From 8ad51948a8befc97e8fa2b0784b69783df2e9c66 Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 16:13:56 +0700
Subject: [PATCH 01/11] Clean empty arrays and objects

---
 ts/server/src/core/extract.spec.ts | 75 +++++++++++++++++++++++-------
 ts/server/src/core/extract.ts      | 55 ++++++++++++++++------
 2 files changed, 98 insertions(+), 32 deletions(-)

diff --git a/ts/server/src/core/extract.spec.ts b/ts/server/src/core/extract.spec.ts
index 6c51d8d..07a48d0 100644
--- a/ts/server/src/core/extract.spec.ts
+++ b/ts/server/src/core/extract.spec.ts
@@ -3,6 +3,38 @@ import { FPMLValidationError, resolveTemplate } from './extract';
 describe('Transformation', () => {
     const resource = { list: [{ key: 1 }, { key: 2 }, { key: 3 }] } as any;
 
+    test.skip('null values are not removed', () => {
+        const resourceWithEmptyArrayNullable = {
+            root: { resourceType: 'Example', list: [null, { nested: null }, null] },
+        } as any;
+        expect(
+            resolveTemplate(
+                resourceWithEmptyArrayNullable,
+                { root: '{{ %Resource.root }}' },
+                { Resource: resourceWithEmptyArrayNullable },
+                null,
+                null,
+                true,
+            ),
+        ).toStrictEqual({ root: { resourceType: 'Example', list: [null, { nested: null }] } });
+    });
+
+    test('undefined value are removed', () => {
+        const resourceWithEmptyArray = {
+            root: { resourceType: 'Example', list: [undefined, { nested: undefined }] },
+        } as any;
+        expect(
+            resolveTemplate(
+                resourceWithEmptyArray,
+                { root: '{{ %Resource.root }}' },
+                { Resource: resourceWithEmptyArray },
+                null,
+                null,
+                true,
+            ),
+        ).toStrictEqual({ root: { resourceType: 'Example' } });
+    });
+
     test('fails on accessing props of resource in strict mode', () => {
         expect(() =>
             resolveTemplate(resource, { key: '{{ list.key }}' }, {}, null, null, true),
@@ -61,12 +93,12 @@ describe('Transformation', () => {
         ).toStrictEqual({ key: 1 });
     });
 
-    test('for empty object return empty object', () => {
-        expect(resolveTemplate(resource, {})).toStrictEqual({});
+    test('for empty object return undefined', () => {
+        expect(resolveTemplate(resource, {})).toBeUndefined();
     });
 
-    test('for empty array return empty array', () => {
-        expect(resolveTemplate(resource, [])).toStrictEqual([]);
+    test('for empty array return undefined', () => {
+        expect(resolveTemplate(resource, [])).toBeUndefined();
     });
 
     test('for array of arrays returns flattened array', () => {
@@ -92,8 +124,12 @@ describe('Transformation', () => {
         expect(resolveTemplate(resource, { key: null })).toStrictEqual({ key: null });
     });
 
-    test('for object with undefined keys returns undefined keys', () => {
-        expect(resolveTemplate(resource, { key: undefined })).toStrictEqual({ key: undefined });
+    test('for object with undefined keys returns undefined', () => {
+        expect(resolveTemplate(resource, { key: undefined })).toBeUndefined();
+    });
+
+    test('for object with undefined keys returns only defined keys', () => {
+        expect(resolveTemplate(resource, { key: undefined, key2: 1 })).toStrictEqual({ key2: 1 });
     });
 
     test('for object with non-null keys returns non-null keys', () => {
@@ -230,13 +266,18 @@ describe('Assign block', () => {
 
     test('works with undefined intermediate values', () => {
         expect(
-            resolveTemplate(resource, {
-                '{% assign %}': [{ varA: '{{ {} }}' }, { varB: '{{ %varA }}' }],
-                valueA: '{{ %varB }}',
-            }),
-        ).toStrictEqual({
-            valueA: undefined,
-        });
+            resolveTemplate(
+                resource,
+                {
+                    '{% assign %}': [{ varA: '{{ {} }}' }, { varB: '{{ %varA }}' }],
+                    valueA: '{{ %varB }}',
+                },
+                null,
+                null,
+                null,
+                true,
+            ),
+        ).toBeUndefined();
     });
 
     test('works with multiple vars as array of objects', () => {
@@ -478,9 +519,7 @@ describe('If block', () => {
                     "{% if key != 'value' %}": { nested: "{{ 'true' + key }}" },
                 },
             }),
-        ).toStrictEqual({
-            result: undefined,
-        });
+        ).toBeUndefined();
     });
 
