package classifiers;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import Main.KeyValue;
import weka.classifiers.misc.InputMappedClassifier;
import weka.core.Attribute;
import weka.core.DenseInstance;
import weka.core.FastVector;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.converters.ArffSaver;
public class SpecPragmaticCreateDataset_posteriori {
Connection conn = null;
Statement stmt = null;
ResultSet rs = null;
String connectionUrl;
String connectionUser;
String connectionPassword;
public static void main(String[] args) {
SpecPragmaticCreateDataset_posteriori sp = new SpecPragmaticCreateDataset_posteriori();
sp.ProcessTables("NotInteresting");
}
public Instances CreateInstances(){
Attribute PMCAttribute = new Attribute("PMC");
Attribute TableIDAttribute = new Attribute("TableID");
Attribute NoRowsAttribute = new Attribute("NoRows");
Attribute NoColumnsAttribute = new Attribute("NoColumn");
Attribute TotalCellsAttribute = new Attribute("TotalCellNo");
Attribute EmptyCellsAttribute = new Attribute("CellEmpty");
Attribute CellNumericAttribute = new Attribute("CellNumeric");
Attribute CellSemiNumericAttribute = new Attribute(
"CellSemiNumeric");
Attribute CellTextAttribute = new Attribute("CellText");
Attribute ContainsAdverseAttribute = new Attribute(
"ContainsAdverse");
Attribute containsAgeAttribute = new Attribute("containsAge");
Attribute containsBaselineAttribute = new Attribute(
"containsBaseline");
Attribute containsCharacteristicCapAttribute = new Attribute(
"containsCharacteristicCap");
Attribute containsDemographicAttribute = new Attribute(
"containsDemographic");
Attribute ContainsExclusionAttribute = new Attribute(
"ContainsExclusion");
Attribute ContainsInclusionAttribute = new Attribute(
"ContainsInclusion");
Attribute containsNAttribute = new Attribute("containsN");
Attribute containsPatientsCapAttribute = new Attribute(
"containsPatientsCap");
Attribute containsPatientsCellAttribute = new Attribute(
"containsPatientsCell");
Attribute ContainsSideEffectAttribute = new Attribute(
"ContainsSideEffect");
Attribute ContainsSignOrSymptomAnnotationAttribute = new Attribute(
"ContainsSignOrSymptomAnnotation");
Attribute containsEglibilityAttribute = new Attribute(
"containsEglibility");
Attribute containsToxicityAttribute = new Attribute(
"containsToxicity");
Attribute containsInclusionExclusionCellAttribute = new Attribute(
"containsInclusionExclusionCell");
Attribute containsHaematologicAttribute = new Attribute(
"containsHaematologic");
Attribute containsTrialCapAttribute = new Attribute(
"containsTrialCap");
Attribute containsCriteriaAttribute = new Attribute(
"containsCriteria");
// Attribute attCaption = new Attribute("Caption");
// Attribute attWholeHeader = new Attribute("WholeHeader");
// Attribute attWholeStub = new Attribute("WholeStub");
// Attribute attWholeSuperRow = new Attribute("SuperRow");
// Attribute attWholeData= new Attribute("Data");
Attribute caption_topic1= new Attribute("Caption_topic1");
Attribute caption_topic2= new Attribute("Caption_topic2");
Attribute caption_topic3= new Attribute("Caption_topic3");
Attribute caption_topic4= new Attribute("Caption_topic4");
Attribute caption_topic5= new Attribute("Caption_topic5");
Attribute caption_topic6= new Attribute("Caption_topic6");
Attribute caption_topic7= new Attribute("Caption_topic7");
Attribute caption_topic8= new Attribute("Caption_topic8");
Attribute caption_topic9= new Attribute("Caption_topic9");
Attribute caption_topic10= new Attribute("Caption_topic10");
Attribute caption_topic11= new Attribute("Caption_topic11");
Attribute caption_topic12= new Attribute("Caption_topic12");
Attribute caption_topic13= new Attribute("Caption_topic13");
Attribute caption_topic14= new Attribute("Caption_topic14");
Attribute caption_topic15= new Attribute("Caption_topic15");
Attribute caption_topic16= new Attribute("Caption_topic16");
Attribute caption_topic17= new Attribute("Caption_topic17");
Attribute caption_topic18= new Attribute("Caption_topic18");
Attribute caption_topic19= new Attribute("Caption_topic19");
Attribute caption_topic20= new Attribute("Caption_topic20");
Attribute caption_topic21= new Attribute("Caption_topic21");
Attribute caption_topic22= new Attribute("Caption_topic22");
Attribute caption_topic23= new Attribute("Caption_topic23");
Attribute caption_topic24= new Attribute("Caption_topic24");
Attribute caption_topic25= new Attribute("Caption_topic25");
Attribute caption_topic26= new Attribute("Caption_topic26");
Attribute caption_topic27= new Attribute("Caption_topic27");
Attribute caption_topic28= new Attribute("Caption_topic28");
Attribute caption_topic29= new Attribute("Caption_topic29");
Attribute caption_topic30= new Attribute("Caption_topic30");
Attribute caption_topic31= new Attribute("Caption_topic31");
Attribute caption_topic32= new Attribute("Caption_topic32");
Attribute caption_topic33= new Attribute("Caption_topic33");
Attribute caption_topic34= new Attribute("Caption_topic34");
Attribute caption_topic35= new Attribute("Caption_topic35");
Attribute caption_topic36= new Attribute("Caption_topic36");
Attribute caption_topic37= new Attribute("Caption_topic37");
Attribute caption_topic38= new Attribute("Caption_topic38");
Attribute caption_topic39= new Attribute("Caption_topic39");
