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Trim whitespace.

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Dannon Baker
2013-03-05 15:44:03 -05:00
parent 4ca14e3dea
commit 8e9bb76611
1 changed files with 65 additions and 65 deletions
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lib/galaxy/web/base/controller.py
+65 -65
View File
@@ -194,7 +194,7 @@ class Datatype( object ):
self.mimetype = mimetype
self.display_in_upload = display_in_upload
#
#
# -- Mixins for working with Galaxy objects. --
#
@@ -221,7 +221,7 @@ class SharableItemSecurityMixin:
class UsesHistoryDatasetAssociationMixin:
""" Mixin for controllers that use HistoryDatasetAssociation objects. """
def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False, check_state=True ):
""" Get an HDA object by id. """
# DEPRECATION: We still support unencoded ids for backward compatibility
@@ -256,13 +256,13 @@ class UsesHistoryDatasetAssociationMixin:
return trans.show_error_message( "Please wait until this dataset finishes uploading "
+ "before attempting to view it." )
return data
def get_history_dataset_association( self, trans, history, dataset_id,
check_ownership=True, check_accessible=False, check_state=False ):
"""Get a HistoryDatasetAssociation from the database by id, verifying ownership."""
self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible )
hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False )
if check_accessible:
if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ):
error( "You are not allowed to access this dataset" )
@@ -270,7 +270,7 @@ class UsesHistoryDatasetAssociationMixin:
if check_state and hda.state == trans.model.Dataset.states.UPLOAD:
error( "Please wait until this dataset finishes uploading before attempting to view it." )
return hda
def get_data( self, dataset, preview=True ):
""" Gets a dataset's data. """
@@ -290,7 +290,7 @@ class UsesHistoryDatasetAssociationMixin:
# For now, cannot get data from non-text datasets.
dataset_data = None
return truncated, dataset_data
def check_dataset_state( self, trans, dataset ):
"""
Returns a message if dataset is not ready to be used in visualization.
@@ -302,7 +302,7 @@ class UsesHistoryDatasetAssociationMixin:
if dataset.state != trans.app.model.Job.states.OK:
return dataset.conversion_messages.PENDING
return None
class UsesLibraryMixin:
def get_library( self, trans, id, check_ownership=False, check_accessible=True ):
@@ -319,10 +319,10 @@ class UsesLibraryMixinItems( SharableItemSecurityMixin ):
def get_library_dataset( self, trans, id, check_ownership=False, check_accessible=True ):
return self.get_object( trans, id, 'LibraryDataset', check_ownership=False, check_accessible=check_accessible )
class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
UsesLibraryMixinItems ):
""" Mixin for controllers that use Visualization objects. """
viz_types = [ "trackster" ]
def create_visualization( self, trans, type, title="Untitled Genome Vis", slug=None, dbkey=None, annotation=None, config={}, save=True ):
@@ -339,26 +339,26 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
session.flush()
return visualization
def save_visualization( self, trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None ):
session = trans.sa_session
# Create/get visualization.
# Create/get visualization.
if not id:
# Create new visualization.
vis = self._create_visualization( trans, title, type, dbkey, slug, annotation )
else:
decoded_id = trans.security.decode_id( id )
vis = session.query( trans.model.Visualization ).get( decoded_id )
# Create new VisualizationRevision that will be attached to the viz
vis_rev = trans.model.VisualizationRevision()
vis_rev.visualization = vis
vis_rev.title = vis.title
vis_rev.dbkey = dbkey
# -- Validate config. --
if vis.type == 'trackster':
def unpack_track( track_json ):
""" Unpack a track from its json. """
@@ -436,12 +436,12 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
# Unpack Trackster config.
latest_revision = visualization.latest_revision
bookmarks = latest_revision.config.get( 'bookmarks', [] )
def pack_track( track_dict ):
dataset_id = track_dict['dataset_id']
hda_ldda = track_dict.get('hda_ldda', 'hda')
if hda_ldda == 'ldda':
