mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Remove memdump, which probably has not worked for many years.
This commit is contained in:
Nate Coraor
@@ -629,10 +629,6 @@ use_interactive = True
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# lot of CPU.
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#use_heartbeat = False
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# Enable the memory debugging interface (careful, negatively impacts server
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# performance).
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#use_memdump = False
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# -- Data Libraries
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# These library upload options are described in much more detail in the wiki:
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@@ -26,7 +26,6 @@ pysam = 0.4.2
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pysqlite = 2.5.6
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python_lzo = 1.08_2.03_static
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PyYAML = 3.10
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guppy = 0.1.10
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SQLAlchemy = 0.7.9
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; msgpack_python = 0.2.4
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+1
-8
@@ -107,10 +107,8 @@ class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
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self.quota_agent = galaxy.quota.QuotaAgent( self.model )
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else:
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self.quota_agent = galaxy.quota.NoQuotaAgent( self.model )
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# Heartbeat and memdump for thread / heap profiling
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# Heartbeat for thread profiling
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self.heartbeat = None
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self.memdump = None
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self.memory_usage = None
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# Container for OpenID authentication routines
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if self.config.enable_openid:
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from galaxy.web.framework import openid_manager
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@@ -125,11 +123,6 @@ class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
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self.heartbeat = heartbeat.Heartbeat( fname=self.config.heartbeat_log )
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self.heartbeat.daemon = True
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self.heartbeat.start()
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# Enable the memdump signal catcher if configured and available
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if self.config.use_memdump:
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from galaxy.util import memdump
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if memdump.Memdump:
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self.memdump = memdump.Memdump()
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# Transfer manager client
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if self.config.get_bool( 'enable_beta_job_managers', False ):
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from galaxy.jobs import transfer_manager
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@@ -227,7 +227,6 @@ class Configuration( object ):
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self.external_chown_script = kwargs.get('external_chown_script', None)
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self.environment_setup_file = kwargs.get( 'environment_setup_file', None )
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self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) )
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self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) )
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self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
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self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
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self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
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@@ -385,8 +385,6 @@ class GalaxyConfig( object ):
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"DRMAA_python": lambda: "sge" in self.config.get( "app:main", "start_job_runners" ).split(","),
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"drmaa": lambda: "drmaa" in self.config.get( "app:main", "start_job_runners" ).split(","),
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"pbs_python": lambda: "pbs" in self.config.get( "app:main", "start_job_runners" ).split(","),
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"threadframe": lambda: self.config.get( "app:main", "use_heartbeat" ),
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"guppy": lambda: self.config.get( "app:main", "use_memdump" ),
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"python_openid": lambda: self.config.get( "app:main", "enable_openid" ),
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"python_daemon": lambda: sys.version_info[:2] >= ( 2, 5 ),
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"pysam": lambda: check_pysam(),
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@@ -1,50 +0,0 @@
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# Attempt to load guppy module, and only define Memdump class
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# if available
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try:
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import pkg_resources
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pkg_resources.require( "guppy" )
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except:
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import sys
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print >> sys.stderr, "No guppy module, Memdump not available"
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Memdump = None
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else:
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import os, sys, signal, time, guppy
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class Memdump( object ):
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def __init__( self, signum=signal.SIGUSR1, fname="memdump.log" ):
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self.fname = fname
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signal.signal( signum, self.dump )
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self.heapy = guppy.hpy()
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self.heap = None
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def dump( self, signum, stack ):
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file = open( self.fname, "a" )
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print >> file, "Memdump for pid %d at %s" % ( os.getpid(), time.asctime() )
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print >> file
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try:
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self.heap = self.heapy.heap()
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print >> file, "heap():"
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print >> file, self.heap
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print >> file, "\nbyrcs:"
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print >> file, self.heap.byrcs
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print >> file, "\nbyrcs[0].byid:"
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print >> file, self.heap.byrcs[0].byid
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print >> file, "\nget_rp():"
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print >> file, self.heap.get_rp()
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self.heapy.setref()
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except AssertionError:
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pass
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print >> file, "\nEnd dump\n"
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file.close()
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def setref( self ):
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self.heapy.setref()
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def get( self, update=False ):
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if update:
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self.heap = self.heapy.heap()
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return self.heap
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@@ -1024,48 +1024,6 @@ class Admin( object ):
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message=message,
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status=status )
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@web.expose
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@web.require_admin
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def memdump( self, trans, ids = 'None', sorts = 'None', pages = 'None', new_id = None, new_sort = None, **kwd ):
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if self.app.memdump is None:
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return trans.show_error_message( "Memdump is not enabled (set <code>use_memdump = True</code> in galaxy.ini)" )
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heap = self.app.memdump.get()
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p = util.Params( kwd )
