latch 2.40.4.dev4__tar.gz → 2.40.4.dev6__tar.gz

latch-2.40.4.dev6/PKG-INFO

@@ -0,0 +1,39 @@
+Metadata-Version: 2.1
+Name: latch
+Version: 2.40.4.dev6
+Summary: The Latch SDK
+Author-email: kenny@latch.bio
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.8,<3.12
+License-File: LICENSE
+Requires-Dist: kubernetes>=24.2.0
+Requires-Dist: pyjwt>=0.2.0
+Requires-Dist: requests>=2.28.1
+Requires-Dist: click>=8.0
+Requires-Dist: docker>=5.0
+Requires-Dist: paramiko>=3.2.0
+Requires-Dist: scp>=0.14.0
+Requires-Dist: boto3>=1.26.0
+Requires-Dist: tqdm>=4.63.0
+Requires-Dist: lytekit==0.15.6
+Requires-Dist: lytekitplugins-pods==0.6.2
+Requires-Dist: typing-extensions==4.7.1
+Requires-Dist: apscheduler==3.9.1
+Requires-Dist: gql==3.4.0
+Requires-Dist: graphql-core==3.2.3
+Requires-Dist: requests-toolbelt==0.10.1
+Requires-Dist: latch-sdk-gql==0.0.6
+Requires-Dist: latch-sdk-config==0.0.4
+Requires-Dist: python-dateutil>=2.8
+Requires-Dist: aioconsole==0.6.1
+Requires-Dist: asyncssh==2.13.2
+Requires-Dist: websockets==11.0.3
+Requires-Dist: watchfiles==0.19.0
+Provides-Extra: snakemake
+Requires-Dist: snakemake<7.30.2,>=7.18.0; extra == "snakemake"
+Requires-Dist: pulp<2.8,>=2.0; extra == "snakemake"
+Provides-Extra: pandas
+Requires-Dist: pandas>=2.0.0; extra == "pandas"

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch/account.py

@@ -258,12 +258,10 @@ class AccountUpdate:
 
         args = l.ArgumentNode()
         args.name = _name_node("input")
-        args.value = _json_value(
-            {
-                "argOwnerId": self.account.id,
-                "argDisplayNames": display_names,
-            }
-        )
+        args.value = _json_value({
+            "argOwnerId": self.account.id,
+            "argDisplayNames": display_names,
+        })
 
         res.alias = _name_node(f"upd{len(mutations)}")
         res.arguments = tuple([args])
@@ -299,11 +297,9 @@ class AccountUpdate:
 
         args = l.ArgumentNode()
         args.name = _name_node("input")
-        args.value = _json_value(
-            {
-                "argIds": ids,
-            }
-        )
+        args.value = _json_value({
+            "argIds": ids,
+        })
 
         res.alias = _name_node(f"upd{len(mutations)}")
         res.arguments = tuple([args])

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch/executions.py

@@ -15,13 +15,13 @@ pod_name_regex = re.compile(
         (?P<node_name>
             (
                 n
-                [0-9]+
+                [^\-]+
                 -
                 [0-9]+
                 -
             )*
             n
-            [0-9]+
+            [^\-]+
         )
         -
         (?P<retry>[0-9]+)

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch/registry/project.py

@@ -228,12 +228,10 @@ class ProjectUpdate:
 
         args = l.ArgumentNode()
         args.name = _name_node("input")
-        args.value = _json_value(
-            {
-                "argProjectId": self.project.id,
-                "argDisplayNames": display_names,
-            }
-        )
+        args.value = _json_value({
+            "argProjectId": self.project.id,
+            "argDisplayNames": display_names,
+        })
 
         res.alias = _name_node(f"upd{len(mutations)}")
         res.arguments = tuple([args])
@@ -267,11 +265,9 @@ class ProjectUpdate:
 
         args = l.ArgumentNode()
         args.name = _name_node("input")
-        args.value = _json_value(
-            {
-                "argIds": ids,
-            }
-        )
+        args.value = _json_value({
+            "argIds": ids,
+        })
 
         res.alias = _name_node(f"upd{len(mutations)}")
         res.arguments = tuple([args])

