Dev new config (#204)

* Tidyup configuration

* Tidyup configuration

* bounce postgresql lib version - vulnerable to SQL Injection

* bounce postgresql lib version 4.6.2 - vulnerable to SQL Injection

Author: w-hayes

JeMPI_Apps/JeMPI_Configuration/src/main/scala/configuration/CustomLinkerBackEnd.scala

@@ -29,6 +29,7 @@ object CustomLinkerBackEnd {
         .mkString(sys.props("line.separator"))
     }
 
+    /*
     def createApplyFunctions(): String = {
 
       def applyFields(): String = {
@@ -59,8 +60,10 @@ object CustomLinkerBackEnd {
          |${" " * 3}                          interaction.uniqueInteractionData(),
          |${" " * 3}                          new CustomDemographicData(${applyFields()}));
          |${" " * 3}}""".stripMargin
+
     }
 
+     */
     config.demographicFields
       .filter(f => f.linkMetaData.isDefined)
       .foreach(f => {
@@ -87,14 +90,12 @@ object CustomLinkerBackEnd {
          |
          |${createGenerateFunctions()}
          |
-         |   ${createApplyFunctions()}
-         |
          |   static void updateGoldenRecordFields(
          |         final LibMPI libMPI,
          |         final float threshold,
          |         final String interactionId,
          |         final String goldenId) {
-         |      final var expandedGoldenRecord = libMPI.findExpandedGoldenRecords(List.of(goldenId)).get(0);
+         |      final var expandedGoldenRecord = libMPI.findExpandedGoldenRecords(List.of(goldenId)).getFirst();
          |      final var goldenRecord = expandedGoldenRecord.goldenRecord();
          |      final var demographicData = goldenRecord.demographicData();
          |      var k = 0;
@@ -105,13 +106,15 @@ object CustomLinkerBackEnd {
       val fieldName = Utils.snakeCaseToCamelCase(field_name)
       writer.println(
         s"""${" " * 6}k += LinkerDWH.helperUpdateGoldenRecordField(libMPI, interactionId, expandedGoldenRecord,
-           |${" " * 6}                                            "$fieldName", demographicData.$fieldName, CustomDemographicData::get${fieldName
-            .charAt(0)
-            .toUpper}${fieldName.substring(1)})
+           |${" " * 6}                                            "$fieldName", demographicData.$fieldName,
+           |${" " * 6}                                            expandedGoldenRecord.interactionsWithScore()
+           |${" " * 6}                                                                .stream()
+           |${" " * 6}                                                                .map(rec -> rec.interaction().demographicData().$fieldName))
            |${" " * 12}? 1
            |${" " * 12}: 0;""".stripMargin
       )
     })
+
     writer.println(s"""
          |${" " * 6}if (k > 0) {
          |${" " * 6}  LinkerDWH.helperUpdateInteractionsScore(libMPI, threshold, expandedGoldenRecord);

JeMPI_Apps/JeMPI_Configuration/src/main/scala/configuration/CustomPatient.scala

@@ -61,7 +61,7 @@ private object CustomPatient {
       )
     }
     writer.println()
-    for (field <- config.demographicFields) {
+    /*    for (field <- config.demographicFields) {
       val typeString = field.fieldType
       val fieldName = Utils.snakeCaseToCamelCase(field.fieldName)
       writer.println(
@@ -73,7 +73,7 @@ private object CustomPatient {
            |""".stripMargin
       )
     }
-
+     */
     writer.println(
       s"""${" " * indent * 1}public $customClassNameCustomDemographicData() {""".stripMargin
     )
@@ -83,6 +83,20 @@ private object CustomPatient {
          |""".stripMargin
     )
 
+    writer.print(
+      s"""${" " * indent * 1}public $customClassNameCustomDemographicData(final $customClassNameCustomDemographicData demographicData) {"""
+    )
+    config.demographicFields.zipWithIndex.foreach { case (field, idx) =>
+      val fieldName = Utils.snakeCaseToCamelCase(field.fieldName)
+      writer.print(
+        s"""
+           |${" " * indent * 2}this.$fieldName = demographicData.$fieldName;""".stripMargin
+      )
+    }
+    writer.println(s"""
+         |${" " * indent * 1}}
+         |""".stripMargin)
+
     writer.println(
       s"""${" " * indent * 1}public $customClassNameCustomDemographicData(""".stripMargin
     )

