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write out to a csv file
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@hongcui
hongcui committed Jul 23, 2014
1 parent aae6c5e commit 111cc7a
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Showing 4 changed files with 112 additions and 10 deletions.
1 change: 1 addition & 0 deletions parsing-gui/.classpath
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Expand Up @@ -44,5 +44,6 @@
<classpathentry combineaccessrules="false" kind="src" path="/PhenoscapeII"/>
<classpathentry kind="lib" path="lib/org.eclipse.swt.win32.win32.x86_64_3.100.1.v4234e.jar"/>
<classpathentry kind="lib" path="lib/evo-inflector-1.0.1.jar"/>
<classpathentry kind="lib" path="lib/owlapi-bin.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
4 changes: 2 additions & 2 deletions parsing-gui/bhlproject.conf
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@@ -1,2 +1,2 @@
C:\Users\updates\CharaParserTest\charaParserEval2013\best\confC:\Users\updates\CharaParserTest\charaParserEval2013\best\sourceC:\Users\updates\CharaParserTest\charaParserEval2013\best\target\
C:\Users\updates\CharaParserTest\charaParserEval2013\best
C:\Users\updates\Desktop\SemanticCharaParser\testdataset\confC:\Users\updates\Desktop\SemanticCharaParser\testdataset\sourceC:\Users\updates\Desktop\SemanticCharaParser\testdataset\target\
C:\Users\updates\Desktop\SemanticCharaParser\testdataset
Binary file added parsing-gui/lib/owlapi-bin.jar
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117 changes: 109 additions & 8 deletions parsing-gui/src/fna/parsing/VolumeFinalizer.java
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Expand Up @@ -3,25 +3,32 @@
*/
package fna.parsing;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.sql.Statement;

import org.apache.log4j.Logger;
import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Display;
import org.eclipse.swt.widgets.Text;
import org.jdom.Comment;
import org.jdom.Element;
import org.semanticweb.owlapi.model.OWLOntology;

import outputter.ApplicationUtilities;
//import outputter.TermEQ2IDEQ;
import outputter.XML2EQ;
import owlaccessor.OWLAccessorImpl;
import fna.charactermarkup.StanfordParser;
import fna.parsing.state.SentenceOrganStateMarker;

import java.sql.Timestamp;
import java.util.Date;
import java.util.Set;


/**
Expand All @@ -37,7 +44,7 @@ public class VolumeFinalizer extends Thread {
private static final Logger LOGGER = Logger.getLogger(VolumeFinalizer.class);
private Connection conn = null;
private String glossaryPrefix;
private static String version="$Id: VolumeFinalizer.java 996 2011-10-07 01:13:47Z hong1.cui $";
private static String version="SemanticCharaParser v-alpha-0.1";
private static boolean standalone = Boolean.valueOf(ApplicationUtilities.getProperty("finalizer.standalone"));//set to true when running only StanfordParser; false when running with GUI.
private static String standalonefolder = "C:/Users/updates/CharaParserTest/EQ-patterns_FixedGloss";
private Text finalLog;
Expand Down Expand Up @@ -101,7 +108,6 @@ public void outputFinal() throws Exception {
sp.parsing();
if(!standalone) this.showOutputMessage("System is annotating sentences...");
sp.extracting();
if(!standalone) this.showOutputMessage("System is generating term-based EQ statements...");
String xmldir = Registry.TargetDirectory+System.getProperty("file.separator")+"final"+System.getProperty("file.separator");
String outputtable = this.dataPrefix+"_xml2eq";
//String benchmarktable = "internalworkbench";
Expand All @@ -112,21 +118,116 @@ public void outputFinal() throws Exception {
String uberon = ontodir+System.getProperty("file.separator")+ApplicationUtilities.getProperty("ontology.uberon")+".owl";
String bspo = ontodir+System.getProperty("file.separator")+ApplicationUtilities.getProperty("ontology.bspo")+".owl";
String pato = ontodir+System.getProperty("file.separator")+ApplicationUtilities.getProperty("ontology.pato")+".owl";
//XML2EQ x2e = new XML2EQ(xmldir, database, outputtable, uberon, bspo, pato);
//x2e.outputEQs();
String spatialtermtable = ApplicationUtilities.getProperty("uniquespatialterms");
XML2EQ x2e = new XML2EQ(xmldir, database, outputtable, uberon, bspo, pato, spatialtermtable, glosstable);
x2e.outputEQs();

