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pep8, cleanup in histories manager.

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This commit is contained in:
Dannon Baker
2015-03-17 13:03:52 -04:00
parent 5e3dc3bad0
commit 8708cc231b
1 changed files with 61 additions and 67 deletions
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lib/galaxy/managers/histories.py
+61 -67
View File
@@ -6,7 +6,6 @@ created (or copied) by users over the course of an analysis.
"""
from galaxy import model
from galaxy.managers import base
from galaxy.managers import sharable
from galaxy.managers import deletable
from galaxy.managers import hdas
@@ -26,7 +25,7 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
annotation_assoc = model.HistoryAnnotationAssociation
rating_assoc = model.HistoryRatingAssociation
#TODO: incorporate imp/exp (or alias to)
# TODO: incorporate imp/exp (or alias to)
def __init__( self, app, *args, **kwargs ):
super( HistoryManager, self ).__init__( app, *args, **kwargs )
@@ -62,7 +61,7 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
return True
return super( HistoryManager, self ).is_owner( trans, history, user )
#TODO: possibly to sharable
# TODO: possibly to sharable
def most_recent( self, trans, user, filters=None, **kwargs ):
"""
Return the most recently update history for the user.
@@ -70,13 +69,13 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
If user is anonymous, return the current history. If the user is anonymous
and the current history is deleted, return None.
"""
#TODO: trans
# TODO: trans
if not user:
current_history = self.get_current( trans )
return None if ( not current_history or current_history.deleted ) else current_history
desc_update_time = self.model_class.table.c.update_time
filters = self._munge_filters( filters, self.model_class.user_id == user.id )
#TODO: normalize this return value
# TODO: normalize this return value
return self.query( trans, filters=filters, order_by=desc_update_time, limit=1, **kwargs ).first()
# .... purgable
@@ -99,14 +98,14 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
"""
Return the current history.
"""
#TODO: trans
# TODO: trans
return trans.get_history()
def set_current( self, trans, history ):
"""
Set the current history.
"""
#TODO: trans
# TODO: trans
trans.set_history( history )
return history
@@ -117,27 +116,23 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
return self.set_current( trans, self.by_id( trans, history_id ) )
# .... serialization
#TODO: move to serializer (i.e. history with contents attr)
# TODO: move to serializer (i.e. history with contents attr)
def _get_history_data( self, trans, history ):
"""
Returns a dictionary containing ``history`` and ``contents``, serialized
history and an array of serialized history contents respectively.
"""
#TODO: instantiate here? really?
# TODO: instantiate here? really?
history_serializer = HistorySerializer( self.app )
hda_serializer = hdas.HDASerializer( self.app )
history_dictionary = {}
contents_dictionaries = []
try:
history_dictionary = history_serializer.serialize_to_view( trans, history, view='detailed' )
#for content in history.contents_iter( **contents_kwds ):
for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ):
contents_dict = {}
if isinstance( content, model.HistoryDatasetAssociation ):
contents_dict = hda_serializer.serialize_to_view( trans, content, view='detailed' )
elif isinstance( content, model.HistoryDatasetCollectionAssociation ):
try:
service = self.app.dataset_collections_service
@@ -147,25 +142,23 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
id=self.app.security.encode_id( content.id ),
)
contents_dict = dictify_dataset_collection_instance( dataset_collection_instance,
security=self.app.security, parent=dataset_collection_instance.history, view="element" )
security=self.app.security,
parent=dataset_collection_instance.history,
view="element" )
except Exception, exc:
log.exception( "Error in history API at listing dataset collection: %s", exc )
#TODO: return some dict with the error
# TODO: return some dict with the error
contents_dictionaries.append( contents_dict )
except Exception, exc:
user_id = str( trans.user.id ) if trans.user else '(anonymous)'
log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) )
message = ( 'An error occurred getting the history data from the server. '
+ 'Please contact a Galaxy administrator if the problem persists.' )
'Please contact a Galaxy administrator if the problem persists.' )
history_dictionary[ 'error' ] = message
return {
'history' : history_dictionary,
'contents' : contents_dictionaries
}
return { 'history': history_dictionary,
'contents': contents_dictionaries }
# remove this
def get_state_counts( self, trans, history, exclude_deleted=True, exclude_hidden=False ):
@@ -173,12 +166,12 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
Return a dictionary keyed to possible dataset states and valued with the number
of datasets in this history that have those states.
