text: """
  Galaxy data model classes
  
  Naming: try to use class names that have a distinct plural form so that
  the relationship cardinalities are obvious (e.g. prefer Dataset to Data)
  """
  import codecs
  import errno
  import json
  import logging
  import numbers
  import operator
  import os
  import socket
  import time
  from datetime import datetime, timedelta
  from string import Template
  from uuid import UUID, uuid4
  
  from six import string_types
  from sqlalchemy import (and_, func, join, not_, or_, select, true, type_coerce,
                          types)
  from sqlalchemy.ext import hybrid
  from sqlalchemy.orm import aliased, joinedload, object_session
  
  import galaxy.model.metadata
  import galaxy.model.orm.now
  import galaxy.security.passwords
  import galaxy.util
  from galaxy.model.item_attrs import UsesAnnotations
  from galaxy.security import get_permitted_actions
  from galaxy.util import (directory_hash_id, Params, ready_name_for_url,
                           restore_text, send_mail, unicodify, unique_id)
  from galaxy.util.bunch import Bunch
  from galaxy.util.dictifiable import Dictifiable
  from galaxy.util.hash_util import new_secure_hash
  from galaxy.util.multi_byte import is_multi_byte
  from galaxy.util.sanitize_html import sanitize_html
  from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField,
                                       PasswordField, SelectField, TextArea, TextField, WorkflowField,
                                       WorkflowMappingField)
  from galaxy.web.framework.helpers import to_unicode
  
  log = logging.getLogger( __name__ )
  
  _datatypes_registry = None
  
  # When constructing filters with in for a fixed set of ids, maximum
  # number of items to place in the IN statement. Different databases
  # are going to have different limits so it is likely best to not let
  # this be unlimited - filter in Python if over this limit.
  MAX_IN_FILTER_LENGTH = 100
  
  
  class NoConverterException(Exception):
      def __init__(self, value):
          self.value = value
  
      def __str__(self):
          return repr(self.value)
  
  
  class ConverterDependencyException(Exception):
      def __init__(self, value):
          self.value = value
  
      def __str__(self):
          return repr(self.value)
  
  
  def _get_datatypes_registry():
      if _datatypes_registry is None:
          raise Exception("galaxy.model.set_datatypes_registry must be called before performing certain DatasetInstance operations.")
      return _datatypes_registry
  
  
  def set_datatypes_registry( d_registry ):
      """
      Set up datatypes_registry
      """
      global _datatypes_registry
      _datatypes_registry = d_registry
  
  
  class HasName:
  
      def get_display_name( self ):
          """
          These objects have a name attribute can be either a string or a unicode
          object. If string, convert to unicode object assuming 'utf-8' format.
          """
          name = self.name
          name = unicodify( name, 'utf-8' )
          return name
  
  
  class JobLike:
  
      def _init_metrics( self ):
          self.text_metrics = []
          self.numeric_metrics = []
  
      def add_metric( self, plugin, metric_name, metric_value ):
          plugin = unicodify( plugin, 'utf-8' )
          metric_name = unicodify( metric_name, 'utf-8' )
          if isinstance( metric_value, numbers.Number ):
              metric = self._numeric_metric( plugin, metric_name, metric_value )
              self.numeric_metrics.append( metric )
          else:
              metric_value = unicodify( metric_value, 'utf-8' )
              if len( metric_value ) > 1022:
                  # Truncate these values - not needed with sqlite
                  # but other backends must need it.
                  metric_value = metric_value[ :1022 ]
              metric = self._text_metric( plugin, metric_name, metric_value )
              self.text_metrics.append( metric )
  
      @property
      def metrics( self ):
          # TODO: Make iterable, concatenate with chain
          return self.text_metrics + self.numeric_metrics
  
      def set_streams( self, stdout, stderr ):
          stdout = galaxy.util.unicodify( stdout )
          stderr = galaxy.util.unicodify( stderr )
          if ( len( stdout ) > galaxy.util.DATABASE_MAX_STRING_SIZE ):
              stdout = galaxy.util.shrink_string_by_size( stdout, galaxy.util.DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
              log.info( "stdout for %s %d is greater than %s, only a portion will be logged to database", type(self), self.id, galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY )
          self.stdout = stdout
          if ( len( stderr ) > galaxy.util.DATABASE_MAX_STRING_SIZE ):
              stderr = galaxy.util.shrink_string_by_size( stderr, galaxy.util.DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
              log.info( "stderr for %s %d is greater than %s, only a portion will be logged to database", type(self), self.id, galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY )
          self.stderr = stderr
  
      def log_str(self):
          extra = ""
          safe_id = getattr(self, "id", None)
          if safe_id is not None:
              extra += "id=%s" % safe_id
          else:
              extra += "unflushed"
  
          return "%s[%s,tool_id=%s]" % (self.__class__.__name__, extra, self.tool_id)
  
  
  class User( object, Dictifiable ):
      use_pbkdf2 = True
      """
      Data for a Galaxy user or admin and relations to their
      histories, credentials, and roles.
      """
      # attributes that will be accessed and returned when calling to_dict( view='collection' )
      dict_collection_visible_keys = ( 'id', 'email', 'username' )
      # attributes that will be accessed and returned when calling to_dict( view='element' )
      dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' )
  
      def __init__( self, email=None, password=None ):
          self.email = email
          self.password = password
          self.external = False
          self.deleted = False
          self.purged = False
          self.active = False
          self.activation_token = None
          self.username = None
          self.last_password_change = None
          # Relationships
          self.histories = []
          self.credentials = []
          # ? self.roles = []
  
      def set_password_cleartext( self, cleartext ):
          """
          Set user password to the digest of `cleartext`.
          """
          if User.use_pbkdf2:
              self.password = galaxy.security.passwords.hash_password( cleartext )
          else:
              self.password = new_secure_hash( text_type=cleartext )
          self.last_password_change = datetime.now()
  
      def check_password( self, cleartext ):
          """
          Check if `cleartext` matches user password when hashed.
          """
          return galaxy.security.passwords.check_password( cleartext, self.password )
  
      def all_roles( self ):
          """
          Return a unique list of Roles associated with this user or any of their groups.
          """
          try:
              db_session = object_session( self )
              user = db_session.query(
                  User
              ).filter_by(  # don't use get, it will use session variant.
                  id=self.id
              ).options(
                  joinedload("roles"),
                  joinedload("roles.role"),
                  joinedload("groups"),
                  joinedload("groups.group"),
                  joinedload("groups.group.roles"),
                  joinedload("groups.group.roles.role")
              ).one()
          except Exception:
              # If not persistent user, just use models normaly and
              # skip optimizations...
              user = self
  
          roles = [ ura.role for ura in user.roles ]
          for group in [ uga.group for uga in user.groups ]:
              for role in [ gra.role for gra in group.roles ]:
                  if role not in roles:
                      roles.append( role )
          return roles
  
      def all_roles_exploiting_cache( self ):
          """
          """
          roles = [ ura.role for ura in self.roles ]
          for group in [ uga.group for uga in self.groups ]:
              for role in [ gra.role for gra in group.roles ]:
                  if role not in roles:
                      roles.append( role )
          return roles
  
      def get_disk_usage( self, nice_size=False ):
          """
          Return byte count of disk space used by user or a human-readable
          string if `nice_size` is `True`.
          """
          rval = 0
          if self.disk_usage is not None:
              rval = self.disk_usage
          if nice_size:
              rval = galaxy.util.nice_size( rval )
          return rval
  
      def set_disk_usage( self, bytes ):
          """
          Manually set the disk space used by a user to `bytes`.
          """
          self.disk_usage = bytes
  
      total_disk_usage = property( get_disk_usage, set_disk_usage )
  
      def adjust_total_disk_usage( self, amount ):
          if amount != 0:
              self.disk_usage = func.coalesce(self.table.c.disk_usage, 0) + amount
  
      @property
      def nice_total_disk_usage( self ):
          """
          Return byte count of disk space used in a human-readable string.
          """
          return self.get_disk_usage( nice_size=True )
  
      def calculate_disk_usage( self ):
          """
          Return byte count total of disk space used by all non-purged, non-library
          HDAs in non-purged histories.
          """
          # maintain a list so that we don't double count
          dataset_ids = []
          total = 0
          # this can be a huge number and can run out of memory, so we avoid the mappers
          db_session = object_session( self )
          for history in db_session.query( History ).enable_eagerloads( False ).filter_by( user_id=self.id, purged=False ).yield_per( 1000 ):
              for hda in db_session.query( HistoryDatasetAssociation ).enable_eagerloads( False ).filter_by( history_id=history.id, purged=False ).yield_per( 1000 ):
                  # TODO: def hda.counts_toward_disk_usage():
                  #   return ( not self.dataset.purged and not self.dataset.library_associations )
                  if hda.dataset.id not in dataset_ids and not hda.dataset.purged and not hda.dataset.library_associations:
                      dataset_ids.append( hda.dataset.id )
                      total += hda.dataset.get_total_size()
          return total
  
      @staticmethod
      def user_template_environment( user ):
          """
  
          >>> env = User.user_template_environment(None)
          >>> env['__user_email__']
          'Anonymous'
          >>> env['__user_id__']
          'Anonymous'
          >>> user = User('foo@example.com')
          >>> user.id = 6
          >>> user.username = 'foo2'
          >>> env = User.user_template_environment(user)
          >>> env['__user_id__']
          '6'
          >>> env['__user_name__']
          'foo2'
          """
          if user:
              user_id = '%d' % user.id
              user_email = str( user.email )
              user_name = str( user.username )
          else:
              user = None
              user_id = 'Anonymous'
              user_email = 'Anonymous'
              user_name = 'Anonymous'
          environment = {}
          environment[ '__user__' ] = user
          environment[ '__user_id__' ] = environment[ 'userId' ] = user_id
          environment[ '__user_email__' ] = environment[ 'userEmail' ] = user_email
          environment[ '__user_name__' ] = user_name
          return environment
  
      @staticmethod
      def expand_user_properties( user, in_string ):
          """
          """
          environment = User.user_template_environment( user )
          return Template( in_string ).safe_substitute( environment )
  
  
  class PasswordResetToken( object ):
      def __init__( self, user, token=None):
          if token:
              self.token = token
          else:
              self.token = unique_id()
          self.user = user
          self.expiration_time = galaxy.model.orm.now.now() + timedelta(hours=24)
  
  
  class BaseJobMetric( object ):
  
      def __init__( self, plugin, metric_name, metric_value ):
          self.plugin = plugin
          self.metric_name = metric_name
          self.metric_value = metric_value
  
  
  class JobMetricText( BaseJobMetric ):
      pass
  
  
  class JobMetricNumeric( BaseJobMetric ):
      pass
  
  
  class TaskMetricText( BaseJobMetric ):
      pass
  
  
  class TaskMetricNumeric( BaseJobMetric ):
      pass
  
  
  class Job( object, JobLike, Dictifiable ):
      dict_collection_visible_keys = [ 'id', 'state', 'exit_code', 'update_time', 'create_time' ]
      dict_element_visible_keys = [ 'id', 'state', 'exit_code', 'update_time', 'create_time'  ]
  
      """
      A job represents a request to run a tool given input datasets, tool
      parameters, and output datasets.
      """
      _numeric_metric = JobMetricNumeric
      _text_metric = JobMetricText
  
      states = Bunch( NEW='new',
                      RESUBMITTED='resubmitted',
                      UPLOAD='upload',
                      WAITING='waiting',
                      QUEUED='queued',
                      RUNNING='running',
                      OK='ok',
                      ERROR='error',
                      PAUSED='paused',
                      DELETED='deleted',
                      DELETED_NEW='deleted_new' )
      terminal_states = [ states.OK,
                          states.ERROR,
                          states.DELETED ]
      #: job states where the job hasn't finished and the model may still change
      non_ready_states = [
          states.NEW,
          states.RESUBMITTED,
          states.UPLOAD,
          states.WAITING,
          states.QUEUED,
          states.RUNNING,
      ]
  
      # Please include an accessor (get/set pair) for any new columns/members.
      def __init__( self ):
          self.session_id = None
          self.user_id = None
          self.tool_id = None
          self.tool_version = None
          self.command_line = None
          self.dependencies = []
          self.param_filename = None
          self.parameters = []
          self.input_datasets = []
          self.output_datasets = []
          self.input_dataset_collections = []
          self.output_dataset_collection_instances = []
          self.output_dataset_collections = []
          self.input_library_datasets = []
          self.output_library_datasets = []
          self.state = Job.states.NEW
          self.info = None
          self.job_runner_name = None
          self.job_runner_external_id = None
          self.destination_id = None
          self.destination_params = None
          self.post_job_actions = []
          self.state_history = []
          self.imported = False
          self.handler = None
          self.exit_code = None
          self._init_metrics()
          self.state_history.append( JobStateHistory( self ) )
  
      @property
      def finished( self ):
          states = self.states
          return self.state in [
              states.OK,
              states.ERROR,
              states.DELETED,
              states.DELETED_NEW,
          ]
  
      # TODO: Add accessors for members defined in SQL Alchemy for the Job table and
      # for the mapper defined to the Job table.
      def get_external_output_metadata( self ):
          """
          The external_output_metadata is currently a reference from Job to
          JobExternalOutputMetadata. It exists for a job but not a task.
          """
          return self.external_output_metadata
  
      def get_session_id( self ):
          return self.session_id
  
      def get_user_id( self ):
          return self.user_id
  
      def get_tool_id( self ):
          return self.tool_id
  
      def get_tool_version( self ):
          return self.tool_version
  
      def get_command_line( self ):
          return self.command_line
  
      def get_dependencies(self):
          return self.dependencies
  
      def get_param_filename( self ):
          return self.param_filename
  
      def get_parameters( self ):
          return self.parameters
  
      def get_input_datasets( self ):
          return self.input_datasets
  
      def get_output_datasets( self ):
          return self.output_datasets
  
      def get_input_library_datasets( self ):
          return self.input_library_datasets
  
      def get_output_library_datasets( self ):
          return self.output_library_datasets
  
      def get_state( self ):
          return self.state
  
      def get_info( self ):
          return self.info
  
      def get_job_runner_name( self ):
          # This differs from the Task class in that job_runner_name is
          # accessed instead of task_runner_name. Note that the field
          # runner_name is not the same thing.
          return self.job_runner_name
  
      def get_job_runner_external_id( self ):
          # This is different from the Task just in the member accessed:
          return self.job_runner_external_id
  
      def get_post_job_actions( self ):
          return self.post_job_actions
  
      def get_imported( self ):
          return self.imported
  
      def get_handler( self ):
          return self.handler
  
      def get_params( self ):
          return self.params
  
      def get_user( self ):
          # This is defined in the SQL Alchemy mapper as a relation to the User.
          return self.user
  
      def get_id( self ):
          # This is defined in the SQL Alchemy's Job table (and not in the model).
          return self.id
  
      def get_tasks( self ):
          # The tasks member is pert of a reference in the SQL Alchemy schema:
          return self.tasks
  
      def get_id_tag( self ):
          """
          Return a tag that can be useful in identifying a Job.
          This returns the Job's get_id
          """
          return "%s" % self.id
  
      def set_session_id( self, session_id ):
          self.session_id = session_id
  
      def set_user_id( self, user_id ):
          self.user_id = user_id
  
      def set_tool_id( self, tool_id ):
          self.tool_id = tool_id
  
      def set_tool_version( self, tool_version ):
          self.tool_version = tool_version
  
      def set_command_line( self, command_line ):
          self.command_line = command_line
  
      def set_dependencies( self, dependencies ):
          self.dependencies = dependencies
  
      def set_param_filename( self, param_filename ):
          self.param_filename = param_filename
  
      def set_parameters( self, parameters ):
          self.parameters = parameters
  
      def set_input_datasets( self, input_datasets ):
          self.input_datasets = input_datasets
  
      def set_output_datasets( self, output_datasets ):
          self.output_datasets = output_datasets
  
      def set_input_library_datasets( self, input_library_datasets ):
          self.input_library_datasets = input_library_datasets
  
      def set_output_library_datasets( self, output_library_datasets ):
          self.output_library_datasets = output_library_datasets
  
      def set_info( self, info ):
          self.info = info
  
      def set_runner_name( self, job_runner_name ):
          self.job_runner_name = job_runner_name
  
      def get_job( self ):
          # Added so job and task have same interface (.get_job() ) to get at
          # underlying job object.
          return self
  
      def set_runner_external_id( self, job_runner_external_id ):
          self.job_runner_external_id = job_runner_external_id
  
      def set_post_job_actions( self, post_job_actions ):
          self.post_job_actions = post_job_actions
  
      def set_imported( self, imported ):
          self.imported = imported
  
      def set_handler( self, handler ):
          self.handler = handler
  
      def set_params( self, params ):
          self.params = params
  
      def add_parameter( self, name, value ):
          self.parameters.append( JobParameter( name, value ) )
  
      def add_input_dataset( self, name, dataset=None, dataset_id=None ):
          assoc = JobToInputDatasetAssociation( name, dataset )
          if dataset is None and dataset_id is not None:
              assoc.dataset_id = dataset_id
          self.input_datasets.append( assoc )
  
      def add_output_dataset( self, name, dataset ):
          self.output_datasets.append( JobToOutputDatasetAssociation( name, dataset ) )
  
      def add_input_dataset_collection( self, name, dataset_collection ):
          self.input_dataset_collections.append( JobToInputDatasetCollectionAssociation( name, dataset_collection ) )
  
      def add_output_dataset_collection( self, name, dataset_collection_instance ):
          self.output_dataset_collection_instances.append( JobToOutputDatasetCollectionAssociation( name, dataset_collection_instance ) )
  
      def add_implicit_output_dataset_collection( self, name, dataset_collection ):
          self.output_dataset_collections.append( JobToImplicitOutputDatasetCollectionAssociation( name, dataset_collection ) )
  
      def add_input_library_dataset( self, name, dataset ):
          self.input_library_datasets.append( JobToInputLibraryDatasetAssociation( name, dataset ) )
  
      def add_output_library_dataset( self, name, dataset ):
          self.output_library_datasets.append( JobToOutputLibraryDatasetAssociation( name, dataset ) )
  
      def add_post_job_action(self, pja):
          self.post_job_actions.append( PostJobActionAssociation( pja, self ) )
  
      def set_state( self, state ):
          """
          Save state history
          """
          self.state = state
          self.state_history.append( JobStateHistory( self ) )
  
      def get_param_values( self, app, ignore_errors=False ):
          """
          Read encoded parameter values from the database and turn back into a
          dict of tool parameter values.
          """
          param_dict = self.raw_param_dict()
          tool = app.toolbox.get_tool( self.tool_id )
          param_dict = tool.params_from_strings( param_dict, app, ignore_errors=ignore_errors )
          return param_dict
  
      def raw_param_dict( self ):
          param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] )
          return param_dict
  
      def check_if_output_datasets_deleted( self ):
          """
          Return true if all of the output datasets associated with this job are
          in the deleted state
          """
          for dataset_assoc in self.output_datasets:
              dataset = dataset_assoc.dataset
              # only the originator of the job can delete a dataset to cause
              # cancellation of the job, no need to loop through history_associations
              if not dataset.deleted:
                  return False
          return True
  
      def mark_deleted( self, track_jobs_in_database=False ):
          """
          Mark this job as deleted, and mark any output datasets as discarded.
          """
          if self.finished:
              # Do not modify the state/outputs of jobs that are already terminal
              return
          if track_jobs_in_database:
              self.state = Job.states.DELETED_NEW
          else:
              self.state = Job.states.DELETED
          self.info = "Job output deleted by user before job completed."
          for dataset_assoc in self.output_datasets:
              dataset = dataset_assoc.dataset
              dataset.deleted = True
              dataset.state = dataset.states.DISCARDED
              for dataset in dataset.dataset.history_associations:
                  # propagate info across shared datasets
                  dataset.deleted = True
                  dataset.blurb = 'deleted'
                  dataset.peek = 'Job deleted'
                  dataset.info = 'Job output deleted by user before job completed'
  
      def to_dict( self, view='collection', system_details=False ):
          rval = super( Job, self ).to_dict( view=view )
          rval['tool_id'] = self.tool_id
          if system_details:
              # System level details that only admins should have.
              rval['external_id'] = self.job_runner_external_id
              rval['command_line'] = self.command_line
  
          if view == 'element':
              param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] )
              rval['params'] = param_dict
  
              input_dict = {}
              for i in self.input_datasets:
                  if i.dataset is not None:
                      input_dict[i.name] = {
                          "id" : i.dataset.id, "src" : "hda",
                          "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                      }
              for i in self.input_library_datasets:
                  if i.dataset is not None:
                      input_dict[i.name] = {
                          "id" : i.dataset.id, "src" : "ldda",
                          "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                      }
              for k in input_dict:
                  if k in param_dict:
                      del param_dict[k]
              rval['inputs'] = input_dict
  
              output_dict = {}
              for i in self.output_datasets:
                  if i.dataset is not None:
                      output_dict[i.name] = {
                          "id" : i.dataset.id, "src" : "hda",
                          "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                      }
              for i in self.output_library_datasets:
                  if i.dataset is not None:
                      output_dict[i.name] = {
                          "id" : i.dataset.id, "src" : "ldda",
                          "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                      }
              rval['outputs'] = output_dict
  
          return rval
  
      def set_final_state( self, final_state ):
          self.set_state( final_state )
          if self.workflow_invocation_step:
              self.workflow_invocation_step.update()
  
      def get_destination_configuration(self, config, key, default=None):
          """ Get a destination parameter that can be defaulted back
          in specified config if it needs to be applied globally.
          """
          param_unspecified = object()
          config_value = (self.destination_params or {}).get(key, param_unspecified)
          if config_value is param_unspecified:
              config_value = getattr(config, key, param_unspecified)
          if config_value is param_unspecified:
              config_value = default
          return config_value
  
