easylink 0.1.18__py3-none-any.whl → 0.1.19__py3-none-any.whl

easylink/_version.py

@@ -1 +1 @@
-__version__ = "0.1.18"
+__version__ = "0.1.19"

easylink/cli.py

@@ -55,7 +55,7 @@ from easylink.utilities.general_utils import (
     configure_logging_to_terminal,
     handle_exceptions,
 )
-from easylink.utilities.paths import CONTAINER_DIR
+from easylink.utilities.paths import DEFAULT_IMAGES_DIR, DEV_IMAGES_DIR
 
 SHARED_OPTIONS = [
     click.option(
@@ -154,6 +154,16 @@ def easylink():
 
 @easylink.command()
 @_pass_shared_options
+@click.option(
+    "-I",
+    "--images",
+    hidden=True,
+    type=click.Path(exists=False, file_okay=False, resolve_path=True),
+    help=(
+        "The directory containing the images to run. If no value is passed, a new "
+        f"directory will be created at the home directory: {DEFAULT_IMAGES_DIR}."
+    ),
+)
 @click.option(
     "-e",
     "--computing-environment",
@@ -171,6 +181,7 @@ def run(
     output_dir: str | None,
     no_timestamp: bool,
     schema: str,
+    images: str,
     computing_environment: str | None,
     verbose: int,
     with_debugger: bool,
@@ -196,6 +207,7 @@ def run(
         input_data=input_data,
         computing_environment=computing_environment,
         results_dir=results_dir,
+        images_dir=images,
         schema_name=schema,
     )
     logger.info("*** FINISHED ***")
@@ -263,7 +275,7 @@ easylink.add_command(devtools)
     type=click.Path(exists=False, dir_okay=True, file_okay=False, resolve_path=True),
     help=(
         "The directory to move the container to. If no value is passed, it will "
-        f"be moved to {CONTAINER_DIR} in a sub-directory named with the username."
+        f"be moved to {DEV_IMAGES_DIR} in a sub-directory named with the username."
     ),
 )
 def create_implementation(
@@ -300,7 +312,7 @@ def create_implementation(
     if not scripts:
         logger.error("No scripts provided.")
         return
-    output_dir = Path(output_dir) if output_dir else Path(f"{CONTAINER_DIR}/{os.getlogin()}")
+    output_dir = Path(output_dir) if output_dir else Path(f"{DEV_IMAGES_DIR}/{os.getlogin()}")
     if not output_dir.exists():
         # make the directory with rwxrwxr-x permissions
         output_dir.mkdir(parents=True, mode=0o775)

easylink/configuration.py

@@ -17,6 +17,7 @@ from layered_config_tree import LayeredConfigTree
 from easylink.pipeline_schema import PipelineSchema
 from easylink.utilities.data_utils import load_yaml
 from easylink.utilities.general_utils import exit_with_validation_error
+from easylink.utilities.paths import DEFAULT_IMAGES_DIR
 
 PIPELINE_ERRORS_KEY = "PIPELINE ERRORS"
 INPUT_DATA_ERRORS_KEY = "INPUT DATA ERRORS"
@@ -66,9 +67,14 @@ class Config(LayeredConfigTree):
     config_params
         A dictionary of all specifications required to run the pipeline. This
         includes the pipeline, input data, and computing environment specifications,
-        as well as the results directory.
+        as well as the results directory and images directory.
     schema_name
         The name of the schema to validate the pipeline configuration against.
+    images_dir
+        The directory containing the images or to download the images to if they
+        don't exist. If None, will default to the :data:`~easylink.utilities.paths.DEFAULT_IMAGES_DIR`.
+    command
+        The EasyLink command being run.
 
     Attributes
     ----------
@@ -82,6 +88,11 @@ class Config(LayeredConfigTree):
         The input data filepaths.
     schema
         The :class:`~easylink.pipeline_schema.PipelineSchema`.
+    images_dir
+        The directory containing the images or to download the images to if they
+        don't exist. If None, will default to ~/.easylink_images.
+    command
+        The EasyLink command being run.
 
