Merge pull request #7 from DiSSCo/feature/add-rollback

Add rollback functionality and remove duplication
DiSSCo · Nov 11, 2022 · f3bef1c · f3bef1c
2 parents 16f351d + 165ba83
commit f3bef1c
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Showing 22 changed files with 948 additions and 190 deletions.
diff --git a/pom.xml b/pom.xml
@@ -146,7 +146,7 @@
   </dependencies>
 
   <build>
-    <defaultGoal>clean package</defaultGoal>
+    <defaultGoal>-B verify</defaultGoal>
     <plugins>
       <plugin>
         <groupId>org.springframework.boot</groupId>

diff --git a/.../java/eu/dissco/core/digitalspecimenprocessor/configuration/ApplicationConfiguration.java b/.../java/eu/dissco/core/digitalspecimenprocessor/configuration/ApplicationConfiguration.java
@@ -2,9 +2,11 @@
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.util.Random;
+import javax.xml.XMLConstants;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
@@ -24,7 +26,16 @@ public Random random() {
   @Bean
   public DocumentBuilder documentBuilder() throws ParserConfigurationException {
     var docFactory = DocumentBuilderFactory.newInstance();
+    docFactory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
     return docFactory.newDocumentBuilder();
   }
 
+  @Bean
+  public TransformerFactory transformerFactory() {
+    var factory = TransformerFactory.newInstance();
+    factory.setAttribute(XMLConstants.ACCESS_EXTERNAL_DTD, "");
+    factory.setAttribute(XMLConstants.ACCESS_EXTERNAL_STYLESHEET, "");
+    return factory;
+  }
+
 }
diff --git a/src/main/java/eu/dissco/core/digitalspecimenprocessor/domain/HandleAttribute.java b/src/main/java/eu/dissco/core/digitalspecimenprocessor/domain/HandleAttribute.java
@@ -1,5 +1,36 @@
 package eu.dissco.core.digitalspecimenprocessor.domain;
 
+import java.util.Arrays;
+import java.util.Objects;
+
 public record HandleAttribute(int index, String type, byte[] data) {
 
+  @Override
+  public boolean equals(Object o) {
+    if (this == o) {
+      return true;
+    }
+    if (o == null || getClass() != o.getClass()) {
+      return false;
+    }
+    HandleAttribute that = (HandleAttribute) o;
+    return index == that.index && Objects.equals(type, that.type)
+        && Arrays.equals(data, that.data);
+  }
+
+  @Override
+  public int hashCode() {
+    int result = Objects.hash(index, type);
+    result = 31 * result + Arrays.hashCode(data);
+    return result;
+  }
+
+  @Override
+  public String toString() {
+    return "HandleAttribute{" +
+        "index=" + index +
+        ", type='" + type + '\'' +
+        ", data=" + Arrays.toString(data) +
+        '}';
+  }
 }
diff --git a/...ain/java/eu/dissco/core/digitalspecimenprocessor/domain/UpdatedDigitalSpecimenRecord.java b/...ain/java/eu/dissco/core/digitalspecimenprocessor/domain/UpdatedDigitalSpecimenRecord.java
@@ -0,0 +1,9 @@
+package eu.dissco.core.digitalspecimenprocessor.domain;
+
+import java.util.List;
+
+public record UpdatedDigitalSpecimenRecord(DigitalSpecimenRecord digitalSpecimenRecord,
+                                           List<String> enrichment,
+                                           DigitalSpecimenRecord currentDigitalSpecimen) {
+
+}
diff --git a/...main/java/eu/dissco/core/digitalspecimenprocessor/domain/UpdatedDigitalSpecimenTuple.java b/...main/java/eu/dissco/core/digitalspecimenprocessor/domain/UpdatedDigitalSpecimenTuple.java
@@ -1,6 +1,6 @@
 package eu.dissco.core.digitalspecimenprocessor.domain;
 
 public record UpdatedDigitalSpecimenTuple(DigitalSpecimenRecord currentSpecimen,
-                                          DigitalSpecimen digitalSpecimen) {
+                                          DigitalSpecimenEvent digitalSpecimenEvent) {
 