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msg = None
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if p.dump:
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heap = self.app.memdump.get( update = True )
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msg = "Heap dump complete"
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elif p.setref:
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self.app.memdump.setref()
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msg = "Reference point set (dump to see delta from this point)"
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ids = ids.split( ',' )
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sorts = sorts.split( ',' )
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if new_id is not None:
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ids.append( new_id )
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sorts.append( 'None' )
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elif new_sort is not None:
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sorts[-1] = new_sort
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breadcrumb = "<a href='%s' class='breadcrumb'>heap</a>" % web.url_for(controller='admin', action='memdump')
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# new lists so we can assemble breadcrumb links
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new_ids = []
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new_sorts = []
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for id, sort in zip( ids, sorts ):
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new_ids.append( id )
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if id != 'None':
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breadcrumb += "<a href='%s' class='breadcrumb'>[%s]</a>" % ( web.url_for(controller='admin', action='memdump', ids=','.join( new_ids ), sorts=','.join( new_sorts ) ), id )
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heap = heap[int(id)]
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new_sorts.append( sort )
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if sort != 'None':
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breadcrumb += "<a href='%s' class='breadcrumb'>.by('%s')</a>" % ( web.url_for(controller='admin', action='memdump', ids=','.join( new_ids ), sorts=','.join( new_sorts ) ), sort )
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heap = heap.by( sort )
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ids = ','.join( new_ids )
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sorts = ','.join( new_sorts )
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if p.theone:
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breadcrumb += ".theone"
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heap = heap.theone
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return trans.fill_template( '/admin/memdump.mako', heap = heap, ids = ids, sorts = sorts, breadcrumb = breadcrumb, msg = msg )
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@web.expose
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@web.require_admin
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def jobs( self, trans, stop = [], stop_msg = None, cutoff = 180, job_lock = None, ajl_submit = None, **kwd ):
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@@ -1,76 +0,0 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/message.mako" import="render_msg" />
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<%def name="title()">Memory Profiling</%def>
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<%
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import re
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from xml.sax.saxutils import escape, unescape
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%>
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<style type="text/css">
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a.breadcrumb:link,
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a.breadcrumb:visited,
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a.breadcrumb:active {
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text-decoration: none;
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}
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a.breadcrumb:hover {
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text-decoration: underline;
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}
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</style>
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<h2>Memory Profiling</h2>
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<ul class="manage-table-actions">
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<li><a class="action-button" href="${h.url_for( controller='admin', action='memdump', dump=True )}">Dump memory (warning: hangs server!)</a></li>
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<li><a class="action-button" href="${h.url_for( controller='admin', action='memdump', setref=True )}">Set reference point</a></li>
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</ul>
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<%def name="htmlize( heap )">
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<%
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s = escape( str( heap ) )
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new_s = ""
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id_re = re.compile('^(\s+)([0-9]+)')
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for line in s.split( '\n' ):
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try:
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id = id_re.search( line ).group( 2 )
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except:
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id = None
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new_s += re.sub( id_re, r'\1<a href="' + h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_id=id ) + r'">\2</a>', line )
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if id and heap[int(id)].count == 1:
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new_s += " <a href='%s'>theone</a>\n" % h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_id=id, theone=True )
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else:
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new_s += "\n"
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return new_s
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%>
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</%def>
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%if message:
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${render_msg( message, status )}
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%endif
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%if heap is None:
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No memory dump available. Click "Dump memory" to create one.
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%else:
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<pre>
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<br/>
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You are here: ${breadcrumb}<br/>
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%if breadcrumb.endswith( 'theone' ):
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${heap|h}
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%else:
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<nobr>
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Sort:
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Class')}">Class</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Clodo' )}">Clodo</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Id' )}">Id</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Idset' )}">Idset</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Module' )}">Module</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Unity' )}">Unity</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Rcs' )}">Rcs</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Size' )}">Size</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Type' )}">Type</a> |
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<a href="${h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_sort='Via' )}">Via</a>
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</nobr>
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${htmlize( heap )}
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%endif
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</pre>
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%endif
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@@ -78,7 +78,6 @@
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<div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_versions' )}" target="galaxy_main">View tool lineage</a></div>
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<div class="toolTitle"><a href="${h.url_for( controller='admin', action='package_tool' )}" target="galaxy_main">Download tool tarball</a></div>
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<div class="toolTitle"><a href="${h.url_for( controller='admin', action='reload_tool' )}" target="galaxy_main">Reload a tool's configuration</a></div>
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<div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div>
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<div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div>
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<div class="toolTitle"><a href="${h.url_for( controller='admin', action='review_tool_migration_stages' )}" target="galaxy_main">Review tool migration stages</a></div>
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%if installing_repository_ids:
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