Attribute caption_topic40= new Attribute("Caption_topic40");
Attribute caption_topic41= new Attribute("Caption_topic41");
Attribute caption_topic42= new Attribute("Caption_topic42");
Attribute caption_topic43= new Attribute("Caption_topic43");
Attribute caption_topic44= new Attribute("Caption_topic44");
Attribute caption_topic45= new Attribute("Caption_topic45");
Attribute caption_topic46= new Attribute("Caption_topic46");
Attribute caption_topic47= new Attribute("Caption_topic47");
Attribute caption_topic48= new Attribute("Caption_topic48");
Attribute caption_topic49= new Attribute("Caption_topic49");
Attribute caption_topic50= new Attribute("Caption_topic50");
Attribute sentence_topic1= new Attribute("sentence_topic1");
Attribute sentence_topic2= new Attribute("sentence_topic2");
Attribute sentence_topic3= new Attribute("sentence_topic3");
Attribute sentence_topic4= new Attribute("sentence_topic4");
Attribute sentence_topic5= new Attribute("sentence_topic5");
Attribute sentence_topic6= new Attribute("sentence_topic6");
Attribute sentence_topic7= new Attribute("sentence_topic7");
Attribute sentence_topic8= new Attribute("sentence_topic8");
Attribute sentence_topic9= new Attribute("sentence_topic9");
Attribute sentence_topic10= new Attribute("sentence_topic10");
Attribute sentence_topic11= new Attribute("sentence_topic11");
Attribute sentence_topic12= new Attribute("sentence_topic12");
Attribute sentence_topic13= new Attribute("sentence_topic13");
Attribute sentence_topic14= new Attribute("sentence_topic14");
Attribute sentence_topic15= new Attribute("sentence_topic15");
Attribute sentence_topic16= new Attribute("sentence_topic16");
Attribute sentence_topic17= new Attribute("sentence_topic17");
Attribute sentence_topic18= new Attribute("sentence_topic18");
Attribute sentence_topic19= new Attribute("sentence_topic19");
Attribute sentence_topic20= new Attribute("sentence_topic20");
Attribute sentence_topic21= new Attribute("sentence_topic21");
Attribute sentence_topic22= new Attribute("sentence_topic22");
Attribute sentence_topic23= new Attribute("sentence_topic23");
Attribute sentence_topic24= new Attribute("sentence_topic24");
Attribute sentence_topic25= new Attribute("sentence_topic25");
Attribute sentence_topic26= new Attribute("sentence_topic26");
Attribute sentence_topic27= new Attribute("sentence_topic27");
Attribute sentence_topic28= new Attribute("sentence_topic28");
Attribute sentence_topic29= new Attribute("sentence_topic29");
Attribute sentence_topic30= new Attribute("sentence_topic30");
Attribute sentence_topic31= new Attribute("sentence_topic31");
Attribute sentence_topic32= new Attribute("sentence_topic32");
Attribute sentence_topic33= new Attribute("sentence_topic33");
Attribute sentence_topic34= new Attribute("sentence_topic34");
Attribute sentence_topic35= new Attribute("sentence_topic35");
Attribute sentence_topic36= new Attribute("sentence_topic36");
Attribute sentence_topic37= new Attribute("sentence_topic37");
Attribute sentence_topic38= new Attribute("sentence_topic38");
Attribute sentence_topic39= new Attribute("sentence_topic39");
Attribute sentence_topic40= new Attribute("sentence_topic40");
Attribute sentence_topic41= new Attribute("sentence_topic41");
Attribute sentence_topic42= new Attribute("sentence_topic42");
Attribute sentence_topic43= new Attribute("sentence_topic43");
Attribute sentence_topic44= new Attribute("sentence_topic44");
Attribute sentence_topic45= new Attribute("sentence_topic45");
Attribute sentence_topic46= new Attribute("sentence_topic46");
Attribute sentence_topic47= new Attribute("sentence_topic47");
Attribute sentence_topic48= new Attribute("sentence_topic48");
Attribute sentence_topic49= new Attribute("sentence_topic49");
Attribute sentence_topic50= new Attribute("sentence_topic50");
FastVector fvClassVal = new FastVector(4);
// AdverseEvent,InclusionExclusion,DontCare,BaselineCharacteristic
fvClassVal.addElement("AdverseEvent");
fvClassVal.addElement("InclusionExclusion");
fvClassVal.addElement("Other");
fvClassVal.addElement("BaselineCharacteristic");
Attribute ClassAttribute = new Attribute("clas", fvClassVal);
// Declare the feature vector
FastVector fvWekaAttributes = new FastVector(128);
fvWekaAttributes.addElement(PMCAttribute);
fvWekaAttributes.addElement(TableIDAttribute);
fvWekaAttributes.addElement(NoRowsAttribute);
fvWekaAttributes.addElement(NoColumnsAttribute);
fvWekaAttributes.addElement(TotalCellsAttribute);
fvWekaAttributes.addElement(EmptyCellsAttribute);
fvWekaAttributes.addElement(CellNumericAttribute);
fvWekaAttributes.addElement(CellSemiNumericAttribute);
fvWekaAttributes.addElement(CellTextAttribute);
fvWekaAttributes.addElement(ContainsAdverseAttribute);
fvWekaAttributes.addElement(containsAgeAttribute);
fvWekaAttributes.addElement(containsBaselineAttribute);
fvWekaAttributes.addElement(containsCharacteristicCapAttribute);
fvWekaAttributes.addElement(containsDemographicAttribute);
fvWekaAttributes.addElement(ContainsExclusionAttribute);
fvWekaAttributes.addElement(ContainsInclusionAttribute);
fvWekaAttributes.addElement(containsNAttribute);
fvWekaAttributes.addElement(containsPatientsCapAttribute);
fvWekaAttributes.addElement(containsPatientsCellAttribute);
fvWekaAttributes.addElement(ContainsSideEffectAttribute);
fvWekaAttributes
