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Merged in nsoranzo/galaxy-central (pull request #551)

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Small bugs, doc and pylint fixes.
This commit is contained in:
John Chilton
2014-11-10 11:04:02 -05:00
parent b60de7d63f 5cd46dc4dd
commit b391883060
9 changed files with 247 additions and 227 deletions
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lib/galaxy/util/bunch.py
+6
View File
@@ -17,6 +17,12 @@ class Bunch( object ):
def items(self):
return self.__dict__.items()
def keys(self):
return self.__dict__.keys()
def values(self):
return self.__dict__.values()
def __str__(self):
return '%s' % self.__dict__
lib/galaxy/web/base/controller.py
+37 -49
View File
@@ -13,7 +13,6 @@ from sqlalchemy import func, and_, select
from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
from paste.httpexceptions import HTTPNotImplemented, HTTPRequestRangeNotSatisfiable
from galaxy import exceptions
from galaxy.exceptions import ItemAccessibilityException, ItemDeletionException, ItemOwnershipException
from galaxy.exceptions import MessageException
@@ -27,7 +26,7 @@ from galaxy.web import error, url_for
from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField
from galaxy.web.form_builder import build_select_field, HistoryField, PasswordField, WorkflowField, WorkflowMappingField
from galaxy.workflow.modules import module_factory, WorkflowModuleInjector, MissingToolException
from galaxy.model.orm import eagerload, eagerload_all, desc, not_
from galaxy.model.orm import eagerload, eagerload_all, desc
from galaxy.security.validate_user_input import validate_publicname
from galaxy.util.sanitize_html import sanitize_html
from galaxy.model.item_attrs import Dictifiable, UsesAnnotations
@@ -85,7 +84,7 @@ class BaseController( object ):
Convenience method to get a model object with the specified checks.
"""
return managers_base.get_object( trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted )
# this should be here - but catching errors from sharable item controllers that *should* have SharableItemMixin
# but *don't* then becomes difficult
#def security_check( self, trans, item, check_ownership=False, check_accessible=False ):
@@ -322,7 +321,7 @@ class UsesHistoryMixin( SharableItemSecurityMixin ):
# Initialize count dict with all states.
state_count_dict = {}
for k, state in trans.app.model.Dataset.states.items():
for state in trans.app.model.Dataset.states.values():
state_count_dict[ state ] = 0
# Process query results, adding to count dict.
@@ -370,7 +369,7 @@ class UsesHistoryMixin( SharableItemSecurityMixin ):
# init counts, ids for each state
state_counts = {}
state_ids = {}
for key, state in trans.app.model.Dataset.states.items():
for state in trans.app.model.Dataset.states.values():
state_counts[ state ] = 0
state_ids[ state ] = []
@@ -566,7 +565,7 @@ class UsesHistoryDatasetAssociationMixin:
# DEPRECATION: We still support unencoded ids for backward compatibility
try:
dataset_id = int( dataset_id )
except ValueError, v_err:
except ValueError:
raise HTTPBadRequest( "Invalid dataset id: %s." % str( dataset_id ) )
try:
@@ -589,7 +588,7 @@ class UsesHistoryDatasetAssociationMixin:
error( "You are not allowed to access this dataset" )
if check_state and data.state == trans.model.Dataset.states.UPLOAD:
return trans.show_error_message( "Please wait until this dataset finishes uploading "
return trans.show_error_message( "Please wait until this dataset finishes uploading "
+ "before attempting to view it." )
return data
@@ -651,7 +650,7 @@ class UsesHistoryDatasetAssociationMixin:
check_ownership=check_ownership,
check_accessible=check_accessible,
check_state=check_state )
except Exception, exception:
except Exception:
pass
hdas.append( hda )
return hdas
@@ -711,7 +710,7 @@ class UsesHistoryDatasetAssociationMixin:
# ---- return here if deleted AND purged OR can't access
purged = ( hda.purged or hda.dataset.purged )
if ( hda.deleted and purged ):
if hda.deleted and purged:
#TODO: to_dict should really go AFTER this - only summary data
return trans.security.encode_dict_ids( hda_dict )
@@ -747,10 +746,6 @@ class UsesHistoryDatasetAssociationMixin:
#TODO: it may also be wiser to remove from here and add as API call that loads the visualizations
# when the visualizations button is clicked (instead of preloading/pre-checking)
# ---- return here if deleted
if hda.deleted and not purged:
return trans.security.encode_dict_ids( hda_dict )
return trans.security.encode_dict_ids( hda_dict )
def get_inaccessible_hda_dict( self, trans, hda ):
@@ -892,7 +887,8 @@ class UsesLibraryMixinItems( SharableItemSecurityMixin ):
# or ( trans.app.security_agent.can_add_library_item( user.all_roles(), item ) ) )
def can_current_user_add_to_library_item( self, trans, item ):
if not trans.user: return False
if not trans.user:
return False
return ( ( trans.user_is_admin() )
or ( trans.app.security_agent.can_add_library_item( trans.get_current_user_roles(), item ) ) )
