Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.webapps.reports.controllers.tools
import collections
import logging
from datetime import timedelta
import sqlalchemy as sa
from markupsafe import escape
from sqlalchemy import and_
import galaxy.model
from galaxy.util import (
restore_text,
unicodify
)
from galaxy.webapps.base.controller import BaseUIController, web
log = logging.getLogger(__name__)
[docs]def int_to_octet(size):
try:
size = float(size)
except ValueError:
return "???"
except TypeError:
if size is None:
return "0 o"
return "???"
units = ("o", "Ko", "Mo", "Go", "To")
no_unit = 0
while (size >= 1000):
size /= 1000.
no_unit += 1
try:
return "%.2f %s" % (size, units[no_unit])
except IndexError:
return "%.0f %s" % (size * ((no_unit - len(units) + 1) * 1000.), units[-1])
[docs]class Tools(BaseUIController):
"""
Class defining functions used by reports to make requests to get
informations and fill templates before being displayed.
The name of function must be the same as as the field "action" of
the "href" dict, in .mako templates (templates/webapps/reports).
"""
[docs] def formatted(self, date, colored=False):
splited = str(date).split(',')
if len(splited) == 2:
returned = "%s %dH" % (splited[0], int(splited[1].split(':')[0]))
if colored:
return '<font color="red">' + returned + '</font>'
return returned
else:
splited = tuple([float(_) for _ in str(date).split(':')])
if splited[0]:
returned = '%d h. %d min.' % splited[:2]
if colored:
return '<font color="orange">' + returned + '</font>'
return returned
if splited[1]:
return "%d min. %d sec." % splited[1:3]
return "%.1f sec." % splited[2]
[docs] @web.expose
def tools_and_job_state(self, trans, **kwd):
"""
fill tools_and_job_state.mako template with
- the name of the tool
- the number of jobs using this tool in state 'ok'
- the number of jobs using this tool in error
"""
message = escape(restore_text(kwd.get('message', '')))
user_cutoff = int(kwd.get('user_cutoff', 60))
# sort by history space, or by user mail or by number of history/dataset
sort_by = kwd.get('sorting', 'Tool')
sorting = 0 if sort_by == 'Tool' else 1 if sort_by == 'ok' else 2
descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
reverse = descending == 1
sort_keys = (
lambda v: v.lower(),
lambda v: tools_and_jobs_ok.get(v, 0),
lambda v: tools_and_jobs_error.get(v, 0))
data = collections.OrderedDict()
# select count(id), tool_id from job where state='ok' group by tool_id;
tools_and_jobs_ok = sa.select((galaxy.model.Job.table.c.tool_id .label('tool'),
sa.func.count(galaxy.model.Job.table.c.id).label('job')),
from_obj=[galaxy.model.Job.table],
whereclause=(galaxy.model.Job.table.c.state == 'ok'),
group_by=['tool'])
# select count(id), tool_id from job where state='error' group by tool_id;
tools_and_jobs_error = sa.select((galaxy.model.Job.table.c.tool_id .label('tool'),
sa.func.count(galaxy.model.Job.table.c.id).label('job')),
from_obj=[galaxy.model.Job.table],
whereclause=(galaxy.model.Job.table.c.state == 'error'),
group_by=['tool'])
tools_and_jobs_ok = dict(list(tools_and_jobs_ok.execute()))
tools_and_jobs_error = dict(list(tools_and_jobs_error.execute()))
# select each job name one time
tools = list(set(tools_and_jobs_ok.keys()) | set(tools_and_jobs_error.keys()))
tools.sort(key=sort_keys[sorting], reverse=reverse)
for tool in tools:
data[tool] = (str(tools_and_jobs_ok.get(tool, '-')), str(tools_and_jobs_error.get(tool, '-')))
return trans.fill_template('/webapps/reports/tools_and_job_state.mako',
data=data,
user_cutoff=user_cutoff,
sorting=sorting,
descending=descending,
message=message)
[docs] @web.expose
def tools_and_job_state_per_month(self, trans, **kwd):
"""
fill tools_and_job_state_per_month.mako template with
- the name of the tool
- the number of jobs using this tool in state 'ok'
- the number of jobs using this tool in error
"""
message = escape(restore_text(kwd.get('message', '')))
user_cutoff = int(kwd.get('user_cutoff', 60))
# sort by history space, or by user mail or by number of history/dataset
# sort_by = kwd.get( 'sorting', 'Tool' )
# sorting = 0 if sort_by == 'Tool' else 1 if sort_by == 'ok' else 2
# descending = 1 if kwd.get( 'descending', 'desc' ) == 'desc' else -1
tool = kwd.get('tool', None)