JeMPI_Apps/JeMPI_Configuration/src/main/scala/configuration/CustomPostgresqlGoldenRecord.scala

@@ -23,17 +23,10 @@ private object CustomPostgresqlGoldenRecord {
          |final class $customClassName extends CustomDemographicData implements NodeData {
          |
          |   $customClassName(final CustomDemographicData customDemographicData) {
-         |      super(${fields
-          .map(field =>
-            s"""customDemographicData.${Utils.snakeCaseToCamelCase(
-                field.fieldName
-              )}"""
-          )
-          .mkString(s",${sys.props("line.separator")}            ")});
+         |      super(customDemographicData);
          |   }
          |
-         |}
-         |""".stripMargin
+         |}""".stripMargin
     )
     writer.close()
   }

JeMPI_Apps/JeMPI_Configuration/src/main/scala/configuration/CustomPostgresqlInteraction.scala

@@ -23,13 +23,7 @@ private object CustomPostgresqlInteraction {
          |final class $customClassName extends CustomDemographicData implements NodeData {
          |
          |   $customClassName(final CustomDemographicData customDemographicData) {
-         |      super(${fields
-          .map(field =>
-            s"""customDemographicData.${Utils.snakeCaseToCamelCase(
-                field.fieldName
-              )}"""
-          )
-          .mkString(s",${sys.props("line.separator")}            ")});
+         |      super(customDemographicData);
          |   }
          |
          |}

JeMPI_Apps/JeMPI_Configuration/src/main/scala/configuration/Main.scala

@@ -44,8 +44,8 @@ object Main {
     CustomLinkerProbabilistic.generate(config)
     CustomLinkerBackEnd.generate(config)
     CustomLinkerMU.generate(config)
-    CustomPostgresqlInteraction.generate(config.demographicFields)
-    CustomPostgresqlGoldenRecord.generate(config.demographicFields)
+//    CustomPostgresqlInteraction.generate(config.demographicFields)
+//    CustomPostgresqlGoldenRecord.generate(config.demographicFields)
     CustomAsyncHelper.generate(config)
     CustomPatient.generate(config)
     CustomFieldTallies.generate(config)

JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/postgresql/CustomGoldenRecordData.java

@@ -0,0 +1,11 @@
+package org.jembi.jempi.libmpi.postgresql;
+
+import org.jembi.jempi.shared.models.CustomDemographicData;
+
+final class GoldenRecordData extends CustomDemographicData implements NodeData {
+
+   GoldenRecordData(final CustomDemographicData customDemographicData) {
+      super(customDemographicData);
+   }
+
+}

JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/postgresql/CustomInteractionData.java

@@ -0,0 +1,12 @@
+package org.jembi.jempi.libmpi.postgresql;
+
+import org.jembi.jempi.shared.models.CustomDemographicData;
+
+final class InteractionData extends CustomDemographicData implements NodeData {
+
+   InteractionData(final CustomDemographicData customDemographicData) {
+      super(customDemographicData);
+   }
+
+}
+

JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/postgresql/GoldenRecordData.java

@@ -7,10 +7,10 @@
 record NodeGoldenRecord(
       NodeType type,
       UUID uid,
-      CustomGoldenRecordData data) implements Node {
+      GoldenRecordData data) implements Node {
 
    NodeGoldenRecord(final CustomDemographicData demographicData) {
-      this(NodeType.GOLDEN_RECORD, null, new CustomGoldenRecordData(demographicData));
+      this(NodeType.GOLDEN_RECORD, null, new GoldenRecordData(demographicData));
    }
 
    public NodeType getType() {

JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/postgresql/InteractionData.java

@@ -7,10 +7,10 @@
 record NodeInteraction(
       NodeType type,
       UUID uid,
-      CustomInteractionData data) implements Node {
+      InteractionData data) implements Node {
 
    NodeInteraction(final CustomDemographicData demographicData) {
-      this(NodeType.INTERACTION, null, new CustomInteractionData(demographicData));
+      this(NodeType.INTERACTION, null, new InteractionData(demographicData));
    }
 
    public NodeType getType() {

JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/postgresql/NodeGoldenRecord.java