      @property
      def seconds_since_update( self ):
          return (galaxy.model.orm.now.now() - self.update_time).total_seconds()
  
  
  class Task( object, JobLike ):
      """
      A task represents a single component of a job.
      """
      _numeric_metric = TaskMetricNumeric
      _text_metric = TaskMetricText
  
      states = Bunch( NEW='new',
                      WAITING='waiting',
                      QUEUED='queued',
                      RUNNING='running',
                      OK='ok',
                      ERROR='error',
                      DELETED='deleted' )
  
      # Please include an accessor (get/set pair) for any new columns/members.
      def __init__( self, job, working_directory, prepare_files_cmd ):
          self.command_line = None
          self.parameters = []
          self.state = Task.states.NEW
          self.info = None
          self.working_directory = working_directory
          self.task_runner_name = None
          self.task_runner_external_id = None
          self.job = job
          self.stdout = ""
          self.stderr = ""
          self.exit_code = None
          self.prepare_input_files_cmd = prepare_files_cmd
          self._init_metrics()
  
      def get_param_values( self, app ):
          """
          Read encoded parameter values from the database and turn back into a
          dict of tool parameter values.
          """
          param_dict = dict( [ ( p.name, p.value ) for p in self.parent_job.parameters ] )
          tool = app.toolbox.get_tool( self.tool_id )
          param_dict = tool.params_from_strings( param_dict, app )
          return param_dict
  
      def get_id( self ):
          # This is defined in the SQL Alchemy schema:
          return self.id
  
      def get_id_tag( self ):
          """
          Return an id tag suitable for identifying the task.
          This combines the task's job id and the task's own id.
          """
          return "%s_%s" % ( self.job.get_id(), self.get_id() )
  
      def get_command_line( self ):
          return self.command_line
  
      def get_parameters( self ):
          return self.parameters
  
      def get_state( self ):
          return self.state
  
      def get_info( self ):
          return self.info
  
      def get_working_directory( self ):
          return self.working_directory
  
      def get_task_runner_name( self ):
          return self.task_runner_name
  
      def get_task_runner_external_id( self ):
          return self.task_runner_external_id
  
      def get_job( self ):
          return self.job
  
      def get_stdout( self ):
          return self.stdout
  
      def get_stderr( self ):
          return self.stderr
  
      def get_prepare_input_files_cmd( self ):
          return self.prepare_input_files_cmd
  
      # The following accessors are for members that are in the Job class but
      # not in the Task class. So they can either refer to the parent Job
      # or return None, depending on whether Tasks need to point to the parent
      # (e.g., for a session) or never use the member (e.g., external output
      # metdata). These can be filled in as needed.
      def get_external_output_metadata( self ):
          """
          The external_output_metadata is currently a backref to
          JobExternalOutputMetadata. It exists for a job but not a task,
          and when a task is cancelled its corresponding parent Job will
          be cancelled. So None is returned now, but that could be changed
          to self.get_job().get_external_output_metadata().
          """
          return None
  
      def get_job_runner_name( self ):
          """
          Since runners currently access Tasks the same way they access Jobs,
          this method just refers to *this* instance's runner.
          """
          return self.task_runner_name
  
      def get_job_runner_external_id( self ):
          """
          Runners will use the same methods to get information about the Task
          class as they will about the Job class, so this method just returns
          the task's external id.
          """
          # TODO: Merge into get_runner_external_id.
          return self.task_runner_external_id
  
      def get_session_id( self ):
          # The Job's galaxy session is equal to the Job's session, so the
          # Job's session is the same as the Task's session.
          return self.get_job().get_session_id()
  
      def set_id( self, id ):
          # This is defined in the SQL Alchemy's mapper and not here.
          # This should never be called.
          self.id = id
  
      def set_command_line( self, command_line ):
          self.command_line = command_line
  
      def set_parameters( self, parameters ):
          self.parameters = parameters
  
      def set_state( self, state ):
          self.state = state
  
      def set_info( self, info ):
          self.info = info
  
      def set_working_directory( self, working_directory ):
          self.working_directory = working_directory
  
      def set_task_runner_name( self, task_runner_name ):
          self.task_runner_name = task_runner_name
  
      def set_job_runner_external_id( self, task_runner_external_id ):
          # This method is available for runners that do not want/need to
          # differentiate between the kinds of Runnable things (Jobs and Tasks)
          # that they're using.
          log.debug( "Task %d: Set external id to %s"
                     % ( self.id, task_runner_external_id ) )
          self.task_runner_external_id = task_runner_external_id
  
      def set_task_runner_external_id( self, task_runner_external_id ):
          self.task_runner_external_id = task_runner_external_id
  
      def set_job( self, job ):
          self.job = job
  
      def set_stdout( self, stdout ):
          self.stdout = stdout
  
      def set_stderr( self, stderr ):
          self.stderr = stderr
  
      def set_prepare_input_files_cmd( self, prepare_input_files_cmd ):
          self.prepare_input_files_cmd = prepare_input_files_cmd
  
  
  class JobParameter( object ):
      def __init__( self, name, value ):
          self.name = name
          self.value = value
  
  
  class JobToInputDatasetAssociation( object ):
      def __init__( self, name, dataset ):
          self.name = name
          self.dataset = dataset
  
  
  class JobToOutputDatasetAssociation( object ):
      def __init__( self, name, dataset ):
          self.name = name
          self.dataset = dataset
  
  
  class JobToInputDatasetCollectionAssociation( object ):
      def __init__( self, name, dataset_collection ):
          self.name = name
          self.dataset_collection = dataset_collection
  
  
  # Many jobs may map to one HistoryDatasetCollection using these for a given
  # tool output (if mapping over an input collection).
  class JobToOutputDatasetCollectionAssociation( object ):
      def __init__( self, name, dataset_collection_instance ):
          self.name = name
          self.dataset_collection_instance = dataset_collection_instance
  
  
  # A DatasetCollection will be mapped to at most one job per tool output
  # using these. (You can think of many of these models as going into the
  # creation of a JobToOutputDatasetCollectionAssociation.)
  class JobToImplicitOutputDatasetCollectionAssociation( object ):
      def __init__( self, name, dataset_collection ):
          self.name = name
          self.dataset_collection = dataset_collection
  
  
  class JobToInputLibraryDatasetAssociation( object ):
      def __init__( self, name, dataset ):
          self.name = name
          self.dataset = dataset
  
  
  class JobToOutputLibraryDatasetAssociation( object ):
      def __init__( self, name, dataset ):
          self.name = name
          self.dataset = dataset
  
  
  class JobStateHistory( object ):
      def __init__( self, job ):
          self.job = job
          self.state = job.state
          self.info = job.info
  
  
  class ImplicitlyCreatedDatasetCollectionInput( object ):
      def __init__( self, name, input_dataset_collection ):
          self.name = name
          self.input_dataset_collection = input_dataset_collection
  
  
  class PostJobAction( object ):
      def __init__( self, action_type, workflow_step, output_name=None, action_arguments=None):
          self.action_type = action_type
          self.output_name = output_name
          self.action_arguments = action_arguments
          self.workflow_step = workflow_step
  
  
  class PostJobActionAssociation( object ):
      def __init__(self, pja, job=None, job_id=None ):
          if job is not None:
              self.job = job
          elif job_id is not None:
              self.job_id = job_id
          else:
              raise Exception("PostJobActionAssociation must be created with a job or a job_id.")
          self.post_job_action = pja
  
  
  class JobExternalOutputMetadata( object ):
      def __init__( self, job=None, dataset=None ):
          self.job = job
          if isinstance( dataset, galaxy.model.HistoryDatasetAssociation ):
              self.history_dataset_association = dataset
          elif isinstance( dataset, galaxy.model.LibraryDatasetDatasetAssociation ):
              self.library_dataset_dataset_association = dataset
  
      @property
      def dataset( self ):
          if self.history_dataset_association:
              return self.history_dataset_association
          elif self.library_dataset_dataset_association:
              return self.library_dataset_dataset_association
          return None
  
  
  class JobExportHistoryArchive( object ):
      def __init__( self, job=None, history=None, dataset=None, compressed=False,
                    history_attrs_filename=None, datasets_attrs_filename=None,
                    jobs_attrs_filename=None ):
          self.job = job
          self.history = history
          self.dataset = dataset
          self.compressed = compressed
          self.history_attrs_filename = history_attrs_filename
          self.datasets_attrs_filename = datasets_attrs_filename
          self.jobs_attrs_filename = jobs_attrs_filename
  
      @property
      def up_to_date( self ):
          """ Return False, if a new export should be generated for corresponding
          history.
          """
          job = self.job
          return job.state not in [ Job.states.ERROR, Job.states.DELETED ] \
              and job.update_time > self.history.update_time
  
      @property
      def ready( self ):
          return self.job.state == Job.states.OK
  
      @property
      def preparing( self ):
          return self.job.state in [ Job.states.RUNNING, Job.states.QUEUED, Job.states.WAITING ]
  
      @property
      def export_name( self ):
          # Stream archive.
          hname = ready_name_for_url( self.history.name )
          hname = "Galaxy-History-%s.tar" % ( hname )
          if self.compressed:
              hname += ".gz"
          return hname
  
  
  class JobImportHistoryArchive( object ):
      def __init__( self, job=None, history=None, archive_dir=None ):
          self.job = job
          self.history = history
          self.archive_dir = archive_dir
  
  
  class GenomeIndexToolData( object ):
      def __init__( self, job=None, params=None, dataset=None, deferred_job=None,
                    transfer_job=None, fasta_path=None, created_time=None, modified_time=None,
                    dbkey=None, user=None, indexer=None ):
          self.job = job
          self.dataset = dataset
          self.fasta_path = fasta_path
          self.user = user
          self.indexer = indexer
          self.created_time = created_time
          self.modified_time = modified_time
          self.deferred = deferred_job
          self.transfer = transfer_job
  
  
  class DeferredJob( object ):
      states = Bunch( NEW='new',
                      WAITING='waiting',
                      QUEUED='queued',
                      RUNNING='running',
                      OK='ok',
                      ERROR='error' )
  
      def __init__( self, state=None, plugin=None, params=None ):
          self.state = state
          self.plugin = plugin
          self.params = params
  
      def get_check_interval( self ):
          if not hasattr( self, '_check_interval' ):
              self._check_interval = None
          return self._check_interval
  
      def set_check_interval( self, seconds ):
          self._check_interval = seconds
      check_interval = property( get_check_interval, set_check_interval )
  
      def get_last_check( self ):
          if not hasattr( self, '_last_check' ):
              self._last_check = 0
          return self._last_check
  
      def set_last_check( self, seconds ):
          try:
              self._last_check = int( seconds )
          except:
              self._last_check = time.time()
      last_check = property( get_last_check, set_last_check )
  
      @property
      def is_check_time( self ):
          if self.check_interval is None:
              return True
          elif ( int( time.time() ) - self.last_check ) > self.check_interval:
              return True
          else:
              return False
  
  
  class Group( object, Dictifiable  ):
      dict_collection_visible_keys = ( 'id', 'name' )
      dict_element_visible_keys = ( 'id', 'name' )
  
      def __init__( self, name=None ):
          self.name = name
          self.deleted = False
  
  
  class UserGroupAssociation( object ):
      def __init__( self, user, group ):
          self.user = user
          self.group = group
  
  
  def is_hda(d):
      return isinstance( d, HistoryDatasetAssociation )
  
  
  class History( object, Dictifiable, UsesAnnotations, HasName ):
  
      dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' )
      dict_element_visible_keys = ( 'id', 'name', 'genome_build', 'deleted', 'purged', 'update_time',
                                    'published', 'importable', 'slug', 'empty' )
      default_name = 'Unnamed history'
  
      def __init__( self, id=None, name=None, user=None ):
          self.id = id
          self.name = name or History.default_name
          self.deleted = False
          self.purged = False
          self.importing = False
          self.genome_build = None
          self.published = False
          # Relationships
          self.user = user
          self.datasets = []
          self.galaxy_sessions = []
          self.tags = []
  
      @property
      def empty( self ):
          return self.hid_counter == 1
  
      def _next_hid( self, n=1 ):
          # this is overriden in mapping.py db_next_hid() method
          if len( self.datasets ) == 0:
              return n
          else:
              last_hid = 0
              for dataset in self.datasets:
                  if dataset.hid > last_hid:
                      last_hid = dataset.hid
              return last_hid + n
  
      def add_galaxy_session( self, galaxy_session, association=None ):
          if association is None:
              self.galaxy_sessions.append( GalaxySessionToHistoryAssociation( galaxy_session, self ) )
          else:
              self.galaxy_sessions.append( association )
  
      def add_dataset( self, dataset, parent_id=None, genome_build=None, set_hid=True, quota=True ):
          if isinstance( dataset, Dataset ):
              dataset = HistoryDatasetAssociation(dataset=dataset)
              object_session( self ).add( dataset )
              object_session( self ).flush()
          elif not isinstance( dataset, HistoryDatasetAssociation ):
              raise TypeError( "You can only add Dataset and HistoryDatasetAssociation instances to a history" +
                               " ( you tried to add %s )." % str( dataset ) )
          if parent_id:
              for data in self.datasets:
                  if data.id == parent_id:
                      dataset.hid = data.hid
                      break
              else:
                  if set_hid:
                      dataset.hid = self._next_hid()
          else:
              if set_hid:
                  dataset.hid = self._next_hid()
          if quota and self.user:
              self.user.adjust_total_disk_usage(dataset.quota_amount(self.user))
          dataset.history = self
          if genome_build not in [None, '?']:
              self.genome_build = genome_build
          dataset.history_id = self.id
          return dataset
  
      def add_datasets( self, sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False ):
          """ Optimized version of add_dataset above that minimizes database
          interactions when adding many datasets to history at once.
          """
          all_hdas = all( is_hda(_) for _ in datasets )
          optimize = len( datasets) > 1 and parent_id is None and all_hdas and set_hid
          if optimize:
              self.__add_datasets_optimized( datasets, genome_build=genome_build )
              if quota and self.user:
                  disk_usage = sum([d.get_total_size() for d in datasets])
                  self.user.adjust_total_disk_usage(disk_usage)
  
              sa_session.add_all( datasets )
              if flush:
                  sa_session.flush()
          else:
              for dataset in datasets:
                  self.add_dataset( dataset, parent_id=parent_id, genome_build=genome_build, set_hid=set_hid, quota=quota )
                  sa_session.add( dataset )
                  if flush:
                      sa_session.flush()
  
      def __add_datasets_optimized( self, datasets, genome_build=None ):
          """ Optimized version of add_dataset above that minimizes database
          interactions when adding many datasets to history at once under
          certain circumstances.
          """
          n = len( datasets )
  
          base_hid = self._next_hid( n=n )
          set_genome = genome_build not in [None, '?']
          for i, dataset in enumerate( datasets ):
              dataset.hid = base_hid + i
              dataset.history = self
              if set_genome:
                  self.genome_build = genome_build
          for dataset in datasets:
              dataset.history_id = self.id
          return datasets
  
      def add_dataset_collection( self, history_dataset_collection, set_hid=True ):
          if set_hid:
              history_dataset_collection.hid = self._next_hid()
          history_dataset_collection.history = self
          # TODO: quota?
          self.dataset_collections.append( history_dataset_collection )
          return history_dataset_collection
  
      def copy( self, name=None, target_user=None, activatable=False, all_datasets=False ):
          """
          Return a copy of this history using the given `name` and `target_user`.
          If `activatable`, copy only non-deleted datasets. If `all_datasets`, copy
          non-deleted, deleted, and purged datasets.
          """
          name = name or self.name
          applies_to_quota = target_user != self.user
  
          # Create new history.
          new_history = History( name=name, user=target_user )
          db_session = object_session( self )
          db_session.add( new_history )
          db_session.flush()
  
          # copy history tags and annotations (if copying user is not anonymous)
          if target_user:
              self.copy_item_annotation( db_session, self.user, self, target_user, new_history )
              new_history.copy_tags_from(target_user=target_user, source_history=self)
  
          # Copy HDAs.
          if activatable:
              hdas = self.activatable_datasets
          elif all_datasets:
              hdas = self.datasets
          else:
              hdas = self.active_datasets
          for hda in hdas:
              # Copy HDA.
              new_hda = hda.copy( copy_children=True )
              new_history.add_dataset( new_hda, set_hid=False, quota=applies_to_quota )
              db_session.add( new_hda )
              db_session.flush()
  
              if target_user:
                  new_hda.copy_item_annotation( db_session, self.user, hda, target_user, new_hda )
                  new_hda.copy_tags_from( target_user, hda )
  
          # Copy history dataset collections
          if all_datasets:
              hdcas = self.dataset_collections
          else:
              hdcas = self.active_dataset_collections
          for hdca in hdcas:
              new_hdca = hdca.copy()
              new_history.add_dataset_collection( new_hdca, set_hid=False )
              db_session.add( new_hdca )
              db_session.flush()
  
              if target_user:
                  new_hdca.copy_item_annotation( db_session, self.user, hdca, target_user, new_hdca )
  
          new_history.hid_counter = self.hid_counter
          db_session.add( new_history )
          db_session.flush()
  
          return new_history
  
      @property
      def activatable_datasets( self ):
          # This needs to be a list
          return [ hda for hda in self.datasets if not hda.dataset.deleted ]
  
      def to_dict( self, view='collection', value_mapper=None ):
  
          # Get basic value.
          rval = super( History, self ).to_dict( view=view, value_mapper=value_mapper )
  
          # Add tags.
          tags_str_list = []
          for tag in self.tags:
              tag_str = tag.user_tname
              if tag.value is not None:
                  tag_str += ":" + tag.user_value
              tags_str_list.append( tag_str )
          rval[ 'tags' ] = tags_str_list
  
          if view == 'element':
              rval[ 'size' ] = int( self.disk_size )
  
          return rval
  
      @property
      def latest_export( self ):
          exports = self.exports
          return exports and exports[ 0 ]
  
      def unhide_datasets( self ):
          for dataset in self.datasets:
              dataset.mark_unhidden()
  
      def resume_paused_jobs( self ):
          for dataset in self.datasets:
              job = dataset.creating_job
              if job is not None and job.state == Job.states.PAUSED:
                  job.set_state(Job.states.NEW)
  
      @hybrid.hybrid_property
      def disk_size( self ):
          """
          Return the size in bytes of this history by summing the 'total_size's of
          all non-purged, unique datasets within it.
          """
          # non-.expression part of hybrid.hybrid_property: called when an instance is the namespace (not the class)
          db_session = object_session( self )
          rval = db_session.query(
              func.sum( db_session.query( HistoryDatasetAssociation.dataset_id, Dataset.total_size ).join( Dataset )
                      .filter( HistoryDatasetAssociation.table.c.history_id == self.id )
                      .filter( HistoryDatasetAssociation.purged != true() )
                      .filter( Dataset.purged != true() )
                      # unique datasets only
                      .distinct().subquery().c.total_size ) ).first()[0]
          if rval is None:
              rval = 0
          return rval
  