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch/registry/table.py

@@ -496,13 +496,11 @@ class TableUpdate:
 
         args = l.ArgumentNode()
         args.name = _name_node("input")
-        args.value = _json_value(
-            {
-                "argExperimentId": self.table.id,
-                "argNames": names,
-                "argData": _var_node(argDataVar),
-            }
-        )
+        args.value = _json_value({
+            "argExperimentId": self.table.id,
+            "argNames": names,
+            "argData": _var_node(argDataVar),
+        })
 
         res.alias = _name_node(f"upd{len(mutations)}")
         res.arguments = tuple([args])
@@ -537,12 +535,10 @@ class TableUpdate:
 
         args = l.ArgumentNode()
         args.name = _name_node("input")
-        args.value = _json_value(
-            {
-                "argExperimentId": self.table.id,
-                "argNames": names,
-            }
-        )
+        args.value = _json_value({
+            "argExperimentId": self.table.id,
+            "argNames": names,
+        })
 
         res.alias = _name_node(f"upd{len(mutations)}")
         res.arguments = tuple([args])
@@ -690,13 +686,11 @@ class TableUpdate:
 
         args = l.ArgumentNode()
         args.name = _name_node("input")
-        args.value = _json_value(
-            {
-                "argExperimentId": self.table.id,
-                "argKeys": keys,
-                "argTypes": _var_node(argTypesVar),
-            }
-        )
+        args.value = _json_value({
+            "argExperimentId": self.table.id,
+            "argKeys": keys,
+            "argTypes": _var_node(argTypesVar),
+        })
 
         res.alias = _name_node(f"upd{len(mutations)}")
         res.arguments = tuple([args])

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch/resources/dynamic.py

@@ -1,7 +1,6 @@
-import json
 import os
 from dataclasses import dataclass
-from typing import Any, Callable, Dict, Union
+from typing import Any, Callable, Dict, Optional, Union
 
 import gql
 from flytekit.configuration import SerializationSettings
@@ -63,9 +62,15 @@ def _override_task_resources(task_config: Pod) -> None:
 
 
 def _dynamic_resource_task(
-    cpu: Union[int, Callable], memory: Union[int, Callable], disk: Union[int, Callable]
+    dynamic_func: Optional[Callable],
+    cpu: Union[int, Callable],
+    memory: Union[int, Callable],
+    disk: Union[int, Callable],
 ):
     def f(**kwargs):
+        if dynamic_func is not None:
+            dynamic_func(**kwargs)
+
         res: Dict[str, int] = {
             "cpu": cpu(**kwargs) if callable(cpu) else cpu,
             "memory": memory(**kwargs) if callable(memory) else memory,
@@ -85,6 +90,7 @@ def _dynamic_resource_task(
 
 @dataclass(frozen=True)
 class DynamicTaskConfig:
+    dynamic_func: Optional[Callable]
     cpu: Union[Callable, int]
     memory: Union[Callable, int]
     storage: Union[Callable, int]
@@ -93,7 +99,10 @@ class DynamicTaskConfig:
 
 class DynamicPythonFunctionTask(PodFunctionTask):
     def __init__(
-        self, task_config: DynamicTaskConfig, task_function: Callable, **kwargs
+        self,
+        task_config: DynamicTaskConfig,
+        task_function: Callable,
+        **kwargs,
     ):
         # validate that the task function inputs are the same as the resource functions
         for resource in [task_config.cpu, task_config.memory, task_config.storage]:
@@ -113,7 +122,10 @@ class DynamicPythonFunctionTask(PodFunctionTask):
                     )
 
         self._pre_task_function = _dynamic_resource_task(
-            task_config.cpu, task_config.memory, task_config.storage
+            task_config.dynamic_func,
+            task_config.cpu,
+            task_config.memory,
+            task_config.storage,
         )
 
         super().__init__(

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch/resources/tasks.py

@@ -26,7 +26,7 @@ exported decorators.
 