@@ -153,7 +153,7 @@ public static List<NodeGoldenRecord> getGoldenRecordsOfInteraction(final UUID ei
          while (rs.next()) {
             final var id = rs.getString("id");
             final var json = rs.getString("fields");
-            final var goldenRecordData = new CustomGoldenRecordData(OBJECT_MAPPER.readValue(json, CustomDemographicData.class));
+            final var goldenRecordData = new GoldenRecordData(OBJECT_MAPPER.readValue(json, CustomDemographicData.class));
             list.add(new NodeGoldenRecord(Node.NodeType.valueOf(rs.getString("type")), UUID.fromString(id), goldenRecordData));
          }
          return list;
@@ -175,7 +175,7 @@ public static List<NodeInteraction> getGoldenRecordInteractions(final UUID gid)
          while (rs.next()) {
             final var id = rs.getString("id");
             final var json = rs.getString("fields");
-            final var interactionData = new CustomInteractionData(OBJECT_MAPPER.readValue(json, CustomDemographicData.class));
+            final var interactionData = new InteractionData(OBJECT_MAPPER.readValue(json, CustomDemographicData.class));
             list.add(new NodeInteraction(Node.NodeType.valueOf(rs.getString("type")), UUID.fromString(id), interactionData));
          }
          return list;
@@ -192,7 +192,7 @@ private static List<GoldenRecord> findCandidatesWorker(final String sql) {
          while (rs.next()) {
             final var id = rs.getString("id");
             final var json = rs.getString("fields");
-            final var goldenRecordData = new CustomGoldenRecordData(OBJECT_MAPPER.readValue(json, CustomDemographicData.class));
+            final var goldenRecordData = new GoldenRecordData(OBJECT_MAPPER.readValue(json, CustomDemographicData.class));
             list.add(new GoldenRecord(id, null, new CustomUniqueGoldenRecordData(null), goldenRecordData));
          }
          return list;
@@ -228,7 +228,7 @@ public static NodeGoldenRecord getGoldenRecord(final UUID gid) {
          if (rs.next()) {
             final var id = rs.getString("id");
             final var goldenRecordData =
-                  new CustomGoldenRecordData(OBJECT_MAPPER.readValue(rs.getString("fields"), CustomDemographicData.class));
+                  new GoldenRecordData(OBJECT_MAPPER.readValue(rs.getString("fields"), CustomDemographicData.class));
             return new NodeGoldenRecord(Node.NodeType.valueOf(rs.getString("type")), UUID.fromString(id), goldenRecordData);
          }
          return null;
@@ -248,7 +248,7 @@ static NodeInteraction getInteraction(final UUID iid) {
          if (rs.next()) {
             final var id = rs.getString("id");
             final var interactionData =
-                  new CustomInteractionData(OBJECT_MAPPER.readValue(rs.getString("fields"), CustomDemographicData.class));
+                  new InteractionData(OBJECT_MAPPER.readValue(rs.getString("fields"), CustomDemographicData.class));
             return new NodeInteraction(Node.NodeType.valueOf(rs.getString("type")), UUID.fromString(id), interactionData);
          }
          return null;

JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/postgresql/NodeInteraction.java

@@ -12,38 +12,20 @@ public class CustomDemographicData {
    public final String phoneNumber;
    public final String nationalId;
 
-   public final String getGivenName() {
-      return givenName;
-   }
-
-   public final String getFamilyName() {
-      return familyName;
-   }
-
-   public final String getGender() {
-      return gender;
-   }
-
-   public final String getDob() {
-      return dob;
-   }
-
-   public final String getCity() {
-      return city;
-   }
-
-   public final String getPhoneNumber() {
-      return phoneNumber;
-   }
-
-   public final String getNationalId() {
-      return nationalId;
-   }
-
    public CustomDemographicData() {
       this(null, null, null, null, null, null, null);
    }
 
+   public CustomDemographicData(final CustomDemographicData demographicData) {
+      this.givenName = demographicData.givenName;
+      this.familyName = demographicData.familyName;
+      this.gender = demographicData.gender;
+      this.dob = demographicData.dob;
+      this.city = demographicData.city;
+      this.phoneNumber = demographicData.phoneNumber;
+      this.nationalId = demographicData.nationalId;
+   }
+
    public CustomDemographicData(
       final String givenName,
       final String familyName,