      @disk_size.expression
      def disk_size( cls ):
          """
          Return a query scalar that will get any history's size in bytes by summing
          the 'total_size's of all non-purged, unique datasets within it.
          """
          # .expression acts as a column_property and should return a scalar
          # first, get the distinct datasets within a history that are not purged
          hda_to_dataset_join = join( HistoryDatasetAssociation, Dataset,
              HistoryDatasetAssociation.table.c.dataset_id == Dataset.table.c.id )
          distinct_datasets = (
              select([
                  # use labels here to better accrss from the query above
                  HistoryDatasetAssociation.table.c.history_id.label( 'history_id' ),
                  Dataset.total_size.label( 'dataset_size' ),
                  Dataset.id.label( 'dataset_id' )
              ])
              .where( HistoryDatasetAssociation.table.c.purged != true() )
              .where( Dataset.table.c.purged != true() )
              .select_from( hda_to_dataset_join )
              # TODO: slow (in general) but most probably here - index total_size for easier sorting/distinct?
              .distinct()
          )
          # postgres needs an alias on FROM
          distinct_datasets_alias = aliased( distinct_datasets, name="datasets" )
          # then, bind as property of history using the cls.id
          size_query = (
              select([
                  func.coalesce( func.sum( distinct_datasets_alias.c.dataset_size ), 0 )
              ])
              .select_from( distinct_datasets_alias )
              .where( distinct_datasets_alias.c.history_id == cls.id )
          )
          # label creates a scalar
          return size_query.label( 'disk_size' )
  
      @property
      def disk_nice_size( self ):
          """Returns human readable size of history on disk."""
          return galaxy.util.nice_size( self.disk_size )
  
      @property
      def active_datasets_and_roles( self ):
          if not hasattr(self, '_active_datasets_and_roles'):
              db_session = object_session( self )
              query = ( db_session.query( HistoryDatasetAssociation )
                        .filter( HistoryDatasetAssociation.table.c.history_id == self.id )
                        .filter( not_( HistoryDatasetAssociation.deleted ) )
                        .order_by( HistoryDatasetAssociation.table.c.hid.asc() )
                        .options( joinedload("dataset"),
                                  joinedload("dataset.actions"),
                                  joinedload("dataset.actions.role"),
                                  ))
              self._active_datasets_and_roles = query.all()
          return self._active_datasets_and_roles
  
      @property
      def active_contents( self ):
          """ Return all active contents ordered by hid.
          """
          return self.contents_iter( types=[ "dataset", "dataset_collection" ], deleted=False, visible=True )
  
      def contents_iter( self, **kwds ):
          """
          Fetch filtered list of contents of history.
          """
          default_contents_types = [
              'dataset',
          ]
          types = kwds.get('types', default_contents_types)
          iters = []
          if 'dataset' in types:
              iters.append( self.__dataset_contents_iter( **kwds ) )
          if 'dataset_collection' in types:
              iters.append( self.__collection_contents_iter( **kwds ) )
          return galaxy.util.merge_sorted_iterables( operator.attrgetter( "hid" ), *iters )
  
      def __dataset_contents_iter(self, **kwds):
          return self.__filter_contents( HistoryDatasetAssociation, **kwds )
  
      def __filter_contents( self, content_class, **kwds ):
          db_session = object_session( self )
          assert db_session is not None
          query = db_session.query( content_class ).filter( content_class.table.c.history_id == self.id )
          query = query.order_by( content_class.table.c.hid.asc() )
          deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) )
          if deleted is not None:
              query = query.filter( content_class.deleted == deleted )
          visible = galaxy.util.string_as_bool_or_none( kwds.get( 'visible', None ) )
          if visible is not None:
              query = query.filter( content_class.visible == visible )
          if 'ids' in kwds:
              ids = kwds['ids']
              max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH)
              if len(ids) < max_in_filter_length:
                  query = query.filter( content_class.id.in_(ids) )
              else:
                  query = (content for content in query if content.id in ids)
          return query
  
      def __collection_contents_iter( self, **kwds ):
          return self.__filter_contents( HistoryDatasetCollectionAssociation, **kwds )
  
      def copy_tags_from(self, target_user, source_history):
          for src_shta in source_history.tags:
              new_shta = src_shta.copy()
              new_shta.user = target_user
              self.tags.append(new_shta)
  
  
  class HistoryUserShareAssociation( object ):
      def __init__( self ):
          self.history = None
          self.user = None
  
  
  class UserRoleAssociation( object ):
      def __init__( self, user, role ):
          self.user = user
          self.role = role
  
  
  class GroupRoleAssociation( object ):
      def __init__( self, group, role ):
          self.group = group
          self.role = role
  
  
  class Role( object, Dictifiable ):
      dict_collection_visible_keys = ( 'id', 'name' )
      dict_element_visible_keys = ( 'id', 'name', 'description', 'type' )
      private_id = None
      types = Bunch(
          PRIVATE='private',
          SYSTEM='system',
          USER='user',
          ADMIN='admin',
          SHARING='sharing'
      )
  
      def __init__( self, name="", description="", type="system", deleted=False ):
          self.name = name
          self.description = description
          self.type = type
          self.deleted = deleted
  
  
  class UserQuotaAssociation( object, Dictifiable ):
      dict_element_visible_keys = ( 'user', )
  
      def __init__( self, user, quota ):
          self.user = user
          self.quota = quota
  
  
  class GroupQuotaAssociation( object, Dictifiable ):
      dict_element_visible_keys = ( 'group', )
  
      def __init__( self, group, quota ):
          self.group = group
          self.quota = quota
  
  
  class Quota( object, Dictifiable ):
      dict_collection_visible_keys = ( 'id', 'name' )
      dict_element_visible_keys = ( 'id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups' )
      valid_operations = ( '+', '-', '=' )
  
      def __init__( self, name="", description="", amount=0, operation="=" ):
          self.name = name
          self.description = description
          if amount is None:
              self.bytes = -1
          else:
              self.bytes = amount
          self.operation = operation
  
      def get_amount( self ):
          if self.bytes == -1:
              return None
          return self.bytes
  
      def set_amount( self, amount ):
          if amount is None:
              self.bytes = -1
          else:
              self.bytes = amount
      amount = property( get_amount, set_amount )
  
      @property
      def display_amount( self ):
          if self.bytes == -1:
              return "unlimited"
          else:
              return galaxy.util.nice_size( self.bytes )
  
  
  class DefaultQuotaAssociation( Quota, Dictifiable ):
      dict_element_visible_keys = ( 'type', )
      types = Bunch(
          UNREGISTERED='unregistered',
          REGISTERED='registered'
      )
  
      def __init__( self, type, quota ):
          assert type in self.types.__dict__.values(), 'Invalid type'
          self.type = type
          self.quota = quota
  
  
  class DatasetPermissions( object ):
      def __init__( self, action, dataset, role=None, role_id=None ):
          self.action = action
          self.dataset = dataset
          if role is not None:
              self.role = role
          else:
              self.role_id = role_id
  
  
  class LibraryPermissions( object ):
      def __init__( self, action, library_item, role ):
          self.action = action
          if isinstance( library_item, Library ):
              self.library = library_item
          else:
              raise Exception( "Invalid Library specified: %s" % library_item.__class__.__name__ )
          self.role = role
  
  
  class LibraryFolderPermissions( object ):
      def __init__( self, action, library_item, role ):
          self.action = action
          if isinstance( library_item, LibraryFolder ):
              self.folder = library_item
          else:
              raise Exception( "Invalid LibraryFolder specified: %s" % library_item.__class__.__name__ )
          self.role = role
  
  
  class LibraryDatasetPermissions( object ):
      def __init__( self, action, library_item, role ):
          self.action = action
          if isinstance( library_item, LibraryDataset ):
              self.library_dataset = library_item
          else:
              raise Exception( "Invalid LibraryDataset specified: %s" % library_item.__class__.__name__ )
          self.role = role
  
  
  class LibraryDatasetDatasetAssociationPermissions( object ):
      def __init__( self, action, library_item, role ):
          self.action = action
          if isinstance( library_item, LibraryDatasetDatasetAssociation ):
              self.library_dataset_dataset_association = library_item
          else:
              raise Exception( "Invalid LibraryDatasetDatasetAssociation specified: %s" % library_item.__class__.__name__ )
          self.role = role
  
  
  class DefaultUserPermissions( object ):
      def __init__( self, user, action, role ):
          self.user = user
          self.action = action
          self.role = role
  
  
  class DefaultHistoryPermissions( object ):
      def __init__( self, history, action, role ):
          self.history = history
          self.action = action
          self.role = role
  
  
  class StorableObject( object ):
  
      def __init__( self, id, **kwargs):
          self.id = id
  
  
  class Dataset( StorableObject ):
      states = Bunch( NEW='new',
                      UPLOAD='upload',
                      QUEUED='queued',
                      RUNNING='running',
                      OK='ok',
                      EMPTY='empty',
                      ERROR='error',
                      DISCARDED='discarded',
                      PAUSED='paused',
                      SETTING_METADATA='setting_metadata',
                      FAILED_METADATA='failed_metadata')
      # failed_metadata is only valid as DatasetInstance state currently
  
      non_ready_states = (
          states.NEW,
          states.UPLOAD,
          states.QUEUED,
          states.RUNNING,
          states.SETTING_METADATA
      )
      ready_states = tuple( set( states.__dict__.values() ) - set( non_ready_states ) )
      valid_input_states = tuple(
          set( states.__dict__.values() ) - set( [states.ERROR, states.DISCARDED] )
      )
      terminal_states = (
          states.OK,
          states.EMPTY,
          states.ERROR,
          states.DISCARDED,
          states.FAILED_METADATA,
      )
  
      conversion_messages = Bunch( PENDING="pending",
                                   NO_DATA="no data",
                                   NO_CHROMOSOME="no chromosome",
                                   NO_CONVERTER="no converter",
                                   NO_TOOL="no tool",
                                   DATA="data",
                                   ERROR="error",
                                   OK="ok" )
  
      permitted_actions = get_permitted_actions( filter='DATASET' )
      file_path = "/tmp/"
      object_store = None  # This get initialized in mapping.py (method init) by app.py
      engine = None
  
      def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None ):
          super(Dataset, self).__init__(id=id)
          self.state = state
          self.deleted = False
          self.purged = False
          self.purgable = purgable
          self.external_filename = external_filename
          self.external_extra_files_path = None
          self._extra_files_path = extra_files_path
          self.file_size = file_size
          if uuid is None:
              self.uuid = uuid4()
          else:
              self.uuid = UUID(str(uuid))
  
      def in_ready_state( self ):
          return self.state in self.ready_states
  
      def get_file_name( self ):
          if not self.external_filename:
              assert self.id is not None, "ID must be set before filename used (commit the object)"
              assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id
              filename = self.object_store.get_filename( self )
              return filename
          else:
              filename = self.external_filename
          # Make filename absolute
          return os.path.abspath( filename )
  
      def set_file_name( self, filename ):
          if not filename:
              self.external_filename = None
          else:
              self.external_filename = filename
      file_name = property( get_file_name, set_file_name )
  
      def get_extra_files_path( self ):
          # Unlike get_file_name - external_extra_files_path is not backed by an
          # actual database column so if SA instantiates this object - the
          # attribute won't exist yet.
          if not getattr( self, "external_extra_files_path", None ):
              return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id )
          else:
              return os.path.abspath( self.external_extra_files_path )
  
      def set_extra_files_path( self, extra_files_path ):
          if not extra_files_path:
              self.external_extra_files_path = None
          else:
              self.external_extra_files_path = extra_files_path
      extra_files_path = property( get_extra_files_path, set_extra_files_path)
  
      def _calculate_size( self ):
          if self.external_filename:
              try:
                  return os.path.getsize(self.external_filename)
              except OSError:
                  return 0
          else:
              return self.object_store.size(self)
  
      def get_size( self, nice_size=False ):
          """Returns the size of the data on disk"""
          if self.file_size:
              if nice_size:
                  return galaxy.util.nice_size( self.file_size )
              else:
                  return self.file_size
          else:
              if nice_size:
                  return galaxy.util.nice_size( self._calculate_size() )
              else:
                  return self._calculate_size()
  
      def set_size( self ):
          """Returns the size of the data on disk"""
          if not self.file_size:
              self.file_size = self._calculate_size()
  
      def get_total_size( self ):
          if self.total_size is not None:
              return self.total_size
          # for backwards compatibility, set if unset
          self.set_total_size()
          db_session = object_session( self )
          db_session.flush()
          return self.total_size
  
      def set_total_size( self ):
          if self.file_size is None:
              self.set_size()
          self.total_size = self.file_size or 0
          if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True):
              for root, dirs, files in os.walk( self.extra_files_path ):
                  self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files if os.path.exists( os.path.join( root, file ) ) ] )
  
      def has_data( self ):
          """Detects whether there is any data"""
          return self.get_size() > 0
  
      def mark_deleted( self, include_children=True ):
          self.deleted = True
  
      def is_multi_byte( self ):
          if not self.has_data():
              return False
          try:
              return is_multi_byte( codecs.open( self.file_name, 'r', 'utf-8' ).read( 100 ) )
          except UnicodeDecodeError:
              return False
      # FIXME: sqlalchemy will replace this
  
      def _delete(self):
          """Remove the file that corresponds to this data"""
          self.object_store.delete(self)
  
      @property
      def user_can_purge( self ):
          return self.purged is False \
              and not bool( self.library_associations ) \
              and len( self.history_associations ) == len( self.purged_history_associations )
  
      def full_delete( self ):
          """Remove the file and extra files, marks deleted and purged"""
          # os.unlink( self.file_name )
          self.object_store.delete(self)
          if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True):
              self.object_store.delete(self, entire_dir=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True)
          # if os.path.exists( self.extra_files_path ):
          #     shutil.rmtree( self.extra_files_path )
          # TODO: purge metadata files
          self.deleted = True
          self.purged = True
  
      def get_access_roles( self, trans ):
          roles = []
          for dp in self.actions:
              if dp.action == trans.app.security_agent.permitted_actions.DATASET_ACCESS.action:
                  roles.append( dp.role )
          return roles
  
      def get_manage_permissions_roles( self, trans ):
          roles = []
          for dp in self.actions:
              if dp.action == trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action:
                  roles.append( dp.role )
          return roles
  
      def has_manage_permissions_roles( self, trans ):
          for dp in self.actions:
              if dp.action == trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action:
                  return True
          return False
  
  
  class DatasetInstance( object ):
      """A base class for all 'dataset instances', HDAs, LDAs, etc"""
      states = Dataset.states
      conversion_messages = Dataset.conversion_messages
      permitted_actions = Dataset.permitted_actions
  
      def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None,
                    dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None,
                    parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None,
                    extended_metadata=None, flush=True ):
          self.name = name or "Unnamed dataset"
          self.id = id
          self.info = info
          self.blurb = blurb
          self.peek = peek
          self.tool_version = tool_version
          self.extension = extension
          self.designation = designation
          # set private variable to None here, since the attribute may be needed in by MetadataCollection.__init__
          self._metadata = None
          self.metadata = metadata or dict()
          self.extended_metadata = extended_metadata
          if dbkey:  # dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata'
              self.dbkey = dbkey
          self.deleted = deleted
          self.visible = visible
          # Relationships
          if not dataset and create_dataset:
              # Had to pass the sqlalchemy session in order to create a new dataset
              dataset = Dataset( state=Dataset.states.NEW )
              if flush:
                  sa_session.add( dataset )
                  sa_session.flush()
          self.dataset = dataset
          self.parent_id = parent_id
          self.validation_errors = validation_errors
  
      @property
      def ext( self ):
          return self.extension
  
      def get_dataset_state( self ):
          # self._state is currently only used when setting metadata externally
          # leave setting the state as-is, we'll currently handle this specially in the external metadata code
          if self._state:
              return self._state
          return self.dataset.state
  
      def raw_set_dataset_state( self, state ):
          if state != self.dataset.state:
              self.dataset.state = state
              return True
          else:
              return False
  
      def set_dataset_state( self, state ):
          if self.raw_set_dataset_state( state ):
              object_session( self ).add( self.dataset )
              object_session( self ).flush()  # flush here, because hda.flush() won't flush the Dataset object
      state = property( get_dataset_state, set_dataset_state )
  
      def get_file_name( self ):
          return self.dataset.get_file_name()
  
      def set_file_name(self, filename):
          return self.dataset.set_file_name( filename )
      file_name = property( get_file_name, set_file_name )
  
      @property
      def extra_files_path( self ):
          return self.dataset.extra_files_path
  
      @property
      def datatype( self ):
          return _get_datatypes_registry().get_datatype_by_extension( self.extension )
  
      def get_metadata( self ):
          # using weakref to store parent (to prevent circ ref),
          #   does a Session.clear() cause parent to be invalidated, while still copying over this non-database attribute?
          if not hasattr( self, '_metadata_collection' ) or self._metadata_collection.parent != self:
              self._metadata_collection = galaxy.model.metadata.MetadataCollection( self )
          return self._metadata_collection
  
      def set_metadata( self, bunch ):
          # Needs to accept a MetadataCollection, a bunch, or a dict
          self._metadata = self.metadata.make_dict_copy( bunch )
      metadata = property( get_metadata, set_metadata )
      # This provide backwards compatibility with using the old dbkey
      # field in the database.  That field now maps to "old_dbkey" (see mapping.py).
  
