def build_tool_dependencies_select_field(app,
tool_shed_repository,
name,
multiple=True,
display='checkboxes',
uninstalled_only=False):
"""
Generate a SelectField consisting of the current list of tool dependency ids
for an installed tool shed repository.
"""
tool_dependencies_select_field = SelectField(name=name,
multiple=multiple,
display=display)
for tool_dependency in tool_shed_repository.tool_dependencies:
if uninstalled_only:
if tool_dependency.status not in [
app.install_model.ToolDependency.installation_status.
NEVER_INSTALLED, app.install_model.ToolDependency.
installation_status.UNINSTALLED
]:
continue
else:
if tool_dependency.status in [
app.install_model.ToolDependency.installation_status.
NEVER_INSTALLED, app.install_model.ToolDependency.
installation_status.UNINSTALLED
]:
continue
option_label = '%s version %s' % (str(
tool_dependency.name), str(tool_dependency.version))
option_value = app.security.encode_id(tool_dependency.id)
tool_dependencies_select_field.add_option(option_label, option_value)
return tool_dependencies_select_field
def build_repository_type_select_field(trans,
repository=None,
name='repository_type'):
"""Called from the Tool Shed to generate the current list of supported repository types."""
if repository:
selected_type = str(repository.type)
else:
selected_type = None
repository_type_select_field = SelectField(name=name)
for type_label, type_class in trans.app.repository_types_registry.repository_types_by_label.items(
):
option_label = str(type_class.label)
option_value = str(type_class.type)
if selected_type and selected_type == option_value:
selected = True
else:
selected = False
if repository:
if repository.type == option_value:
repository_type_select_field.add_option(option_label,
option_value,
selected=selected)
elif type_class.is_valid_for_type(trans.app, repository):
repository_type_select_field.add_option(option_label,
option_value,
selected=selected)
else:
repository_type_select_field.add_option(option_label,
option_value,
selected=selected)
return repository_type_select_field
def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True,
downloadable=False, reviewed=False, not_reviewed=False ):
"""
Build a SelectField whose options are the changeset_rev strings of certain revisions of the
received repository.
"""
options = []
changeset_tups = []
refresh_on_change_values = []
if downloadable:
# Restrict the options to downloadable revisions.
repository_metadata_revisions = repository.downloadable_revisions
elif reviewed:
# Restrict the options to revisions that have been reviewed.
repository_metadata_revisions = []
metadata_changeset_revision_hashes = []
for metadata_revision in repository.metadata_revisions:
metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision )
for review in repository.reviews:
if review.changeset_revision in metadata_changeset_revision_hashes:
repository_metadata_revisions.append( review.repository_metadata )
elif not_reviewed:
# Restrict the options to revisions that have not yet been reviewed.
repository_metadata_revisions = []
reviewed_metadata_changeset_revision_hashes = []
for review in repository.reviews:
reviewed_metadata_changeset_revision_hashes.append( review.changeset_revision )
for metadata_revision in repository.metadata_revisions:
if metadata_revision.changeset_revision not in reviewed_metadata_changeset_revision_hashes:
repository_metadata_revisions.append( metadata_revision )
else:
# Restrict the options to all revisions that have associated metadata.
repository_metadata_revisions = repository.metadata_revisions
for repository_metadata in repository_metadata_revisions:
rev, label, changeset_revision = \
hg_util.get_rev_label_changeset_revision_from_repository_metadata( trans.app,
repository_metadata,
repository=repository,
include_date=True,
include_hash=False )
changeset_tups.append( ( rev, label, changeset_revision ) )
refresh_on_change_values.append( changeset_revision )
# Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time,
# the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time.
for changeset_tup in sorted( changeset_tups ):
# Display the latest revision first.
options.insert( 0, ( changeset_tup[ 1 ], changeset_tup[ 2 ] ) )
if add_id_to_name:
name = 'changeset_revision_%d' % repository.id
else:
name = 'changeset_revision'
select_field = SelectField( name=name,
refresh_on_change=True,
refresh_on_change_values=refresh_on_change_values )
for option_tup in options:
selected = selected_value and option_tup[ 1 ] == selected_value
select_field.add_option( option_tup[ 0 ], option_tup[ 1 ], selected=selected )
return select_field
def build_tool_panel_section_select_field(app):
"""Build a SelectField whose options are the sections of the current in-memory toolbox."""