 }
diff --git a/...n/java/eu/dissco/core/digitalspecimenprocessor/exception/DisscoJsonBMappingException.java b/...n/java/eu/dissco/core/digitalspecimenprocessor/exception/DisscoJsonBMappingException.java
@@ -0,0 +1,10 @@
+package eu.dissco.core.digitalspecimenprocessor.exception;
+
+import org.springframework.dao.DataAccessException;
+
+public class DisscoJsonBMappingException extends DataAccessException {
+
+  public DisscoJsonBMappingException(String msg, Throwable cause) {
+    super(msg, cause);
+  }
+}
diff --git a/...ain/java/eu/dissco/core/digitalspecimenprocessor/exception/DisscoRepositoryException.java b/...ain/java/eu/dissco/core/digitalspecimenprocessor/exception/DisscoRepositoryException.java
@@ -0,0 +1,12 @@
+package eu.dissco.core.digitalspecimenprocessor.exception;
+
+public class DisscoRepositoryException extends Exception{
+
+  public DisscoRepositoryException(String message) {
+    super(message);
+  }
+
+  public DisscoRepositoryException(String message, Throwable cause) {
+    super(message, cause);
+  }
+}
diff --git a/...in/java/eu/dissco/core/digitalspecimenprocessor/repository/DigitalSpecimenRepository.java b/...in/java/eu/dissco/core/digitalspecimenprocessor/repository/DigitalSpecimenRepository.java
@@ -3,9 +3,12 @@
 import static eu.dissco.core.digitalspecimenprocessor.database.jooq.Tables.NEW_DIGITAL_SPECIMEN;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dissco.core.digitalspecimenprocessor.domain.DigitalSpecimen;
 import eu.dissco.core.digitalspecimenprocessor.domain.DigitalSpecimenRecord;
+import eu.dissco.core.digitalspecimenprocessor.exception.DisscoJsonBMappingException;
+import eu.dissco.core.digitalspecimenprocessor.exception.DisscoRepositoryException;
 import java.time.Instant;
 import java.util.Collection;
 import java.util.List;
@@ -14,6 +17,7 @@
 import org.jooq.JSONB;
 import org.jooq.Query;
 import org.jooq.Record;
+import org.jooq.exception.DataAccessException;
 import org.springframework.stereotype.Repository;
 
 @Repository
@@ -25,21 +29,18 @@ public class DigitalSpecimenRepository {
 
   private DigitalSpecimenRecord mapDigitalSpecimen(Record dbRecord) {
     DigitalSpecimen digitalSpecimen = null;
-    try {
-      digitalSpecimen = new DigitalSpecimen(dbRecord.get(NEW_DIGITAL_SPECIMEN.TYPE),
-          dbRecord.get(NEW_DIGITAL_SPECIMEN.PHYSICAL_SPECIMEN_ID),
-          dbRecord.get(NEW_DIGITAL_SPECIMEN.PHYSICAL_SPECIMEN_TYPE),
-          dbRecord.get(NEW_DIGITAL_SPECIMEN.SPECIMEN_NAME),
-          dbRecord.get(NEW_DIGITAL_SPECIMEN.ORGANIZATION_ID),
-          dbRecord.get(NEW_DIGITAL_SPECIMEN.DATASET),
-          dbRecord.get(NEW_DIGITAL_SPECIMEN.PHYSICAL_SPECIMEN_COLLECTION),
-          dbRecord.get(NEW_DIGITAL_SPECIMEN.SOURCE_SYSTEM_ID),
-          mapper.readTree(dbRecord.get(NEW_DIGITAL_SPECIMEN.DATA).data()),
-          mapper.readTree(dbRecord.get(NEW_DIGITAL_SPECIMEN.ORIGINAL_DATA).data()),
-          dbRecord.get(NEW_DIGITAL_SPECIMEN.DWCA_ID));
-    } catch (JsonProcessingException e) {
-      throw new RuntimeException(e);
-    }
+    digitalSpecimen = new DigitalSpecimen(dbRecord.get(NEW_DIGITAL_SPECIMEN.TYPE),
+        dbRecord.get(NEW_DIGITAL_SPECIMEN.PHYSICAL_SPECIMEN_ID),
+        dbRecord.get(NEW_DIGITAL_SPECIMEN.PHYSICAL_SPECIMEN_TYPE),
+        dbRecord.get(NEW_DIGITAL_SPECIMEN.SPECIMEN_NAME),
+        dbRecord.get(NEW_DIGITAL_SPECIMEN.ORGANIZATION_ID),
+        dbRecord.get(NEW_DIGITAL_SPECIMEN.DATASET),
+        dbRecord.get(NEW_DIGITAL_SPECIMEN.PHYSICAL_SPECIMEN_COLLECTION),
+        dbRecord.get(NEW_DIGITAL_SPECIMEN.SOURCE_SYSTEM_ID),
+        mapToJson(dbRecord.get(NEW_DIGITAL_SPECIMEN.DATA)),
+        mapToJson(dbRecord.get(NEW_DIGITAL_SPECIMEN.ORIGINAL_DATA)),
+        dbRecord.get(NEW_DIGITAL_SPECIMEN.DWCA_ID));
+
     return new DigitalSpecimenRecord(
         dbRecord.get(NEW_DIGITAL_SPECIMEN.ID),
         dbRecord.get(NEW_DIGITAL_SPECIMEN.MIDSLEVEL),
@@ -48,6 +49,16 @@ private DigitalSpecimenRecord mapDigitalSpecimen(Record dbRecord) {
         digitalSpecimen);
   }
 
