import calendar, operator, os, socket
from datetime import datetime, date, timedelta
from time import mktime, strftime, localtime
from galaxy.web.base.controller import BaseUIController, web
from galaxy import model, util
from galaxy.web.framework.helpers import time_ago, iff, grids
from galaxy.model.orm import and_, not_, or_
import pkg_resources
pkg_resources.require( "SQLAlchemy >= 0.4" )
import sqlalchemy as sa
import logging
log = logging.getLogger( __name__ )
[docs]class SpecifiedDateListGrid( grids.Grid ):
[docs] class JobIdColumn( grids.IntegerColumn ):
[docs] def get_value( self, trans, grid, job ):
return job.id
[docs] class StateColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, job ):
return '<div class="count-box state-color-%s">%s</div>' % ( job.state, job.state )
[docs] def filter( self, trans, user, query, column_filter ):
if column_filter == 'Unfinished':
return query.filter( not_( or_( model.Job.table.c.state == model.Job.states.OK,
model.Job.table.c.state == model.Job.states.ERROR,
model.Job.table.c.state == model.Job.states.DELETED ) ) )
return query
[docs] class CreateTimeColumn( grids.DateTimeColumn ):
[docs] def get_value( self, trans, grid, job ):
return job.create_time.strftime("%b %d, %Y, %H:%M:%S")
[docs] class UserColumn( grids.GridColumn ):
[docs] def get_value( self, trans, grid, job ):
if job.user:
return job.user.email
return 'anonymous'
[docs] class EmailColumn( grids.GridColumn ):
[docs] def filter( self, trans, user, query, column_filter ):
if column_filter == 'All':
return query
return query.filter( and_( model.Job.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == column_filter ) )
[docs] class SpecifiedDateColumn( grids.GridColumn ):
[docs] def filter( self, trans, user, query, column_filter ):
if column_filter == 'All':
return query
# We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM,
# so we need to figure out which type of date we have
if column_filter.count( '-' ) == 2: # We are filtering on a date like YYYY-MM-DD
year, month, day = map( int, column_filter.split( "-" ) )
start_date = date( year, month, day )
end_date = start_date + timedelta( days=1 )
if column_filter.count( '-' ) == 1: # We are filtering on a month like YYYY-MM
year, month = map( int, column_filter.split( "-" ) )
start_date = date( year, month, 1 )
end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] )
return query.filter( and_( self.model_class.table.c.create_time >= start_date,
self.model_class.table.c.create_time < end_date ) )
# Grid definition
use_async = False
model_class = model.Job
title = "Jobs"
template = '/webapps/reports/grid.mako'
default_sort_key = "id"
columns = [
JobIdColumn( "Id",
key="id",
link=( lambda item: dict( operation="job_info", id=item.id, webapp="reports" ) ),
attach_popup=False,
filterable="advanced" ),
StateColumn( "State",
key="state",
attach_popup=False ),
ToolColumn( "Tool Id",
key="tool_id",
link=( lambda item: dict( operation="tool_per_month", id=item.id, webapp="reports" ) ),
attach_popup=False ),
CreateTimeColumn( "Creation Time",
key="create_time",
attach_popup=False ),
UserColumn( "User",
key="email",
model_class=model.User,
link=( lambda item: dict( operation="user_per_month", id=item.id, webapp="reports" ) ),
attach_popup=False ),
# Columns that are valid for filtering but are not visible.
SpecifiedDateColumn( "Specified Date",
key="specified_date",
visible=False ),
EmailColumn( "Email",
key="email",
model_class=model.User,
visible=False ),
grids.StateColumn( "State",
key="state",
visible=False,
filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search",
cols_to_filter=[ columns[1], columns[2] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
standard_filters = []
default_filter = { 'specified_date' : 'All' }
num_rows_per_page = 50
preserve_state = False
use_paging = True
[docs] def build_initial_query( self, trans, **kwd ):
params = util.Params( kwd )
monitor_email = params.get( 'monitor_email', 'monitor@bx.psu.edu' )
monitor_user_id = get_monitor_id( trans, monitor_email )
return trans.sa_session.query( self.model_class ) \
.join( model.User ) \
.filter( model.Job.table.c.user_id != monitor_user_id )\
.enable_eagerloads( False )
[docs]class Jobs( BaseUIController ):
"""
Class contains functions for querying data requested by user via the webapp. It exposes the functions and
responds to requests with the filled .mako templates.