      def get_dbkey( self ):
          dbkey = self.metadata.dbkey
          if not isinstance(dbkey, list):
              dbkey = [dbkey]
          if dbkey in [[None], []]:
              return "?"
          return dbkey[0]
  
      def set_dbkey( self, value ):
          if "dbkey" in self.datatype.metadata_spec:
              if not isinstance(value, list):
                  self.metadata.dbkey = [value]
              else:
                  self.metadata.dbkey = value
      dbkey = property( get_dbkey, set_dbkey )
  
      def change_datatype( self, new_ext ):
          self.clear_associated_files()
          _get_datatypes_registry().change_datatype( self, new_ext )
  
      def get_size( self, nice_size=False ):
          """Returns the size of the data on disk"""
          if nice_size:
              return galaxy.util.nice_size( self.dataset.get_size() )
          return self.dataset.get_size()
  
      def set_size( self ):
          """Returns the size of the data on disk"""
          return self.dataset.set_size()
  
      def get_total_size( self ):
          return self.dataset.get_total_size()
  
      def set_total_size( self ):
          return self.dataset.set_total_size()
  
      def has_data( self ):
          """Detects whether there is any data"""
          return self.dataset.has_data()
  
      def get_raw_data( self ):
          """Returns the full data. To stream it open the file_name and read/write as needed"""
          return self.datatype.get_raw_data( self )
  
      def write_from_stream( self, stream ):
          """Writes data from a stream"""
          self.datatype.write_from_stream(self, stream)
  
      def set_raw_data( self, data ):
          """Saves the data on the disc"""
          self.datatype.set_raw_data(self, data)
  
      def get_mime( self ):
          """Returns the mime type of the data"""
          try:
              return _get_datatypes_registry().get_mimetype_by_extension( self.extension.lower() )
          except AttributeError:
              # extension is None
              return 'data'
  
      def is_multi_byte( self ):
          """Data consists of multi-byte characters"""
          return self.dataset.is_multi_byte()
  
      def set_peek( self, is_multi_byte=False ):
          return self.datatype.set_peek( self, is_multi_byte=is_multi_byte )
  
      def init_meta( self, copy_from=None ):
          return self.datatype.init_meta( self, copy_from=copy_from )
  
      def set_meta( self, **kwd ):
          self.clear_associated_files( metadata_safe=True )
          return self.datatype.set_meta( self, **kwd )
  
      def missing_meta( self, **kwd ):
          return self.datatype.missing_meta( self, **kwd )
  
      def as_display_type( self, type, **kwd ):
          return self.datatype.as_display_type( self, type, **kwd )
  
      def display_peek( self ):
          return self.datatype.display_peek( self )
  
      def display_name( self ):
          return self.datatype.display_name( self )
  
      def display_info( self ):
          return self.datatype.display_info( self )
  
      def get_converted_files_by_type( self, file_type ):
          for assoc in self.implicitly_converted_datasets:
              if not assoc.deleted and assoc.type == file_type:
                  if assoc.dataset:
                      return assoc.dataset
                  return assoc.dataset_ldda
          return None
  
      def get_converted_dataset_deps(self, trans, target_ext):
          """
          Returns dict of { "dependency" => HDA }
          """
          # List of string of dependencies
          try:
              depends_list = trans.app.datatypes_registry.converter_deps[self.extension][target_ext]
          except KeyError:
              depends_list = []
          return dict([ (dep, self.get_converted_dataset(trans, dep)) for dep in depends_list ])
  
      def get_converted_dataset(self, trans, target_ext, target_context=None, history=None):
          """
          Return converted dataset(s) if they exist, along with a dict of dependencies.
          If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
          """
          # See if we can convert the dataset
          if target_ext not in self.get_converter_types():
              raise NoConverterException("Conversion from '%s' to '%s' not possible" % (self.extension, target_ext) )
          deps = {}
          # List of string of dependencies
          try:
              depends_list = trans.app.datatypes_registry.converter_deps[self.extension][target_ext]
          except KeyError:
              depends_list = []
          # See if converted dataset already exists, either in metadata in conversions.
          converted_dataset = self.get_metadata_dataset( target_ext )
          if converted_dataset:
              return converted_dataset
          converted_dataset = self.get_converted_files_by_type( target_ext )
          if converted_dataset:
              return converted_dataset
          # Conversion is possible but hasn't been done yet, run converter.
          # Check if we have dependencies
          try:
              for dependency in depends_list:
                  dep_dataset = self.get_converted_dataset(trans, dependency)
                  if dep_dataset is None:
                      # None means converter is running first time
                      return None
                  elif dep_dataset.state == Job.states.ERROR:
                      raise ConverterDependencyException("A dependency (%s) was in an error state." % dependency)
                  elif dep_dataset.state != Job.states.OK:
                      # Pending
                      return None
                  deps[dependency] = dep_dataset
          except NoConverterException:
              raise NoConverterException("A dependency (%s) is missing a converter." % dependency)
          except KeyError:
              pass  # No deps
          new_dataset = next(iter(self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, target_context=target_context, history=history ).values()))
          new_dataset.name = self.name
          self.copy_attributes( new_dataset )
          assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False )
          session = trans.sa_session
          session.add( new_dataset )
          session.add( assoc )
          session.flush()
          return new_dataset
  
      def copy_attributes( self, new_dataset ):
          """
          Copies attributes to a new datasets, used for implicit conversions
          """
          pass
  
      def get_metadata_dataset( self, dataset_ext ):
          """
          Returns an HDA that points to a metadata file which contains a
          converted data with the requested extension.
          """
          for name, value in self.metadata.items():
              # HACK: MetadataFile objects do not have a type/ext, so need to use metadata name
              # to determine type.
              if dataset_ext == 'bai' and name == 'bam_index' and isinstance( value, MetadataFile ):
                  # HACK: MetadataFile objects cannot be used by tools, so return
                  # a fake HDA that points to metadata file.
                  fake_dataset = Dataset( state=Dataset.states.OK, external_filename=value.file_name )
                  fake_hda = HistoryDatasetAssociation( dataset=fake_dataset )
                  return fake_hda
  
      def clear_associated_files( self, metadata_safe=False, purge=False ):
          raise Exception( "Unimplemented" )
  
      def get_child_by_designation(self, designation):
          for child in self.children:
              if child.designation == designation:
                  return child
          return None
  
      def get_converter_types(self):
          return self.datatype.get_converter_types( self, _get_datatypes_registry() )
  
      def can_convert_to(self, format):
          return format in self.get_converter_types()
  
      def find_conversion_destination( self, accepted_formats, **kwd ):
          """Returns ( target_ext, existing converted dataset )"""
          return self.datatype.find_conversion_destination( self, accepted_formats, _get_datatypes_registry(), **kwd )
  
      def add_validation_error( self, validation_error ):
          self.validation_errors.append( validation_error )
  
      def extend_validation_errors( self, validation_errors ):
          self.validation_errors.extend(validation_errors)
  
      def mark_deleted( self, include_children=True ):
          self.deleted = True
          if include_children:
              for child in self.children:
                  child.mark_deleted()
  
      def mark_undeleted( self, include_children=True ):
          self.deleted = False
          if include_children:
              for child in self.children:
                  child.mark_undeleted()
  
      def mark_unhidden( self, include_children=True ):
          self.visible = True
          if include_children:
              for child in self.children:
                  child.mark_unhidden()
  
      def undeletable( self ):
          if self.purged:
              return False
          return True
  
      @property
      def is_ok(self):
          return self.state == self.states.OK
  
      @property
      def is_pending( self ):
          """
          Return true if the dataset is neither ready nor in error
          """
          return self.state in ( self.states.NEW, self.states.UPLOAD,
                                 self.states.QUEUED, self.states.RUNNING,
                                 self.states.SETTING_METADATA )
  
      @property
      def source_library_dataset( self ):
          def get_source( dataset ):
              if isinstance( dataset, LibraryDatasetDatasetAssociation ):
                  if dataset.library_dataset:
                      return ( dataset, dataset.library_dataset )
              if dataset.copied_from_library_dataset_dataset_association:
                  source = get_source( dataset.copied_from_library_dataset_dataset_association )
                  if source:
                      return source
              if dataset.copied_from_history_dataset_association:
                  source = get_source( dataset.copied_from_history_dataset_association )
                  if source:
                      return source
              return ( None, None )
          return get_source( self )
  
      @property
      def source_dataset_chain( self ):
          def _source_dataset_chain( dataset, lst ):
              try:
                  cp_from_ldda = dataset.copied_from_library_dataset_dataset_association
                  if cp_from_ldda:
                      lst.append( (cp_from_ldda, "(Data Library)") )
                      return _source_dataset_chain( cp_from_ldda, lst )
              except Exception as e:
                  log.warning( e )
              try:
                  cp_from_hda = dataset.copied_from_history_dataset_association
                  if cp_from_hda:
                      lst.append( (cp_from_hda, cp_from_hda.history.name) )
                      return _source_dataset_chain( cp_from_hda, lst )
              except Exception as e:
                  log.warning( e )
              return lst
          return _source_dataset_chain( self, [] )
  
      @property
      def creating_job( self ):
          creating_job_associations = None
          if self.creating_job_associations:
              creating_job_associations = self.creating_job_associations
          else:
              inherit_chain = self.source_dataset_chain
              if inherit_chain:
                  creating_job_associations = inherit_chain[-1][0].creating_job_associations
          if creating_job_associations:
              return creating_job_associations[0].job
          return None
  
      def get_display_applications( self, trans ):
          return self.datatype.get_display_applications_by_dataset( self, trans )
  
      def get_visualizations( self ):
          return self.datatype.get_visualizations( self )
  
      def get_datasources( self, trans ):
          """
          Returns datasources for dataset; if datasources are not available
          due to indexing, indexing is started. Return value is a dictionary
          with entries of type
          (<datasource_type> : {<datasource_name>, <indexing_message>}).
          """
          data_sources_dict = {}
          msg = None
          for source_type, source_list in self.datatype.data_sources.items():
              data_source = None
              if source_type == "data_standalone":
                  # Nothing to do.
                  msg = None
                  data_source = source_list
              else:
                  # Convert.
                  if isinstance( source_list, string_types ):
                      source_list = [ source_list ]
  
                  # Loop through sources until viable one is found.
                  for source in source_list:
                      msg = self.convert_dataset( trans, source )
                      # No message or PENDING means that source is viable. No
                      # message indicates conversion was done and is successful.
                      if not msg or msg == self.conversion_messages.PENDING:
                          data_source = source
                          break
  
              # Store msg.
              data_sources_dict[ source_type ] = { "name": data_source, "message": msg }
  
          return data_sources_dict
  
      def convert_dataset( self, trans, target_type ):
          """
          Converts a dataset to the target_type and returns a message indicating
          status of the conversion. None is returned to indicate that dataset
          was converted successfully.
          """
  
          # Get converted dataset; this will start the conversion if necessary.
          try:
              converted_dataset = self.get_converted_dataset( trans, target_type )
          except NoConverterException:
              return self.conversion_messages.NO_CONVERTER
          except ConverterDependencyException as dep_error:
              return { 'kind': self.conversion_messages.ERROR, 'message': dep_error.value }
  
          # Check dataset state and return any messages.
          msg = None
          if converted_dataset and converted_dataset.state == Dataset.states.ERROR:
              job_id = trans.sa_session.query( JobToOutputDatasetAssociation ) \
                  .filter_by( dataset_id=converted_dataset.id ).first().job_id
              job = trans.sa_session.query( Job ).get( job_id )
              msg = { 'kind': self.conversion_messages.ERROR, 'message': job.stderr }
          elif not converted_dataset or converted_dataset.state != Dataset.states.OK:
              msg = self.conversion_messages.PENDING
  
          return msg
  
  
  class HistoryDatasetAssociation( DatasetInstance, Dictifiable, UsesAnnotations, HasName ):
      """
      Resource class that creates a relation between a dataset and a user history.
      """
  
      def __init__( self,
                    hid=None,
                    history=None,
                    copied_from_history_dataset_association=None,
                    copied_from_library_dataset_dataset_association=None,
                    sa_session=None,
                    **kwd ):
          """
          Create a a new HDA and associate it with the given history.
          """
          # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
          # parameter is True so that the new object can be flushed.  Is there a better way?
          DatasetInstance.__init__( self, sa_session=sa_session, **kwd )
          self.hid = hid
          # Relationships
          self.history = history
          self.copied_from_history_dataset_association = copied_from_history_dataset_association
          self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association
  
      def copy( self, copy_children=False, parent_id=None ):
          """
          Create a copy of this HDA.
          """
          hda = HistoryDatasetAssociation( hid=self.hid,
                                           name=self.name,
                                           info=self.info,
                                           blurb=self.blurb,
                                           peek=self.peek,
                                           tool_version=self.tool_version,
                                           extension=self.extension,
                                           dbkey=self.dbkey,
                                           dataset=self.dataset,
                                           visible=self.visible,
                                           deleted=self.deleted,
                                           parent_id=parent_id,
                                           copied_from_history_dataset_association=self )
          # update init non-keywords as well
          hda.purged = self.purged
  
          object_session( self ).add( hda )
          object_session( self ).flush()
          hda.set_size()
          # Need to set after flushed, as MetadataFiles require dataset.id
          hda.metadata = self.metadata
          if copy_children:
              for child in self.children:
                  child.copy( copy_children=copy_children, parent_id=hda.id )
          if not self.datatype.copy_safe_peek:
              # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
              hda.set_peek()
          object_session( self ).flush()
          return hda
  
      def copy_attributes( self, new_dataset ):
          new_dataset.hid = self.hid
  
      def to_library_dataset_dataset_association( self, trans, target_folder,
                                                  replace_dataset=None, parent_id=None, user=None, roles=None, ldda_message='' ):
          """
          Copy this HDA to a library optionally replacing an existing LDDA.
          """
          if replace_dataset:
              # The replace_dataset param ( when not None ) refers to a LibraryDataset that
              #   is being replaced with a new version.
              library_dataset = replace_dataset
          else:
              # If replace_dataset is None, the Library level permissions will be taken from the folder and
              #   applied to the new LibraryDataset, and the current user's DefaultUserPermissions will be applied
              #   to the associated Dataset.
              library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info )
              object_session( self ).add( library_dataset )
              object_session( self ).flush()
          if not user:
              # This should never happen since users must be authenticated to upload to a data library
              user = self.history.user
          ldda = LibraryDatasetDatasetAssociation( name=self.name,
                                                   info=self.info,
                                                   blurb=self.blurb,
                                                   peek=self.peek,
                                                   tool_version=self.tool_version,
                                                   extension=self.extension,
                                                   dbkey=self.dbkey,
                                                   dataset=self.dataset,
                                                   library_dataset=library_dataset,
                                                   visible=self.visible,
                                                   deleted=self.deleted,
                                                   parent_id=parent_id,
                                                   copied_from_history_dataset_association=self,
                                                   user=user )
          object_session( self ).add( ldda )
          object_session( self ).flush()
          # If roles were selected on the upload form, restrict access to the Dataset to those roles
          roles = roles or []
          for role in roles:
              dp = trans.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action,
                                                   ldda.dataset, role )
              trans.sa_session.add( dp )
              trans.sa_session.flush()
          # Must set metadata after ldda flushed, as MetadataFiles require ldda.id
          ldda.metadata = self.metadata
          if ldda_message:
              ldda.message = ldda_message
          if not replace_dataset:
              target_folder.add_library_dataset( library_dataset, genome_build=ldda.dbkey )
              object_session( self ).add( target_folder )
              object_session( self ).flush()
          library_dataset.library_dataset_dataset_association_id = ldda.id
          object_session( self ).add( library_dataset )
          object_session( self ).flush()
          for child in self.children:
              child.to_library_dataset_dataset_association( trans,
                                                            target_folder=target_folder,
                                                            replace_dataset=replace_dataset,
                                                            parent_id=ldda.id,
                                                            user=ldda.user )
          if not self.datatype.copy_safe_peek:
              # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
              ldda.set_peek()
          object_session( self ).flush()
          return ldda
  
      def clear_associated_files( self, metadata_safe=False, purge=False ):
          """
          """
          # metadata_safe = True means to only clear when assoc.metadata_safe == False
          for assoc in self.implicitly_converted_datasets:
              if not assoc.deleted and ( not metadata_safe or not assoc.metadata_safe ):
                  assoc.clear( purge=purge )
          for assoc in self.implicitly_converted_parent_datasets:
              assoc.clear( purge=purge, delete_dataset=False )
  
      def get_access_roles( self, trans ):
          """
          Return The access roles associated with this HDA's dataset.
          """
          return self.dataset.get_access_roles( trans )
  
      def quota_amount( self, user ):
          """
          Return the disk space used for this HDA relevant to user quotas.
  
          If the user has multiple instances of this dataset, it will not affect their
          disk usage statistic.
          """
          rval = 0
          # Anon users are handled just by their single history size.
          if not user:
              return rval
          # Gets an HDA and its children's disk usage, if the user does not already
          #   have an association of the same dataset
          if not self.dataset.library_associations and not self.purged and not self.dataset.purged:
              for hda in self.dataset.history_associations:
                  if hda.id == self.id:
                      continue
                  if not hda.purged and hda.history and hda.history.user and hda.history.user == user:
                      break
              else:
                  rval += self.get_total_size()
          for child in self.children:
              rval += child.get_disk_usage( user )
          return rval
  
      def to_dict( self, view='collection', expose_dataset_path=False ):
          """
          Return attributes of this HDA that are exposed using the API.
          """
          # Since this class is a proxy to rather complex attributes we want to
          # display in other objects, we can't use the simpler method used by
          # other model classes.
          hda = self
          rval = dict( id=hda.id,
                       hda_ldda='hda',
                       uuid=( lambda uuid: str( uuid ) if uuid else None )( hda.dataset.uuid ),
                       hid=hda.hid,
                       file_ext=hda.ext,
                       peek=( lambda hda: hda.display_peek() if hda.peek and hda.peek != 'no peek' else None )( hda ),
                       model_class=self.__class__.__name__,
                       name=hda.name,
                       deleted=hda.deleted,
                       purged=hda.purged,
                       visible=hda.visible,
                       state=hda.state,
                       history_content_type=hda.history_content_type,
                       file_size=int( hda.get_size() ),
                       create_time=hda.create_time.isoformat(),
                       update_time=hda.update_time.isoformat(),
                       data_type=hda.datatype.__class__.__module__ + '.' + hda.datatype.__class__.__name__,
                       genome_build=hda.dbkey,
                       misc_info=hda.info.strip() if isinstance( hda.info, string_types ) else hda.info,
                       misc_blurb=hda.blurb )
  
          # add tags string list
          tags_str_list = []
          for tag in self.tags:
              tag_str = tag.user_tname
              if tag.value is not None:
                  tag_str += ":" + tag.user_value
              tags_str_list.append( tag_str )
          rval[ 'tags' ] = tags_str_list
  
          if hda.copied_from_library_dataset_dataset_association is not None:
              rval['copied_from_ldda_id'] = hda.copied_from_library_dataset_dataset_association.id
  
          if hda.history is not None:
              rval['history_id'] = hda.history.id
  
          if hda.extended_metadata is not None:
              rval['extended_metadata'] = hda.extended_metadata.data
  
          rval[ 'peek' ] = to_unicode( hda.display_peek() )
  
          for name, spec in hda.metadata.spec.items():
              val = hda.metadata.get( name )
              if isinstance( val, MetadataFile ):
                  # only when explicitly set: fetching filepaths can be expensive
                  if not expose_dataset_path:
                      continue
                  val = val.file_name
              # If no value for metadata, look in datatype for metadata.
              elif val is None and hasattr( hda.datatype, name ):
                  val = getattr( hda.datatype, name )
              rval['metadata_' + name] = val
          return rval
  
      @property
      def history_content_type( self ):
          return "dataset"
  
      # TODO: down into DatasetInstance
      content_type = u'dataset'
  
      @hybrid.hybrid_property
      def type_id( self ):
          return u'-'.join([ self.content_type, str( self.id ) ])
  
      @type_id.expression
      def type_id( cls ):
          return (( type_coerce( cls.content_type, types.Unicode ) + u'-' +
                    type_coerce( cls.id, types.Unicode ) ).label( 'type_id' ))
  
      def copy_tags_from( self, target_user, source_hda ):
          """
          Copy tags from `source_hda` to this HDA and assign them the user `target_user`.
          """
          for source_tag_assoc in source_hda.tags:
              new_tag_assoc = source_tag_assoc.copy()
              new_tag_assoc.user = target_user
              self.tags.append( new_tag_assoc )
  
  
  class HistoryDatasetAssociationDisplayAtAuthorization( object ):
      def __init__( self, hda=None, user=None, site=None ):
          self.history_dataset_association = hda
          self.user = user
          self.site = site
  
  
  class HistoryDatasetAssociationSubset( object ):
      def __init__(self, hda, subset, location):
          self.hda = hda
          self.subset = subset
          self.location = location
  
  
  class Library( object, Dictifiable, HasName ):
      permitted_actions = get_permitted_actions( filter='LIBRARY' )
      dict_collection_visible_keys = ( 'id', 'name' )
      dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id', 'create_time' )
  
      def __init__( self, name=None, description=None, synopsis=None, root_folder=None ):
          self.name = name or "Unnamed library"
          self.description = description
          self.synopsis = synopsis
          self.root_folder = root_folder
  
      def to_dict( self, view='collection', value_mapper=None ):
          """
          We prepend an F to folders.
          """
          rval = super( Library, self ).to_dict( view=view, value_mapper=value_mapper )
          if 'root_folder_id' in rval:
              rval[ 'root_folder_id' ] = 'F' + str(rval[ 'root_folder_id' ])
          return rval
  
      def get_active_folders( self, folder, folders=None ):
          # TODO: should we make sure the library is not deleted?
          def sort_by_attr( seq, attr ):
              """
              Sort the sequence of objects by object's attribute
              Arguments:
              seq  - the list or any sequence (including immutable one) of objects to sort.
              attr - the name of attribute to sort by
              """
              # Use the "Schwartzian transform"
              # Create the auxiliary list of tuples where every i-th tuple has form
              # (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not
              # only to provide stable sorting, but mainly to eliminate comparison of objects
              # (which can be expensive or prohibited) in case of equal attribute values.
              intermed = map( None, (getattr(_, attr) for _ in seq), range( len( seq ) ), seq )
              intermed.sort()
              return [_[-1] for _ in intermed]
          if folders is None:
              active_folders = [ folder ]
          for active_folder in folder.active_folders:
              active_folders.extend( self.get_active_folders( active_folder, folders ) )
          return sort_by_attr( active_folders, 'id' )
  
      def get_info_association( self, restrict=False, inherited=False ):
          if self.info_association:
              if not inherited or self.info_association[0].inheritable:
                  return self.info_association[0], inherited
              else:
                  return None, inherited
          return None, inherited
  
      def get_template_widgets( self, trans, get_contents=True ):
          # See if we have any associated templates - the returned value for
          # inherited is not applicable at the library level.  The get_contents
          # param is passed by callers that are inheriting a template - these
          # are usually new library datsets for which we want to include template
          # fields on the upload form, but not necessarily the contents of the
          # inherited template saved for the parent.
          info_association, inherited = self.get_info_association()
          if info_association:
              template = info_association.template
              if get_contents:
                  # See if we have any field contents
                  info = info_association.info
                  if info:
                      return template.get_widgets( trans.user, contents=info.content )
              return template.get_widgets( trans.user )
          return []
  
      def get_access_roles( self, trans ):
          roles = []
          for lp in self.actions:
              if lp.action == trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action:
                  roles.append( lp.role )
          return roles
  
  
  class LibraryFolder( object, Dictifiable, HasName ):
      dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted' )
  
      def __init__( self, name=None, description=None, item_count=0, order_id=None ):
          self.name = name or "Unnamed folder"
          self.description = description
          self.item_count = item_count
          self.order_id = order_id
          self.genome_build = None
  
      def add_library_dataset( self, library_dataset, genome_build=None ):
          library_dataset.folder_id = self.id
          library_dataset.order_id = self.item_count
          self.item_count += 1
          if genome_build not in [None, '?']:
              self.genome_build = genome_build
  
      def add_folder( self, folder ):
          folder.parent_id = self.id
          folder.order_id = self.item_count
          self.item_count += 1
  
      def get_info_association( self, restrict=False, inherited=False ):
          # If restrict is True, we will return this folder's info_association, not inheriting.
          # If restrict is False, we'll return the next available info_association in the
          # inheritable hierarchy if it is "inheritable".  True is also returned if the
          # info_association was inherited and False if not.  This enables us to eliminate
          # displaying any contents of the inherited template.
          if self.info_association:
              if not inherited or self.info_association[0].inheritable:
                  return self.info_association[0], inherited
              else:
                  return None, inherited
          if restrict:
              return None, inherited
          if self.parent:
              return self.parent.get_info_association( inherited=True )
          if self.library_root:
              return self.library_root[0].get_info_association( inherited=True )
          return None, inherited
  
      def get_template_widgets( self, trans, get_contents=True ):
          # See if we have any associated templates.  The get_contents
          # param is passed by callers that are inheriting a template - these
          # are usually new library datsets for which we want to include template
          # fields on the upload form.
          info_association, inherited = self.get_info_association()
          if info_association:
              if inherited:
                  template = info_association.template.current.latest_form
              else:
                  template = info_association.template
              # See if we have any field contents, but only if the info_association was
              # not inherited ( we do not want to display the inherited contents ).
              # (gvk: 8/30/10) Based on conversations with Dan, we agreed to ALWAYS inherit
              # contents.  We'll use this behavior until we hear from the community that
              # contents should not be inherited.  If we don't hear anything for a while,
              # eliminate the old commented out behavior.
              # if not inherited and get_contents:
              if get_contents:
                  info = info_association.info
                  if info:
                      return template.get_widgets( trans.user, info.content )
              else:
                  return template.get_widgets( trans.user )
          return []
  