.addElement(ContainsSignOrSymptomAnnotationAttribute);
fvWekaAttributes.addElement(containsEglibilityAttribute);
fvWekaAttributes.addElement(containsToxicityAttribute);
fvWekaAttributes
.addElement(containsInclusionExclusionCellAttribute);
fvWekaAttributes.addElement(containsHaematologicAttribute);
fvWekaAttributes.addElement(containsTrialCapAttribute);
fvWekaAttributes.addElement(containsCriteriaAttribute);
// fvWekaAttributes.addElement(new Attribute("WholeHeader", (FastVector) null));
// fvWekaAttributes.addElement(new Attribute("WholeStub", (FastVector) null));
// fvWekaAttributes.addElement(new Attribute("WholeSuperRow", (FastVector) null));
// fvWekaAttributes.addElement(new Attribute("WholeData", (FastVector) null));
// fvWekaAttributes.addElement(new Attribute("Caption", (FastVector) null));
fvWekaAttributes.addElement(caption_topic1);
fvWekaAttributes.addElement(caption_topic2);
fvWekaAttributes.addElement(caption_topic3);
fvWekaAttributes.addElement(caption_topic4);
fvWekaAttributes.addElement(caption_topic5);
fvWekaAttributes.addElement(caption_topic6);
fvWekaAttributes.addElement(caption_topic7);
fvWekaAttributes.addElement(caption_topic8);
fvWekaAttributes.addElement(caption_topic9);
fvWekaAttributes.addElement(caption_topic10);
fvWekaAttributes.addElement(caption_topic11);
fvWekaAttributes.addElement(caption_topic12);
fvWekaAttributes.addElement(caption_topic13);
fvWekaAttributes.addElement(caption_topic14);
fvWekaAttributes.addElement(caption_topic15);
fvWekaAttributes.addElement(caption_topic16);
fvWekaAttributes.addElement(caption_topic17);
fvWekaAttributes.addElement(caption_topic18);
fvWekaAttributes.addElement(caption_topic19);
fvWekaAttributes.addElement(caption_topic20);
fvWekaAttributes.addElement(caption_topic21);
fvWekaAttributes.addElement(caption_topic22);
fvWekaAttributes.addElement(caption_topic23);
fvWekaAttributes.addElement(caption_topic24);
fvWekaAttributes.addElement(caption_topic25);
fvWekaAttributes.addElement(caption_topic26);
fvWekaAttributes.addElement(caption_topic27);
fvWekaAttributes.addElement(caption_topic28);
fvWekaAttributes.addElement(caption_topic29);
fvWekaAttributes.addElement(caption_topic30);
fvWekaAttributes.addElement(caption_topic31);
fvWekaAttributes.addElement(caption_topic32);
fvWekaAttributes.addElement(caption_topic33);
fvWekaAttributes.addElement(caption_topic34);
fvWekaAttributes.addElement(caption_topic35);
fvWekaAttributes.addElement(caption_topic36);
fvWekaAttributes.addElement(caption_topic37);
fvWekaAttributes.addElement(caption_topic38);
fvWekaAttributes.addElement(caption_topic39);
fvWekaAttributes.addElement(caption_topic40);
fvWekaAttributes.addElement(caption_topic41);
fvWekaAttributes.addElement(caption_topic42);
fvWekaAttributes.addElement(caption_topic43);
fvWekaAttributes.addElement(caption_topic44);
fvWekaAttributes.addElement(caption_topic45);
fvWekaAttributes.addElement(caption_topic46);
fvWekaAttributes.addElement(caption_topic47);
fvWekaAttributes.addElement(caption_topic48);
fvWekaAttributes.addElement(caption_topic49);
fvWekaAttributes.addElement(caption_topic50);
fvWekaAttributes.addElement(sentence_topic1);
fvWekaAttributes.addElement(sentence_topic2);
fvWekaAttributes.addElement(sentence_topic3);
fvWekaAttributes.addElement(sentence_topic4);
fvWekaAttributes.addElement(sentence_topic5);
fvWekaAttributes.addElement(sentence_topic6);
fvWekaAttributes.addElement(sentence_topic7);
fvWekaAttributes.addElement(sentence_topic8);
fvWekaAttributes.addElement(sentence_topic9);
fvWekaAttributes.addElement(sentence_topic10);
fvWekaAttributes.addElement(sentence_topic11);
fvWekaAttributes.addElement(sentence_topic12);
fvWekaAttributes.addElement(sentence_topic13);
fvWekaAttributes.addElement(sentence_topic14);
fvWekaAttributes.addElement(sentence_topic15);
fvWekaAttributes.addElement(sentence_topic16);
fvWekaAttributes.addElement(sentence_topic17);
fvWekaAttributes.addElement(sentence_topic18);
fvWekaAttributes.addElement(sentence_topic19);
fvWekaAttributes.addElement(sentence_topic20);
fvWekaAttributes.addElement(sentence_topic21);
fvWekaAttributes.addElement(sentence_topic22);
fvWekaAttributes.addElement(sentence_topic23);
fvWekaAttributes.addElement(sentence_topic24);
fvWekaAttributes.addElement(sentence_topic25);
fvWekaAttributes.addElement(sentence_topic26);
fvWekaAttributes.addElement(sentence_topic27);
fvWekaAttributes.addElement(sentence_topic28);
fvWekaAttributes.addElement(sentence_topic29);
fvWekaAttributes.addElement(sentence_topic30);
fvWekaAttributes.addElement(sentence_topic31);
fvWekaAttributes.addElement(sentence_topic32);
fvWekaAttributes.addElement(sentence_topic33);
fvWekaAttributes.addElement(sentence_topic34);
fvWekaAttributes.addElement(sentence_topic35);
fvWekaAttributes.addElement(sentence_topic36);
fvWekaAttributes.addElement(sentence_topic37);
fvWekaAttributes.addElement(sentence_topic38);
fvWekaAttributes.addElement(sentence_topic39);
fvWekaAttributes.addElement(sentence_topic40);
fvWekaAttributes.addElement(sentence_topic41);
fvWekaAttributes.addElement(sentence_topic42);
fvWekaAttributes.addElement(sentence_topic43);
fvWekaAttributes.addElement(sentence_topic44);
fvWekaAttributes.addElement(sentence_topic45);
fvWekaAttributes.addElement(sentence_topic46);
fvWekaAttributes.addElement(sentence_topic47);