     test('returns null for falsy condition with nullable else branch', () => {
@@ -600,7 +639,7 @@ describe('If block', () => {
             resolveTemplate(resource, {
                 result: {
                     myKey: 1,
-                    "{% if key = 'value' %}": [],
+                    "{% if key = 'value' %}": [{ key1: true }],
                 },
             }),
         ).toThrow(FPMLValidationError);
@@ -612,7 +651,7 @@ describe('If block', () => {
                 result: {
                     myKey: 1,
                     "{% if key != 'value' %}": {},
-                    '{% else %}': [],
+                    '{% else %}': [{ key1: true }],
                 },
             }),
         ).toThrow(FPMLValidationError);
diff --git a/ts/server/src/core/extract.ts b/ts/server/src/core/extract.ts
index a1633ea..f92fc77 100644
--- a/ts/server/src/core/extract.ts
+++ b/ts/server/src/core/extract.ts
@@ -106,7 +106,7 @@ function resolveTemplateRecur(
 
             return { node, context };
         },
-    )[rootNodeKey];
+    )?.[rootNodeKey];
 }
 
 function processTemplateString(
@@ -164,7 +164,6 @@ function processAssignBlock(
 ): { node: any; context: Context } {
     const extendedContext = { ...context };
     const keys = Object.keys(node);
-
     const assignRegExp = /{%\s*assign\s*%}/;
     const assignKey = keys.find((k) => k.match(assignRegExp));
     if (assignKey) {
@@ -177,8 +176,17 @@ function processAssignBlock(
                     );
                 }
 
-                Object.entries(
-                    resolveTemplateRecur(path, resource, obj, extendedContext, model, fpOptions),
+                return Object.entries(
+                    mapValues(obj, (objValue) =>
+                        resolveTemplateRecur(
+                            path,
+                            resource,
+                            objValue,
+                            extendedContext,
+                            model,
+                            fpOptions,
+                        ),
+                    ),
                 ).forEach(([key, value]) => {
                     extendedContext[key] = value;
                 });
@@ -191,13 +199,15 @@ function processAssignBlock(
                 );
             }
             Object.entries(
-                resolveTemplateRecur(
-                    path,
-                    resource,
-                    node[assignKey],
-                    extendedContext,
-                    model,
-                    fpOptions,
+                mapValues(node[assignKey], (objValue) =>
+                    resolveTemplateRecur(
+                        path,
+                        resource,
+                        objValue,
+                        extendedContext,
+                        model,
+                        fpOptions,
+                    ),
                 ),
             ).forEach(([key, value]) => {
                 extendedContext[key] = value;
@@ -398,19 +408,36 @@ type Transformer = (path: Path, node: any, context: Context) => { node: any; con
 function iterateObject(startPath: Path, obj: any, context: Context, transform: Transformer): any {
     if (Array.isArray(obj)) {
         // Arrays are flattened and null/undefined values are removed here
-        return obj
+        const cleanedArray = obj
             .flatMap((value, index) => {
                 const result = transform([...startPath, index], value, context);
 
-                return iterateObject([...startPath, index], result.node, result.context, transform);
+                const testResult = iterateObject(
+                    [...startPath, index],
+                    result.node,
+                    result.context,
+                    transform,
+                );
+                console.log(testResult);
+                return testResult;
             })
             .filter((x) => x !== null && x !== undefined);
+        return cleanedArray.length ? cleanedArray : undefined;
     } else if (isPlainObject(obj)) {
-        return mapValues(obj, (value, key) => {
+        const objResult = mapValues(obj, (value, key) => {
             const result = transform([...startPath, key], value, context);
 
             return iterateObject([...startPath, key], result.node, result.context, transform);
         });
+
+        if (isPlainObject(objResult)) {
+            const cleanedObject = Object.entries(objResult).filter(([, value]) => value !== undefined);
+            if (!cleanedObject.length) {
+                return undefined;
+            }
+            return Object.fromEntries(cleanedObject);
+        }
+        return objResult;
     }
 
     return transform(startPath, obj, context).node;

From 2c250b76b385619f6fd1ce9fa55ea7989c1f4bc7 Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 17:44:19 +0700
Subject: [PATCH 02/11] Python vestion: remove undefined and empty array values

---
 python/fpml/core/extract.py       | 39 ++++++++++++++++++++-----------
 python/tests/core/test_extract.py | 33 ++++++++++++++------------
 2 files changed, 44 insertions(+), 28 deletions(-)

diff --git a/python/fpml/core/extract.py b/python/fpml/core/extract.py
index 1ed170a..d47eab4 100644
--- a/python/fpml/core/extract.py
+++ b/python/fpml/core/extract.py
@@ -42,7 +42,7 @@ def resolve_template(
         context (Optional[Context], optional): Additional context data. Defaults to None.
         fp_options (Optional[FPOptions], optional): Options for controlling FHIRPath evaluation. Defaults to None.
         strict (bool, optional): Whether to enforce strict mode. Defaults to False.
-            See more details on 
+            See more details on
             [strict mode](https://github.com/beda-software/FHIRPathMappingLanguage/tree/main?tab=readme-ov-file#strict-mode).
 