+  private JsonNode mapToJson(JSONB jsonb) {
+    try {
+      return mapper.readTree(jsonb.data());
+    } catch (JsonProcessingException e) {
+      throw new DisscoJsonBMappingException(
+          "Failed to parse jsonb field to json: " + jsonb.data(), e);
+    }
+  }
+
+
   public int[] createDigitalSpecimenRecord(
       Collection<DigitalSpecimenRecord> digitalSpecimenRecords) {
     var queries = digitalSpecimenRecords.stream().map(this::specimenToQuery).toList();
@@ -89,12 +100,31 @@ public int updateLastChecked(List<String> currentDigitalSpecimen) {
         .execute();
   }
 
-  public List<DigitalSpecimenRecord> getDigitalSpecimens(List<String> specimenList) {
-    return context.select(NEW_DIGITAL_SPECIMEN.asterisk())
-        .distinctOn(NEW_DIGITAL_SPECIMEN.ID)
-        .from(NEW_DIGITAL_SPECIMEN)
-        .where(NEW_DIGITAL_SPECIMEN.PHYSICAL_SPECIMEN_ID.in(specimenList))
-        .orderBy(NEW_DIGITAL_SPECIMEN.ID, NEW_DIGITAL_SPECIMEN.VERSION.desc())
-        .fetch(this::mapDigitalSpecimen);
+  public List<DigitalSpecimenRecord> getDigitalSpecimens(List<String> specimenList)
+      throws DisscoRepositoryException {
+    try {
+      return context.select(NEW_DIGITAL_SPECIMEN.asterisk())
+          .distinctOn(NEW_DIGITAL_SPECIMEN.ID)
+          .from(NEW_DIGITAL_SPECIMEN)
+          .where(NEW_DIGITAL_SPECIMEN.PHYSICAL_SPECIMEN_ID.in(specimenList))
+          .orderBy(NEW_DIGITAL_SPECIMEN.ID, NEW_DIGITAL_SPECIMEN.VERSION.desc())
+          .fetch(this::mapDigitalSpecimen);
+    } catch (DataAccessException ex) {
+      throw new DisscoRepositoryException(
+          "Failed to get specimen from repository: " + specimenList);
+    }
+  }
+
+  public void rollbackSpecimen(String handle) {
+    context.delete(NEW_DIGITAL_SPECIMEN)
+        .where(NEW_DIGITAL_SPECIMEN.ID.eq(handle))
+        .execute();
+  }
+
+  public void deleteVersion(DigitalSpecimenRecord digitalSpecimenRecord) {
+    context.delete(NEW_DIGITAL_SPECIMEN)
+        .where(NEW_DIGITAL_SPECIMEN.ID.eq(digitalSpecimenRecord.id()))
+        .and(NEW_DIGITAL_SPECIMEN.VERSION.eq(digitalSpecimenRecord.version()))
+        .execute();
   }
 }
diff --git a/...main/java/eu/dissco/core/digitalspecimenprocessor/repository/ElasticSearchRepository.java b/...main/java/eu/dissco/core/digitalspecimenprocessor/repository/ElasticSearchRepository.java
@@ -3,6 +3,7 @@
 import co.elastic.clients.elasticsearch.ElasticsearchClient;
 import co.elastic.clients.elasticsearch.core.BulkRequest;
 import co.elastic.clients.elasticsearch.core.BulkResponse;
+import co.elastic.clients.elasticsearch.core.DeleteResponse;
 import eu.dissco.core.digitalspecimenprocessor.domain.DigitalSpecimenRecord;
 import eu.dissco.core.digitalspecimenprocessor.property.ElasticSearchProperties;
 import java.io.IOException;
@@ -30,4 +31,14 @@ public BulkResponse indexDigitalSpecimen(Collection<DigitalSpecimenRecord> digit
     }
     return client.bulk(bulkRequest.build());
   }
+
+  public DeleteResponse rollbackSpecimen(DigitalSpecimenRecord digitalSpecimenRecord)
+      throws IOException {
+    return client.delete(d -> d.index(properties.getIndexName()).id(digitalSpecimenRecord.id()));
+  }
+
+  public void rollbackVersion(DigitalSpecimenRecord currentDigitalSpecimen) throws IOException {
+    client.index(i -> i.index(properties.getIndexName()).id(currentDigitalSpecimen.id())
+        .document(currentDigitalSpecimen));
+  }
 }
diff --git a/src/main/java/eu/dissco/core/digitalspecimenprocessor/repository/HandleRepository.java b/src/main/java/eu/dissco/core/digitalspecimenprocessor/repository/HandleRepository.java
@@ -39,7 +39,7 @@ public void createHandle(String handle, Instant recordTimestamp,
   }
 
