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DictifiableMixin cleanup: (a) remove 'Mixin' from name and (b) rename dictify to to_dict.

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This commit is contained in:
Jeremy Goecks
2013-08-30 14:17:23 -04:00
parent efaf9936c9
commit 7421a130fd
32 changed files with 161 additions and 161 deletions
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lib/galaxy/model/__init__.py
+37 -37
View File
@@ -23,7 +23,7 @@ import galaxy.datatypes
import galaxy.datatypes.registry
import galaxy.security.passwords
from galaxy.datatypes.metadata import MetadataCollection
from galaxy.model.item_attrs import DictifiableMixin, UsesAnnotations
from galaxy.model.item_attrs import Dictifiable, UsesAnnotations
from galaxy.security import get_permitted_actions
from galaxy.util import is_multi_byte, nice_size, Params, restore_text, send_mail
from galaxy.util.bunch import Bunch
@@ -61,15 +61,15 @@ def set_datatypes_registry( d_registry ):
datatypes_registry = d_registry
class User( object, DictifiableMixin ):
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 dictify( view='collection' )
# attributes that will be accessed and returned when calling to_dict( view='collection' )
dict_collection_visible_keys = ( 'id', 'email' )
# attributes that will be accessed and returned when calling dictify( view='element' )
# 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 ):
@@ -157,7 +157,7 @@ class User( object, DictifiableMixin ):
return total
class Job( object, DictifiableMixin ):
class Job( object, Dictifiable ):
dict_collection_visible_keys = [ 'id' ]
dict_element_visible_keys = [ 'id' ]
@@ -363,8 +363,8 @@ class Job( object, DictifiableMixin ):
dataset.blurb = 'deleted'
dataset.peek = 'Job deleted'
dataset.info = 'Job output deleted by user before job completed'
def dictify( self, view='collection' ):
rval = super( Job, self ).dictify( view=view )
def to_dict( self, view='collection' ):
rval = super( Job, self ).to_dict( view=view )
rval['tool_name'] = self.tool_id
param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] )
rval['params'] = param_dict
@@ -649,7 +649,7 @@ class DeferredJob( object ):
else:
return False
class Group( object, DictifiableMixin ):
class Group( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'name' )
dict_element_visible_keys = ( 'id', 'name' )
@@ -662,7 +662,7 @@ class UserGroupAssociation( object ):
self.user = user
self.group = group
class History( object, DictifiableMixin, UsesAnnotations ):
class History( object, Dictifiable, UsesAnnotations ):
dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' )
dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged' )
@@ -780,10 +780,10 @@ class History( object, DictifiableMixin, UsesAnnotations ):
history_name = unicode(history_name, 'utf-8')
return history_name
def dictify( self, view='collection', value_mapper = None ):
def to_dict( self, view='collection', value_mapper = None ):
# Get basic value.
rval = super( History, self ).dictify( view=view, value_mapper=value_mapper )
rval = super( History, self ).to_dict( view=view, value_mapper=value_mapper )
# Add tags.
tags_str_list = []
@@ -869,7 +869,7 @@ class GroupRoleAssociation( object ):
self.group = group
self.role = role
class Role( object, DictifiableMixin ):
class Role( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'name' )
dict_element_visible_keys = ( 'id', 'name', 'description', 'type' )
private_id = None
@@ -886,19 +886,19 @@ class Role( object, DictifiableMixin ):
self.type = type
self.deleted = deleted
class UserQuotaAssociation( object, DictifiableMixin ):
class UserQuotaAssociation( object, Dictifiable ):
dict_element_visible_keys = ( 'user', )
def __init__( self, user, quota ):
self.user = user
self.quota = quota
class GroupQuotaAssociation( object, DictifiableMixin ):
class GroupQuotaAssociation( object, Dictifiable ):
dict_element_visible_keys = ( 'group', )
def __init__( self, group, quota ):
self.group = group
self.quota = quota
class Quota( object, DictifiableMixin ):
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 = ( '+', '-', '=' )
@@ -927,7 +927,7 @@ class Quota( object, DictifiableMixin ):
else:
return nice_size( self.bytes )
class DefaultQuotaAssociation( Quota, DictifiableMixin ):
class DefaultQuotaAssociation( Quota, Dictifiable ):
dict_element_visible_keys = ( 'type', )
types = Bunch(
UNREGISTERED = 'unregistered',
@@ -1508,7 +1508,7 @@ class DatasetInstance( object ):
return msg
class HistoryDatasetAssociation( DatasetInstance, DictifiableMixin, UsesAnnotations ):
class HistoryDatasetAssociation( DatasetInstance, Dictifiable, UsesAnnotations ):
"""
Resource class that creates a relation between a dataset and a user history.
"""
@@ -1680,7 +1680,7 @@ class HistoryDatasetAssociation( DatasetInstance, DictifiableMixin, UsesAnnotati
rval += child.get_disk_usage( user )
return rval
def dictify( self, view='collection' ):
def to_dict( self, view='collection' ):
"""
Return attributes of this HDA that are exposed using the API.
"""
@@ -1759,7 +1759,7 @@ class HistoryDatasetAssociationSubset( object ):
self.subset = subset
self.location = location
class Library( object, DictifiableMixin ):
class Library( object, Dictifiable ):
permitted_actions = get_permitted_actions( filter='LIBRARY' )
dict_collection_visible_keys = ( 'id', 'name' )
dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' )
@@ -1828,7 +1828,7 @@ class Library( object, DictifiableMixin ):
name = unicode( name, 'utf-8' )
return name
class LibraryFolder( object, DictifiableMixin ):
class LibraryFolder( object, Dictifiable ):
dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' )
def __init__( self, name=None, description=None, item_count=0, order_id=None ):
self.name = name or "Unnamed folder"
@@ -1900,8 +1900,8 @@ class LibraryFolder( object, DictifiableMixin ):
if isinstance( name, str ):
name = unicode( name, 'utf-8' )
return name
def dictify( self, view='collection' ):
rval = super( LibraryFolder, self ).dictify( view=view )
def to_dict( self, view='collection' ):
rval = super( LibraryFolder, self ).to_dict( view=view )
info_association, inherited = self.get_info_association()
if info_association:
if inherited:
@@ -1966,7 +1966,7 @@ class LibraryDataset( object ):
name = property( get_name, set_name )
def display_name( self ):
self.library_dataset_dataset_association.display_name()
def dictify( self, view='collection' ):
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.
