Feature/fix matix multi

CHANGELOG.md

@@ -5,6 +5,7 @@ Note: version releases in the 0.x.y range may introduce breaking changes.
 ## [unreleased]
  ### Added 
  ### Fixed 
+-  new Matrix serialisation use rm-model for index and fix section handling ([#386](https://github.com/ehrbase/openEHR_SDK/pull/386))
 
 ## [1.20.0]
  ### Added 

serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/CompositionToMatrixWalker.java

@@ -44,12 +44,12 @@
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import org.apache.commons.lang3.StringUtils;
 import org.ehrbase.aql.dto.path.AqlPath;
 import org.ehrbase.serialisation.walker.Context;
 import org.ehrbase.serialisation.walker.FromCompositionWalker;
 import org.ehrbase.serialisation.walker.RmPrimitive;
 import org.ehrbase.util.exception.SdkException;
+import org.ehrbase.webtemplate.interpreter.Interpreter;
 import org.ehrbase.webtemplate.model.WebTemplateNode;
 
 /**
@@ -58,12 +58,19 @@
 public class CompositionToMatrixWalker extends FromCompositionWalker<FromWalkerDto> {
 
     public static final String MAGNITUDE = "/magnitude";
-    private List<String> resolveTo = List.of("OBSERVATION", "EVALUATION", "INSTRUCTION", "ACTION", "ADMIN_ENTRY");
+    private List<String> resolveTo =
+            List.of("OBSERVATION", "EVALUATION", "INSTRUCTION", "ACTION", "ADMIN_ENTRY", "SECTION");
 
     @Override
     protected FromWalkerDto extract(
             Context<FromWalkerDto> context, WebTemplateNode child, boolean isChoice, Integer i) {
 
+        if (i == null
+                && Interpreter.findRmAttributeInfo(context.getNodeDeque().peek(), child)
+                        .isMultipleValued()) {
+            i = 0;
+        }
+
         FromWalkerDto next = new FromWalkerDto(context.getObjectDeque().peek());
 
         // this belongs to composition thus COMPOSITION is the root
@@ -73,14 +80,12 @@ protected FromWalkerDto extract(
         }
 
         // Is this a RM type to which we resolve to, then add a new Entity
-        if (child.getNodeId() != null
-                && findTypeName(child.getNodeId()) != null
-                && resolveTo.contains(findTypeName(child.getNodeId()))) {
+        if (child.getNodeId() != null && resolveTo.contains(child.getRmType())) {
 
             Entity nextEntity = new Entity(next.getCurrentEntity());
             nextEntity.setArchetypeId(child.getNodeId());
-            nextEntity.setPathFromRoot(
-                    child.getAqlPathDto().removeStart(next.getCurrentEntity().getPathFromRoot()));
+            nextEntity.setRmType(child.getRmType());
+            nextEntity.setPathFromRoot(child.getAqlPathDto());
             if (i != null) {
                 nextEntity.getEntityIdx().add(child.getAqlPath(), i);
             }
@@ -288,18 +293,4 @@ private void add(FromWalkerDto fromWalkerDto, AqlPath relativ, Object o) {
                     .putAll(flatten(relativ, MARSHAL_OM.valueToTree(o)));
         }
     }
-
-    static String findTypeName(String atCode) {
-        String typeName = null;
-
-        if (atCode.contains("openEHR-EHR-")) {
-
-            typeName = StringUtils.substringBetween(atCode, "openEHR-EHR-", ".");
-        } else if (atCode.startsWith("at")) {
-            typeName = null;
-        } else {
-            typeName = atCode;
-        }
-        return typeName;
-    }
 }

serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Entity.java

@@ -28,6 +28,8 @@ class Entity {
     private AqlPath pathFromRoot;
     private String archetypeId;
 
+    private String rmType;
+
     private Index entityIdx = new Index();
 
     public Entity() {}
@@ -36,6 +38,7 @@ public Entity(Entity other) {
         this.pathFromRoot = AqlPath.parse(other.pathFromRoot.getPath());
         this.archetypeId = other.archetypeId;
         this.entityIdx = new Index(other.entityIdx);
+        this.rmType = other.getRmType();
     }
 
     public AqlPath getPathFromRoot() {
@@ -62,8 +65,17 @@ public void setEntityIdx(Index entityIdx) {
         this.entityIdx = entityIdx;
     }
 
+    public String getRmType() {
+        return rmType;
+    }
+
+    public void setRmType(String rmType) {
+        this.rmType = rmType;
+    }
+
     @Override
     public boolean equals(Object o) {
+
         if (this == o) {
             return true;
         }
@@ -73,19 +85,21 @@ public boolean equals(Object o) {
         Entity entity = (Entity) o;
         return Objects.equals(pathFromRoot, entity.pathFromRoot)
                 && Objects.equals(archetypeId, entity.archetypeId)
+                && Objects.equals(rmType, entity.rmType)
                 && Objects.equals(entityIdx, entity.entityIdx);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(pathFromRoot, archetypeId, entityIdx);
+        return Objects.hash(pathFromRoot, archetypeId, rmType, entityIdx);
     }
 