# HACK: need to encode library dataset ID because get_hda_or_ldda
# HACK: need to encode library dataset ID because get_hda_or_ldda
# only works for encoded datasets.
dataset_id = trans.security.encode_id( dataset_id )
dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )
@@ -452,10 +452,10 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
prefs = {}
track_type, _ = dataset.datatype.get_track_type()
track_data_provider = trans.app.data_provider_registry.get_data_provider( trans,
original_dataset=dataset,
track_data_provider = trans.app.data_provider_registry.get_data_provider( trans,
original_dataset=dataset,
source='data' )
return {
"track_type": track_type,
"name": track_dict['name'],
@@ -467,7 +467,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
"tool": get_tool_def( trans, dataset ),
"tool_state": track_dict.get( 'tool_state', {} )
}
def pack_collection( collection_dict ):
drawables = []
for drawable_dict in collection_dict[ 'drawables' ]:
@@ -482,10 +482,10 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
'prefs': collection_dict.get( 'prefs', [] ),
'filters': collection_dict.get( 'filters', {} )
}
def encode_dbkey( dbkey ):
"""
Encodes dbkey as needed. For now, prepends user's public name
"""
Encodes dbkey as needed. For now, prepends user's public name
to custom dbkey keys.
"""
encoded_dbkey = dbkey
@@ -493,7 +493,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
if 'dbkeys' in user.preferences and dbkey in user.preferences[ 'dbkeys' ]:
encoded_dbkey = "%s:%s" % ( user.username, dbkey )
return encoded_dbkey
# Set tracks.
tracks = []
if 'tracks' in latest_revision.config:
@@ -506,12 +506,12 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
tracks.append( pack_track( drawable_dict ) )
else:
tracks.append( pack_collection( drawable_dict ) )
config = { "title": visualization.title,
config = { "title": visualization.title,
"vis_id": trans.security.encode_id( visualization.id ),
"tracks": tracks,
"bookmarks": bookmarks,
"chrom": "",
"tracks": tracks,
"bookmarks": bookmarks,
"chrom": "",
"dbkey": encode_dbkey( visualization.dbkey ) }
if 'viewport' in latest_revision.config:
@@ -522,7 +522,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
config = latest_revision.config
return config
def get_new_track_config( self, trans, dataset ):
"""
Returns track configuration dict for a dataset.
@@ -530,13 +530,13 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
# Get data provider.
track_type, _ = dataset.datatype.get_track_type()
track_data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset )
if isinstance( dataset, trans.app.model.HistoryDatasetAssociation ):
hda_ldda = "hda"
elif isinstance( dataset, trans.app.model.LibraryDatasetDatasetAssociation ):
hda_ldda = "ldda"
# Get track definition.
return {
"track_type": track_type,
@@ -548,16 +548,16 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
"tool": get_tool_def( trans, dataset ),
"tool_state": {}
}
def get_hda_or_ldda( self, trans, hda_ldda, dataset_id ):
""" Returns either HDA or LDDA for hda/ldda and id combination. """
if hda_ldda == "hda":
return self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )
else:
return self.get_library_dataset_dataset_association( trans, dataset_id )
# -- Helper functions --
def _create_visualization( self, trans, title, type, dbkey=None, slug=None, annotation=None, save=True ):
""" Create visualization but not first revision. Returns Visualization object. """
user = trans.get_user()
@@ -573,7 +573,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
if title_err or slug_err:
return { 'title_err': title_err, 'slug_err': slug_err }
# Create visualization
visualization = trans.model.Visualization( user=user, title=title, dbkey=dbkey, type=type )
@@ -616,13 +616,13 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
if isinstance( dataset.datatype, ChromatinInteractions ):
source = 'data'
data_provider = trans.app.data_provider_registry.get_data_provider( trans,
original_dataset=dataset,
data_provider = trans.app.data_provider_registry.get_data_provider( trans,
original_dataset=dataset,
source=source )
# HACK: pass in additional params which are used for only some
# types of data providers; level, cutoffs used for summary tree,
# HACK: pass in additional params which are used for only some
# types of data providers; level, cutoffs used for summary tree,
# num_samples for BBI, and interchromosomal used for chromatin interactions.
rval = data_provider.get_genome_data( chroms_info,
rval = data_provider.get_genome_data( chroms_info,
level=4, detail_cutoff=0, draw_cutoff=0,
num_samples=150,
interchromosomal=True )
@@ -635,7 +635,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
Returns highest priority message from a list of messages.