@@ -1411,11 +1407,6 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix
# Get data provider.
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": dataset.datatype.track_type,
@@ -1705,7 +1696,7 @@ class UsesStoredWorkflowMixin( SharableItemSecurityMixin, UsesAnnotations ):
data['name'] = workflow.name
data['annotation'] = annotation_str
if workflow.uuid is not None:
data['uuid'] = str(workflow.uuid)
data['uuid'] = str(workflow.uuid)
data['steps'] = {}
# For each step, rebuild the form and encode the state
for step in workflow.steps:
@@ -1743,18 +1734,16 @@ class UsesStoredWorkflowMixin( SharableItemSecurityMixin, UsesAnnotations ):
step_dict['inputs'] = module.get_runtime_input_dicts( annotation_str )
# User outputs
step_dict['user_outputs'] = []
"""
module_outputs = module.get_data_outputs()
step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step )
for output in step_outputs:
name = output.output_name
annotation = ""
for module_output in module_outputs:
if module_output.get( 'name', None ) == name:
output_type = module_output.get( 'extension', '' )
break
data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type }
"""
# module_outputs = module.get_data_outputs()
# step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step )
# for output in step_outputs:
# name = output.output_name
# annotation = ""
# for module_output in module_outputs:
# if module_output.get( 'name', None ) == name:
# output_type = module_output.get( 'extension', '' )
# break
# data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type }
# All step outputs
step_dict['outputs'] = []
@@ -2139,7 +2128,7 @@ class UsesFormDefinitionsMixin:
# We need the type of each template field widget
widgets = item.get_template_widgets( trans )
# The list of widgets may include an AddressField which we need to save if it is new
for index, widget_dict in enumerate( widgets ):
for widget_dict in widgets:
widget = widget_dict[ 'widget' ]
if isinstance( widget, AddressField ):
value = util.restore_text( params.get( widget.name, '' ) )
@@ -2220,7 +2209,7 @@ class UsesFormDefinitionsMixin:
trans.sa_session.flush()
info_association = sra.run
else:
info_association = assoc.run
info_association = assoc.run
else:
info_association = None
if info_association:
@@ -2364,7 +2353,7 @@ class UsesFormDefinitionsMixin:
def widget_fields_have_contents( self, widgets ):
# Return True if any of the fields in widgets contain contents, widgets is a list of dictionaries that looks something like:
# [{'widget': <galaxy.web.form_builder.TextField object at 0x10867aa10>, 'helptext': 'Field 0 help (Optional)', 'label': 'Field 0'}]
for i, field in enumerate( widgets ):
for field in widgets:
if ( isinstance( field[ 'widget' ], TextArea ) or isinstance( field[ 'widget' ], TextField ) ) and field[ 'widget' ].value:
return True
if isinstance( field[ 'widget' ], SelectField ) and field[ 'widget' ].options:
@@ -2385,7 +2374,7 @@ class UsesFormDefinitionsMixin:
def clean_field_contents( self, widgets, **kwd ):
field_contents = {}
for index, widget_dict in enumerate( widgets ):
for widget_dict in widgets:
widget = widget_dict[ 'widget' ]
value = kwd.get( widget.name, '' )
if isinstance( widget, CheckboxField ):
@@ -2434,7 +2423,7 @@ class UsesFormDefinitionsMixin:
'''
params = util.Params( kwd )
values = {}
for index, field in enumerate( form_definition.fields ):
for field in form_definition.fields:
field_type = field[ 'type' ]
field_name = field[ 'name' ]
input_value = params.get( field_name, '' )
@@ -2586,7 +2575,7 @@ class SharableMixin:
if message:
return trans.fill_template( '/sharing_base.mako', item=self.get_item( trans, id ), message=message, status='error' )
user.username = username
trans.sa_session.flush
trans.sa_session.flush()
return self.sharing( trans, id, **kwargs )
@web.expose
@@ -2648,34 +2637,34 @@ class SharableMixin:
@web.require_login( "share Galaxy items" )
def sharing( self, trans, id, **kwargs ):
""" Handle item sharing. """
raise "Unimplemented Method"
raise NotImplementedError()
@web.expose
@web.require_login( "share Galaxy items" )
def share( self, trans, id=None, email="", **kwd ):
""" Handle sharing an item with a particular user. """
raise "Unimplemented Method"
raise NotImplementedError()
@web.expose
def display_by_username_and_slug( self, trans, username, slug ):
""" Display item by username and slug. """
