def render_title(context):
context.caller_stack._push_frame()
try:
_import_ns = {}
_mako_get_namespace(context, '__anon_0x7f313c4cda10')._populate(
_import_ns, [u'*'])
_mako_get_namespace(context, '__anon_0x7f313c4cd310')._populate(
_import_ns, [
u'render_individual_tagging_element',
u'render_community_tagging_element'
])
item = _import_ns.get('item', context.get('item', UNDEFINED))
get_class_display_name = _import_ns.get(
'get_class_display_name',
context.get('get_class_display_name', UNDEFINED))
get_item_name = _import_ns.get('get_item_name',
context.get('get_item_name', UNDEFINED))
__M_writer = context.writer()
# SOURCE LINE 19
__M_writer(u'\n Galaxy | ')
# SOURCE LINE 20
__M_writer(
unicode(
iff(
item.published, "Published ",
iff(item.importable, "Accessible ",
iff(item.users_shared_with, "Shared ", "Private "))) +
get_class_display_name(item.__class__)))
__M_writer(u' | ')
__M_writer(filters.html_escape(unicode(get_item_name(item))))
__M_writer(u'\n')
return ''
finally:
context.caller_stack._pop_frame()
class FormsGrid( grids.Grid ):
# Custom column types
class NameColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.name
class DescriptionColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.desc
class TypeColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.type
class DeletedColumn( grids.GridColumn ):
def get_accepted_filters( self ):
""" Returns a list of accepted filters for this column. """
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) )
return accepted_filters
# Grid definition
title = "Forms"
template = "admin/forms/grid.mako"
model_class = model.FormDefinitionCurrent
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict( deleted="False" )
columns = [
NameColumn( "Name",
key="name",
model_class=model.FormDefinition,
link=( lambda item: iff( item.deleted, None, dict( operation="view", id=item.id ) ) ),
attach_popup=True,
filterable="advanced" ),
DescriptionColumn( "Description",
key='desc',
model_class=model.FormDefinition,
filterable="advanced" ),
TypeColumn( "Type" ),
DeletedColumn( "Deleted",
key="deleted",
visible=False,
filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
operations = [
grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted ) ),
grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
]
global_actions = [
grids.GridAction( "Create new form", dict( controller='forms',
action='new' ) )
]
def _list_undelete(self, trans, histories):
"""Undelete histories"""
n_undeleted = 0
n_already_purged = 0
for history in histories:
if history.purged:
n_already_purged += 1
if history.deleted:
history.deleted = False
if not history.default_permissions:
# For backward compatibility - for a while we were deleting all DefaultHistoryPermissions on
# the history when we deleted the history. We are no longer doing this.
# Need to add default DefaultHistoryPermissions in case they were deleted when the history was deleted
default_action = trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS
private_user_role = trans.app.security_agent.get_private_user_role(history.user)
default_permissions = {}
default_permissions[default_action] = [private_user_role]
trans.app.security_agent.history_set_default_permissions(history, default_permissions)
n_undeleted += 1
trans.log_event("History (%s) %d marked as undeleted" % (history.name, history.id))
status = SUCCESS
message_parts = []
if n_undeleted:
message_parts.append("Undeleted %d %s. " % (n_undeleted, iff(n_undeleted != 1, "histories", "history")))
if n_already_purged:
message_parts.append("%d histories have already been purged and cannot be undeleted." % n_already_purged)
status = WARNING
return status, "".join(message_parts)
class FormsGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return escape(form.latest_form.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return escape(form.latest_form.desc)
class TypeColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return form.latest_form.type
# Grid definition
title = "Forms"
template = "admin/forms/grid.mako"
model_class = model.FormDefinitionCurrent
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict(deleted="False")
columns = [
NameColumn("Name",
key="name",
model_class=model.FormDefinition,
link=(lambda item: iff(item.deleted, None, dict(operation="view_latest_form_definition",
id=item.id))),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description",
key='desc',
model_class=model.FormDefinition,
filterable="advanced"),
TypeColumn("Type"),
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Edit", allow_multiple=False, condition=(lambda item: not item.deleted)),
grids.GridOperation("Delete", allow_multiple=True, condition=(lambda item: not item.deleted)),
grids.GridOperation("Undelete", condition=(lambda item: item.deleted)),
]
global_actions = [
grids.GridAction("Create new form", dict(controller='forms', action='create_form_definition'))
]
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join(model.FormDefinition, self.model_class.latest_form_id == model.FormDefinition.id)
def render_title(context):
context.caller_stack._push_frame()
try:
_import_ns = {}
_mako_get_namespace(context, '__anon_0x1135ad290')._populate(_import_ns, [u'render_individual_tagging_element', u'render_community_tagging_element', u'community_tag_js'])
_mako_get_namespace(context, '__anon_0x1135ad890')._populate(_import_ns, [u'*'])
item = _import_ns.get('item', context.get('item', UNDEFINED))
get_class_display_name = _import_ns.get('get_class_display_name', context.get('get_class_display_name', UNDEFINED))
get_item_name = _import_ns.get('get_item_name', context.get('get_item_name', UNDEFINED))
__M_writer = context.writer()
# SOURCE LINE 19
__M_writer(u'\n Galaxy | ')
# SOURCE LINE 20
__M_writer(unicode(iff( item.published, "Published ", iff( item.importable , "Accessible ", iff( item.users_shared_with, "Shared ", "Private " ) ) ) + get_class_display_name( item.__class__ )))
__M_writer(u' | ')
__M_writer(filters.html_escape(unicode(get_item_name( item ) )))
__M_writer(u'\n')
return ''
finally:
context.caller_stack._pop_frame()
def _list_delete(self, trans, histories, purge=False):
"""Delete histories"""
n_deleted = 0
deleted_current = False
message_parts = []
status = SUCCESS
current_history = trans.get_history()
for history in histories:
try:
if history.users_shared_with:
raise exceptions.ObjectAttributeInvalidException(
f"History ({history.name}) has been shared with others, unshare it before deleting it."
