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Source code for galaxy.jobs.runners.util.pykube_util

"""Interface layer for pykube library shared between Galaxy and Pulsar."""
import logging
import os
import re
from pathlib import PurePath

try:
    from pykube.config import KubeConfig
    from pykube.exceptions import HTTPError
    from pykube.http import HTTPClient
    from pykube.objects import (
        Ingress,
        Job,
        Pod,
        Service,
    )
except ImportError as exc:
    KubeConfig = None
    Ingress = None
    Job = None
    Pod = None
    Service = None
    HTTPError = None
    K8S_IMPORT_MESSAGE = (
        "The Python pykube package is required to use "
        "this feature, please install it or correct the "
        "following error:\nImportError %s" % str(exc)
    )

log = logging.getLogger(__name__)

DEFAULT_JOB_API_VERSION = "batch/v1"
DEFAULT_SERVICE_API_VERSION = "v1"
DEFAULT_INGRESS_API_VERSION = "extensions/v1beta1"
DEFAULT_NAMESPACE = "default"
INSTANCE_ID_INVALID_MESSAGE = (
    "Galaxy instance [%s] is either too long "
    "(>20 characters) or it includes non DNS "
    "acceptable characters, ignoring it."
)


[docs]def ensure_pykube(): if KubeConfig is None: raise Exception(K8S_IMPORT_MESSAGE)
[docs]def pykube_client_from_dict(params): if "k8s_use_service_account" in params and params["k8s_use_service_account"]: pykube_client = HTTPClient(KubeConfig.from_service_account()) else: config_path = params.get("k8s_config_path") if config_path is None: config_path = os.environ.get("KUBECONFIG", None) if config_path is None: config_path = "~/.kube/config" pykube_client = HTTPClient(KubeConfig.from_file(config_path)) return pykube_client
[docs]def produce_k8s_job_prefix(app_prefix=None, instance_id=None): job_name_elems = [app_prefix or "", instance_id or ""] return "-".join(elem for elem in job_name_elems if elem)
[docs]def pull_policy(params): # If this doesn't validate it returns None, that seems odd? if "k8s_pull_policy" in params: if params["k8s_pull_policy"] in ["Always", "IfNotPresent", "Never"]: return params["k8s_pull_policy"] return None
[docs]def find_service_object_by_name(pykube_api, service_name, namespace=None): if not service_name: raise ValueError("service name must not be empty") return Service.objects(pykube_api).filter(field_selector={"metadata.name": service_name}, namespace=namespace)
[docs]def find_ingress_object_by_name(pykube_api, ingress_name, namespace=None): if not ingress_name: raise ValueError("ingress name must not be empty") return Ingress.objects(pykube_api).filter(field_selector={"metadata.name": ingress_name}, namespace=namespace)
[docs]def find_job_object_by_name(pykube_api, job_name, namespace=None): if not job_name: raise ValueError("job name must not be empty") return Job.objects(pykube_api).filter(field_selector={"metadata.name": job_name}, namespace=namespace)
[docs]def find_pod_object_by_name(pykube_api, job_name, namespace=None): return Pod.objects(pykube_api).filter(selector=f"job-name={job_name}", namespace=namespace)
[docs]def is_pod_unschedulable(pykube_api, pod, namespace=None): is_unschedulable = any(c.get("reason") == "Unschedulable" for c in pod.obj["status"].get("conditions", [])) if pod.obj["status"].get("phase") == "Pending" and is_unschedulable: return True return False
[docs]def delete_job(job, cleanup="always"): job_failed = job.obj["status"]["failed"] > 0 if "failed" in job.obj["status"] else False # Scale down the job just in case even if cleanup is never job.scale(replicas=0) api_delete = cleanup == "always" if not api_delete and cleanup == "onsuccess" and not job_failed: api_delete = True if api_delete: delete_options = {"apiVersion": "v1", "kind": "DeleteOptions", "propagationPolicy": "Background"} r = job.api.delete(json=delete_options, **job.api_kwargs()) job.api.raise_for_status(r)
[docs]def delete_ingress(ingress, cleanup="always", job_failed=False): api_delete = cleanup == "always" if not api_delete and cleanup == "onsuccess" and not job_failed: api_delete = True if api_delete: delete_options = {"apiVersion": "v1", "kind": "DeleteOptions", "propagationPolicy": "Background"} r = ingress.api.delete(json=delete_options, **ingress.api_kwargs()) ingress.api.raise_for_status(r)
[docs]def delete_service(service, cleanup="always", job_failed=False): api_delete = cleanup == "always" if not api_delete and cleanup == "onsuccess" and not job_failed: api_delete = True if api_delete: delete_options = {"apiVersion": "v1", "kind": "DeleteOptions", "propagationPolicy": "Background"} r = service.api.delete(json=delete_options, **service.api_kwargs()) service.api.raise_for_status(r)
[docs]def job_object_dict(params, job_prefix, spec): k8s_job_obj = { "apiVersion": params.get("k8s_job_api_version", DEFAULT_JOB_API_VERSION), "kind": "Job", "metadata": { "generateName": f"{job_prefix}-", "namespace": params.get("k8s_namespace", DEFAULT_NAMESPACE), }, "spec": spec, } return k8s_job_obj
