {
String text = (String) strength;
String strengthNumText = "";
String subText = "";
boolean containsNums = false;
boolean doneHere = false;
int textSize = text.length();
int pos = 0;
Integer posInt = null;
while (!doneHere && (textSize > pos) && (textSize >= 1)) {
try {
String numString = text.substring(pos, pos + 1);
if (numString.compareTo(".") == 0) {
subText = text.substring(pos + 1, textSize);
pos++;
strengthNumText = strengthNumText + numString;
}
else {
Integer posNum = Integer.decode(numString);
int checkInt = posNum.intValue();
if ((checkInt >= 0) && (checkInt <= 9)) {
containsNums = true;
subText = text.substring(pos + 1, textSize);
pos++;
strengthNumText = strengthNumText + numString;
} else
return 0;
}
}
catch (NullPointerException npe) {
return 0;
} catch (NumberFormatException nfe) {
if (!containsNums)
return 0;
else
doneHere = true;
}
}
return new Double(strengthNumText).doubleValue();
}
public String convertFromTextToNum(String firstTerm) {
// First see if the text consists of a number range and take the
// greater of the two
int hyph = firstTerm.lastIndexOf('-');
if (hyph > 0){
firstTerm = firstTerm.substring(0, hyph);
int hyphChild = firstTerm.lastIndexOf('-');
if (hyphChild > 0 )
firstTerm = firstTerm.substring(0, hyphChild);
int lastHyph = firstTerm.indexOf('-');
if (lastHyph > 0)
firstTerm = firstTerm.substring(0, lastHyph);
}
int space = firstTerm.indexOf(' ');
if (space > 0)
firstTerm = firstTerm.substring(0, space);
if ((firstTerm.compareToIgnoreCase("first") == 0)
|| (firstTerm.compareToIgnoreCase("one") == 0)
|| (firstTerm.compareToIgnoreCase("daily") == 0)
|| (firstTerm.compareToIgnoreCase(FrequencyUnitElement.DAILY) == 0)
|| (firstTerm.compareToIgnoreCase("once") == 0)) {
return "1";
} else if ((firstTerm.compareToIgnoreCase("twice") == 0)
|| (firstTerm.compareToIgnoreCase("second") == 0)
|| (firstTerm.compareToIgnoreCase("two") == 0)) {
return "2";
} else if ((firstTerm.compareToIgnoreCase("third") == 0)
|| (firstTerm.compareToIgnoreCase("three") == 0)) {
return "3";
} else if ((firstTerm.compareToIgnoreCase("forth") == 0)
|| (firstTerm.compareToIgnoreCase("four") == 0)) {
return "4";
} else if ((firstTerm.compareToIgnoreCase("fifth") == 0)
|| (firstTerm.compareToIgnoreCase("five") == 0)) {
return "5";
} else if (firstTerm.compareToIgnoreCase("six") == 0) {
return "6";
} else if (firstTerm.compareToIgnoreCase("seven") == 0) {
return "7";
} else if (firstTerm.compareToIgnoreCase("eight") == 0) {
return "8";
} else if (firstTerm.compareToIgnoreCase("nine") == 0) {
return "9";
} else if (firstTerm.compareToIgnoreCase("ten") == 0) {
return "10";
} else if ((firstTerm.compareToIgnoreCase("half") == 0)
|| (firstTerm
.compareToIgnoreCase(FrequencyUnitElement.EVERYOTHERDAY) == 0)) {
return ".5";
} else if ((firstTerm.compareToIgnoreCase(FrequencyUnitElement.WEEKLY) == 0)
|| (firstTerm.compareToIgnoreCase("weekly") == 0)){
return ".14";
} else if ((firstTerm.compareToIgnoreCase(FrequencyUnitElement.MONTHLY) == 0)
|| (firstTerm.compareToIgnoreCase("monthly") == 0)){
return ".03";
} else if ((firstTerm.compareToIgnoreCase(FrequencyUnitElement.HOURLY) == 0)
|| (firstTerm.compareToIgnoreCase("hourly") == 0)){
return "24";
}else
return firstTerm;
}
public String convertToChangeStatus(String firstTerm) {
if ((firstTerm.compareToIgnoreCase(DrugChangeStatusElement.STOP_STATUS) == 0)