)
if purge:
self.history_manager.purge(history)
else:
self.history_manager.delete(history)
if history == current_history:
deleted_current = True
except Exception as e:
message_parts.append(unicodify(e))
status = ERROR
else:
trans.log_event(f"History ({history.name}) marked as deleted")
n_deleted += 1
if n_deleted:
part = "Deleted %d %s" % (n_deleted, iff(n_deleted != 1, "histories", "history"))
if purge and trans.app.config.allow_user_dataset_purge:
part += f" and removed {iff(n_deleted != 1, 'their', 'its')} dataset{iff(n_deleted != 1, 's', '')} from disk"
elif purge:
part += " but the datasets were not removed from disk because that feature is not enabled in this Galaxy instance"
message_parts.append(f"{part}. ")
if deleted_current:
# if this history is the current history for this session,
# - attempt to find the most recently used, undeleted history and switch to it.
# - If no suitable recent history is found, create a new one and switch
# note: this needs to come after commits above or will use an empty history that was deleted above
not_deleted_or_purged = [model.History.deleted == false(), model.History.purged == false()]
most_recent_history = self.history_manager.most_recent(user=trans.user, filters=not_deleted_or_purged)
if most_recent_history:
self.history_manager.set_current(trans, most_recent_history)
else:
trans.get_or_create_default_history()
message_parts.append("Your active history was deleted, a new empty history is now active. ")
status = INFO
return (status, " ".join(message_parts))
def render_render_tagging_element_html(context,elt_id=None,tags=None,editable=True,use_toggle_link=True,input_size='15',in_form=False,tag_type='individual',render_add_tag_button=True):
context.caller_stack._push_frame()
try:
h = context.get('h', UNDEFINED)
unicode = context.get('unicode', UNDEFINED)
isinstance = context.get('isinstance', UNDEFINED)
len = context.get('len', UNDEFINED)
str = context.get('str', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 20
__M_writer(u'\n')
# SOURCE LINE 22
__M_writer(u' ')
num_tags = len( tags )
# SOURCE LINE 24
__M_writer(u'\n <div class="tag-element"\n')
# SOURCE LINE 26
if elt_id:
# SOURCE LINE 27
__M_writer(u' id="')
__M_writer(unicode(elt_id))
__M_writer(u'"\n')
pass
# SOURCE LINE 30
if num_tags == 0 and not editable:
# SOURCE LINE 31
__M_writer(u' style="display: none"\n')
pass
# SOURCE LINE 33
__M_writer(u' >\n')
# SOURCE LINE 34
if use_toggle_link:
# SOURCE LINE 35
__M_writer(u' <a class="toggle-link" href="#">')
__M_writer(unicode(num_tags))
__M_writer(u' Tag')
__M_writer(unicode(iff( num_tags == 1, "", "s")))
__M_writer(u'</a>\n')
pass
# SOURCE LINE 37
__M_writer(u' <div class="tag-area \n')
# SOURCE LINE 38
if tag_type == 'individual':
# SOURCE LINE 39
__M_writer(u' individual-tag-area\n')
pass
# SOURCE LINE 41
__M_writer(u' ">\n\n')
# SOURCE LINE 44
for tag in tags:
# SOURCE LINE 45
__M_writer(u' ')
## Handle both Tag and ItemTagAssociation objects.
if isinstance( tag, Tag ):
tag_name = tag.name
tag_value = None
elif isinstance( tag, ItemTagAssociation ):
tag_name = tag.user_tname
tag_value = tag.user_value
## Convert tag name, value to unicode.
if isinstance( tag_name, str ):
tag_name = unicode( escape( tag_name ), 'utf-8' )
if tag_value:
tag_value = unicode( escape( tag_value ), 'utf-8' )
if tag_value:
tag_str = tag_name + ":" + tag_value
else:
tag_str = tag_name
# SOURCE LINE 62
__M_writer(u'\n <span class="tag-button">\n <span class="tag-name">')
# SOURCE LINE 64
__M_writer(unicode(tag_str))
__M_writer(u'</span>\n')
# SOURCE LINE 65
if editable:
# SOURCE LINE 66
__M_writer(u' <img class="delete-tag-img" src="')
__M_writer(unicode(h.url_for('/static/images/delete_tag_icon_gray.png')))
__M_writer(u'"/>\n')
pass
# SOURCE LINE 68
__M_writer(u' </span>\n')
pass
# SOURCE LINE 70
__M_writer(u' \n')
# SOURCE LINE 72
if editable:
# SOURCE LINE 73
if in_form:
# SOURCE LINE 74
__M_writer(u' <textarea class="tag-input" rows=\'1\' cols=\'')
__M_writer(unicode(input_size))
__M_writer(u"'></textarea>\n")
# SOURCE LINE 75
else:
# SOURCE LINE 76
__M_writer(u' <input class="tag-input" type=\'text\' size=\'')
__M_writer(unicode(input_size))
__M_writer(u"'/>\n")
pass
# SOURCE LINE 79
if render_add_tag_button:
# SOURCE LINE 80
__M_writer(u" <img src='")
__M_writer(unicode(h.url_for('/static/images/fugue/tag--plus.png')))
__M_writer(u'\' class="add-tag-button tooltip" title="Add tags"/>\n')
pass
pass
# SOURCE LINE 83
__M_writer(u' </div>\n </div>\n')
return ''
finally:
context.caller_stack._pop_frame()
def __call__(self, trans, **kwargs):
status = kwargs.get('status', None)
message = kwargs.get('message', None)
session = trans.sa_session
# Build a base filter and sort key that is the combination of the saved state and defaults. Saved state takes preference over defaults.
