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Sumarize sort by #256

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Dec 14, 2023
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Sumarize sort by #256

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79 changes: 49 additions & 30 deletions abm/lib/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,37 +192,41 @@ def find_executable(name):
# "swaptotal",
# "uname"

table_header = [
"id",
"history_id",
"history_name",
"state",
"tool_id",
"invocation_id",
"workflow_id",
"cpuacct.usage",
# "end_epoch",
"galaxy_memory_mb",
"galaxy_slots",
# "memory.failcnt",
"memory.limit_in_bytes",
"memory.max_usage_in_bytes",
# "memory.memsw.limit_in_bytes",
# "memory.memsw.max_usage_in_bytes",
# "memory.oom_control.oom_kill_disable",
# "memory.oom_control.under_oom",
"memory.soft_limit_in_bytes",
"memtotal",
"processor_count",
"runtime_seconds",
# "start_epoch",
# "swaptotal",
# "uname"
]

def print_table_header():
print(','.join(table_header))


def summarize_metrics(gi, jobs: list):
table = []
header = [
"id",
"history_id",
"history_name",
"state",
"tool_id",
"invocation_id",
"workflow_id",
"cpuacct.usage",
# "end_epoch",
"galaxy_memory_mb",
"galaxy_slots",
# "memory.failcnt",
"memory.limit_in_bytes",
"memory.max_usage_in_bytes",
# "memory.memsw.limit_in_bytes",
# "memory.memsw.max_usage_in_bytes",
# "memory.oom_control.oom_kill_disable",
# "memory.oom_control.under_oom",
"memory.soft_limit_in_bytes",
"memtotal",
"processor_count",
"runtime_seconds",
# "start_epoch",
# "swaptotal",
# "uname"
]
table.append(header)
# table.append(header)
# print(','.join(header))
for job in jobs:
job_metrics = gi.jobs.get_metrics(job['id'])
Expand All @@ -231,14 +235,14 @@ def summarize_metrics(gi, jobs: list):
if '/' in toolid:
parts = toolid.split('/')
toolid = f'{parts[-2]}/{parts[-1]}'
metrics = metrics_to_dict(job_metrics, header)
metrics = metrics_to_dict(job_metrics, table_header)
metrics['id'] = job.get('id', 'unknown')
metrics['history_id'] = job.get('history_id', 'unknown')
metrics['history_name'] = job.get('history_name', 'unknown')
metrics['state'] = job.get('state', 'unknown')
metrics['tool_id'] = toolid
metrics['invocation_id'] = job.get('invocation_id', 'unknown')
for key in header:
for key in table_header:
if key in metrics:
row.append(metrics[key])
else:
Expand Down Expand Up @@ -334,3 +338,18 @@ def make_result(data):
def _make_dataset_element(name, value):
# print(f"Making dataset element for {name} = {value}({type(value)})")
return dataset_collections.HistoryDatasetElement(name=name, id=value)

def get_float_key(column: int):
def get_key(row: list):
if row[column] == '':
return -1
return float(row[column])
return get_key

def get_str_key(column: int):
# print(f"Getting string key for column {column}")
def get_key(row: list):
# print(f"Sorting by column {column} key {row[column]}")
return row[column]
return get_key

70 changes: 22 additions & 48 deletions abm/lib/experiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
import benchmark
import helm
import yaml
from common import Context, load_profiles, print_markdown_table
from common import Context, load_profiles, print_markdown_table, get_str_key, get_float_key

INVOCATIONS_DIR = "invocations"
METRICS_DIR = "metrics"
Expand Down Expand Up @@ -124,46 +124,16 @@ def summarize(context: Context, args: list):
"""
markdown = False
separator = None
input_dirs = []
make_row = make_table_row
header_row = "Run,Cloud,Job Conf,Workflow,History,Inputs,Tool,Tool Version,State,Slots,Memory,Runtime (Sec),CPU,Memory Limit (Bytes),Memory Max usage (Bytes)"
# for arg in args:
# if arg in ['-t', '--tsv']:
# if separator is not None or markdown:
# print('ERROR: The output format is specified more than once')
# return
# print('tsv')
# separator = '\t'
# elif arg in ['-c', '--csv']:
# if separator is not None or markdown:
# print('ERROR: The output format is specified more than once')
# return
# separator = ','
# print('csv')
# elif arg in ['-m', '--model']:
# if separator is not None or markdown:
# print('ERROR: The output format is specified more than once')
# return
# print('making a model')
# separator = ','
# make_row = make_model_row
# header_row = "job_id,tool_id,tool_version,state,memory.max_usage_in_bytes,cpuacct.usage,process_count,galaxy_slots,runtime_seconds,ref_data_size,input_data_size_1,input_data_size_2"
# elif arg == '--markdown':
# if separator is not None or markdown:
# print('ERROR: The output format is specified more than once')
# return
# markdown = True
# else:
# # print(f"Input dir {arg}")
# input_dirs.append(arg)