@@ -2096,7 +2096,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
if restrict:
return None, inherited
return self.library_dataset.folder.get_info_association( inherited=True )
def dictify( self, view='collection' ):
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.
@@ -2323,7 +2323,7 @@ class UCI( object ):
self.id = None
self.user = None
class StoredWorkflow( object, DictifiableMixin):
class StoredWorkflow( object, Dictifiable):
dict_collection_visible_keys = ( 'id', 'name', 'published' )
dict_element_visible_keys = ( 'id', 'name', 'published' )
def __init__( self ):
@@ -2341,8 +2341,8 @@ class StoredWorkflow( object, DictifiableMixin):
new_swta.user = target_user
self.tags.append(new_swta)
def dictify( self, view='collection', value_mapper = None ):
rval = super( StoredWorkflow, self ).dictify(self, view=view, value_mapper = value_mapper)
def to_dict( self, view='collection', value_mapper = None ):
rval = super( StoredWorkflow, self ).to_dict(self, view=view, value_mapper = value_mapper)
tags_str_list = []
for tag in self.tags:
tag_str = tag.user_tname
@@ -2434,7 +2434,7 @@ class MetadataFile( object ):
return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
class FormDefinition( object, DictifiableMixin ):
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',
@@ -2562,7 +2562,7 @@ class FormValues( object ):
self.form_definition = form_def
self.content = content
class Request( object, DictifiableMixin ):
class Request( object, Dictifiable ):
states = Bunch( NEW = 'New',
SUBMITTED = 'In Progress',
REJECTED = 'Rejected',
@@ -2753,7 +2753,7 @@ class ExternalService( object ):
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, DictifiableMixin ):
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',
@@ -2839,7 +2839,7 @@ class RequestTypePermissions( object ):
self.request_type = request_type
self.role = role
class Sample( object, DictifiableMixin ):
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',
@@ -3169,7 +3169,7 @@ class Tag ( object ):
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, DictifiableMixin ):
class ItemTagAssociation ( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'user_tname', 'user_value' )
dict_element_visible_keys = dict_collection_visible_keys
@@ -3350,7 +3350,7 @@ class ToolShedRepository( object ):
self.error_message = error_message
def as_dict( self, value_mapper=None ):
return self.dictify( view='element', value_mapper=value_mapper )
return self.to_dict( view='element', value_mapper=value_mapper )
@property
def can_install( self ):
@@ -3372,7 +3372,7 @@ class ToolShedRepository( object ):
def can_reinstall_or_activate( self ):
return self.deleted
def dictify( self, view='collection', value_mapper=None ):
def to_dict( self, view='collection', value_mapper=None ):
if value_mapper is None:
value_mapper = {}
rval = {}
@@ -3772,7 +3772,7 @@ class ToolDependency( object ):
self.tool_shed_repository.name,
self.tool_shed_repository.installed_changeset_revision )
class ToolVersion( object, DictifiableMixin ):
class ToolVersion( object, Dictifiable ):
dict_element_visible_keys = ( 'id', 'tool_shed_repository' )
def __init__( self, id=None, create_time=None, tool_id=None, tool_shed_repository=None ):
self.id = id
@@ -3830,8 +3830,8 @@ class ToolVersion( object, DictifiableMixin ):
return version_ids
return [ tool_version.tool_id for tool_version in self.get_versions( app ) ]
def dictify( self, view='element' ):
rval = super( ToolVersion, self ).dictify( self, view )
def to_dict( self, view='element' ):
rval = super( ToolVersion, self ).to_dict( self, view )
rval['tool_name'] = self.tool_id
for a in self.parent_tool_association:
rval['parent_tool_id'] = a.parent_id
lib/galaxy/model/item_attrs.py
+5 -5
View File
@@ -158,12 +158,12 @@ class UsesAnnotations:
class_name = '%sAnnotationAssociation' % item.__class__.__name__
return getattr( galaxy.model, class_name, None )
class DictifiableMixin:
class Dictifiable:
""" Mixin that enables objects to be converted to dictionaries. This is useful
when for sharing objects across boundaries, such as the API, tool scripts,
and JavaScript code. """
def dictify( self, view='collection', value_mapper=None ):
def to_dict( self, view='collection', value_mapper=None ):
"""
Return item dictionary.
"""
@@ -176,9 +176,9 @@ class DictifiableMixin:
Recursive helper function to get item values.
"""
# FIXME: why use exception here? Why not look for key in value_mapper
# first and then default to dictify?
# first and then default to to_dict?
try:
return item.dictify( view=view, value_mapper=value_mapper )
return item.to_dict( view=view, value_mapper=value_mapper )
except:
if key in value_mapper:
return value_mapper.get( key )( item )
@@ -193,7 +193,7 @@ class DictifiableMixin:
try:
visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' )
except AttributeError:
raise Exception( 'Unknown DictifiableMixin view: %s' % view )
raise Exception( 'Unknown Dictifiable view: %s' % view )
for key in visible_keys:
try:
item = self.__getattribute__( key )
lib/galaxy/model/search.py
+1 -1
View File
@@ -560,7 +560,7 @@ class SearchQuery:
return self.view.get_results(True)
def item_to_api_value(self, item):
r = item.dictify( view='element' )
r = item.to_dict( view='element' )
if self.query.field_list.count("*"):
return r
o = {}
lib/galaxy/tools/__init__.py
+21 -21
View File
@@ -59,7 +59,7 @@ from galaxy.util.odict import odict
from galaxy.util.template import fill_template
from galaxy.web import url_for
from galaxy.web.form_builder import SelectField
from galaxy.model.item_attrs import DictifiableMixin
from galaxy.model.item_attrs import Dictifiable
from tool_shed.util import shed_util_common
from .loader import load_tool, template_macro_params
@@ -93,16 +93,16 @@ class StdioErrorLevel( object ):
class ToolNotFoundException( Exception ):
pass
def dictify_helper( obj, kwargs ):
""" Helper function that provides the appropriate kwargs to dictify an object. """
def to_dict_helper( obj, kwargs ):
""" Helper function that provides the appropriate kwargs to to_dict an object. """
# Label.dictify cannot have kwargs.
# Label.to_dict cannot have kwargs.
if isinstance( obj, ToolSectionLabel ):
kwargs = {}
return obj.dictify( **kwargs )
return obj.to_dict( **kwargs )
class ToolBox( object, DictifiableMixin ):
class ToolBox( object, Dictifiable ):
"""Container for a collection of tools"""
def __init__( self, config_filenames, tool_root_dir, app ):
@@ -711,9 +711,9 @@ class ToolBox( object, DictifiableMixin ):
"""
return self.app.model.context
def dictify( self, trans, in_panel=True, **kwds ):
def to_dict( self, trans, in_panel=True, **kwds ):
"""
Dictify toolbox.
to_dict toolbox.