     Returns:
@@ -72,12 +72,16 @@ def resolve_template_recur(
     context: Context,
     fp_options: Optional[FPOptions] = None,
 ) -> Any:
-    return iterate_node(
+    result = iterate_node(
         start_path,
         {root_node_key: template},
         context or {},
         lambda path, node, context: process_node(path, resource, node, context, fp_options),
-    ).get(root_node_key, None)
+    )
+    if isinstance(result, dict):
+        return result.get(root_node_key, None)
+
+    return None
 
 
 def process_node(
@@ -113,7 +117,7 @@ def process_node(
 def iterate_node(start_path: Path, node: Node, context: Context, transform: Transformer) -> Node:
     if isinstance(node, list):
         # Arrays are flattened and null/undefined values are removed here
-        return flatten(
+        cleaned_array = flatten(
             [
                 value
                 for value in [
@@ -127,9 +131,11 @@ def iterate_node(start_path: Path, node: Node, context: Context, transform: Tran
                 if value is not None and value is not undefined
             ]
         )
+
+        return cleaned_array or undefined
     if isinstance(node, dict):
         # undefined values are removed from dicts, but nulls are preserved
-        return {
+        cleaned_object = {
             key: value
             for key, value in {
                 key: iterate_node(
@@ -142,6 +148,11 @@ def iterate_node(start_path: Path, node: Node, context: Context, transform: Tran
             if value is not undefined
         }
 
+        if len(cleaned_object) == 0:
+            return undefined
+
+        return cleaned_object
+
     return transform(start_path, node, context)[0]
 
 
@@ -354,18 +365,20 @@ def process_assign_block(
                     raise FPMLValidationError(
                         "Assign block must accept only one key per object", path
                     )
-                result = resolve_template_recur(path, resource, obj, extended_context, fp_options)
+                result = {
+                    key: resolve_template_recur(
+                        path, resource, obj_value, extended_context, fp_options
+                    )
+                    for key, obj_value in obj.items()
+                }
                 key = next(iter(obj.keys()))
                 extended_context.update({key: result.get(key, None)})
         elif isinstance(node[assign_key], dict) and len(node[assign_key]) == 1:
             obj = node[assign_key]
-            result = resolve_template_recur(
-                path,
-                resource,
-                obj,
-                extended_context,
-                fp_options,
-            )
+            result = {
+                key: resolve_template_recur(path, resource, obj_value, extended_context, fp_options)
+                for key, obj_value in obj.items()
+            }
             key = next(iter(obj.keys()))
             extended_context.update({key: result.get(key, None)})
         else:
diff --git a/python/tests/core/test_extract.py b/python/tests/core/test_extract.py
index b5b6796..00d331a 100644
--- a/python/tests/core/test_extract.py
+++ b/python/tests/core/test_extract.py
@@ -58,11 +58,11 @@ def test_transformation_works_on_accessing_props_of_implicit_context_in_strict_m
 
 
 def test_transformation_for_empty_object_return_empty_object() -> None:
-    assert resolve_template({}, {}) == {}
+    assert resolve_template({}, {}) is None
 
 
 def test_transformation_for_empty_array_return_empty_array() -> None:
-    assert resolve_template({}, []) == []
+    assert resolve_template({}, []) is None
 
 
 def test_transformation_for_array_of_arrays_returns_flattened_array() -> None:
@@ -82,7 +82,7 @@ def test_transformation_for_object_with_null_keys_returns_null_keys() -> None:
 
 
 def test_transformation_for_object_with_undefined_keys_clears_undefined_keys() -> None:
-    assert resolve_template({}, {"key": undefined}) == {}
+    assert resolve_template({}, {"key": undefined}) is None
 
 
 def test_transformation_for_object_with_non_null_keys_returns_non_null_keys() -> None:
@@ -123,7 +123,7 @@ def test_transformation_for_non_empty_array_expression_return_first_element() ->
 
 def test_transformation_for_empty_array_expression_clears_undefined_keys() -> None:
     resource: Resource = {"list": []}
-    assert resolve_template(resource, {"result": "{{ list.where($this = 0) }}"}) == {}
+    assert resolve_template(resource, {"result": "{{ list.where($this = 0) }}"})is None
 
 
 def test_transformation_for_empty_array_nullable_expression_returns_null() -> None:
@@ -141,23 +141,26 @@ def test_transformation_for_template_expression_returns_resolved_template() -> N
     )
 
 
-def test_transformation_for_empty_array_template_expression_clears_undefined_keys() -> None:
+def test_transformation_for_empty_array_template_expression_returns_undefined() -> None:
     resource: Resource = {"list": [{"key": 1}, {"key": 2}, {"key": 3}]}
     assert (
         resolve_template(
             resource,
-            {"result": "/Patient/{{ list.where($this = 0) }}/_history/{{ list.last() }}"},
+            "/Patient/{{ list.where($this = 0) }}/_history/{{ list.last() }}",
         )
-        == {}
+        is None
     )
 
 
 def test_transformation_for_empty_array_nullable_template_expression_returns_null() -> None:
     resource: Resource = {"list": [{"key": 1}, {"key": 2}, {"key": 3}]}
-    assert resolve_template(
-        resource,
-        {"result": "/Patient/{{+ list.where($this = 0) +}}/_history/{{ list.last() }}"},
-    ) == {"result": None}
+    assert (
+        resolve_template(
+            resource,
+            "/Patient/{{+ list.where($this = 0) +}}/_history/{{ list.last() }}",
+        )
+        is None
+    )
 
 
 def test_transformation_for_multiline_template_works_properly() -> None:
@@ -234,7 +237,7 @@ def test_assign_block_with_undefined_intermediate_values() -> None:
                 "valueA": "{{ %varB }}",
             },
         )
-        == {}
+        is None
     )
 
 
@@ -508,7 +511,7 @@ def test_if_block_clears_undefined_keys_for_falsy_condition_without_else_branch(
             },
         },
     )
-    assert result == {}
+    assert result is None
 
 
 def test_if_block_returns_null_for_falsy_condition_with_nullable_else_branch() -> None:
@@ -622,7 +625,7 @@ def test_if_block_fails_on_implicit_merge_with_non_object_returned_from_if_branc
             {
                 "result": {
                     "myKey": 1,
-                    "{% if key = 'value' %}": [],
+                    "{% if key = 'value' %}": [{"key1": True}],
                 },
             },
         )
@@ -639,7 +642,7 @@ def test_if_block_fails_on_implicit_merge_with_non_object_returned_from_else_bra
                 "result": {
                     "myKey": 1,
                     "{% if key != 'value' %}": {},
-                    "{% else %}": [],
+                    "{% else %}": [{"key1": True}],
                 },
             },
         )

From bcf40c029e562b3668ea5b910fcfdd0cce73957f Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 17:46:27 +0700
Subject: [PATCH 03/11] Fix linter errors

---
 python/fpml/core/extract.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/fpml/core/extract.py b/python/fpml/core/extract.py
index d47eab4..9f38f36 100644
--- a/python/fpml/core/extract.py
+++ b/python/fpml/core/extract.py
@@ -372,7 +372,7 @@ def process_assign_block(
                     for key, obj_value in obj.items()
                 }
                 key = next(iter(obj.keys()))
-                extended_context.update({key: result.get(key, None)})
+                extended_context.update({key: result.get(key)})
         elif isinstance(node[assign_key], dict) and len(node[assign_key]) == 1:
             obj = node[assign_key]
             result = {
@@ -380,7 +380,7 @@ def process_assign_block(
                 for key, obj_value in obj.items()
             }
             key = next(iter(obj.keys()))
-            extended_context.update({key: result.get(key, None)})
+            extended_context.update({key: result.get(key)})
         else:
             raise FPMLValidationError("Assign block must accept array or object", path)
         return omit_key(node, assign_key), extended_context

From dabeee2b2ea79ea85411ece849384da6ae7ddd03 Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 19:43:52 +0700
Subject: [PATCH 04/11] Fix review notes in python code

---
 python/fpml/core/extract.py       | 19 +++++++++----------
 python/tests/core/test_extract.py | 18 +++++++++---------
 2 files changed, 18 insertions(+), 19 deletions(-)

diff --git a/python/fpml/core/extract.py b/python/fpml/core/extract.py
index 9f38f36..57ac249 100644
--- a/python/fpml/core/extract.py
+++ b/python/fpml/core/extract.py
@@ -79,9 +79,9 @@ def resolve_template_recur(
         lambda path, node, context: process_node(path, resource, node, context, fp_options),
     )
     if isinstance(result, dict):
-        return result.get(root_node_key, None)
+        return result.get(root_node_key, undefined)
 
-    return None
+    return undefined
 
 
 def process_node(
@@ -148,10 +148,7 @@ def iterate_node(start_path: Path, node: Node, context: Context, transform: Tran
             if value is not undefined
         }
 
-        if len(cleaned_object) == 0:
-            return undefined
-
-        return cleaned_object
+        return cleaned_object or undefined
 
     return transform(start_path, node, context)[0]
 
@@ -367,20 +364,22 @@ def process_assign_block(
                     )
                 result = {
                     key: resolve_template_recur(
-                        path, resource, obj_value, extended_context, fp_options
+                        [*path, key], resource, obj_value, extended_context, fp_options
                     )
                     for key, obj_value in obj.items()
                 }
                 key = next(iter(obj.keys()))
-                extended_context.update({key: result.get(key)})
+                extended_context.update({key: result[key] if result[key] != undefined else None})
         elif isinstance(node[assign_key], dict) and len(node[assign_key]) == 1:
             obj = node[assign_key]
             result = {
-                key: resolve_template_recur(path, resource, obj_value, extended_context, fp_options)
+                key: resolve_template_recur(
+                    [*path, key], resource, obj_value, extended_context, fp_options
+                )
                 for key, obj_value in obj.items()
             }
             key = next(iter(obj.keys()))
-            extended_context.update({key: result.get(key)})
+            extended_context.update({key: result[key] if result[key] != undefined else None})
         else:
             raise FPMLValidationError("Assign block must accept array or object", path)
         return omit_key(node, assign_key), extended_context
diff --git a/python/tests/core/test_extract.py b/python/tests/core/test_extract.py
index 00d331a..17840dc 100644
--- a/python/tests/core/test_extract.py
+++ b/python/tests/core/test_extract.py
@@ -58,11 +58,11 @@ def test_transformation_works_on_accessing_props_of_implicit_context_in_strict_m
 
 
 def test_transformation_for_empty_object_return_empty_object() -> None:
-    assert resolve_template({}, {}) is None
+    assert resolve_template({}, {}) == undefined
 
 
 def test_transformation_for_empty_array_return_empty_array() -> None:
-    assert resolve_template({}, []) is None
+    assert resolve_template({}, [])  == undefined
 
 
 def test_transformation_for_array_of_arrays_returns_flattened_array() -> None:
@@ -82,7 +82,7 @@ def test_transformation_for_object_with_null_keys_returns_null_keys() -> None:
 
 
 def test_transformation_for_object_with_undefined_keys_clears_undefined_keys() -> None:
-    assert resolve_template({}, {"key": undefined}) is None
+    assert resolve_template({}, {"key": undefined})  == undefined
 
 
 def test_transformation_for_object_with_non_null_keys_returns_non_null_keys() -> None:
@@ -97,7 +97,7 @@ def test_transformation_for_array_of_objects_returns_original_array() -> None:
 
 
 def test_transformation_for_null_returns_null() -> None:
-    assert resolve_template({}, None) is None
+    assert resolve_template({}, None)  == undefined
 
 
 def test_transformation_for_constant_string_returns_constant_string() -> None:
@@ -123,7 +123,7 @@ def test_transformation_for_non_empty_array_expression_return_first_element() ->
 
 def test_transformation_for_empty_array_expression_clears_undefined_keys() -> None:
     resource: Resource = {"list": []}
-    assert resolve_template(resource, {"result": "{{ list.where($this = 0) }}"})is None
+    assert resolve_template(resource, {"result": "{{ list.where($this = 0) }}"}) == undefined
 
 
 def test_transformation_for_empty_array_nullable_expression_returns_null() -> None:
@@ -148,7 +148,7 @@ def test_transformation_for_empty_array_template_expression_returns_undefined()
             resource,
             "/Patient/{{ list.where($this = 0) }}/_history/{{ list.last() }}",
         )
-        is None
+        == undefined
     )
 
 
@@ -159,7 +159,7 @@ def test_transformation_for_empty_array_nullable_template_expression_returns_nul
             resource,
             "/Patient/{{+ list.where($this = 0) +}}/_history/{{ list.last() }}",
         )
-        is None
+        == undefined
     )
 
 
@@ -237,7 +237,7 @@ def test_assign_block_with_undefined_intermediate_values() -> None:
                 "valueA": "{{ %varB }}",
             },
         )
-        is None
+        == undefined
     )
 
 
@@ -511,7 +511,7 @@ def test_if_block_clears_undefined_keys_for_falsy_condition_without_else_branch(
             },
         },
     )
-    assert result is None
+    assert result == undefined
 
 
 def test_if_block_returns_null_for_falsy_condition_with_nullable_else_branch() -> None:

From e3b1bf7f761fb34cefdb945c09393b8c0bd7bd79 Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 19:44:28 +0700
Subject: [PATCH 05/11] Fix review notes in JS code

---
 ts/server/src/core/extract.ts | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/ts/server/src/core/extract.ts b/ts/server/src/core/extract.ts
index f92fc77..1dffea8 100644
--- a/ts/server/src/core/extract.ts
+++ b/ts/server/src/core/extract.ts
@@ -177,9 +177,9 @@ function processAssignBlock(
                 }
 
                 return Object.entries(
-                    mapValues(obj, (objValue) =>
+                    mapValues(obj, (objValue, objKey) =>
                         resolveTemplateRecur(
-                            path,
+                            [...path, objKey],
                             resource,
                             objValue,
                             extendedContext,
@@ -199,9 +199,9 @@ function processAssignBlock(
                 );
             }
             Object.entries(
-                mapValues(node[assignKey], (objValue) =>
+                mapValues(node[assignKey], (objValue, objKey) =>
                     resolveTemplateRecur(
-                        path,
+                        [...path, objKey],
                         resource,
                         objValue,
                         extendedContext,
@@ -412,14 +412,12 @@ function iterateObject(startPath: Path, obj: any, context: Context, transform: T
             .flatMap((value, index) => {
                 const result = transform([...startPath, index], value, context);
 
