WIP Java program

drugs/java/src/main/java/fr/erias/frenchdrugs/comparators/CDcomp.java

+package fr.erias.frenchdrugs.comparators;
+
+import fr.erias.frenchdrugs.models.ClinicalDrug;
+
+public abstract class CDcomp {
+	protected final ClinicalDrug cd;
+	
+	public CDcomp(ClinicalDrug cd) {
+		this.cd = cd;
+	}
+	
+	public ClinicalDrug getCD() {
+		return(this.cd);
+	}
+
+	public abstract boolean isEquals(Object o);
+	
+	protected boolean isSameIngredientSize(Object o) {
+		if (o == this) { 
+			return true; 
+		}
+		
+		if (!(o instanceof CDcomp)) { 
+			return false; 
+		} 
+		
+		CDcomp c = (CDcomp) o; 
+		
+		// compare number of ClinicalDrugComponent
+		int size1 = cd.getCDCs().size();
+		int size2 = c.getCD().getCDCs().size();
+		if (size1 != size2) {
+			return(false);
+		}
+		return(true);
+	}
+	
+	public abstract int getHashCode();
+	
+    @Override
+    public boolean equals(Object o) {
+    	return(isEquals(o));
+    }
+    
+    @Override
+    public int hashCode() {
+    	return(getHashCode());
+    }
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/comparators/CDcompIN.java

+package fr.erias.frenchdrugs.comparators;
+
+import fr.erias.frenchdrugs.models.ClinicalDrug;
+import fr.erias.frenchdrugs.models.ClinicalDrugComponent;
+
+public class CDcompIN extends CDcomp  {
+
+	public CDcompIN(ClinicalDrug cd) {
+		super(cd);
+	}
+	
+	public static boolean checkSameIngredients(ClinicalDrug cd1, ClinicalDrug cd2) {
+		// compare number of ClinicalDrugComponent
+		int size1 = cd1.getCDCs().size();
+		int size2 = cd2.getCDCs().size();
+		if (size1 != size2) {
+			return(false);
+		}
+		
+		// compare the substance:
+		for (int i = 0; i<size1; i++) {
+			ClinicalDrugComponent cdc1 = cd1.getCDCs().get(i);
+			String substanceId1 = cdc1.getSubstanceStrength().getSubstanceId();
+			
+			ClinicalDrugComponent cdc2 = cd2.getCDCs().get(i);
+			String substanceId2 = cdc2.getSubstanceStrength().getSubstanceId();
+			
+			// they are ordered by substanceId
+			if (!substanceId1.equals(substanceId2)) {
+				return(false);
+			}
+		}
+		return(true);
+	}
+	
+	@Override
+	public boolean isEquals(Object o) {
+		if (o == this) { 
+			return true; 
+		}
+		
+		if (!(o instanceof CDcompIN)) { 
+			return false; 
+		} 
+		
+		CDcompIN c = (CDcompIN) o; 
+		return(checkSameIngredients(this.cd, c.getCD()));
+	}
+	
+    @Override
+    public int getHashCode() {
+        int result = 17;
+        for (ClinicalDrugComponent cdc1 : cd.getCDCs()) {
+            result = result + 31 * cdc1.getSubstanceStrength().getSubstanceId().hashCode();
+        }
+        return result;
+    }
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/comparators/CDcompINDoseForm.java

+package fr.erias.frenchdrugs.comparators;
+
+import fr.erias.frenchdrugs.models.ClinicalDrug;
+import fr.erias.frenchdrugs.models.ClinicalDrugComponent;
+import fr.erias.frenchdrugs.models.DoseForm;
+
+public class CDcompINDoseForm extends CDcomp {
+
+	public CDcompINDoseForm(ClinicalDrug cd) {
+		super(cd);
+	}
+
+	public static boolean checkDoseForm(ClinicalDrug cd1, ClinicalDrug cd2) {
+		DoseForm df1 = cd1.getDoseForm();
+		DoseForm df2 = cd2.getDoseForm();
+		if (!df1.equals(df2)) {
+			return(false);
+		} else {
+			return(true);
+		}
+	}
+	
+	@Override
+	public boolean isEquals(Object o) {
+		if (o == this) { 
+			return true; 
+		}
+		
+		if (!(o instanceof CDcompINDoseForm)) { 
+			return false; 
+		} 
+		CDcompINDoseForm c = (CDcompINDoseForm) o;
+		
+		// check same ingredient:
+		CDcompIN.checkSameIngredients(this.getCD(), c.getCD());
+		
+		// check same dose form:
+		if (!CDcompINDoseForm.checkDoseForm(c.getCD(), this.getCD())) {
+			return(false);
+		}
+		
+		return(true);
+	}
+
+	@Override
+	public int getHashCode() {
+        int result = 17;
+        for (ClinicalDrugComponent cdc1 : cd.getCDCs()) {
+            result = result + 31 * cdc1.getSubstanceStrength().getSubstanceId().hashCode();
+        }
+        result = result + this.cd.getDoseForm().hashCode();
+        return result;
+	}
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/comparators/CDcompINstrength.java

