from .MarkdownTable import MarkdownTable # noqa
import time
import json
from os import system, name
from IPython.display import display, clear_output, Markdown
import ipywidgets as widgets
[docs]class Job:
"""
Job class
Attributes:
client (obj): Client that this job requests information from
maintainer (obj): Maintainer pool that this job is in
isJupyter (bool): Whether or not this is running in Jupyter
jupyterhubApiToken (str): API token needed to send requests
using the JupyterHub API
id (str): Id assigned to this job by the client
hpc (str): HPC that this job will be submitted to
"""
# static variables
basicEventTypes = [
'JOB_QUEUED', 'JOB_REGISTERED', 'JOB_INIT',
'GLOBUS_TRANSFER_INIT_SUCCESS', 'JOB_ENDED', 'JOB_FAILED']
def __init__(self, maintainer=None, hpc=None, id=None, hpcUsername=None, hpcPassword=None,
client=None, isJupyter=None, jupyterhubApiToken=None, printJob=True):
# TODO: we can make this better
if (jupyterhubApiToken is None):
raise Exception('please login to jupyter first')
self.client = client
self.maintainer = maintainer
self.isJupyter = isJupyter
self.jupyterhubApiToken = jupyterhubApiToken
job = None
if (id is None):
# create new job
if maintainer is None:
raise Exception('maintainer cannot by NoneType')
req = {'maintainer': maintainer, 'jupyterhubApiToken': jupyterhubApiToken}
if (hpc is not None):
req['hpc'] = hpc
if (hpcUsername is None):
job = self.client.request('POST', '/job', req)
else:
req['user'] = hpcUsername
req['password'] = hpcPassword
job = self.client.request('POST', '/job', req)
hpc = job['hpc']
id = job['id']
else:
# reinstate existing job
job = self.client.request('GET', '/job/' + id, {'jupyterhubApiToken': jupyterhubApiToken})
hpc = job['hpc']
if (hpcPassword is not None):
print('⚠️ HPC password input detected, change your code to use .get_job_by_id() instead')
print('🙅♂️ it\'s not safe to distribute code with login credentials')
self.id = id
self.hpc = hpc
if printJob:
self._print_job_formatted(job)
[docs] def submit(self):
"""
Submits this job to the client, and prints the output
Returns:
Job: This job
"""
body = {'jupyterhubApiToken': self.jupyterhubApiToken}
job = self.client.request('POST', '/job/' + self.id + '/submit', body)
print('✅ job submitted')
self._print_job_formatted(job)
return self
[docs] def set(self, localExecutableFolder=None, localDataFolder=None, localResultFolder=None, param=None, env=None,
slurm=None, printJob=True):
"""
PUT requests information about this job to the client
so it can be submitted to the hpc. Displays information
about this job unless specified otherwise.
Args:
executableFolder (str): Path of the executable folder
dataFolder (str): Path of the data folder
resultFolder (str): Path of the result folder
param (dict): Rules for input data
env (dict): Enviorment variables required by the appliation
slurm (dict): Slurm input rules
printJob (bool): If the status of the job should be printed
"""
body = {'jupyterhubApiToken': self.jupyterhubApiToken}
if localExecutableFolder:
body['localExecutableFolder'] = localExecutableFolder
if localDataFolder:
body['localDataFolder'] = localDataFolder
if localResultFolder:
body['localResultFolder'] = localResultFolder
if param:
body['param'] = param
if env:
body['env'] = env
if slurm:
body['slurm'] = slurm
if (len(list(body)) == 1):
print('❌ please set at least one parmeter')
job = self.client.request('PUT', '/job/' + self.id, body)
if printJob:
self._print_job(job)
[docs] def events(
self, raw=False,
basic=True,
refreshRateInSeconds=10):
"""
While the job is running, display the events generated by the client
Args:
raw (bool): If true, return a list of the events
generated by status
liveOutput (bool):
basic (bool): If true, exclude non-basicEventType events
RefreshRateInSeconds (int): Number of seconds to wait before
refreshing status
Todo:
Modify function to include liveOutput or remove it
from the arguments
"""
if raw:
return self.status(raw=True)['events']
isEnd = False
while (not isEnd):
self._clear()
status = self.status(raw=True)
out = status['events']
headers = ['types', 'message', 'time']
events = []
for o in out:
# if o['type'] not in self.basicEventTypes and basic:
# continue
events.append([
o['type'],
o['message'],
o['createdAt']
])
isEnd = isEnd or o['type'] == 'JOB_ENDED' or o[
'type'] == 'JOB_FAILED'
print('📮 Job ID: ' + self.id)
if 'slurmId' in status:
print('🤖 Slurm ID: ' + str(status['slurmId']))
def markdown_widget(text):
out = widgets.Output()
with out:
display(Markdown(text))
return out
markdown = MarkdownTable.render(events, headers)
markdown_table = markdown_widget(markdown)
table_exp = widgets.Accordion(children=[markdown_table], selected_index=None)
table_exp.set_title(0, "See events")
if len(events) > 0:
if self.isJupyter:
display(table_exp)
else:
print(markdown)
if not isEnd:
time.sleep(refreshRateInSeconds)
[docs] def logs(self, raw=False, liveOutput=True, refreshRateInSeconds=15):
"""
While the job is running, display the logs generated by the client.
Args:
raw (bool): If true, return a list of the events
generated by status
liveOutput (bool):
RefreshRateInSeconds (int): Number of seconds to wait
before refreshing status
Returns:
list: List of logs generated by the client.
Only returned if raw is true.