[docs]def service_object_dict(params, service_name, spec): k8s_service_obj = { "apiVersion": params.get("k8s_service_api_version", DEFAULT_SERVICE_API_VERSION), "kind": "Service", "metadata": { "name": service_name, "namespace": params.get("k8s_namespace", DEFAULT_NAMESPACE), }, } k8s_service_obj["metadata"].update(spec.pop("metadata", {})) k8s_service_obj.update(spec) return k8s_service_obj
[docs]def ingress_object_dict(params, ingress_name, spec): k8s_ingress_obj = { "apiVersion": params.get("k8s_ingress_api_version", DEFAULT_INGRESS_API_VERSION), "kind": "Ingress", "metadata": { "name": ingress_name, "namespace": params.get("k8s_namespace", DEFAULT_NAMESPACE), # TODO: Add default annotations }, } k8s_ingress_obj["metadata"].update(spec.pop("metadata", {})) k8s_ingress_obj.update(spec) return k8s_ingress_obj
[docs]def parse_pvc_param_line(pvc_param): """ :type pvc_param: str :param pvc_param: the pvc mount param in the format ``pvc-name/subpath/desired:/mountpath/desired[:r]`` :rtype: dict :return: a dict like:: {"name": "pvc-name", "subPath": "subpath/desired", "mountPath": "/mountpath/desired", "readOnly": False} """ claim, _, rest = pvc_param.partition(":") mount_path, _, mode = rest.partition(":") read_only = mode == "r" claim_name, _, subpath = claim.partition("/") return { "name": claim_name.strip(), "subPath": subpath.strip(), "mountPath": mount_path.strip(), "readOnly": read_only, }
def generate_relative_mounts(pvc_param, files): """ Maps a list of files as mounts, relative to the base volume mount. For example, given the pvc mount: { 'name': 'my_pvc', 'mountPath': '/galaxy/database/jobs', 'subPath': 'data', 'readOnly': False } and files: ['/galaxy/database/jobs/01/input.txt', '/galaxy/database/jobs/01/working'] returns each file as a relative mount as follows: [ { 'name': 'my_pvc', 'mountPath': '/galaxy/database/jobs/01/input.txt', 'subPath': 'data/01/input.txt', 'readOnly': False }, { 'name': 'my_pvc', 'mountPath': '/galaxy/database/jobs/01/working', 'subPath': 'data/01/working', 'readOnly': False } ] :param pvc_param: the pvc claim dict :param files: a list of file or folder names :return: A list of volume mounts """ if not pvc_param: return param_claim = parse_pvc_param_line(pvc_param) claim_name = param_claim["name"] base_subpath = PurePath(param_claim.get("subPath", "")) base_mount = PurePath(param_claim["mountPath"]) read_only = param_claim["readOnly"] volume_mounts = [] for f in files: file_path = PurePath(str(f)) if base_mount not in file_path.parents: # force relative directory, needed for the job working directory in particular file_path = base_mount.joinpath(file_path.relative_to("/") if file_path.is_absolute() else file_path) relpath = file_path.relative_to(base_mount) subpath = base_subpath.joinpath(relpath) volume_mounts.append( {"name": claim_name, "mountPath": str(file_path), "subPath": str(subpath), "readOnly": read_only} ) return volume_mounts def deduplicate_entries(obj_list): # remove duplicate entries in a list of dictionaries # based on: https://stackoverflow.com/a/9428041 return [i for n, i in enumerate(obj_list) if i not in obj_list[n + 1 :]]
[docs]def get_volume_mounts_for_job(job_wrapper, data_claim=None, working_claim=None): volume_mounts = [] if data_claim: volume_mounts.extend(generate_relative_mounts(data_claim, job_wrapper.job_io.get_input_fnames())) # for individual output files, mount the parent folder of each output as there could be wildcard outputs output_folders = deduplicate_entries( [str(PurePath(str(f)).parent) for f in job_wrapper.job_io.get_output_fnames()] ) volume_mounts.extend(generate_relative_mounts(data_claim, output_folders)) if working_claim: volume_mounts.extend(generate_relative_mounts(working_claim, [job_wrapper.working_directory])) return deduplicate_entries(volume_mounts)
[docs]def galaxy_instance_id(params): """Parse and validate the id of the Galaxy instance from supplied dict. This will be added to Jobs and Pods names, so it needs to be DNS friendly, this means: `The Internet standards (Requests for Comments) for protocols mandate that component hostname labels may contain only the ASCII letters 'a' through 'z' (in a case-insensitive manner), the digits '0' through '9', and the minus sign ('-').` It looks for the value set on params['k8s_galaxy_instance_id'], which might or not be set. The idea behind this is to allow the Galaxy instance to trust (or not) existing k8s Jobs and Pods that match the setup of a Job that is being recovered or restarted after a downtime/reboot. """ if "k8s_galaxy_instance_id" in params: raw_value = params["k8s_galaxy_instance_id"] if re.match(r"(?!-)[a-z\d-]{1,20}(?<!-)$", raw_value): return raw_value else: log.error(INSTANCE_ID_INVALID_MESSAGE % raw_value) return None
__all__ = ( "DEFAULT_JOB_API_VERSION", "DEFAULT_SERVICE_API_VERSION", "DEFAULT_INGRESS_API_VERSION", "ensure_pykube", "find_service_object_by_name", "find_ingress_object_by_name", "find_job_object_by_name", "find_pod_object_by_name", "galaxy_instance_id", "HTTPError", "is_pod_unschedulable", "Job", "Service", "Ingress", "job_object_dict", "service_object_dict", "ingress_object_dict", "Pod", "produce_k8s_job_prefix", "pull_policy", "pykube_client_from_dict", "delete_job", "delete_service", "delete_ingress", "get_volume_mounts_for_job", "parse_pvc_param_line", )