raise "Unimplemented Method"
raise NotImplementedError()
@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"
raise NotImplementedError()
@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"
raise NotImplementedError()
def get_item( self, trans, id ):
""" Return item based on id. """
raise "Unimplemented Method"
raise NotImplementedError()
class UsesQuotaMixin( object ):
@@ -2692,7 +2681,7 @@ class UsesTagsMixin( SharableItemSecurityMixin ):
def _get_user_tags( self, trans, item_class_name, id ):
user = trans.user
tagged_item = self._get_tagged_item( trans, item_class_name, id )
return [ tag for tag in tagged_item.tags if ( tag.user == user ) ]
return [ tag for tag in tagged_item.tags if tag.user == user ]
def _get_tagged_item( self, trans, item_class_name, id, check_ownership=True ):
tagged_item = self.get_object( trans, id, item_class_name, check_ownership=check_ownership, check_accessible=True )
@@ -2756,7 +2745,6 @@ class UsesTagsMixin( SharableItemSecurityMixin ):
return sorted( tags )
class UsesExtendedMetadataMixin( SharableItemSecurityMixin ):
""" Mixin for getting and setting item extended metadata. """
@@ -2846,10 +2834,10 @@ class UsesExtendedMetadataMixin( SharableItemSecurityMixin ):
yield prefix, ("%s" % (meta)).encode("utf8", errors='replace')
"""
Deprecated: `BaseController` used to be available under the name `Root`
"""
class ControllerUnavailable( Exception ):
"""
Deprecated: `BaseController` used to be available under the name `Root`
"""
pass
## ---- Utility methods -------------------------------------------------------
lib/galaxy/web/framework/webapp.py
+2 -7
View File
@@ -504,9 +504,9 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
for char in filter( lambda x: x not in string.ascii_lowercase + string.digits + '-', username ):
username = username.replace( char, '-' )
# Find a unique username - user can change it later
if ( self.sa_session.query( self.app.model.User ).filter_by( username=username ).first() ):
if self.sa_session.query( self.app.model.User ).filter_by( username=username ).first():
i = 1
while ( self.sa_session.query( self.app.model.User ).filter_by( username=(username + '-' + str(i) ) ).first() ):
while self.sa_session.query( self.app.model.User ).filter_by( username=(username + '-' + str(i) ) ).first():
i += 1
username += '-' + str(i)
user.username = username
@@ -701,11 +701,6 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
def template_context( self ):
return dict()
def make_form_data( self, name, **kwargs ):
rval = self.template_context[name] = FormData()
rval.values.update( kwargs )
return rval
def set_message( self, message, type=None ):
"""
Convenience method for setting the 'message' and 'message_type'
lib/galaxy/webapps/demo_sequencer/framework/__init__.py
+1 -4
View File
@@ -116,10 +116,7 @@ class DemoWebTransaction( galaxy.web.framework.base.DefaultWebTransaction ):
@galaxy.web.framework.base.lazy_property
def template_context( self ):
return dict()
def make_form_data( self, name, **kwargs ):
rval = self.template_context[name] = FormData()
rval.values.update( kwargs )
return rval
def set_message( self, message, type=None ):
"""
Convenience method for setting the 'message' and 'message_type'
lib/galaxy/webapps/galaxy/api/histories.py
+1 -1
View File
@@ -92,7 +92,7 @@ class HistoriesController( BaseAPIController, UsesHistoryMixin, UsesTagsMixin,
:rtype: dictionary
:returns: detailed history information from
:func:`galaxy.web.base.controller.UsesHistoryDatasetAssociationMixin.get_history_dict`
:func:`galaxy.web.base.controller.UsesHistoryMixin.get_history_dict`
"""
history_id = id
deleted = string_as_bool( deleted )
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+115 -115
View File
@@ -480,7 +480,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
tool.update_state( trans, tool.inputs_by_page[ 0 ], state.inputs, kwd )
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.iteritems():
for input in tool.inputs.itervalues():
if input.type == "upload_dataset":
dataset_upload_inputs.append( input )
library_bunch = upload_common.handle_library_params( trans, {}, trans.security.encode_id( folder.id ) )
@@ -536,7 +536,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
* POST /api/libraries/datasets/download/{format}
Downloads requested datasets (identified by encoded IDs) in requested format.