"""
return_message = None
# For now, priority is: job error (dict), no converter, pending.
for message in message_list:
if message is not None:
@@ -714,14 +714,14 @@ class UsesHistoryMixin( SharableItemSecurityMixin ):
def get_hda_state_counts( self, trans, history, include_deleted=False, include_hidden=False ):
"""
Returns a dictionary with state counts for history's HDAs. Key is a
Returns a dictionary with state counts for history's HDAs. Key is a
dataset state, value is the number of states in that count.
"""
# Build query to get (state, count) pairs.
cols_to_select = [ trans.app.model.Dataset.table.c.state, func.count( '*' ) ]
cols_to_select = [ trans.app.model.Dataset.table.c.state, func.count( '*' ) ]
from_obj = trans.app.model.HistoryDatasetAssociation.table.join( trans.app.model.Dataset.table )
conditions = [ trans.app.model.HistoryDatasetAssociation.table.c.history_id == history.id ]
if not include_deleted:
# Only count datasets that have not been deleted.
@@ -729,7 +729,7 @@ class UsesHistoryMixin( SharableItemSecurityMixin ):
if not include_hidden:
# Only count datasets that are visible.
conditions.append( trans.app.model.HistoryDatasetAssociation.table.c.visible == True )
group_by = trans.app.model.Dataset.table.c.state
query = select( columns=cols_to_select,
from_obj=from_obj,
@@ -740,7 +740,7 @@ class UsesHistoryMixin( SharableItemSecurityMixin ):
state_count_dict = {}
for k, state in trans.app.model.Dataset.states.items():
state_count_dict[ state ] = 0
# Process query results, adding to count dict.
for row in trans.sa_session.execute( query ):
state, count = row
@@ -1501,13 +1501,13 @@ class UsesFormDefinitionsMixin:
class SharableMixin:
""" Mixin for a controller that manages an item that can be shared. """
# -- Implemented methods. --
def _is_valid_slug( self, slug ):
""" Returns true if slug is valid. """
return _is_valid_slug( slug )
@web.expose
@web.require_login( "share Galaxy items" )
def set_public_username( self, trans, id, username, **kwargs ):
@@ -1526,7 +1526,7 @@ class SharableMixin:
item = self.get_item( trans, id )
if item:
# Only update slug if slug is not already in use.
if trans.sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug, importable=True ).count() == 0:
if trans.sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug, importable=True ).count() == 0:
item.slug = new_slug
trans.sa_session.flush()
@@ -1534,15 +1534,15 @@ class SharableMixin:
def _make_item_accessible( self, sa_session, item ):
""" Makes item accessible--viewable and importable--and sets item's slug.
Does not flush/commit changes, however. Item must have name, user,
Does not flush/commit changes, however. Item must have name, user,
importable, and slug attributes. """
item.importable = True
self.create_item_slug( sa_session, item )
def create_item_slug( self, sa_session, item ):
""" Create/set item slug. Slug is unique among user's importable items
for item's class. Returns true if item's slug was set/changed; false
otherwise.
""" Create/set item slug. Slug is unique among user's importable items
for item's class. Returns true if item's slug was set/changed; false
otherwise.
"""
cur_slug = item.slug
@@ -1563,7 +1563,7 @@ class SharableMixin:
else:
slug_base = cur_slug
# Using slug base, find a slug that is not taken. If slug is taken,
# Using slug base, find a slug that is not taken. If slug is taken,
# add integer to end.
new_slug = slug_base
count = 1
@@ -1572,13 +1572,13 @@ class SharableMixin:
# handle numerous items with the same name gracefully.
new_slug = '%s-%i' % ( slug_base, count )
count += 1
# Set slug and return.
item.slug = new_slug
return item.slug == cur_slug
# -- Abstract methods. --
# -- Abstract methods. --
@web.expose
@web.require_login( "share Galaxy items" )
def sharing( self, trans, id, **kwargs ):
@@ -1595,19 +1595,19 @@ class SharableMixin:
def display_by_username_and_slug( self, trans, username, slug ):
""" Display item by username and slug. """
raise "Unimplemented Method"
@web.json
@web.require_login( "get item name and link" )
def get_name_and_link_async( self, trans, id=None ):
""" Returns item's name and link. """
raise "Unimplemented Method"
@web.expose
@web.require_login("get item content asynchronously")
def get_item_content_async( self, trans, id ):
""" Returns item content in HTML format. """
raise "Unimplemented Method"
def get_item( self, trans, id ):
""" Return item based on id. """
raise "Unimplemented Method"