"""
context = Bunch( toolbox=self, trans=trans, **kwds )
@@ -736,11 +736,11 @@ class ToolBox( object, DictifiableMixin ):
link_details = True
)
for elt in panel_elts:
rval.append( dictify_helper( elt, kwargs ) )
rval.append( to_dict_helper( elt, kwargs ) )
else:
tools = []
for id, tool in self.tools_by_id.items():
tools.append( tool.dictify( trans, link_details=True ) )
tools.append( tool.to_dict( trans, link_details=True ) )
rval = tools
return rval
@@ -801,7 +801,7 @@ def _filter_for_panel( item, filters, context ):
class ToolSection( object, DictifiableMixin ):
class ToolSection( object, Dictifiable ):
"""
A group of tools with similar type/purpose that will be displayed as a
group in the user interface.
@@ -824,22 +824,22 @@ class ToolSection( object, DictifiableMixin ):
copy.elems = self.elems.copy()
return copy
def dictify( self, trans, link_details=False ):
def to_dict( self, trans, link_details=False ):
""" Return a dict that includes section's attributes. """
section_dict = super( ToolSection, self ).dictify()
section_dict = super( ToolSection, self ).to_dict()
section_elts = []
kwargs = dict(
trans = trans,
link_details = link_details
)
for elt in self.elems.values():
section_elts.append( dictify_helper( elt, kwargs ) )
section_elts.append( to_dict_helper( elt, kwargs ) )
section_dict[ 'elems' ] = section_elts
return section_dict
class ToolSectionLabel( object, DictifiableMixin ):
class ToolSectionLabel( object, Dictifiable ):
"""
A label for a set of tools that can be displayed above groups of tools
and sections in the user interface
@@ -898,7 +898,7 @@ class DefaultToolState( object ):
self.rerun_remap_job_id = None
self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True )
class ToolOutput( object, DictifiableMixin ):
class ToolOutput( object, Dictifiable ):
"""
Represents an output datasets produced by a tool. For backward
compatibility this behaves as if it were the tuple::
@@ -948,7 +948,7 @@ class ToolRequirement( object ):
self.type = type
self.version = version
class Tool( object, DictifiableMixin ):
class Tool( object, Dictifiable ):
"""
Represents a computational tool that can be executed through Galaxy.
"""
@@ -2962,11 +2962,11 @@ class Tool( object, DictifiableMixin ):
self.sa_session.flush()
return primary_datasets
def dictify( self, trans, link_details=False, io_details=False ):
def to_dict( self, trans, link_details=False, io_details=False ):
""" Returns dict of tool. """
# Basic information
tool_dict = super( Tool, self ).dictify()
tool_dict = super( Tool, self ).to_dict()
# Add link details.
if link_details:
@@ -2983,8 +2983,8 @@ class Tool( object, DictifiableMixin ):
# Add input and output details.
if io_details:
tool_dict[ 'inputs' ] = [ input.dictify( trans ) for input in self.inputs.values() ]
tool_dict[ 'outputs' ] = [ output.dictify() for output in self.outputs.values() ]
tool_dict[ 'inputs' ] = [ input.to_dict( trans ) for input in self.inputs.values() ]
tool_dict[ 'outputs' ] = [ output.to_dict() for output in self.outputs.values() ]
return tool_dict
lib/galaxy/tools/parameters/basic.py
+7 -7
View File
@@ -12,12 +12,12 @@ from sanitize import ToolParameterSanitizer
import validation, dynamic_options
# For BaseURLToolParameter
from galaxy.web import url_for
from galaxy.model.item_attrs import DictifiableMixin
from galaxy.model.item_attrs import Dictifiable
import galaxy.model
log = logging.getLogger(__name__)
class ToolParameter( object, DictifiableMixin ):
class ToolParameter( object, Dictifiable ):
"""
Describes a parameter accepted by a tool. This is just a simple stub at the
moment but in the future should encapsulate more complex parameters (lists
@@ -170,10 +170,10 @@ class ToolParameter( object, DictifiableMixin ):
for validator in self.validators:
validator.validate( value, history )
def dictify( self, trans, view='collection', value_mapper=None ):
""" Dictify tool parameter. This can be overridden by subclasses. """
def to_dict( self, trans, view='collection', value_mapper=None ):
""" to_dict tool parameter. This can be overridden by subclasses. """
tool_dict = super( ToolParameter, self ).dictify()
tool_dict = super( ToolParameter, self ).to_dict()
tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) )
if hasattr( self, 'value' ):
tool_dict[ 'value' ] = self.value
@@ -872,8 +872,8 @@ class SelectToolParameter( ToolParameter ):
else:
return []
def dictify( self, trans, view='collection', value_mapper=None ):
d = super( SelectToolParameter, self ).dictify( trans )
def to_dict( self, trans, view='collection', value_mapper=None ):
d = super( SelectToolParameter, self ).to_dict( trans )
# Get options, value.
options = self.get_options( trans, [] )
lib/galaxy/tools/parameters/grouping.py
+5 -5
View File
@@ -15,9 +15,9 @@ from galaxy.util import relpath
from galaxy.util import sanitize_for_filename
from galaxy.util.bunch import Bunch
from galaxy.util.expressions import ExpressionContext
from galaxy.model.item_attrs import DictifiableMixin
from galaxy.model.item_attrs import Dictifiable
class Group( object, DictifiableMixin ):
class Group( object, Dictifiable ):
dict_collection_visible_keys = ( 'name', 'type' )
@@ -48,9 +48,9 @@ class Group( object, DictifiableMixin ):
"""
raise TypeError( "Not implemented" )
def dictify( self, trans, view='collection', value_mapper=None ):
# TODO: need to dictify conditions.
group_dict = super( Group, self ).dictify( view=view, value_mapper=value_mapper )
def to_dict( self, trans, view='collection', value_mapper=None ):
# TODO: need to to_dict conditions.
group_dict = super( Group, self ).to_dict( view=view, value_mapper=value_mapper )
return group_dict
class Repeat( Group ):
lib/galaxy/visualization/genomes.py
+2 -2
View File
@@ -73,7 +73,7 @@ class Genome( object ):
self.len_file = len_file
self.twobit_file = twobit_file
def dictify( self, num=None, chrom=None, low=None ):
def to_dict( self, num=None, chrom=None, low=None ):
"""
Returns representation of self as a dictionary.
