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#############################################################
# #
# Author: Herve Menager #
# Organization:'Biological Software and Databases' Group, #
# Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the #
# COPYING.LIB document. #
# #
#############################################################
"""
Registry.py
This module holds:
- The Registry class that describes the list of installed/imported services
and their servers
- The DefNode class, an abstract class that describes an element (node or
leaf) of the services tree
- The ProgramDef class that describes a service (leaf in the services tree)
- The CategoryDef class that describes a category (node in the services tree)
- The ServerDef class that describes a server (node in the services tree)
"""
import os
from hashlib import md5
from glob import glob
from Mobyle.ConfigManager import Config
_cfg = Config()
from logging import getLogger
r_log = getLogger( __name__ )
class DefNode(object):
"""
DefNode is the class that provides the tree structure to the
server/categories/program hierarchy
"""
def __init__(self):
self.name = None
self.children = []
self.parents = []
def getDescendants(self):
"""
Returns the descendants of the node recursively
@return: the list of descendant nodes
@rtype: list
"""
r = []
r.extend(self.children)
for p in self.children:
r.extend(p.getDescendants())
return r
def getAncestors(self):
"""
Returns the ancestors of the node recursively
@return: the list of ancestor nodes
@rtype: list
"""
r = []
r.extend(self.parents)
for p in self.parents:
r.extend(p.getAncestors())
return r
def addDescendant(self, subpath):
"""
Adds a descendant to the node, by recursively adding the descendants from the provided subpath if they do not exist
@param subpath: the subpath, a list of descendant objects
(e.g.: [CategoryDef, CategoryDef, ProgramDef])
@type subpath: string
"""
if len(subpath)==0:
return
else:
c = [c for c in self.children if (c.name == subpath[0].name and (not(hasattr(c,'server')) or c.server == subpath[0].server))]
if not(c):
c = subpath[0]
self.children.append(c)
c.parents.append(self)
else:
c = c[0]
c.addDescendant(subpath[1:])
def __cmp__(self, other):
"""
Comparison operator that allows to classify the tree structure alphabetically
based on node names
@param other: the other node to which self is compared
@type other: DefNode
@return: the comparison result
@rtype: boolean
"""
return cmp(self.name.lower(), other.name.lower())
def getChildCategories(self):
"""
Returns child categories, i.e. child nodes which happen to be CategoryDef instances
@return: a list of category nodes
@rtype: list
"""
l = [c for c in self.children if not(isinstance(c, ServiceDef))]
l.sort()
return l
def getChildServices(self):
"""
Returns child programs, i.e. child nodes which happen to be ServiceDef instances
@return: a list of program nodes
@rtype: list
"""
l = [c for c in self.children if isinstance(c, ServiceDef)]
l.sort()
return l
class Registry(DefNode):
#__shared_state = {}
def __init__( self ):
#self.__dict__ = self.__shared_state
DefNode.__init__(self)
self.programs = []
self.workflows = []
self.viewers = []
self.tutorials = []
self.servers = []
self.serversByName = {}
self.serversByUrl = {}
self.programsByUrl = {}
self.workflowsByUrl={}
self.viewersByUrl = {}
self.tutorialsByUrl= {}
self.servers_path=_cfg.servers_path()
def load( self):
"""
"""
serverProperties = self._getServerProperties()
for name, properties in serverProperties.items():
server = ServerDef( name = name,
url = properties[ 'url' ] ,
help = properties[ 'help' ],
repository = properties[ 'repository' ],
jobsBase = properties[ 'jobsBase' ] ,
)
self.addServer(server)
for name in properties[ 'programs' ]:
try:
url = self.getProgramUrl( name, server.name )
path = self._computeProgramPath( name, server.name)
program = ProgramDef( name = name,
url = url,
path = path,
server = server
)
# service disabled
if _cfg.isDisabled( portalID = "%s.%s" %( server.name , program.name ) ):
program.disabled = True
# service with restricted access
if not( _cfg.isAuthorized( url )):
program.authorized = False
self.addProgram( program )
except IndexError, e:
r_log.error("Error while loading %s: %s" % (name, e))
for name in properties[ 'workflows' ]:
try:
url = self.getWorkflowUrl( name, server.name)
path = self._computeWorkflowPath( name, server.name)
wf = WorkflowDef( name = name,
url = url,
path = path,
server = server
)
# service disabled
if _cfg.isDisabled( portalID = "%s.%s" %( server.name , wf.name ) ):
wf.disabled = True
# service with restricted access
if not( _cfg.isAuthorized( url )):
wf.authorized = False
self.addWorkflow( wf )
except IndexError, e:
r_log.error("Error while loading %s: %s" % (name, e))
if server.name == 'local':
for name in properties['viewers']:
try:
url = self.getViewerUrl( name )
path = self.getViewerPath( name )
viewer = ViewerDef( name= name,
url= url,
path=path,
server=server
)
self.addViewer(viewer)
except IndexError, e:
r_log.error("Error while loading %s: %s" % (name, e))
for name in properties[ 'tutorials' ]:
try:
url = self.getTutorialUrl(name)
path = self._computeTutorialPath(name)
tt = TutorialDef( name = name,
url = url,
path = path,
server = server
)
# service disabled
if _cfg.isDisabled( portalID = "%s.%s" %( server.name, name ) ):
tt.disabled = True
# service with restricted access
if not( _cfg.isAuthorized( url )):
tt.authorized = False
self.addTutorial( tt )
except IndexError, e:
r_log.error("Error while loading %s: %s" % (name, e))
def addServer(self, server):
self.servers.append( server )
self.serversByName[ server.name ] = server
self.serversByUrl[ server.url ] = server
def addProgram( self, program ):
self.programs.append( program )
self.programsByUrl[ program.url ] = program
self.serversByName[ program.server.name ].programs.append( program )
self.serversByName[ program.server.name ].programsByName[ program.name ] = program
def addWorkflow(self, workflow ):
self.workflows.append( workflow )
self.workflowsByUrl[ workflow.url ] = workflow
self.serversByName[ workflow.server.name ].workflows.append( workflow )
self.serversByName[ workflow.server.name ].workflowsByName[ workflow.name ] = workflow
def addViewer(self, viewer ):
self.viewers.append( viewer )
self.viewersByUrl[ viewer.url ] = viewer
self.serversByName[ viewer.server.name ].viewers.append( viewer )
self.serversByName[ viewer.server.name ].viewersByName[ viewer.name ] = viewer
def addTutorial(self, tutorial ):
self.tutorials.append( tutorial )
self.tutorialsByUrl[ tutorial.url ] = tutorial
self.serversByName[ tutorial.server.name ].tutorials.append( tutorial )
self.serversByName[ tutorial.server.name ].tutorialsByName[ tutorial.name ] = tutorial
def has_service(self , service ):
"""
@param service: the service to test the existance.
@type service: a ServiceDef instance
@return: True if the service exists in this registry, False otherwise.
@rtype: boolean.
"""
if isinstance( service , ProgramDef ):
try:
self.serversByName[ service.server.name ].programsByName[ service.name ]
return True
except KeyError:
return False
elif isinstance( service , WorkflowDef ):
try:
self.serversByName[ service.server.name ].workflowsByName[ service.name ]
return True
except KeyError:
return False
elif isinstance( service , ViewerDef ):
try:
self.serversByName[ service.server.name ].viewersByName[ service.name ]
return True
except KeyError :
return False
elif isinstance( service , TutorialDef ):
try:
self.serversByName[ service.server.name ].tutorialsByName[ service.name ]
return True
except KeyError :
return False
def pruneService(self, service):
"""
remove a Service Definition from the registry
@param service: the Service to remove
@type service: a ServiceDef instance
"""
if isinstance( service , ProgramDef ):
if self.has_service(service):
self.programs.remove(service)
del self.programsByUrl[service.url]
self.serversByName[service.server.name].programs.remove(service)
del self.serversByName[service.server.name].\
programsByName[service.name]
# if (len(service.server.services)==0):
# del self.serversByName[service.server.name]
# self.servers.remove(service.server)
elif isinstance( service , WorkflowDef ):
if self.has_service(service):
self.workflows.remove(service)
del self.workflowsByUrl[service.url]
self.serversByName[service.server.name].workflows.remove(service)
del self.serversByName[service.server.name].\
workflowsByName[service.name]
# if (len(service.server.services)==0):
# del self.serversByName[service.server.name]
# self.servers.remove(service.server)
elif isinstance( service , ViewerDef ):
if self.has_service(service):
self.viewers.remove(service)
del self.viewersByUrl[service.url]
self.serversByName[service.server.name].viewers.remove(service)
del self.serversByName[service.server.name].\
