feat: add k8s client wrapper and constants (#201)

README.md

@@ -66,3 +66,17 @@ and the taskmaster ends, completing the task.
   need either an FTP account or a PVC that can be accessed from within or from
   outside of the cluster by the workflow manager (more in the
   [deployment](deployment/documentation/deployment.md) page).
+
+### Environment Variables
+
+| **Environment Variable**                        | **Default Value**                                  | **Description**                                |
+|-------------------------------------------------|----------------------------------------------------|------------------------------------------------|
+| `TESK_API_TASKMASTER_FILER_IMAGE_NAME`          | `docker.io/elixircloud/tesk-core-filer`            | Name of the filer image                        |
+| `TESK_API_TASKMASTER_FILER_IMAGE_VERSION`       | `latest`                                           | Version of the filer image                     |
+| `TESK_API_TASKMASTER_IMAGE_NAME`                | `docker.io/elixircloud/tesk-core-taskmaster`       | Name of the taskmaster image                   |
+| `TESK_API_TASKMASTER_IMAGE_VERSION`             | `latest`                                           | Version of the taskmaster image                |
+| `TESK_API_K8S_NAMESPACE`                        | `tesk`                                             | Namespace in which TESK creates K8s resources  |
+| `TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME`      | `taskmaster`                                       | Taskmaster service account name                |
+| `ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT`            | `6`                                                | Backoff limit for taskmaster execution         |
+| `FILER_BACKOFF_LIMIT`                           | `2`                                                | Backoff limit for filer job                    |
+| `EXECUTOR_BACKOFF_LIMIT`                        | `2`                                                | Backoff limit for executor job                 |

docs/source/pages/tesk/tesk.api.ga4gh.rst

@@ -0,0 +1,18 @@
+tesk.api.ga4gh package
+======================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tesk.api.ga4gh.tes
+
+Module contents
+---------------
+
+.. automodule:: tesk.api.ga4gh
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tesk/tesk.api.ga4gh.tes.rst

@@ -0,0 +1,37 @@
+tesk.api.ga4gh.tes package
+==========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tesk.api.ga4gh.tes.service_info
+
+Submodules
+----------
+
+tesk.api.ga4gh.tes.controllers module
+-------------------------------------
+
+.. automodule:: tesk.api.ga4gh.tes.controllers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.api.ga4gh.tes.models module
+--------------------------------
+
+.. automodule:: tesk.api.ga4gh.tes.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tesk.api.ga4gh.tes
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tesk/tesk.api.ga4gh.tes.service_info.rst

@@ -0,0 +1,21 @@
+tesk.api.ga4gh.tes.service\_info package
+========================================
+
+Submodules
+----------
+
+tesk.api.ga4gh.tes.service\_info.service\_info module
+-----------------------------------------------------
+
+.. automodule:: tesk.api.ga4gh.tes.service_info.service_info
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tesk.api.ga4gh.tes.service_info
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tesk/tesk.api.rst

@@ -0,0 +1,18 @@
+tesk.api package
+================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tesk.api.ga4gh
+
+Module contents
+---------------
+
+.. automodule:: tesk.api
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tesk/tesk.k8s.rst

@@ -0,0 +1,29 @@
+tesk.k8s package
+================
+
+Submodules
+----------
+
+tesk.k8s.constants module
+-------------------------
+
+.. automodule:: tesk.k8s.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.k8s.wrapper module
+-----------------------
+
+.. automodule:: tesk.k8s.wrapper
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tesk.k8s
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tesk/tesk.rst

@@ -7,8 +7,53 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
+   tesk.api
+   tesk.k8s
    tesk.services
 
+Submodules
+----------
+
+tesk.app module
+---------------
+
+.. automodule:: tesk.app
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.constants module
+---------------------
+
+.. automodule:: tesk.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.custom\_config module
+--------------------------
+
+.. automodule:: tesk.custom_config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.exceptions module
+----------------------
+
+.. automodule:: tesk.exceptions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.utils module
+-----------------
+
+.. automodule:: tesk.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 

pyproject.toml

@@ -32,7 +32,7 @@ boto3 = "1.34.104"
 foca = "^0.13.0"
 kubernetes = "^29.0.0"
 python = "^3.11"
-requests = ">=2.20.0"
+werkzeug = "==2.2.3" # Remove when FOCA updates this dependency.
 urllib3 = "^2.2.2"
 