"""
@@ -289,7 +289,7 @@ class Genomes( object ):
# Set up return value or log exception if genome not found for key.
rval = None
if genome:
rval = genome.dictify( num=num, chrom=chrom, low=low )
rval = genome.to_dict( num=num, chrom=chrom, low=low )
else:
log.exception( 'genome not found for key %s' % dbkey )
lib/galaxy/web/base/controller.py
+11 -11
View File
@@ -32,7 +32,7 @@ from galaxy.workflow.modules import module_factory
from galaxy.model.orm import eagerload, eagerload_all
from galaxy.security.validate_user_input import validate_publicname
from galaxy.util.sanitize_html import sanitize_html
from galaxy.model.item_attrs import DictifiableMixin
from galaxy.model.item_attrs import Dictifiable
from galaxy.datatypes.interval import ChromatinInteractions
from galaxy.datatypes.data import Text
@@ -422,7 +422,7 @@ class UsesHistoryMixin( SharableItemSecurityMixin ):
def get_history_dict( self, trans, history, hda_dictionaries=None ):
"""Returns history data in the form of a dictionary.
"""
history_dict = history.dictify( view='element', value_mapper={ 'id':trans.security.encode_id })
history_dict = history.to_dict( view='element', value_mapper={ 'id':trans.security.encode_id })
history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True )
history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, trans.user, history )
@@ -583,7 +583,7 @@ class UsesHistoryDatasetAssociationMixin:
"""
#precondition: the user's access to this hda has already been checked
#TODO:?? postcondition: all ids are encoded (is this really what we want at this level?)
hda_dict = hda.dictify( view='element' )
hda_dict = hda.to_dict( view='element' )
hda_dict[ 'api_type' ] = "file"
# Add additional attributes that depend on trans can hence must be added here rather than at the model level.
@@ -594,7 +594,7 @@ class UsesHistoryDatasetAssociationMixin:
# ---- return here if deleted AND purged OR can't access
purged = ( hda.purged or hda.dataset.purged )
if ( hda.deleted and purged ):
#TODO: dictify should really go AFTER this - only summary data
#TODO: to_dict should really go AFTER this - only summary data
return trans.security.encode_dict_ids( hda_dict )
if trans.user_is_admin() or trans.app.config.expose_dataset_path:
@@ -920,7 +920,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix
return query
return query.all()
#TODO: move into model (dictify)
#TODO: move into model (to_dict)
def get_visualization_summary_dict( self, visualization ):
"""
Return a set of summary attributes for a visualization in dictionary form.
@@ -949,7 +949,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix
'user_id' : visualization.user.id,
'dbkey' : visualization.dbkey,
'slug' : visualization.slug,
# dictify only the latest revision (allow older to be fetched elsewhere)
# to_dict only the latest revision (allow older to be fetched elsewhere)
'latest_revision' : self.get_visualization_revision_dict( visualization.latest_revision ),
'revisions' : [ r.id for r in visualization.revisions ],
}
@@ -1129,7 +1129,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix
return None
# Get tool definition and add input values from job.
tool_dict = tool.dictify( trans, io_details=True )
tool_dict = tool.to_dict( trans, io_details=True )
inputs_dict = tool_dict[ 'inputs' ]
tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] )
tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True )
@@ -1139,8 +1139,8 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix
name = t_input[ 'name' ]
if name in tool_param_values:
value = tool_param_values[ name ]
if isinstance( value, DictifiableMixin ):
value = value.dictify()
if isinstance( value, Dictifiable ):
value = value.to_dict()
t_input[ 'value' ] = value
return tool_dict
@@ -1172,7 +1172,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix
source='data' )
return {
"track_type": dataset.datatype.track_type,
"dataset": trans.security.encode_dict_ids( dataset.dictify() ),
"dataset": trans.security.encode_dict_ids( dataset.to_dict() ),
"name": track_dict['name'],
"prefs": prefs,
"mode": track_dict.get( 'mode', 'Auto' ),
@@ -1252,7 +1252,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix
return {
"track_type": dataset.datatype.track_type,
"name": dataset.name,
"dataset": trans.security.encode_dict_ids( dataset.dictify() ),
"dataset": trans.security.encode_dict_ids( dataset.to_dict() ),
"prefs": {},
"filters": { 'filters' : track_data_provider.get_filters() },
"tool": self.get_tool_def( trans, dataset ),
lib/galaxy/webapps/galaxy/api/datasets.py
+1 -1
View File
@@ -60,7 +60,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistory
rval[ 'display_types' ] = self.get_old_display_applications( trans, dataset )
rval[ 'display_apps' ] = self.get_display_apps( trans, dataset )
else:
rval = dataset.dictify()
rval = dataset.to_dict()
except Exception, e:
rval = "Error in dataset API at listing contents: " + str( e )