      @property
      def activatable_library_datasets( self ):
          # This needs to be a list
          return [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted ]
  
      def to_dict( self, view='collection', value_mapper=None ):
          rval = super( LibraryFolder, self ).to_dict( view=view, value_mapper=value_mapper  )
          info_association, inherited = self.get_info_association()
          if info_association:
              if inherited:
                  template = info_association.template.current.latest_form
              else:
                  template = info_association.template
              rval['data_template'] = template.name
          rval['library_path'] = self.library_path
          rval['parent_library_id'] = self.parent_library.id
          return rval
  
      @property
      def library_path(self):
          l_path = []
          f = self
          while f.parent:
              l_path.insert(0, f.name)
              f = f.parent
          return l_path
  
      @property
      def parent_library( self ):
          f = self
          while f.parent:
              f = f.parent
          return f.library_root[0]
  
  
  class LibraryDataset( object ):
      # This class acts as a proxy to the currently selected LDDA
      upload_options = [ ( 'upload_file', 'Upload files' ),
                         ( 'upload_directory', 'Upload directory of files' ),
                         ( 'upload_paths', 'Upload files from filesystem paths' ),
                         ( 'import_from_history', 'Import datasets from your current history' ) ]
  
      def __init__( self, folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd ):
          self.folder = folder
          self.order_id = order_id
          self.name = name
          self.info = info
          self.library_dataset_dataset_association = library_dataset_dataset_association
  
      def set_library_dataset_dataset_association( self, ldda ):
          self.library_dataset_dataset_association = ldda
          ldda.library_dataset = self
          object_session( self ).add_all( ( ldda, self ) )
          object_session( self ).flush()
  
      def get_info( self ):
          if self.library_dataset_dataset_association:
              return self.library_dataset_dataset_association.info
          elif self._info:
              return self._info
          else:
              return 'no info'
  
      def set_info( self, info ):
          self._info = info
      info = property( get_info, set_info )
  
      def get_name( self ):
          if self.library_dataset_dataset_association:
              return self.library_dataset_dataset_association.name
          elif self._name:
              return self._name
          else:
              return 'Unnamed dataset'
  
      def set_name( self, name ):
          self._name = name
      name = property( get_name, set_name )
  
      def display_name( self ):
          self.library_dataset_dataset_association.display_name()
  
      def to_dict( self, view='collection' ):
          # Since this class is a proxy to rather complex attributes we want to
          # display in other objects, we can't use the simpler method used by
          # other model classes.
          ldda = self.library_dataset_dataset_association
          template_data = {}
          for temp_info in ldda.info_association:
              template = temp_info.template
              content = temp_info.info.content
              tmp_dict = {}
              for field in template.fields:
                  tmp_dict[field['label']] = content[field['name']]
              template_data[template.name] = tmp_dict
  
          rval = dict( id=self.id,
                       ldda_id=ldda.id,
                       parent_library_id=self.folder.parent_library.id,
                       folder_id=self.folder_id,
                       model_class=self.__class__.__name__,
                       state=ldda.state,
                       name=ldda.name,
                       file_name=ldda.file_name,
                       uploaded_by=ldda.user.email,
                       message=ldda.message,
                       date_uploaded=ldda.create_time.isoformat(),
                       file_size=int( ldda.get_size() ),
                       file_ext=ldda.ext,
                       data_type=ldda.datatype.__class__.__module__ + '.' + ldda.datatype.__class__.__name__,
                       genome_build=ldda.dbkey,
                       misc_info=ldda.info,
                       misc_blurb=ldda.blurb,
                       peek=( lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None )( ldda ),
                       template_data=template_data )
          if ldda.dataset.uuid is None:
              rval['uuid'] = None
          else:
              rval['uuid'] = str(ldda.dataset.uuid)
          for name, spec in ldda.metadata.spec.items():
              val = ldda.metadata.get( name )
              if isinstance( val, MetadataFile ):
                  val = val.file_name
              elif isinstance( val, list ):
                  val = ', '.join( [str(v) for v in val] )
              rval['metadata_' + name] = val
          return rval
  
  
  class LibraryDatasetDatasetAssociation( DatasetInstance, HasName ):
      def __init__( self,
                    copied_from_history_dataset_association=None,
                    copied_from_library_dataset_dataset_association=None,
                    library_dataset=None,
                    user=None,
                    sa_session=None,
                    **kwd ):
          # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
          # parameter in kwd is True so that the new object can be flushed.  Is there a better way?
          DatasetInstance.__init__( self, sa_session=sa_session, **kwd )
          if copied_from_history_dataset_association:
              self.copied_from_history_dataset_association_id = copied_from_history_dataset_association.id
          if copied_from_library_dataset_dataset_association:
              self.copied_from_library_dataset_dataset_association_id = copied_from_library_dataset_dataset_association.id
          self.library_dataset = library_dataset
          self.user = user
  
      def to_history_dataset_association( self, target_history, parent_id=None, add_to_history=False ):
          hda = HistoryDatasetAssociation( name=self.name,
                                           info=self.info,
                                           blurb=self.blurb,
                                           peek=self.peek,
                                           tool_version=self.tool_version,
                                           extension=self.extension,
                                           dbkey=self.dbkey,
                                           dataset=self.dataset,
                                           visible=self.visible,
                                           deleted=self.deleted,
                                           parent_id=parent_id,
                                           copied_from_library_dataset_dataset_association=self,
                                           history=target_history )
          object_session( self ).add( hda )
          object_session( self ).flush()
          hda.metadata = self.metadata  # need to set after flushed, as MetadataFiles require dataset.id
          if add_to_history and target_history:
              target_history.add_dataset( hda )
          for child in self.children:
              child.to_history_dataset_association( target_history=target_history, parent_id=hda.id, add_to_history=False )
          if not self.datatype.copy_safe_peek:
              hda.set_peek()  # in some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
          object_session( self ).flush()
          return hda
  
      def copy( self, copy_children=False, parent_id=None, target_folder=None ):
          ldda = LibraryDatasetDatasetAssociation( name=self.name,
                                                   info=self.info,
                                                   blurb=self.blurb,
                                                   peek=self.peek,
                                                   tool_version=self.tool_version,
                                                   extension=self.extension,
                                                   dbkey=self.dbkey,
                                                   dataset=self.dataset,
                                                   visible=self.visible,
                                                   deleted=self.deleted,
                                                   parent_id=parent_id,
                                                   copied_from_library_dataset_dataset_association=self,
                                                   folder=target_folder )
          object_session( self ).add( ldda )
          object_session( self ).flush()
          # Need to set after flushed, as MetadataFiles require dataset.id
          ldda.metadata = self.metadata
          if copy_children:
              for child in self.children:
                  child.copy( copy_children=copy_children, parent_id=ldda.id )
          if not self.datatype.copy_safe_peek:
              # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
              ldda.set_peek()
          object_session( self ).flush()
          return ldda
  
      def clear_associated_files( self, metadata_safe=False, purge=False ):
          return
  
      def get_access_roles( self, trans ):
          return self.dataset.get_access_roles( trans )
  
      def get_manage_permissions_roles( self, trans ):
          return self.dataset.get_manage_permissions_roles( trans )
  
      def has_manage_permissions_roles( self, trans ):
          return self.dataset.has_manage_permissions_roles( trans )
  
      def get_info_association( self, restrict=False, inherited=False ):
          # If restrict is True, we will return this ldda's info_association whether it
          # exists or not ( in which case None will be returned ).  If restrict is False,
          # we'll return the next available info_association in the inheritable hierarchy.
          # True is also returned if the info_association was inherited, and False if not.
          # This enables us to eliminate displaying any contents of the inherited template.
          # SM: Accessing self.info_association can cause a query to be emitted
          if self.info_association:
              return self.info_association[0], inherited
          if restrict:
              return None, inherited
          return self.library_dataset.folder.get_info_association( inherited=True )
  
      def to_dict( self, view='collection' ):
          # Since this class is a proxy to rather complex attributes we want to
          # display in other objects, we can't use the simpler method used by
          # other model classes.
          ldda = self
          try:
              file_size = int( ldda.get_size() )
          except OSError:
              file_size = 0
  
          rval = dict( id=ldda.id,
                       hda_ldda='ldda',
                       model_class=self.__class__.__name__,
                       name=ldda.name,
                       deleted=ldda.deleted,
                       visible=ldda.visible,
                       state=ldda.state,
                       library_dataset_id=ldda.library_dataset_id,
                       file_size=file_size,
                       file_name=ldda.file_name,
                       update_time=ldda.update_time.isoformat(),
                       file_ext=ldda.ext,
                       data_type=ldda.datatype.__class__.__module__ + '.' + ldda.datatype.__class__.__name__,
                       genome_build=ldda.dbkey,
                       misc_info=ldda.info,
                       misc_blurb=ldda.blurb )
          if ldda.dataset.uuid is None:
              rval['uuid'] = None
          else:
              rval['uuid'] = str(ldda.dataset.uuid)
          rval['parent_library_id'] = ldda.library_dataset.folder.parent_library.id
          if ldda.extended_metadata is not None:
              rval['extended_metadata'] = ldda.extended_metadata.data
          for name, spec in ldda.metadata.spec.items():
              val = ldda.metadata.get( name )
              if isinstance( val, MetadataFile ):
                  val = val.file_name
              # If no value for metadata, look in datatype for metadata.
              elif val is None and hasattr( ldda.datatype, name ):
                  val = getattr( ldda.datatype, name )
              rval['metadata_' + name] = val
          return rval
  
      def get_template_widgets( self, trans, get_contents=True ):
          # See if we have any associated templatesThe get_contents
          # param is passed by callers that are inheriting a template - these
          # are usually new library datsets for which we want to include template
          # fields on the upload form, but not necessarily the contents of the
          # inherited template saved for the parent.
          info_association, inherited = self.get_info_association()
          if info_association:
              if inherited:
                  template = info_association.template.current.latest_form
              else:
                  template = info_association.template
              # See if we have any field contents, but only if the info_association was
              # not inherited ( we do not want to display the inherited contents ).
              # (gvk: 8/30/10) Based on conversations with Dan, we agreed to ALWAYS inherit
              # contents.  We'll use this behavior until we hear from the community that
              # contents should not be inherited.  If we don't hear anything for a while,
              # eliminate the old commented out behavior.
              # if not inherited and get_contents:
              if get_contents:
                  info = info_association.info
                  if info:
                      return template.get_widgets( trans.user, info.content )
              else:
                  return template.get_widgets( trans.user )
          return []
  
      def templates_dict( self, use_name=False ):
          """
          Returns a dict of template info
          """
          # TODO: Should have a method that allows names and labels to be returned together in a structured way
          template_data = {}
          for temp_info in self.info_association:
              template = temp_info.template
              content = temp_info.info.content
              tmp_dict = {}
              for field in template.fields:
                  if use_name:
                      name = field[ 'name' ]
                  else:
                      name = field[ 'label' ]
                  tmp_dict[ name ] = content.get( field[ 'name' ] )
              template_data[template.name] = tmp_dict
          return template_data
  
      def templates_json( self, use_name=False ):
          return json.dumps( self.templates_dict( use_name=use_name ) )
  
  
  class ExtendedMetadata( object ):
      def __init__(self, data):
          self.data = data
  
  
  class ExtendedMetadataIndex( object ):
      def __init__( self, extended_metadata, path, value):
          self.extended_metadata = extended_metadata
          self.path = path
          self.value = value
  
  
  class LibraryInfoAssociation( object ):
      def __init__( self, library, form_definition, info, inheritable=False ):
          self.library = library
          self.template = form_definition
          self.info = info
          self.inheritable = inheritable
  
  
  class LibraryFolderInfoAssociation( object ):
      def __init__( self, folder, form_definition, info, inheritable=False ):
          self.folder = folder
          self.template = form_definition
          self.info = info
          self.inheritable = inheritable
  
  
  class LibraryDatasetDatasetInfoAssociation( object ):
      def __init__( self, library_dataset_dataset_association, form_definition, info ):
          # TODO: need to figure out if this should be inheritable to the associated LibraryDataset
          self.library_dataset_dataset_association = library_dataset_dataset_association
          self.template = form_definition
          self.info = info
  
      @property
      def inheritable( self ):
          return True  # always allow inheriting, used for replacement
  
  
  class ValidationError( object ):
      def __init__( self, message=None, err_type=None, attributes=None ):
          self.message = message
          self.err_type = err_type
          self.attributes = attributes
  
  
  class DatasetToValidationErrorAssociation( object ):
      def __init__( self, dataset, validation_error ):
          self.dataset = dataset
          self.validation_error = validation_error
  
  
  class ImplicitlyConvertedDatasetAssociation( object ):
  
      def __init__( self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True ):
          self.id = id
          if isinstance(dataset, HistoryDatasetAssociation):
              self.dataset = dataset
          elif isinstance(dataset, LibraryDatasetDatasetAssociation):
              self.dataset_ldda = dataset
          else:
              raise AttributeError( 'Unknown dataset type provided for dataset: %s' % type( dataset ) )
          if isinstance(parent, HistoryDatasetAssociation):
              self.parent_hda = parent
          elif isinstance(parent, LibraryDatasetDatasetAssociation):
              self.parent_ldda = parent
          else:
              raise AttributeError( 'Unknown dataset type provided for parent: %s' % type( parent ) )
          self.type = file_type
          self.deleted = deleted
          self.purged = purged
          self.metadata_safe = metadata_safe
  
      def clear( self, purge=False, delete_dataset=True ):
          self.deleted = True
          if self.dataset:
              if delete_dataset:
                  self.dataset.deleted = True
              if purge:
                  self.dataset.purged = True
          if purge and self.dataset.deleted:  # do something with purging
              self.purged = True
              try:
                  os.unlink( self.file_name )
              except Exception as e:
                  log.error( "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e ) )
  
  
  DEFAULT_COLLECTION_NAME = "Unnamed Collection"
  
  
  class DatasetCollection( object, Dictifiable, UsesAnnotations ):
      """
      """
      dict_collection_visible_keys = ( 'id', 'collection_type' )
      dict_element_visible_keys = ( 'id', 'collection_type' )
      populated_states = Bunch(
          NEW='new',  # New dataset collection, unpopulated elements
          OK='ok',  # Collection elements populated (HDAs may or may not have errors)
          FAILED='failed',  # some problem populating state, won't be populated
      )
  
      def __init__(
          self,
          id=None,
          collection_type=None,
          populated=True,
      ):
          self.id = id
          self.collection_type = collection_type
          if not populated:
              self.populated_state = DatasetCollection.populated_states.NEW
  
      @property
      def populated( self ):
          top_level_populated = self.populated_state == DatasetCollection.populated_states.OK
          if top_level_populated and self.has_subcollections:
              return all(e.child_collection.populated for e in self.elements)
          return top_level_populated
  
      @property
      def waiting_for_elements( self ):
          top_level_waiting = self.populated_state == DatasetCollection.populated_states.NEW
          if not top_level_waiting and self.has_subcollections:
              return any(e.child_collection.waiting_for_elements for e in self.elements)
          return top_level_waiting
  
      def mark_as_populated( self ):
          self.populated_state = DatasetCollection.populated_states.OK
  
      def handle_population_failed( self, message ):
          self.populated_state = DatasetCollection.populated_states.FAILED
          self.populated_state_message = message
  
      @property
      def dataset_instances( self ):
          instances = []
          for element in self.elements:
              if element.is_collection:
                  instances.extend( element.child_collection.dataset_instances )
              else:
                  instance = element.dataset_instance
                  instances.append( instance )
          return instances
  
      @property
      def dataset_elements( self ):
          elements = []
          for element in self.elements:
              if element.is_collection:
                  elements.extend( element.child_collection.dataset_elements )
              else:
                  elements.append( element )
          return elements
  
      @property
      def state( self ):
          # TODO: DatasetCollection state handling...
          return 'ok'
  
      def validate( self ):
          if self.collection_type is None:
              raise Exception("Each dataset collection must define a collection type.")
  
      def __getitem__( self, key ):
          get_by_attribute = "element_index" if isinstance( key, int ) else "element_identifier"
          for element in self.elements:
              if getattr( element, get_by_attribute ) == key:
                  return element
          error_message = "Dataset collection has no %s with key %s." % ( get_by_attribute, key )
          raise KeyError( error_message )
  
      def copy( self, destination=None, element_destination=None ):
          new_collection = DatasetCollection(
              collection_type=self.collection_type,
          )
          for element in self.elements:
              element.copy_to_collection(
                  new_collection,
                  destination=destination,
                  element_destination=element_destination,
              )
          object_session( self ).add( new_collection )
          object_session( self ).flush()
          return new_collection
  
      def set_from_dict( self, new_data ):
          # Nothing currently editable in this class.
          return {}
  
      @property
      def has_subcollections(self):
          return ":" in self.collection_type
  
  
  class DatasetCollectionInstance( object, HasName ):
      """
      """
      def __init__(
          self,
          collection=None,
          deleted=False,
      ):
          # Relationships
          self.collection = collection
          # Since deleted property is shared between history and dataset collections,
          # it could be on either table - some places in the code however it is convient
          # it is on instance instead of collection.
          self.deleted = deleted
  
      @property
      def state( self ):
          return self.collection.state
  
      @property
      def populated( self ):
          return self.collection.populated
  
      @property
      def dataset_instances( self ):
          return self.collection.dataset_instances
  
      def display_name( self ):
          return self.get_display_name()
  
      def _base_to_dict( self, view ):
          return dict(
              id=self.id,
              name=self.name,
              collection_type=self.collection.collection_type,
              populated=self.populated,
              populated_state=self.collection.populated_state,
              populated_state_message=self.collection.populated_state_message,
              type="collection",  # contents type (distinguished from file or folder (in case of library))
          )
  
      def set_from_dict( self, new_data ):
          """
          Set object attributes to the values in dictionary new_data limiting
          to only those keys in dict_element_visible_keys.
  