if tool is None:
raise TypeError("Tool can't be None")
data = collections.OrderedDict()
# select count(id), create_time from job where state='ok' and tool_id=$tool group by date;
date_and_jobs_ok = sa.select((sa.func.date(galaxy.model.Job.table.c.create_time).label('date'),
sa.func.count(galaxy.model.Job.table.c.id).label('job')),
from_obj=[galaxy.model.Job.table],
whereclause=and_(galaxy.model.Job.table.c.state == 'ok', galaxy.model.Job.table.c.tool_id == tool),
group_by=['date'])
# select count(id), create_time from job where state='error' and tool_id=$tool group by date;
date_and_jobs_error = sa.select((sa.func.date(galaxy.model.Job.table.c.create_time).label('date'),
sa.func.count(galaxy.model.Job.table.c.id).label('job')),
from_obj=[galaxy.model.Job.table],
whereclause=and_(galaxy.model.Job.table.c.state == 'error', galaxy.model.Job.table.c.tool_id == tool),
group_by=['date'])
date_and_jobs_ok = dict(list(date_and_jobs_ok.execute()))
date_and_jobs_error = dict(list(date_and_jobs_error.execute()))
# select each date
dates = list(set(date_and_jobs_ok.keys()) | set(date_and_jobs_error.keys()))
dates.sort(reverse=True)
for date in dates:
date_key = date.strftime("%B %Y")
if date_key not in data:
data[date_key] = [int(date_and_jobs_ok.get(date, 0)), int(date_and_jobs_error.get(date, 0))]
else:
data[date_key][0] += int(date_and_jobs_ok.get(date, 0))
data[date_key][1] += int(date_and_jobs_error.get(date, 0))
return trans.fill_template('/webapps/reports/tools_and_job_state_per_month.mako',
data=data,
tool=tool,
user_cutoff=user_cutoff,
message=message)
[docs] @web.expose
def tool_execution_time(self, trans, **kwd):
"""
Fill the template tool_execution_time.mako with informations:
- Tool name
- Tool average execution time
- last job execution time
- min and max execution time
"""
# liste des tools + temps moyen d'exec du job + temps d'execution du dernier job + tps min et max / mois (?)
user_cutoff = int(kwd.get("user_cutoff", 60))
sort_by = kwd.get("sort_by", "tool")
descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
reverse = descending == 1
sort_by = 0 if sort_by == "tool" else 1 if sort_by == "avg" else 2 if sort_by == "min" else 3
color = True if kwd.get("color", '') == "True" else False
data = {}
ordered_data = collections.OrderedDict()
sort_keys = (
lambda v: v.lower(),
lambda v: data[v]['avg'],
lambda v: data[v]['min'],
lambda v: data[v]['max'])
jobs_times = sa.select((galaxy.model.Job.table.c.tool_id.label("name"),
galaxy.model.Job.table.c.create_time.label("create_time"),
galaxy.model.Job.table.c.update_time.label("update_time"),
galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
from_obj=[galaxy.model.Job.table])
jobs_times = [(name, (create, update, time)) for name, create, update, time in jobs_times.execute()]
for tool, attr in jobs_times:
if tool not in data:
data[tool] = {"last": [(attr[1], attr[0])], "avg": [attr[2]]}
else:
data[tool]["last"].append((attr[1], attr[0]))
data[tool]["avg"].append(attr[2])
for tool in data:
data[tool]["min"] = min(data[tool]["avg"])
data[tool]["max"] = max(data[tool]["avg"])
last = max(data[tool]["last"])
data[tool]["last"] = last[0] - last[1]
data[tool]["avg"] = sum(data[tool]["avg"], timedelta()) / len(data[tool]["avg"])
tools = list(data.keys())
if user_cutoff:
tools = tools[:user_cutoff]
tools.sort(key=sort_keys[sort_by], reverse=reverse)
for tool in tools:
ordered_data[tool] = {"min": self.formatted(data[tool]["min"], color),
"max": self.formatted(data[tool]["max"], color),
"avg": self.formatted(data[tool]["avg"], color),
"last": self.formatted(data[tool]["last"], color)}
return trans.fill_template('/webapps/reports/tool_execution_time.mako',
data=ordered_data,
descending=descending,
user_cutoff=user_cutoff,
sort_by=sort_by)
[docs] @web.expose
def tool_execution_time_per_month(self, trans, **kwd):
"""
Fill the template tool_execution_time_per_month.mako with informations:
- Tool average execution time
- last job execution time
- min and max execution time
"""