options = []
for section_id, section_name in app.toolbox.get_sections():
options.append((section_name, section_id))
select_field = SelectField(name='tool_panel_section_id', display='radio')
for option_tup in options:
select_field.add_option(option_tup[0], option_tup[1])
return select_field
def build_repository_ids_select_field( self, name='repository_ids', multiple=True, display='checkboxes' ):
"""Generate the current list of repositories for resetting metadata."""
repositories_select_field = SelectField( name=name, multiple=multiple, display=display )
query = self.get_query_for_setting_metadata_on_repositories( order=True )
for repository in query:
owner = str( repository.owner )
option_label = '%s (%s)' % ( str( repository.name ), owner )
option_value = '%s' % self.app.security.encode_id( repository.id )
repositories_select_field.add_option( option_label, option_value )
return repositories_select_field
def build_tool_panel_section_select_field( app ):
"""Build a SelectField whose options are the sections of the current in-memory toolbox."""
options = []
for k, v in app.toolbox.tool_panel.items():
if isinstance( v, galaxy.tools.ToolSection ):
options.append( ( v.name, v.id ) )
select_field = SelectField( name='tool_panel_section_id', display='radio' )
for option_tup in options:
select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] )
return select_field
def build_approved_select_field(trans, name, selected_value=None, for_component=True):
options = [('No', trans.model.ComponentReview.approved_states.NO),
('Yes', trans.model.ComponentReview.approved_states.YES)]
if for_component:
options.append(('Not applicable', trans.model.ComponentReview.approved_states.NA))
if selected_value is None:
selected_value = trans.model.ComponentReview.approved_states.NA
select_field = SelectField(name=name)
for option_tup in options:
selected = selected_value and option_tup[1] == selected_value
select_field.add_option(option_tup[0], option_tup[1], selected=selected)
return select_field
def build_shed_tool_conf_select_field(app):
"""Build a SelectField whose options are the keys in app.toolbox.shed_tool_confs."""
options = []
for dynamic_tool_conf_filename in app.toolbox.dynamic_conf_filenames():
if dynamic_tool_conf_filename.startswith('./'):
option_label = dynamic_tool_conf_filename.replace('./', '', 1)
else:
option_label = dynamic_tool_conf_filename
options.append((option_label, dynamic_tool_conf_filename))
select_field = SelectField(name='shed_tool_conf')
for option_tup in options:
select_field.add_option(option_tup[0], option_tup[1])
return select_field
def __build_form_types_widget(self, trans, selected='none'):
form_type_select_field = SelectField('form_type_select_field')
if selected == 'none':
form_type_select_field.add_option('Select one', 'none', selected=True)
else:
form_type_select_field.add_option('Select one', 'none')
fd_types = trans.app.model.FormDefinition.types.items()
fd_types.sort()
for ft in fd_types:
if selected == ft[1]:
form_type_select_field.add_option(ft[1], ft[1], selected=True)
else:
form_type_select_field.add_option(ft[1], ft[1])
return form_type_select_field
def build_shed_tool_conf_select_field( app ):
"""Build a SelectField whose options are the keys in app.toolbox.shed_tool_confs."""
