Add IsDeleted check in search queries

src/Microsoft.Health.Fhir.SqlServer/Features/Search/Expressions/Visitors/QueryGenerators/SqlQueryGenerator.cs

@@ -253,10 +253,7 @@ public override object VisitSqlRoot(SqlRootExpression expression, SearchOptions
 
                     AppendHistoryClause(delimitedClause, context.ResourceVersionTypes); // This does not hurt today, but will be neded with resource history separation
 
-                    if (expression.SearchParamTableExpressions.Count == 0)
-                    {
-                        AppendDeletedClause(delimitedClause, context.ResourceVersionTypes);
-                    }
+                    AppendDeletedClause(delimitedClause, context.ResourceVersionTypes);
                 }
 
                 if (!searchOptions.CountOnly)

src/Microsoft.Health.Fhir.Tests.Common/Microsoft.Health.Fhir.Tests.Common.csproj

@@ -22,6 +22,7 @@
   <ItemGroup>
 	  <EmbeddedResource Include="TestFiles\Normative\Bundle-BatchWithDuplicatedItems.json" />
 	  <EmbeddedResource Include="TestFiles\Normative\Bundle-BatchWithConditionalUpdateByIdentifier.json" />
+	  <EmbeddedResource Include="TestFiles\Normative\Flag.json" />
 	  <EmbeddedResource Include="TestFiles\Normative\Import-Observation.ndjson" />
     <EmbeddedResource Include="TestFiles\Normative\LegacyRawReindexJobRecord.json" />
     <EmbeddedResource Include="DefinitionFiles\R5\SearchParameters.json" />

src/Microsoft.Health.Fhir.Tests.Common/TestFiles/Normative/Flag.json

@@ -0,0 +1,48 @@
+{
+    "resourceType": "Flag",
+    "id": "example",
+    "text": {
+        "status": "generated",
+        "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Large Dog warning for Peter Patient</div>"
+    },
+    "identifier": [
+        {
+            "value": "12345"
+        }
+    ],
+    "status": "inactive",
+    "category": [
+        {
+            "coding": [
+                {
+                    "system": "http://terminology.hl7.org/CodeSystem/flag-category",
+                    "code": "safety",
+                    "display": "Safety"
+                }
+            ],
+            "text": "Safety"
+        }
+    ],
+    "code": {
+        "coding": [
+            {
+                "system": "http://example.org/local",
+                "code": "bigdog",
+                "display": "Big dog"
+            }
+        ],
+        "text": "Patient has a big dog at his home. Always always wear a suit of armor or take other active counter-measures"
+    },
+    "subject": {
+        "reference": "Patient/example",
+        "display": "Peter Patient"
+    },
+    "period": {
+        "start": "2015-01-17",
+        "end": "2016-12-01"
+    },
+    "author": {
+        "reference": "Practitioner/example",
+        "display": "Nancy Nurse"
+    }
+}

test/Microsoft.Health.Fhir.Shared.Tests.E2E/Rest/DeleteTests.cs

@@ -73,6 +73,19 @@
             }
         }
 
+        [Fact]
+        public async Task GivenADeletedResource_WhenSearchWithNotModifier_ThenDeletedResourcesShouldNotBeReturned()
+        {
+            FhirResponse<Flag> response = await _client.CreateAsync(Samples.GetJsonSample("Flag").ToPoco<Flag>());
+
+            // Delete all Flag resources
+            await _client.DeleteAllResources(ResourceType.Flag, null);
+
+            var searchResults = await _client.SearchAsync("Flag?identifier:not=123");
+
+            Assert.True(searchResults.Resource.Entry == null || searchResults.Resource.Entry.Count == 0);
+        }
+
         [Fact]
         [Trait(Traits.Priority, Priority.One)]
         public async Task GivenAResource_WhenHardDeleting_ThenServerShouldDeleteAllRelatedResourcesSuccessfully()