base_filter = {}
if self.default_filter:
base_filter = self.default_filter.copy()
base_sort_key = self.default_sort_key
if self.preserve_state:
pref_name = unicode(self.__class__.__name__ +
self.cur_filter_pref_name)
if pref_name in trans.get_user().preferences:
saved_filter = from_json_string(
trans.get_user().preferences[pref_name])
base_filter.update(saved_filter)
pref_name = unicode(self.__class__.__name__ +
self.cur_sort_key_pref_name)
if pref_name in trans.get_user().preferences:
base_sort_key = from_json_string(
trans.get_user().preferences[pref_name])
# Build initial query
query = self.build_initial_query(session)
query = self.apply_default_filter(trans, query, **kwargs)
# Maintain sort state in generated urls
extra_url_args = {}
# Determine whether use_default_filter flag is set.
use_default_filter_str = kwargs.get('use_default_filter')
use_default_filter = False
if use_default_filter_str:
use_default_filter = (use_default_filter_str.lower() == 'true')
# Process filtering arguments to (a) build a query that represents the filter and (b) builds a
# dictionary that denotes the current filter.
cur_filter_dict = {}
for column in self.columns:
if column.key:
# Get the filter criterion for the column. Precedence is (a) if using default filter, only look there; otherwise,
# (b) look in kwargs; and (c) look in base filter.
column_filter = None
if use_default_filter:
if self.default_filter:
column_filter = self.default_filter.get(column.key)
elif "f-" + column.key in kwargs:
column_filter = kwargs.get("f-" + column.key)
elif column.key in base_filter:
column_filter = base_filter.get(column.key)
# Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings.
def from_json_string_recurse(item):
decoded_list = []
if isinstance(item, basestring):
try:
# Not clear what we're decoding, so recurse to ensure that we catch everything.
decoded_item = from_json_string(item)
if isinstance(decoded_item, list):
decoded_list = from_json_string_recurse(
decoded_item)
else:
decoded_list = [unicode(decoded_item)]
except ValueError:
decoded_list = [unicode(item)]
elif isinstance(item, list):
return_val = []
for element in item:
a_list = from_json_string_recurse(element)
decoded_list = decoded_list + a_list
return decoded_list
# If column filter found, apply it.
if column_filter is not None:
# TextColumns may have a mix of json and strings.
if isinstance(column, TextColumn):
column_filter = from_json_string_recurse(column_filter)
if len(column_filter) == 1:
column_filter = column_filter[0]
# If filter criterion is empty, do nothing.
if column_filter == '':
continue
# Update query.
query = column.filter(trans.sa_session, query,
column_filter)
# Upate current filter dict.
cur_filter_dict[column.key] = column_filter
# Carry filter along to newly generated urls; make sure filter is a string so
# that we can encode to UTF-8 and thus handle user input to filters.
if isinstance(column_filter, list):
# Filter is a list; process each item.
for filter in column_filter:
if not isinstance(filter, basestring):
filter = unicode(filter).encode("utf-8")
extra_url_args["f-" + column.key] = to_json_string(
column_filter)
else:
# Process singleton filter.
if not isinstance(column_filter, basestring):
column_filter = unicode(column_filter)
extra_url_args[
"f-" + column.key] = column_filter.encode("utf-8")
# Process sort arguments.
sort_key = sort_order = None
if 'sort' in kwargs:
sort_key = kwargs['sort']
elif base_sort_key:
sort_key = base_sort_key
encoded_sort_key = sort_key
if sort_key:
if sort_key.startswith("-"):
sort_key = sort_key[1:]
sort_order = 'desc'
query = query.order_by(
self.model_class.table.c.get(sort_key).desc())
else:
sort_order = 'asc'
query = query.order_by(
self.model_class.table.c.get(sort_key).asc())
extra_url_args['sort'] = encoded_sort_key
# There might be a current row
current_item = self.get_current_item(trans)
# Process page number.
if self.use_paging:
if 'page' in kwargs:
if kwargs['page'] == 'all':
page_num = 0
else:
page_num = int(kwargs['page'])
else:
page_num = 1
if page_num == 0:
# Show all rows in page.
total_num_rows = query.count()
page_num = 1
num_pages = 1
else:
# Show a limited number of rows. Before modifying query, get the total number of rows that query
# returns so that the total number of pages can be computed.
total_num_rows = query.count()
query = query.limit(self.num_rows_per_page).offset(
(page_num - 1) * self.num_rows_per_page)
num_pages = int(
math.ceil(float(total_num_rows) / self.num_rows_per_page))
else:
# Defaults.
page_num = 1
num_pages = 1
# Preserve grid state: save current filter and sort key.
if self.preserve_state:
pref_name = unicode(self.__class__.__name__ +
self.cur_filter_pref_name)
trans.get_user().preferences[pref_name] = unicode(
to_json_string(cur_filter_dict))
if sort_key:
pref_name = unicode(self.__class__.__name__ +
self.cur_sort_key_pref_name)
trans.get_user().preferences[pref_name] = unicode(
to_json_string(sort_key))
trans.sa_session.flush()