viewersByName[service.name]
# if (len(service.server.services)==0):
# del self.serversByName[service.server.name]
# self.servers.remove(service.server)
elif isinstance( service , TutorialDef ):
if self.has_service(service):
self.tutorials.remove(service)
del self.tutorialsByUrl[service.url]
self.serversByName[service.server.name].tutorials.remove(service)
del self.serversByName[service.server.name].\
tutorialsByName[service.name]
# if (len(service.server.services)==0):
# del self.serversByName[service.server.name]
# self.servers.remove(service.server)
def _getServerProperties(self):
"""
@return: a dict of all deployed servers associated with their respective properties
@rtype: { server_name :{ 'url': string ,
'help': string,
'repository':string ,
'jobBase': string ,
'programs': [] ,
'workflows' : [] ,
'viewers': [] #available only for local server ,
'tutorials': [] #available only for local server }
"""
imported_portals = _cfg.portals()
properties = {}
all_server_dir_path = glob( os.path.join(self.servers_path , '*' ) )
for server_dir_path in all_server_dir_path:
if not os.path.isdir(server_dir_path):
continue
else:
server_name = os.path.basename( server_dir_path )
properties[ server_name ] = {}
deployed_programs_path = glob( os.path.join( server_dir_path , ProgramDef.directory_basename ,'*.xml') )
deployed_workflows_path = glob( os.path.join( server_dir_path , WorkflowDef.directory_basename ,'*.xml') )
properties[ server_name ][ 'programs' ] = [ os.path.basename( p )[:-4] for p in deployed_programs_path ]
properties[ server_name ][ 'workflows' ] = [ os.path.basename( p )[:-4] for p in deployed_workflows_path ]
if server_name == 'local':
properties[ server_name ][ 'url' ] = _cfg.cgi_url()
properties[ server_name ][ 'help' ] = _cfg.mailHelp()
properties[ server_name ][ 'repository' ] = _cfg.repository_url()
deployed_viewers_path = glob(os.path.join( server_dir_path , ViewerDef.directory_basename ,"*.xml") )
properties[ server_name ][ 'viewers' ] = [ os.path.basename( p )[:-4] for p in deployed_viewers_path ]
deployed_tutorials_path = glob(os.path.join( server_dir_path , TutorialDef.directory_basename ,"*.xml") )
properties[ server_name ][ 'tutorials' ] = [ os.path.basename( p )[:-4] for p in deployed_tutorials_path ]
properties[ server_name ][ 'jobsBase' ] = _cfg.results_url()
elif server_name in imported_portals:
properties[ server_name ][ 'url' ] = imported_portals[ server_name ][ 'url' ]
properties[ server_name ][ 'help' ] = imported_portals[ server_name ][ 'help' ]
properties[ server_name ][ 'repository' ] = imported_portals[ server_name ][ 'repository' ]
properties[ server_name ][ 'repository' ] = imported_portals[ server_name ][ 'repository' ]
properties[ server_name ][ 'jobsBase' ] = "%s/jobs" %properties[ server_name ][ 'repository' ]
else:
r_log.warning("the server '%s' is deployed but not appear in the configuration (skip in registry)" % server_name)
del properties[ server_name ]
return properties
def getProgramUrl(self , name , server='local'):
#the server.repository point to services_path
return "%s/services/servers/local/%s/%s.xml" %( self.serversByName[server].repository ,
ProgramDef.directory_basename ,
name )
def getWorkflowUrl(self , name , server='local'):
return "%s/services/servers/local/%s/%s.xml" %( self.serversByName[server].repository ,
WorkflowDef.directory_basename ,
name )
def getViewerUrl(self, name ):
return "%s/services/servers/local/%s/%s.xml" %( self.serversByName[ 'local' ].repository,
ViewerDef.directory_basename ,
name )
def getTutorialUrl(self, name ):
return "%s/services/servers/local/%s/%s.xml" %( self.serversByName[ 'local' ].repository,
TutorialDef.directory_basename ,
name )
def getJobPID(self, url):
"""
@param url: the url of
@type url: string
@return: the portal identifier for this job
@rtype: string
"""
server = self.getServerByJobId(url)
jobPID = url.replace(server.jobsBase,'').lstrip('/').replace('/','.')
if server.name != 'local':
jobPID = server.name + '.' + jobPID
return jobPID
def isJobLocal(self, url):
"""
@param url: the url of
@type url: string
@return: true if the job is local, false otherwise
@rtype: boolean
"""
return self.getJobPID(url).find('.')>-1 or self.getJobPID(url).startswith('local.')
def getJobURL(self, pid):
# if the PID is composite (i.e. it's a workflow task), only take the last part into account.
pid = pid.split('::').pop()
l = pid.split('.')
if (len(l)==2):
server_name = 'local'
else:
server_name = l[0]
l = l[1:]
return self.serversByName[server_name].jobsBase + '/' + '/'.join(l)
def getViewerPath(self, name):
return os.path.join( self.servers_path , 'local', ViewerDef.directory_basename , name + '.xml')
def getTutorialPath(self, name):
return os.path.join( self.servers_path , 'local', TutorialDef.directory_basename , name + '.xml')
def getProgramPath(self, name, server_name ='local'):
if server_name in self.serversByName:
if name in self.serversByName[ server_name ].programsByName:
return self.serversByName[ server_name ].programsByName[ name ].path
else:
raise KeyError , "unknown service %s for server %s " %( name , server_name )
else:
raise KeyError , "unknown server %s" %server_name
def _computeProgramPath( self , name , server_name= 'local' ):
return os.path.join( self.servers_path , server_name, ProgramDef.directory_basename , name + '.xml')
def _computeWorkflowPath( self , name , server_name= 'local' ):
return os.path.join( self.servers_path , server_name, WorkflowDef.directory_basename , name + '.xml')
def _computeTutorialPath( self , name , server_name= 'local' ):
return os.path.join( self.servers_path , server_name, TutorialDef.directory_basename , name + '.xml')
def getServerByJobId(self,jobId):
for server in self.servers:
if jobId.startswith(server.jobsBase):
return server
class ServiceDef(DefNode):
"""
ServiceDef is the superclass that provides the service information to the registry
"""
directory_basename = None
def __init__(self, url, name=None, path=None, server=None):
"""
@param url: the url of the definition of the program on the server where it is executed
@type url: String
@param name: the name of the program
@type name: String
@param path: the os path to the local version of the file (local file definition or local cache of distant service)
@type path: String
@param server: the execution server definition
@type server: ServerDef
"""
DefNode.__init__(self)
self.url = url
self.name = name
self.path = path
self.server = server
self.categories = []
if (self.server.name == 'local'):
"""portal id"""
self.pid = self.name
else:
self.pid = '%s.%s' % (self.server.name, self.name)
self.disabled = False
self.authorized = True
def isExported(self):
return self.server.name == 'local' and self.name in _cfg.exported_services()
def __eq__(self , other ):
return self.server.name == other.server.name and self.name == other.name
class ProgramDef(ServiceDef):
"""
ProgramDef is the class that provides the service information to the registry
"""
type = "program"
directory_basename = "programs"
class WorkflowDef(ServiceDef):
"""
WorkflowDef is the class that provides the workflow information to the registry
"""
type = "workflow"
directory_basename = "workflows"
class ViewerDef(ServiceDef):
"""
ViewerDef is the class that provides the viewer information to the registry
"""
type = "viewer"
directory_basename = "viewers"
class TutorialDef(ServiceDef):
"""
TutorialDef is the class that provides the tutorial information to the registry
"""
type = "tutorial"
directory_basename = "tutorials"
class ServerDef(DefNode):
"""
ServerDef is the class that provides the server information to the registry
"""
def __init__(self, name, url, help, repository, jobsBase ):
"""
@param name: the short name, as displayed for instance in the services tree menu
@type name: String
@param url: the url of the server (cgi-bin base url for now)
@type url: String
@param help: the help email contact
@type help: String
@param repository: the url wher to find programs, workflows, etc...
@type repository: String
@param jobsBase: the url of the directory that contains all of the server's jobs
@type jobsBase: String
"""
DefNode.__init__(self)
self.name = name
self.url = url
self.help = help
self.repository = repository
"""top-level categories"""
self.categories = [] # top-level categories
"""the url to revieve a job"""
self.jobsBase = jobsBase
""" """
self.programs = []
""" """
self.programsByName = {}
""" """
self.workflows = []
""" """
self.workflowsByName = {}
self.viewers = []
self.viewersByName = {}
self.tutorials = []
self.tutorialsByName = {}
self.path = os.path.join( _cfg.services_path() , self.name )
def __cmp__(self, other):
"""
Comparison operator that allows to classify the servers alphabetically
based on node names, except local server which is first
@param other: the other node to which self is compared
@type other: DefNode
@return: the comparison result
@rtype: boolean
"""
if self.name=='local':
return -1
else:
return cmp(self.name.lower(), other.name.lower())
class CategoryDef(DefNode):
"""
CategoryDef is the class that provides the category information to the registry
"""
def __init__ (self, name, parentCategory=None, server=None):
"""
@param name: the name of the category
@type name: String
@param parentCategory: the parent category (if any)
@type parentCategory: CategoryDef
@param server: the server to which the Category belongs
@type server: ServerDef
"""
DefNode.__init__(self)
self.name = name
self.parentCategory = parentCategory
self.server = server
self.services = [] # top-level services
self.categories = [] # top-level categories
class ServiceTypeDef(CategoryDef):
def __cmp__(self, other):
"""
Comparison operator that allows to classify the service types
with tutorials at the end
@param other: the other node to which self is compared
@type other: DefNode
@return: the comparison result
@rtype: boolean
"""
if other.name=='Tutorials':
return -1
elif self.name=='Tutorials':
return 1
else:
return cmp(self.name.lower(), other.name.lower())
registry = Registry()
registry.load()
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