example: ``GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828``
example: ``GET localhost:8080/api/libraries/datasets/download/tbz?ld_ids%255B%255D=a0d84b45643a2678&ld_ids%255B%255D=fe38c84dcd46c828``
.. note:: supported format values are: 'zip', 'tgz', 'tbz', 'uncompressed'
@@ -554,7 +554,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
datasets_to_download = kwd.get( 'ld_ids%5B%5D', None )
if datasets_to_download is None:
datasets_to_download = kwd.get( 'ld_ids', None )
if ( datasets_to_download is not None ):
if datasets_to_download is not None:
datasets_to_download = util.listify( datasets_to_download )
for dataset_id in datasets_to_download:
try:
@@ -570,128 +570,128 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
raise exceptions.RequestParameterMissingException( 'Request has to contain a list of dataset ids to download.' )
if format in [ 'zip', 'tgz', 'tbz' ]:
# error = False
killme = string.punctuation + string.whitespace
trantab = string.maketrans( killme, '_'*len( killme ) )
try:
outext = 'zip'
if format == 'zip':
# Can't use mkstemp - the file must not exist first
tmpd = tempfile.mkdtemp()
util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid )
tmpf = os.path.join( tmpd, 'library_download.' + format )
if trans.app.config.upstream_gzip:
archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True )
else:
archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
archive.add = lambda x, y: archive.write( x, y.encode( 'CP437' ) )
elif format == 'tgz':
if trans.app.config.upstream_gzip:
archive = StreamBall( 'w|' )
outext = 'tar'
else:
archive = StreamBall( 'w|gz' )
outext = 'tgz'
elif format == 'tbz':
archive = StreamBall( 'w|bz2' )
outext = 'tbz2'
except ( OSError, zipfile.BadZipfile ):
log.exception( "Unable to create archive for download" )
raise exceptions.InternalServerError( "Unable to create archive for download." )
except Exception:
log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[ 0 ] )
raise exceptions.InternalServerError( "Unable to create archive for download." )
composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
seen = []
for ld in library_datasets:
ldda = ld.library_dataset_dataset_association
ext = ldda.extension
is_composite = ext in composite_extensions
path = ""
parent_folder = ldda.library_dataset.folder
while parent_folder is not None:
# Exclude the now-hidden "root folder"
if parent_folder.parent is None:
path = os.path.join( parent_folder.library_root[ 0 ].name, path )
break
path = os.path.join( parent_folder.name, path )
parent_folder = parent_folder.parent
path += ldda.name
while path in seen:
path += '_'
seen.append( path )
zpath = os.path.split(path)[ -1 ] # comes as base_name/fname
outfname, zpathext = os.path.splitext( zpath )
# error = False
killme = string.punctuation + string.whitespace
trantab = string.maketrans( killme, '_'*len( killme ) )
try:
outext = 'zip'
if format == 'zip':
# Can't use mkstemp - the file must not exist first
tmpd = tempfile.mkdtemp()
util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid )
tmpf = os.path.join( tmpd, 'library_download.' + format )
if trans.app.config.upstream_gzip:
archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True )
else:
archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
archive.add = lambda x, y: archive.write( x, y.encode( 'CP437' ) )
elif format == 'tgz':
if trans.app.config.upstream_gzip:
archive = StreamBall( 'w|' )
outext = 'tar'
else:
archive = StreamBall( 'w|gz' )
outext = 'tgz'
elif format == 'tbz':
archive = StreamBall( 'w|bz2' )
outext = 'tbz2'
except ( OSError, zipfile.BadZipfile ):
log.exception( "Unable to create archive for download" )
raise exceptions.InternalServerError( "Unable to create archive for download." )
except Exception:
log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[ 0 ] )
raise exceptions.InternalServerError( "Unable to create archive for download." )
composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
seen = []
for ld in library_datasets:
ldda = ld.library_dataset_dataset_association
ext = ldda.extension
is_composite = ext in composite_extensions
path = ""
parent_folder = ldda.library_dataset.folder
while parent_folder is not None:
# Exclude the now-hidden "root folder"
if parent_folder.parent is None:
path = os.path.join( parent_folder.library_root[ 0 ].name, path )
break
path = os.path.join( parent_folder.name, path )
parent_folder = parent_folder.parent
path += ldda.name
while path in seen:
path += '_'
seen.append( path )
zpath = os.path.split(path)[ -1 ] # comes as base_name/fname
outfname, zpathext = os.path.splitext( zpath )
if is_composite: # need to add all the components from the extra_files_path to the zip
if zpathext == '':
zpath = '%s.html' % zpath # fake the real nature of the html file
if is_composite: # need to add all the components from the extra_files_path to the zip
if zpathext == '':