 [tool.poetry.group.docs.dependencies]

tesk/constants.py

@@ -0,0 +1,78 @@
+"""Tesk scoped constants."""
+
+import os
+
+from pydantic import BaseModel
+
+
+class TeskConstants(BaseModel):
+    """Tesk's K8s scoped constants.
+
+    Attributes:
+        FILER_IMAGE_NAME: Name of the filer image
+        FILER_IMAGE_VERSION: Version of the filer image
+        TASKMASTER_IMAGE_NAME:  Name of the taskmaster image
+        TASKMASTER_IMAGE_VERSION: Version of the taskmaster image
+        TESK_NAMESPACE: Namespace in which api will create K8s resources from TES
+            request
+        TASKMASTER_SERVICE_ACCOUNT_NAME: Taskmaster service account name
+        TASKMASTER_ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT:  Backoff limit for taskmaster env
+        FILER_BACKOFF_LIMIT: Backoff limit got filer job
+        EXECUTOR_BACKOFF_LIMIT: Backoff limit for executor job
+
+    Note:
+        Below are the mentioned environment variable with which these constants can be
+        configured, otherwise mentioned default will be assigned.
+
+        variable:
+            ENV_VARIABLE = default
+
+        FILER_IMAGE_NAME:
+            TESK_API_TASKMASTER_FILER_IMAGE_NAME = docker.io/elixircloud/tesk-core-filer
+        FILER_IMAGE_VERSION:
+            TESK_API_TASKMASTER_FILER_IMAGE_VERSION = latest
+        TASKMASTER_IMAGE_NAME:
+            TESK_API_TASKMASTER_IMAGE_NAME = docker.io/elixircloud/tesk-core-taskmaster
+        TASKMASTER_IMAGE_VERSION:
+            TESK_API_TASKMASTER_IMAGE_VERSION = latest
+        TESK_NAMESPACE:
+            TESK_API_K8S_NAMESPACE = tesk
+        TASKMASTER_SERVICE_ACCOUNT_NAME:
+            TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME = taskmaster
+        TASKMASTER_ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT:
+            ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT = 6
+        FILER_BACKOFF_LIMIT:
+            FILER_BACKOFF_LIMIT = 2
+        EXECUTOR_BACKOFF_LIMIT:
+            EXECUTOR_BACKOFF_LIMIT = 2
+    """
+
+    FILER_IMAGE_NAME: str = os.getenv(
+        "TESK_API_TASKMASTER_FILER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-filer"
+    )
+    FILER_IMAGE_VERSION: str = os.getenv(
+        "TESK_API_TASKMASTER_FILER_IMAGE_VERSION", "latest"
+    )
+    TASKMASTER_IMAGE_NAME: str = os.getenv(
+        "TESK_API_TASKMASTER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-taskmaster"
+    )
+    TASKMASTER_IMAGE_VERSION: str = os.getenv(
+        "TESK_API_TASKMASTER_IMAGE_VERSION", "latest"
+    )
+    TESK_NAMESPACE: str = os.getenv("TESK_API_K8S_NAMESPACE", "tesk")
+    TASKMASTER_SERVICE_ACCOUNT_NAME: str = os.getenv(
+        "TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME", "taskmaster"
+    )
+    TASKMASTER_ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT: str = os.getenv(
+        "ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT", "6"
+    )
+    FILER_BACKOFF_LIMIT: str = os.getenv("FILER_BACKOFF_LIMIT", "2")
+    EXECUTOR_BACKOFF_LIMIT: str = os.getenv("EXECUTOR_BACKOFF_LIMIT", "2")
+
+    class Config:
+        """Configuration for class."""
+
+        frozen = True
+
+
+tesk_constants = TeskConstants()

tesk/exceptions.py

@@ -7,6 +7,7 @@
     OAuthProblem,
     Unauthorized,
 )
+from kubernetes.client.exceptions import ApiException
 from werkzeug.exceptions import (
     BadRequest,
     InternalServerError,
@@ -18,6 +19,10 @@ class ConfigNotFoundError(FileNotFoundError):
     """Configuration file not found error."""
 
 
+class KubernetesError(ApiException):
+    """Kubernetes error."""
+
+
 # exceptions raised in app context
 exceptions = {
     Exception: {

tesk/k8s/__init__.py

@@ -0,0 +1 @@
+"""Kubernetes API module for TESK."""