# Log grid view.
context = unicode(self.__class__.__name__)
params = cur_filter_dict.copy()
params['sort'] = sort_key
params['async'] = ('async' in kwargs)
trans.log_action(unicode("grid.view"), context, params)
# Render grid.
def url(*args, **kwargs):
# Only include sort/filter arguments if not linking to another
# page. This is a bit of a hack.
if 'action' in kwargs:
new_kwargs = dict()
else:
new_kwargs = dict(extra_url_args)
# Extend new_kwargs with first argument if found
if len(args) > 0:
new_kwargs.update(args[0])
new_kwargs.update(kwargs)
# We need to encode item ids
if 'id' in new_kwargs:
id = new_kwargs['id']
if isinstance(id, list):
new_args['id'] = [trans.security.encode_id(i) for i in id]
else:
new_kwargs['id'] = trans.security.encode_id(id)
return url_for(**new_kwargs)
async_request = ((self.use_async) and ('async' in kwargs)
and (kwargs['async'] in ['True', 'true']))
return trans.fill_template(
iff(async_request, self.async_template, self.template),
grid=self,
query=query,
cur_page_num=page_num,
num_pages=num_pages,
default_filter_dict=self.default_filter,
cur_filter_dict=cur_filter_dict,
sort_key=sort_key,
encoded_sort_key=encoded_sort_key,
sort_order=sort_order,
current_item=current_item,
ids=kwargs.get('id', []),
url=url,
message_type=status,
message=message,
# Pass back kwargs so that grid template can set and use args without grid explicitly having to pass them.
kwargs=kwargs)
class InstalledRepositoryGrid(grids.Grid):
class ToolShedStatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
if tool_shed_repository.tool_shed_status:
tool_shed_status_str = ''
if tool_shed_repository.is_deprecated_in_tool_shed:
tool_shed_status_str += generate_deprecated_repository_img_str(
include_mouse_over=True)
if tool_shed_repository.is_latest_installable_revision:
tool_shed_status_str += generate_latest_revision_img_str(
include_mouse_over=True)
if tool_shed_repository.revision_update_available:
tool_shed_status_str += generate_revision_updates_img_str(
include_mouse_over=True)
if tool_shed_repository.upgrade_available:
tool_shed_status_str += generate_revision_upgrades_img_str(
include_mouse_over=True)
if tool_shed_repository.includes_workflows:
tool_shed_status_str += generate_includes_workflows_img_str(
include_mouse_over=True)
else:
tool_shed_status_str = generate_unknown_img_str(
include_mouse_over=True)
return tool_shed_status_str
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return util.unicodify(tool_shed_repository.description)
class OwnerColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.owner)
class RevisionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.changeset_revision)
class StatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return suc.get_tool_shed_repository_status_label(
trans.app, tool_shed_repository)
class ToolShedColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.tool_shed
class DeletedColumn(grids.DeletedColumn):
def get_accepted_filters(self):
""" Returns a list of accepted filters for this column. """
accepted_filter_labels_and_vals = {
"Active": "False",
"Deactivated or uninstalled": "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))
return accepted_filters
# Grid definition
title = "Installed tool shed repositories"
model_class = tool_shed_install.ToolShedRepository
template = '/admin/tool_shed_repository/grid.mako'
default_sort_key = "name"
columns = [
ToolShedStatusColumn(label=""),
NameColumn(
label="Name",
key="name",
link=(lambda item: iff(
item.status in [
tool_shed_install.ToolShedRepository.installation_status.
CLONING
], None, dict(operation="manage_repository", id=item.id))),
attach_popup=True),
DescriptionColumn(label="Description"),
OwnerColumn(label="Owner"),
RevisionColumn(label="Revision"),
StatusColumn(label="Installation Status", filterable="advanced"),
ToolShedColumn(label="Tool shed"),
# Columns that are valid for filtering but are not visible.
DeletedColumn(label="Status",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction(
label="Update tool shed status",
url_args=dict(
controller='admin_toolshed',
action='update_tool_shed_status_for_installed_repository',
all_installed_repositories=True),
inbound=False)
]
operations = [ grids.GridOperation( label="Update tool shed status",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='update tool shed status' ) ),
grids.GridOperation( label="Get updates",
condition=( lambda item: \
not item.deleted and \
item.revision_update_available and \
item.status not in \
[ tool_shed_install.ToolShedRepository.installation_status.ERROR,
tool_shed_install.ToolShedRepository.installation_status.NEW ] ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='get updates' ) ),
grids.GridOperation( label="Install latest revision",
condition=( lambda item: item.upgrade_available ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='install latest revision' ) ),
grids.GridOperation( label="Install",
condition=( lambda item: \
not item.deleted and \
item.status == tool_shed_install.ToolShedRepository.installation_status.NEW ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='manage_repository',
operation='install' ) ),
grids.GridOperation( label="Deactivate or uninstall",
condition=( lambda item: \
not item.deleted and \
item.status != tool_shed_install.ToolShedRepository.installation_status.NEW ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='deactivate or uninstall' ) ),
grids.GridOperation( label="Reset to install",
condition=( lambda item: \
( item.status == tool_shed_install.ToolShedRepository.installation_status.ERROR ) ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='reset to install' ) ),
grids.GridOperation( label="Activate or reinstall",
condition=( lambda item: item.deleted ),
allow_multiple=False,
target=None,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='activate or reinstall' ) ),
grids.GridOperation( label="Purge",
condition=( lambda item: item.is_new ),
allow_multiple=False,
target=None,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='purge' ) ) ]
standard_filters = []
default_filter = dict(deleted="False")
num_rows_per_page = 50
preserve_state = False
use_paging = False
def build_initial_query(self, trans, **kwd):
return trans.install_model.context.query( self.model_class ) \
.order_by( self.model_class.table.c.tool_shed,
self.model_class.table.c.name,
self.model_class.table.c.owner,
self.model_class.table.c.ctx_rev )
@property
def legend(self):
legend_str = '%s Updates are available in the Tool Shed for this revision<br/>' % generate_revision_updates_img_str(
)
legend_str += '%s A newer installable revision is available for this repository<br/>' % generate_revision_upgrades_img_str(
)
legend_str += '%s This is the latest installable revision of this repository<br/>' % generate_latest_revision_img_str(
)
legend_str += '%s This repository is deprecated in the Tool Shed<br/>' % generate_deprecated_repository_img_str(
)
legend_str += '%s This repository contains exported workflows<br/>' % generate_includes_workflows_img_str(
)
legend_str += '%s Unable to get information from the Tool Shed<br/>' % generate_unknown_img_str(
)
return legend_str
class RepositoryInstallationGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.name
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.description
class OwnerColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.owner
class RevisionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.changeset_revision
class StatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
status_label = tool_shed_repository.status
if tool_shed_repository.status in [
trans.install_model.ToolShedRepository.installation_status.