"""
#TODO: the default flags above may not make a lot of sense (T,T?)
# TODO: the default flags above may not make a lot of sense (T,T?)
state_counts = {}
for state in model.Dataset.states.values():
state_counts[ state ] = 0
#TODO:?? collections and coll. states?
# TODO:?? collections and coll. states?
for hda in history.datasets:
if exclude_deleted and hda.deleted:
continue
@@ -197,14 +190,14 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
for state in model.Dataset.states.values():
state_ids[ state ] = []
#TODO:?? collections and coll. states?
# TODO:?? collections and coll. states?
for hda in history.datasets:
#TODO: do not encode ids at this layer
# TODO: do not encode ids at this layer
encoded_id = self.app.security.encode_id( hda.id )
state_ids[ hda.state ].append( encoded_id )
return state_ids
#TODO: remove this (is state used/useful?)
# TODO: remove this (is state used/useful?)
def get_history_state( self, trans, history ):
"""
Returns the history state based on the states of the HDAs it contains.
@@ -214,7 +207,7 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
# (default to ERROR)
state = states.ERROR
#TODO: history_state and state_counts are classically calc'd at the same time
# TODO: history_state and state_counts are classically calc'd at the same time
# so this is rel. ineff. - if we keep this...
hda_state_counts = self.get_state_counts( trans, history, exclude_deleted=False )
num_hdas = sum( hda_state_counts.values() )
@@ -222,17 +215,17 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
state = states.NEW
else:
if( ( hda_state_counts[ states.RUNNING ] > 0 )
or ( hda_state_counts[ states.SETTING_METADATA ] > 0 )
or ( hda_state_counts[ states.UPLOAD ] > 0 ) ):
if ( hda_state_counts[ states.RUNNING ] > 0
or hda_state_counts[ states.SETTING_METADATA ] > 0
or hda_state_counts[ states.UPLOAD ] > 0 ):
state = states.RUNNING
#TODO: this method may be more useful if we *also* polled the histories jobs here too
# TODO: this method may be more useful if we *also* polled the histories jobs here too
elif hda_state_counts[ states.QUEUED ] > 0:
state = states.QUEUED
elif( ( hda_state_counts[ states.ERROR ] > 0 )
or ( hda_state_counts[ states.FAILED_METADATA ] > 0 ) ):
elif ( hda_state_counts[ states.ERROR ] > 0
or hda_state_counts[ states.FAILED_METADATA ] > 0 ):
state = states.ERROR
elif hda_state_counts[ states.OK ] == num_hdas:
@@ -261,53 +254,52 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
'name',
'deleted',
'purged',
#'count'
# 'count'
'url',
#TODO: why these?