lib/galaxy/webapps/galaxy/api/folders.py
+1 -1
View File
@@ -35,7 +35,7 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
# check_ownership=false since we are only displaying it.
content = self.get_library_folder( trans, id, check_ownership=False,
check_accessible=True )
return self.encode_all_ids( trans, content.dictify( view='element' ) )
return self.encode_all_ids( trans, content.to_dict( view='element' ) )
@web.expose_api
def create( self, trans, payload, **kwd ):
lib/galaxy/webapps/galaxy/api/forms.py
+3 -3
View File
@@ -23,7 +23,7 @@ class FormDefinitionAPIController( BaseAPIController ):
query = trans.sa_session.query( trans.app.model.FormDefinition )#.filter( trans.app.model.FormDefinition.table.c.deleted == False )
rval = []
for form_definition in query:
item = form_definition.dictify( value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item = form_definition.to_dict( value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item['url'] = url_for( 'form', id=trans.security.encode_id( form_definition.id ) )
rval.append( item )
return rval
@@ -47,7 +47,7 @@ class FormDefinitionAPIController( BaseAPIController ):
if not form_definition or not trans.user_is_admin():
trans.response.status = 400
return "Invalid form definition id ( %s ) specified." % str( form_definition_id )
item = form_definition.dictify( view='element', value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item = form_definition.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item['url'] = url_for( 'form', id=form_definition_id )
return item
@@ -69,6 +69,6 @@ class FormDefinitionAPIController( BaseAPIController ):
trans.sa_session.add( form_definition )
trans.sa_session.flush()
encoded_id = trans.security.encode_id( form_definition.id )
item = form_definition.dictify( view='element', value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item = form_definition.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item['url'] = url_for( 'form', id=encoded_id )
return [ item ]
lib/galaxy/webapps/galaxy/api/groups.py
+3 -3
View File
@@ -21,7 +21,7 @@ class GroupAPIController( BaseAPIController ):
rval = []
for group in trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.deleted == False ):
if trans.user_is_admin():
item = group.dictify( value_mapper={ 'id': trans.security.encode_id } )
item = group.to_dict( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( group.id )
item['url'] = url_for( 'group', id=encoded_id )
rval.append( item )
@@ -65,7 +65,7 @@ class GroupAPIController( BaseAPIController ):
"""
trans.sa_session.flush()
encoded_id = trans.security.encode_id( group.id )
item = group.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
item = group.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'group', id=encoded_id )
return [ item ]
@@ -89,7 +89,7 @@ class GroupAPIController( BaseAPIController ):
if not group:
trans.response.status = 400
return "Invalid group id ( %s ) specified." % str( group_id )
item = group.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
item = group.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'group', id=group_id )
item['users_url'] = url_for( 'group_users', group_id=group_id )
item['roles_url'] = url_for( 'group_roles', group_id=group_id )
lib/galaxy/webapps/galaxy/api/histories.py
+4 -4
View File
@@ -46,14 +46,14 @@ class HistoriesController( BaseAPIController, UsesHistoryMixin ):
.order_by( desc( trans.app.model.History.table.c.update_time ) )
.all() )
for history in query:
item = history.dictify(value_mapper={'id':trans.security.encode_id})
item = history.to_dict(value_mapper={'id':trans.security.encode_id})
item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) )
rval.append( item )
elif trans.galaxy_session.current_history:
#No user, this must be session authentication with an anonymous user.
history = trans.galaxy_session.current_history
item = history.dictify(value_mapper={'id':trans.security.encode_id})
item = history.to_dict(value_mapper={'id':trans.security.encode_id})
item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) )
rval.append(item)
@@ -139,7 +139,7 @@ class HistoriesController( BaseAPIController, UsesHistoryMixin ):
trans.sa_session.add( new_history )
trans.sa_session.flush()
item = new_history.dictify(view='element', value_mapper={'id':trans.security.encode_id})
item = new_history.to_dict(view='element', value_mapper={'id':trans.security.encode_id})
item['url'] = url_for( 'history', id=item['id'] )
#TODO: copy own history
@@ -254,7 +254,7 @@ class HistoriesController( BaseAPIController, UsesHistoryMixin ):
:param id: the encoded id of the history to undelete
:type payload: dict
:param payload: a dictionary containing any or all the
fields in :func:`galaxy.model.History.dictify` and/or the following:
fields in :func:`galaxy.model.History.to_dict` and/or the following:
* annotation: an annotation for the history
lib/galaxy/webapps/galaxy/api/history_contents.py
+2 -2
View File
@@ -190,7 +190,7 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio
hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True )
trans.sa_session.flush()
return hda.dictify()
return hda.to_dict()
else:
# TODO: implement other "upload" methods here.
@@ -210,7 +210,7 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio
:param id: the encoded id of the history to undelete
:type payload: dict
:param payload: a dictionary containing any or all the
fields in :func:`galaxy.model.HistoryDatasetAssociation.dictify`
fields in :func:`galaxy.model.HistoryDatasetAssociation.to_dict`
and/or the following:
* annotation: an annotation for the HDA
lib/galaxy/webapps/galaxy/api/item_tags.py
+1 -1
View File
@@ -49,7 +49,7 @@ class BaseItemTagsController( BaseAPIController, UsesTagsMixin ):
return 'OK'
def _api_value( self, tag, trans, view='element' ):
return tag.dictify( view=view, value_mapper={ 'id': trans.security.encode_id } )
return tag.to_dict( view=view, value_mapper={ 'id': trans.security.encode_id } )
class HistoryContentTagsController( BaseItemTagsController ):
controller_name = "history_content_tags"
lib/galaxy/webapps/galaxy/api/libraries.py
+3 -3
View File
@@ -49,7 +49,7 @@ class LibrariesController( BaseAPIController ):
trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) )
rval = []
for library in query:
item = library.dictify()
item = library.to_dict()
item['url'] = url_for( route, id=trans.security.encode_id( library.id ) )
item['id'] = trans.security.encode_id( item['id'] )
rval.append( item )
@@ -87,7 +87,7 @@ class LibrariesController( BaseAPIController ):
library = None
if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), library ) ):
raise HTTPBadRequest( detail='Invalid library id ( %s ) specified.' % id )
item = library.dictify( view='element' )
item = library.to_dict( view='element' )
#item['contents_url'] = url_for( 'contents', library_id=library_id )
item['contents_url'] = url_for( 'library_contents', library_id=library_id )
return item
@@ -162,4 +162,4 @@ class LibrariesController( BaseAPIController ):
library.deleted = True
trans.sa_session.add( library )
trans.sa_session.flush()
return library.dictify( view='element', value_mapper={ 'id' : trans.security.encode_id } )
return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id } )
lib/galaxy/webapps/galaxy/api/library_contents.py
+3 -3
View File
@@ -105,7 +105,7 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
:rtype: dict
:returns: detailed library item information
.. seealso::
:func:`galaxy.model.LibraryDataset.dictify` and
:func:`galaxy.model.LibraryDataset.to_dict` and
:attr:`galaxy.model.LibraryFolder.dict_element_visible_keys`
"""
class_name, content_id = self.__decode_library_content_id( trans, id )
@@ -113,7 +113,7 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True )
else:
content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True )
return self.encode_all_ids( trans, content.dictify( view='element' ) )
return self.encode_all_ids( trans, content.to_dict( view='element' ) )
@web.expose_api
def create( self, trans, library_id, payload, **kwd ):
@@ -266,7 +266,7 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
return { 'error' : 'user has no permission to add to library folder (%s)' %( folder_id ) }
ldda = self.copy_hda_to_library_folder( trans, hda, folder, ldda_message=ldda_message )
ldda_dict = ldda.dictify()
ldda_dict = ldda.to_dict()
rval = trans.security.encode_dict_ids( ldda_dict )
except Exception, exc:
lib/galaxy/webapps/galaxy/api/permissions.py
+1 -1
View File
@@ -47,6 +47,6 @@ class PermissionsController( BaseAPIController ):
trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder )
message = "Permissions updated for library '%s'." % library.name
item = library.dictify( view='element' )
item = library.to_dict( view='element' )
return item
lib/galaxy/webapps/galaxy/api/quotas.py
+3 -3
View File
@@ -34,7 +34,7 @@ class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuotaMixin
route = 'quota'
query = query.filter( trans.app.model.Quota.table.c.deleted == False )
for quota in query:
item = quota.dictify( value_mapper={ 'id': trans.security.encode_id } )
item = quota.to_dict( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( quota.id )
item['url'] = url_for( route, id=encoded_id )
rval.append( item )
@@ -49,7 +49,7 @@ class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuotaMixin
Displays information about a quota.
