latch 2.40.4.dev8__tar.gz → 2.40.4.dev10__tar.gz

{latch-2.40.4.dev8/latch.egg-info → latch-2.40.4.dev10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.40.4.dev8
+Version: 2.40.4.dev10
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.40.4.dev8 → latch-2.40.4.dev10}/latch/types/directory.py

@@ -115,8 +115,10 @@ class LatchDir(FlyteDirectory):
 
         if is_valid_url(self.path) and remote_path is None:
             self._remote_directory = self.path
+            self.raw_remote_path = str(path)
         else:
             self._remote_directory = None if remote_path is None else str(remote_path)
+            self.raw_remote_path = self._remote_directory
 
         if kwargs.get("downloader") is not None:
             super().__init__(self.path, kwargs["downloader"], self._remote_directory)

{latch-2.40.4.dev8 → latch-2.40.4.dev10/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.40.4.dev8
+Version: 2.40.4.dev10
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.40.4.dev8 → latch-2.40.4.dev10}/latch.egg-info/SOURCES.txt

@@ -136,7 +136,13 @@ latch_cli/services/execute/utils.py
 latch_cli/services/init/__init__.py
 latch_cli/services/init/init.py
 latch_cli/services/init/__pycache__/__init__.cpython-310.pyc
+latch_cli/services/init/__pycache__/__init__.cpython-311.pyc
+latch_cli/services/init/__pycache__/__init__.cpython-38.pyc
+latch_cli/services/init/__pycache__/__init__.cpython-39.pyc
 latch_cli/services/init/__pycache__/init.cpython-310.pyc
+latch_cli/services/init/__pycache__/init.cpython-311.pyc
+latch_cli/services/init/__pycache__/init.cpython-38.pyc
+latch_cli/services/init/__pycache__/init.cpython-39.pyc
 latch_cli/services/init/assemble_and_sort/.env
 latch_cli/services/init/assemble_and_sort/LICENSE
 latch_cli/services/init/assemble_and_sort/README.md
@@ -144,21 +150,25 @@ latch_cli/services/init/assemble_and_sort/__init__.py
 latch_cli/services/init/assemble_and_sort/assemble.py
 latch_cli/services/init/assemble_and_sort/sort.py
 latch_cli/services/init/assemble_and_sort/system-requirements.txt
+latch_cli/services/init/assemble_and_sort/__pycache__/__init__.cpython-310.pyc
 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_conda/__pycache__/__init__.cpython-310.pyc
 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_cli/services/init/example_nextflow/nextflow.config
 latch_cli/services/init/example_nextflow/workflow.nf
+latch_cli/services/init/example_nf_integration/latch_metadata/__pycache__/__init__.cpython-311.pyc
 latch_cli/services/init/example_nfcore/Dockerfile
 latch_cli/services/init/example_nfcore/__init__.py
 latch_cli/services/init/example_nfcore/task.py
 latch_cli/services/init/example_r/__init__.py
 latch_cli/services/init/example_r/environment.R
 latch_cli/services/init/example_r/r_task.py
+latch_cli/services/init/example_r/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/init/example_snakemake/Dockerfile
 latch_cli/services/init/example_snakemake/Snakefile
 latch_cli/services/init/example_snakemake/config.yaml
@@ -171,6 +181,7 @@ latch_cli/services/init/template/LICENSE
 latch_cli/services/init/template/README.md
 latch_cli/services/init/template/__init__.py
 latch_cli/services/init/template/task.py
+latch_cli/services/init/template/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/register/__init__.py
 latch_cli/services/register/constants.py
 latch_cli/services/register/register.py

{latch-2.40.4.dev8 → latch-2.40.4.dev10}/latch_cli/extras/common/config/utils.py

@@ -1,4 +1,5 @@
 from dataclasses import fields, is_dataclass, make_dataclass
+from enum import Enum
 from typing import Any, Dict, List, Optional, Type, Union, get_args, get_origin
 
 from flytekit.core.annotation import FlyteAnnotation
@@ -220,6 +221,13 @@ def get_preamble(typ: Type, *, make_optionals: bool = False) -> str:
             [get_preamble(t, make_optionals=make_optionals) for t in get_args(typ)]
         )
 
+    if issubclass(typ, Enum):
+        lines = [f"class {typ.__name__}(Enum):"]
+        for k, v in typ._member_map_.items():
+            lines.append(f"    {k} = {repr(v.value)}")
+
+        return "\n".join(lines) + "\n\n\n"
+
     assert is_dataclass(typ), typ
 
     preambles = []

