chore(docs): run sphinx-apidocs

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

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+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

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+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.kubernetes.rst

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+tesk.api.kubernetes package
+===========================
+
+Submodules
+----------
+
+tesk.api.kubernetes.constants module
+------------------------------------
+
+.. automodule:: tesk.api.kubernetes.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.api.kubernetes.wrapper module
+----------------------------------
+
+.. automodule:: tesk.api.kubernetes.wrapper
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tesk.api.kubernetes
+   :members:
+   :undoc-members:
+   :show-inheritance:

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

@@ -0,0 +1,19 @@
+tesk.api package
+================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tesk.api.ga4gh
+   tesk.api.kubernetes
+
+Module contents
+---------------
+
+.. automodule:: tesk.api
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tesk/tesk.rst

@@ -7,8 +7,52 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
+   tesk.api
    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
 ---------------
 

tesk/api/kubernetes/__init__.py

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+"""Kubernetes API module for TESK."""

tesk/api/kubernetes/constants.py

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+"""Constants for Kubernetes API."""
+
+from enum import Enum
+from typing import Set
+
+from pydantic import BaseModel, Field
+
+
+class Constants(BaseModel):
+    """Constants related to job and tasks."""
+
+    taskmaster_input: str = Field(
+        default="JSON_INPUT",
+        description="ENV var that serves as taskmaster script input (JSON format)",
+    )
+    taskmaster_input_exec_key: str = Field(
+        default="executors",
+        description="Key in JSON taskmaster input, which holds list of executors",
+    )
+    volume_name: str = Field(default="PVC", description="Volume name")
+    job_create_attempts_no: int = Field(
+        default=5,
+        description="Number of attempts of job creation in case of name collision",
+    )
+    job_name_taskm_prefix: str = Field(
+        default="task-",
+        description="Constant prefix of taskmaster's job name (== TES task ID)",
+    )
+    job_name_exec_prefix: str = Field(
+        default="-ex-",
+        description="Part of executor's job name, that follows taskmaster's name",
+    )
+    job_name_taskm_rand_part_length: int = Field(
+        default=4,
+        description=(
+            "No of bytes of random part of task master's name (which end up "
+            "encoded to hex)"
+        ),
+    )
+    job_name_exec_no_length: int = Field(
+        default=2,
+        description="No of digits reserved for executor number in executor's job name."
+        " Ends up padded with '0' for numbers < 10",
+    )
+    job_name_filer_suf: str = Field(
+        default="-outputs-filer", description="Output filer name suffix"
+    )
+    ann_testask_name_key: str = Field(
+        default="tes-task-name",
+        description=(
+            "Key of the annotation, that stores name of TES task in both taskmaster's "
+            "job and executor's jobs"
+        ),
+    )
+    ann_json_input_key: str = Field(
+        default="json-input",
+        description="Key of the annotation, that stores whole input TES task serialized"
+        " to JSON",
+    )
+    label_testask_id_key: str = Field(
+        default="taskmaster-name",
+        description="Key of the label, that stores taskmaster's name (==TES task "
+        "generated ID) in executor jobs",
+    )
+    label_jobtype_key: str = Field(
+        default="job-type",
+        description="Key of the label, that stores type of a job (taskmaster or "
+        "executor)",
+    )
+    label_jobtype_value_taskm: str = Field(
+        default="taskmaster",
+        description="Value of the label with taskmaster's job type",
+    )
+    label_jobtype_value_exec: str = Field(
+        default="executor", description="Value of the label with executor's job type"
+    )
+    label_execno_key: str = Field(
+        default="executor-no",
+        description="Key of the label, that holds executor number for executor jobs",
+    )
+    label_taskstate_key: str = Field(
+        default="task-status",
+        description="Key of the label, that holds executor's state",
+    )
+    label_taskstate_value_canc: str = Field(
+        default="Cancelled",
+        description="Value of the label, that holds executor's Cancelled state",
+    )
+    label_userid_key: str = Field(
+        default="creator-user-id", description="Key of the label, that holds user id"
+    )
+    label_groupname_key: str = Field(
+        default="creator-group-name",
+        description="Key of the label, that holds user's group name",
+    )
+    absolute_path_regexp: str = Field(
+        default="^\\/.*", description="Pattern to validate paths"
+    )
+    absolute_path_message: str = Field(
+        default="must be an absolute path",
+        description="Message for absolute path validation (to avoid "
+        "message.properties)",
+    )
+    resource_disk_default: float = Field(
+        default=0.1, description="Default resource disk value"
+    )
+    completed_states: Set[str] = Field(
+        default={"CANCELED", "COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR"},
+        description="TES task states, indicating task is not running and cannot be "
+        "cancelled",
+    )
+    ftp_secret_username_env: str = Field(
+        default="TESK_FTP_USERNAME",
+        description="Name of taskmaster's ENV variable with username of FTP account "
+        "used for storage",
+    )
+    ftp_secret_password_env: str = Field(
+        default="TESK_FTP_PASSWORD",
+        description="Name of taskmaster's ENV variable with password of FTP account "
+        "used for storage",
+    )
+    cancel_patch: str = Field(
+        default='{"metadata":{"labels":{"task-status":"Cancelled"}}}',
+        description="Patch object passed to job API, when cancelling task",
+    )
+    executor_backoff_limit: str = Field(
+        default="EXECUTOR_BACKOFF_LIMIT",
+        description="Set a number of retries of a job execution.",
+    )
+    filer_backoff_limit: str = Field(
+        default="FILER_BACKOFF_LIMIT",
+        description="Set a number of retries of a filer job execution.",
+    )
+
+
+class K8sConstants(BaseModel):
+    """Constants related to Kubernetes."""
+
+    k8s_batch_api_version: str = Field(
+        default="batch/v1", description="Kubernetes Batch API version"
+    )
+    k8s_batch_api_job_type: str = Field(
+        default="Job", description="Kubernetes Job object type"
+    )
+    job_restart_policy: str = Field(
+        default="Never", description="Kubernetes Job restart policy"
+    )
+    resource_cpu_key: str = Field("cpu", description="Executor CPU resource label")
+    resource_mem_key: str = Field(
+        default="memory", description="Executor memory resource label"
+    )
+    resource_mem_unit: str = Field(
+        default="Gi", description="Executor memory resource unit"
+    )
+    resource_mem_one_gb: int = Field(
+        default=1073741824, description="One Gibibyte (Gi) in bytes"
+    )
+
+    class PodPhase(Enum):
+        """Pod state."""
+
+        PENDING = "Pending"
+
+        def get_code(self) -> str:
+            """Return the pod state."""
+            return self.value