     @Override
     public String toString() {
-        return "Resolve{" + "pathFromRoot="
+        return "Entity{" + "pathFromRoot="
                 + pathFromRoot + ", archetypeId='"
-                + archetypeId + '\'' + ", count="
+                + archetypeId + '\'' + ", rmType='"
+                + rmType + '\'' + ", entityIdx="
                 + entityIdx + '}';
     }
 }

serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixFormat.java

@@ -17,8 +17,6 @@
  */
 package org.ehrbase.serialisation.matrixencoding;
 
-import static org.ehrbase.serialisation.matrixencoding.CompositionToMatrixWalker.findTypeName;
-
 import com.fasterxml.jackson.core.JsonGenerator;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -100,6 +98,7 @@ Map<Entity, Map<Index, Map<AqlPath, Object>>> toMatrix(Composition composition)
         Entity currentEntity = new Entity();
         currentEntity.setPathFromRoot(AqlPath.ROOT_PATH);
         currentEntity.setArchetypeId(composition.getArchetypeNodeId());
+        currentEntity.setRmType("COMPOSITION");
         FromWalkerDto fromWalkerDto = new FromWalkerDto();
         fromWalkerDto.updateEntity(currentEntity);
         new CompositionToMatrixWalker()
@@ -123,6 +122,9 @@ public List<Row> toTable(Composition composition) {
             flatten.forEach(this::encode);
         }
 
+        flatten.forEach(r -> r.setTemplateId(
+                composition.getArchetypeDetails().getTemplateId().getValue()));
+
         return flatten;
     }
 
@@ -146,6 +148,7 @@ private Row toRow(Entity entity, Map.Entry<Index, Map<AqlPath, Object>> e) {
         row.setEntityIdx(entity.getEntityIdx().getRepetitions());
         row.setArchetypeId(entity.getArchetypeId());
         row.setEntityPath(entity.getPathFromRoot());
+        row.setRmType(entity.getRmType());
         row.setFields(e.getValue());
         row.setFieldIdx(e.getKey().getRepetitions());
         return row;
@@ -187,6 +190,7 @@ private Row toRow(CSVRecord csvRecord) {
         row.setEntityIdx(buildArray(csvRecord.get(HEADERS.ENTITY_IDX)));
         row.setFieldIdx(buildArray(csvRecord.get(HEADERS.FIELD_IDX)));
         row.setArchetypeId(csvRecord.get(HEADERS.ENTITY_CONCEPT));
+        row.setRmType(csvRecord.get(HEADERS.RM_ENTITY));
         row.setEntityPath(AqlPath.parse(csvRecord.get(HEADERS.ENTITY_PATH)));
         try {
             Map<String, Object> map = MAPPER.readValue(
@@ -240,7 +244,7 @@ private static void printRow(CSVPrinter printer, Row r) {
             printer.printRecord(
                     r.getNum(),
                     r.getArchetypeId(),
-                    findTypeName(r.getArchetypeId()),
+                    r.getRmType(),
                     r.getEntityPath().format(AqlPath.OtherPredicatesFormat.SHORTED, true),
                     printArray(r.getEntityIdx()),
                     printArray(r.getFieldIdx()),

serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixToCompositionWalker.java

@@ -43,6 +43,7 @@
 import org.ehrbase.serialisation.walker.Context;
 import org.ehrbase.serialisation.walker.ToCompositionWalker;
 import org.ehrbase.util.exception.SdkException;
+import org.ehrbase.webtemplate.interpreter.Interpreter;
 import org.ehrbase.webtemplate.model.WebTemplateNode;
 
 /**
@@ -87,6 +88,12 @@ protected List<ToWalkerDto> extract(
             return null;
         }
 
+        if (i == null
+                && Interpreter.findRmAttributeInfo(context.getNodeDeque().peek(), child)
+                        .isMultipleValued()) {
+            i = 0;
+        }
+
         List<ToWalkerDto> filter = filter(context.getObjectDeque().peek(), child.getAqlPathDto(), i != null, i);
 
         // Check that the type is correct
@@ -101,6 +108,9 @@ && filter(filter, child.getAqlPathDto().addEnd("/_type"), false, null).stream()
         if (filter.isEmpty()) {
             return null;
         }
+        if (i != null) {
+            filter = filter.stream().map(MatrixToCompositionWalker::removeIndex).collect(Collectors.toList());
+        }
         return filter;
     }
 
@@ -199,6 +209,10 @@ private static Map<String, Object> unflatten(List<ToWalkerDto> entries) {
                 .collect(Collectors.groupingBy(e -> e.path.getBaseNode().getName()));
 
         return collect.entrySet().stream().collect(Collectors.toMap(Map.Entry::getKey, e -> {
+            if (e.getKey() == null) {
+                System.out.println("ff");
+            }
+
             // Elementar Value found
             if (e.getValue().size() == 1 && e.getValue().get(0).path.getNodeCount() <= 1) {
                 return e.getValue().get(0).value;
@@ -346,4 +360,11 @@ private static boolean matches(ToWalkerDto toWalkerDto, AqlPath path, boolean ch
 
         return index == null || toWalkerDto.index.get(0).equals(index);
     }
+
+    private static ToWalkerDto removeIndex(ToWalkerDto current) {
+
+        ToWalkerDto toWalkerDto = new ToWalkerDto(current);
+        toWalkerDto.index.remove(0);
+        return toWalkerDto;
+    }
 }

serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Row.java

@@ -31,6 +31,10 @@ public class Row {
     private AqlPath entityPath;
     private String archetypeId;
 