parser = argparse.ArgumentParser()
parser.add_argument('dirs', nargs='*')
parser.add_argument('-c', '--csv', action='store_true')
parser.add_argument('-t', '--tsv', action='store_true')
parser.add_argument('-m', '--model', action='store_true')
parser.add_argument('--markdown', action='store_true')
parser.add_argument('-s', '--sort-by', choices=['cpu', 'runtime', 'memory'])
parser.add_argument('-s', '--sort-by', choices=['runtime', 'memory', 'tool'])
argv = parser.parse_args(args)

count = 0
Expand Down Expand Up @@ -197,8 +167,8 @@ def summarize(context: Context, args: list):
separator = ','

if markdown:
print("|Run|Job Conf|Tool|State|Runtime (Sec)|CPU (Sec) |Max Memory (GB)|")
print("|---|---|---|---|---:|---:|---:|")
print("|Run|Inputs|Job Conf|Tool|State|Runtime (Sec)|Max Memory (GB)|")
print("|---|---|---|---|---|---:|---:|")
else:
print(header_row)

Expand All @@ -218,34 +188,38 @@ def summarize(context: Context, args: list):
row = make_row(data)
table.append(row)
except Exception as e:
# Silently fail to allow the remainder of the table to be generated.
print(f"Unable to process {input_path}")
print(e)
traceback.print_exc()
# Silently fail to allow the remainder of the table to be generated.
# pass

def comparator(row):
print('key', row[key])
print('type', type(row[key]))
return row[key]

reverse = True
if argv.sort_by:
key = 0
comp = get_str_key(6)
if argv.sort_by == 'runtime':
key = 10
elif argv.sort_by == 'cpu':
key = 11
# key = 10
comp = get_float_key(10)
# elif argv.sort_by == 'cpu':
# comp = get_float_comparator(11)
# #key = 11
elif argv.sort_by == 'memory':
key = 13
table.sort(key=lambda row: -1 if row[key] == '' else float(row[key]), reverse=True)
comp = get_float_key(13)
# key = 13
elif argv.sort_by == 'tool':
# print('Getting string key accessor.')
comp = get_str_key(6)
reverse = False
# table.sort(key=lambda row: -1 if row[key] == '' else float(row[key]), reverse=True)
table.sort(key=comp, reverse=reverse)

if markdown:
for row in table:
runtime = '' if len(row[10]) == 0 else f"{float(row[10]):4.1f}"
cpu = '' if len(row[11]) == 0 else f"{float(row[11])/10**9:4.1f}"
# cpu = '' if len(row[11]) == 0 else f"{float(row[11])/10**9:4.1f}"
memory = '' if len(row[13]) == 0 else f"{float(row[13])/GB:4.3f}"
# memory = float(row[13]) / GB
print(f"| {row[0]} | {row[2]} | {row[6]} | {row[7]} | {runtime} | {cpu} | {memory} |")
print(f"| {row[0]} | {row[5].split(' ')[0]} |{row[2]} | {row[6]} | {row[7]} | {runtime} | {memory} |")
else:
for row in table:
print(separator.join([str(x) for x in row]))
Expand Down
51 changes: 25 additions & 26 deletions abm/lib/history.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import argparse
import json
import os
import sys
Expand All @@ -8,7 +9,8 @@
import yaml
from bioblend.galaxy.objects import GalaxyInstance
from lib.common import (Context, connect, find_history, parse_profile,
print_json, summarize_metrics, print_markdown_table)
print_json, summarize_metrics, print_markdown_table,
get_float_key, get_str_key, print_table_header)