options = []
for shed_tool_conf_dict in app.toolbox.shed_tool_confs:
shed_tool_conf_filename = shed_tool_conf_dict[ 'config_filename' ]
if shed_tool_conf_filename != app.config.migrated_tools_config:
if shed_tool_conf_filename.startswith( './' ):
option_label = shed_tool_conf_filename.replace( './', '', 1 )
else:
option_label = shed_tool_conf_filename
options.append( ( option_label, shed_tool_conf_filename ) )
select_field = SelectField( name='shed_tool_conf' )
for option_tup in options:
select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] )
return select_field
def __build_external_service_type_select_field(
self,
trans,
selected_value,
refresh_on_change=True,
visible_external_service_types_only=False):
external_service_types = trans.app.external_service_types.all_external_service_types
if visible_external_service_types_only:
objs_list = [
external_service_types[seq_type_id] for seq_type_id in
trans.app.external_service_types.visible_external_service_types
]
else:
objs_list = external_service_types.values()
refresh_on_change_values = ['none']
refresh_on_change_values.extend(
[trans.security.encode_id(obj.id) for obj in objs_list])
select_external_service_type = SelectField(
'external_service_type_id',
refresh_on_change=refresh_on_change,
refresh_on_change_values=refresh_on_change_values)
if selected_value == 'none':
select_external_service_type.add_option('Select one',
'none',
selected=True)
else:
select_external_service_type.add_option('Select one', 'none')
for seq_type in objs_list:
if seq_type.version:
option_name = " ".join(
[seq_type.name, "version", seq_type.version])
else:
option_name = seq_type.name
if selected_value == seq_type.id:
select_external_service_type.add_option(option_name,
seq_type.id,
selected=True)
else:
select_external_service_type.add_option(
option_name, seq_type.id)
return select_external_service_type
def build_form_definition_field_widgets(self, trans, layout_grids,
field_index, field, form_type):
'''
This method returns a list of widgets which describes a form definition field. This
includes the field label, helptext, type, selectfield options, required/optional & layout
'''
# field label
label = TextField('field_label_' + str(field_index), 40,
field['label'])
# help text
helptext = TextField('field_helptext_' + str(field_index), 40,
field['helptext'])
# field type
field_type_select_field = SelectField(
'field_type_' + str(field_index),
refresh_on_change=True,
refresh_on_change_values=[SelectField.__name__])
# fill up the field type selectfield options
field_type_options = []
# if the form is for defining samples, then use the sample field types
# which does not include TextArea & AddressField
if form_type == trans.model.FormDefinition.types.SAMPLE:
for supported_field_type in trans.model.Sample.supported_field_types:
if supported_field_type.__name__ == field['type']:
field_type_select_field.add_option(
supported_field_type.__name__,
supported_field_type.__name__,
selected=True)
if supported_field_type.__name__ == SelectField.__name__:
# when field type is Selectfield, add option Textfields
field_type_options = self.__build_field_type_select_field_options(
field, field_index)
else:
field_type_select_field.add_option(
supported_field_type.__name__,
supported_field_type.__name__)
else:
for supported_field_type in trans.model.FormDefinition.supported_field_types:
if supported_field_type.__name__ == field['type']:
field_type_select_field.add_option(
supported_field_type.__name__,
supported_field_type.__name__,
selected=True)
if supported_field_type.__name__ == SelectField.__name__:
# when field type is Selectfield, add option Textfields
field_type_options = self.__build_field_type_select_field_options(
field, field_index)
else:
field_type_select_field.add_option(
supported_field_type.__name__,
supported_field_type.__name__)
# required/optional radio button
required = SelectField('field_required_' + str(field_index),
display='radio')
if field['required'] == 'required':
required.add_option('Required', 'required', selected=True)
required.add_option('Optional', 'optional')
else:
required.add_option('Required', 'required')
required.add_option('Optional', 'optional', selected=True)
# layout grid option select_field
if layout_grids and form_type == trans.model.FormDefinition.types.SAMPLE:
layout_select_field = SelectField('field_layout_' +
str(field_index))
for index, grid_name in enumerate(layout_grids):
if str(field.get('layout', None)) == str(
index
): # existing behavior: integer indexes are stored as strings.
grid_selected = True
else:
grid_selected = False
layout_select_field.add_option("%i. %s" %
(index + 1, grid_name),
index,
selected=grid_selected)
# default value
default_value = TextField('field_default_' + str(field_index), 40,
field.get('default', ''))
# field name
name = TextField('field_name_' + str(field_index), 40, field['name'])
name_helptext = "The field name must be unique for each field and must contain only alphanumeric characters and underscore ."
if layout_grids and form_type == trans.model.FormDefinition.types.SAMPLE:
return [('Field label', label), ('Help text', helptext),
('Type', field_type_select_field, "Add options below",
field_type_options), ('Default value', default_value),
('', required),
('Select the grid layout to place this field',
layout_select_field), ('Field name', name, name_helptext)]
return [('Field label', label), ('Help text', helptext),
('Type', field_type_select_field, "Add options below",
field_type_options), ('Default value', default_value),
('', required), ('Field name', name, name_helptext)]