zpath = '%s.html' % zpath # fake the real nature of the html file
try:
if format == 'zip':
archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set
else:
archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set
except IOError:
log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name )
raise exceptions.InternalServerError( "Unable to create archive for download." )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
raise exceptions.ObjectNotFound( "Requested dataset not found. " )
except Exception, e:
log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name )
raise exceptions.InternalServerError( "Unable to add composite parent to temporary library download archive. " + str( e ) )
flist = glob.glob(os.path.join(ldda.dataset.extra_files_path, '*.*')) # glob returns full paths
for fpath in flist:
efp, fname = os.path.split(fpath)
if fname > '':
fname = fname.translate(trantab)
try:
if format == 'zip':
archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set
archive.add( fpath, fname )
else:
archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set
archive.add( fpath, fname, check_file=True )
except IOError:
log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name )
log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname) )
raise exceptions.InternalServerError( "Unable to create archive for download." )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
raise exceptions.ObjectNotFound( "Requested dataset not found. " )
except Exception, e:
log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name )
raise exceptions.InternalServerError( "Unable to add composite parent to temporary library download archive. " + str( e ) )
flist = glob.glob(os.path.join(ldda.dataset.extra_files_path, '*.*')) # glob returns full paths
for fpath in flist:
efp, fname = os.path.split(fpath)
if fname > '':
fname = fname.translate(trantab)
try:
if format == 'zip':
archive.add( fpath, fname )
else:
archive.add( fpath, fname, check_file=True )
except IOError:
log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname) )
raise exceptions.InternalServerError( "Unable to create archive for download." )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % fpath )
raise exceptions.ObjectNotFound( "Requested dataset not found." )
except Exception, e:
log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname ) )
raise exceptions.InternalServerError( "Unable to add dataset to temporary library download archive . " + str( e ) )
else: # simple case
try:
if format == 'zip':
archive.add( ldda.dataset.file_name, path )
else:
archive.add( ldda.dataset.file_name, path, check_file=True )
except IOError:
log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name )
raise exceptions.InternalServerError( "Unable to create archive for download" )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
log.exception( "Requested dataset %s does not exist on the host." % fpath )
raise exceptions.ObjectNotFound( "Requested dataset not found." )
except Exception, e:
log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname ) )
raise exceptions.InternalServerError( "Unknown error. " + str( e ) )
lname = 'selected_dataset'
fname = lname.replace( ' ', '_' ) + '_files'
if format == 'zip':
archive.close()
trans.response.set_content_type( "application/octet-stream" )
trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % ( fname, outext )
archive = util.streamball.ZipBall( tmpf, tmpd )
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream
else:
trans.response.set_content_type( "application/x-tar" )
trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % ( fname, outext )
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream
raise exceptions.InternalServerError( "Unable to add dataset to temporary library download archive . " + str( e ) )
else: # simple case
try:
if format == 'zip':
archive.add( ldda.dataset.file_name, path )
else:
archive.add( ldda.dataset.file_name, path, check_file=True )
except IOError:
log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name )
raise exceptions.InternalServerError( "Unable to create archive for download" )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
raise exceptions.ObjectNotFound( "Requested dataset not found." )
except Exception, e:
log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname ) )
raise exceptions.InternalServerError( "Unknown error. " + str( e ) )
lname = 'selected_dataset'
fname = lname.replace( ' ', '_' ) + '_files'
if format == 'zip':
archive.close()
trans.response.set_content_type( "application/octet-stream" )
trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % ( fname, outext )
archive = util.streamball.ZipBall( tmpf, tmpd )
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream
else:
trans.response.set_content_type( "application/x-tar" )
trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % ( fname, outext )