//Appending new date to the csv and txt output - Hariharan task1
Date d = new Date();
String time = new Timestamp(d.getTime())+"";
String csv = (Registry.TargetDirectory+System.getProperty("file.separator")+dataPrefix+"_"+time.replaceAll("[:-]","_")+"_EQ.csv").replaceAll("\\\\+", "/");
String txt = (Registry.TargetDirectory+System.getProperty("file.separator")+dataPrefix+"_"+time.replaceAll("[:-]","_")+"_version.txt").replaceAll("\\\\+", "/");
String txt = (Registry.TargetDirectory+System.getProperty("file.separator")+dataPrefix+"_"+time.replaceAll("[:-]","_")+"_versions.txt").replaceAll("\\\\+", "/");
writeCSVandVersionFiles(outputtable, csv, txt);

if(!standalone){
this.showOutputMessage("Operations completed.");
this.showOutputMessage("Check result file in "+csv);
this.showOutputMessage("Check result file in the database table: "+outputtable+" and in the files: "+csv+" and "+txt);
LOGGER.debug("Check result file in the database table: "+outputtable+" and in the files: "+csv+" and "+txt);
}
}



private void writeCSVandVersionFiles(String outputtable, String csv,
String txt) throws SQLException {
//output a csv file
File csvfile = new File(csv);
if(csvfile.exists()) csvfile.delete();
String fieldlist ="source, characterID, characterlabel, stateID, statelabel, entity, entitylabel, entityid, " +
"quality, qualitylabel, qualityid, relatedentity, relatedentitylabel, relatedentityid, " +
"unontologizedentity, unontologizedquality, unontologizedrelatedentity";
String header = "'"+fieldlist.replaceAll("\\s*,\\s*", "','")+"'";
String export = "(SELECT "+header+ ") UNION (SELECT "+fieldlist+ " From "+ outputtable+
" INTO OUTFILE '"+csv+"' FIELDS TERMINATED BY ',' "+
" OPTIONALLY ENCLOSED BY '\\\"' "+
" ESCAPED BY '\\\\' LINES TERMINATED BY '\\n')";
/*String export = "SELECT * "+
" INTO OUTFILE '"+csv+"' FIELDS TERMINATED BY ',' "+
" OPTIONALLY ENCLOSED BY '\\\"' "+
" ESCAPED BY '\\\\' LINES TERMINATED BY '\\n' FROM ("+
" SELECT "+header+ " UNION SELECT "+fieldlist+ " From "+ outputtable+") a"; */

/*(SELECT 'source','characterID','characterlabel','stateID','statelabel','entity','entitylabel','entityid','quality','qualitylabel','qualityid','relatedentity','relatedentitylabel','relatedentityid','unontologizedentity','unontologizedquality','unontologizedrelatedentity')
UNION
(SELECT source,characterID,characterlabel,stateID,statelabel,entity,entitylabel,entityid,quality,qualitylabel,qualityid,relatedentity,relatedentitylabel,relatedentityid,unontologizedentity,unontologizedquality,unontologizedrelatedentity
FROM test_xml2eq
INTO OUTFILE 'C:/Users/updates/Desktop/SemanticCharaParser/testdataset/target/eq.csv'
FIELDS TERMINATED BY ','
OPTIONALLY ENCLOSED BY '"'
ESCAPED BY '\\'
LINES TERMINATED BY '\r\n'); */
Statement stmt = null;
try{
stmt = conn.createStatement();
stmt.execute(export);
}catch(Exception e){
e.printStackTrace();
LOGGER.error("Error: Export EQ to csv format failed "+ export);
LOGGER.error("MySQL exception ", e);
}finally{
if(stmt!=null) stmt.close();
if(conn!=null) conn.close();
}
//String ontologyfolder =new File(new File(Registry.TargetDirectory).getParent(), "ontologies").getAbsolutePath();
//TermEQ2IDEQ t2id = new TermEQ2IDEQ(database, outputtable, dataPrefix, ontologyfolder, csv,txt,version);

//output the version file with charaparser and ontology versions
StringBuffer versions = new StringBuffer();

for(OWLAccessorImpl api: XML2EQ.ontoutil.OWLqualityOntoAPIs)
{
OWLOntology temp=null;
String S[]=api.getSource().split("[\\\\.]");
versions.append((S[S.length-2].toUpperCase())+" version:");
temp = api.getManager().getOntologies().iterator().next();
versions.append((temp.getOntologyID().getVersionIRI())+System.getProperty("line.separator"));
}

for(OWLAccessorImpl api1: XML2EQ.ontoutil.OWLentityOntoAPIs)
{
OWLOntology temp=null;
String S[]=api1.getSource().split("[\\\\.]");
versions.append((S[S.length-2].toUpperCase())+" version:");
Set<OWLOntology> ontologies = api1.getManager().getOntologies();
for(OWLOntology ontology:ontologies)
{
if(ontology.getOntologyID().getVersionIRI()!=null){
temp = ontology;
break;
}
/*if(ontology.toString().contains(S[S.length-2]))
{
temp = ontology;
break;
}*/
}
versions.append(temp!=null?(temp.getOntologyID().getVersionIRI()):"");
versions.append(System.getProperty("line.separator"));
}
versions.append("Semantic CharaParser version:"+ version+System.getProperty("line.separator"));
//write versions to the txt file
try {
File file = new File(txt);
if (!file.exists()) {
file.createNewFile();
}

FileWriter fw = new FileWriter(file.getAbsoluteFile());
BufferedWriter bw = new BufferedWriter(fw);
bw.write(versions.toString());
bw.close();
} catch (Exception e) {
e.printStackTrace();
LOGGER.error("IO exception ", e);
}
}

public static void outputFinalXML(Element root, String fileindex, String targetstring) {
Expand Down

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