fvWekaAttributes.addElement(sentence_topic48);
fvWekaAttributes.addElement(sentence_topic49);
fvWekaAttributes.addElement(sentence_topic50);
fvWekaAttributes.addElement(ClassAttribute);
Instances Instances = new Instances("Rel", fvWekaAttributes, 0);
Instances.setClassIndex(127);
return Instances;
}
public void ProcessTables(String tableType)
{
DataBase();
int execCount = 0;
try {
String SQL = "SELECT * from ArtTable where HasXML='yes' and specPragmatic='"+tableType+"' order by RAND() limit 200";
Statement st = conn.createStatement();
Instances instances = CreateInstances();
FastVector fvWekaAttributes = new FastVector(128);
rs = st.executeQuery(SQL);
while (rs.next()) {
Instance iExample = processTable(rs.getInt(1));
instances.add(iExample);
execCount ++;
if(execCount>10000){
conn.close();
DataBase();
execCount = 0;
}
}
System.out.println(instances.toString());
ArffSaver saver = new ArffSaver();
saver.setInstances(instances);
saver.setFile(new File("spptest.arff"));
//saver.setDestination(new File("./data/test.arff")); // **not** necessary in 3.5.4 and later
saver.writeBatch();
} catch (Exception ex) {
ex.printStackTrace();
}
}
public void DataBase() {
try {
BufferedReader br = new BufferedReader(new FileReader(
"settings.cfg"));
// StringBuilder sb = new StringBuilder();
String line = br.readLine();
String host = "";
String database_name = "";
String database_username = "";
String database_password = "";
String database_port = "";
while (line != null) {
KeyValue kv = new KeyValue();
String[] parts = line.split(";");
kv.key = parts[0];
kv.value = parts[1];
if (kv.key.equals("database_host")) {
host = kv.value;
}
if (kv.key.equals("database_name")) {
database_name = kv.value;
}
if (kv.key.equals("database_username")) {
database_username = kv.value;
}
if (kv.key.equals("database_password")) {
database_password = kv.value;
}
if (kv.key.equals("database_port")) {
database_port = kv.value;
}
line = br.readLine();
}
database_password = database_password.replace("\"", "");
Class.forName("com.mysql.jdbc.Driver").newInstance();
connectionUrl = "jdbc:mysql://" + host + ":" + database_port
+ "/" + database_name;
connectionUser = database_username;
connectionPassword = database_password;
conn = DriverManager.getConnection(connectionUrl, connectionUser,
connectionPassword);
} catch (SQLException ex) {
ex.printStackTrace();
System.out.println("SQLException: " + ex.getMessage());
System.out.println("SQLState: " + ex.getSQLState());
System.out.println("VendorError: " + ex.getErrorCode());
} catch (Exception ex) {
ex.printStackTrace();
}
}
public Instance processTable(int tableid) {
String classification = "NotInteresting";
Instance iExample = null;
try {
int containsDemographic = 0;
int containsPatientsCap = 0;
int containsPatientsCell = 0;
int containsBaseline = 0;
int containsAge = 0;
int containsN = 0;
int containsTrialCap = 0;
int containsCharacteristicCap = 0;
int NoColumn = 0;
int NoRows = 0;
int ContainsInclusion = 0;
int ContainsExclusion = 0;
int containsEglibility = 0;
int containsInclusionExclusionCell = 0;
int containsToxicity = 0;
int containsHaematologic = 0;
float CellNumeric = 0;
float CellText = 0;
float CellEmpty = 0;
float CellSemiNumeric = 0;
int TotalCellNo = 0;
int ContainsAdverse = 0;
int ContainsSideEffect = 0;
int ContainsSignOrSymptomAnnotation = 0;
int containsCriteria = 0;
String Caption = "";
String WholeHeader = "";
String WholeStub = "";
String WholeSuperRow="";
String WholeData = "";
int PMC = 0;
int[] caption_topics = new int[50];
int[] ref_sentence_topic = new int[50];
String SQL = "select * from ArtTable inner join article on article.idArticle=ArtTable.Article_idArticle where idTable=" + tableid;
Statement st = conn.createStatement();
ResultSet rs = st.executeQuery(SQL);
// iterate through the java resultset
while (rs.next()) {
Caption = rs.getString(3);
PMC = rs.getInt(12);
}
SQL = "select * from Cell where Table_idTable=" + tableid;
Statement st2 = conn.createStatement();
ResultSet rs2 = st2.executeQuery(SQL);
// iterate through the java resultset
while (rs2.next()) {
int cell_id = rs2.getInt(1);
String SQL2 = "select * from cellroles inner join cell on cell.idCell=cellroles.Cell_idCell where Cell_idCell=" + cell_id;
Statement st3 = conn.createStatement();
ResultSet rs3 = st3.executeQuery(SQL2);
while (rs3.next()) {
int CellRole = rs3.getInt(2);
if(CellRole==1)
{
WholeHeader+="; "+rs3.getString(13).toLowerCase();
}
if(CellRole==2)
{
WholeStub+="; "+rs3.getString(13).toLowerCase();
}
if(CellRole==3)
{
WholeData+="; "+rs3.getString(13).toLowerCase();
}
if(CellRole==4)
{
WholeSuperRow+="; "+rs3.getString(13).toLowerCase();
}
}
String SQL4 = "select * from topics_captions where Table_id=" + tableid;
Statement st4 = conn.createStatement();
ResultSet rs4 = st4.executeQuery(SQL4);
while (rs4.next()) {
String num = rs4.getString(3);
caption_topics[Integer.parseInt(num)]=1;
}
String SQL5 = "SELECT * FROM table_db.tablesentences inner join sentence_topic on idTableSentences = SentenceID where Table_idTable=" + tableid;
Statement st5 = conn.createStatement();
ResultSet rs5 = st5.executeQuery(SQL5);
while (rs5.next()) {
ref_sentence_topic[rs5.getInt(8)]=1;
}
String CellType = rs2.getString(3);
if (CellType.equalsIgnoreCase("Empty")) {
CellEmpty++;
}
if (CellType.equalsIgnoreCase("Partially Numeric")) {
