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annotation/from_NER/009575f9-74e8-4a6d-9fa6-3cae72fd01c3.txt-PROCESSED.xml
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annotation/from_NER/01243d39-ccf2-43ce-b9bf-b445b9c22c75.txt-PROCESSED.xml
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annotation/from_NER/b3e740ad-46d9-48f5-85ab-7c319919ceb1.txt-PROCESSED.xml
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annotation/to_NER/009575f9-74e8-4a6d-9fa6-3cae72fd01c3.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,103 @@ | ||
| package Annotation; | ||
| import java.sql.PreparedStatement; | ||
| import java.sql.ResultSet; | ||
| import java.sql.SQLException; | ||
| import java.sql.Statement; | ||
| import java.text.DateFormat; | ||
| import java.text.SimpleDateFormat; | ||
| import java.util.Date; | ||
| import java.util.LinkedList; | ||
|
|
||
| import DataBase.DataBaseAnnotationSaver; | ||
| import Main.MarvinSemAnnotator; | ||
| import Main.Word; | ||
| import Main.WordMeaningOutputElement; | ||
|
|
||
|
|
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| public class MetaMapAnnotatorMain { | ||
|
|
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| public static void main(String[] args) { | ||
| // TODO Auto-generated method stub | ||
| DataBaseAnnotationSaver dbas = new DataBaseAnnotationSaver(); | ||
| try { | ||
| Statement stmt = dbas.conn.createStatement(); | ||
| String insertTableSQL = "SELECT * FROM Cell where idCell > 489245"; // change this to be idCell that was available before running the last TableAnnotator load. Currently 489245. | ||
| ResultSet rs = stmt.executeQuery(insertTableSQL); | ||
| MarvinSemAnnotator marvin = new MarvinSemAnnotator(); | ||
| while (rs.next()) { | ||
| int idCell = rs.getInt("idCell"); | ||
| String CellID = rs.getString("CellID"); | ||
| String CellType = rs.getString("CellType"); | ||
| int Table_idTable = rs.getInt("Table_idTable"); | ||
| int RowN = rs.getInt("RowN"); | ||
| int ColumnN = rs.getInt("ColumnN"); | ||
| String Content = rs.getString("Content"); | ||
| System.out.println("Processing cell record - \n\tidCell: " + idCell + "\n\tCellID: " + CellID + "\n\tCellType: " + CellType + "\n\tTable_idTable: " + Table_idTable + "\n\tRowN: " + RowN + "\n\tColumnN: " + ColumnN); | ||
| System.out.println("Cell content:" + Content); | ||
| if(Content==null) | ||
| { | ||
| Content = ""; | ||
| } | ||
| int mathTypeIndex = Content.indexOf("MathType@"); | ||
| if(mathTypeIndex>0) | ||
| { | ||
| Content = Content.substring(0, mathTypeIndex); | ||
| } | ||
| LinkedList<Word> words = null; | ||
| if(Content!=null){ | ||
| Content = Content.trim(); | ||
| words = marvin.annotate(Content); | ||
| if(words == null){ | ||
| System.out.println("ERROR: Marvin returned NULL when annotating content (see above) - this cell will be skipped for now "); | ||
| System.out.println("ERROR: letting process rest and then initiating a new marvin metamap annotation connection...."); | ||
| try { | ||
| Thread.sleep(1000); //1000 milliseconds is one second. | ||
| } catch(InterruptedException ex) { | ||
| Thread.currentThread().interrupt(); | ||
| } | ||
| marvin = new MarvinSemAnnotator(); | ||
| continue; | ||
| } | ||
|
|
||
| for(Word w:words) | ||
| { | ||
|
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| for(WordMeaningOutputElement wm: w.wordmeanings) | ||
| { | ||
| System.out.println(wm.AgentName); | ||
| Statement stmt8 = dbas.conn.createStatement(); | ||
| String insertTableSQL8 = "INSERT INTO Annotation (Content,Start,End,AnnotationID,AgentType,AgentName,AnnotationURL,EnvironmentDescription,Cell_idCell,AnnotationDescription,AnnotationSchemaVersion,DateOfAction, Location) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?)"; | ||
| PreparedStatement preparedStatement8 = dbas.conn.prepareStatement(insertTableSQL8,Statement.RETURN_GENERATED_KEYS); | ||
| preparedStatement8.setString(1,wm.appearingWord); | ||
| preparedStatement8.setInt(2,wm.startAt); | ||
| preparedStatement8.setInt(3,wm.endAt); | ||
| preparedStatement8.setString(4,wm.id); | ||
| preparedStatement8.setString(5,"Software"); | ||
| preparedStatement8.setString(6,wm.AgentName); | ||
| preparedStatement8.setString(7,wm.URL); | ||
| preparedStatement8.setString(8,wm.EnvironmentDesc); | ||
| preparedStatement8.setInt(9,idCell); | ||
| preparedStatement8.setString(10,wm.Description); | ||
| preparedStatement8.setString(11,wm.AgentVersion);// Should be version | ||
| //DateFormat dateFormat = new SimpleDateFormat("dd/MM/yyyy"); | ||
| DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd"); | ||
| Date date = new Date(); | ||
| preparedStatement8.setString(12,dateFormat.format(date)); | ||
| preparedStatement8.setString(13,wm.Location); // Should be location | ||
| // execute insert SQL stetement | ||
| preparedStatement8.executeUpdate(); | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
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| dbas.CloseDBConnection(); | ||
|
|
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| } catch (SQLException e) { | ||
| // TODO Auto-generated catch block | ||
| e.printStackTrace(); | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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