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream
elif format == 'uncompressed':
if len(library_datasets) != 1:
raise exceptions.RequestParameterInvalidException( "You can download only one uncompressed file at once." )
lib/galaxy/webapps/galaxy/api/library_contents.py
+10 -8
View File
@@ -146,17 +146,21 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
the HDA's encoded id in ``from_hda_id`` (and optionally ``ldda_message``).
:type library_id: str
:param library_id: encoded id string of the library that contains this item
:param library_id: encoded id string of the library where to create the new item
:type payload: dict
:param payload: dictionary structure containing:
* folder_id: the parent folder of the new item
* create_type: the type of item to create ('file' or 'folder')
* create_type: the type of item to create ('file', 'folder' or 'collection')
* from_hda_id: (optional) the id of an accessible HDA to copy into the
library
* ldda_message: (optional) the new message attribute of the LDDA created
* extended_metadata: (optional) dub-dictionary containing any extended
metadata to associate with the item
* link_data_only: (optional) either 'copy_files' (default) or 'link_to_files'
* upload_option: (optional) one of 'upload_file' (default), 'upload_directory' or 'upload_paths'
* server_dir: (optional) only if upload_option is 'upload_directory'
* filesystem_paths: (optional) only if upload_option is 'upload_paths' and the user is an admin
:rtype: dict
:returns: a dictionary containing the id, name,
@@ -217,11 +221,9 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
return output
else:
rval = []
for k, v in output.items():
for v in output.values():
if ex_meta_payload is not None:
"""
If there is extended metadata, store it, attach it to the dataset, and index it
"""
# If there is extended metadata, store it, attach it to the dataset, and index it
ex_meta = ExtendedMetadata(ex_meta_payload)
trans.sa_session.add( ex_meta )
v.extended_metadata = ex_meta
@@ -343,9 +345,9 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
trans.sa_session.flush()
def __decode_library_content_id( self, trans, content_id ):
if ( len( content_id ) % 16 == 0 ):
if len( content_id ) % 16 == 0:
return 'LibraryDataset', content_id
elif ( content_id.startswith( 'F' ) ):
elif content_id.startswith( 'F' ):
return 'LibraryFolder', content_id[ 1: ]
else:
raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) )
lib/galaxy/webapps/galaxy/controllers/dataset.py
+36 -42
View File
@@ -1,8 +1,6 @@
import logging
import os
import tempfile
import urllib
import zipfile
from galaxy import datatypes, eggs, model, util, web
from galaxy.datatypes.display_applications.util import decode_dataset_user, encode_dataset_user
@@ -43,8 +41,8 @@ class HistoryDatasetAssociationListGrid( grids.Grid ):
accepted_filter_labels_and_vals = { "Active" : "False", "Deleted" : "True", "All": "All" }
accepted_filters = []
for label, val in accepted_filter_labels_and_vals.items():
args = { self.key: val }
accepted_filters.append( grids.GridColumnFilter( label, args) )
args = { self.key: val }
accepted_filters.append( grids.GridColumnFilter( label, args) )
return accepted_filters
# Grid definition
@@ -147,7 +145,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, Use
trans.response.set_content_type( 'text/plain' )
exit_code = ""
try:
job = self._get_job_for_dataset( dataset_id )
job = self._get_job_for_dataset( trans, dataset_id )
exit_code = job.exit_code
except:
exit_code = "Invalid dataset ID or you are not allowed to access this dataset"
@@ -323,40 +321,38 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, Use
if params.annotation:
annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' )
self.add_item_annotation( trans.sa_session, trans.get_user(), data, annotation )
"""
# This block on controller code is inactive until the 'extended_metadata' edit box is added back into the UI
# Add or delete extended metadata
if params.extended_metadata:
em_string = params.extended_metadata
if len(em_string):
em_payload = None
try:
em_payload = loads(em_string)
except Exception, e:
message = 'Invalid JSON input'
error = True
if em_payload is not None:
if data is not None:
ex_obj = self.get_item_extended_metadata_obj(trans, data)
if ex_obj is not None:
self.unset_item_extended_metadata_obj(trans, data)
self.delete_extended_metadata(trans, ex_obj)
ex_obj = self.create_extended_metadata(trans, em_payload)
self.set_item_extended_metadata_obj(trans, data, ex_obj)
message = "Updated Extended metadata '%s'." % data.name
status = 'done'
else:
message = "data not found"
error = True
else:
if data is not None:
ex_obj = self.get_item_extended_metadata_obj(trans, data)
if ex_obj is not None:
self.unset_item_extended_metadata_obj(trans, data)
self.delete_extended_metadata(trans, ex_obj)
message = "Deleted Extended metadata '%s'." % data.name
status = 'done'
"""