# liste des tools + temps moyen d'exec du job + temps d'execution du dernier job + tps min et max / mois(?)
user_cutoff = int(kwd.get("user_cutoff", 60))
sort_by = kwd.get("sort_by", "month")
descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
reverse = descending == 1
sort_by = 0 if sort_by == "month" else 1 if sort_by == "min" else 2 if sort_by == "max" else 3
tool = kwd.get("tool", None)
color = True if kwd.get("color", '') == "True" else False
if tool is None:
raise ValueError("Tool can't be None")
ordered_data = collections.OrderedDict()
sort_keys = [(lambda v, i=i: v[i]) for i in range(4)]
jobs_times = sa.select((sa.func.date_trunc('month', galaxy.model.Job.table.c.create_time).label('date'),
sa.func.max(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
sa.func.avg(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
sa.func.min(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time)),
from_obj=[galaxy.model.Job.table],
whereclause=galaxy.model.Job.table.c.tool_id == tool,
group_by=['date'])
months = list(jobs_times.execute())
months.sort(key=sort_keys[sort_by], reverse=reverse)
if user_cutoff:
months = months[:user_cutoff]
for month in months:
ordered_data[str(month[0]).split(' ')[0][:-3]] = (self.formatted(month[1], color),
self.formatted(month[2], color),
self.formatted(month[3], color))
return trans.fill_template('/webapps/reports/tool_execution_time_per_month.mako',
data=ordered_data,
tool=tool,
descending=descending,
user_cutoff=user_cutoff,
sort_by=sort_by)
[docs] @web.expose
def tool_error_messages(self, trans, **kwd):
tool_name = kwd.get("tool", None)
descending = 1 if kwd.get("descending", 'desc') == "desc" else -1
reverse = descending == 1
sort_by = 0 if kwd.get("sort_by", "time") == "time" else 1
cutoff = int(kwd.get("user_cutoff", 60))
sort_keys = (
lambda v: counter[v][1],
lambda v: counter[v][0])
if tool_name is None:
raise ValueError("Tool can't be none")
tool_errors = [[unicodify(a), b] for a, b in
sa.select((galaxy.model.Job.table.c.stderr, galaxy.model.Job.table.c.create_time),
from_obj=[galaxy.model.Job.table],
whereclause=and_(galaxy.model.Job.table.c.tool_id == tool_name,
galaxy.model.Job.table.c.state == 'error')).execute()]
counter = {}
for error in tool_errors:
if error[0] in counter:
counter[error[0]][0] += 1
else:
counter[error[0]] = [1, error[1]]
data = collections.OrderedDict()
keys = list(counter.keys())
if cutoff:
keys = keys[:cutoff]
keys.sort(key=sort_keys[sort_by], reverse=reverse)
spaces = [' ', '\t', ' ']
for key in keys:
new_key = '</br>'.join(_ for _ in key.split('\n') if _ and _ not in spaces)
if len(new_key) >= 100:
to_replace = []
words = key.split('\n')
for word in words:
if word in to_replace:
continue
if words.count(word) > 1:
to_replace.append(word)
for word in to_replace:
sentence = ("</br>" + word) * 2
count = 2
while sentence + "</br>" + word in new_key:
sentence += "</br>" + word
count += 1
if sentence in new_key:
new_key = new_key.replace(sentence, '</br>' + word + " [this line in %d times]" % (count))
data[new_key] = counter[key]
return trans.fill_template("/webapps/reports/tool_error_messages.mako",
data=data,
descending=descending,
tool_name=tool_name,
sort_by=sort_by,
user_cutoff=cutoff)