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iv-request.py
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iv-request.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 26 08:44:21 2022
@author: kkmattil
"""
import json
import datetime
import time
import re
import os
import swiftclient
from swiftclient.multithreading import OutputManager
from swiftclient.service import SwiftError, SwiftService, SwiftUploadObject
import getpass
############################################################################
##upload a large file
#return job description information as a python dictionary
def get_task_json(target_task):
#print("jobs/"+_user+"/"+target_task+"/task.json")
task_json_link=("jobs/"+_user+"/"+target_task+"/task.json")
task_json=conn.get_object(bucket, task_json_link)[1]
task_description=json.loads(task_json)
return task_description
#return biobank specific job description information as a python dictionary
def get_task_json_biobank(target_task, biobank):
task_json_link=("jobs/"+_user+"/"+target_task+"/"+biobank+"/task.json")
task_json=conn.get_object(bucket, task_json_link)[1]
task_description=json.loads(task_json)
return task_description
#Upload process that allows uploading over 5 GB files
def upload_large_file(bucket_name, object_name):
# limit upload threads to 4
if os.path.isfile(object_name):
#limit upload threads to 4
opts = {'object_uu_threads': 4, 'os_auth_url' : _authurl, 'os_username' : _user, 'os_password' : _key, 'os_project_name' : _project, 'os_project_domain_name' : 'Default' }
with SwiftService(options=opts) as swift:
for r in swift.upload(bucket_name, [ object_name ], { 'segment_size': 5000000000}):
if r['success']:
if 'object' in r:
print(r['object'])
elif 'for_object' in r:
print(
'%s segment %s' % (r['for_object'],
r['segment_index'])
)
else:
print(r)
else:
print("ERROR: File "+object_name+" not found.")
exit()
#Download process that allows downloading over 5 GB files
def download_large_file(bucket_name, object_name, out_file):
# limit upload threads to 4
opts = {'object_uu_threads': 4, 'os_auth_url' : _authurl, 'os_username' : _user, 'os_password' : _key, 'os_project_name' : _project, 'os_project_domain_name' : 'Default', 'out_file' : out_file }
with SwiftService(options=opts) as swift:
for r in swift.download(bucket_name, [ object_name ]):
if r['success']:
if 'object' in r:
print(r['object'])
elif 'for_object' in r:
print(
'%s segment %s' % (r['for_object'],
r['segment_index'])
)
else:
print(r)
#Subroutine to manage selection from several options
def selectFromDict(options, name, atric):
index = 0
indexValidList = []
print('Select '+atric+' ' + name + ':')
for optionName in options:
index = index + 1
indexValidList.extend([options[optionName]])
print(str(index) + ') ' + optionName)
inputValid = False
while not inputValid:
inputRaw = input(name + ': ')
if str.isdigit(inputRaw):
inputNo = int(inputRaw) - 1
if inputNo > -1 and inputNo < len(indexValidList):
selected = indexValidList[inputNo]
print('Selected ' + name + ': ' + selected)
inputValid = True
break
else:
print('Please select a valid ' + name + ' number')
else:
print(inputRaw+" is not a valid selection. Please select again. " )
return selected
###
##parameters for prs-pipe test run
def set_prspipe_parameters():
# inputs=["2004504-prspipe/prspipe_8.7.22.tar"]
inputs=[
{
"name": "infile",
"description": "tar-package containing all data neede",
"bucket": "2004504-prspipe",
"object": "prspipe_8.7.22.tar",
"url": "/2004504-prspipe/prspipe_8.7.22.tar",
"path": "./prspipe_8.7.22.tar",
"type": "FILE"
},
]
output_names=["prspipe_results.zip"]
instructions=[
{
"bucket": "2004504-prspipe",
"object": "/prspipe_README.md"
}
]
requirements=["singularity"]
resources= {
"cpuCores": 4,
"ramGb": 8.0,
"diskGb": 100.0,
"timeHours": 2,
"preemptible": False
},
return(inputs, output_names, instructions, requirements, resources)
## parameters for pgsc_calc test run
def set_pgsc_calc_parameters():
requirements=["singularity", "nextflow"]
# inputs=["2004504-prspipe/prspipe_8.7.22.tar"]
resources= {
"cpuCores": 4,
"ramGb": 16.0,
"diskGb": 100.0,
"timeHours": 2,
"preemptible": False
},
inputs=[
{
"name": "pgsc_calc_7.10.22.tar",
"description": "tar-package containing pgsc_calc",
"bucket": "2004504-pgsc_calc",
"object": "gsc_calc_7.10.22.tar",
"url": "/2004504-pgsc_calc/pgsc_calc_7.10.22.tar",
"path": "./pgsc_calc_7.10.22.tar",
"type": "FILE"
}
]
output_names=["pgsc_calc_results.zip"]
#input file
instructions=[
{
"bucket": "2004504-pgsc_calc",
"object": "/pgsc_calc_README.md"
}
]
return(inputs, output_names, instructions, requirements, resources)
## tool to pick target biobanks
def select_biobanks():
all_biobanks=["HUS", "Estonia_Biobank", "HUNT", "FIMM", "CSC"]
print("Select target biobanks:")
run_selection=True
while run_selection:
selected_biobanks=[]
for biobank in all_biobanks:
ansver=input("Include biobank "+biobank+"(y/n)?")
if ansver == "y" or ansver == "Y" or ansver == "yes":
selected_biobanks.append(biobank)
print("Selected biobanks:")
print(selected_biobanks)
ansver=input("Is this section OK(y/n)?")
if ansver == "y" or ansver == "Y" or ansver == "yes":
run_selection=False
return(selected_biobanks)
###
#parameters for job file
def upload_new_task(_user,conn):
# Currently availalble tasks
available_tasks = {}
available_tasks['prspipe'] = 'prspipe'
available_tasks['pgsc_calc'] = 'pgsc_calc'
available_tasks['other'] = 'other'
available_tasks['none'] = 'none'
tasktype=selectFromDict(available_tasks, "analysis pipeline", "an")
if tasktype=="none":
return()
taskname=input("Give a name for your task:")
print("\n")
email=input("Give contact email address: ")
available_biobanks=select_biobanks()
#available_biobanks=["HUS", "Estonia_Biobank"]
jobid=(str(int(time.time()))+"-"+_user)
workdir=(_user+"/"+str(jobid))
storage="allas"
general_task_description="none"
print("\n")
if tasktype == "prspipe":
general_task_description="Predefined PRSPIPE fucntionality test."
task_parameters=set_prspipe_parameters()
inputs=task_parameters[0]
output_names=task_parameters[1]
instructions=task_parameters[2]
requirements=task_parameters[3]
resources=task_parameters[4]
if tasktype == "pgsc_calc":
general_task_description="Predefined PGSC_CALC fucntionality test."
task_parameters=set_pgsc_calc_parameters()
inputs=task_parameters[0]
output_names=task_parameters[1]
instructions=task_parameters[2]
requirements=task_parameters[3]
resources=task_parameters[4]
input_file=input("Give pgsc_calc input data file: ")
pseudofolder=("jobs/"+workdir+"/input")
upload_large_file(bucket+"/"+pseudofolder, input_file)
input_definition={
"name": input_file,
"description": "input provided by requestor",
"bucket": bucket,
"object": (pseudofolder+input_file),
"url": (bucket+"/"+pseudofolder+"/"+input_file),
"path": input_file,
"type": "FILE"
}
inputs.append(input_definition)
if tasktype == "other":
general_task_description="User specified task"
pseudofolder=("jobs/"+workdir+"/input")
#Define input files
inputs = []
input_file = "x"
print("\n")
print("Give the names of input files including the sorfware containers.")
print("Give empty file name to stop importing new input files.")
while input_file != "":
input_file=input("Give new input data file: ")
print("\n")
if input_file != "":
upload_large_file(bucket+"/"+pseudofolder, input_file)
input_definition={
"name": input_file,
"description": "input provided by requestor",
"bucket": bucket,
"object": pseudofolder+"/"+input_file,
"url": (bucket+"/"+pseudofolder+"/"+input_file),
"path": input_file,
"type": "FILE"
}
inputs.append(input_definition)
#Define output files
output_names = []
output_file = "x"
print("\n")
print("Give the names of output files to be returned.")
print("Give empty file name to stop importing new output files.")
while output_file != "":
print("\n")
output_file=input("Give new output data file: ")
if output_file != "":
output_names.append(output_file)
#Define requirements
requirements = []
requirement = "x"
print("\n")
print("Give the techincal requirements of the task.")
print("Give empty name to stop importing new requirements.")
while requirement != "":
if requirement != "":
print("\n")
requirement=input("Give requirement: ")
requirements.append(requirement)
#resource request
print("Give the resouce requirements of the task.")
cores = input("How many cores should be used(default 1):") or 1
ram = input("How much memory is needed (GB, default 2):") or 2
disk=input("Hom much disk space is needed (GB, default 20): ") or 20
hours=input("Maximum runtime in hours (default 1): ") or 1
resources= {
"cpuCores": cores,
"ramGb": ram,
"diskGb": disk,
"timeHours": hours,
"preemptible": False
},
#Define instructions
print("\n")
print("Give the file that contains instructios to run the task.")
instructions_file=input("Give instructions data file: ")
upload_large_file(bucket+"/"+pseudofolder, instructions_file)
instructions=[
{
"bucket": bucket,
"object": (pseudofolder+"/"+instructions_file)
}
]
#create task directories and files for each biobank
for biobank in available_biobanks:
job_file_name="task.json"
outputs= []
for ofile in output_names:
o_item= {
"bucket": bucket,
"object": ("jobs/"+workdir+"/"+biobank+"/results/"+ofile),
"url" : (bucket+"/jobs/"+workdir+"/"+biobank+"/results/"+ofile),
"path" : ("./"+ofile)
}
outputs.append(o_item)
task_json = {"ID": jobid,
"name": taskname,
"description": general_task_description,
"csc-user": _user,
"requestor": email,
"date": str(datetime.datetime.now()),
"biobanks": available_biobanks,
"requirements": requirements,
"resources": resources,
"storageserver": storage,
"inputs": inputs,
"outputs": outputs,
"instructions": instructions
}
print("Uploading job "+jobid+" to "+bucket+" for "+biobank)
#move object to allas
object_dir=("jobs/"+workdir+"/"+biobank)
object_name=(object_dir+"/"+job_file_name)
conn.put_object(bucket, object_name, contents=json.dumps(task_json, indent=2), content_type='text/plain')
# copy_large_file(object_dir, job_file_name)
full_allas_path=(object_dir+"/"+job_file_name)
#create status object
status_object=("jobs/"+workdir+"/"+biobank+"/status/submitted")
conn.put_object(bucket, status_object ,
contents=(task_json["date"]),
content_type='text/plain')
#make a note file for biobak.
note_object=(biobank+"/requests/"+jobid)
conn.put_object(bucket, note_object ,
contents=(full_allas_path),
content_type='text/plain')
#add common json file
object_name=("jobs/"+workdir+"/task.json")
conn.put_object(bucket, object_name, contents=json.dumps(task_json, indent=2), content_type='text/plain')
def update_task_lists(conn):
#this function returns updated my_tasks list and task_status_info that
# is a list of dictionaries
#list all objects in the bucket
all_objs=conn.get_container(bucket)[1]
#print("Debug1:")
#print(all_objs)
my_tasks=[]
task_status_info=[]
task_status_dict={}
if len(all_objs) == 0 :
return(my_tasks,task_status_info)
#print("Collecting task information.")
print(" ")
for j in all_objs:
if re.search("jobs/"+_user+"/", j["name"] ):
#if re.search("/status/", j["name"] ):
task_row=(j["name"])
#print("Task row: "+task_row)
task=task_row.split("/")[2]
if task not in my_tasks:
my_tasks.append(task)
#print("Adding:"+task)
#print("Debug 3 ")
#print(my_tasks)
for task in my_tasks:
task_desc=get_task_json(task)
biobanks=task_desc["biobanks"]
#print(task+" : ")
#print(biobanks)
task_status_dict={"id": task}
#print("Evaluating "+task+" in ")
#print(biobanks)
for biobank in biobanks:
task_stat_num=0
# check all object for given biobank and task combibation
for jj in all_objs:
if re.search(task+"/"+biobank+"/status/ready", jj["name"]):
task_stat_num=task_stat_num+4
#print(jj["name"]+" ready"+task_stat_num)
if re.search(task+"/"+biobank+"/status/processing", jj["name"]):
task_stat_num=task_stat_num+2
#print(jj["name"]+" proc")
if re.search(task+"/"+biobank+"/status/submitted", jj["name"]):
task_stat_num=task_stat_num+1
#print(jj["name"]+" submitted")
# infer the status of tasks based on checks
if task_stat_num==7 or task_stat_num==5 or task_stat_num==4:
task_status_dict[biobank]="ready"
#print("Debug:"+task+" "+biobank+"ready")
if task_stat_num==3:
task_status_dict[biobank]="processing"
if task_stat_num==1:
task_status_dict[biobank]="submitted"
task_status_info.append(task_status_dict)
return(my_tasks,task_status_info)
####################################################################
# Main program starts here
#
_authurl = 'https://pouta.csc.fi:5001/v3'
_auth_version = '3'
_user = input('CSC username: \n')
_key = getpass.getpass('CSC password: \n')
storage="allas"
_os_options = {
'user_domain_name': 'Default',
'project_domain_name': 'Default',
'project_name': 'project_2004504'
}
_project = _os_options["project_name"]
bucket=(_project+"-intervene-tasks")
conn = swiftclient.Connection(
authurl=_authurl,
user=_user,
key=_key,
os_options=_os_options,
auth_version=_auth_version
)
print("parameters for allas connection")
#_authurl = 'https://pouta.csc.fi:5001/v3'
#_auth_version = '3'
#_user = input('CSC username: \n')
#_key = getpass.getpass('CSC password: \n')
#
#
#_os_options = {
# 'user_domain_name': 'Default',
# 'project_domain_name': 'Default',
# 'project_name': 'project_2004504'
#}
dothis = "start"
#####################
##List my tasks
my_tasks=[]
task_selection_dict = {}
task_download_dict= {}
task_upload_dict={}
################
my_tasks, task_status_info = update_task_lists(conn)
job_operations = {}
job_operations['list'] = 'list'
job_operations['submit'] = 'submit'
job_operations['download'] = 'download'
job_operations['delete'] = 'delete'
job_operations['update task list'] = 'update task list'
job_operations['quit'] = 'quit'
#biobanks=["HUS","Estonia_Biobank"]
while dothis != "quit":
dothis=selectFromDict(job_operations, "operation", "an")
print("")
if dothis == "update task list":
my_tasks, task_status_info = update_task_lists(conn)
if dothis == "list":
##List my tasks
print("Tasks submitted by user "+_user)
for task_status_dict in task_status_info:
print("Task:"+task_status_dict["id"])
task_desc=get_task_json(task_status_dict["id"])
biobanks=task_desc["biobanks"]
for biobank in biobanks:
#print out status of each biobank
print(" "+biobank+": "+task_status_dict[biobank])
print(" ")
if dothis == "submit":
upload_new_task(_user, conn)
my_tasks, task_status_info = update_task_lists(conn)
if dothis == "delete":
#previous_jobid="x"
job_dict = {}
for jobid in my_tasks:
job_dict[jobid] = jobid
job_dict["None"] = "None"
jobid=selectFromDict(job_dict, "task", "a")
#print(job_status_objects.split("/")[3])
if jobid != "None" :
for j in conn.get_container(bucket)[1]:
print(j["name"])
if re.search(jobid, j["name"]):
print("Deleting object "+j["name"])
conn.delete_object(bucket,j["name"])
# update task list after deleting
my_tasks, task_status_info = update_task_lists(conn)
if dothis == "download":
print("Listing ready tasks")
tasks_ready=[]
# check taks that are ready for download
my_tasks, task_status_info = update_task_lists(conn)
for task_status_dict in task_status_info:
task=task_status_dict["id"]
#print("Task:"+task)
task_desc=get_task_json(task)
biobanks=task_desc["biobanks"]
non_ready_biobanks=0
ready_biobanks=0
for biobank in biobanks:
#print out status of each biobank
if task_status_dict[biobank] != "ready":
non_ready_biobanks=(non_ready_biobanks + 1)
if task_status_dict[biobank] == "ready":
ready_biobanks=(ready_biobanks +1 )
if non_ready_biobanks == 0 :
tasks_ready.append(task)
print(task+" ready")
else:
print(task+" "+str(ready_biobanks)+" bioanks ready. " +str(non_ready_biobanks)+" biobanks missing." )
task_download_dict={}
for task in tasks_ready:
task_download_dict[task]=task
task_download_dict["none"]="none"
download_task=selectFromDict(task_download_dict, "task", "a")
# Download the output files or selected task
if download_task != "none":
task_desc=get_task_json(download_task)
downloaddir=download_task
isExist = os.path.exists(downloaddir)
#print("Dir test")
if not isExist:
# Create a new directory because it does not exist
os.makedirs(downloaddir)
for biobank in task_desc["biobanks"]:
#create biobank specific subdeirectories
isExist = os.path.exists(downloaddir+"/"+biobank)
if not isExist:
os.makedirs(downloaddir+"/"+biobank)
task_biobank_desc=get_task_json_biobank(download_task, biobank)
for output_file in task_biobank_desc["outputs"]:
print(" ")
print("Downloading "+output_file["url"]+" to "+download_task+"/"+biobank+"/"+output_file["path"])
download_large_file(bucket, output_file["object"], download_task+"/"+biobank+"/"+output_file["path"])