#
# History related functions
Expand Down Expand Up @@ -339,44 +341,44 @@ def tag(context: Context, args: list):


def summarize(context: Context, args: list):
markdown = False
if '--markdown' in args:
markdown = True
args.remove('--markdown')
parser = argparse.ArgumentParser()
parser.add_argument('id_list', nargs='+')
parser.add_argument('--markdown', action='store_true')
parser.add_argument('-s', '--sort-by', choices=['runtime', 'memory', 'tool'])
argv = parser.parse_args(args)

if len(args) == 0:
if len(argv.id_list) == 0:
print("ERROR: Provide one or more history ID values.")
return
gi = connect(context)
all_jobs = []
while len(args) > 0:
hid = find_history(gi, args.pop(0))
id_list = argv.id_list
while len(id_list) > 0:
hid = find_history(gi, id_list.pop(0))
history = gi.histories.show_history(history_id=hid)
jobs = gi.jobs.get_jobs(history_id=hid)
for job in jobs:
job['invocation_id'] = ''
job['history_id'] = hid
job['history_name'] = history['name']
job['workflow_id'] = ''
# if 'workflow_id' in invocation:
# job['workflow_id'] = invocation['workflow_id']
all_jobs.append(job)
# invocations = gi.invocations.get_invocations(history_id=hid)
# for invocation in invocations:
# id = invocation['id']
# #jobs = gi.jobs.get_jobs(history_id=hid, invocation_id=id)
# jobs = gi.jobs.get_jobs(history_id=hid)
# for job in jobs:
# job['invocation_id'] = id
# job['history_id'] = hid
# if 'workflow_id' in invocation:
# job['workflow_id'] = invocation['workflow_id']
# all_jobs.append(job)
# summarize_metrics(gi, gi.jobs.get_jobs(history_id=args[0]))
table = summarize_metrics(gi, all_jobs)
if markdown:
if argv.sort_by:
reverse = True
get_key = None
if argv.sort_by == 'runtime':
get_key = get_float_key(15)
elif argv.sort_by == 'memory':
get_key = get_float_key(11)
elif argv.sort_by == 'tool':
get_key = get_str_key(4)
reverse = False
table.sort(key=get_key, reverse=reverse)
if argv.markdown:
print_markdown_table(table)
else:
print_table_header()
for row in table:
print(','.join(row))

Expand Down Expand Up @@ -437,9 +439,6 @@ def wait_for(gi: GalaxyInstance, history_id: str):
waiting = False
if waiting:
time.sleep(30)
# elif state == 'paused':
# paused += 1
# print(f"{job['id']}\t{job['state']}\t{job['update_time']}\t{job['tool_id']}")


class JobStates:
Expand Down
31 changes: 21 additions & 10 deletions abm/lib/invocation.py
View file
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
from common import Context, connect, print_json, summarize_metrics, print_markdown_table
import argparse
from common import Context, connect, print_json, summarize_metrics, print_markdown_table, get_float_key, get_str_key, \
print_table_header


def doList(context: Context, args: list):
Expand All @@ -25,14 +27,11 @@ def doList(context: Context, args: list):


def summarize(context: Context, args: list):
markdown = False
if '--markdown' in args:
markdown = True
args.remove('--markdown')

if len(args) == 0:
print("ERROR: Provide one or more invocation ID values.")
return
parser = argparse.ArgumentParser()
parser.add_argument('id', nargs=1)
parser.add_argument('--markdown', action='store_true')
parser.add_argument('-s', '--sort-by', choices=['runtime', 'memory', 'tool'])
argv = parser.parse_args(args)
gi = connect(context)
id = args[0]
all_jobs = []
Expand All @@ -42,8 +41,20 @@ def summarize(context: Context, args: list):
job['workflow_id'] = ''
all_jobs.append(job)
table = summarize_metrics(gi, all_jobs)
if markdown:
if argv.sort_by:
reverse = True
get_key = None
if argv.sort_by == 'runtime':
get_key = get_float_key(15)
elif argv.sort_by == 'memory':
get_key = get_float_key(11)
elif argv.sort_by == 'tool':
get_key = get_str_key(4)
reverse = False
table.sort(key=get_key, reverse=reverse)
if argv.markdown:
print_markdown_table(table)
else:
print_table_header()
for row in table:
print(','.join(row))
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