          Returns a dictionary of the keys, values that have been changed.
          """
          # precondition: keys are proper, values are parsed and validated
          changed = self.collection.set_from_dict( new_data )
  
          # unknown keys are ignored here
          for key in ( k for k in new_data.keys() if k in self.editable_keys ):
              new_val = new_data[ key ]
              old_val = self.__getattribute__( key )
              if new_val == old_val:
                  continue
  
              self.__setattr__( key, new_val )
              changed[ key ] = new_val
  
          return changed
  
  
  class HistoryDatasetCollectionAssociation( DatasetCollectionInstance, UsesAnnotations, Dictifiable ):
      """ Associates a DatasetCollection with a History. """
      editable_keys = ( 'name', 'deleted', 'visible' )
  
      def __init__(
          self,
          id=None,
          hid=None,
          collection=None,
          history=None,
          name=None,
          deleted=False,
          visible=True,
          copied_from_history_dataset_collection_association=None,
          implicit_output_name=None,
          implicit_input_collections=[],
      ):
          super( HistoryDatasetCollectionAssociation, self ).__init__(
              collection=collection,
              deleted=deleted,
          )
          self.id = id
          self.hid = hid
          self.history = history
          self.name = name
          self.visible = visible
          self.copied_from_history_dataset_collection_association = copied_from_history_dataset_collection_association
          self.implicit_output_name = implicit_output_name
          self.implicit_input_collections = implicit_input_collections
  
      @property
      def history_content_type( self ):
          return "dataset_collection"
  
      # TODO: down into DatasetCollectionInstance
      content_type = u'dataset_collection'
  
      @hybrid.hybrid_property
      def type_id( self ):
          return u'-'.join([ self.content_type, str( self.id ) ])
  
      @type_id.expression
      def type_id( cls ):
          return (( type_coerce( cls.content_type, types.Unicode ) + u'-' +
                    type_coerce( cls.id, types.Unicode ) ).label( 'type_id' ))
  
      def to_hda_representative( self, multiple=False ):
          rval = []
          for dataset in self.collection.dataset_elements:
              rval.append( dataset.dataset_instance )
              if multiple is False:
                  break
          if len( rval ) > 0:
              return rval if multiple else rval[ 0 ]
  
      def to_dict( self, view='collection' ):
          dict_value = dict(
              hid=self.hid,
              history_id=self.history.id,
              history_content_type=self.history_content_type,
              visible=self.visible,
              deleted=self.deleted,
              **self._base_to_dict(view=view)
          )
          return dict_value
  
      def add_implicit_input_collection( self, name, history_dataset_collection ):
          self.implicit_input_collections.append( ImplicitlyCreatedDatasetCollectionInput( name, history_dataset_collection)  )
  
      def find_implicit_input_collection( self, name ):
          matching_collection = None
          for implicit_input_collection in self.implicit_input_collections:
              if implicit_input_collection.name == name:
                  matching_collection = implicit_input_collection.input_dataset_collection
                  break
          return matching_collection
  
      def copy( self, element_destination=None ):
          """
          Create a copy of this history dataset collection association. Copy
          underlying collection.
          """
          hdca = HistoryDatasetCollectionAssociation(
              hid=self.hid,
              collection=None,
              visible=self.visible,
              deleted=self.deleted,
              name=self.name,
              copied_from_history_dataset_collection_association=self,
          )
          collection_copy = self.collection.copy(
              destination=hdca,
              element_destination=element_destination,
          )
          hdca.collection = collection_copy
          object_session( self ).add( hdca )
          object_session( self ).flush()
          return hdca
  
  
  class LibraryDatasetCollectionAssociation( DatasetCollectionInstance, Dictifiable ):
      """ Associates a DatasetCollection with a library folder. """
      editable_keys = ( 'name', 'deleted' )
  
      def __init__(
          self,
          id=None,
          collection=None,
          name=None,
          deleted=False,
          folder=None,
      ):
          super(LibraryDatasetCollectionAssociation, self).__init__(
              collection=collection,
              deleted=deleted,
          )
          self.id = id
          self.folder = folder
          self.name = name
  
      def to_dict( self, view='collection' ):
          dict_value = dict(
              folder_id=self.folder.id,
              **self._base_to_dict(view=view)
          )
          return dict_value
  
  
  class DatasetCollectionElement( object, Dictifiable ):
      """ Associates a DatasetInstance (hda or ldda) with a DatasetCollection. """
      # actionable dataset id needs to be available via API...
      dict_collection_visible_keys = ( 'id', 'element_type', 'element_index', 'element_identifier' )
      dict_element_visible_keys = ( 'id', 'element_type', 'element_index', 'element_identifier' )
  
      def __init__(
          self,
          id=None,
          collection=None,
          element=None,
          element_index=None,
          element_identifier=None,
      ):
          if isinstance(element, HistoryDatasetAssociation):
              self.hda = element
          elif isinstance(element, LibraryDatasetDatasetAssociation):
              self.ldda = element
          elif isinstance( element, DatasetCollection ):
              self.child_collection = element
          else:
              raise AttributeError( 'Unknown element type provided: %s' % type( element ) )
  
          self.id = id
          self.collection = collection
          self.element_index = element_index
          self.element_identifier = element_identifier or str(element_index)
  
      @property
      def element_type( self ):
          if self.hda:
              return "hda"
          elif self.ldda:
              return "ldda"
          elif self.child_collection:
              # TOOD: Rename element_type to element_type.
              return "dataset_collection"
          else:
              raise Exception( "Unknown element instance type" )
  
      @property
      def is_collection( self ):
          return self.element_type == "dataset_collection"
  
      @property
      def element_object( self ):
          if self.hda:
              return self.hda
          elif self.ldda:
              return self.ldda
          elif self.child_collection:
              return self.child_collection
          else:
              raise Exception( "Unknown element instance type" )
  
      @property
      def dataset_instance( self ):
          element_object = self.element_object
          if isinstance( element_object, DatasetCollection ):
              raise AttributeError( "Nested collection has no associated dataset_instance." )
          return element_object
  
      @property
      def dataset( self ):
          return self.dataset_instance.dataset
  
      def first_dataset_instance( self ):
          element_object = self.element_object
          if isinstance( element_object, DatasetCollection ):
              return element_object.dataset_instances[ 0 ]
          else:
              return element_object
  
      def copy_to_collection( self, collection, destination=None, element_destination=None ):
          element_object = self.element_object
          if element_destination:
              if self.is_collection:
                  element_object = element_object.copy(
                      destination=destination,
                      element_destination=element_destination
                  )
              else:
                  new_element_object = element_object.copy( copy_children=True )
                  if destination is not None and element_object.hidden_beneath_collection_instance:
                      new_element_object.hidden_beneath_collection_instance = destination
                  # Ideally we would not need to give the following
                  # element an HID and it would exist in the history only
                  # as an element of the containing collection.
                  element_destination.add_dataset( new_element_object )
                  element_object = new_element_object
  
          new_element = DatasetCollectionElement(
              element=element_object,
              collection=collection,
              element_index=self.element_index,
              element_identifier=self.element_identifier,
          )
          return new_element
  
  
  class Event( object ):
      def __init__( self, message=None, history=None, user=None, galaxy_session=None ):
          self.history = history
          self.galaxy_session = galaxy_session
          self.user = user
          self.tool_id = None
          self.message = message
  
  
  class GalaxySession( object ):
      def __init__( self,
                    id=None,
                    user=None,
                    remote_host=None,
                    remote_addr=None,
                    referer=None,
                    current_history=None,
                    session_key=None,
                    is_valid=False,
                    prev_session_id=None,
                    last_action=None ):
          self.id = id
          self.user = user
          self.remote_host = remote_host
          self.remote_addr = remote_addr
          self.referer = referer
          self.current_history = current_history
          self.session_key = session_key
          self.is_valid = is_valid
          self.prev_session_id = prev_session_id
          self.histories = []
          self.last_action = last_action or datetime.now()
  
      def add_history( self, history, association=None ):
          if association is None:
              self.histories.append( GalaxySessionToHistoryAssociation( self, history ) )
          else:
              self.histories.append( association )
  
      def get_disk_usage( self ):
          if self.disk_usage is None:
              return 0
          return self.disk_usage
  
      def set_disk_usage( self, bytes ):
          self.disk_usage = bytes
      total_disk_usage = property( get_disk_usage, set_disk_usage )
  
  
  class GalaxySessionToHistoryAssociation( object ):
      def __init__( self, galaxy_session, history ):
          self.galaxy_session = galaxy_session
          self.history = history
  
  
  class UCI( object ):
      def __init__( self ):
          self.id = None
          self.user = None
  
  
  class StoredWorkflow( object, Dictifiable):
  
      dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' )
      dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted' )
  
      def __init__( self ):
          self.id = None
          self.user = None
          self.name = None
          self.slug = None
          self.published = False
          self.latest_workflow_id = None
          self.workflows = []
  
      def copy_tags_from(self, target_user, source_workflow):
          for src_swta in source_workflow.owner_tags:
              new_swta = src_swta.copy()
              new_swta.user = target_user
              self.tags.append(new_swta)
  
      def to_dict( self, view='collection', value_mapper=None ):
          rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper=value_mapper )
          tags_str_list = []
          for tag in self.tags:
              tag_str = tag.user_tname
              if tag.value is not None:
                  tag_str += ":" + tag.user_value
              tags_str_list.append( tag_str )
          rval['tags'] = tags_str_list
          rval['latest_workflow_uuid'] = ( lambda uuid: str( uuid ) if self.latest_workflow.uuid else None )( self.latest_workflow.uuid )
          return rval
  
  
  class Workflow( object, Dictifiable ):
  
      dict_collection_visible_keys = ( 'name', 'has_cycles', 'has_errors' )
      dict_element_visible_keys = ( 'name', 'has_cycles', 'has_errors' )
      input_step_types = ['data_input', 'data_collection_input', 'parameter_input']
  
      def __init__( self, uuid=None ):
          self.user = None
          self.name = None
          self.has_cycles = None
          self.has_errors = None
          self.steps = []
          if uuid is None:
              self.uuid = uuid4()
          else:
              self.uuid = UUID(str(uuid))
  
      def has_outputs_defined(self):
          """
          Returns true or false indicating whether or not a workflow has outputs defined.
          """
          for step in self.steps:
              if step.workflow_outputs:
                  return True
          return False
  
      def to_dict( self, view='collection', value_mapper=None):
          rval = super( Workflow, self ).to_dict( view=view, value_mapper=value_mapper )
          rval['uuid'] = ( lambda uuid: str( uuid ) if uuid else None )( self.uuid )
          return rval
  
      @property
      def steps_by_id( self ):
          steps = {}
          for step in self.steps:
              step_id = step.id
              steps[ step_id ] = step
          return steps
  
      def step_by_index(self, order_index):
          for step in self.steps:
              if order_index == step.order_index:
                  return step
          raise KeyError("Workflow has no step with order_index '%s'" % order_index)
  
      @property
      def input_steps(self):
          for step in self.steps:
              if step.type in Workflow.input_step_types:
                  yield step
  
      @property
      def workflow_outputs(self):
          for step in self.steps:
              for workflow_output in step.workflow_outputs:
                  yield workflow_output
  
      @property
      def top_level_workflow( self ):
          """ If this workflow is not attached to stored workflow directly,
          recursively grab its parents until it is the top level workflow
          which must have a stored workflow associated with it.
          """
          top_level_workflow = self
          if self.stored_workflow is None:
              # TODO: enforce this at creation...
              assert len(self.parent_workflow_steps) == 1
              return self.parent_workflow_steps[0].workflow.top_level_workflow
          return top_level_workflow
  
      @property
      def top_level_stored_workflow( self ):
          """ If this workflow is not attached to stored workflow directly,
          recursively grab its parents until it is the top level workflow
          which must have a stored workflow associated with it and then
          grab that stored workflow.
          """
          return self.top_level_workflow.stored_workflow
  
      def copy(self):
          """ Copy a workflow (without user information) for a new
          StoredWorkflow object.
          """
          copied_workflow = Workflow()
          copied_workflow.name = self.name
          copied_workflow.has_cycles = self.has_cycles
          copied_workflow.has_errors = self.has_errors
  
          # Map old step ids to new steps
          step_mapping = {}
          copied_steps = []
          for step in self.steps:
              copied_step = WorkflowStep()
              copied_steps.append(copied_step)
              step_mapping[step.id] = copied_step
  
          for old_step, new_step in zip(self.steps, copied_steps):
              old_step.copy_to(new_step, step_mapping)
          copied_workflow.steps = copied_steps
          return copied_workflow
  
      def log_str(self):
          extra = ""
          if self.stored_workflow:
              extra = ",name=%s" % self.stored_workflow.name
          return "Workflow[id=%d%s]" % (self.id, extra)
  
  
  class WorkflowStep( object ):
  
      def __init__( self ):
          self.id = None
          self.type = None
          self.tool_id = None
          self.tool_inputs = None
          self.tool_errors = None
          self.position = None
          self.input_connections = []
          self.config = None
          self.label = None
          self.uuid = uuid4()
          self.workflow_outputs = []
          self._input_connections_by_name = None
  
      @property
      def unique_workflow_outputs(self):
          # Older Galaxy workflows may have multiple WorkflowOutputs
          # per "output_name", when serving these back to the editor
          # feed only a "best" output per "output_name.""
          outputs = {}
          for workflow_output in self.workflow_outputs:
              output_name = workflow_output.output_name
  
              if output_name in outputs:
                  found_output = outputs[output_name]
                  if found_output.label is None and workflow_output.label is not None:
                      outputs[output_name] = workflow_output
              else:
                  outputs[output_name] = workflow_output
          return list(outputs.values())
  
      @property
      def content_id( self ):
          content_id = None
          if self.type == "tool":
              content_id = self.tool_id
          elif self.type == "subworkflow":
              content_id = self.subworkflow.id
          else:
              content_id = None
          return content_id
  
      @property
      def input_connections_by_name(self):
          if self._input_connections_by_name is None:
              self.setup_input_connections_by_name()
          return self._input_connections_by_name
  
      def setup_input_connections_by_name(self):
          # Ensure input_connections has already been set.
  
          # Make connection information available on each step by input name.
          input_connections_by_name = {}
          for conn in self.input_connections:
              input_name = conn.input_name
              if input_name not in input_connections_by_name:
                  input_connections_by_name[input_name] = []
              input_connections_by_name[input_name].append(conn)
          self._input_connections_by_name = input_connections_by_name
  
      def create_or_update_workflow_output(self, output_name, label, uuid):
          output = self.workflow_output_for(output_name)
          if output is None:
              output = WorkflowOutput(workflow_step=self, output_name=output_name)
          if uuid is not None:
              output.uuid = uuid
          if label is not None:
              output.label = label
          return output
  
      def workflow_output_for(self, output_name):
          target_output = None
          for workflow_output in self.workflow_outputs:
              if workflow_output.output_name == output_name:
                  target_output = workflow_output
                  break
          return target_output
  
      def copy_to(self, copied_step, step_mapping):
          copied_step.order_index = self.order_index
          copied_step.type = self.type
          copied_step.tool_id = self.tool_id
          copied_step.tool_inputs = self.tool_inputs
          copied_step.tool_errors = self.tool_errors
          copied_step.position = self.position
          copied_step.config = self.config
          copied_step.label = self.label
          copied_step.input_connections = copy_list(self.input_connections)
  
          subworkflow_step_mapping = {}
          subworkflow = self.subworkflow
          if subworkflow:
              copied_subworkflow = subworkflow.copy()
              copied_step.subworkflow = copied_subworkflow
              for subworkflow_step, copied_subworkflow_step in zip(subworkflow.steps, copied_subworkflow.steps):
                  subworkflow_step_mapping[subworkflow_step.id] = copied_subworkflow_step
  
          for old_conn, new_conn in zip(self.input_connections, copied_step.input_connections):
              # new_conn.input_step = new_
              new_conn.input_step = step_mapping[old_conn.input_step_id]
              new_conn.output_step = step_mapping[old_conn.output_step_id]
              if old_conn.input_subworkflow_step_id:
                  new_conn.input_subworkflow_step = subworkflow_step_mapping[old_conn.input_subworkflow_step_id]
          for orig_pja in self.post_job_actions:
              PostJobAction( orig_pja.action_type,
                             copied_step,
                             output_name=orig_pja.output_name,
                             action_arguments=orig_pja.action_arguments )
          copied_step.workflow_outputs = copy_list(self.workflow_outputs, copied_step)
  
      def log_str(self):
          return "WorkflowStep[index=%d,type=%s]" % (self.order_index, self.type)
  
  
  class WorkflowStepConnection( object ):
      # Constant used in lieu of output_name and input_name to indicate an
      # implicit connection between two steps that is not dependent on a dataset
      # or a dataset collection. Allowing for instance data manager steps to setup
      # index data before a normal tool runs or for workflows that manage data
      # outside of Galaxy.
      NON_DATA_CONNECTION = "__NO_INPUT_OUTPUT_NAME__"
  
      def __init__( self ):
          self.output_step_id = None
          self.output_name = None
          self.input_step_id = None
          self.input_name = None
  
      def set_non_data_connection(self):
          self.output_name = WorkflowStepConnection.NON_DATA_CONNECTION
          self.input_name = WorkflowStepConnection.NON_DATA_CONNECTION
  
      @property
      def non_data_connection(self):
          return (self.output_name == WorkflowStepConnection.NON_DATA_CONNECTION and
                  self.input_name == WorkflowStepConnection.NON_DATA_CONNECTION)
  
      def copy(self):
          # TODO: handle subworkflow ids...
          copied_connection = WorkflowStepConnection()
          copied_connection.output_name = self.output_name
          copied_connection.input_name = self.input_name
          return copied_connection
  
  
  class WorkflowOutput(object):
  
      def __init__( self, workflow_step, output_name=None, label=None, uuid=None):
          self.workflow_step = workflow_step
          self.output_name = output_name
          self.label = label
          if uuid is None:
              self.uuid = uuid4()
          else:
              self.uuid = UUID(str(uuid))
  
      def copy(self, copied_step):
          copied_output = WorkflowOutput(copied_step)
          copied_output.output_name = self.output_name
          copied_output.label = self.label
          return copied_output
  
  
  class StoredWorkflowUserShareAssociation( object ):
  
      def __init__( self ):
          self.stored_workflow = None
          self.user = None
  
  
  class StoredWorkflowMenuEntry( object ):
  
      def __init__( self ):
          self.stored_workflow = None
          self.user = None
          self.order_index = None
  
  
  class WorkflowInvocation( object, Dictifiable ):
      dict_collection_visible_keys = ( 'id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state' )
      dict_element_visible_keys = ( 'id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state' )
      states = Bunch(
          NEW='new',  # Brand new workflow invocation... maybe this should be same as READY
          READY='ready',  # Workflow ready for another iteration of scheduling.
          SCHEDULED='scheduled',  # Workflow has been scheduled.
          CANCELLED='cancelled',
          FAILED='failed',
      )
  
      def __init__(self):
          self.subworkflow_invocations = []
          self.step_states = []
          self.steps = []
  
      def create_subworkflow_invocation_for_step( self, step ):
          assert step.type == "subworkflow"
          subworkflow_invocation = WorkflowInvocation()
          return self.attach_subworkflow_invocation_for_step( step, subworkflow_invocation )
  
      def attach_subworkflow_invocation_for_step( self, step, subworkflow_invocation ):
          assert step.type == "subworkflow"
          assoc = WorkflowInvocationToSubworkflowInvocationAssociation()
          assoc.workflow_invocation = self
          assoc.workflow_step = step
          subworkflow_invocation.history = self.history
          subworkflow_invocation.workflow = step.subworkflow
          assoc.subworkflow_invocation = subworkflow_invocation
          self.subworkflow_invocations.append(assoc)
          return assoc
  
      def get_subworkflow_invocation_for_step( self, step ):
          assoc = self.get_subworkflow_invocation_association_for_step(step)
          return assoc.subworkflow_invocation
  
      def get_subworkflow_invocation_association_for_step( self, step ):
          assert step.type == "subworkflow"
          assoc = None
          for subworkflow_invocation in self.subworkflow_invocations:
              if subworkflow_invocation.workflow_step == step:
                  assoc = subworkflow_invocation
                  break
          return assoc
  