     """
 
@@ -89,6 +100,8 @@ class Config(LayeredConfigTree):
         self,
         config_params: dict[str, Any],
         schema_name: str = "main",
+        images_dir: str | Path | None = None,
+        command: str = "run",
     ) -> None:
         super().__init__(layers=["initial_data", "default", "user_configured"])
         self.update(DEFAULT_ENVIRONMENT, layer="default")
@@ -101,6 +114,14 @@ class Config(LayeredConfigTree):
             self.update({"environment": {"slurm": {}}}, layer="default")
         self.update({"schema": self._get_schema(schema_name)}, layer="initial_data")
         self.schema.configure_pipeline(self.pipeline, self.input_data)
+        # use the images_dir if provided, otherwise use default
+        self.update(
+            {
+                "images_dir": Path(images_dir) if images_dir else DEFAULT_IMAGES_DIR,
+            },
+            layer="user_configured",
+        )
+        self.update({"command": command}, layer="user_configured")
         self._validate()
         self.freeze()
 
@@ -303,7 +324,9 @@ def _load_input_data_paths(
             f"Input was: '{input_data_paths}'"
         )
     filepath_dict = {
-        filename: Path(filepath).resolve() for filename, filepath in input_data_paths.items()
+        # Resolve paths relative to location of the YAML file
+        filename: (Path(input_data_specification_path).parent / Path(filepath)).resolve()
+        for filename, filepath in input_data_paths.items()
     }
     return filepath_dict
 

easylink/devtools/implementation_creator.py

@@ -69,8 +69,6 @@ class ImplementationCreator:
         for the container.
     implementation_name
         The name of the implementation. It is by definition the name of the script.
-    requirements
-        The install requirements for the implementation (if any).
     step
         The name of the step that this implementation implements.
     output_slot
@@ -93,20 +91,30 @@ class ImplementationCreator:
         for the container."""
         self.implementation_name = script_path.stem
         """The name of the implementation. It is by definition the name of the script."""
-        self.requirements = self._extract_requirements(script_path)
-        """The install requirements for the implementation (if any)."""
         self.step = self._extract_implemented_step(script_path)
         """The name of the step that this implementation implements."""
+        self.has_custom_recipe = self._extract_has_custom_recipe(script_path)
+        """Whether the user has already written the recipe for this implementation."""
+        self.script_base_command = self._extract_script_base_command(script_path)
+        """The base command to use to run the script in this implementation."""
         self.output_slot = self._extract_output_slot(script_path, self.step)
         """The name of the output slot that this implementation sends results to."""
 
     def create_recipe(self) -> None:
         """Builds the singularity recipe and writes it to disk."""
-
-        recipe = PythonRecipe(self.script_path, self.recipe_path, self.requirements)
+        if self.has_custom_recipe:
+            if not self.recipe_path.exists():
+                raise ValueError(f"Could not find a custom recipe at {self.recipe_path}.")
+            return
+
+        recipe = PythonRecipe(
+            self.script_path,
+            self.recipe_path,
+            ImplementationCreator._extract_requirements(self.script_path),
+            self.script_base_command,
+        )
         recipe.build()
         recipe.write()
-        pass
 
     def build_container(self) -> None:
         """Builds the container from the recipe.
@@ -190,7 +198,7 @@ class ImplementationCreator:
         info[self.implementation_name] = {
             "steps": [self.step],
             "image_path": str(self.hosted_container_path),
-            "script_cmd": f"python /{self.script_path.name}",
+            "script_cmd": f"{self.script_base_command} /{self.script_path.name}",
             "outputs": {
                 self.output_slot: "result.parquet",
             },
@@ -241,6 +249,22 @@ class ImplementationCreator:
             )
         return steps[0]
 
+    @staticmethod
+    def _extract_has_custom_recipe(script_path: Path) -> bool:
+        """Extracts whether the user has already written the recipe for this implementation.
+
+        The expectation is that this flag is specified within the script
+        as a comment of the format:
+
+        .. code-block:: python
+            # HAS_CUSTOM_RECIPE: true
+        """
+        has_custom_recipe = _extract_metadata("HAS_CUSTOM_RECIPE", script_path)
+        if len(has_custom_recipe) == 0:
+            return False
+        else:
+            return str(has_custom_recipe[0]).strip().lower() in ["true", "yes"]
+
     @staticmethod
     def _extract_output_slot(script_path: Path, step_name: str) -> str:
         """Extracts the name of the output slot that this script is implementing."""
@@ -307,7 +331,7 @@ class ImplementationCreator:
     def _extract_pipeline_schema_name(script_path: Path) -> str:
         """Extracts the relevant pipeline schema name.
 
-        The expectation is that the output slot's name is specified within the script
+        The expectation is that the pipeline schema's name is specified within the script
         as a comment of the format:
 
         .. code-block:: python
@@ -321,6 +345,22 @@ class ImplementationCreator:
             raise ValueError(f"Pipeline schema '{schema_name}' is not supported.")
         return schema_name
 
+    @staticmethod
+    def _extract_script_base_command(script_path: Path) -> str:
+        """Extracts the base command to be used to run the script.
+
+        The expectation is that the base command is specified within the script
+        as a comment of the format:
+
+        .. code-block:: python
+            # SCRIPT_BASE_COMMAND: python
+
+        If no pipeline schema is specified, "python" will be used by default.
+        """
+        base_command_list: list[str] = _extract_metadata("SCRIPT_BASE_COMMAND", script_path)
+        base_command = base_command_list[0] if base_command_list else "python"
+        return base_command
+
     @staticmethod
     def _write_metadata(info: dict[str, dict[str, str]]) -> None:
         """Writes the implementation metadata to disk.
@@ -341,10 +381,17 @@ class PythonRecipe:
         "python@sha256:1c26c25390307b64e8ff73e7edf34b4fbeac59d41da41c08da28dc316a721899"
     )
 
-    def __init__(self, script_path: Path, recipe_path: Path, requirements: str) -> None:
+    def __init__(
+        self,
+        script_path: Path,
+        recipe_path: Path,
+        requirements: str,
+        script_base_command: str,
+    ) -> None:
         self.script_path = script_path
         self.recipe_path = recipe_path
         self.requirements = requirements
+        self.script_base_command = script_base_command
         self.text: str | None = None
 
     def build(self) -> None:
@@ -373,7 +420,7 @@ From: {self.BASE_IMAGE}
     export LC_ALL=C
 
 %runscript
-    python /{script_name} '$@'"""
+    {self.script_base_command} /{script_name} '$@'"""
 
     def write(self) -> None:
         """Writes the recipe to disk.

easylink/implementation.py

@@ -16,9 +16,14 @@ from pathlib import Path
 from typing import TYPE_CHECKING
 
 from layered_config_tree import LayeredConfigTree
+from loguru import logger
 
 from easylink.utilities import paths
-from easylink.utilities.data_utils import load_yaml
+from easylink.utilities.data_utils import (
+    calculate_md5_checksum,
+    download_image,
+    load_yaml,
+)
 
 if TYPE_CHECKING:
     from easylink.graph_components import InputSlot, OutputSlot
@@ -74,14 +79,14 @@ class Implementation:
     def __repr__(self) -> str:
         return f"Implementation.{self.name}"
 
-    def validate(self) -> list[str]:
+    def validate(self, skip_image_validation: bool, images_dir: str | Path) -> list[str]:
         """Validates individual ``Implementation`` instances.
 
         Returns
         -------
             A list of logs containing any validation errors. Each item in the list
             is a distinct message about a particular validation error (e.g. if a
-            required container does not exist).
+            required image does not exist).
 
         Notes
         -----
@@ -89,7 +94,8 @@ class Implementation:
         """
         logs = []
         logs = self._validate_expected_steps(logs)
-        logs = self._validate_container_exists(logs)
+        if not skip_image_validation:
+            logs = self._download_and_validate_image(logs, images_dir)
         return logs
 
     ##################
@@ -110,11 +116,82 @@ class Implementation:
             )
         return logs
 
-    def _validate_container_exists(self, logs: list[str]) -> list[str]:
-        """Validates that the container to run exists."""
-        err_str = f"Container '{self.singularity_image_path}' does not exist."
-        if not Path(self.singularity_image_path).exists():
-            logs.append(err_str)
+    def _download_and_validate_image(
+        self, logs: list[str], images_dir: str | Path
+    ) -> list[str]:
+        """Downloads the image if required and validates it exists.
+
+        If the image does not exist in the specified images directory, it will
+        attempt to download it.
+        """
+        # HACK: We manually create the image path here as well as later when writing
+        # each implementations Snakefile rule.
+        image_path = Path(images_dir) / self.singularity_image_name
+        expected_md5_checksum = self._metadata.get("md5_checksum", None)
+        record_id = self._metadata.get("zenodo_record_id", None)
+        if image_path.exists():
+            self._handle_conflicting_checksums(
+                logs, image_path, expected_md5_checksum, record_id
+            )
+        else:
+            if not record_id:
+                logs.append(
+                    f"Image '{str(image_path)}' does not exist and no Zenodo record ID "
+                    "is provided to download it."
+                )
+            if not expected_md5_checksum:
+                logs.append(
+                    f"Image '{str(image_path)}' does not exist and no MD5 checksum "
+                    "is provided to verify from the host."
+                )
+            if not record_id or not expected_md5_checksum:
+                return logs
+            download_image(
+                images_dir=images_dir,
+                record_id=record_id,
+                filename=self.singularity_image_name,
+                md5_checksum=expected_md5_checksum,
+            )
+        if not image_path.exists():
+            logs.append(
+                f"Image '{str(image_path)}' does not exist and could not be downloaded."
+            )
+        return logs
+
+    @staticmethod
+    def _handle_conflicting_checksums(
+        logs: list[str],
+        image_path: Path,
+        expected_md5_checksum: str | None,
+        record_id: str | None,
+    ) -> list[str]:
+        # TODO: Strengthen the following logic to better handle image updates.
+        # If using the default images directory and the image already exists
+        # but with a different checksum than in the implementation metadata,
+        # re-download.
+        calculated_md5_checksum = calculate_md5_checksum(image_path)
+        if (
+            image_path.parent == paths.DEFAULT_IMAGES_DIR
+            and expected_md5_checksum
+            and calculated_md5_checksum != expected_md5_checksum
+        ):
+            if not record_id:
+                logs.append(
+                    f"Image '{str(image_path)}' exists but has a different MD5 checksum "
+                    f"({calculated_md5_checksum}) than expected ({expected_md5_checksum}). "
+                    "No Zenodo record ID is provided to re-download the image."
+                )
+            logger.info(
+                f"Image '{str(image_path)}' exists but has a different MD5 checksum "
+                f"({calculated_md5_checksum}) than expected ({expected_md5_checksum}). "
+                "Re-downloading the image."
+            )
+            download_image(
+                images_dir=image_path.parent,
+                record_id=record_id,
+                filename=image_path.name,
+                md5_checksum=expected_md5_checksum,
+            )
         return logs
 
     def _get_env_vars(self, implementation_config: LayeredConfigTree) -> dict[str, str]:
@@ -124,9 +201,9 @@ class Implementation:
         return env_vars
 
     @property
-    def singularity_image_path(self) -> str:
+    def singularity_image_name(self) -> str:
         """The path to the required Singularity image."""
-        return self._metadata["image_path"]
+        return self._metadata["image_name"]
 
     @property
     def script_cmd(self) -> str: