Commit 15:18

javadoc

Projet.iml

@@ -7,5 +7,39 @@
     </content>
     <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module-library" scope="TEST">
+      <library name="JUnit6">
+        <CLASSES>
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/jupiter/junit-jupiter/6.0.0/junit-jupiter-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/jupiter/junit-jupiter-api/6.0.0/junit-jupiter-api-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/opentest4j/opentest4j/1.3.0/opentest4j-1.3.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/platform/junit-platform-commons/6.0.0/junit-platform-commons-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/apiguardian/apiguardian-api/1.1.2/apiguardian-api-1.1.2.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/jspecify/jspecify/1.0.0/jspecify-1.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/jupiter/junit-jupiter-params/6.0.0/junit-jupiter-params-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/jupiter/junit-jupiter-engine/6.0.0/junit-jupiter-engine-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/platform/junit-platform-engine/6.0.0/junit-platform-engine-6.0.0.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
+    <orderEntry type="module-library">
+      <library>
+        <CLASSES>
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/jupiter/junit-jupiter/6.0.0/junit-jupiter-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/jupiter/junit-jupiter-api/6.0.0/junit-jupiter-api-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/opentest4j/opentest4j/1.3.0/opentest4j-1.3.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/platform/junit-platform-commons/6.0.0/junit-platform-commons-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/apiguardian/apiguardian-api/1.1.2/apiguardian-api-1.1.2.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/jspecify/jspecify/1.0.0/jspecify-1.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/jupiter/junit-jupiter-params/6.0.0/junit-jupiter-params-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/jupiter/junit-jupiter-engine/6.0.0/junit-jupiter-engine-6.0.0.jar!/" />
+          <root url="jar://$MAVEN_REPOSITORY$/org/junit/platform/junit-platform-engine/6.0.0/junit-platform-engine-6.0.0.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
   </component>
 </module>

UML/classes.puml

@@ -46,7 +46,7 @@ namespace ecoparasite {
     namespace ecoparasite.poissons {
 
         class Poisson {
-            - String specie
+            - String id
             - Double length
             - Double weight
             - Double infestation

data/test.csv

@@ -0,0 +1,4 @@
+Sample_code;Station;Latitude;Longitude;Depth;d13C_raw;d13C_corr;d15N;C_N;StandardLength;TrophicLevel;Anisakis_abdominalcavity;Anisakis_Liver;Anisakis_gonads;Anisakis_stomach;NParasitesViscera;Anisakis_Muscle_Right;Anisakis_Muscle_Left;Aniskis_Muscle_total;NParasitesTotal
+TRACTRA_S0575_A0439;S0575;48.8692264;-4.3976635;96.84;-20.09735065;-19.14374028;12.52361179;4.316778148;257;3.117572211;7;1;0;1;9;1;3;4;13
+TRACTRA_S0575_A0440;S0575;48.8692264;-4.3976635;96.84;-20.02738845;-19.42703789;12.25444555;3.959950061;252;3.038405671;263;5;0;21;289;12;11;23;312
+TRACTRA_S0575_A0441;S0575;48.8692264;-4.3976635;96.84;-19.82735569;-18.83090708;12.97020596;4.360049101;254;3.248923438;51;1;12;1;65;2;3;5;70

src/ecoparasite/input/DataParsing.java

@@ -4,7 +4,10 @@ import ecoparasite.poisson.Poisson;
 
 import java.util.HashSet;
 
+/**
+ * Interface définissant la fonction de Parsing des données
+ */
 public interface DataParsing {
 
-    public HashSet<Poisson> parse(RawData data);
+    public HashSet<Poisson> parse(RawData data) throws RawDataOverflow;
 }

src/ecoparasite/input/RawDataTest.java

@@ -0,0 +1,43 @@
+package ecoparasite.input;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.*;
+import ecoparasite.input.RawData;
+
+import java.util.HashSet;
+
+class RawDataTest {
+
+
+    @Test
+    void getColumnsNames() throws InputFileException {
+        RawData test = InputFactory.readData("test.csv");
+
+        HashSet<String> d = new HashSet<>();
+
+        for (int i = 0; i < test.getData().size(); i++){
+            d.add(test.getData().get(i).getFirst());
+        }
+
+        System.out.println(test.getColumnsNames());
+        System.out.println(d);
+
+        assertIterableEquals(test.getColumnsNames(),d);
+    }
+
+    @Test
+    void getDataFromColumn() throws InputFileException {
+        RawData test = InputFactory.readData("test.csv");
+
+        System.out.println(test.getDataFromColumn("Sample_code"));
+
+    }
+
+    @Test
+    void getEntry() throws InputFileException, RawDataOverflow {
+        RawData test = InputFactory.readData("test.csv");
+
+        System.out.println(test.getEntry(2));
+    }
+}

src/ecoparasite/poisson/Mackerel.java

@@ -2,24 +2,48 @@ package ecoparasite.poisson;
 
 import ecoparasite.input.DataParsing;
 import ecoparasite.input.RawData;
+import ecoparasite.input.RawDataOverflow;
 
+import java.util.HashMap;
 import java.util.HashSet;
 
+import static java.lang.Double.valueOf;
+
 /**
  * Hérite de Poisson.
  * Ajoute les fonctions de Parsing liés aux données collectées sur le Mackerel.
  */
 public class Mackerel extends Poisson implements DataParsing {
-    public Mackerel(String species, Double length, Double infestation) {
+
-        super(species, length, null, infestation);
+    /**
+     * Constructeur de Mackerel
+     * @param length
+     * @param infestation
+     */
+    public Mackerel(String id, Double length, Double infestation) {
+        super(id, length, null, infestation);
     }
 