      @property
      def active( self ):
          """ Indicates the workflow invocation is somehow active - and in
          particular valid actions may be performed on its
          WorkflowInvocationSteps.
          """
          states = WorkflowInvocation.states
          return self.state in [ states.NEW, states.READY ]
  
      def cancel( self ):
          if not self.active:
              return False
          else:
              self.state = WorkflowInvocation.states.CANCELLED
              return True
  
      def fail( self ):
          self.state = WorkflowInvocation.states.FAILED
  
      def step_states_by_step_id( self ):
          step_states = {}
          for step_state in self.step_states:
              step_id = step_state.workflow_step_id
              step_states[ step_id ] = step_state
          return step_states
  
      def step_invocations_by_step_id( self ):
          step_invocations = {}
          for invocation_step in self.steps:
              step_id = invocation_step.workflow_step_id
              if step_id not in step_invocations:
                  step_invocations[ step_id ] = []
              step_invocations[ step_id ].append( invocation_step )
          return step_invocations
  
      def step_invocations_for_step_id( self, step_id ):
          step_invocations = []
          for invocation_step in self.steps:
              if step_id == invocation_step.workflow_step_id:
                  step_invocations.append( invocation_step )
          return step_invocations
  
      @staticmethod
      def poll_active_workflow_ids(
          sa_session,
          scheduler=None,
          handler=None
      ):
          and_conditions = [
              or_(
                  WorkflowInvocation.state == WorkflowInvocation.states.NEW,
                  WorkflowInvocation.state == WorkflowInvocation.states.READY
              ),
          ]
          if scheduler is not None:
              and_conditions.append( WorkflowInvocation.scheduler == scheduler )
          if handler is not None:
              and_conditions.append( WorkflowInvocation.handler == handler )
  
          query = sa_session.query(
              WorkflowInvocation.id
          ).filter( and_( *and_conditions ) ).order_by( WorkflowInvocation.table.c.id.asc() )
          # Immediately just load all ids into memory so time slicing logic
          # is relatively intutitive.
          return [wid for wid in query.all()]
  
      def to_dict( self, view='collection', value_mapper=None, step_details=False ):
          rval = super( WorkflowInvocation, self ).to_dict( view=view, value_mapper=value_mapper )
          if view == 'element':
              steps = []
              for step in self.steps:
                  if step_details:
                      v = step.to_dict(view='element')
                  else:
                      v = step.to_dict(view='collection')
                  steps.append( v )
              rval['steps'] = steps
  
              inputs = {}
              for step in self.steps:
                  if step.workflow_step.type == 'tool':
                      for step_input in step.workflow_step.input_connections:
                          output_step_type = step_input.output_step.type
                          if output_step_type in [ 'data_input', 'data_collection_input' ]:
                              src = "hda" if output_step_type == 'data_input' else 'hdca'
                              for job_input in step.job.input_datasets:
                                  if job_input.name == step_input.input_name:
                                      inputs[str(step_input.output_step.order_index)] = {
                                          "id": job_input.dataset_id, "src": src,
                                          "uuid" : str(job_input.dataset.dataset.uuid) if job_input.dataset.dataset.uuid is not None else None
                                      }
              rval['inputs'] = inputs
          return rval
  
      def update( self ):
          self.update_time = galaxy.model.orm.now.now()
  
      def add_input( self, content, step_id ):
          history_content_type = getattr(content, "history_content_type", None)
          if history_content_type == "dataset":
              request_to_content = WorkflowRequestToInputDatasetAssociation()
              request_to_content.dataset = content
              request_to_content.workflow_step_id = step_id
              self.input_datasets.append( request_to_content )
          elif history_content_type == "dataset_collection":
              request_to_content = WorkflowRequestToInputDatasetCollectionAssociation()
              request_to_content.dataset_collection = content
              request_to_content.workflow_step_id = step_id
              self.input_dataset_collections.append( request_to_content )
          else:
              request_to_content = WorkflowRequestInputStepParmeter()
              request_to_content.parameter_value = content
              request_to_content.workflow_step_id = step_id
              self.input_step_parameters.append( request_to_content )
  
      def has_input_for_step( self, step_id ):
          for content in self.input_datasets:
              if content.workflow_step_id == step_id:
                  return True
          for content in self.input_dataset_collections:
              if content.workflow_step_id == step_id:
                  return True
          return False
  
      @property
      def seconds_since_created( self ):
          create_time = self.create_time or galaxy.model.orm.now.now()  # In case not flushed yet
          return (galaxy.model.orm.now.now() - create_time).total_seconds()
  
  
  class WorkflowInvocationToSubworkflowInvocationAssociation( object, Dictifiable ):
      dict_collection_visible_keys = ( 'id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id' )
      dict_element_visible_keys = ( 'id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id' )
  
  
  class WorkflowInvocationStep( object, Dictifiable ):
      dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' )
      dict_element_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' )
  
      def update( self ):
          self.workflow_invocation.update()
  
      def to_dict( self, view='collection', value_mapper=None ):
          rval = super( WorkflowInvocationStep, self ).to_dict( view=view, value_mapper=value_mapper )
          rval['order_index'] = self.workflow_step.order_index
          rval['workflow_step_label'] = self.workflow_step.label
          rval['workflow_step_uuid'] = str(self.workflow_step.uuid)
          rval['state'] = self.job.state if self.job is not None else None
          if self.job is not None and view == 'element':
              output_dict = {}
              for i in self.job.output_datasets:
                  if i.dataset is not None:
                      output_dict[i.name] = {
                          "id" : i.dataset.id, "src" : "hda",
                          "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                      }
              for i in self.job.output_library_datasets:
                  if i.dataset is not None:
                      output_dict[i.name] = {
                          "id" : i.dataset.id, "src" : "ldda",
                          "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                      }
              rval['outputs'] = output_dict
          return rval
  
  
  class WorkflowRequest( object, Dictifiable ):
      dict_collection_visible_keys = [ 'id', 'name', 'type', 'state', 'history_id', 'workflow_id' ]
      dict_element_visible_keys = [ 'id', 'name', 'type', 'state', 'history_id', 'workflow_id' ]
  
      def to_dict( self, view='collection', value_mapper=None ):
          rval = super( WorkflowRequest, self ).to_dict( view=view, value_mapper=value_mapper )
          return rval
  
  
  class WorkflowRequestInputParameter(object, Dictifiable):
      """ Workflow-related parameters not tied to steps or inputs.
      """
      dict_collection_visible_keys = ['id', 'name', 'value', 'type']
      types = Bunch(
          REPLACEMENT_PARAMETERS='replacements',
          META_PARAMETERS='meta',  #
      )
  
      def __init__( self, name=None, value=None, type=None ):
          self.name = name
          self.value = value
          self.type = type
  
  
  class WorkflowRequestStepState(object, Dictifiable):
      """ Workflow step value parameters.
      """
      dict_collection_visible_keys = ['id', 'name', 'value', 'workflow_step_id']
  
      def __init__( self, workflow_step=None, name=None, value=None ):
          self.workflow_step = workflow_step
          self.name = name
          self.value = value
          self.type = type
  
  
  class WorkflowRequestToInputDatasetAssociation(object, Dictifiable):
      """ Workflow step input dataset parameters.
      """
      dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name' ]
  
  
  class WorkflowRequestToInputDatasetCollectionAssociation(object, Dictifiable):
      """ Workflow step input dataset collection parameters.
      """
      dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name' ]
  
  
  class WorkflowRequestInputStepParmeter(object, Dictifiable):
      """ Workflow step parameter inputs.
      """
      dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'parameter_value' ]
  
  
  class MetadataFile( StorableObject ):
  
      def __init__( self, dataset=None, name=None ):
          super(MetadataFile, self).__init__(id=None)
          if isinstance( dataset, HistoryDatasetAssociation ):
              self.history_dataset = dataset
          elif isinstance( dataset, LibraryDatasetDatasetAssociation ):
              self.library_dataset = dataset
          self.name = name
  
      @property
      def file_name( self ):
          assert self.id is not None, "ID must be set before filename used (commit the object)"
          # Ensure the directory structure and the metadata file object exist
          try:
              da = self.history_dataset or self.library_dataset
              if self.object_store_id is None and da is not None:
                  self.object_store_id = da.dataset.object_store_id
              if not da.dataset.object_store.exists( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ):
                  da.dataset.object_store.create( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
              path = da.dataset.object_store.get_filename( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
              return path
          except AttributeError:
              # In case we're not working with the history_dataset
              # print "Caught AttributeError"
              path = os.path.join( Dataset.file_path, '_metadata_files', *directory_hash_id( self.id ) )
              # Create directory if it does not exist
              try:
                  os.makedirs( path )
              except OSError as e:
                  # File Exists is okay, otherwise reraise
                  if e.errno != errno.EEXIST:
                      raise
              # Return filename inside hashed directory
              return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
  
  
  class FormDefinition( object, Dictifiable ):
      # The following form_builder classes are supported by the FormDefinition class.
      supported_field_types = [ AddressField, CheckboxField, PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField ]
      types = Bunch( REQUEST='Sequencing Request Form',
                     SAMPLE='Sequencing Sample Form',
                     EXTERNAL_SERVICE='External Service Information Form',
                     RUN_DETAILS_TEMPLATE='Sample run details template',
                     LIBRARY_INFO_TEMPLATE='Library information template',
                     USER_INFO='User Information' )
      dict_collection_visible_keys = ( 'id', 'name' )
      dict_element_visible_keys = ( 'id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout' )
  
      def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ):
          self.name = name
          self.desc = desc
          self.fields = fields
          self.form_definition_current = form_definition_current
          self.type = form_type
          self.layout = layout
  
      def to_dict( self, user=None, values=None, security=None ):
          values = values or {}
          form_def = { 'id': security.encode_id( self.id ) if security else self.id, 'name': self.name, 'inputs': [] }
          for field in self.fields:
              FieldClass = ( { 'AddressField'         : AddressField,
                               'CheckboxField'        : CheckboxField,
                               'HistoryField'         : HistoryField,
                               'PasswordField'        : PasswordField,
                               'SelectField'          : SelectField,
                               'TextArea'             : TextArea,
                               'TextField'            : TextField,
                               'WorkflowField'        : WorkflowField } ).get( field[ 'type' ], TextField )
              form_def[ 'inputs' ].append( FieldClass( user=user, value=values.get( field[ 'name' ], field[ 'default' ] ), security=security, **field ).to_dict() )
          return form_def
  
      def grid_fields( self, grid_index ):
          # Returns a dictionary whose keys are integers corresponding to field positions
          # on the grid and whose values are the field.
          gridfields = {}
          for i, f in enumerate( self.fields ):
              if str( f[ 'layout' ] ) == str( grid_index ):
                  gridfields[i] = f
          return gridfields
  
      def get_widgets( self, user, contents={}, **kwd ):
          '''
          Return the list of widgets that comprise a form definition,
          including field contents if any.
          '''
          params = Params( kwd )
          widgets = []
          for index, field in enumerate( self.fields ):
              field_type = field[ 'type' ]
              if 'name' in field:
                  field_name = field[ 'name' ]
              else:
                  # Default to names like field_0, field_1, etc for backward compatibility
                  # (not sure this is necessary)...
                  field_name = 'field_%i' % index
              # Determine the value of the field
              if field_name in kwd:
                  # The form was submitted via refresh_on_change
                  if field_type == 'CheckboxField':
                      value = CheckboxField.is_checked( params.get( field_name, False ) )
                  else:
                      value = restore_text( params.get( field_name, '' ) )
              elif contents:
                  try:
                      # This field has a saved value.
                      value = str( contents[ field[ 'name' ] ] )
                  except:
                      # If there was an error getting the saved value, we'll still
                      # display the widget, but it will be empty.
                      if field_type == 'AddressField':
                          value = 'none'
                      elif field_type == 'CheckboxField':
                          # Since we do not have contents, set checkbox value to False
                          value = False
                      else:
                          # Set other field types to empty string
                          value = ''
              else:
                  # If none of the above, then leave the field empty
                  if field_type == 'AddressField':
                      value = 'none'
                  elif field_type == 'CheckboxField':
                      # Since we do not have contents, set checkbox value to False
                      value = False
                  else:
                      # Set other field types to the default value of the field
                      value = field.get( 'default', '' )
              # Create the field widget
              field_widget = eval( field_type )( field_name )
              if field_type in [ 'TextField', 'PasswordField' ]:
                  field_widget.set_size( 40 )
                  field_widget.value = value
              elif field_type == 'TextArea':
                  field_widget.set_size( 3, 40 )
                  field_widget.value = value
              elif field_type in ['AddressField', 'WorkflowField', 'WorkflowMappingField', 'HistoryField']:
                  field_widget.user = user
                  field_widget.value = value
                  field_widget.params = params
              elif field_type == 'SelectField':
                  for option in field[ 'selectlist' ]:
                      if option == value:
                          field_widget.add_option( option, option, selected=True )
                      else:
                          field_widget.add_option( option, option )
              elif field_type == 'CheckboxField':
                  field_widget.set_checked( value )
              if field[ 'required' ] == 'required':
                  req = 'Required'
              else:
                  req = 'Optional'
              if field[ 'helptext' ]:
                  helptext = '%s (%s)' % ( field[ 'helptext' ], req )
              else:
                  helptext = '(%s)' % req
              widgets.append( dict( label=field[ 'label' ], widget=field_widget, helptext=helptext ) )
          return widgets
  
      def field_as_html( self, field ):
          """Generates disabled html for a field"""
          type = field[ 'type' ]
          form_field = None
          for field_type in self.supported_field_types:
              if type == field_type.__name__:
                  # Name it AddressField, CheckboxField, etc.
                  form_field = field_type( type )
                  break
          if form_field:
              return form_field.get_html( disabled=True )
          # Return None if unsupported field type
          return None
  
  
  class FormDefinitionCurrent( object ):
      def __init__(self, form_definition=None):
          self.latest_form = form_definition
  
  
  class FormValues( object ):
      def __init__(self, form_def=None, content=None):
          self.form_definition = form_def
          self.content = content
  
  
  class Request( object, Dictifiable ):
      states = Bunch( NEW='New',
                      SUBMITTED='In Progress',
                      REJECTED='Rejected',
                      COMPLETE='Complete' )
      dict_collection_visible_keys = ( 'id', 'name', 'state' )
  
      def __init__( self, name=None, desc=None, request_type=None, user=None, form_values=None, notification=None ):
          self.name = name
          self.desc = desc
          self.type = request_type
          self.values = form_values
          self.user = user
          self.notification = notification
          self.samples_list = []
  
      @property
      def state( self ):
          latest_event = self.latest_event
          if latest_event:
              return latest_event.state
          return None
  
      @property
      def latest_event( self ):
          if self.events:
              return self.events[0]
          return None
  
      @property
      def samples_have_common_state( self ):
          """
          Returns the state of this request's samples when they are all
          in one common state. Otherwise returns False.
          """
          state_for_comparison = self.samples[0].state
          if state_for_comparison is None:
              for s in self.samples:
                  if s.state is not None:
                      return False
          for s in self.samples:
              if s.state.id != state_for_comparison.id:
                  return False
          return state_for_comparison
  
      @property
      def last_comment( self ):
          latest_event = self.latest_event
          if latest_event:
              if latest_event.comment:
                  return latest_event.comment
              return ''
          return 'No comment'
  
      def get_sample( self, sample_name ):
          for sample in self.samples:
              if sample.name == sample_name:
                  return sample
          return None
  
      @property
      def is_unsubmitted( self ):
          return self.state in [ self.states.REJECTED, self.states.NEW ]
  
      @property
      def is_rejected( self ):
          return self.state == self.states.REJECTED
  
      @property
      def is_submitted( self ):
          return self.state == self.states.SUBMITTED
  
      @property
      def is_new( self ):
  
          return self.state == self.states.NEW
  
      @property
      def is_complete( self ):
          return self.state == self.states.COMPLETE
  
      @property
      def samples_without_library_destinations( self ):
          # Return all samples that are not associated with a library
          samples = []
          for sample in self.samples:
              if not sample.library:
                  samples.append( sample )
          return samples
  
      @property
      def samples_with_bar_code( self ):
          # Return all samples that have associated bar code
          samples = []
          for sample in self.samples:
              if sample.bar_code:
                  samples.append( sample )
          return samples
  
      def send_email_notification( self, trans, common_state, final_state=False ):
          # Check if an email notification is configured to be sent when the samples
          # are in this state
          if self.notification and common_state.id not in self.notification[ 'sample_states' ]:
              return
          comments = ''
          # Send email
          if trans.app.config.smtp_server is not None and self.notification and self.notification[ 'email' ]:
              body = """
  Galaxy Sample Tracking Notification
  ===================================
  
  User:                     %(user)s
  
  Sequencing request:       %(request_name)s
  Sequencer configuration:  %(request_type)s
  Sequencing request state: %(request_state)s
  
  Number of samples:        %(num_samples)s
  All samples in state:     %(sample_state)s
  
  """
              values = dict( user=self.user.email,
                             request_name=self.name,
                             request_type=self.type.name,
                             request_state=self.state,
                             num_samples=str( len( self.samples ) ),
                             sample_state=common_state.name,
                             create_time=self.create_time,
                             submit_time=self.create_time )
              body = body % values
              # check if this is the final state of the samples
              if final_state:
                  txt = "Sample Name -> Data Library/Folder\r\n"
                  for s in self.samples:
                      if s.library:
                          library_name = s.library.name
                          folder_name = s.folder.name
                      else:
                          library_name = 'No target data library'
                          folder_name = 'No target data library folder'
                      txt = txt + "%s -> %s/%s\r\n" % ( s.name, library_name, folder_name )
                  body = body + txt
              to = self.notification['email']
              frm = trans.app.config.email_from
              if frm is None:
                  host = trans.request.host.split( ':' )[0]
                  if host in [ 'localhost', '127.0.0.1', '0.0.0.0' ]:
                      host = socket.getfqdn()
                  frm = 'galaxy-no-reply@' + host
              subject = "Galaxy Sample Tracking notification: '%s' sequencing request" % self.name
              try:
                  send_mail( frm, to, subject, body, trans.app.config )
                  comments = "Email notification sent to %s." % ", ".join( to ).strip().strip( ',' )
              except Exception as e:
                  comments = "Email notification failed. (%s)" % str(e)
              # update the request history with the email notification event
          elif not trans.app.config.smtp_server:
              comments = "Email notification failed as SMTP server not set in config file"
          if comments:
              event = RequestEvent( self, self.state, comments )
              trans.sa_session.add( event )
              trans.sa_session.flush()
          return comments
  
  
  class RequestEvent( object ):
      def __init__(self, request=None, request_state=None, comment=''):
          self.request = request
          self.state = request_state
          self.comment = comment
  
  
  class ExternalService( object ):
      data_transfer_protocol = Bunch( HTTP='http',
                                      HTTPS='https',
                                      SCP='scp' )
  
      def __init__( self, name=None, description=None, external_service_type_id=None, version=None, form_definition_id=None, form_values_id=None, deleted=None ):
          self.name = name
          self.description = description
          self.external_service_type_id = external_service_type_id
          self.version = version
          self.form_definition_id = form_definition_id
          self.form_values_id = form_values_id
          self.deleted = deleted
          self.label = None  # Used in the request_type controller's __build_external_service_select_field() method
  
      def get_external_service_type( self, trans ):
          return trans.app.external_service_types.all_external_service_types[ self.external_service_type_id ]
  
      def load_data_transfer_settings( self, trans ):
          trans.app.external_service_types.reload( self.external_service_type_id )
          self.data_transfer = {}
          external_service_type = self.get_external_service_type( trans )
          for data_transfer_protocol, data_transfer_obj in external_service_type.data_transfer.items():
              if data_transfer_protocol == self.data_transfer_protocol.SCP:
                  scp_configs = {}
                  automatic_transfer = data_transfer_obj.config.get( 'automatic_transfer', 'false' )
                  scp_configs[ 'automatic_transfer' ] = galaxy.util.string_as_bool( automatic_transfer )
                  scp_configs[ 'host' ] = self.form_values.content.get( data_transfer_obj.config.get( 'host', '' ), '' )
                  scp_configs[ 'user_name' ] = self.form_values.content.get( data_transfer_obj.config.get( 'user_name', '' ), '' )
                  scp_configs[ 'password' ] = self.form_values.content.get( data_transfer_obj.config.get( 'password', '' ), '' )
                  scp_configs[ 'data_location' ] = self.form_values.content.get( data_transfer_obj.config.get( 'data_location', '' ), '' )
                  scp_configs[ 'rename_dataset' ] = self.form_values.content.get( data_transfer_obj.config.get( 'rename_dataset', '' ), '' )
                  self.data_transfer[ self.data_transfer_protocol.SCP ] = scp_configs
              if data_transfer_protocol == self.data_transfer_protocol.HTTP:
                  http_configs = {}
                  automatic_transfer = data_transfer_obj.config.get( 'automatic_transfer', 'false' )
                  http_configs[ 'automatic_transfer' ] = galaxy.util.string_as_bool( automatic_transfer )
                  self.data_transfer[ self.data_transfer_protocol.HTTP ] = http_configs
  
      def populate_actions( self, trans, item, param_dict=None ):
          return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict )
  
  
  class RequestType( object, Dictifiable ):
      dict_collection_visible_keys = ( 'id', 'name', 'desc' )
      dict_element_visible_keys = ( 'id', 'name', 'desc', 'request_form_id', 'sample_form_id' )
      rename_dataset_options = Bunch( NO='Do not rename',
                                      SAMPLE_NAME='Preprend sample name',
                                      EXPERIMENT_NAME='Prepend experiment name',
                                      EXPERIMENT_AND_SAMPLE_NAME='Prepend experiment and sample name')
      permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' )
  
      def __init__( self, name=None, desc=None, request_form=None, sample_form=None ):
          self.name = name
          self.desc = desc
          self.request_form = request_form
          self.sample_form = sample_form
  