"""
specified_date_list_grid = SpecifiedDateListGrid()
@web.expose
[docs] def specified_date_handler( self, trans, **kwd ):
# We add params to the keyword dict in this method in order to rename the param
# with an "f-" prefix, simulating filtering by clicking a search link. We have
# to take this approach because the "-" character is illegal in HTTP requests.
if 'f-specified_date' in kwd and 'specified_date' not in kwd:
# The user clicked a State link in the Advanced Search box, so 'specified_date'
# will have been eliminated.
pass
elif 'specified_date' not in kwd:
kwd[ 'f-specified_date' ] = 'All'
else:
kwd[ 'f-specified_date' ] = kwd[ 'specified_date' ]
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "job_info":
return trans.response.send_redirect( web.url_for( controller='jobs',
action='job_info',
**kwd ) )
elif operation == "tool_for_month":
kwd[ 'f-tool_id' ] = kwd[ 'tool_id' ]
elif operation == "tool_per_month":
# The received id is the job id, so we need to get the job's tool_id.
job_id = kwd.get( 'id', None )
job = get_job( trans, job_id )
kwd[ 'tool_id' ] = job.tool_id
return trans.response.send_redirect( web.url_for( controller='jobs',
action='tool_per_month',
**kwd ) )
elif operation == "user_for_month":
kwd[ 'f-email' ] = util.restore_text( kwd[ 'email' ] )
elif operation == "user_per_month":
# The received id is the job id, so we need to get the id of the user
# that submitted the job.
job_id = kwd.get( 'id', None )
job = get_job( trans, job_id )
if job.user:
kwd[ 'email' ] = job.user.email
else:
kwd[ 'email' ] = None # For anonymous users
return trans.response.send_redirect( web.url_for( controller='jobs',
action='user_per_month',
**kwd ) )
elif operation == "specified_date_in_error":
kwd[ 'f-state' ] = 'error'
elif operation == "unfinished":
kwd[ 'f-state' ] = 'Unfinished'
return self.specified_date_list_grid( trans, **kwd )
@web.expose
[docs] def specified_month_all( self, trans, **kwd ):
"""
Queries the DB for all jobs in given month, defaults to current month.
"""
message = ''
params = util.Params( kwd )
monitor_email = params.get( 'monitor_email', 'monitor@bx.psu.edu' )
# In case we don't know which is the monitor user we will query for all jobs
monitor_user_id = get_monitor_id( trans, monitor_email )
# If specified_date is not received, we'll default to the current month
specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) )
specified_month = specified_date[ :7 ]
year, month = map( int, specified_month.split( "-" ) )
start_date = date( year, month, 1 )
end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] )
month_label = start_date.strftime( "%B" )
year_label = start_date.strftime( "%Y" )
month_jobs = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ),
sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ),
whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id,
model.Job.table.c.create_time >= start_date,
model.Job.table.c.create_time < end_date ),
from_obj=[ model.Job.table ],
group_by=[ 'date' ],
order_by=[ sa.desc( 'date' ) ] )
jobs = []
for row in month_jobs.execute():
jobs.append( ( row.date.strftime( "%A" ),
row.date.strftime( "%d" ),
row.total_jobs,
row.date
) )
return trans.fill_template( '/webapps/reports/jobs_specified_month_all.mako',
month_label=month_label,
year_label=year_label,
month=month,
jobs=jobs,
is_user_jobs_only=monitor_user_id,
message=message )
@web.expose
[docs] def specified_month_in_error( self, trans, **kwd ):
"""
Queries the DB for the user jobs in error.
"""
message = ''
params = util.Params( kwd )
monitor_email = params.get( 'monitor_email', 'monitor@bx.psu.edu' )
# In case we don't know which is the monitor user we will query for all jobs instead
monitor_user_id = get_monitor_id( trans, monitor_email )
# If specified_date is not received, we'll default to the current month
specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) )
specified_month = specified_date[ :7 ]
year, month = map( int, specified_month.split( "-" ) )
start_date = date( year, month, 1 )
end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] )
month_label = start_date.strftime( "%B" )
year_label = start_date.strftime( "%Y" )
month_jobs_in_error = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ),
sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ),
whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id,
model.Job.table.c.state == 'error',
model.Job.table.c.create_time >= start_date,
model.Job.table.c.create_time < end_date ),
from_obj=[ model.Job.table ],
group_by=[ 'date' ],
order_by=[ sa.desc( 'date' ) ] )
jobs = []
for row in month_jobs_in_error.execute():
jobs.append( ( row.date.strftime( "%A" ),
row.date,
row.total_jobs,
row.date.strftime( "%d" ) ) )
return trans.fill_template( '/webapps/reports/jobs_specified_month_in_error.mako',
month_label=month_label,
year_label=year_label,
month=month,
jobs=jobs,
message=message,
is_user_jobs_only=monitor_user_id )
@web.expose
[docs] def per_month_all( self, trans, **kwd ):
"""
Queries the DB for all jobs. Avoids monitor jobs.