Todo:
Modify function to include liveOutput
or remove it from the arguments
"""
if raw:
return self.status(raw=True)['logs']
logs = []
isEnd = False
while (not isEnd):
self._clear()
status = self.status(raw=True)
headers = ['message', 'time']
logs = []
for o in status['events']:
isEnd = isEnd or o['type'] == 'JOB_ENDED' or o[
'type'] == 'JOB_FAILED'
for o in status['logs']:
i = [
o['message'],
o['createdAt']
]
logs.append(i)
print('📮 Job ID: ' + self.id)
if 'slurmId' in status:
print('🤖 Slurm ID: ' + str(status['slurmId']))
def markdown_widget(text):
out = widgets.Output()
with out:
display(Markdown(text))
return out
markdown = MarkdownTable.render(logs, headers)
markdown_table = markdown_widget(markdown)
table_exp = widgets.Accordion(children=[markdown_table], selected_index=None)
table_exp.set_title(0, "See logs")
if len(logs) > 0:
if self.isJupyter:
display(table_exp)
else:
print(markdown)
if not isEnd:
time.sleep(refreshRateInSeconds)
[docs] def status(self, raw=False):
"""
Displays the status of this job, and returns it if specified.
Args:
raw (bool): If information about this job should be returned
Returns:
dict: Infomation about this job returned by
the client. This includes the job's 'id', 'hpc',
'executableFolder', 'dataFolder', 'resultFolder',
'param', 'slurm', 'userId', 'maintainer', 'createdAt', and 'events'
Raises:
Exception: If the 'id' attribute is None
"""
if self.id is None:
raise Exception('missing job ID, submit/register job first')
job = self.client.request('GET', '/job/' + self.id, {
'jupyterhubApiToken': self.jupyterhubApiToken
})
if raw:
return job
self._print_job_formatted(job)
[docs] def result_folder_content(self):
"""
Returns the results from the job
Returns:
dict: Results from running the job
Raises:
Exception: If the id is None
"""
if self.id is None:
raise Exception('missing job ID, submit/register job first')
out = self.client.request('GET', '/job/' + self.id + '/result-folder-content', {'jupyterhubApiToken': self.jupyterhubApiToken})
return out
[docs] def download_result_folder_by_globus(self, localPath=None, localEndpoint=None, remotePath=None, raw=False):
"""
Downloads the folder with results from the job using Globus
Args:
remotePath (string): Path to the remote result folder
raw (bool): If the function should return the
output from the client
Returns:
dict: Output from the client when downloading the
results using globus. Only returned when raw is true.
Raises:
Exception: If the job ID is None
Exception: If the key 'resultFolder' is not returned with status
Exception: If the result folder is formatted improperly
"""
if self.id is None:
raise Exception('missing job ID, submit/register job first')
jobStatus = self.status(raw=True)
if 'remoteResultFolder' not in jobStatus:
raise Exception('executable folder is not ready')
folderId = jobStatus['remoteResultFolder']['id']
# init globus transfer
self.client.request('POST', '/folder/' + folderId + '/download/globus-init', {
"jobId": self.id,
"jupyterhubApiToken": self.jupyterhubApiToken,
"fromPath": remotePath,
"toPath": localPath,
"toEndpoint": localEndpoint
})
status = None
while status not in ['SUCCEEDED', 'FAILED']:
self._clear()
print('⏳ waiting for file to download using Globus')
out = self.client.request('GET', '/folder/' + folderId + '/download/globus-status', {
"jupyterhubApiToken": self.jupyterhubApiToken
})
status = out['status']
if raw:
return out
# exit loop
self._clear()
if status == 'SUCCEEDED':
print('✅ download success!')
else:
print('❌ download fail!')
# Helpers
def _clear(self):
"""
Clears output
"""
if self.isJupyter:
clear_output(wait=True)
# for windows
if name == 'nt':
_ = system('cls')
# for mac and linux(here, os.name is 'posix')
else:
_ = system('clear')
def _print_job(self, job):
"""
Displays information about this job
Args:
job (dict): Information about this job returned by the client
"""
if job is None:
return
headers = [
'id', 'slurmId', 'hpc', 'remoteExecutableFolder', 'remoteDataFolder',
'remoteResultFolder', 'param', 'slurm', 'userId', 'maintainer',
'createdAt']
data = [[
job['id'],
job['slurmId'],
job['hpc'],
job['remoteExecutableFolder'],
job['remoteDataFolder'],
job['remoteResultFolder'],
json.dumps(job['param']),
json.dumps(job['slurm']),
job['userId'],
job['maintainer'],
job['createdAt'],
]]
if self.isJupyter:
display(Markdown(MarkdownTable.render(data, headers)))
else:
print(MarkdownTable.render(data, headers))
def _print_job_formatted(self, job):
"""
Displays information about the job formatted in a way that can be read with no horizonal scroll bar
"""
if job is None:
return
if job['localExecutableFolder'] is None:
modelName = "None"
else:
modelName = job['localExecutableFolder']['gitId']
headersCol1 = [
'id', 'slurmId', 'hpc', 'remoteExecutableFolder', 'remoteDataFolder',
'remoteResultFolder']
headersCol2 = [
'param', 'slurm', 'userId', 'maintainer',
'createdAt', 'modelName']
dataCol1 = [[
job['id'],
job['slurmId'],
job['hpc'],
job['remoteExecutableFolder'],
job['remoteDataFolder'],
job['remoteResultFolder'],
]]
dataCol2 = [[
json.dumps(job['param']),
json.dumps(job['slurm']),
job['userId'],
job['maintainer'],
job['createdAt'],
modelName
]]
if self.isJupyter:
display(Markdown(MarkdownTable.render(dataCol1, headersCol1)))
display(Markdown(MarkdownTable.render(dataCol2, headersCol2)))
else:
print(MarkdownTable.render(dataCol1, headersCol1))
print(MarkdownTable.render(dataCol2, headersCol2))