CLONING, trans.install_model.ToolShedRepository.
installation_status.SETTING_TOOL_VERSIONS,
trans.install_model.ToolShedRepository.installation_status.
INSTALLING_TOOL_DEPENDENCIES,
trans.install_model.ToolShedRepository.installation_status.
LOADING_PROPRIETARY_DATATYPES
]:
bgcolor = trans.install_model.ToolShedRepository.states.INSTALLING
elif tool_shed_repository.status in [
trans.install_model.ToolShedRepository.installation_status.
NEW, trans.install_model.ToolShedRepository.
installation_status.UNINSTALLED
]:
bgcolor = trans.install_model.ToolShedRepository.states.UNINSTALLED
elif tool_shed_repository.status in [
trans.install_model.ToolShedRepository.installation_status.
ERROR
]:
bgcolor = trans.install_model.ToolShedRepository.states.ERROR
elif tool_shed_repository.status in [
trans.install_model.ToolShedRepository.installation_status.
DEACTIVATED
]:
bgcolor = trans.install_model.ToolShedRepository.states.WARNING
elif tool_shed_repository.status in [
trans.install_model.ToolShedRepository.installation_status.
INSTALLED
]:
if tool_shed_repository.missing_tool_dependencies or tool_shed_repository.missing_repository_dependencies:
bgcolor = trans.install_model.ToolShedRepository.states.WARNING
if tool_shed_repository.missing_tool_dependencies and not tool_shed_repository.missing_repository_dependencies:
status_label = '%s, missing tool dependencies' % status_label
if tool_shed_repository.missing_repository_dependencies and not tool_shed_repository.missing_tool_dependencies:
status_label = '%s, missing repository dependencies' % status_label
if tool_shed_repository.missing_tool_dependencies and tool_shed_repository.missing_repository_dependencies:
status_label = '%s, missing both tool and repository dependencies' % status_label
if not tool_shed_repository.missing_tool_dependencies and not tool_shed_repository.missing_repository_dependencies:
bgcolor = trans.install_model.ToolShedRepository.states.OK
else:
bgcolor = trans.install_model.ToolShedRepository.states.ERROR
rval = '<div class="count-box state-color-%s" id="RepositoryStatus-%s">%s</div>' % \
( bgcolor, trans.security.encode_id( tool_shed_repository.id ), status_label )
return rval
title = "Monitor installing tool shed repositories"
template = "admin/tool_shed_repository/repository_installation_grid.mako"
model_class = tool_shed_install.ToolShedRepository
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = False
columns = [
NameColumn( "Name",
link=( lambda item: iff( item.status in \
[ tool_shed_install.ToolShedRepository.installation_status.NEW,
tool_shed_install.ToolShedRepository.installation_status.CLONING,
tool_shed_install.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
tool_shed_install.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
tool_shed_install.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
tool_shed_install.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES,
tool_shed_install.ToolShedRepository.installation_status.UNINSTALLED ], \
None, dict( action="manage_repository", id=item.id ) ) ),
filterable="advanced" ),
DescriptionColumn( "Description",
filterable="advanced" ),
OwnerColumn( "Owner",
filterable="advanced" ),
RevisionColumn( "Revision",
filterable="advanced" ),
StatusColumn( "Installation Status",
filterable="advanced",
label_id_prefix="RepositoryStatus-" )
]
operations = []
def build_initial_query(self, trans, **kwd):
clause_list = []
tool_shed_repository_ids = util.listify(
kwd.get('tool_shed_repository_ids', None))
if tool_shed_repository_ids:
for tool_shed_repository_id in tool_shed_repository_ids:
clause_list.append(self.model_class.table.c.id == trans.
security.decode_id(tool_shed_repository_id))
if clause_list:
return trans.install_model.context.query( self.model_class ) \
.filter( or_( *clause_list ) )
for tool_shed_repository in trans.install_model.context.query( self.model_class ) \
.filter( self.model_class.table.c.deleted == False ):
if tool_shed_repository.status in [
trans.install_model.ToolShedRepository.installation_status.
NEW, trans.install_model.ToolShedRepository.
installation_status.CLONING,
trans.install_model.ToolShedRepository.installation_status.