+package fr.erias.frenchdrugs.comparators;
+
+import fr.erias.frenchdrugs.models.ClinicalDrug;
+import fr.erias.frenchdrugs.models.ClinicalDrugComponent;
+import fr.erias.frenchdrugs.models.ISubstanceStrength;
+
+public class CDcompINstrength extends CDcomp {
+
+	public CDcompINstrength(ClinicalDrug cd) {
+		super(cd);
+	}
+
+	public static boolean checkSubstanceStrength(ClinicalDrug cd1, ClinicalDrug cd2) {
+		// compare number of ClinicalDrugComponent
+		int size1 = cd1.getCDCs().size();
+		int size2 = cd2.getCDCs().size();
+		if (size1 != size2) {
+			return(false);
+		}
+		
+		// compare the substance:
+		for (int i = 0; i<size1; i++) {
+			ClinicalDrugComponent cdc1 = cd1.getCDCs().get(i);
+			ISubstanceStrength substanceStrength1 = cdc1.getSubstanceStrength();
+			
+			ClinicalDrugComponent cdc2 = cd2.getCDCs().get(i);
+			ISubstanceStrength substanceStrength2 = cdc2.getSubstanceStrength();
+			
+			// they are ordered by substanceId
+			if (!substanceStrength1.equals(substanceStrength2)) {
+				return(false);
+			}
+		}
+		return(true);
+	}
+	
+	@Override
+	public boolean isEquals(Object o) {
+		if (o == this) { 
+			return true; 
+		}
+		
+		if (!(o instanceof CDcompINstrength)) { 
+			return false; 
+		} 
+		CDcompINstrength c = (CDcompINstrength) o;
+		
+		if (!CDcompINstrength.checkSubstanceStrength(c.getCD(), this.getCD())) {
+			return(false);
+		}
+		
+		return(true);
+	}
+
+	@Override
+	public int getHashCode() {
+        int result = 17;
+        for (ClinicalDrugComponent cdc1 : cd.getCDCs()) {
+            result = result + 31 * cdc1.getSubstanceStrength().hashCode();
+        }
+        return result;
+	}
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/load/Compo.java

+package fr.erias.frenchdrugs.load;
+
+public class Compo {
+	
+	private int cis;
+	private String dosageform;
+	private int typecode;
+	private String sacode;
+	private String sastrength;
+	private String sawikidata;
+	private float saamount;
+	private String saucumunit;
+	private String ftcode;
+	private String ftstrength;
+	private String ftwikidata;
+	private float ftamount;
+	private String ftucumunit;
+	
+	public Compo(int cis, String dosageform, int typecode, String sacode) {
+		this.cis = cis;
+		this.dosageform = dosageform;
+	}
+	
+	public static void main(String[] args) {
+
+	}
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/load/InvalidFileException.java

+package fr.erias.frenchdrugs.load;
+
+public class InvalidFileException extends Exception {
+
+	public InvalidFileException(String string) {
+		super(string);
+	}
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/load/LoadCompo.java

+package fr.erias.frenchdrugs.load;
+
+import java.io.IOException;
+
+public class LoadCompo extends LoadFile {
+	
+	public LoadCompo() {
+		this.filename = "drug_composition.tsv";
+		this.header = "cis	dosageform	typecode	sacode	sastrength	sawikidata	saamount	saucumunit	ftcode	ftstrength	ftwikidata	ftamount	ftucumunit";
+		this.nColumns = 13;
+		this.sep = "\t";
+	}
+	
+	@Override
+	public void handleColumns(String[] columns) {
+		
+	}
+	
+	public static void main(String[] args) throws IOException, InvalidFileException {
+		new LoadCompo().loadFile();
+	}
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/load/LoadFile.java