CellSemiNumeric++;
}
if (CellType.equalsIgnoreCase("Numeric")) {
CellNumeric++;
}
if (CellType.equalsIgnoreCase("Text")) {
CellText++;
}
TotalCellNo++;
if (NoRows < rs2.getInt(5))
NoRows = rs2.getInt(5);
if (NoColumn < rs2.getInt(6))
NoColumn = rs2.getInt(6);
if (rs2.getString(10).toLowerCase().contains("patient"))
containsPatientsCell = 1;
if (rs2.getString(10).toLowerCase().contains("age"))
containsAge = 1;
if (rs2.getString(10).toLowerCase().contains("n=")
|| rs2.getString(10).toLowerCase().contains("n ="))
containsN = 1;
if (rs2.getString(10).toLowerCase().contains("inclusion")
|| rs2.getString(10).toLowerCase()
.contains("exclusion"))
containsInclusionExclusionCell = 1;
}
NoRows++;
NoColumn++;
if(tableid == 260)
{
System.out.println("I am here!");
}
if (Caption.toLowerCase().contains("patient"))
containsPatientsCap = 1;
if (Caption.toLowerCase().contains("characteristic"))
containsCharacteristicCap = 1;
if (Caption.toLowerCase().contains("demograph"))
containsDemographic = 1;
if (Caption.toLowerCase().contains("baseline"))
containsBaseline = 1;
if (Caption.toLowerCase().contains("trial"))
containsBaseline = 1;
if (Caption.toLowerCase().contains("inclusion"))
ContainsInclusion = 1;
if (Caption.toLowerCase().contains("exclusion"))
ContainsExclusion = 1;
if (Caption.toLowerCase().contains("adverse"))
ContainsAdverse = 1;
if (Caption.toLowerCase().contains("side effect"))
ContainsAdverse = 1;
if (Caption.toLowerCase().contains("eligibi"))
containsEglibility = 1;
if (Caption.toLowerCase().contains("toxicity"))
containsToxicity = 1;
if (Caption.toLowerCase().contains("haematologic"))
containsToxicity = 1;
if (Caption.toLowerCase().contains("criteria"))
containsCriteria = 1;
SQL = "select * from Annotation inner join Cell on Cell.idCell=Annotation.Cell_idCell where Annotation.AgentName='MetaMap' and AnnotationDescription LIKE '%Symptom%' and Table_idTable="
+ tableid;
Statement st3 = conn.createStatement();
ResultSet rs3 = st3.executeQuery(SQL);
rs3.last();
int size = rs3.getRow();
rs3.beforeFirst();
if (size > 0) {
ContainsSignOrSymptomAnnotation = 1;
}
CellEmpty = ((float) (CellEmpty)) / ((float) (TotalCellNo)) * 100;
CellText = ((float) (CellText)) / ((float) (TotalCellNo)) * 100;
CellNumeric = ((float) (CellNumeric)) / ((float) (TotalCellNo))
* 100;
CellSemiNumeric = ((float) (CellSemiNumeric))
/ ((float) (TotalCellNo)) * 100;
String prediction = "";
Instances ins = null;
Attribute PMCAttribute = new Attribute("PMC");
Attribute TableIDAttribute = new Attribute("TableID");
Attribute NoRowsAttribute = new Attribute("NoRows");
Attribute NoColumnsAttribute = new Attribute("NoColumn");
Attribute TotalCellsAttribute = new Attribute("TotalCellNo");
Attribute EmptyCellsAttribute = new Attribute("CellEmpty");
Attribute CellNumericAttribute = new Attribute("CellNumeric");
Attribute CellSemiNumericAttribute = new Attribute(
"CellSemiNumeric");
Attribute CellTextAttribute = new Attribute("CellText");
Attribute ContainsAdverseAttribute = new Attribute(
"ContainsAdverse");
Attribute containsAgeAttribute = new Attribute("containsAge");
Attribute containsBaselineAttribute = new Attribute(
"containsBaseline");
Attribute containsCharacteristicCapAttribute = new Attribute(
"containsCharacteristicCap");
Attribute containsDemographicAttribute = new Attribute(
"containsDemographic");
Attribute ContainsExclusionAttribute = new Attribute(
"ContainsExclusion");
Attribute ContainsInclusionAttribute = new Attribute(
"ContainsInclusion");
Attribute containsNAttribute = new Attribute("containsN");
Attribute containsPatientsCapAttribute = new Attribute(
"containsPatientsCap");
Attribute containsPatientsCellAttribute = new Attribute(
"containsPatientsCell");
Attribute ContainsSideEffectAttribute = new Attribute(
"ContainsSideEffect");
Attribute ContainsSignOrSymptomAnnotationAttribute = new Attribute(
"ContainsSignOrSymptomAnnotation");
Attribute containsEglibilityAttribute = new Attribute(
"containsEglibility");
Attribute containsToxicityAttribute = new Attribute(
"containsToxicity");
Attribute containsInclusionExclusionCellAttribute = new Attribute(
"containsInclusionExclusionCell");
Attribute containsHaematologicAttribute = new Attribute(
"containsHaematologic");
Attribute containsTrialCapAttribute = new Attribute(
"containsTrialCap");
Attribute containsCriteriaAttribute = new Attribute(
"containsCriteria");
// Attribute attCaption = new Attribute("Caption");
// Attribute attWholeHeader = new Attribute("WholeHeader");
// Attribute attWholeStub = new Attribute("WholeStub");
// Attribute attWholeSuperRow = new Attribute("SuperRow");
// Attribute attWholeData= new Attribute("Data");
Attribute caption_topic1= new Attribute("Caption_topic1");
Attribute caption_topic2= new Attribute("Caption_topic2");
Attribute caption_topic3= new Attribute("Caption_topic3");
Attribute caption_topic4= new Attribute("Caption_topic4");
Attribute caption_topic5= new Attribute("Caption_topic5");
Attribute caption_topic6= new Attribute("Caption_topic6");
Attribute caption_topic7= new Attribute("Caption_topic7");
Attribute caption_topic8= new Attribute("Caption_topic8");
Attribute caption_topic9= new Attribute("Caption_topic9");
Attribute caption_topic10= new Attribute("Caption_topic10");
Attribute caption_topic11= new Attribute("Caption_topic11");