SETTING_TOOL_VERSIONS,
trans.install_model.ToolShedRepository.installation_status.
INSTALLING_TOOL_DEPENDENCIES,
trans.install_model.ToolShedRepository.installation_status.
LOADING_PROPRIETARY_DATATYPES
]:
clause_list.append(
self.model_class.table.c.id == tool_shed_repository.id)
if clause_list:
return trans.install_model.context.query( self.model_class ) \
.filter( or_( *clause_list ) )
return trans.install_model.context.query( self.model_class ) \
.filter( self.model_class.table.c.status == trans.install_model.ToolShedRepository.installation_status.NEW )
def apply_query_filter(self, trans, query, **kwd):
tool_shed_repository_id = kwd.get('tool_shed_repository_id', None)
if tool_shed_repository_id:
return query.filter_by(tool_shed_repository_id=trans.security.
decode_id(tool_shed_repository_id))
return query
def __call__(self, trans, **kwargs):
# Get basics.
webapp = kwargs.get('webapp', 'galaxy')
status = kwargs.get('status', None)
message = kwargs.get('message', None)
# Build a base filter and sort key that is the combination of the saved state and defaults.
# Saved state takes preference over defaults.
base_filter = {}
if self.default_filter:
# default_filter is a dictionary that provides a default set of filters based on the grid's columns.
base_filter = self.default_filter.copy()
base_sort_key = self.default_sort_key
if self.preserve_state:
pref_name = unicode(self.__class__.__name__ +
self.cur_filter_pref_name)
if pref_name in trans.get_user().preferences:
saved_filter = from_json_string(
trans.get_user().preferences[pref_name])
base_filter.update(saved_filter)
pref_name = unicode(self.__class__.__name__ +
self.cur_sort_key_pref_name)
if pref_name in trans.get_user().preferences:
base_sort_key = from_json_string(
trans.get_user().preferences[pref_name])
# Build initial query
query = self.build_initial_query(trans, **kwargs)
query = self.apply_query_filter(trans, query, **kwargs)
# Maintain sort state in generated urls
extra_url_args = {}
# Determine whether use_default_filter flag is set.
use_default_filter_str = kwargs.get('use_default_filter')
use_default_filter = False
if use_default_filter_str:
use_default_filter = (use_default_filter_str.lower() == 'true')
# Process filtering arguments to (a) build a query that represents the filter and (b) build a
# dictionary that denotes the current filter.
cur_filter_dict = {}
for column in self.columns:
if column.key:
# Get the filter criterion for the column. Precedence is (a) if using default filter, only look there; otherwise,
# (b) look in kwargs; and (c) look in base filter.
column_filter = None
if use_default_filter:
if self.default_filter:
column_filter = self.default_filter.get(column.key)
elif "f-" + column.model_class.__name__ + ".%s" % column.key in kwargs:
# Queries that include table joins cannot guarantee unique column names. This problem is
# handled by setting the column_filter value to <TableName>.<ColumnName>.
column_filter = kwargs.get("f-" +
column.model_class.__name__ +
".%s" % column.key)
elif "f-" + column.key in kwargs:
column_filter = kwargs.get("f-" + column.key)
elif column.key in base_filter:
column_filter = base_filter.get(column.key)
# Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings.
def from_json_string_recurse(item):
decoded_list = []
if isinstance(item, basestring):
try:
# Not clear what we're decoding, so recurse to ensure that we catch everything.
decoded_item = from_json_string(item)
if isinstance(decoded_item, list):
decoded_list = from_json_string_recurse(
decoded_item)
else:
decoded_list = [unicode(decoded_item)]
except ValueError:
decoded_list = [unicode(item)]
elif isinstance(item, list):
return_val = []
for element in item:
a_list = from_json_string_recurse(element)
decoded_list = decoded_list + a_list
return decoded_list
# If column filter found, apply it.
if column_filter is not None:
# TextColumns may have a mix of json and strings.
if isinstance(column, TextColumn):
column_filter = from_json_string_recurse(column_filter)
if len(column_filter) == 1:
column_filter = column_filter[0]
# Interpret ',' as a separator for multiple terms.
if isinstance(
column_filter,
basestring) and column_filter.find(',') != -1:
column_filter = column_filter.split(',')
# If filter criterion is empty, do nothing.
if column_filter == '':
continue
# Update query.
query = column.filter(trans, trans.user, query,
column_filter)
# Upate current filter dict.
cur_filter_dict[column.key] = column_filter
# Carry filter along to newly generated urls; make sure filter is a string so
# that we can encode to UTF-8 and thus handle user input to filters.
if isinstance(column_filter, list):
# Filter is a list; process each item.
for filter in column_filter:
if not isinstance(filter, basestring):
filter = unicode(filter).encode("utf-8")
extra_url_args["f-" + column.key] = to_json_string(
column_filter)
else:
# Process singleton filter.
if not isinstance(column_filter, basestring):
column_filter = unicode(column_filter)
extra_url_args[
"f-" + column.key] = column_filter.encode("utf-8")
# Process sort arguments.
sort_key = None
if 'sort' in kwargs:
sort_key = kwargs['sort']
elif base_sort_key:
sort_key = base_sort_key
if sort_key:
ascending = not (sort_key.startswith("-"))
# Queries that include table joins cannot guarantee unique column names. This problem is
# handled by setting the column_filter value to <TableName>.<ColumnName>.
table_name = None
if sort_key.find('.') > -1:
a_list = sort_key.split('.')