+package fr.erias.frenchdrugs.load;
+
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+public abstract class  LoadFile {
+	protected String filename = "some_file_name";
+	protected String sep = "\t";
+	protected String header = "col1 col2 col3";
+	protected int nColumns = 3;
+	
+	public void loadFile() throws IOException, InvalidFileException {
+		FileInputStream in = new FileInputStream(filename);
+		String line = null;
+		BufferedReader br = new BufferedReader(new InputStreamReader(in,"UTF-8"));
+		String header = br.readLine();
+		checkHeader(header);
+		int lineNumber = 1;
+		while ((line = br.readLine()) != null) {
+			String[] columns = getColumns(line, lineNumber);
+			handleColumns(columns);
+			lineNumber += 1;
+		}
+		br.close();
+	}
+	
+	public abstract void handleColumns(String[] columns);
+	
+	public void checkHeader(String header) throws InvalidFileException {
+		if (!header.equals(this.header)) {
+			throw new InvalidFileException("header doesn't match");
+		}
+	}
+	
+	public String[] getColumns(String line, int lineNumber) {
+		String[] columns = line.split(sep, -1);
+		if (columns.length != nColumns) {
+			String error = String.format("Incorrect number of columns %d:"
+					+ "\nline %d: ----> %s", columns.length, lineNumber, line);
+			throw new ArrayIndexOutOfBoundsException(error);
+		}
+		return(columns);
+	}
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/models/ClinicalDrug.java

+package fr.erias.frenchdrugs.models;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashSet;
+
+/**
+ * Ingredient + Strength + Dose Form ; ex: Fluoxetine 4 MG/ML Oral Solution
+ * It may contain multiple substance
+ * @author Sebastien Cossin
+ *
+ */
+public class ClinicalDrug {
+	
+	/**
+	 * Sorted arrayList by substance name
+	 */
+	private final ArrayList<ClinicalDrugComponent> cdcs;
+	
+	private final DoseForm df;
+	
+	public ClinicalDrug(Collection<ClinicalDrugComponent> cdcs, DoseForm df) {
+		this.cdcs = new ArrayList<ClinicalDrugComponent>();
+
+		for (ClinicalDrugComponent cdc : cdcs) {
+			this.cdcs.add(cdc);
+		}
+		// sort by substanceId
+		Collections.sort(this.cdcs,new Comparator<ClinicalDrugComponent>() {
+			@Override
+			public int compare(ClinicalDrugComponent o1, ClinicalDrugComponent o2) {
+				String substance1 = o1.getSubstanceStrength().getSubstanceId();
+				String substance2 = o2.getSubstanceStrength().getSubstanceId();
+				return substance1.compareTo(substance2);
+			}
+		});
+		
+		this.df = df;
+	}
+	
+	public ArrayList<ClinicalDrugComponent> getCDCs() {
+		return(this.cdcs);
+	}
+	
+	public HashSet<ClinicalDrugComponent> getSetCDCs() {
+		return(this.getSetCDCs());
+	}
+	
+	public DoseForm getDoseForm() {
+		return(this.df);
+	}
+	
+	/**
+	 * copy the arraylist to sort for the toString method
+	 * @return
+	 */
+	private ArrayList<ClinicalDrugComponent> getCopyArrayList() { 
+		ArrayList<ClinicalDrugComponent> newArrayList = new ArrayList<ClinicalDrugComponent>();
+		for (ClinicalDrugComponent cdc : this.cdcs) {
+			newArrayList.add(cdc);
+		}
+		return(newArrayList);
+	}
+	
+
+	
+	public String toString() {
+		// sort alphabetic substance name order
+		ArrayList<ClinicalDrugComponent> newArrayList = getCopyArrayList();
+		Collections.sort(newArrayList,new Comparator<ClinicalDrugComponent>() {
+			@Override
+			public int compare(ClinicalDrugComponent o1, ClinicalDrugComponent o2) {
+				String prefLabel1 = o1.getSubstanceStrength().terminology();
+				String prefLabel2 = o2.getSubstanceStrength().terminology();
+				return prefLabel1.compareTo(prefLabel2);
+			}
+		});
+		
+		StringBuilder sb = new StringBuilder();
+		for (ClinicalDrugComponent cdc : newArrayList) {
+			sb.append(cdc.toString());
+			sb.append(" / ");
+		}
+		sb.setLength(sb.length() - 2); // remove the "/ " before inserting the dose form
+		sb.append(df.toString());
+		return(sb.toString());
+	}
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/models/ClinicalDrugComponent.java

