mampok 3.0.4__py3-none-any.whl

mampok/__init__.py

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+"""Mampok — Kubernetes deployment manager for bioinformatics pipelines."""
+
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("mampok")
+except PackageNotFoundError:
+    __version__ = "unknown"

mampok/config/__init__.py

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+"""Mampok configuration module."""
+
+from mampok.config.config import AuthProxyConfig, ClusterConfig, MampokConfig, S3Config
+
+__all__ = ["MampokConfig", "ClusterConfig", "S3Config", "AuthProxyConfig"]

mampok/config/config.py

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+"""MampokConfig — typed configuration for Mampok v2."""
+
+from __future__ import annotations
+
+import importlib.resources
+import json
+import logging
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import TYPE_CHECKING, ClassVar
+
+import jsonschema
+from packaging.specifiers import InvalidSpecifier, SpecifierSet
+
+from mampok import __version__
+
+if TYPE_CHECKING:
+    from mampok.kubernetes.manager import DeploymentManager
+    from mampok.s3.s3 import S3
+
+logger = logging.getLogger(__name__)
+
+
+def _load_config_defaults() -> tuple[dict, dict, dict]:
+    schema_ref = (
+        importlib.resources.files("mampok.config")
+        .joinpath("schemas")
+        .joinpath("config_schema.json")
+    )
+    with schema_ref.open("r", encoding="utf-8") as f:
+        schema = json.load(f)
+    cluster_props = schema["definitions"]["ClusterConfig"]["properties"]
+    ap_props = schema["properties"]["auth_proxy"]["properties"]
+    s3_props = schema["properties"]["s3"]["properties"]
+    return (
+        {k: v["default"] for k, v in cluster_props.items() if "default" in v},
+        {k: v["default"] for k, v in ap_props.items() if "default" in v},
+        {k: v["default"] for k, v in s3_props.items() if "default" in v},
+    )
+
+
+_CLUSTER_DEFAULTS, _AUTH_PROXY_DEFAULTS, _S3_DEFAULTS = _load_config_defaults()
+
+
+@dataclass
+class AuthProxyConfig:
+    """Auth proxy configuration for the Gatekeeper sidecar.
+
+    Args:
+        auth_proxy_image: Docker image of the Gatekeeper container.
+        proxy_port: Port on which the Gatekeeper listens.
+        auth_annotations: Extra Ingress annotations when auth=True.
+        image_pull_secrets: Pull secrets for the proxy image.
+    """
+
+    auth_proxy_image: str
+    proxy_port: int = 8080
+    auth_annotations: dict = field(default_factory=dict)
+    image_pull_secrets: list[str] = field(default_factory=list)
+    project_auth_path: str = ""
+
+
+@dataclass
+class ClusterConfig:
+    """Configuration for a single Kubernetes cluster profile.
+
+    Args:
+        host: Ingress host for this cluster.
+        namespace: Kubernetes namespace for deployments.
+        kubeconfig_path: Path to the kubeconfig file for this cluster.
+        annotations: Kubernetes Ingress annotations.
+        ingress_class: Ingress class name.
+        dnsissuer: Cert-manager issuer name for TLS.
+        dnssecret: DNS secret name for ACME challenge.
+    """
+
+    host: str
+    namespace: str
+    kubeconfig_path: str
+    annotations: dict = field(default_factory=dict)
+    ingress_class: str = ""
+    dnsissuer: str = ""
+    dnssecret: str = ""
+
+
+@dataclass
+class S3Config:
+    """S3-compatible storage credentials.
+
+    Args:
+        endpoint: S3 endpoint URL.
+        access_key: S3 access key ID.
+        secret_key: S3 secret access key.
+        secretname: Name of the pre-existing K8s Secret holding S3 credentials.
+        prefix: Optional prefix for S3 bucket names.
+    """
+
+    endpoint: str
+    access_key: str
+    secret_key: str
+    secretname: str
+    prefix: str = ""
+
+
+@dataclass
+class MampokConfig:
+    """Typed configuration for Mampok v2.
+
+    Loaded from a JSON file and validated against the config schema.
+    Provides factory methods to create Kubernetes and S3 clients.
+
+    Args:
+        clusters: Named cluster profiles (e.g. {'BN': ClusterConfig(...)}).
+        s3: S3 storage credentials.
+        mamplan_repo: Path to the Mamplan repository directory.
+        mamplates_path: Path to the Mamplates directory.
+        lifetime_days: Default deployment lifetime in days.
+    """
+
+    clusters: dict[str, ClusterConfig]
+    s3: S3Config
+    mamplan_repo: Path
+    mamplates_path: Path
+    lifetime_days: int
+    mampok_version: str
+    default_cluster: str | None = None
+    auth_proxy: AuthProxyConfig | None = None
+    """Gatekeeper proxy configuration. Required when deployments use auth=True."""
+
+    _schema_cache: ClassVar[dict | None] = None
+
+    def get_cluster(self, name: str) -> ClusterConfig:
+        """Return the named cluster profile.
+
+        Args:
+            name: Cluster name as used in the config and Mamplan.
+
+        Returns:
+            The ClusterConfig for the given name.
+
+        Raises:
+            KeyError: If the cluster name is not found in the config.
+        """
+        if name not in self.clusters:
+            raise KeyError(
+                f"Unknown cluster: {name!r}. Available: {list(self.clusters)}"
+            )
+        return self.clusters[name]
+
+    def build_deployment_manager(self, cluster_name: str) -> "DeploymentManager":
+        """Create a DeploymentManager for the named cluster profile.
+
+        Loads the kubeconfig, creates a Kubernetes ApiClient, wraps it in a
+        KubeClient, and returns a DeploymentManager. Used by interface layers.
+
+        Args:
+            cluster_name: Name of the cluster profile to connect to.
+
+        Returns:
+            Configured DeploymentManager for the cluster.
+        """
+        import kubernetes
+        from mampok.kubernetes.client import KubeClient
+        from mampok.kubernetes.manager import DeploymentManager
+
+        cluster = self.get_cluster(cluster_name)
+        kubernetes.config.load_kube_config(config_file=cluster.kubeconfig_path)
+        api_client = kubernetes.client.ApiClient()
+        kube_client = KubeClient(namespace=cluster.namespace, api_client=api_client)
+        return DeploymentManager(kube_client)
+
+    def build_s3_client(self, bucket: str) -> "S3":
+        """Create an S3 client with the configured credentials.
+
+        Used by interface layers to create the S3 dependency for Mampok.
+
+        Args:
+            bucket: S3 bucket name for this deployment.
+
+        Returns:
+            Configured S3 client.
+        """
+        from mampok.s3.s3 import S3
+
+        return S3(
+            bucket=bucket,
+            endpoint_url=self.s3.endpoint,
+            access_key=self.s3.access_key,
+            secret_key=self.s3.secret_key,
+        )
+
+    @classmethod
+    def from_dict(cls, data: dict) -> "MampokConfig":
+        """Create a MampokConfig from a dict, validated against the JSON schema.
+
+        Args:
+            data: Configuration dict (as loaded from JSON).
+
+        Returns:
+            Validated MampokConfig instance.
+
+        Raises:
+            jsonschema.ValidationError: If the data violates the schema.
+        """
+        if cls._schema_cache is None:
+            schema_ref = (
+                importlib.resources.files("mampok.config")
+                .joinpath("schemas")
+                .joinpath("config_schema.json")
+            )
+            with schema_ref.open("r", encoding="utf-8") as f:
+                cls._schema_cache = json.load(f)
+
+        jsonschema.validate(data, cls._schema_cache)
+
+        raw_version_spec = data["mampok_version"]
+        try:
+            spec = SpecifierSet(raw_version_spec)
+        except InvalidSpecifier as exc:
+            raise ValueError(
+                f"Invalid mampok_version specifier in config: {raw_version_spec!r}"
+            ) from exc
+        if __version__ not in spec:
+            raise ValueError(
+                f"Mampok version mismatch: config requires {raw_version_spec!r}, "
+                f"but installed version is {__version__!r}."
+            )
+
+        clusters = {
+            name: ClusterConfig(**{**_CLUSTER_DEFAULTS, **cluster_data})
+            for name, cluster_data in data["cluster"].items()
+        }
+
+        s3 = S3Config(**{**_S3_DEFAULTS, **data["s3"]})
+
+        auth_proxy = None
+        if _ap := data.get("auth_proxy"):
+            auth_proxy = AuthProxyConfig(**{**_AUTH_PROXY_DEFAULTS, **_ap})
+
+        return cls(
+            clusters=clusters,
+            s3=s3,
+            mamplan_repo=Path(data["mamplan_repo"]),
+            mamplates_path=Path(data["mamplates_path"]),
+            lifetime_days=data["lifetime_days"],
+            mampok_version=data["mampok_version"],
+            default_cluster=data.get("default_cluster"),
+            auth_proxy=auth_proxy,
+        )
+
+    @classmethod
+    def from_file(cls, path: Path) -> "MampokConfig":
+        """Load a MampokConfig from a JSON file.
+
+        Args:
+            path: Path to the JSON config file.
+
+        Returns:
+            Validated MampokConfig instance.
+
+        Raises:
+            FileNotFoundError: If the file does not exist.
+            json.JSONDecodeError: If the file is not valid JSON.
+            jsonschema.ValidationError: If the content violates the schema.
+        """
+        path = Path(path)
+        if not path.exists():
+            raise FileNotFoundError(f"Config file not found: {path}")
+        logger.info("loading config: %s", path)
+        with path.open("r", encoding="utf-8") as f:
+            data = json.load(f)
+        return cls.from_dict(data)

mampok/config/schemas/config_schema.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "MampokConfig",
+  "description": "Schema for Mampok v2 configuration files.",
+  "type": "object",
+  "required": ["cluster", "s3", "mamplan_repo", "mamplates_path", "lifetime_days", "mampok_version"],
+  "additionalProperties": false,
+  "properties": {
+    "cluster": {
+      "type": "object",
+      "description": "Named cluster profiles. Each key is a cluster name (e.g. 'BN', 'BN_public').",
+      "minProperties": 1,
+      "additionalProperties": {
+        "$ref": "#/definitions/ClusterConfig"
+      }
+    },
+    "s3": {
+      "type": "object",
+      "description": "S3-compatible storage credentials (shared across all clusters).",
+      "required": ["endpoint", "access_key", "secret_key", "secretname"],
+      "additionalProperties": false,
+      "properties": {
+        "endpoint": {
+          "type": "string",
+          "description": "S3 endpoint URL (e.g. 'https://s3.example.com')."
+        },
+        "access_key": {
+          "type": "string",
+          "description": "S3 access key ID."
+        },
+        "secret_key": {
+          "type": "string",
+          "description": "S3 secret access key."
+        },
+        "secretname": {
+          "type": "string",
+          "description": "Name of the pre-existing Kubernetes Secret holding S3 credentials (e.g. 'mpis')."
+        },
+        "prefix": {
+          "type": "string",
+          "description": "Optional prefix for S3 bucket names.",
+          "default": ""
+        }
+      }
+    },
+    "mamplan_repo": {
+      "type": "string",
+      "description": "Path to the Mamplan repository directory."
+    },
+    "mamplates_path": {
+      "type": "string",
+      "description": "Path to the Mamplates directory."
+    },
+    "lifetime_days": {
+      "type": "integer",
+      "description": "Default deployment lifetime in days.",
+      "minimum": 1
+    },
+    "default_cluster": {
+      "type": "string",
+      "description": "Default cluster name used when no cluster is specified (e.g. for Software Hub deployments). Must match a key in the 'cluster' object."
+    },
+    "auth_proxy": {
+      "type": "object",
+      "description": "Gatekeeper proxy configuration. Only needed when deployments use auth=True.",
+      "required": ["auth_proxy_image"],
+      "additionalProperties": false,
+      "properties": {
+        "auth_proxy_image": {
+          "type": "string",
+          "description": "Docker image of the Gatekeeper container."
+        },
+        "proxy_port": {
+          "type": "integer",
+          "description": "Port on which the Gatekeeper listens.",
+          "default": 8080,
+          "minimum": 1,
+          "maximum": 65535
+        },
+        "auth_annotations": {
+          "type": "object",
+          "description": "Extra Ingress annotations when auth=True.",
+          "additionalProperties": {"type": "string"},
+          "default": {}
+        },
+        "image_pull_secrets": {
+          "type": "array",
+          "description": "Pull secret names for the proxy image.",
+          "items": {"type": "string"},
+          "default": []
+        },
+        "project_auth_path": {
+          "type": "string",
+          "description": "Absolute path to project_auth.json (for the Flask API /openProject endpoint).",
+          "default": ""
+        }
+      }
+    },
+    "mampok_version": {
+      "type": "string",
+      "description": "PEP 440 version specifier restricting which Mampok versions may run on this repository (e.g. '>=2.0.0,<3.0.0'). Required."
+    }
+  },
+  "definitions": {
+    "ClusterConfig": {
+      "type": "object",
+      "description": "Configuration for a single Kubernetes cluster.",
+      "required": ["host", "namespace", "kubeconfig_path"],
+      "additionalProperties": false,
+      "properties": {
+        "host": {
+          "type": "string",
+          "description": "Ingress host for this cluster (e.g. 'bioinformatics-cluster.example.com')."
+        },
+        "namespace": {
+          "type": "string",
+          "description": "Kubernetes namespace for deployments on this cluster."
+        },
+        "kubeconfig_path": {
+          "type": "string",
+          "description": "Absolute path to the kubeconfig file for this cluster."
+        },
+        "annotations": {
+          "type": "object",
+          "description": "Kubernetes Ingress annotations for this cluster.",
+          "additionalProperties": {
+            "type": "string"
+          },
+          "default": {}
+        },
+        "ingress_class": {
+          "type": "string",
+          "description": "Kubernetes Ingress class name (e.g. 'nginx').",
+          "default": ""
+        },
+        "dnsissuer": {
+          "type": "string",
+          "description": "Cert-manager issuer name for TLS certificates (optional).",
+          "default": ""
+        },
+        "dnssecret": {
+          "type": "string",
+          "description": "DNS secret name for ACME challenge (optional).",
+          "default": ""
+        }
+      }
+    }
+  }
+}

mampok/interfaces/__init__.py

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+"""Interfaces module — CLI (Typer) and Python API."""