   public void updateHandleAttributes(String id, Instant recordTimestamp,
-      List<HandleAttribute> handleAttributes) {
+      List<HandleAttribute> handleAttributes, boolean versionIncrement) {
     var queryList = new ArrayList<Query>();
     for (var handleAttribute : handleAttributes) {
       var query = context.update(HANDLES)
@@ -49,24 +49,37 @@ public void updateHandleAttributes(String id, Instant recordTimestamp,
           .and(HANDLES.IDX.eq(handleAttribute.index()));
       queryList.add(query);
     }
-    queryList.add(versionIncrement(id, recordTimestamp));
+    queryList.add(versionIncrement(id, recordTimestamp, versionIncrement));
     context.batch(queryList).execute();
   }
 
-  private Query versionIncrement(String pid, Instant recordTimestamp) {
+  private Query versionIncrement(String pid, Instant recordTimestamp, boolean versionIncrement) {
     var currentVersion =
         Integer.parseInt(context.select(HANDLES.DATA)
             .from(HANDLES)
             .where(HANDLES.HANDLE.eq(pid.getBytes(
                 StandardCharsets.UTF_8)))
             .and(HANDLES.TYPE.eq("issueNumber".getBytes(StandardCharsets.UTF_8)))
             .fetchOne(dbRecord -> new String(dbRecord.value1())));
-    var version = currentVersion + 1;
+    int version;
+    if (versionIncrement){
+       version = currentVersion + 1;
+    } else {
+      version = currentVersion - 1;
+    }
+
     return context.update(HANDLES)
         .set(HANDLES.DATA, String.valueOf(version).getBytes(StandardCharsets.UTF_8))
         .set(HANDLES.TIMESTAMP, recordTimestamp.getEpochSecond())
         .where(HANDLES.HANDLE.eq(pid.getBytes(
             StandardCharsets.UTF_8)))
         .and(HANDLES.TYPE.eq("issueNumber".getBytes(StandardCharsets.UTF_8)));
   }
+
+  public void rollbackHandleCreation(String id) {
+    context.delete(HANDLES)
+        .where(HANDLES.HANDLE.eq(id.getBytes(StandardCharsets.UTF_8)))
+        .execute();
+  }
+
 }