{latch-2.40.4.dev8 → latch-2.40.4.dev10}/latch_cli/extras/nextflow/build.py

@@ -531,6 +531,7 @@ def generate_nf_entrypoint(
 
         from flytekit.extras.persistence import LatchPersistence
         from latch_cli.extras.nextflow.file_persistence import download_files, upload_files
+        from latch_cli.extras.nextflow.workflow import get_flags
         from latch_cli.extras.nextflow.channel import get_mapper_inputs, get_boolean_value, get_mapper_outputs
         from latch_cli.utils import check_exists_and_rename, get_parameter_json_value, urljoins
         from latch_cli.utils.workflow import _override_task_status
@@ -551,7 +552,7 @@ def generate_nf_entrypoint(
     if any([is_samplesheet_param(t) for t in wf.python_interface.inputs.values()]):
         preamble += reindent(
             r"""
-            from latch_metadata.parameters import  construct_samplesheet
+            from latch_metadata.parameters import construct_samplesheet
             """,
             0,
         )

{latch-2.40.4.dev8 → latch-2.40.4.dev10}/latch_cli/extras/nextflow/tasks/operator.py

@@ -129,9 +129,6 @@ class NextflowOperatorTask(NextflowBaseTask):
             "lib",
         ]
 
-        for flag, val in self.wf.flags_to_params.items():
-            run_task_entrypoint.extend([flag, str(val)])
-
         code_block += reindent(
             """
             wf_paths = {}
@@ -191,23 +188,32 @@ class NextflowOperatorTask(NextflowBaseTask):
         upload_str = ""
         download_str = ""
         if do_file_io:
-            download_str = rf"""download_files(channel_vals, LatchDir({repr(self.wf.output_directory.remote_path)}))"""
-            upload_str = rf"""upload_files(out_channels, LatchDir({repr(self.wf.output_directory.remote_path)}))"""
+            download_str = rf"""download_files(channel_vals, LatchDir({repr(self.wf.output_directory.raw_remote_path)}))"""
+            upload_str = rf"""upload_files(out_channels, LatchDir({repr(self.wf.output_directory.raw_remote_path)}))"""
 
         if self.script_path.resolve() != self.wf.nf_script.resolve():
             stem = self.script_path.resolve().relative_to(self.wf.pkg_root.resolve())
             run_task_entrypoint[2] = str(Path("/root") / stem)
             run_task_entrypoint.extend(["-entry", self.calling_subwf_name])
 
+        flag_args = {}
+        for param in self.wf_inputs:
+            key = param[len("wf_") :]
+            flag_args[key] = param
+
         code_block += reindent(
             rf"""
+
+
                     channel_vals = [{", ".join([f"json.loads({x})" for x in self.channel_inputs])}]
 
                     {download_str}
 
+                    flags = get_flags(wf_paths, {", ".join([f"{k}={v}" for k, v in flag_args.items()])})
+
                     try:
                         subprocess.run(
-                            [{', '.join([f"str({x})" if x.startswith("wf_") else repr(x) for x in run_task_entrypoint])}],
+                            [{', '.join([repr(x) for x in run_task_entrypoint])}, *flags],
                             env={{
                                 **os.environ,
                                 "LATCH_CONFIG_DIR_OVERRIDE": str(Path.cwd()),

{latch-2.40.4.dev8 → latch-2.40.4.dev10}/latch_cli/extras/nextflow/tasks/process.py

@@ -97,9 +97,6 @@ class NextflowProcessTask(NextflowBaseTask):
         if self.execution_profile is not None:
             run_task_entrypoint.extend(["-profile", self.execution_profile])
 
-        for flag, val in self.wf.flags_to_params.items():
-            run_task_entrypoint.extend([flag, str(val)])
-
         for k, typ in self.wf_inputs.items():
             code_block += reindent(
                 f"""
@@ -177,17 +174,24 @@ class NextflowProcessTask(NextflowBaseTask):
                 0,
             )
 
+        flag_args = {}
+        for param in self.wf_inputs:
+            key = param[len("wf_") :]
+            flag_args[key] = param
+
         code_block += reindent(
             rf"""
 
             channel_vals = [{','.join([f"json.loads(default.{x})" for x in self.channel_inputs])}]
 
             if not {pre_execute}:
-                download_files(channel_vals, LatchDir({repr(self.wf.output_directory.remote_path)}))
+                download_files(channel_vals, LatchDir({repr(self.wf.output_directory.raw_remote_path)}))
+
+            flags = get_flags(wf_paths, {", ".join([f"{k}={v}" for k, v in flag_args.items()])})
 
             try:
                 subprocess.run(
-                    [{','.join([f"str({x})" if x.startswith("wf_") else repr(x) for x in run_task_entrypoint])}],
+                    [{','.join([repr(x) for x in run_task_entrypoint])}, *flags],
                     env={{
                         **os.environ,
                         "LATCH_BIN_DIR_OVERRIDE": str(Path.cwd() / "bin"),
@@ -301,7 +305,7 @@ class NextflowProcessTask(NextflowBaseTask):
             print(out_channels)
 
