fix get elements at commit if element was deleted after commit

.circleci/config.yml

@@ -20,19 +20,20 @@ jobs:
 
       - setup_remote_docker
 
-      - run: 
+      - run:
           name: "Create and start all services from the docker-compose configuration"
           command: |
             cp example/src/main/resources/application.properties.example ./example/src/main/resources/application.properties
             docker-compose up --build -d
             docker run --network container:mms curlimages/curl --retry 8 --retry-delay 10 --retry-max-time 90 --retry-connrefused http://mms:8080/healthcheck
 
-      - run: 
+      - run:
           name: "Run and test Postman Collection"
           command: |
             docker create -v /etc/newman --name mms_test_configs alpine:3.4 /bin/true
             docker cp example/. mms_test_configs:/etc/newman
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run crud.postman_collection.json -e test-env.json --delay-request 500
+            docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run getAtCommits.postman_collection.json -e test-env.json --delay-request 500  
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run cameo.postman_collection.json -e test-env.json --delay-request 1000
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run jupyter.postman_collection.json -e test-env.json --delay-request 500
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run localauth.postman_collection.json -e test-env.json --delay-request 500

core/src/main/java/org/openmbee/mms/core/dao/CommitIndexDAO.java

@@ -25,6 +25,8 @@ public interface CommitIndexDAO {
 
     List<CommitJson> elementHistory(String id, Set<String> commitIds);
 
+    List<CommitJson> elementDeletedHistory(String id, Collection<String> commitIds);
+
     CommitJson update(CommitJson commitJson);
 
 }

crud/src/main/java/org/openmbee/mms/crud/services/NodeGetHelper.java

@@ -13,14 +13,24 @@
 import org.openmbee.mms.data.domains.scoped.Branch;
 import org.openmbee.mms.data.domains.scoped.Commit;
 import org.openmbee.mms.data.domains.scoped.Node;
+import org.openmbee.mms.core.dao.CommitIndexDAO;
+import org.openmbee.mms.json.CommitJson;
 import org.openmbee.mms.json.ElementJson;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 import static org.openmbee.mms.core.config.ContextHolder.getContext;
 
 @Service
 public class NodeGetHelper extends NodeOperation {
 
+    protected CommitIndexDAO commitIndex;
+
+    @Autowired
+    public void setCommitIndex(CommitIndexDAO commitIndex) {
+        this.commitIndex = commitIndex;
+    }
+
     public NodeGetInfo processGetJsonFromNodes(List<Node> nodes, NodeService service) {
         NodeGetInfo info = initInfoFromNodes(nodes, null);
         return processLatest(info, service);
@@ -122,21 +132,45 @@ private NodeGetInfo processCommit(NodeGetInfo info, String commitId, NodeService
                 Optional<ElementJson> e = nodeIndex.getElementLessThanOrEqualTimestamp(nodeId,
                     formatter.format(time), refCommitIds);
                 if (e.isPresent()) { // found version of element at commit time
-                    //TODO determine if element was deleted at the time?
-                    e.get().setRefId(ContextHolder.getContext().getBranchId());
-                    info.getActiveElementMap().put(nodeId, e.get());
+                    Instant realModified = Instant.from(formatter.parse(e.get().getModified()));
+                    if (elementDeleted(nodeId, commitId, time, realModified, refCommitIds)) {
+                        rejectDeleted(info, nodeId, e.get());
+                    } else {
+                        e.get().setRefId(ContextHolder.getContext().getBranchId());
+                        info.getActiveElementMap().put(nodeId, e.get());
+                    }
                 } else {
                     rejectNotFound(info, nodeId); // element not found at commit time
                 }
             } else if (info.getExistingNodeMap().get(nodeId).isDeleted()) { // latest element is before commit, but deleted
-                rejectDeleted(info, nodeId, indexElement);
+                if (refCommitIds == null) { // need list of commitIds of current ref to filter on
+                    refCommitIds = getRefCommitIds(time);
+                }
+                if (elementDeleted(nodeId, commitId, time, modified, refCommitIds)) {
+                    rejectDeleted(info, nodeId, indexElement);
+                } else {
+                    info.getActiveElementMap().put(nodeId, indexElement);
+                }
             } else { // latest element version is version at commit, not deleted
                 info.getActiveElementMap().put(nodeId, indexElement);
             }
         }
         return info;
     }
 
+    private boolean elementDeleted(String nodeId, String commitId, Instant time, Instant modified, List<String> refCommitIds) {
+        List<CommitJson> commits = commitIndex.elementDeletedHistory(nodeId, refCommitIds);
+        for (CommitJson c: commits) {
+            Instant deletedTime = Instant.from(formatter.parse(c.getCreated()));
+            if ((deletedTime.isBefore(time) || c.getId().equals(commitId)) && deletedTime.isAfter(modified)) {
+                //there's a delete between element last modified time and requested commit time
+                //or element is deleted at commit
+                return true;
+            }
+        }
+        return false;
+    }
+
     public NodeGetInfo processGetJson(List<ElementJson> elements, Instant time, NodeService service) {
         Optional<Branch> ref = branchRepository.findByBranchId(getContext().getBranchId());
         if (ref.isPresent()) {

elastic/src/main/java/org/openmbee/mms/elastic/CommitElasticDAOImpl.java

@@ -124,6 +124,33 @@ private QueryBuilder getCommitHistoryQuery(String id, Set<String> commitIds) {
         return query;
     }
 
+    @Override
+    public List<CommitJson> elementDeletedHistory(String id, Collection<String> commitIds) {
+        QueryBuilder query = QueryBuilders.boolQuery()
+            .filter(QueryBuilders.termQuery("deleted.id", id))
+            .filter(QueryBuilders.termsQuery(CommitJson.ID, commitIds));
+        try {
+            List<CommitJson> commits = new ArrayList<>();
+            SearchHits hits = getCommitResults(query);
+            if (hits.getTotalHits().value == 0) {
+                return new ArrayList<>();
+            }
+            for (SearchHit hit : hits.getHits()) {
+                Map<String, Object> source = hit.getSourceAsMap();// gets "_source"
+                CommitJson ob = newInstance();
+                ob.putAll(source);
+                ob.remove(CommitJson.ADDED);
+                ob.remove(CommitJson.UPDATED);
+                ob.remove(CommitJson.DELETED);
+                commits.add(ob);
+            }
+            return commits;
+        } catch (IOException e) {
+            logger.error(e.getMessage(), e);
+            throw new InternalErrorException(e);
+        }
+    }
+
     /**
      * Returns the commit history of a element
      * <p> Returns a list of commit metadata for the specified id