"""
quota = self.get_quota( trans, id, deleted=util.string_as_bool( deleted ) )
return quota.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
return quota.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
@web.expose_api
@web.require_admin
@@ -67,7 +67,7 @@ class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuotaMixin
quota, message = self._create_quota( params )
except ActionInputError, e:
raise HTTPBadRequest( detail=str( e ) )
item = quota.dictify( value_mapper={ 'id': trans.security.encode_id } )
item = quota.to_dict( value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'quota', id=trans.security.encode_id( quota.id ) )
item['message'] = message
return item
lib/galaxy/webapps/galaxy/api/request_types.py
+3 -3
View File
@@ -19,7 +19,7 @@ class RequestTypeAPIController( BaseAPIController ):
"""
rval = []
for request_type in trans.app.security_agent.get_accessible_request_types( trans, trans.user ):
item = request_type.dictify( value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
item = request_type.to_dict( value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( request_type.id )
item['url'] = url_for( 'request_type', id=encoded_id )
rval.append( item )
@@ -47,7 +47,7 @@ class RequestTypeAPIController( BaseAPIController ):
if not trans.app.security_agent.can_access_request_type( trans.user.all_roles(), request_type ):
trans.response.status = 400
return "No permission to access request_type ( %s )." % str( request_type_id )
item = request_type.dictify( view='element', value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
item = request_type.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
item['url'] = url_for( 'request_type', id=request_type_id )
return item
@@ -97,6 +97,6 @@ class RequestTypeAPIController( BaseAPIController ):
trans.sa_session.add( request_type )
trans.sa_session.flush()
encoded_id = trans.security.encode_id( request_type.id )
item = request_type.dictify( view='element', value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
item = request_type.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
item['url'] = url_for( 'request_type', id=encoded_id )
return [ item ]
lib/galaxy/webapps/galaxy/api/requests.py
+2 -2
View File
@@ -30,7 +30,7 @@ class RequestsAPIController( BaseAPIController ):
.all()
rval = []
for request in query:
item = request.dictify()
item = request.to_dict()
item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) )
item['id'] = trans.security.encode_id( item['id'] )
if trans.user_is_admin():
@@ -55,7 +55,7 @@ class RequestsAPIController( BaseAPIController ):
if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ):
trans.response.status = 400
return "Invalid request id ( %s ) specified." % str( request_id )
item = request.dictify()
item = request.to_dict()
item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) )
item['id'] = trans.security.encode_id( item['id'] )
item['user'] = request.user.email
lib/galaxy/webapps/galaxy/api/roles.py
+3 -3
View File
@@ -18,7 +18,7 @@ class RoleAPIController( BaseAPIController ):
rval = []
for role in trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.deleted == False ):
if trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role ):
item = role.dictify( value_mapper={ 'id': trans.security.encode_id } )
item = role.to_dict( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( role.id )
item['url'] = url_for( 'role', id=encoded_id )
rval.append( item )
@@ -43,7 +43,7 @@ class RoleAPIController( BaseAPIController ):
if not role or not (trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role )):
trans.response.status = 400
return "Invalid role id ( %s ) specified." % str( role_id )
item = role.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
item = role.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'role', id=role_id )
return item
@@ -81,6 +81,6 @@ class RoleAPIController( BaseAPIController ):
trans.app.security_agent.associate_group_role( group, role )
trans.sa_session.flush()
encoded_id = trans.security.encode_id( role.id )
item = role.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
item = role.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'role', id=encoded_id )
return [ item ]
lib/galaxy/webapps/galaxy/api/samples.py
+1 -1
View File
@@ -35,7 +35,7 @@ class SamplesAPIController( BaseAPIController ):
return "Invalid request id ( %s ) specified." % str( request_id )
rval = []
for sample in request.samples:
item = sample.dictify()
item = sample.to_dict()
item['url'] = url_for( 'samples',
request_id=trans.security.encode_id( request_id ),
id=trans.security.encode_id( sample.id ) )
lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+2 -2
View File
@@ -45,7 +45,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
.order_by( trans.app.model.ToolShedRepository.table.c.name ) \
.all()
for tool_shed_repository in query:
tool_shed_repository_dict = tool_shed_repository.dictify( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) )
tool_shed_repository_dict = tool_shed_repository.to_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) )
tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id( tool_shed_repository.id ) )
@@ -402,7 +402,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
repair_dict = repository_util.repair_tool_shed_repository( trans,
repository,
encoding_util.tool_shed_encode( repo_info_dict ) )
repository_dict = repository.dictify( value_mapper=default_tool_shed_repository_value_mapper( trans, repository ) )
repository_dict = repository.to_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
lib/galaxy/webapps/galaxy/api/tools.py
+4 -4
View File
@@ -32,7 +32,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
# Create return value.
try:
return self.app.toolbox.dictify( trans, in_panel=in_panel, trackster=trackster )
return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster )
except Exception, exc:
log.error( 'could not convert toolbox to dictionary: %s', str( exc ), exc_info=True )
trans.response.status = 500
@@ -45,7 +45,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
Returns tool information, including parameters and inputs.