+    /**
+     * Implémentation de la fonction parse de Dataparsing
+     * @param data
+     * @return tableau des poissons
+     */
     @Override
-    public HashSet<Poisson> parse(RawData data) {
+    public HashSet<Poisson> parse(RawData data) throws RawDataOverflow {
+
+        HashMap<String,String> temp = new HashMap<>();
 
         HashSet<Poisson> fishSet;
         fishSet = new HashSet<>();
 
+        for (int i = 0; i < data.getData().getFirst().size(); i++) {
+            temp = data.getEntry(i);
+            Poisson newP = new Mackerel(temp.get("Sample_code"),valueOf(temp.get("StandardLength")),valueOf(temp.get("NParasitesViscera")));
+
+            fishSet.add(newP);
+        }
+
 
         return fishSet;
     }

src/ecoparasite/poisson/Merlu.java

@@ -2,9 +2,13 @@ package ecoparasite.poisson;
 
 import ecoparasite.input.DataParsing;
 import ecoparasite.input.RawData;
+import ecoparasite.input.RawDataOverflow;
 
+import java.util.HashMap;
 import java.util.HashSet;
 
+import static java.lang.Double.valueOf;
+
 /**
  * Hérite de Poisson.
  * Ajoute les fonctions de Parsing liés aux données collectées sur le Merlu.
@@ -16,8 +20,8 @@ public class Merlu extends Poisson implements DataParsing {
      * @param length Un Wrapper Double representant la longueur/taille du poisson
      * @param infestation Un Wrapper Double representant le taux de parasite du poisson
      */
-    public Merlu(Double length, Double infestation) {
+    public Merlu(String id, Double length, Double infestation) {
-        super("Merlu", length, null, infestation);
+        super(id, length, null, infestation);
     }
 
     /**
@@ -26,11 +30,20 @@ public class Merlu extends Poisson implements DataParsing {
      * @return tableau des poissons
      */
     @Override
-    public HashSet<Poisson> parse(RawData data) { //TODO
+    public HashSet<Poisson> parse(RawData data) throws RawDataOverflow {
+
+        HashMap<String,String> temp = new HashMap<>();
 
         HashSet<Poisson> fishSet;
         fishSet = new HashSet<>();
 
+        for (int i = 0; i < data.getData().getFirst().size(); i++) {
+            temp = data.getEntry(i);
+            Poisson newP = new Merlu(temp.get("nom.merlu"),valueOf(temp.get("m.size")),valueOf(temp.get("number of Anisakis sp L3")));
+
+            fishSet.add(newP);
+        }
+
 
         return fishSet;
     }

src/ecoparasite/poisson/Poisson.java

@@ -8,7 +8,7 @@ import java.util.HashSet;
  */
 public class Poisson{
 
-    private String specie;
+    private String id;
     private Double length;
     private Double weight;
     private Double infestation;
@@ -16,13 +16,13 @@ public class Poisson{
 
     /**
      * Constructeur de l'objet Poisson
-     * @param specie Une String representant l'espece du poisson
+     * @param id Une String representant l'espece du poisson
      * @param length Un Wrapper Double representant la longueur/taille du poisson
      * @param weight Un Wrapper Double representant le poids du poisson
      * @param infestation Un Wrapper Double representant le taux de parasite du poisson
      */
-    public Poisson(String specie, Double length, Double weight, Double infestation){
+    public Poisson(String id, Double length, Double weight, Double infestation){
-        this.specie = specie;
+        this.id = id;
         this.length = length;
         this.weight = weight;
         this.infestation = infestation;
@@ -30,11 +30,11 @@ public class Poisson{
     }
 
     /**
-     * Getter de l'attribut specie
+     * Getter de l'attribut Id
-     * @return La string de l'attribut specie
+     * @return La string de l'attribut Id
      */
-    public String getSpecie() {
+    public String getId() {
-        return specie;
+        return id;
     }
 
     /**

src/ecoparasite/test/InputFactoryTest.java

@@ -0,0 +1,36 @@
+package ecoparasite.test;
+
+
+import static ecoparasite.input.InputFactory.*;
+import static org.junit.jupiter.api.Assertions.assertArrayEquals;
+
+import ecoparasite.input.InputFactory;
+import ecoparasite.input.InputFileException;
+import ecoparasite.input.RawData;
+import org.junit.jupiter.api.Test;
+
+class InputFactoryTest{
+
+    @org.junit.jupiter.api.Test
+    void buildDataPath() {
+
+        String d = "data/Campagne/mackerel.97442.csv";
+        String e = "data/Campagne/merlu2018_75164.csv";
+
+        assertArrayEquals(d.toCharArray(), InputFactory.buildDataPath("Campagne/mackerel.97442.csv").toCharArray());
+        assertArrayEquals(e.toCharArray(), InputFactory.buildDataPath("Campagne/merlu2018_75164.csv").toCharArray());
+
+    }
+
+    @org.junit.jupiter.api.Test
+    void readData() throws InputFileException {
+        RawData test = InputFactory.readData("test.csv");
+
+        System.out.println(test.getData());
+
+    }
+
+    @org.junit.jupiter.api.Test
+    void testReadData() {
+    }
+}