+    private String rmType;
+
+    private String templateId;
+
     private Integer[] entityIdx;
 
     private Integer[] fieldIdx;
@@ -76,6 +80,22 @@ public void setFields(Map<AqlPath, Object> fields) {
         this.fields = fields;
     }
 
+    public String getTemplateId() {
+        return templateId;
+    }
+
+    public void setTemplateId(String templateId) {
+        this.templateId = templateId;
+    }
+
+    public String getRmType() {
+        return rmType;
+    }
+
+    public void setRmType(String rmType) {
+        this.rmType = rmType;
+    }
+
     public int getNum() {
         return num;
     }
@@ -96,14 +116,16 @@ public boolean equals(Object o) {
         return num == row.num
                 && Objects.equals(entityPath, row.entityPath)
                 && Objects.equals(archetypeId, row.archetypeId)
+                && Objects.equals(rmType, row.rmType)
+                && Objects.equals(templateId, row.templateId)
                 && Arrays.equals(entityIdx, row.entityIdx)
                 && Arrays.equals(fieldIdx, row.fieldIdx)
                 && Objects.equals(fields, row.fields);
     }
 
     @Override
     public int hashCode() {
-        int result = Objects.hash(num, entityPath, archetypeId, fields);
+        int result = Objects.hash(num, entityPath, archetypeId, rmType, templateId, fields);
         result = 31 * result + Arrays.hashCode(entityIdx);
         result = 31 * result + Arrays.hashCode(fieldIdx);
         return result;
@@ -112,11 +134,13 @@ public int hashCode() {
     @Override
     public String toString() {
         return "Row{" + "num="
-                + num + ", pathFromRoot="
+                + num + ", entityPath="
                 + entityPath + ", archetypeId='"
-                + archetypeId + '\'' + ", count="
-                + Arrays.toString(entityIdx) + ", index="
-                + Arrays.toString(fieldIdx) + ", other="
+                + archetypeId + '\'' + ", rmType='"
+                + rmType + '\'' + ", templateId='"
+                + templateId + '\'' + ", entityIdx="
+                + Arrays.toString(entityIdx) + ", fieldIdx="
+                + Arrays.toString(fieldIdx) + ", fields="
                 + fields + '}';
     }
 }

serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/ToWalkerDto.java

@@ -17,6 +17,7 @@
  */
 package org.ehrbase.serialisation.matrixencoding;
 
+import java.util.ArrayList;
 import java.util.List;
 import org.ehrbase.aql.dto.path.AqlPath;
 
@@ -28,4 +29,12 @@ class ToWalkerDto {
     AqlPath path;
     List<Integer> index;
     Object value;
+
+    public ToWalkerDto() {}
+
+    public ToWalkerDto(ToWalkerDto other) {
+        this.path = other.path;
+        this.index = new ArrayList<>(other.index);
+        this.value = other.value;
+    }
 }

serialisation/src/test/java/org/ehrbase/serialisation/matrixencoding/MatrixFormatTest.java

@@ -79,36 +79,6 @@ void toMatrixIPS() throws IOException {
         assertThat(actual).isEqualToNormalizingNewlines(expected);
     }
 
-    @Test
-    void toMatrixIPSEncode() throws IOException {
-
-        String corona = IOUtils.toString(CompositionTestDataCanonicalJson.IPS.getStream(), StandardCharsets.UTF_8);
-
-        MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider(), new FixedCodeSetEncoder());
-
-        String actual = cut.marshal(new CanonicalJson().unmarshal(corona));
-
-        String expected =
-                IOUtils.toString(MatrixFormat.class.getResourceAsStream("/csv/IPSEncode.csv"), StandardCharsets.UTF_8);
-
-        assertThat(actual).isEqualToNormalizingNewlines(expected);
-    }
-
-    @Test
-    void toMatrixCoronaEncode() throws IOException {
-
-        String corona = IOUtils.toString(CompositionTestDataCanonicalJson.CORONA.getStream(), StandardCharsets.UTF_8);
-
-        MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider(), new FixedCodeSetEncoder());
-
-        String actual = cut.marshal(new CanonicalJson().unmarshal(corona));
-
-        String expected = IOUtils.toString(
-                MatrixFormat.class.getResourceAsStream("/csv/CORONAEncode.csv"), StandardCharsets.UTF_8);
-
-        assertThat(actual).isEqualToNormalizingNewlines(expected);
-    }
-
     @Test
     void fromMatrix() throws IOException {
         MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider());