merge

Author: JaeAeich

.safety-policy.yml

@@ -25,6 +25,15 @@ security:
     70624:
       reason: 'No fix available.'
       expires: '2025-5-27'
+    71595:
+      reason: 'Foca needs to update werkzeug to >=2.3.8.'
+      expires: '2025-7-21'
+    71594:
+      reason: 'Foca needs to update werkzeug to >=3.0.3.'
+      expires: '2025-7-21'
+    71636:
+      reason: 'Foca needs to update authlib to >=1.3.0.'
+      expires: '2025-7-21'
 
 report:
   dependency-vulnerabilities:

deployment/config.yaml

@@ -6,7 +6,7 @@
 # Server configuration
 # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.ServerConfig
 server:
-  host: "0.0.0.0"
+  host: '0.0.0.0'
   port: 8080
   debug: True
   environment: development
@@ -48,7 +48,31 @@ api:
           swagger_ui: True
           serve_spec: True
 
+# Custom configuration
+# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.CustomConfig
 custom:
+  # ServiceInfo configuration based on ServiceInfo model
+  service_info:
+    id: org.ga4gh.myservice
+    name: TESK
+    type:
+      group: org.ga4gh
+      artifact: tes
+      version: 1.1.0
+    description: TES on Kubernetes
+    organization:
+      name: My organization
+      url: https://example.com
+    contactUrl: mailto:support@example.com
+    documentationUrl: https://docs.myservice.example.com
+    createdAt: '2019-06-04T12:58:19Z'
+    updatedAt: '2019-06-04T12:58:19Z'
+    environment: test
+    version: 1.0.0
+    tesResources_backend_parameters:
+      - VmSize
+      - ParamToRecogniseDataComingFromConfig
+  # Taskmaster configuration
   taskmaster_template:
     apiVersion: batch/v1
     kind: Job
@@ -96,6 +120,7 @@ custom:
                 fieldRef:
                   fieldPath: metadata.labels
           restartPolicy: Never
+  # Taskmaster environment properties
   taskmaster_env_properties:
     # Taskmaster image name
     imageName: docker.io/elixircloud/tesk-core-taskmaster
@@ -128,8 +153,8 @@ log:
   formatters:
     standard:
       class: logging.Formatter
-      style: "{"
-      format: "[{asctime}: {levelname:<8}] {message} [{name}]"
+      style: '{'
+      format: '[{asctime}: {levelname:<8}] {message} [{name}]'
   handlers:
     console:
       class: logging.StreamHandler
@@ -143,9 +168,9 @@ log:
 # Exception configuration
 # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.ExceptionConfig
 exceptions:
-    required_members: [['detail'], ['status'], ['title']]
-    status_member: ['status']
-    exceptions: tesk.exceptions.exceptions
+  required_members: [['detail'], ['status'], ['title']]
+  status_member: ['status']
+  exceptions: tesk.exceptions.exceptions
 
 storeLogs:
   execution_trace: True

poetry.lock

@@ -33,7 +33,7 @@ foca = "^0.13.0"
 kubernetes = "^30.1.0"
 python = "^3.11"
 requests = ">=2.20.0"
-urllib3 = "^2.2.1"
+urllib3 = "^2.2.2"
 
 [tool.poetry.group.docs.dependencies]
 added-value = "^0.24.0"

pyproject.toml

@@ -4,12 +4,12 @@
 
 from foca.utils.logging import log_traffic  # type: ignore
 
-from tesk.api.kubernetes.template import KubernetesTemplateSupplier
 from tesk.api.ga4gh.tes.models import TesTask
-from tesk.utils import get_custom_config
+from tesk.api.ga4gh.tes.service_info.service_info import ServiceInfo
 from tesk.api.kubernetes.converter import TesKubernetesConverter
+from tesk.api.kubernetes.template import KubernetesTemplateSupplier
 from tesk.exceptions import BadRequest, InternalServerError
-# from tesk.api.ga4gh.tes.task.create_task import CreateTask as TaskCreater
+from tesk.utils import get_custom_config
 
 # Get logger instance
 logger = logging.getLogger(__name__)
@@ -48,14 +48,10 @@ def CreateTask(**kwargs) -> dict:  # type: ignore
 
 # GET /tasks/service-info
 @log_traffic
-def GetServiceInfo(*args, **kwargs) -> dict:  # type: ignore
-    """Get service info.
-
-    Args:
-        *args: Variable length argument list.
-        **kwargs: Arbitrary keyword arguments.
-    """
-    pass
+def GetServiceInfo() -> dict:  # type: ignore
+    """Get service info."""
+    service_info = ServiceInfo()
+    return service_info.response()
 