 import datetime
 import functools
-from typing import Callable, Union
+from typing import Callable, Optional, Union
 from warnings import warn
 
 from flytekit import task
@@ -470,6 +470,9 @@ def custom_task(
     *,
     storage_gib: Union[Callable, int] = 500,
     timeout: Union[datetime.timedelta, int] = 0,
+    cache: bool = False,
+    retries: int = 0,
+    pre_execute: Optional[Callable] = None,
 ):
     """Returns a custom task configuration requesting
     the specified CPU/RAM allocations
@@ -481,13 +484,20 @@ def custom_task(
     """
     if callable(cpu) or callable(memory) or callable(storage_gib):
         task_config = DynamicTaskConfig(
+            dynamic_func=pre_execute,
             cpu=cpu,
             memory=memory,
             storage=storage_gib,
-            pod_config=_get_small_pod(),
+            pod_config=_custom_task_config(1, 1, 50),
+        )
+        return functools.partial(
+            task, task_config=task_config, timeout=timeout, cache=cache, retries=retries
         )
-        return functools.partial(task, task_config=task_config, timeout=timeout)
 
     return functools.partial(
-        task, task_config=_custom_task_config(cpu, memory, storage_gib), timeout=timeout
+        task,
+        task_config=_custom_task_config(cpu, memory, storage_gib),
+        timeout=timeout,
+        cache=cache,
+        retries=retries,
     )

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch/verified/deseq2.py

@@ -19,17 +19,13 @@ def deseq2_wf(
     raw_count_table: Optional[
         Annotated[
             LatchFile,
-            FlyteAnnotation(
-                {
-                    "_tmp_hack_deseq2": "counts_table",
-                    "rules": [
-                        {
-                            "regex": r".*\.(csv|tsv|xlsx)$",
-                            "message": "Expected a CSV, TSV, or XLSX file",
-                        }
-                    ],
-                }
-            ),
+            FlyteAnnotation({
+                "_tmp_hack_deseq2": "counts_table",
+                "rules": [{
+                    "regex": r".*\.(csv|tsv|xlsx)$",
+                    "message": "Expected a CSV, TSV, or XLSX file",
+                }],
+            }),
         ]
     ] = None,
     raw_count_tables: List[LatchFile] = [],
@@ -44,17 +40,13 @@ def deseq2_wf(
     conditions_table: Optional[
         Annotated[
             LatchFile,
-            FlyteAnnotation(
-                {
-                    "_tmp_hack_deseq2": "design_matrix",
-                    "rules": [
-                        {
-                            "regex": r".*\.(csv|tsv|xlsx)$",
-                            "message": "Expected a CSV, TSV, or XLSX file",
-                        }
-                    ],
-                }
-            ),
+            FlyteAnnotation({
+                "_tmp_hack_deseq2": "design_matrix",
+                "rules": [{
+                    "regex": r".*\.(csv|tsv|xlsx)$",
+                    "message": "Expected a CSV, TSV, or XLSX file",
+                }],
+            }),
         ]
     ] = None,
     design_matrix_sample_id_column: Optional[
@@ -62,12 +54,10 @@ def deseq2_wf(
     ] = None,
     design_formula: Annotated[
         List[List[str]],
-        FlyteAnnotation(
-            {
-                "_tmp_hack_deseq2": "design_formula",
-                "_tmp_hack_deseq2_allow_clustering": True,
-            }
-        ),
+        FlyteAnnotation({
+            "_tmp_hack_deseq2": "design_formula",
+            "_tmp_hack_deseq2_allow_clustering": True,
+        }),
     ] = [],
     number_of_genes_to_plot: int = 30,
 ) -> LatchDir: ...