Attribute caption_topic12= new Attribute("Caption_topic12");
Attribute caption_topic13= new Attribute("Caption_topic13");
Attribute caption_topic14= new Attribute("Caption_topic14");
Attribute caption_topic15= new Attribute("Caption_topic15");
Attribute caption_topic16= new Attribute("Caption_topic16");
Attribute caption_topic17= new Attribute("Caption_topic17");
Attribute caption_topic18= new Attribute("Caption_topic18");
Attribute caption_topic19= new Attribute("Caption_topic19");
Attribute caption_topic20= new Attribute("Caption_topic20");
Attribute caption_topic21= new Attribute("Caption_topic21");
Attribute caption_topic22= new Attribute("Caption_topic22");
Attribute caption_topic23= new Attribute("Caption_topic23");
Attribute caption_topic24= new Attribute("Caption_topic24");
Attribute caption_topic25= new Attribute("Caption_topic25");
Attribute caption_topic26= new Attribute("Caption_topic26");
Attribute caption_topic27= new Attribute("Caption_topic27");
Attribute caption_topic28= new Attribute("Caption_topic28");
Attribute caption_topic29= new Attribute("Caption_topic29");
Attribute caption_topic30= new Attribute("Caption_topic30");
Attribute caption_topic31= new Attribute("Caption_topic31");
Attribute caption_topic32= new Attribute("Caption_topic32");
Attribute caption_topic33= new Attribute("Caption_topic33");
Attribute caption_topic34= new Attribute("Caption_topic34");
Attribute caption_topic35= new Attribute("Caption_topic35");
Attribute caption_topic36= new Attribute("Caption_topic36");
Attribute caption_topic37= new Attribute("Caption_topic37");
Attribute caption_topic38= new Attribute("Caption_topic38");
Attribute caption_topic39= new Attribute("Caption_topic39");
Attribute caption_topic40= new Attribute("Caption_topic40");
Attribute caption_topic41= new Attribute("Caption_topic41");
Attribute caption_topic42= new Attribute("Caption_topic42");
Attribute caption_topic43= new Attribute("Caption_topic43");
Attribute caption_topic44= new Attribute("Caption_topic44");
Attribute caption_topic45= new Attribute("Caption_topic45");
Attribute caption_topic46= new Attribute("Caption_topic46");
Attribute caption_topic47= new Attribute("Caption_topic47");
Attribute caption_topic48= new Attribute("Caption_topic48");
Attribute caption_topic49= new Attribute("Caption_topic49");
Attribute caption_topic50= new Attribute("Caption_topic50");
Attribute sentence_topic1= new Attribute("sentence_topic1");
Attribute sentence_topic2= new Attribute("sentence_topic2");
Attribute sentence_topic3= new Attribute("sentence_topic3");
Attribute sentence_topic4= new Attribute("sentence_topic4");
Attribute sentence_topic5= new Attribute("sentence_topic5");
Attribute sentence_topic6= new Attribute("sentence_topic6");
Attribute sentence_topic7= new Attribute("sentence_topic7");
Attribute sentence_topic8= new Attribute("sentence_topic8");
Attribute sentence_topic9= new Attribute("sentence_topic9");
Attribute sentence_topic10= new Attribute("sentence_topic10");
Attribute sentence_topic11= new Attribute("sentence_topic11");
Attribute sentence_topic12= new Attribute("sentence_topic12");
Attribute sentence_topic13= new Attribute("sentence_topic13");
Attribute sentence_topic14= new Attribute("sentence_topic14");
Attribute sentence_topic15= new Attribute("sentence_topic15");
Attribute sentence_topic16= new Attribute("sentence_topic16");
Attribute sentence_topic17= new Attribute("sentence_topic17");
Attribute sentence_topic18= new Attribute("sentence_topic18");
Attribute sentence_topic19= new Attribute("sentence_topic19");
Attribute sentence_topic20= new Attribute("sentence_topic20");
Attribute sentence_topic21= new Attribute("sentence_topic21");
Attribute sentence_topic22= new Attribute("sentence_topic22");
Attribute sentence_topic23= new Attribute("sentence_topic23");
Attribute sentence_topic24= new Attribute("sentence_topic24");
Attribute sentence_topic25= new Attribute("sentence_topic25");
Attribute sentence_topic26= new Attribute("sentence_topic26");
Attribute sentence_topic27= new Attribute("sentence_topic27");
Attribute sentence_topic28= new Attribute("sentence_topic28");
Attribute sentence_topic29= new Attribute("sentence_topic29");
Attribute sentence_topic30= new Attribute("sentence_topic30");
Attribute sentence_topic31= new Attribute("sentence_topic31");
Attribute sentence_topic32= new Attribute("sentence_topic32");
Attribute sentence_topic33= new Attribute("sentence_topic33");
Attribute sentence_topic34= new Attribute("sentence_topic34");
Attribute sentence_topic35= new Attribute("sentence_topic35");
Attribute sentence_topic36= new Attribute("sentence_topic36");
Attribute sentence_topic37= new Attribute("sentence_topic37");
Attribute sentence_topic38= new Attribute("sentence_topic38");
Attribute sentence_topic39= new Attribute("sentence_topic39");
Attribute sentence_topic40= new Attribute("sentence_topic40");
Attribute sentence_topic41= new Attribute("sentence_topic41");
Attribute sentence_topic42= new Attribute("sentence_topic42");
Attribute sentence_topic43= new Attribute("sentence_topic43");
Attribute sentence_topic44= new Attribute("sentence_topic44");
Attribute sentence_topic45= new Attribute("sentence_topic45");
Attribute sentence_topic46= new Attribute("sentence_topic46");
Attribute sentence_topic47= new Attribute("sentence_topic47");