 
 # GET /tasks

tesk/api/ga4gh/tes/controllers.py

@@ -86,7 +86,7 @@ class TesExecutor(BaseModel):
         example={"BLASTDB": "/data/GRC38", "HMMERDB": "/data/hmmer"},
     )
     ignore_error: Optional[bool] = Field(
-        default=False,
+        default=None,
         description="Default behavior of running an array of executors is that "
         "execution\nstops on the first error. If `ignore_error` is `True`, then "
         "the\nrunner will record error exit codes, but will continue on to the "
@@ -154,7 +154,7 @@ class TesInput(BaseModel):
         description="Path of the file inside the container.\nMust be an absolute path.",
         example="/data/file1",
     )
-    type: Optional[TesFileType] = Field(default=TesFileType.FILE)
+    type: Optional[TesFileType] = TesFileType.FILE
     content: Optional[str] = Field(
         default=None,
         description="File content literal.\n\nImplementations should support a minimum "
@@ -337,9 +337,9 @@ class Service(BaseModel):
     id: str = Field(
         ...,
         description="Unique ID of this service. Reverse domain name notation is "
-        "recommended, though not required. The identifier should attempt to be globally"
-        " unique so it can be used in downstream aggregator services e.g. Service "
-        "Registry.",
+        "recommended, though not required. The identifier should attempt to be "
+        "globally unique so it can be used in downstream aggregator services e.g. "
+        "Service Registry.",
         example="org.ga4gh.myservice",
     )
     name: str = Field(
@@ -357,7 +357,7 @@ class Service(BaseModel):
     organization: Organization = Field(
         ..., description="Organization providing the service"
     )
-    contactUrl: Optional[AnyUrl] = Field(
+    contactUrl: Optional[str] = Field(
         default=None,
         description="URL of the contact for the provider of this service, e.g. a link "
         "to a contact form (RFC 3986 format), or an email (RFC 2368 format).",
@@ -486,7 +486,7 @@ class TesTask(BaseModel):
         description="Task identifier assigned by the server.",
         example="job-0012345",
     )
-    state: Optional[TesState] = Field(default=TesState.UNKNOWN)
+    state: Optional[TesState] = TesState.UNKNOWN
     name: Optional[str] = Field(None, description="User-provided task name.")
     description: Optional[str] = Field(
         default=None,

tesk/api/ga4gh/tes/models.py

@@ -0,0 +1 @@
+"""Package for the TES Service Info endpoint."""

tesk/api/ga4gh/tes/service_info/__init__.py

@@ -0,0 +1,92 @@
+"""Service info for TES API."""
+
+import json
+import logging
+from typing import Any, Optional
+
+from foca import Foca
+from pydantic import AnyUrl
+
+from tesk.api.ga4gh.tes.models import (
+    Artifact,
+    Organization,
+    TesServiceInfo,
+    TesServiceType,
+)
+from tesk.exceptions import ConfigNotFoundError
+from tesk.utils import get_config_path
+
+logger = logging.getLogger(__name__)
+
+
+class ServiceInfo:
+    """Service info for TES API."""
+
+    def __init__(self) -> None:
+        """Initializes the BaseServiceInfoRequest class."""
+        self.service_info: Optional[TesServiceInfo] = None
+        self.config = Foca(config_file=get_config_path()).conf
+
+    def get_default_service_info(self) -> TesServiceInfo:
+        """Get the default service info.
+
+        if service info is not provided in the config,
+        this method will return the default service info.
+
+        Returns:
+            TesServiceInfo: Default service info.
+        """
+        logger.warning("Service info not found in config. Using default service info.")
+        return TesServiceInfo(
+            id="org.ga4gh.tes",
+            name="TES",
+            type=TesServiceType(
+                group="org.ga4gh",
+                artifact=Artifact.tes,
+                version="1.1.0",
+            ),
+            organization=Organization(
+                name="my_organization",
+                url=AnyUrl("https://example.com"),
+            ),
+            version="1.0.0",
+        )
+
+    def get_service_info_from_config(self) -> TesServiceInfo:
+        """Returns service info from config.
+
+        Returns:
+          TesServiceInfo: Service info from config.
+
+        Raises:
+          ConfigNotFoundError: If custom config or part of it is not found
+            in the config file.
+        """
+        if not self.config.custom:
+            raise ConfigNotFoundError("Custom configuration not found.")
+
+        service_info_data = self.config.custom.get("service_info")
+        if not service_info_data:
+            raise ConfigNotFoundError("Service info not found in custom configuration.")
+
+        try:
+            service_info = TesServiceInfo(**service_info_data)
+        except TypeError as e:
+            logging.error(f"Exception occurred: {e}")
+            raise ConfigNotFoundError(f"Invalid service info format: {e}") from None
+
+        return service_info
+
+    def response(self) -> dict[str, Any]:
+        """Returns serialized response for /service-info.
+
+        Returns:
+          dict: Serialized response.
+        """
+        if self.service_info is None:
+            try:
+                self.service_info = self.get_service_info_from_config()
+            except ConfigNotFoundError:
+                self.service_info = self.get_default_service_info()
+
+        return dict(json.loads(self.service_info.json()))

tesk/api/ga4gh/tes/service_info/service_info.py

@@ -4,6 +4,7 @@
 
 from pydantic import BaseModel, Field
 
+from tesk.api.ga4gh.tes.models import Service
 from tesk.constants import TeskConstants
 
 
@@ -151,5 +152,7 @@ class Job(BaseModel):
 class CustomConfig(BaseModel):
     """Custom configuration model for the FOCA app."""
 
+    # Define custom configuration fields here
+    service_info: Service
     taskmaster_template: Job  # This is Pydantic model for V1Job
     taskmaster_env_properties: TaskmasterEnvProperties