latch-2.40.4.dev6/latch.egg-info/PKG-INFO

@@ -0,0 +1,39 @@
+Metadata-Version: 2.1
+Name: latch
+Version: 2.40.4.dev6
+Summary: The Latch SDK
+Author-email: kenny@latch.bio
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.8,<3.12
+License-File: LICENSE
+Requires-Dist: kubernetes>=24.2.0
+Requires-Dist: pyjwt>=0.2.0
+Requires-Dist: requests>=2.28.1
+Requires-Dist: click>=8.0
+Requires-Dist: docker>=5.0
+Requires-Dist: paramiko>=3.2.0
+Requires-Dist: scp>=0.14.0
+Requires-Dist: boto3>=1.26.0
+Requires-Dist: tqdm>=4.63.0
+Requires-Dist: lytekit==0.15.6
+Requires-Dist: lytekitplugins-pods==0.6.2
+Requires-Dist: typing-extensions==4.7.1
+Requires-Dist: apscheduler==3.9.1
+Requires-Dist: gql==3.4.0
+Requires-Dist: graphql-core==3.2.3
+Requires-Dist: requests-toolbelt==0.10.1
+Requires-Dist: latch-sdk-gql==0.0.6
+Requires-Dist: latch-sdk-config==0.0.4
+Requires-Dist: python-dateutil>=2.8
+Requires-Dist: aioconsole==0.6.1
+Requires-Dist: asyncssh==2.13.2
+Requires-Dist: websockets==11.0.3
+Requires-Dist: watchfiles==0.19.0
+Provides-Extra: snakemake
+Requires-Dist: snakemake<7.30.2,>=7.18.0; extra == "snakemake"
+Requires-Dist: pulp<2.8,>=2.0; extra == "snakemake"
+Provides-Extra: pandas
+Requires-Dist: pandas>=2.0.0; extra == "pandas"

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch.egg-info/SOURCES.txt

@@ -148,9 +148,6 @@ latch_cli/services/init/common/.dockerignore
 latch_cli/services/init/example_conda/__init__.py
 latch_cli/services/init/example_conda/conda_task.py
 latch_cli/services/init/example_conda/environment.yaml
-latch_cli/services/init/example_docker/.__init__.py.swn
-latch_cli/services/init/example_docker/.__init__.py.swo
-latch_cli/services/init/example_docker/.__init__.py.swp
 latch_cli/services/init/example_docker/__init__.py
 latch_cli/services/init/example_docker/task.py
 latch_cli/services/init/example_nextflow/main.nf

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch_cli/centromere/utils.py

@@ -2,6 +2,7 @@ import builtins
 import contextlib
 import os
 import random
+import shutil
 import string
 import sys
 import tempfile
@@ -261,6 +262,9 @@ class MaybeRemoteDir:
             return
 
         if self._tempdir is not None and not isinstance(self._tempdir, str):
+            if os.environ.get("LATCH_SAVE_PROTO") is not None:
+                shutil.copytree(Path(self._tempdir.name), Path.cwd() / "protos")
+
             self._tempdir.cleanup()
 
 

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch_cli/extras/common/serialize.py

@@ -1,3 +1,4 @@
+import os
 import sys
 from dataclasses import fields
 from pathlib import Path
@@ -302,8 +303,11 @@ def serialize(
     image_name: str,
     dkr_repo: str,
     *,
-    write_spec: bool = False,
+    write_spec: Optional[bool] = None,
 ):
+    if write_spec is None:
+        write_spec = os.environ.get("LATCH_DUMP_SPEC") is not None
+
     image_name_no_version, version = image_name.split(":")
     default_img = Image(
         name=image_name,

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch_cli/extras/nextflow/build.py

@@ -29,7 +29,7 @@ from latch_cli.extras.nextflow.tasks.base import NextflowBaseTask, NFTaskType
 
 from ...click_utils import italic
 from ...menus import select_tui
-from ...utils import current_workspace, identifier_from_str
+from ...utils import identifier_from_str
 from ..common.serialize import binding_from_python
 from ..common.utils import is_samplesheet_param, reindent
 from .dag import DAG, VertexType
@@ -50,7 +50,10 @@ def get_node_name(vertex_id: str) -> str:
 
 
 def build_from_nextflow_dag(
-    wf: NextflowWorkflow, *, execution_profile: Optional[str] = None
+    wf: NextflowWorkflow,
+    *,
+    execution_profile: Optional[str] = None,
+    ephemeral_storage_gib: int = 500,
 ):
     global_start_node = Node(
         id=_common_constants.GLOBAL_INPUT_NODE_ID,
@@ -105,18 +108,22 @@ def build_from_nextflow_dag(
             else:
                 input_name = f"channel_{dep.id}"
 