# if params.extended_metadata:
# em_string = params.extended_metadata
# if len(em_string):
# em_payload = None
# try:
# em_payload = loads(em_string)
# except Exception, e:
# message = 'Invalid JSON input'
# error = True
# if em_payload is not None:
# if data is not None:
# ex_obj = self.get_item_extended_metadata_obj(trans, data)
# if ex_obj is not None:
# self.unset_item_extended_metadata_obj(trans, data)
# self.delete_extended_metadata(trans, ex_obj)
# ex_obj = self.create_extended_metadata(trans, em_payload)
# self.set_item_extended_metadata_obj(trans, data, ex_obj)
# message = "Updated Extended metadata '%s'." % data.name
# status = 'done'
# else:
# message = "data not found"
# error = True
# else:
# if data is not None:
# ex_obj = self.get_item_extended_metadata_obj(trans, data)
# if ex_obj is not None:
# self.unset_item_extended_metadata_obj(trans, data)
# self.delete_extended_metadata(trans, ex_obj)
# message = "Deleted Extended metadata '%s'." % data.name
# status = 'done'
# If setting metadata previously failed and all required elements have now been set, clear the failed state.
if data._state == trans.model.Dataset.states.FAILED_METADATA and not data.missing_meta():
@@ -954,13 +950,11 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, Use
has_parameter_errors = False
inherit_chain = hda.source_dataset_chain
if inherit_chain:
job_dataset_association, dataset_association_container_name = inherit_chain[-1]
job_dataset_association = inherit_chain[-1][0]
else:
job_dataset_association = hda
if job_dataset_association.creating_job_associations:
for assoc in job_dataset_association.creating_job_associations:
job = assoc.job
break
job = job_dataset_association.creating_job_associations[0].job
if job:
# Get the tool object
try:
@@ -1024,7 +1018,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, Use
trans.sa_session.flush()
target_history_ids.append( new_history.id )
if user:
target_histories = [ hist for hist in map( trans.sa_session.query( trans.app.model.History ).get, target_history_ids ) if ( hist is not None and hist.user == user )]
target_histories = [ hist for hist in map( trans.sa_session.query( trans.app.model.History ).get, target_history_ids ) if hist is not None and hist.user == user ]
else:
target_histories = [ history ]
if len( target_histories ) != len( target_history_ids ):
lib/galaxy/webapps/galaxy/controllers/library_common.py
+39 -1
View File
@@ -162,6 +162,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
default_action=default_action,
message=util.sanitize_text( message ),
status=status ) )
@web.expose
def library_info( self, trans, cntrller, **kwd ):
params = util.Params( kwd )
@@ -222,6 +223,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
inherited=inherited,
message=message,
status=status )
@web.expose
def library_permissions( self, trans, cntrller, **kwd ):
params = util.Params( kwd )
@@ -269,6 +271,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=message,
status=status )
@web.expose
def create_folder( self, trans, cntrller, parent_id, library_id, **kwd ):
params = util.Params( kwd )
@@ -346,6 +349,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=message,
status=status )
@web.expose
def folder_info( self, trans, cntrller, id, library_id, **kwd ):
params = util.Params( kwd )
@@ -403,6 +407,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
inherited=inherited,
message=message,
status=status )
@web.expose
def folder_permissions( self, trans, cntrller, id, library_id, **kwd ):
params = util.Params( kwd )
@@ -453,6 +458,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=message,
status=status )
@web.expose
def ldda_edit_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
params = util.Params( kwd )
@@ -606,6 +612,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
inherited=inherited,
message=message,
status=status )
@web.expose
def ldda_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
params = util.Params( kwd )
@@ -655,6 +662,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
inherited=inherited,
message=message,
status=status )
@web.expose
def ldda_permissions( self, trans, cntrller, library_id, folder_id, id, **kwd ):
params = util.Params( kwd )
@@ -793,6 +801,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=message,
status=status )
@web.expose
def upload_library_dataset( self, trans, cntrller, library_id, folder_id, **kwd ):
params = util.Params( kwd )
@@ -1042,6 +1051,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
ldda_message=ldda_message,
message=message,
status=status )
def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ):
# Set up the traditional tool state/params
tool_id = 'upload1'
@@ -1132,6 +1142,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
trans.sa_session.add( job )
trans.sa_session.flush()
return output
def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ):
link_data_only = params.get( 'link_data_only', 'copy_files' )
uuid_str = params.get( 'uuid', None )
@@ -1166,6 +1177,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
trans.sa_session.add_all( ( uploaded_dataset.data, uploaded_dataset.data.dataset ) )
trans.sa_session.flush()
return uploaded_dataset
def get_server_dir_uploaded_datasets( self, trans, cntrller, params, full_dir, import_dir_desc, library_bunch, response_code, message ):
dir_response = self._get_server_dir_files(params, full_dir, import_dir_desc)
files = dir_response[0]
@@ -1176,6 +1188,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
name = os.path.basename( file )
uploaded_datasets.append( self.make_library_uploaded_dataset( trans, cntrller, params, name, file, 'server_dir', library_bunch ) )
return uploaded_datasets, 200, None
def _get_server_dir_files( self, params, full_dir, import_dir_desc ):
files = []
try:
@@ -1212,6 +1225,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
response_code = 400
return None, response_code, message
return files, None, None
def get_path_paste_uploaded_datasets( self, trans, cntrller, params, library_bunch, response_code, message ):
preserve_dirs = util.string_as_bool( params.get( 'preserve_dirs', False ) )
uploaded_datasets = []
@@ -1246,6 +1260,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
in_folder = None
files_and_folders.append((file_path, file, in_folder))
return files_and_folders
def _paths_list(self, params):
return [ (l.strip(), os.path.abspath(l.strip())) for l in params.filesystem_paths.splitlines() if l.strip() ]
@@ -1463,6 +1478,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
ldda_message=ldda_message,
message=message,
status=status )
def _build_roles_select_list( self, trans, cntrller, library, selected_role_ids=[] ):
# Get the list of legitimate roles to display on the upload form. If the library is public,
# all active roles are legitimate. If the library is restricted by the LIBRARY_ACCESS permission, only
@@ -1478,10 +1494,11 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
return roles_select_list
else:
return None
def _build_upload_option_select_list( self, trans, upload_option, is_admin, do_not_include_values=[] ):
# Build the upload_option select list. The do_not_include_values param can contain options that
# should not be included in the list. For example, the 'upload_directory' option should not be
# included if uploading a new version of a librar dataset.
# included if uploading a new version of a library dataset.
upload_refresh_on_change_values = []
for option_value, option_label in trans.model.LibraryDataset.upload_options:
if option_value not in do_not_include_values:
@@ -1508,6 +1525,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
continue
upload_option_select_list.add_option( option_label, option_value, selected=option_value==upload_option )
return upload_option_select_list
def _get_populated_widgets( self, folder ):