"""
try:
return self.app.toolbox.tools_by_id[ id ].dictify( trans, for_display=True )
return self.app.toolbox.tools_by_id[ id ].to_dict( trans, for_display=True )
except Exception, exc:
log.error( 'could not convert tool (%s) to dictionary: %s', id, str( exc ), exc_info=True )
trans.response.status = 500
@@ -105,7 +105,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
outputs = rval[ "outputs" ]
#TODO:?? poss. only return ids?
for output in output_datasets:
output_dict = output.dictify()
output_dict = output.to_dict()
outputs.append( trans.security.encode_dict_ids( output_dict ) )
return rval
@@ -411,7 +411,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
if joda.name == output_name:
output_dataset = joda.dataset
dataset_dict = output_dataset.dictify()
dataset_dict = output_dataset.to_dict()
dataset_dict[ 'id' ] = trans.security.encode_id( dataset_dict[ 'id' ] )
dataset_dict[ 'track_config' ] = self.get_new_track_config( trans, output_dataset );
return dataset_dict
lib/galaxy/webapps/galaxy/api/users.py
+4 -4
View File
@@ -33,13 +33,13 @@ class UserAPIController( BaseAPIController ):
query = query.filter( trans.app.model.User.table.c.deleted == False )
# special case: user can see only their own user
if not trans.user_is_admin():
item = trans.user.dictify( value_mapper={ 'id': trans.security.encode_id } )
item = trans.user.to_dict( value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( route, id=item['id'] )
item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans )
return [item]
for user in query:
item = user.dictify( value_mapper={ 'id': trans.security.encode_id } )
item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } )
#TODO: move into api_values
item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans )
item['url'] = url_for( route, id=item['id'] )
@@ -77,7 +77,7 @@ class UserAPIController( BaseAPIController ):
raise
else:
raise HTTPBadRequest( detail='Invalid user id ( %s ) specified' % id )
item = user.dictify( view='element', value_mapper={ 'id': trans.security.encode_id,
item = user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id,
'total_disk_usage': float } )
#TODO: move into api_values (needs trans, tho - can we do that with api_keys/@property??)
#TODO: works with other users (from admin)??
@@ -94,7 +94,7 @@ class UserAPIController( BaseAPIController ):
raise HTTPNotImplemented( detail='User creation is not allowed in this Galaxy instance' )
if trans.app.config.use_remote_user and trans.user_is_admin():
user = trans.get_or_create_remote_user(remote_user_email=payload['remote_user_email'])
item = user.dictify( view='element', value_mapper={ 'id': trans.security.encode_id,
item = user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id,
'total_disk_usage': float } )
else:
raise HTTPNotImplemented()
lib/galaxy/webapps/galaxy/api/visualizations.py
+1 -1
View File
@@ -212,7 +212,7 @@ class VisualizationsController( BaseAPIController, UsesVisualizationMixin, UsesA
# this allows PUT'ing an entire model back to the server without attribute errors on uneditable attrs
valid_but_uneditable_keys = (
'id', 'model_class'
#TODO: fill out when we create dictify, get_dict, whatevs
#TODO: fill out when we create to_dict, get_dict, whatevs
)
#TODO: deleted
#TODO: importable
lib/galaxy/webapps/galaxy/api/workflows.py
+4 -4
View File
@@ -31,7 +31,7 @@ class WorkflowsAPIController(BaseAPIController, UsesAnnotations):
for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).filter_by(
user=trans.user, deleted=False).order_by(
desc(trans.app.model.StoredWorkflow.table.c.update_time)).all():
item = wf.dictify(value_mapper={'id':trans.security.encode_id})
item = wf.to_dict(value_mapper={'id':trans.security.encode_id})
encoded_id = trans.security.encode_id(wf.id)
item['url'] = url_for('workflow', id=encoded_id)
rval.append(item)
@@ -39,7 +39,7 @@ class WorkflowsAPIController(BaseAPIController, UsesAnnotations):
user=trans.user ).join( 'stored_workflow' ).filter(
trans.app.model.StoredWorkflow.deleted == False ).order_by(
desc( trans.app.model.StoredWorkflow.update_time ) ).all():
item = wf_sa.stored_workflow.dictify(value_mapper={'id':trans.security.encode_id})
item = wf_sa.stored_workflow.to_dict(value_mapper={'id':trans.security.encode_id})
encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
item['url'] = url_for('workflow', id=encoded_id)
rval.append(item)
@@ -67,7 +67,7 @@ class WorkflowsAPIController(BaseAPIController, UsesAnnotations):
except:
trans.response.status = 400
return "That workflow does not exist."
item = stored_workflow.dictify(view='element', value_mapper={'id':trans.security.encode_id})
item = stored_workflow.to_dict(view='element', value_mapper={'id':trans.security.encode_id})
item['url'] = url_for('workflow', id=workflow_id)
latest_workflow = stored_workflow.latest_workflow
inputs = {}
@@ -329,7 +329,7 @@ class WorkflowsAPIController(BaseAPIController, UsesAnnotations):
# return list
rval= [];
item = workflow.dictify(value_mapper={'id':trans.security.encode_id})
item = workflow.to_dict(value_mapper={'id':trans.security.encode_id})
item['url'] = url_for('workflow', id=encoded_id)
rval.append(item);
lib/galaxy/webapps/galaxy/controllers/visualization.py
+2 -2
View File
@@ -873,8 +873,8 @@ class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations,