-                output_name = "res"
+                dep_output_name = "res"
                 if len(dep.outputNames) > 0:
                     idx = int(edge.label or "0")
                     input_name = f"{input_name}_{idx}"
-                    output_name = dep.outputNames[idx]
+                    dep_output_name = dep.outputNames[idx]
 
                 if vertex.type == VertexType.Merge:
-                    merge_sources[output_name].append(input_name)
+                    vertex_output_name = "res"
+                    if len(vertex.outputNames) > 0:
+                        vertex_output_name = dep_output_name
+
+                    merge_sources[vertex_output_name].append(input_name)
 
                 task_inputs[input_name] = Optional[str]
 
-                node = NodeOutput(node=node_map[dep.id], var=output_name)
+                node = NodeOutput(node=node_map[dep.id], var=dep_output_name)
 
             task_bindings.append(
                 literals_models.Binding(
@@ -177,6 +184,7 @@ def build_from_nextflow_dag(
                 wf=wf,
                 cpu=vertex.cpu,
                 memory=vertex.memoryBytes,
+                storage_gib=ephemeral_storage_gib,
             )
 
             wf.nextflow_tasks.append(process_task)
@@ -220,9 +228,21 @@ def build_from_nextflow_dag(
                                 ),
                             ).ref
                         ),
-                    )
+                    ),
+                    literals_models.Binding(
+                        var="is_skipped",
+                        binding=literals_models.BindingData(
+                            promise=Promise(
+                                var="is_skipped",
+                                val=NodeOutput(
+                                    node=pre_adapter_node,
+                                    var="is_skipped",
+                                ),
+                            ).ref
+                        ),
+                    ),
                 ],
-                upstream_nodes=[mapped_process_node],
+                upstream_nodes=[mapped_process_node, pre_adapter_node],
                 flyte_entity=post_adapter_task,
             )
 
@@ -396,6 +416,7 @@ def build_nf_wf(
     *,
     redownload_dependencies: bool = False,
     execution_profile: Optional[str] = None,
+    ephemeral_storage_gib: int = 500,
 ) -> NextflowWorkflow:
     ensure_nf_dependencies(pkg_root, force_redownload=redownload_dependencies)
 
@@ -474,7 +495,11 @@ def build_nf_wf(
 
     wf = NextflowWorkflow(pkg_root, nf_script, version, main_dag)
 
-    build_from_nextflow_dag(wf, execution_profile=execution_profile)
+    build_from_nextflow_dag(
+        wf,
+        execution_profile=execution_profile,
+        ephemeral_storage_gib=ephemeral_storage_gib,
+    )
 
     return wf
 

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch_cli/extras/nextflow/channel.py

@@ -64,8 +64,16 @@ def get_mapper_inputs(
 NT = TypeVar("NT", bound=NamedTuple)
 
 
-def get_mapper_outputs(adapter_output_cls: Type[NT], mapper_outputs: List[DC]) -> NT:
-    kwargs: Dict[str, str] = {}
+def get_mapper_outputs(
+    adapter_output_cls: Type[NT], mapper_outputs: List[DC], is_skipped: bool
+) -> NT:
+
+    kwargs: Dict[str, Optional[str]] = {}
+    if is_skipped:
+        for f in adapter_output_cls._fields:
+            kwargs[f] = None
+
+        return adapter_output_cls(**kwargs)
 
     if len(mapper_outputs) == 1:
         output = mapper_outputs[0]

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch_cli/extras/nextflow/file_persistence.py

@@ -1,8 +1,8 @@
+import json
 import os
-import shutil
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Dict, List, Optional, Set, Union
+from typing import Dict, List, Optional, Set, Union, cast
 from urllib.parse import urlparse
 
 import click
@@ -17,6 +17,7 @@ from latch.ldata.type import LDataNodeType
 from latch.types.directory import LatchDir
 from latch.types.file import LatchFile
 from latch_cli.utils import urljoins
+from latch_cli.utils.path import is_remote_path
 