Attribute sentence_topic48= new Attribute("sentence_topic48");
Attribute sentence_topic49= new Attribute("sentence_topic49");
Attribute sentence_topic50= new Attribute("sentence_topic50");
FastVector fvClassVal = new FastVector(4);
// AdverseEvent,InclusionExclusion,DontCare,BaselineCharacteristic
fvClassVal.addElement("AdverseEvent");
fvClassVal.addElement("InclusionExclusion");
fvClassVal.addElement("Other");
fvClassVal.addElement("BaselineCharacteristic");
Attribute ClassAttribute = new Attribute("clas", fvClassVal);
// Declare the feature vector
FastVector fvWekaAttributes = new FastVector(128);
fvWekaAttributes.addElement(PMCAttribute);
fvWekaAttributes.addElement(TableIDAttribute);
fvWekaAttributes.addElement(NoRowsAttribute);
fvWekaAttributes.addElement(NoColumnsAttribute);
fvWekaAttributes.addElement(TotalCellsAttribute);
fvWekaAttributes.addElement(EmptyCellsAttribute);
fvWekaAttributes.addElement(CellNumericAttribute);
fvWekaAttributes.addElement(CellSemiNumericAttribute);
fvWekaAttributes.addElement(CellTextAttribute);
fvWekaAttributes.addElement(ContainsAdverseAttribute);
fvWekaAttributes.addElement(containsAgeAttribute);
fvWekaAttributes.addElement(containsBaselineAttribute);
fvWekaAttributes.addElement(containsCharacteristicCapAttribute);
fvWekaAttributes.addElement(containsDemographicAttribute);
fvWekaAttributes.addElement(ContainsExclusionAttribute);
fvWekaAttributes.addElement(ContainsInclusionAttribute);
fvWekaAttributes.addElement(containsNAttribute);
fvWekaAttributes.addElement(containsPatientsCapAttribute);
fvWekaAttributes.addElement(containsPatientsCellAttribute);
fvWekaAttributes.addElement(ContainsSideEffectAttribute);
fvWekaAttributes
.addElement(ContainsSignOrSymptomAnnotationAttribute);
fvWekaAttributes.addElement(containsEglibilityAttribute);
fvWekaAttributes.addElement(containsToxicityAttribute);
fvWekaAttributes
.addElement(containsInclusionExclusionCellAttribute);
fvWekaAttributes.addElement(containsHaematologicAttribute);
fvWekaAttributes.addElement(containsTrialCapAttribute);
fvWekaAttributes.addElement(containsCriteriaAttribute);
// fvWekaAttributes.addElement(new Attribute("WholeHeader", (FastVector) null));
// fvWekaAttributes.addElement(new Attribute("WholeStub", (FastVector) null));
// fvWekaAttributes.addElement(new Attribute("WholeSuperRow", (FastVector) null));
// fvWekaAttributes.addElement(new Attribute("WholeData", (FastVector) null));
// fvWekaAttributes.addElement(new Attribute("Caption", (FastVector) null));
fvWekaAttributes.addElement(caption_topic1);
fvWekaAttributes.addElement(caption_topic2);
fvWekaAttributes.addElement(caption_topic3);
fvWekaAttributes.addElement(caption_topic4);
fvWekaAttributes.addElement(caption_topic5);
fvWekaAttributes.addElement(caption_topic6);
fvWekaAttributes.addElement(caption_topic7);
fvWekaAttributes.addElement(caption_topic8);
fvWekaAttributes.addElement(caption_topic9);
fvWekaAttributes.addElement(caption_topic10);
fvWekaAttributes.addElement(caption_topic11);
fvWekaAttributes.addElement(caption_topic12);
fvWekaAttributes.addElement(caption_topic13);
fvWekaAttributes.addElement(caption_topic14);
fvWekaAttributes.addElement(caption_topic15);
fvWekaAttributes.addElement(caption_topic16);
fvWekaAttributes.addElement(caption_topic17);
fvWekaAttributes.addElement(caption_topic18);
fvWekaAttributes.addElement(caption_topic19);
fvWekaAttributes.addElement(caption_topic20);
fvWekaAttributes.addElement(caption_topic21);
fvWekaAttributes.addElement(caption_topic22);
fvWekaAttributes.addElement(caption_topic23);
fvWekaAttributes.addElement(caption_topic24);
fvWekaAttributes.addElement(caption_topic25);
fvWekaAttributes.addElement(caption_topic26);
fvWekaAttributes.addElement(caption_topic27);
fvWekaAttributes.addElement(caption_topic28);
fvWekaAttributes.addElement(caption_topic29);
fvWekaAttributes.addElement(caption_topic30);
fvWekaAttributes.addElement(caption_topic31);
fvWekaAttributes.addElement(caption_topic32);
fvWekaAttributes.addElement(caption_topic33);
fvWekaAttributes.addElement(caption_topic34);
fvWekaAttributes.addElement(caption_topic35);
fvWekaAttributes.addElement(caption_topic36);
fvWekaAttributes.addElement(caption_topic37);
fvWekaAttributes.addElement(caption_topic38);
fvWekaAttributes.addElement(caption_topic39);
fvWekaAttributes.addElement(caption_topic40);
fvWekaAttributes.addElement(caption_topic41);
fvWekaAttributes.addElement(caption_topic42);
fvWekaAttributes.addElement(caption_topic43);
fvWekaAttributes.addElement(caption_topic44);
fvWekaAttributes.addElement(caption_topic45);
fvWekaAttributes.addElement(caption_topic46);
fvWekaAttributes.addElement(caption_topic47);
fvWekaAttributes.addElement(caption_topic48);
fvWekaAttributes.addElement(caption_topic49);
fvWekaAttributes.addElement(caption_topic50);
fvWekaAttributes.addElement(sentence_topic1);
fvWekaAttributes.addElement(sentence_topic2);
fvWekaAttributes.addElement(sentence_topic3);
fvWekaAttributes.addElement(sentence_topic4);
fvWekaAttributes.addElement(sentence_topic5);
fvWekaAttributes.addElement(sentence_topic6);
fvWekaAttributes.addElement(sentence_topic7);
fvWekaAttributes.addElement(sentence_topic8);
fvWekaAttributes.addElement(sentence_topic9);
fvWekaAttributes.addElement(sentence_topic10);
fvWekaAttributes.addElement(sentence_topic11);