             publish_dir = {self.wf.publish_dir_param}
-            upload_files(out_channels, LatchDir({repr(self.wf.output_directory.remote_path)}), publish_dir)
+            upload_files(out_channels, LatchDir({repr(self.wf.output_directory.raw_remote_path)}), publish_dir)
 
             out_channels = {{k: json.dumps(v) for k, v in out_channels.items()}}
 

{latch-2.40.4.dev8 → latch-2.40.4.dev10}/latch_cli/extras/nextflow/workflow.py

@@ -1,6 +1,7 @@
 from dataclasses import fields, is_dataclass
+from enum import Enum
 from pathlib import Path
-from typing import Any, Dict, List, Tuple, Type
+from typing import Any, Dict, List, Tuple, Type, TypeVar, Union, get_args, get_origin
 
 import click
 from flytekit.core.class_based_resolver import ClassStorageTaskResolver
@@ -15,6 +16,7 @@ from flytekit.core.workflow import (
 from flytekit.exceptions import scopes as exception_scopes
 
 from latch.types import metadata
+from latch.types.file import LatchFile
 from latch_cli.extras.common.utils import (
     is_blob_type,
     is_downloadable_blob_type,
@@ -23,30 +25,52 @@ from latch_cli.extras.common.utils import (
 
 from .dag import DAG
 
-# def _get_flattened_inputs(
-#     key: str, t: Type, val: Any, inputs: Dict[str, Tuple[Type, Any]]
-# ):
-#     if not is_dataclass(t):
-#         inputs[key] = (t, val)
-#         return
 
-#     for f in fields(t):
-#         v = val
-#         if val is not None:
-#             v = getattr()
+def get_flags(wf_paths: Dict[str, Path], **kwargs) -> List[str]:
+    assert metadata._nextflow_metadata is not None
 
+    flags = []
+    for key in kwargs.keys():
+        param = metadata._nextflow_metadata.parameters.get(key)
+        assert param is not None, f"Param {key} is not a workflow parameter"
 
-def _get_flags_to_params(key: str, t: Type, flags: Dict[str, str]):
-    if is_output_dir(t):
+        t = param.type
+        if param.samplesheet:
+            t = LatchFile
+            wf_paths[f"wf_{key}"] = kwargs[key]
+
+        v = kwargs[key]
+
+        _add_flags(key, t, v, flags, wf_paths)
+
+    return flags
+
+
+T = TypeVar("T")
+
+
+def _add_flags(key: str, t: Type[T], v: T, flags: List[str], wf_paths: Dict[str, Path]):
+    if v is None or is_output_dir(t):
         return
 
-    if is_blob_type(t):
-        flags[f"--{key}"] = f"wf_paths['wf_{key}']"
+    if get_origin(t) is Union:
+        for arg in get_args(t):
+            if isinstance(v, arg):
+                _add_flags(key, arg, v, flags, wf_paths)
+                return
+
+    if t is bool:
+        if v:
+            flags.append(f"--{key}")
+    elif is_blob_type(t):
+        flags.extend([f"--{key}", str(wf_paths[f"wf_{key}"])])
     elif is_dataclass(t):
         for f in fields(t):
-            _get_flags_to_params(f"{key}.{f.name}", f.type, flags)
+            _add_flags(f"{key}.{f.name}", f.type, getattr(v, f.name), flags, wf_paths)
+    elif issubclass(t, Enum):
+        flags.extend([f"--{key}", getattr(v, "value")])
     else:
-        flags[f"--{key}"] = f"wf_{key}"
+        flags.extend([f"--{key}", str(v)])
 
 
 class NextflowWorkflow(WorkflowBase, ClassStorageTaskResolver):
@@ -67,6 +91,7 @@ class NextflowWorkflow(WorkflowBase, ClassStorageTaskResolver):
                 "to your workflow metadata to populate this page.\nMore information",
                 "[here](https://wiki.latch.bio/docs/nextflow/quickstart).",
             )
+
         docstring = Docstring(
             f"{metadata._nextflow_metadata.display_name}\n\n{markdown_content}\n\n"
             + str(metadata._nextflow_metadata)
@@ -81,13 +106,6 @@ class NextflowWorkflow(WorkflowBase, ClassStorageTaskResolver):
             docstring=docstring,
         )
 
-        self.flattened_inputs = {}
-
-        self.flags_to_params = {}
-        for k, v in metadata._nextflow_metadata.parameters.items():
-            assert v.type is not None
-            _get_flags_to_params(k, v.type, self.flags_to_params)
-
         self.downloadable_params = {
             k
             for k, v in metadata._nextflow_metadata.parameters.items()

{latch-2.40.4.dev8 → latch-2.40.4.dev10}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.40.4.dev8",
+    version="v2.40.4.dev10",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),