if ascending:
table_name = a_list[0]
else:
table_name = a_list[0][1:]
column_name = a_list[1]
elif ascending:
column_name = sort_key
else:
column_name = sort_key[1:]
# Sort key is a column key.
for column in self.columns:
if column.key and column.key.find('.') > -1:
column_key = column.key.split('.')[1]
else:
column_key = column.key
if (table_name is None
or table_name == column.model_class.__name__
) and column_key == column_name:
query = column.sort(trans,
query,
ascending,
column_name=column_name)
break
extra_url_args['sort'] = sort_key
# There might be a current row
current_item = self.get_current_item(trans, **kwargs)
# Process page number.
if self.use_paging:
if 'page' in kwargs:
if kwargs['page'] == 'all':
page_num = 0
else:
page_num = int(kwargs['page'])
else:
page_num = 1
if page_num == 0:
# Show all rows in page.
total_num_rows = query.count()
page_num = 1
num_pages = 1
else:
# Show a limited number of rows. Before modifying query, get the total number of rows that query
# returns so that the total number of pages can be computed.
total_num_rows = query.count()
query = query.limit(self.num_rows_per_page).offset(
(page_num - 1) * self.num_rows_per_page)
num_pages = int(
math.ceil(float(total_num_rows) / self.num_rows_per_page))
else:
# Defaults.
page_num = 1
num_pages = 1
# There are some places in grid templates where it's useful for a grid
# to have its current filter.
self.cur_filter_dict = cur_filter_dict
# Preserve grid state: save current filter and sort key.
if self.preserve_state:
pref_name = unicode(self.__class__.__name__ +
self.cur_filter_pref_name)
trans.get_user().preferences[pref_name] = unicode(
to_json_string(cur_filter_dict))
if sort_key:
pref_name = unicode(self.__class__.__name__ +
self.cur_sort_key_pref_name)
trans.get_user().preferences[pref_name] = unicode(
to_json_string(sort_key))
trans.sa_session.flush()
# Log grid view.
context = unicode(self.__class__.__name__)
params = cur_filter_dict.copy()
params['sort'] = sort_key
params['async'] = ('async' in kwargs)
params['webapp'] = webapp
trans.log_action(trans.get_user(), unicode("grid.view"), context,
params)
# Render grid.
def url(*args, **kwargs):
# Only include sort/filter arguments if not linking to another
# page. This is a bit of a hack.
if 'action' in kwargs:
new_kwargs = dict()
else:
new_kwargs = dict(extra_url_args)
# Extend new_kwargs with first argument if found
if len(args) > 0:
new_kwargs.update(args[0])
new_kwargs.update(kwargs)
# We need to encode item ids
if 'id' in new_kwargs:
id = new_kwargs['id']
if isinstance(id, list):
new_args['id'] = [trans.security.encode_id(i) for i in id]
else:
new_kwargs['id'] = trans.security.encode_id(id)
return url_for(**new_kwargs)
self.use_panels = (kwargs.get('use_panels', False)
in [True, 'True', 'true'])
async_request = ((self.use_async) and (kwargs.get('async', False)
in [True, 'True', 'true']))
# Currently, filling the template returns a str object; this requires decoding the string into a
# unicode object within mako templates. What probably should be done is to return the template as
# utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid
# results via a controller method, which is require substantial changes. Hence, for now, return grid
# as str.
return trans.fill_template(
iff(async_request, self.async_template, self.template),
grid=self,
query=query,
cur_page_num=page_num,
num_pages=num_pages,
num_page_links=self.num_page_links,
default_filter_dict=self.default_filter,
cur_filter_dict=cur_filter_dict,
sort_key=sort_key,
current_item=current_item,
ids=kwargs.get('id', []),
url=url,
status=status,
message=message,
use_panels=self.use_panels,
webapp=webapp,
show_item_checkboxes=(kwargs.get('show_item_checkboxes', '')
in ['True', 'true']),
# Pass back kwargs so that grid template can set and use args without
# grid explicitly having to pass them.
kwargs=kwargs)
class RequestTypeGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, request_type):
return escape(request_type.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, request_type):
return escape(request_type.desc)
class RequestFormColumn(grids.TextColumn):
def get_value(self, trans, grid, request_type):
return escape(request_type.request_form.name)
class SampleFormColumn(grids.TextColumn):
def get_value(self, trans, grid, request_type):
return escape(request_type.sample_form.name)
class ExternalServiceColumn(grids.IntegerColumn):
def get_value(self, trans, grid, request_type):
if request_type.external_services:
return len(request_type.external_services)
return 'No external service assigned'
# Grid definition
title = "Request Types"
template = "admin/request_type/grid.mako"
model_class = model.RequestType
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict(deleted="False")
columns = [
NameColumn("Name",
key="name",
link=(lambda item: iff(
item.deleted, None,
dict(operation="view_request_type", id=item.id))),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description", key='desc', filterable="advanced"),
RequestFormColumn("Request Form",
link=(lambda item: iff(
item.deleted, None,
dict(operation="view_form_definition",