# TODO: why these?
'published',
'annotation',
'tags',
])
self.add_view( 'detailed', [
'contents_url',
#'hdas',
# 'hdas',
'empty',
'size', 'nice_size',
'user_id',
'create_time', 'update_time',
'importable', 'slug', 'username_and_slug',
'genome_build',
#TODO: remove the next three - instead getting the same info from the 'hdas' list
# TODO: remove the next three - instead getting the same info from the 'hdas' list
'state',
'state_details',
'state_ids',
# in the Historys' case, each of these views includes the keys from the previous
# in the Historys' case, each of these views includes the keys from the previous
], include_keys_from='summary' )
#assumes: outgoing to json.dumps and sanitized
# assumes: outgoing to json.dumps and sanitized
def add_serializers( self ):
super( HistorySerializer, self ).add_serializers()
deletable.PurgableSerializerMixin.add_serializers( self )
self.serializers.update({
'model_class' : lambda *a: 'History',
'id' : self.serialize_id,
'create_time' : self.serialize_date,
'update_time' : self.serialize_date,
'size' : lambda t, i, k: int( i.get_disk_size() ),
'nice_size' : lambda t, i, k: i.get_disk_size( nice_size=True ),
'state' : lambda t, i, k: self.history_manager.get_history_state( t, i ),
'model_class': lambda *a: 'History',
'id': self.serialize_id,
'create_time': self.serialize_date,
'update_time': self.serialize_date,
'size': lambda t, i, k: int( i.get_disk_size() ),
'nice_size': lambda t, i, k: i.get_disk_size( nice_size=True ),
'state': lambda t, i, k: self.history_manager.get_history_state( t, i ),
'url' : lambda t, i, k: self.url_for( 'history', id=t.security.encode_id( i.id ) ),
'contents_url' : lambda t, i, k:
self.url_for( 'history_contents', history_id=t.security.encode_id( i.id ) ),
'url': lambda t, i, k: self.url_for( 'history', id=t.security.encode_id( i.id ) ),
'contents_url': lambda t, i, k: self.url_for( 'history_contents', history_id=t.security.encode_id( i.id ) ),
'empty' : lambda t, i, k: len( i.datasets ) <= 0,
'count' : lambda trans, item, key: len( item.datasets ),
'hdas' : lambda t, i, k: [ t.security.encode_id( hda.id ) for hda in i.datasets ],
'state_details' : lambda t, i, k: self.history_manager.get_state_counts( t, i ),
'state_ids' : lambda t, i, k: self.history_manager.get_state_ids( t, i ),
'contents' : self.serialize_contents
'empty': lambda t, i, k: len( i.datasets ) <= 0,
'count': lambda trans, item, key: len( item.datasets ),
'hdas': lambda t, i, k: [ t.security.encode_id( hda.id ) for hda in i.datasets ],
'state_details': lambda t, i, k: self.history_manager.get_state_counts( t, i ),
'state_ids': lambda t, i, k: self.history_manager.get_state_ids( t, i ),
'contents': self.serialize_contents
})
def serialize_contents( self, trans, history, *args ):
@@ -329,7 +321,9 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
id=self.security.encode_id( collection.id ),
)
return dictify_dataset_collection_instance( dataset_collection_instance,
security=self.app.security, parent=dataset_collection_instance.history, view="element" )
security=self.app.security,
parent=dataset_collection_instance.history,
view="element" )
class HistoryDeserializer( sharable.SharableModelDeserializer, deletable.PurgableDeserializerMixin ):
@@ -347,8 +341,8 @@ class HistoryDeserializer( sharable.SharableModelDeserializer, deletable.Purgabl
deletable.PurgableDeserializerMixin.add_deserializers( self )
self.deserializers.update({
'name' : self.deserialize_basestring,
'genome_build' : self.deserialize_genome_build,
'name': self.deserialize_basestring,
'genome_build': self.deserialize_genome_build,
})
@@ -361,18 +355,18 @@ class HistoryFilters( sharable.SharableModelFilters, deletable.PurgableFiltersMi
self.orm_filter_parsers.update({
# history specific
'name' : { 'op': ( 'eq', 'contains', 'like' ) },
'genome_build' : { 'op': ( 'eq', 'contains', 'like' ) },
'name': { 'op': ( 'eq', 'contains', 'like' ) },
'genome_build': { 'op': ( 'eq', 'contains', 'like' ) },
})
#TODO: I'm not entirely convinced this (or tags) are a good idea for filters since they involve a/the user
# TODO: I'm not entirely convinced this (or tags) are a good idea for filters since they involve a/the user
self.fn_filter_parsers.update({
#TODO: add this in annotatable mixin
'annotation' : { 'op': { 'has' : self.filter_annotation_contains, } },
#TODO: add this in taggable mixin
'tag' : {
# TODO: add this in annotatable mixin
'annotation': { 'op': { 'has': self.filter_annotation_contains, } },
# TODO: add this in taggable mixin
'tag': {
'op': {
'eq' : self.filter_has_tag,
'eq': self.filter_has_tag,
'has': self.filter_has_partial_tag,
}
}