 JSONValue: TypeAlias = Union[
     int,
@@ -76,7 +77,17 @@ def _extract_paths(parameter: JSONValue, res: List[PathData]):
             return
 
         res.append(PathData(parameter=parameter, local=local, remote=remote))
+    elif "string" in parameter:
+        v = parameter["string"]
+        assert isinstance(v, str)
+
+        if not is_remote_path(v):
+            return
 
+        parameter["path"] = v
+        del parameter["string"]
+
+        _extract_paths(parameter, res)
     elif "list" in parameter:
         v = parameter["list"]
         assert isinstance(v, List)
@@ -230,5 +241,18 @@ def upload_files(channels: Dict[str, List[JSONValue]], outdir: LatchDir):
         local_to_remote[local] = remote
         data.parameter["remote"] = remote
 
+    published_files: List[str] = []
+    try:
+        with open(".latch/published.json", "r") as f:
+            data = f.read()
+        conf = json.loads(data)
+        published_files = conf.get("files", [])
+    except FileNotFoundError:
+        pass
+
+    for file in published_files:
+        relative_path = Path(file).relative_to(Path.home())
+        local_to_remote[file] = urljoins(remote_parent, str(relative_path))
+
     for local, remote in local_to_remote.items():
         _upload(local, remote)

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch_cli/extras/nextflow/serialize.py

@@ -3,10 +3,10 @@ from typing import cast
 import gql
 from latch_sdk_gql.execute import execute
 
+from latch.utils import current_workspace
 from latch_cli.extras.common.serialize import serialize
 from latch_cli.extras.nextflow.tasks.base import NextflowBaseTask
 from latch_cli.extras.nextflow.workflow import NextflowWorkflow
-from latch_cli.utils import current_workspace
 
 
 def serialize_nf(

{latch-2.40.4.dev4 → latch-2.40.4.dev6}/latch_cli/extras/nextflow/tasks/adapters.py

@@ -66,7 +66,7 @@ class NextflowProcessPreAdapterTask(NextflowBaseTask):
 
         super().__init__(
             inputs,
-            {"default": List[self.dataclass]},
+            {"default": List[self.dataclass], "is_skipped": bool},
             id,
             name,
             branches,
@@ -96,6 +96,7 @@ class NextflowProcessPreAdapterTask(NextflowBaseTask):
 
             class Res_{self.id}(NamedTuple):
                 default: {type_repr(output_typ)}
+                is_skipped: bool
 
             """,
             0,
@@ -114,7 +115,9 @@ class NextflowProcessPreAdapterTask(NextflowBaseTask):
         return res
 
     def get_fn_return_stmt(self):
-        return reindent(f"return Res_{self.id}(default=result)", 1)
+        return reindent(
+            f"return Res_{self.id}(default=result, is_skipped = not cond)", 1
+        )
 
     def get_fn_code(self, nf_script_path_in_container: Path):
         code_block = self.get_fn_interface()
@@ -173,7 +176,7 @@ class NextflowProcessPostAdapterTask(NextflowBaseTask):
         self.dataclass = dataclass_from_python_params(outputs, id)
 
         super().__init__(
-            {"default": List[self.dataclass]},
+            {"default": List[self.dataclass], "is_skipped": bool},
             outputs,
             id,
             name,
@@ -210,7 +213,8 @@ class NextflowProcessPostAdapterTask(NextflowBaseTask):
             rf"""
             @task(cache=True)
             def {self.name}(
-                default: List[Dataclass_{self.id}]
+                default: List[Dataclass_{self.id}],
+                is_skipped: bool,
             ) -> Res{self.name}:
             """,
             0,
@@ -221,7 +225,7 @@ class NextflowProcessPostAdapterTask(NextflowBaseTask):
     def get_fn_return_stmt(self):
         return reindent(
             rf"""
-            return get_mapper_outputs(Res{self.name}, default)
+            return get_mapper_outputs(Res{self.name}, default, is_skipped)
             """,
             1,
         )