+package fr.erias.frenchdrugs.models;
+
+import fr.erias.frenchdrugs.solvent.Concentration;
+import fr.erias.frenchdrugs.solvent.ISolvent;
+
+/**
+ * Clinical Drug Component. Ex: Fluoxetine 4 MG/ML
+ * {@link IN} + {@link Strength}  	
+ * @author Sebastien Cossin
+ *
+ */
+public class ClinicalDrugComponent {
+	
+	private final ISubstanceStrength substanceStrength;
+	
+	private final ISolvent solvent;
+	
+	public ClinicalDrugComponent(ISubstanceStrength substanceStrength, ISolvent solvent) {
+		this.substanceStrength = substanceStrength;
+		this.solvent = solvent;
+	}
+	
+	public ISubstanceStrength getSubstanceStrength() {
+		return substanceStrength;
+	}
+
+	public ISolvent getSolvent() {
+		return solvent;
+	}
+	
+	public String toString() {
+		Concentration con = new Concentration(substanceStrength.getStrength(), this.solvent);
+		StringBuilder sb = new StringBuilder();
+		sb.append(substanceStrength.terminology().trim());
+		sb.append(" ");
+		sb.append(con.getConcentration());
+		return(sb.toString());
+	}
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/models/DoseForm.java

+package fr.erias.frenchdrugs.models;
+
+
+/**
+ * Dose Form. Ex: Oral Solution
+ * @author Sebastien Cossin
+ *
+ */
+public class DoseForm {
+
+	private final String doseFormId;
+	
+	private final String prefLabel;
+	
+	public DoseForm(String id, String prefLabel) {
+		this.doseFormId = id;
+		this.prefLabel = prefLabel;
+	}
+	
+	public String getDoseFormId() {
+		return doseFormId;
+	}
+
+	public String getPrefLabel() {
+		return prefLabel;
+	}
+	
+	public String toString() {
+		return(this.prefLabel);
+	}
+	
+	@Override
+	public boolean equals(Object o) {
+		if (o == this) { 
+			return true; 
+		} 
+
+		if (!(o instanceof DoseForm)) { 
+			return false; 
+		} 
+
+		DoseForm c = (DoseForm) o; 
+
+		return this.doseFormId.equals(c.getDoseFormId()); 
+	}
+	
+    @Override
+    public int hashCode() {
+        return(this.doseFormId.hashCode());
+    }
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/models/IN.java

+package fr.erias.frenchdrugs.models;
+
+
+/**
+ * Ingredient. Ex: Fluoxetine 
+ * A compound or moiety that gives the drug its distinctive clinical properties. Ingredients generally use the United States Adopted Name (USAN).
+ * @author Sebastien Cossin
+ *
+ */
+public class IN implements ISubstance {
+
+	private final String substanceId;
+
+	private final String prefLabel;
+
+	public IN(String substanceId, String prefLabel) {
+		this.substanceId = substanceId;
+		this.prefLabel = prefLabel;
+	}
+
+	public String getSubstanceId() {
+		return substanceId;
+	}
+
+	public String terminology() {
+		return prefLabel;
+	}
+
+	/**
+	 * return true if same substanceId
+	 */
+	@Override
+	public boolean equals(Object o) {
+		if (o == this) { 
+			return true; 
+		} 
+
+		if (!(o instanceof ISubstance)) { 
+			return false; 
+		} 
+
+		ISubstance c = (ISubstance) o; 
+
+		return this.substanceId.equals(c.getSubstanceId()); 
+	}
+	
+    @Override
+    public int hashCode() {
+        return(this.substanceId.hashCode());
+    }
+}

drugs/java/src/main/java/fr/erias/frenchdrugs/models/INStrength.java

+package fr.erias.frenchdrugs.models;
+
+public class INStrength implements ISubstanceStrength {
+	
+	private final IN in;
+	
+	private final Strength strength;
+