"""
message = ''
params = util.Params( kwd )
monitor_email = params.get( 'monitor_email', 'monitor@bx.psu.edu' )
# In case we don't know which is the monitor user we will query for all jobs
monitor_user_id = get_monitor_id( trans, monitor_email )
jobs_by_month = sa.select( ( sa.func.date_trunc( 'month', model.Job.table.c.create_time ).label( 'date' ),
sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ),
whereclause=model.Job.table.c.user_id != monitor_user_id,
from_obj=[ model.Job.table ],
group_by=[ 'date' ],
order_by=[ sa.desc( 'date' ) ] )
jobs = []
for row in jobs_by_month.execute():
jobs.append( (
row.date.strftime( "%Y-%m" ),
row.total_jobs,
row.date.strftime( "%B" ),
row.date.strftime( "%y" )
) )
return trans.fill_template( '/webapps/reports/jobs_per_month_all.mako',
jobs=jobs,
is_user_jobs_only=monitor_user_id,
message=message )
@web.expose
[docs] def per_month_in_error( self, trans, **kwd ):
"""
Queries the DB for user jobs in error. Filters out monitor jobs.
"""
message = ''
params = util.Params( kwd )
monitor_email = params.get( 'monitor_email', 'monitor@bx.psu.edu' )
# In case we don't know which is the monitor user we will query for all jobs
monitor_user_id = get_monitor_id( trans, monitor_email )
jobs_in_error_by_month = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ),
sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ),
whereclause=sa.and_ ( model.Job.table.c.state == 'error',
model.Job.table.c.user_id != monitor_user_id ),
from_obj=[ model.Job.table ],
group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ],
order_by=[ sa.desc( 'date' ) ] )
jobs = []
for row in jobs_in_error_by_month.execute():
jobs.append( ( row.date.strftime( "%Y-%m" ),
row.total_jobs,
row.date.strftime( "%B" ),
row.date.strftime( "%y" ) ) )
return trans.fill_template( '/webapps/reports/jobs_per_month_in_error.mako',
jobs=jobs,
message=message,
is_user_jobs_only=monitor_user_id )
@web.expose
[docs] def per_user( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
monitor_email = params.get( 'monitor_email', 'monitor@bx.psu.edu' )
jobs = []
jobs_per_user = sa.select( ( model.User.table.c.email.label( 'user_email' ),
sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ),
from_obj=[ sa.outerjoin( model.Job.table, model.User.table ) ],
group_by=[ 'user_email' ],
order_by=[ sa.desc( 'total_jobs' ), 'user_email' ] )
for row in jobs_per_user.execute():
if ( row.user_email == None ):
jobs.append ( ( 'Anonymous',
row.total_jobs ) )
elif ( row.user_email == monitor_email ):
continue
else:
jobs.append( ( row.user_email,
row.total_jobs ) )
return trans.fill_template( '/webapps/reports/jobs_per_user.mako',
jobs=jobs,
message=message )
@web.expose
[docs] def user_per_month( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
email = util.restore_text( params.get( 'email', '' ) )
q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ),
sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ),
whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id,
model.GalaxySession.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == email
),
from_obj=[ sa.join( model.Job.table, model.User.table ) ],
group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ],
order_by=[ sa.desc( 'date' ) ] )
jobs = []
for row in q.execute():
jobs.append( ( row.date.strftime( "%Y-%m" ),
row.total_jobs,
row.date.strftime( "%B" ),
row.date.strftime( "%Y" ) ) )
return trans.fill_template( '/webapps/reports/jobs_user_per_month.mako',
email=util.sanitize_text( email ),
jobs=jobs, message=message )
@web.expose
@web.expose
@web.expose
[docs] def job_info( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
job = trans.sa_session.query( model.Job ) \
.get( trans.security.decode_id( kwd.get( 'id', '' ) ) )
return trans.fill_template( '/webapps/reports/job_info.mako',
job=job,
message=message )
## ---- Utility methods -------------------------------------------------------
[docs]def get_job( trans, id ):
return trans.sa_session.query( trans.model.Job ).get( trans.security.decode_id( id ) )
[docs]def get_monitor_id( trans, monitor_email ):
"""
A convenience method to obtain the monitor job id.
"""
monitor_user_id = None
monitor_row = trans.sa_session.query( trans.model.User.table.c.id ) \
.filter( trans.model.User.table.c.email == monitor_email ) \
.first()
if monitor_row is not None:
monitor_user_id = monitor_row[0]
return monitor_user_id