latch 2.40.4.dev2__tar.gz → 2.40.4.dev3__tar.gz

{latch-2.40.4.dev2/latch.egg-info → latch-2.40.4.dev3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.40.4.dev2
+Version: 2.40.4.dev3
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.40.4.dev2 → latch-2.40.4.dev3}/latch/types/metadata.py

@@ -4,7 +4,9 @@ from enum import Enum
 from pathlib import Path
 from textwrap import indent
 from typing import (
+    Annotated,
     Any,
+    Callable,
     ClassVar,
     Collection,
     Dict,
@@ -478,6 +480,10 @@ class NextflowParameter(Generic[T], LatchParameter):
     """
     default: Optional[T] = None
 
+    def __post_init__(self):
+        if self.samplesheet is True:
+            self.type = Annotated[self.type, "samplesheet"]
+
 
 @dataclass
 class NextflowFileParameter(NextflowParameter[Union[LatchFile, LatchDir]]):

{latch-2.40.4.dev2 → latch-2.40.4.dev3/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.40.4.dev2
+Version: 2.40.4.dev3
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.40.4.dev2 → latch-2.40.4.dev3}/latch_cli/extras/common/utils.py

@@ -37,13 +37,23 @@ def is_blob_type(typ: Type) -> TypeGuard[Union[Type[LatchFile], Type[LatchDir]]]
 
 
 def is_downloadable_blob_type(typ: Type):
-    if not is_blob_type(typ):
+    if not is_blob_type(typ) or typ is LatchOutputDir:
         return False
 
-    return typ is not LatchOutputDir
+    origin = get_origin(typ)
+    if origin is not None:
+        return all([
+            is_downloadable_blob_type(sub_typ) or sub_typ is type(None)
+            for sub_typ in get_args(typ)
+        ])
+
+    return True
 
 
 def type_repr(t: Type, *, add_namespace: bool = False) -> str:
+    if get_origin(t) == Annotated:
+        return type_repr(get_args(t)[0])
+
     if getattr(t, "__name__", None) == "NoneType":
         return "None"
 
@@ -70,3 +80,7 @@ def type_repr(t: Type, *, add_namespace: bool = False) -> str:
         )
 
     return getattr(t, "__name__", repr(t))
+
+
+def is_samplesheet_param(t: Type) -> bool:
+    return get_origin(t) == Annotated and get_args(t)[-1] == "samplesheet"

{latch-2.40.4.dev2 → latch-2.40.4.dev3}/latch_cli/extras/nextflow/build.py

@@ -31,7 +31,7 @@ from ...click_utils import italic
 from ...menus import select_tui
 from ...utils import current_workspace, identifier_from_str
 from ..common.serialize import binding_from_python
-from ..common.utils import reindent
+from ..common.utils import is_samplesheet_param, reindent
 from .dag import DAG, VertexType
 from .tasks.adapters import (
     NextflowProcessPostAdapterTask,
@@ -523,6 +523,14 @@ def generate_nf_entrypoint(
         0,
     )
 
+    if any([is_samplesheet_param(t) for t in wf.python_interface.inputs.values()]):
+        preamble += reindent(
+            r"""
+            from latch_metadata.parameters import  construct_samplesheet
+            """,
+            0,
+        )
+
     for t in wf.python_interface.inputs.values():
         preamble += get_preamble(t, make_optionals=True)
 

{latch-2.40.4.dev2 → latch-2.40.4.dev3}/latch_cli/extras/nextflow/tasks/operator.py

@@ -1,12 +1,12 @@
 import json
 from pathlib import Path
-from typing import Dict, List, Mapping, Type
+from typing import Annotated, Dict, List, Mapping, Type, get_args, get_origin
 
 from latch.types.directory import LatchDir
 from latch.types.file import LatchFile
 from latch.types.metadata import ParameterType
 
-from ...common.utils import is_blob_type, reindent, type_repr
+from ...common.utils import is_blob_type, is_samplesheet_param, reindent, type_repr
 from ..workflow import NextflowWorkflow
 from .base import NextflowBaseTask, NFTaskType
 
@@ -151,6 +151,13 @@ class NextflowOperatorTask(NextflowBaseTask):
                     """,
                     2,
                 )
+            elif is_samplesheet_param(typ):
+                code_block += reindent(
+                    f"""
+                    {k} = construct_samplesheet({k})
+                    """,
+                    2,
+                )
 
         # todo(ayush): figure out how to make this work
         do_file_io = False

{latch-2.40.4.dev2 → latch-2.40.4.dev3}/latch_cli/extras/nextflow/tasks/process.py

@@ -1,13 +1,18 @@
 import json
 from dataclasses import fields, is_dataclass
 from pathlib import Path
-from typing import List, Mapping, Optional, Type
+from typing import Annotated, List, Mapping, Optional, Type
+
+try:
+    from typing import get_args, get_origin
+except ImportError:
+    from typing_extensions import get_args, get_origin
 
 from latch.types.directory import LatchDir
 from latch.types.file import LatchFile
 from latch.types.metadata import ParameterType
 
-from ...common.utils import is_blob_type, reindent, type_repr
+from ...common.utils import is_blob_type, is_samplesheet_param, reindent, type_repr
 from ..workflow import NextflowWorkflow
 from .base import NextflowBaseTask, NFTaskType
 
@@ -165,6 +170,13 @@ class NextflowProcessTask(NextflowBaseTask):
                     """,
                     1,
                 )
+            elif is_samplesheet_param(typ):
+                code_block += reindent(
+                    f"""
+                    {k} = construct_samplesheet({k})
+                    """,
+                    1,
+                )
 
         if self.script_path.resolve() != self.wf.nf_script.resolve():
             stem = self.script_path.resolve().relative_to(self.wf.pkg_root.resolve())

{latch-2.40.4.dev2 → latch-2.40.4.dev3}/latch_cli/main.py

@@ -81,8 +81,6 @@ def main():
             fg="yellow",
         )
 
-    # crash_handler.init()
-
 
 """
 LOGIN COMMANDS

{latch-2.40.4.dev2 → latch-2.40.4.dev3}/latch_cli/services/register/utils.py

@@ -102,7 +102,6 @@ def build_image(
         tag=f"{ctx.dkr_repo}/{image_name}",
         decode=True,
     )
-
     return build_logs
 
 

{latch-2.40.4.dev2 → latch-2.40.4.dev3}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.40.4.dev2",
+    version="v2.40.4.dev3",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),