[WOR-1696] Soft delete PAOs (#101)

common/openapi.yml

@@ -119,6 +119,8 @@ paths:
           $ref: '#/components/responses/ServerError'
     get:
       summary: Retrieve a Policy Attribute Object
+      parameters:
+        - $ref: '#/components/parameters/IncludeDeleted'
       operationId: getPao
       tags: [Tps]
       responses:
@@ -489,6 +491,15 @@ components:
       schema:
         $ref: '#/components/schemas/TpsDepth'
 
+    IncludeDeleted:
+      name: includeDeleted
+      in: query
+      description: |
+        Include deleted policy attribute objects in the response. Defaults to false.
+      required: false
+      schema:
+        type: boolean
+
   responses:
     # Error Responses
     BadRequest:

service/src/main/java/bio/terra/policy/app/controller/TpsApiController.java

@@ -107,8 +107,11 @@ private ApiTpsPolicyExplanation convertExplanation(ExplainGraphNode node) {
   }
 
   @Override
-  public ResponseEntity<ApiTpsPaoGetResult> getPao(UUID objectId) {
-    Pao pao = paoService.getPao(objectId);
+  public ResponseEntity<ApiTpsPaoGetResult> getPao(UUID objectId, Boolean includeDeleted) {
+    if (includeDeleted == null) {
+      includeDeleted = false;
+    }
+    Pao pao = paoService.getPao(objectId, includeDeleted);
     ApiTpsPaoGetResult result = ConversionUtils.paoToApi(pao);
     MetricsUtils.incrementPaoGet();
     return new ResponseEntity<>(result, HttpStatus.OK);

service/src/main/java/bio/terra/policy/db/PaoDao.java

@@ -16,7 +16,6 @@
 import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -103,11 +102,6 @@ public void createPao(
         effectiveSetId);
   }
 
-  @WriteTransaction
-  public void deletePaos(Collection<DbPao> paos) {
-    paos.forEach((DbPao pao) -> removeDbPao(pao));
-  }
-
   /**
    * Set the 'deleted' field on the PAO to true.
    *
@@ -122,8 +116,8 @@ public void markPaoDeleted(UUID objectId) {
   }
 
   @ReadTransaction
-  public Pao getPao(UUID objectId) {
-    DbPao dbPao = getDbPao(objectId);
+  public Pao getPao(UUID objectId, boolean includeDeleted) {
+    DbPao dbPao = getDbPao(objectId, includeDeleted);
     Map<String, PolicyInputs> attributeSetMap =
         getAttributeSets(List.of(dbPao.attributeSetId(), dbPao.effectiveSetId()));
     return Pao.fromDb(dbPao, attributeSetMap);
@@ -236,7 +230,7 @@ private void updatePao(GraphNode change) {
     PolicyInputs effectiveAttributes = change.getEffectivePolicyAttributes();
 
     // Get the dbPao and the attribute sets from the db for comparison
-    DbPao dbPao = getDbPao(pao.getObjectId());
+    DbPao dbPao = getDbPao(pao.getObjectId(), true);
     Map<String, PolicyInputs> attributeSetMap =
         getAttributeSets(List.of(dbPao.attributeSetId(), dbPao.effectiveSetId()));
     PolicyInputs dbAttributes = attributeSetMap.get(dbPao.attributeSetId());
@@ -395,13 +389,17 @@ private void deleteAttributeSet(String setId) {
     tpsJdbcTemplate.update(sql, params);
   }
 
-  public DbPao getDbPao(UUID objectId) {
-    final String sql =
+  public DbPao getDbPao(UUID objectId, boolean includeDeleted) {
+    String sql =
         """
         SELECT object_id, component, object_type, attribute_set_id, effective_set_id, sources, deleted, created, last_updated
         FROM policy_object WHERE object_id = :object_id
         """;
 