      @property
      def external_services( self ):
          external_services = []
          for rtesa in self.external_service_associations:
              external_services.append( rtesa.external_service )
          return external_services
  
      def get_external_service( self, external_service_type_id ):
          for rtesa in self.external_service_associations:
              if rtesa.external_service.external_service_type_id == external_service_type_id:
                  return rtesa.external_service
          return None
  
      def get_external_services_for_manual_data_transfer( self, trans ):
          '''Returns all external services that use manual data transfer'''
          external_services = []
          for rtesa in self.external_service_associations:
              external_service = rtesa.external_service
              # load data transfer settings
              external_service.load_data_transfer_settings( trans )
              if external_service.data_transfer:
                  for transfer_type, transfer_type_settings in external_service.data_transfer.items():
                      if not transfer_type_settings[ 'automatic_transfer' ]:
                          external_services.append( external_service )
          return external_services
  
      def delete_external_service_associations( self, trans ):
          '''Deletes all external service associations.'''
          flush_needed = False
          for rtesa in self.external_service_associations:
              trans.sa_session.delete( rtesa )
              flush_needed = True
          if flush_needed:
              trans.sa_session.flush()
  
      def add_external_service_association( self, trans, external_service ):
          rtesa = trans.model.RequestTypeExternalServiceAssociation( self, external_service )
          trans.sa_session.add( rtesa )
          trans.sa_session.flush()
  
      @property
      def final_sample_state( self ):
          # The states mapper for this object orders ascending
          return self.states[-1]
  
      @property
      def run_details( self ):
          if self.run:
              # self.run[0] is [RequestTypeRunAssociation]
              return self.run[0]
          return None
  
      def get_template_widgets( self, trans, get_contents=True ):
          # See if we have any associated templates.  The get_contents param
          # is passed by callers that are inheriting a template - these are
          # usually new samples for which we want to include template fields,
          # but not necessarily the contents of the inherited template.
          rtra = self.run_details
          if rtra:
              run = rtra.run
              template = run.template
              if get_contents:
                  # See if we have any field contents
                  info = run.info
                  if info:
                      return template.get_widgets( trans.user, contents=info.content )
              return template.get_widgets( trans.user )
          return []
  
  
  class RequestTypeExternalServiceAssociation( object ):
      def __init__( self, request_type, external_service ):
          self.request_type = request_type
          self.external_service = external_service
  
  
  class RequestTypePermissions( object ):
      def __init__( self, action, request_type, role ):
          self.action = action
          self.request_type = request_type
          self.role = role
  
  
  class Sample( object, Dictifiable ):
      # The following form_builder classes are supported by the Sample class.
      supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField, WorkflowMappingField, HistoryField ]
      bulk_operations = Bunch( CHANGE_STATE='Change state',
                               SELECT_LIBRARY='Select data library and folder' )
      dict_collection_visible_keys = ( 'id', 'name' )
  
      def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None):
          self.name = name
          self.desc = desc
          self.request = request
          self.values = form_values
          self.bar_code = bar_code
          self.library = library
          self.folder = folder
          self.history = history
          self.workflow = workflow
  
      @property
      def state( self ):
          latest_event = self.latest_event
          if latest_event:
              return latest_event.state
          return None
  
      @property
      def latest_event( self ):
          if self.events:
              return self.events[0]
          return None
  
      @property
      def adding_to_library_dataset_files( self ):
          adding_to_library_datasets = []
          for dataset in self.datasets:
              if dataset.status == SampleDataset.transfer_status.ADD_TO_LIBRARY:
                  adding_to_library_datasets.append( dataset )
          return adding_to_library_datasets
  
      @property
      def inprogress_dataset_files( self ):
          inprogress_datasets = []
          for dataset in self.datasets:
              if dataset.status not in [ SampleDataset.transfer_status.NOT_STARTED, SampleDataset.transfer_status.COMPLETE ]:
                  inprogress_datasets.append( dataset )
          return inprogress_datasets
  
      @property
      def queued_dataset_files( self ):
          queued_datasets = []
          for dataset in self.datasets:
              if dataset.status == SampleDataset.transfer_status.IN_QUEUE:
                  queued_datasets.append( dataset )
          return queued_datasets
  
      @property
      def transfer_error_dataset_files( self ):
          transfer_error_datasets = []
          for dataset in self.datasets:
              if dataset.status == SampleDataset.transfer_status.ERROR:
                  transfer_error_datasets.append( dataset )
          return transfer_error_datasets
  
      @property
      def transferred_dataset_files( self ):
          transferred_datasets = []
          for dataset in self.datasets:
              if dataset.status == SampleDataset.transfer_status.COMPLETE:
                  transferred_datasets.append( dataset )
          return transferred_datasets
  
      @property
      def transferring_dataset_files( self ):
          transferring_datasets = []
          for dataset in self.datasets:
              if dataset.status == SampleDataset.transfer_status.TRANSFERRING:
                  transferring_datasets.append( dataset )
          return transferring_datasets
  
      @property
      def untransferred_dataset_files( self ):
          untransferred_datasets = []
          for dataset in self.datasets:
              if dataset.status != SampleDataset.transfer_status.COMPLETE:
                  untransferred_datasets.append( dataset )
          return untransferred_datasets
  
      @property
      def run_details( self ):
          # self.runs is a list of SampleRunAssociations ordered descending on update_time.
          if self.runs:
              # Always use the latest run details template, self.runs[0] is a SampleRunAssociation
              return self.runs[0]
          # Inherit this sample's RequestType run details, if one exists.
          return self.request.type.run_details
  
      def get_template_widgets( self, trans, get_contents=True ):
          # Samples have a one-to-many relationship with run details, so we return the
          # widgets for last associated template.  The get_contents param will populate
          # the widget fields with values from the template inherited from the sample's
          # RequestType.
          template = None
          if self.runs:
              # The self.runs mapper orders descending on update_time.
              run = self.runs[0].run
              template = run.template
          if template is None:
              # There are no run details associated with this sample, so inherit the
              # run details template from the sample's RequestType.
              rtra = self.request.type.run_details
              if rtra:
                  run = rtra.run
                  template = run.template
          if template:
              if get_contents:
                  # See if we have any field contents
                  info = run.info
                  if info:
                      return template.get_widgets( trans.user, contents=info.content )
              return template.get_widgets( trans.user )
          return []
  
      def populate_external_services( self, param_dict=None, trans=None ):
          if self.request and self.request.type:
              return [ service.populate_actions( item=self, param_dict=param_dict, trans=trans ) for service in self.request.type.external_services ]
  
  
  class SampleState( object ):
      def __init__(self, name=None, desc=None, request_type=None):
          self.name = name
          self.desc = desc
          self.request_type = request_type
  
  
  class SampleEvent( object ):
      def __init__(self, sample=None, sample_state=None, comment=''):
          self.sample = sample
          self.state = sample_state
          self.comment = comment
  
  
  class SampleDataset( object ):
      transfer_status = Bunch( NOT_STARTED='Not started',
                               IN_QUEUE='In queue',
                               TRANSFERRING='Transferring dataset',
                               ADD_TO_LIBRARY='Adding to data library',
                               COMPLETE='Complete',
                               ERROR='Error' )
  
      def __init__( self, sample=None, name=None, file_path=None, status=None, error_msg=None, size=None, external_service=None ):
          self.sample = sample
          self.name = name
          self.file_path = file_path
          self.status = status
          self.error_msg = error_msg
          self.size = size
          self.external_service = external_service
  
  
  class Run( object ):
      def __init__( self, form_definition, form_values, subindex=None ):
          self.template = form_definition
          self.info = form_values
          self.subindex = subindex
  
  
  class RequestTypeRunAssociation( object ):
      def __init__( self, request_type, run ):
          self.request_type = request_type
          self.run = run
  
  
  class SampleRunAssociation( object ):
      def __init__( self, sample, run ):
          self.sample = sample
          self.run = run
  
  
  class UserAddress( object ):
      def __init__( self, user=None, desc=None, name=None, institution=None,
                    address=None, city=None, state=None, postal_code=None,
                    country=None, phone=None ):
          self.user = user
          self.desc = desc
          self.name = name
          self.institution = institution
          self.address = address
          self.city = city
          self.state = state
          self.postal_code = postal_code
          self.country = country
          self.phone = phone
  
      def to_dict( self, trans ):
          return { 'id'           : trans.security.encode_id( self.id ),
                   'name'         : sanitize_html( self.name ),
                   'desc'         : sanitize_html( self.desc ),
                   'institution'  : sanitize_html( self.institution ),
                   'address'      : sanitize_html( self.address ),
                   'city'         : sanitize_html( self.city ),
                   'state'        : sanitize_html( self.state ),
                   'postal_code'  : sanitize_html( self.postal_code ),
                   'country'      : sanitize_html( self.country ),
                   'phone'        : sanitize_html( self.phone ) }
  
      def get_html(self):
          # This should probably be deprecated eventually.  It should currently
          # sanitize.
          # TODO Find out where else uses this and replace with
          # templates
          html = ''
          if self.name:
              html = html + sanitize_html(self.name)
          if self.institution:
              html = html + '<br/>' + sanitize_html(self.institution)
          if self.address:
              html = html + '<br/>' + sanitize_html(self.address)
          if self.city:
              html = html + '<br/>' + sanitize_html(self.city)
          if self.state:
              html = html + ' ' + sanitize_html(self.state)
          if self.postal_code:
              html = html + ' ' + sanitize_html(self.postal_code)
          if self.country:
              html = html + '<br/>' + sanitize_html(self.country)
          if self.phone:
              html = html + '<br/>' + 'phone: ' + sanitize_html(self.phone)
          return html
  
  
  class UserOpenID( object ):
      def __init__( self, user=None, session=None, openid=None ):
          self.user = user
          self.session = session
          self.openid = openid
  
  
  class Page( object, Dictifiable ):
      dict_element_visible_keys = [ 'id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted' ]
  
      def __init__( self ):
          self.id = None
          self.user = None
          self.title = None
          self.slug = None
          self.latest_revision_id = None
          self.revisions = []
          self.importable = None
          self.published = None
  
      def to_dict( self, view='element' ):
          rval = super( Page, self ).to_dict( view=view )
          rev = []
          for a in self.revisions:
              rev.append(a.id)
          rval['revision_ids'] = rev
          return rval
  
  
  class PageRevision( object, Dictifiable ):
      dict_element_visible_keys = [ 'id', 'page_id', 'title', 'content' ]
  
      def __init__( self ):
          self.user = None
          self.title = None
          self.content = None
  
      def to_dict( self, view='element' ):
          rval = super( PageRevision, self ).to_dict( view=view )
          rval['create_time'] = str(self.create_time)
          rval['update_time'] = str(self.update_time)
          return rval
  
  
  class PageUserShareAssociation( object ):
      def __init__( self ):
          self.page = None
          self.user = None
  
  
  class Visualization( object ):
      def __init__( self, id=None, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None ):
          self.id = id
          self.user = user
          self.type = type
          self.title = title
          self.dbkey = dbkey
          self.slug = slug
          self.latest_revision = latest_revision
          self.revisions = []
          if self.latest_revision:
              self.revisions.append( latest_revision )
  
      def copy( self, user=None, title=None ):
          """
          Provide copy of visualization with only its latest revision.
          """
          # NOTE: a shallow copy is done: the config is copied as is but datasets
          # are not copied nor are the dataset ids changed. This means that the
          # user does not have a copy of the data in his/her history and the
          # user who owns the datasets may delete them, making them inaccessible
          # for the current user.
          # TODO: a deep copy option is needed.
  
          if not user:
              user = self.user
          if not title:
              title = self.title
  
          copy_viz = Visualization( user=user, type=self.type, title=title, dbkey=self.dbkey )
          copy_revision = self.latest_revision.copy( visualization=copy_viz )
          copy_viz.latest_revision = copy_revision
          return copy_viz
  
  
  class VisualizationRevision( object ):
      def __init__( self, visualization=None, title=None, dbkey=None, config=None ):
          self.id = None
          self.visualization = visualization
          self.title = title
          self.dbkey = dbkey
          self.config = config
  
      def copy( self, visualization=None ):
          """
          Returns a copy of this object.
          """
          if not visualization:
              visualization = self.visualization
  
          return VisualizationRevision(
              visualization=visualization,
              title=self.title,
              dbkey=self.dbkey,
              config=self.config
          )
  
  
  class VisualizationUserShareAssociation( object ):
      def __init__( self ):
          self.visualization = None
          self.user = None
  
  
  class TransferJob( object ):
      # These states are used both by the transfer manager's IPC and the object
      # state in the database.  Not all states are used by both.
      states = Bunch( NEW='new',
                      UNKNOWN='unknown',
                      PROGRESS='progress',
                      RUNNING='running',
                      ERROR='error',
                      DONE='done' )
      terminal_states = [ states.ERROR,
                          states.DONE ]
  
      def __init__( self, state=None, path=None, info=None, pid=None, socket=None, params=None ):
          self.state = state
          self.path = path
          self.info = info
          self.pid = pid
          self.socket = socket
          self.params = params
  
  
  class Tag ( object ):
      def __init__( self, id=None, type=None, parent_id=None, name=None ):
          self.id = id
          self.type = type
          self.parent_id = parent_id
          self.name = name
  
      def __str__( self ):
          return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name )
  
  
  class ItemTagAssociation ( object, Dictifiable ):
      dict_collection_visible_keys = ( 'id', 'user_tname', 'user_value' )
      dict_element_visible_keys = dict_collection_visible_keys
  
      def __init__( self, id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None ):
          self.id = id
          self.user = user
          self.item_id = item_id
          self.tag_id = tag_id
          self.user_tname = user_tname
          self.value = None
          self.user_value = None
  
      def copy(self):
          new_ta = type(self)()
          new_ta.tag_id = self.tag_id
          new_ta.user_tname = self.user_tname
          new_ta.value = self.value
          new_ta.user_value = self.user_value
          return new_ta
  
  
  class HistoryTagAssociation ( ItemTagAssociation ):
      pass
  
  
  class DatasetTagAssociation ( ItemTagAssociation ):
      pass
  
  
  class HistoryDatasetAssociationTagAssociation ( ItemTagAssociation ):
      pass
  
  
  class PageTagAssociation ( ItemTagAssociation ):
      pass
  
  
  class WorkflowStepTagAssociation ( ItemTagAssociation ):
      pass
  
  
  class StoredWorkflowTagAssociation ( ItemTagAssociation ):
      pass
  
  
  class VisualizationTagAssociation ( ItemTagAssociation ):
      pass
  
  
  class HistoryDatasetCollectionTagAssociation( ItemTagAssociation ):
      pass
  
  
  class LibraryDatasetCollectionTagAssociation( ItemTagAssociation ):
      pass
  
  
  class ToolTagAssociation( ItemTagAssociation ):
      def __init__( self, id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None ):
          self.id = id
          self.user = user
          self.tool_id = tool_id
          self.tag_id = tag_id
          self.user_tname = user_tname
          self.value = None
          self.user_value = None
  
  
  class WorkRequestTagAssociation( ItemTagAssociation ):
      def __init__( self, id=None, user=None, workflow_request_id=None, tag_id=None, user_tname=None, value=None ):
          self.id = id
          self.user = user
          self.workflow_request_id = workflow_request_id
          self.tag_id = tag_id
          self.user_tname = user_tname
          self.value = None
          self.user_value = None
  
  
  # Item annotation classes.
  class HistoryAnnotationAssociation( object ):
      pass
  
  
  class HistoryDatasetAssociationAnnotationAssociation( object ):
      pass
  
  
  class StoredWorkflowAnnotationAssociation( object ):
      pass
  
  
  class WorkflowStepAnnotationAssociation( object ):
      pass
  
  
  class PageAnnotationAssociation( object ):
      pass
  
  
  class VisualizationAnnotationAssociation( object ):
      pass
  
  
  class HistoryDatasetCollectionAnnotationAssociation( object ):
      pass
  
  
  class LibraryDatasetCollectionAnnotationAssociation( object ):
      pass
  
  
  # Item rating classes.
  
  class ItemRatingAssociation( object ):
      def __init__( self, id=None, user=None, item=None, rating=0 ):
          self.id = id
          self.user = user
          self.item = item
          self.rating = rating
  
      def set_item( self, item ):
          """ Set association's item. """
          pass
  
  
  class HistoryRatingAssociation( ItemRatingAssociation ):
      def set_item( self, history ):
          self.history = history
  
  
  class HistoryDatasetAssociationRatingAssociation( ItemRatingAssociation ):
      def set_item( self, history_dataset_association ):
          self.history_dataset_association = history_dataset_association
  
  
  class StoredWorkflowRatingAssociation( ItemRatingAssociation ):
      def set_item( self, stored_workflow ):
          self.stored_workflow = stored_workflow
  
  
  class PageRatingAssociation( ItemRatingAssociation ):
      def set_item( self, page ):
          self.page = page
  
  
  class VisualizationRatingAssociation( ItemRatingAssociation ):
      def set_item( self, visualization ):
          self.visualization = visualization
  
  
  class HistoryDatasetCollectionRatingAssociation( ItemRatingAssociation ):
      def set_item( self, dataset_collection ):
          self.dataset_collection = dataset_collection
  
  
  class LibraryDatasetCollectionRatingAssociation( ItemRatingAssociation ):
      def set_item( self, dataset_collection ):
          self.dataset_collection = dataset_collection
  
  
  # Data Manager Classes
  class DataManagerHistoryAssociation( object ):
      def __init__( self, id=None, history=None, user=None ):
          self.id = id
          self.history = history
          self.user = user
  
  
  class DataManagerJobAssociation( object ):
      def __init__( self, id=None, job=None, data_manager_id=None ):
          self.id = id
          self.job = job
          self.data_manager_id = data_manager_id
  # end of Data Manager Classes
  
  
  class UserPreference ( object ):
      def __init__( self, name=None, value=None):
          self.name = name
          self.value = value
  
  
  class UserAction( object ):
      def __init__( self, id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None):
          self.id = id
          self.create_time = create_time
          self.user_id = user_id
          self.session_id = session_id
          self.action = action
          self.params = params
          self.context = context
  
  
  class APIKeys( object ):
      def __init__( self, id=None, user_id=None, key=None):
          self.id = id
          self.user_id = user_id
          self.key = key
  
  
  def copy_list(lst, *args, **kwds):
      if lst is None:
          return lst
      else:
          return [el.copy(*args, **kwds) for el in lst]
  