|| (firstTerm.compareToIgnoreCase("stopped") == 0)
|| (firstTerm.compareToIgnoreCase("past") == 0)
|| (firstTerm.compareToIgnoreCase("stopping") == 0)
|| (firstTerm.compareToIgnoreCase("discontinue") == 0)
|| (firstTerm.compareToIgnoreCase("discontinued") == 0)
|| (firstTerm.compareToIgnoreCase("DISCONTINUED MEDICATIONS") == 0)
|| (firstTerm.compareToIgnoreCase("DISCONTINUE MEDICATIONS") == 0)) {
return DrugChangeStatusElement.STOP_STATUS;
} else if ((firstTerm.compareToIgnoreCase("new") == 0)
|| (firstTerm.compareToIgnoreCase("new dose") == 0)
|| (firstTerm.compareToIgnoreCase("start") == 0)
|| (firstTerm.compareToIgnoreCase("started") == 0)
|| (firstTerm.compareToIgnoreCase("new medication") == 0)
|| (firstTerm.compareToIgnoreCase("NEW MEDICATIONS") == 0)) {
return DrugChangeStatusElement.START_STATUS;
} else if ((firstTerm.compareToIgnoreCase("increase") == 0)
|| (firstTerm.compareToIgnoreCase("increased") == 0)) {
return DrugChangeStatusElement.INCREASE_STATUS;
} else if ((firstTerm.compareToIgnoreCase("decrease") == 0)
|| (firstTerm.compareToIgnoreCase("lower") == 0)
|| (firstTerm.compareToIgnoreCase("decreased") == 0)) {
return DrugChangeStatusElement.DECREASE_STATUS;
} else if ((firstTerm.compareToIgnoreCase("then") == 0)
|| (firstTerm.compareToIgnoreCase("changed") == 0)
|| (firstTerm.compareToIgnoreCase("change") == 0)) {
return "change";
} else if ((firstTerm.compareToIgnoreCase("and") == 0)
|| (firstTerm.compareToIgnoreCase("plus") == 0)) {
return "add";
} else
return DrugChangeStatusElement.NOCHANGE_STATUS;
}
// -------------------------- PUBLIC STATIC METHODS
// --------------------------
public int getDosageBegin() {
return dosage.getBeginOffset();
}
public int getDosageEnd() {
return dosage.getEndOffset();
}
public int getFrequencyBegin() {
return frequency.getBeginOffset();
}
public int getFrequencyEnd() {
return frequency.getEndOffset();
}
public int getFUBegin() {
return frequencyUnit.getBeginOffset();
}
public int getFUENd() {
return frequencyUnit.getEndOffset();
}
public int getFormBegin() {
return form.getBeginOffset();
}
public int getFormEnd() {
return form.getEndOffset();
}
public int getDuratationBegin() {
return duration.getBeginOffset();
}
public int getDuratationEnd() {
return duration.getEndOffset();
}
public int getRouteBegin() {
return route.getBeginOffset();
}
public int getRouteEnd() {
return route.getEndOffset();
}
public int getStrengthUnitBegin() {
return strengthUnit.getBeginOffset();
}
public int getStrengthUnitEnd() {
return strengthUnit.getEndOffset();
}
public int getStrengthBegin() {
return strength.getBeginOffset();
}
public int getStrengthEnd() {
return strength.getEndOffset();
}
// Add drug change status offsets begin
public int getChangeStatusBegin() {
return changeStatus.getBeginOffset();
}
public int getChangeStatusEnd() {
return changeStatus.getEndOffset();
}
// Add drug change status offsets end
/**
* Scan a string for the first occurrence of some regex Pattern.
*
* @param lookForAlpha
* the pattern to look for
* @param lookIn
* the String to scan.
* @return offset relative to start of lookIn where it first found the
* pattern, -1 if not found.
*/
public static int indexOfRegex(String lookIn, Pattern lookFor) {
Matcher m = lookFor.matcher(lookIn);
if (m.find()) {
return m.start();
} else {
return -1;
}
}
private double holdLargestPeriod = -1;
}