-                const testResult = iterateObject(
+                return iterateObject(
                     [...startPath, index],
                     result.node,
                     result.context,
                     transform,
                 );
-                console.log(testResult);
-                return testResult;
             })
             .filter((x) => x !== null && x !== undefined);
         return cleanedArray.length ? cleanedArray : undefined;
@@ -430,14 +428,9 @@ function iterateObject(startPath: Path, obj: any, context: Context, transform: T
             return iterateObject([...startPath, key], result.node, result.context, transform);
         });
 
-        if (isPlainObject(objResult)) {
-            const cleanedObject = Object.entries(objResult).filter(([, value]) => value !== undefined);
-            if (!cleanedObject.length) {
-                return undefined;
-            }
-            return Object.fromEntries(cleanedObject);
-        }
-        return objResult;
+        const cleanedObject = filterValues(objResult, (_key, value) => value !== undefined);
+
+        return Object.entries(cleanedObject).length ? cleanedObject : undefined;
     }
 
     return transform(startPath, obj, context).node;
@@ -455,6 +448,14 @@ function mapValues(obj: object, fn: (value: any, key: string) => any) {
     );
 }
 
+function filterValues(obj: object, fn: (value: any, key: string) => any) {
+    return Object.fromEntries(
+        Object.entries(obj).filter(([key, value]) => {
+            return [key, fn(value, key)];
+        }),
+    );
+}
+
 function omitKey(obj: any, key: string) {
     // eslint-disable-next-line @typescript-eslint/no-unused-vars
     const { [key]: _, ...rest } = obj;

From 19c0cd72be7d1132414f40c72372b5f11497ccf9 Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 19:46:22 +0700
Subject: [PATCH 06/11] Fix wrong refactored tests

---
 python/tests/core/test_extract.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/tests/core/test_extract.py b/python/tests/core/test_extract.py
index 17840dc..f2f29c1 100644
--- a/python/tests/core/test_extract.py
+++ b/python/tests/core/test_extract.py
@@ -97,7 +97,7 @@ def test_transformation_for_array_of_objects_returns_original_array() -> None:
 
 
 def test_transformation_for_null_returns_null() -> None:
-    assert resolve_template({}, None)  == undefined
+    assert resolve_template({}, None) is None
 
 
 def test_transformation_for_constant_string_returns_constant_string() -> None:
@@ -159,7 +159,7 @@ def test_transformation_for_empty_array_nullable_template_expression_returns_nul
             resource,
             "/Patient/{{+ list.where($this = 0) +}}/_history/{{ list.last() }}",
         )
-        == undefined
+        is None
     )
 
 

From 63be0493bf96178c4b9570987bc6e08257abdbdf Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 19:55:37 +0700
Subject: [PATCH 07/11] Fix JS tests

---
 ts/server/src/core/extract.ts | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/ts/server/src/core/extract.ts b/ts/server/src/core/extract.ts
index 1dffea8..5eef09a 100644
--- a/ts/server/src/core/extract.ts
+++ b/ts/server/src/core/extract.ts
@@ -428,9 +428,11 @@ function iterateObject(startPath: Path, obj: any, context: Context, transform: T
             return iterateObject([...startPath, key], result.node, result.context, transform);
         });
 
-        const cleanedObject = filterValues(objResult, (_key, value) => value !== undefined);
-
-        return Object.entries(cleanedObject).length ? cleanedObject : undefined;
+        const cleanedObject = Object.entries(objResult).filter(([, value]) => value !== undefined);
+        if (!cleanedObject.length) {
+            return undefined;
+        }
+        return Object.fromEntries(cleanedObject);
     }
 
     return transform(startPath, obj, context).node;
@@ -448,14 +450,6 @@ function mapValues(obj: object, fn: (value: any, key: string) => any) {
     );
 }
 
-function filterValues(obj: object, fn: (value: any, key: string) => any) {
-    return Object.fromEntries(
-        Object.entries(obj).filter(([key, value]) => {
-            return [key, fn(value, key)];
-        }),
-    );
-}
-
 function omitKey(obj: any, key: string) {
     // eslint-disable-next-line @typescript-eslint/no-unused-vars
     const { [key]: _, ...rest } = obj;

From 0eddd47457247b7505aaf12791be849700aa761f Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 20:04:55 +0700
Subject: [PATCH 08/11] [Python] Return None instead of undefined from
 resolve_template

because undefined is for internal puprposes only
---
 python/fpml/core/extract.py       |  4 +++-
 python/tests/core/test_extract.py | 14 +++++++-------
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/python/fpml/core/extract.py b/python/fpml/core/extract.py
index 57ac249..38241d0 100644
--- a/python/fpml/core/extract.py
+++ b/python/fpml/core/extract.py
@@ -55,7 +55,7 @@ def resolve_template(
         FHIRPathMappingLanguage Specification:
         https://github.com/beda-software/FHIRPathMappingLanguage/tree/main?tab=readme-ov-file#specification
     """  # noqa: E501
-    return resolve_template_recur(
+    result = resolve_template_recur(
         [],
         guarded_resource if strict else resource,
         template,
@@ -64,6 +64,8 @@ def resolve_template(
         fp_options=fp_options,
     )
 