# See if we have any inherited templates.
info_association, inherited = folder.get_info_association( inherited=True )
@@ -1517,6 +1535,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
return self.populate_widgets_from_kwd( trans, widgets, **kwd )
else:
return []
@web.expose
def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ):
"""Catches the dataset id and displays file contents as directed"""
@@ -1557,6 +1576,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=util.sanitize_text( message ),
status='error' ) )
@web.expose
def library_dataset_info( self, trans, cntrller, id, library_id, **kwd ):
params = util.Params( kwd )
@@ -1606,6 +1626,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=message,
status=status )
@web.expose
def library_dataset_permissions( self, trans, cntrller, id, library_id, **kwd ):
params = util.Params( kwd )
@@ -1654,6 +1675,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=message,
status=status )
@web.expose
def make_library_item_public( self, trans, cntrller, library_id, item_type, id, **kwd ):
params = util.Params( kwd )
@@ -1696,6 +1718,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=util.sanitize_text( message ),
status=status ) )
@web.expose
def act_on_multiple_datasets( self, trans, cntrller, library_id=None, ldda_ids='', **kwd ):
# This method is called from 1 of 3 places:
@@ -2113,6 +2136,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
use_panels=use_panels,
message=message,
status=status )
@web.expose
def manage_template_inheritance( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ):
params = util.Params( kwd )
@@ -2159,6 +2183,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=util.sanitize_text( message ),
status='done' ) )
@web.expose
def move_library_item( self, trans, cntrller, item_type, item_id, source_library_id='', make_target_current=True, **kwd ):
# This method is called from one of the following places:
@@ -2374,6 +2399,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
use_panels=use_panels,
message=message,
status=status )
@web.expose
def delete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ):
# This action will handle deleting all types of library items. State is saved for libraries and
@@ -2441,6 +2467,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=message,
status=status ) )
@web.expose
def undelete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ):
# This action will handle undeleting all types of library items
@@ -2509,6 +2536,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=message,
status=status ) )
def _check_access( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ):
can_access = True
if isinstance( item, trans.model.HistoryDatasetAssociation ):
@@ -2551,6 +2579,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=util.sanitize_text( message ),
status='error' ) )
def _check_add( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ):
# Deny access if the user is not an admin and does not have the LIBRARY_ADD permission.
if not ( is_admin or trans.app.security_agent.can_add_library_item( current_user_roles, item ) ):
@@ -2566,6 +2595,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
show_deleted=show_deleted,
message=util.sanitize_text( message ),
status='error' ) )
def _check_manage( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ):
if isinstance( item, trans.model.LibraryDataset ):
# Deny access if the user is not an admin and does not have the LIBRARY_MANAGE and DATASET_MANAGE_PERMISSIONS permissions.
@@ -2594,6 +2624,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
use_panels=use_panels,
message=util.sanitize_text( message ),
status='error' ) )
def _check_modify( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ):
# Deny modification if the user is not an admin and does not have the LIBRARY_MODIFY permission.
if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
@@ -2619,6 +2650,7 @@ def active_folders( trans, folder ):
.options( eagerload_all( "actions" ) ) \
.order_by( trans.app.model.LibraryFolder.table.c.name ) \
.all()
def activatable_folders( trans, folder ):
return trans.sa_session.query( trans.app.model.LibraryFolder ) \
.filter_by( parent=folder, purged=False ) \
@@ -2685,6 +2717,7 @@ def branch_deleted( folder ):
if folder.parent:
return branch_deleted( folder.parent )
return False
def get_containing_library_from_library_dataset( trans, library_dataset ):
"""Given a library_dataset, get the containing library"""
folder = library_dataset.folder
@@ -2698,6 +2731,7 @@ def get_containing_library_from_library_dataset( trans, library_dataset ):
if library.root_folder == folder:
return library
return None
def get_comptypes( trans ):
comptypes_t = comptypes
if trans.app.config.nginx_x_archive_files_base:
@@ -2710,6 +2744,7 @@ def get_comptypes( trans ):
except:
pass
return comptypes_t
def get_sorted_accessible_library_items( trans, cntrller, items, sort_attr ):
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
if is_admin:
@@ -2723,6 +2758,7 @@ def get_sorted_accessible_library_items( trans, cntrller, items, sort_attr ):
accessible_items.append( item )
# Sort by name
return sort_by_attr( [ item for item in accessible_items ], sort_attr )
def sort_by_attr( seq, attr ):
"""
Sort the sequence of objects by object's attribute
@@ -2738,6 +2774,7 @@ def sort_by_attr( seq, attr ):
intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq )
intermed.sort()
return map( operator.getitem, intermed, ( -1, ) * len( intermed ) )
def lucene_search( trans, cntrller, search_term, search_url, **kwd ):
"""Return display of results from a full-text lucene search of data libraries."""
params = util.Params( kwd )
@@ -2749,6 +2786,7 @@ def lucene_search( trans, cntrller, search_term, search_url, **kwd ):
response.close()
lddas = [ trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id ) for ldda_id in ldda_ids ]
return status, message, get_sorted_accessible_library_items( trans, cntrller, lddas, 'name' )
def whoosh_search( trans, cntrller, search_term, **kwd ):
"""Return display of results from a full-text whoosh search of data libraries."""
params = util.Params( kwd )