# Add tool, dataset attributes to config based on id.
tool = trans.app.toolbox.get_tool( viz_config[ 'tool_id' ] )
viz_config[ 'tool' ] = tool.dictify( trans, io_details=True )
viz_config[ 'dataset' ] = trans.security.encode_dict_ids( dataset.dictify() )
viz_config[ 'tool' ] = tool.to_dict( trans, io_details=True )
viz_config[ 'dataset' ] = trans.security.encode_dict_ids( dataset.to_dict() )
return trans.fill_template_mako( "visualization/sweepster.mako", config=viz_config )
lib/galaxy/webapps/tool_shed/api/repositories.py
+4 -4
View File
@@ -113,7 +113,7 @@ class RepositoriesController( BaseAPIController ):
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
encoded_repository_id = trans.security.encode_id( repository.id )
repository_dict = repository.dictify( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict = repository.to_dict( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=encoded_repository_id )
@@ -129,7 +129,7 @@ class RepositoriesController( BaseAPIController ):
changeset_revision = new_changeset_revision
if repository_metadata:
encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id )
repository_metadata_dict = repository_metadata.dictify( view='collection',
repository_metadata_dict = repository_metadata.to_dict( view='collection',
value_mapper=default_repository_metadata_value_mapper( trans, repository_metadata ) )
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
@@ -164,7 +164,7 @@ class RepositoriesController( BaseAPIController ):
.order_by( trans.app.model.Repository.table.c.name ) \
.all()
for repository in query:
repository_dict = repository.dictify( view='collection', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict = repository.to_dict( view='collection', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
@@ -187,7 +187,7 @@ class RepositoriesController( BaseAPIController ):
# Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
try:
repository = suc.get_repository_in_tool_shed( trans, id )
repository_dict = repository.dictify( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict = repository.to_dict( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
lib/galaxy/webapps/tool_shed/api/repository_revisions.py
+1 -1
View File
@@ -127,7 +127,7 @@ class RepositoryRevisionsController( BaseAPIController ):
.order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \
.all()
for repository_metadata in query:
repository_metadata_dict = repository_metadata.dictify( view='collection',
repository_metadata_dict = repository_metadata.to_dict( view='collection',
value_mapper=default_value_mapper( trans, repository_metadata ) )
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
lib/galaxy/webapps/tool_shed/model/__init__.py
+16 -16
View File
@@ -4,7 +4,7 @@ import os
from galaxy import util
from galaxy.util.bunch import Bunch
from galaxy.util.hash_util import new_secure_hash
from galaxy.model.item_attrs import DictifiableMixin
from galaxy.model.item_attrs import Dictifiable
import tool_shed.repository_types.util as rt_util
from galaxy import eggs
@@ -19,7 +19,7 @@ class APIKeys( object ):
pass
class User( object, DictifiableMixin ):
class User( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'email' )
dict_element_visible_keys = ( 'id', 'email', 'username' )
@@ -61,7 +61,7 @@ class User( object, DictifiableMixin ):
return 0
class Group( object, DictifiableMixin ):
class Group( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'name' )
dict_element_visible_keys = ( 'id', 'name' )
@@ -70,7 +70,7 @@ class Group( object, DictifiableMixin ):
self.deleted = False
class Role( object, DictifiableMixin ):
class Role( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'name' )
dict_element_visible_keys = ( 'id', 'name', 'description', 'type' )
private_id = None
@@ -130,7 +130,7 @@ class GalaxySession( object ):
self.prev_session_id = prev_session_id
class Repository( object, DictifiableMixin ):
class Repository( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' )
dict_element_visible_keys = ( 'id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded',
'deprecated' )
@@ -155,7 +155,7 @@ class Repository( object, DictifiableMixin ):
self.deprecated = deprecated
def as_dict( self, value_mapper=None ):
return self.dictify( view='element', value_mapper=value_mapper )
return self.to_dict( view='element', value_mapper=value_mapper )
def can_change_type( self, app ):
# Allow changing the type only if the repository has no contents, has never been installed, or has never been changed from
@@ -175,7 +175,7 @@ class Repository( object, DictifiableMixin ):
return True
return False
def dictify( self, view='collection', value_mapper=None ):
def to_dict( self, view='collection', value_mapper=None ):
if value_mapper is None:
value_mapper = {}
rval = {}
@@ -244,7 +244,7 @@ class Repository( object, DictifiableMixin ):
fp.close()
class RepositoryMetadata( object, DictifiableMixin ):
class RepositoryMetadata( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'has_repository_dependencies', 'includes_datatypes',
'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows' )
dict_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', 'do_not_test',
@@ -284,9 +284,9 @@ class RepositoryMetadata( object, DictifiableMixin ):
return False
def as_dict( self, value_mapper=None ):
return self.dictify( view='element', value_mapper=value_mapper )
return self.to_dict( view='element', value_mapper=value_mapper )
def dictify( self, view='collection', value_mapper=None ):
def to_dict( self, view='collection', value_mapper=None ):
if value_mapper is None:
value_mapper = {}
rval = {}
@@ -304,7 +304,7 @@ class RepositoryMetadata( object, DictifiableMixin ):
return rval
class SkipToolTest( object, DictifiableMixin ):
class SkipToolTest( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'repository_metadata_id', 'initial_changeset_revision' )
dict_element_visible_keys = ( 'id', 'repository_metadata_id', 'initial_changeset_revision', 'comment' )
@@ -315,9 +315,9 @@ class SkipToolTest( object, DictifiableMixin ):
self.comment = comment
def as_dict( self, value_mapper=None ):
return self.dictify( view='element', value_mapper=value_mapper )
return self.to_dict( view='element', value_mapper=value_mapper )
def dictify( self, view='collection', value_mapper=None ):
def to_dict( self, view='collection', value_mapper=None ):
if value_mapper is None:
value_mapper = {}
rval = {}
@@ -335,7 +335,7 @@ class SkipToolTest( object, DictifiableMixin ):
return rval
class RepositoryReview( object, DictifiableMixin ):
class RepositoryReview( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted' )
dict_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted' )
approved_states = Bunch( NO='no', YES='yes' )
@@ -347,7 +347,7 @@ class RepositoryReview( object, DictifiableMixin ):
self.rating = rating
self.deleted = deleted
class ComponentReview( object, DictifiableMixin ):
class ComponentReview( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted' )
dict_element_visible_keys = ( 'id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted' )
approved_states = Bunch( NO='no', YES='yes', NA='not_applicable' )
@@ -389,7 +389,7 @@ class RepositoryRatingAssociation( ItemRatingAssociation ):
self.repository = repository
class Category( object, DictifiableMixin ):
class Category( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'name', 'description', 'deleted' )
dict_element_visible_keys = ( 'id', 'name', 'description', 'deleted' )