+    return None if result == undefined else result
+
 
 def resolve_template_recur(
     start_path: Path,
diff --git a/python/tests/core/test_extract.py b/python/tests/core/test_extract.py
index f2f29c1..13b0d1e 100644
--- a/python/tests/core/test_extract.py
+++ b/python/tests/core/test_extract.py
@@ -58,11 +58,11 @@ def test_transformation_works_on_accessing_props_of_implicit_context_in_strict_m
 
 
 def test_transformation_for_empty_object_return_empty_object() -> None:
-    assert resolve_template({}, {}) == undefined
+    assert resolve_template({}, {}) is None
 
 
 def test_transformation_for_empty_array_return_empty_array() -> None:
-    assert resolve_template({}, [])  == undefined
+    assert resolve_template({}, [])  is None
 
 
 def test_transformation_for_array_of_arrays_returns_flattened_array() -> None:
@@ -82,7 +82,7 @@ def test_transformation_for_object_with_null_keys_returns_null_keys() -> None:
 
 
 def test_transformation_for_object_with_undefined_keys_clears_undefined_keys() -> None:
-    assert resolve_template({}, {"key": undefined})  == undefined
+    assert resolve_template({}, {"key": undefined}) is None
 
 
 def test_transformation_for_object_with_non_null_keys_returns_non_null_keys() -> None:
@@ -123,7 +123,7 @@ def test_transformation_for_non_empty_array_expression_return_first_element() ->
 
 def test_transformation_for_empty_array_expression_clears_undefined_keys() -> None:
     resource: Resource = {"list": []}
-    assert resolve_template(resource, {"result": "{{ list.where($this = 0) }}"}) == undefined
+    assert resolve_template(resource, {"result": "{{ list.where($this = 0) }}"}) is None
 
 
 def test_transformation_for_empty_array_nullable_expression_returns_null() -> None:
@@ -148,7 +148,7 @@ def test_transformation_for_empty_array_template_expression_returns_undefined()
             resource,
             "/Patient/{{ list.where($this = 0) }}/_history/{{ list.last() }}",
         )
-        == undefined
+        is None
     )
 
 
@@ -237,7 +237,7 @@ def test_assign_block_with_undefined_intermediate_values() -> None:
                 "valueA": "{{ %varB }}",
             },
         )
-        == undefined
+        is None
     )
 
 
@@ -511,7 +511,7 @@ def test_if_block_clears_undefined_keys_for_falsy_condition_without_else_branch(
             },
         },
     )
-    assert result == undefined
+    assert result is None
 
 
 def test_if_block_returns_null_for_falsy_condition_with_nullable_else_branch() -> None:

From 5d24c3f0e5e53a71ff82942523d3d65c0a9c1503 Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 20:15:35 +0700
Subject: [PATCH 09/11] Fix formatter issue

---
 python/tests/core/test_extract.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/tests/core/test_extract.py b/python/tests/core/test_extract.py
index 13b0d1e..fa14cc4 100644
--- a/python/tests/core/test_extract.py
+++ b/python/tests/core/test_extract.py
@@ -62,7 +62,7 @@ def test_transformation_for_empty_object_return_empty_object() -> None:
 
 
 def test_transformation_for_empty_array_return_empty_array() -> None:
-    assert resolve_template({}, [])  is None
+    assert resolve_template({}, []) is None
 
 
 def test_transformation_for_array_of_arrays_returns_flattened_array() -> None:

From 39c1a85951354b6e2ac764061a7653a75103e95b Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 20:16:03 +0700
Subject: [PATCH 10/11] Add python skipped test for preserve nulls in arrays

---
 python/tests/core/test_extract.py  | 14 ++++++++++++++
 ts/server/src/core/extract.spec.ts |  1 +
 2 files changed, 15 insertions(+)

diff --git a/python/tests/core/test_extract.py b/python/tests/core/test_extract.py
index fa14cc4..c095807 100644
--- a/python/tests/core/test_extract.py
+++ b/python/tests/core/test_extract.py
@@ -763,3 +763,17 @@ def test_merge_block_fails_on_merge_with_non_object() -> None:
                 "{% merge %}": [1, 2],
             },
         )
+
+
+@pytest.mark.skip(reason="https://github.com/beda-software/FHIRPathMappingLanguage/issues/30")
+def test_null_values_are_not_removed_from_array() -> None:
+    resource_with_empty_array_nullable = {
+        "root": {"resourceType": "Example", "list": [None, {"nested": None}, None]},
+    }
+
+    result = resolve_template(
+        resource_with_empty_array_nullable,
+        {"root": "{{ %Resource.root }}"},
+        {"Resource": resource_with_empty_array_nullable},
+    )
+    assert result == {"root": {"resourceType": "Example", "list": [None, {"nested": None}]}}
diff --git a/ts/server/src/core/extract.spec.ts b/ts/server/src/core/extract.spec.ts
index 07a48d0..bde149d 100644
--- a/ts/server/src/core/extract.spec.ts
+++ b/ts/server/src/core/extract.spec.ts
@@ -3,6 +3,7 @@ import { FPMLValidationError, resolveTemplate } from './extract';
 describe('Transformation', () => {
     const resource = { list: [{ key: 1 }, { key: 2 }, { key: 3 }] } as any;
 