+    if (!includeDeleted) {
+      sql += " AND (deleted is null or not deleted)";
+    }
+
     MapSqlParameterSource params =
         new MapSqlParameterSource().addValue("object_id", objectId.toString());
 

service/src/main/java/bio/terra/policy/service/pao/PaoService.java

@@ -8,9 +8,7 @@
 import bio.terra.policy.common.exception.InvalidInputException;
 import bio.terra.policy.common.model.PolicyInput;
 import bio.terra.policy.common.model.PolicyInputs;
-import bio.terra.policy.db.DbPao;
 import bio.terra.policy.db.PaoDao;
-import bio.terra.policy.service.pao.graph.DeleteWalker;
 import bio.terra.policy.service.pao.graph.ExplainWalker;
 import bio.terra.policy.service.pao.graph.Walker;
 import bio.terra.policy.service.pao.graph.model.ExplainGraph;
@@ -70,9 +68,6 @@ public void createPao(
   public void deletePao(UUID objectId) {
     logger.info("Delete PAO id {}", objectId);
     paoDao.markPaoDeleted(objectId);
-    DeleteWalker walker = new DeleteWalker(paoDao, objectId);
-    Set<DbPao> toRemove = walker.findRemovablePaos();
-    paoDao.deletePaos(toRemove);
   }
 
   /**
@@ -87,9 +82,14 @@ public ExplainGraph explainPao(UUID objectId, int depth) {
     return walker.getExplainGraph();
   }
 
-  public Pao getPao(UUID objectId) {
+  public Pao getPao(UUID objectId, boolean includeDeleted) {
     logger.info("Get PAO id {}", objectId);
-    return paoDao.getPao(objectId);
+
+    return paoDao.getPao(objectId, includeDeleted);
+  }
+
+  public Pao getPao(UUID objectId) {
+    return getPao(objectId, false);
   }
 
   @ReadTransaction
@@ -114,7 +114,7 @@ public PolicyUpdateResult linkSourcePao(
     logger.info(
         "LinkSourcePao: dependent {} source {} mode {}", objectId, sourceObjectId, updateMode);
 
-    Pao targetPao = paoDao.getPao(objectId);
+    Pao targetPao = paoDao.getPao(objectId, false);
     boolean newSource = targetPao.getSourceObjectIds().add(sourceObjectId);
 
     // We didn't actually change the source list, so we are done
@@ -164,8 +164,8 @@ public PolicyUpdateResult mergeFromPao(
         "Merge from PAO id {} to {} mode {}", sourceObjectId, destinationObjectId, updateMode);
 
     // Step 0: get the paos. This will throw if they are not present
-    Pao sourcePao = paoDao.getPao(sourceObjectId);
-    Pao destinationPao = paoDao.getPao(destinationObjectId);
+    Pao sourcePao = paoDao.getPao(sourceObjectId, false);
+    Pao destinationPao = paoDao.getPao(destinationObjectId, false);
 
     // If the source and destination are the same PAO, there is nothing to do
     if (sourceObjectId.equals(destinationObjectId)) {
@@ -211,7 +211,7 @@ public PolicyUpdateResult replacePao(
         replacementAttributes,
         updateMode);
     validatePolicyInputs(replacementAttributes);
-    Pao targetPao = paoDao.getPao(targetPaoId);
+    Pao targetPao = paoDao.getPao(targetPaoId, false);
     return updateAttributesWorker(replacementAttributes, targetPao, updateMode);
   }
 
@@ -236,7 +236,7 @@ public PolicyUpdateResult updatePao(
         removeAttributes,
         updateMode);
 
-    Pao targetPao = paoDao.getPao(targetPaoId);
+    Pao targetPao = paoDao.getPao(targetPaoId, false);
     PolicyInputs attributesToUpdate = new PolicyInputs(targetPao.getAttributes());
 
     // We do the removes first, so we don't remove newly added things

service/src/main/java/bio/terra/policy/service/pao/graph/ExplainWalker.java

@@ -170,7 +170,7 @@ public ExplainGraph getExplainGraph() {
   private Pao getPao(UUID objectId) {
     Pao pao = paoMap.get(objectId);
     if (pao == null) {
-      pao = paoDao.getPao(objectId);
+      pao = paoDao.getPao(objectId, true);
       paoMap.put(objectId, pao);
     }
     return pao;