fvWekaAttributes.addElement(sentence_topic12);
fvWekaAttributes.addElement(sentence_topic13);
fvWekaAttributes.addElement(sentence_topic14);
fvWekaAttributes.addElement(sentence_topic15);
fvWekaAttributes.addElement(sentence_topic16);
fvWekaAttributes.addElement(sentence_topic17);
fvWekaAttributes.addElement(sentence_topic18);
fvWekaAttributes.addElement(sentence_topic19);
fvWekaAttributes.addElement(sentence_topic20);
fvWekaAttributes.addElement(sentence_topic21);
fvWekaAttributes.addElement(sentence_topic22);
fvWekaAttributes.addElement(sentence_topic23);
fvWekaAttributes.addElement(sentence_topic24);
fvWekaAttributes.addElement(sentence_topic25);
fvWekaAttributes.addElement(sentence_topic26);
fvWekaAttributes.addElement(sentence_topic27);
fvWekaAttributes.addElement(sentence_topic28);
fvWekaAttributes.addElement(sentence_topic29);
fvWekaAttributes.addElement(sentence_topic30);
fvWekaAttributes.addElement(sentence_topic31);
fvWekaAttributes.addElement(sentence_topic32);
fvWekaAttributes.addElement(sentence_topic33);
fvWekaAttributes.addElement(sentence_topic34);
fvWekaAttributes.addElement(sentence_topic35);
fvWekaAttributes.addElement(sentence_topic36);
fvWekaAttributes.addElement(sentence_topic37);
fvWekaAttributes.addElement(sentence_topic38);
fvWekaAttributes.addElement(sentence_topic39);
fvWekaAttributes.addElement(sentence_topic40);
fvWekaAttributes.addElement(sentence_topic41);
fvWekaAttributes.addElement(sentence_topic42);
fvWekaAttributes.addElement(sentence_topic43);
fvWekaAttributes.addElement(sentence_topic44);
fvWekaAttributes.addElement(sentence_topic45);
fvWekaAttributes.addElement(sentence_topic46);
fvWekaAttributes.addElement(sentence_topic47);
fvWekaAttributes.addElement(sentence_topic48);
fvWekaAttributes.addElement(sentence_topic49);
fvWekaAttributes.addElement(sentence_topic50);
fvWekaAttributes.addElement(ClassAttribute);
Instances Instances = new Instances("Rel", fvWekaAttributes, 0);
iExample = new DenseInstance(128);
Attribute attribute = (Attribute) fvWekaAttributes.elementAt(0);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(0), PMC);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(1), tableid);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(2), NoRows);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(3),
NoColumn);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(4),
TotalCellNo);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(5),
CellEmpty);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(6),
CellNumeric);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(7),
CellSemiNumeric);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(8),
CellText);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(9),
ContainsAdverse);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(10),
containsAge);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(11),
containsBaseline);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(12),
containsCharacteristicCap);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(13),
containsDemographic);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(14),
ContainsExclusion);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(15),
ContainsInclusion);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(16),
containsN);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(17),
containsPatientsCap);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(18),
containsPatientsCell);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(19),
ContainsSideEffect);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(20),
ContainsSignOrSymptomAnnotation);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(21),
containsEglibility);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(22),
containsToxicity);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(23),
containsInclusionExclusionCell);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(24),
containsHaematologic);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(25),
containsTrialCap);
iExample.setValue((Attribute) fvWekaAttributes.elementAt(26),
containsCriteria);
WholeHeader = WholeHeader.replace("'", "");
WholeStub = WholeStub.replace("'", "");
WholeSuperRow = WholeSuperRow.replace("'", "");
WholeData = WholeData.replace("'", "");
Caption = Caption.replace("'", "");
System.out.println("WholeHeader:"+WholeHeader);
System.out.println("WholeStub:"+WholeStub);
System.out.println("WholeSuperRow:"+WholeSuperRow);
System.out.println("WholeData:"+WholeData);
System.out.println("Caption:"+Caption);
// iExample.setValue((Attribute) fvWekaAttributes.elementAt(25),
// WholeHeader);
// iExample.setValue((Attribute) fvWekaAttributes.elementAt(26),
// WholeStub);
// iExample.setValue((Attribute) fvWekaAttributes.elementAt(27),
// WholeSuperRow);
// iExample.setValue((Attribute) fvWekaAttributes.elementAt(28),
// WholeData);
// iExample.setValue((Attribute) fvWekaAttributes.elementAt(25),
// Caption);
for(int i = 27;i<77;i++)
{
iExample.setValue((Attribute) fvWekaAttributes.elementAt(i),
caption_topics[i-27]);
}
for(int i = 77;i<127;i++)
{
iExample.setValue((Attribute) fvWekaAttributes.elementAt(i),
ref_sentence_topic[i-77]);
}
Instances.add(iExample);
Instances.setClassIndex(127);
} catch (Exception ex) {
ex.printStackTrace();
}
return iExample;
}
}