+    // https://github.com/beda-software/FHIRPathMappingLanguage/issues/30
     test.skip('null values are not removed', () => {
         const resourceWithEmptyArrayNullable = {
             root: { resourceType: 'Example', list: [null, { nested: null }, null] },

From 699da1c1bfd74cf76014db3a10291853eb3e8643 Mon Sep 17 00:00:00 2001
From: Dmitry Shutov <dmitry.s@beda.software>
Date: Mon, 30 Jun 2025 20:25:30 +0700
Subject: [PATCH 11/11] [JS] resolveTemplate erturn null instead of undefined

same as python implementation. For better maintenance
---
 ts/server/src/core/extract.spec.ts | 14 +++++++-------
 ts/server/src/core/extract.ts      | 12 +++++-------
 2 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/ts/server/src/core/extract.spec.ts b/ts/server/src/core/extract.spec.ts
index bde149d..a42ef4b 100644
--- a/ts/server/src/core/extract.spec.ts
+++ b/ts/server/src/core/extract.spec.ts
@@ -95,11 +95,11 @@ describe('Transformation', () => {
     });
 
     test('for empty object return undefined', () => {
-        expect(resolveTemplate(resource, {})).toBeUndefined();
+        expect(resolveTemplate(resource, {})).toBeNull();
     });
 
     test('for empty array return undefined', () => {
-        expect(resolveTemplate(resource, [])).toBeUndefined();
+        expect(resolveTemplate(resource, [])).toBeNull();
     });
 
     test('for array of arrays returns flattened array', () => {
@@ -126,7 +126,7 @@ describe('Transformation', () => {
     });
 
     test('for object with undefined keys returns undefined', () => {
-        expect(resolveTemplate(resource, { key: undefined })).toBeUndefined();
+        expect(resolveTemplate(resource, { key: undefined })).toBeNull();
     });
 
     test('for object with undefined keys returns only defined keys', () => {
@@ -168,7 +168,7 @@ describe('Transformation', () => {
     });
 
     test('for empty array expression returns undefined', () => {
-        expect(resolveTemplate(resource, '{{ list.where($this = 0) }}')).toStrictEqual(undefined);
+        expect(resolveTemplate(resource, '{{ list.where($this = 0) }}')).toBeNull();
     });
 
     test('for empty array nullable expression returns null', () => {
@@ -187,7 +187,7 @@ describe('Transformation', () => {
                 resource,
                 '/Patient/{{ list.where($this = 0) }}/_history/{{ list.last() }}',
             ),
-        ).toStrictEqual(undefined);
+        ).toBeNull();
     });
 
     test('for empty array nullable template expression returns null', () => {
@@ -278,7 +278,7 @@ describe('Assign block', () => {
                 null,
                 true,
             ),
-        ).toBeUndefined();
+        ).toBeNull();
     });
 
     test('works with multiple vars as array of objects', () => {
@@ -520,7 +520,7 @@ describe('If block', () => {
                     "{% if key != 'value' %}": { nested: "{{ 'true' + key }}" },
                 },
             }),
-        ).toBeUndefined();
+        ).toBeNull();
     });
 
     test('returns null for falsy condition with nullable else branch', () => {
diff --git a/ts/server/src/core/extract.ts b/ts/server/src/core/extract.ts
index 5eef09a..94e88bd 100644
--- a/ts/server/src/core/extract.ts
+++ b/ts/server/src/core/extract.ts
@@ -50,7 +50,7 @@ export function resolveTemplate(
     fpOptions?: FPOptions,
     strict?: boolean,
 ): any {
-    return resolveTemplateRecur(
+    const result = resolveTemplateRecur(
         [],
         strict ? guardedResourceFactory(resource) : resource,
         template,
@@ -58,6 +58,9 @@ export function resolveTemplate(
         model,
         fpOptions,
     );
+
+    // NOTE: for synchronization with Python implementation
+    return result === undefined ? null : result;
 }
 
 function resolveTemplateRecur(
@@ -412,12 +415,7 @@ function iterateObject(startPath: Path, obj: any, context: Context, transform: T
             .flatMap((value, index) => {
                 const result = transform([...startPath, index], value, context);
 
-                return iterateObject(
-                    [...startPath, index],
-                    result.node,
-                    result.context,
-                    transform,
-                );
+                return iterateObject([...startPath, index], result.node, result.context, transform);
             })
             .filter((x) => x !== null && x !== undefined);
         return cleanedArray.length ? cleanedArray : undefined;