id=item.request_form.id)))),
SampleFormColumn(
"Sample Form",
link=(lambda item: iff(
item.deleted, None,
dict(operation="view_form_definition", id=item.sample_form.id))
)),
ExternalServiceColumn("External Services"),
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Edit request type",
allow_multiple=False,
condition=(lambda item: not item.deleted)),
grids.GridOperation("Edit permissions",
allow_multiple=False,
condition=(lambda item: not item.deleted)),
grids.GridOperation(
"Use run details template",
allow_multiple=False,
condition=(
lambda item: not item.deleted and not item.run_details)),
grids.GridOperation("Delete",
allow_multiple=True,
condition=(lambda item: not item.deleted)),
grids.GridOperation("Undelete", condition=(lambda item: item.deleted)),
]
global_actions = [
grids.GridAction(
"Create new request type",
dict(controller='request_type', action='create_request_type'))
]
def render_render_grid_column_filter(context, grid, column):
context.caller_stack._push_frame()
try:
basestring = context.get('basestring', UNDEFINED)
cur_filter_dict = context.get('cur_filter_dict', UNDEFINED)
url = context.get('url', UNDEFINED)
h = context.get('h', UNDEFINED)
list = context.get('list', UNDEFINED)
len = context.get('len', UNDEFINED)
dict = context.get('dict', UNDEFINED)
enumerate = context.get('enumerate', UNDEFINED)
isinstance = context.get('isinstance', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 7
__M_writer(u'\n <tr>\n ')
# SOURCE LINE 9
column_label = column.label
if column.filterable == "advanced":
column_label = column_label.lower()
# SOURCE LINE 13
__M_writer(u'\n')
# SOURCE LINE 14
if column.filterable == "advanced":
# SOURCE LINE 15
__M_writer(
u' <td align="left" style="padding-left: 10px">')
__M_writer(unicode(column_label))
__M_writer(u':</td>\n')
# SOURCE LINE 17
__M_writer(u' <td style="padding: 0;">\n')
# SOURCE LINE 18
if isinstance(column, TextColumn):
# SOURCE LINE 19
__M_writer(
u' <form class="text-filter-form" column_key="')
__M_writer(unicode(column.key))
__M_writer(u'" action="')
__M_writer(unicode(url(dict())))
__M_writer(u'" method="get" >\n')
# SOURCE LINE 21
for temp_column in grid.columns:
# SOURCE LINE 22
if temp_column.key in cur_filter_dict:
# SOURCE LINE 23
__M_writer(u' ')
value = cur_filter_dict[temp_column.key]
__M_writer(u'\n')
# SOURCE LINE 24
if value != "All":
# SOURCE LINE 25
__M_writer(u' ')
if isinstance(temp_column, TextColumn):
value = h.to_json_string(value)
# SOURCE LINE 28
__M_writer(
u'\n <input type="hidden" id="'
)
# SOURCE LINE 29
__M_writer(unicode(temp_column.key))
__M_writer(u'" name="f-')
__M_writer(unicode(temp_column.key))
__M_writer(u'" value=\'')
__M_writer(unicode(value))
__M_writer(u"'/>\n")
# SOURCE LINE 33
__M_writer(u' \n')
# SOURCE LINE 35
__M_writer(u' <span id="')
__M_writer(unicode(column.key))
__M_writer(u'-filtering-criteria">\n')
# SOURCE LINE 36
if column.key in cur_filter_dict:
# SOURCE LINE 37
__M_writer(u' ')
column_filter = cur_filter_dict[column.key]
__M_writer(u'\n')
# SOURCE LINE 38
if isinstance(column_filter, basestring):
# SOURCE LINE 39
if column_filter != "All":
# SOURCE LINE 40
__M_writer(
u" <span class='text-filter-val'>\n "
)
# SOURCE LINE 41
__M_writer(unicode(cur_filter_dict[column.key]))
__M_writer(
u'\n ')
# SOURCE LINE 42
filter_all = GridColumnFilter("", {column.key: "All"})
__M_writer(
u'\n <a href="'
)
# SOURCE LINE 43
__M_writer(unicode(url(filter_all.get_url_args())))
__M_writer(
u'"><span class="delete-search-icon" /></a> \n </span>\n'
)
# SOURCE LINE 46
elif isinstance(column_filter, list):
# SOURCE LINE 47
for i, filter in enumerate(column_filter):
# SOURCE LINE 48
if i > 0:
# SOURCE LINE 49
__M_writer(
u' ,\n')
# SOURCE LINE 51
__M_writer(
u" <span class='text-filter-val'>"
)
__M_writer(unicode(filter))
__M_writer(
u'\n ')
# SOURCE LINE 52
new_filter = list(column_filter)
del new_filter[i]
new_column_filter = GridColumnFilter(
"", {column.key: h.to_json_string(new_filter)})
# SOURCE LINE 56
__M_writer(
u'\n <a href="'
)
# SOURCE LINE 57
__M_writer(
unicode(url(new_column_filter.get_url_args())))
__M_writer(
u'"><span class="delete-search-icon" /></a>\n </span>\n'
)
# SOURCE LINE 62
__M_writer(u' </span>\n')
# SOURCE LINE 64
__M_writer(
u' <span class="search-box">\n '
)
# SOURCE LINE 65
# Set value, size of search input field. Minimum size is 20 characters.
value = iff(column.filterable == "standard", column.label.lower(),
"")
size = len(value)
if size < 20:
size = 20
# +4 to account for search icon/button.
size = size + 4
# SOURCE LINE 73
__M_writer(
u'\n <input class="search-box-input" id="input-'
)
# SOURCE LINE 74
__M_writer(unicode(column.key))
__M_writer(u'-filter" name="f-')
__M_writer(unicode(column.key))
__M_writer(u'" type="text" value="')
__M_writer(unicode(value))
__M_writer(u'" size="')
__M_writer(unicode(size))
__M_writer(
u'"/>\n <button class="submit-image" type="submit" title=\'Search\'><span style="display: none;"></button>\n </span>\n </form>\n'
)
# SOURCE LINE 78
else:
# SOURCE LINE 79
__M_writer(u' <span id="')
__M_writer(unicode(column.key))
__M_writer(u'-filtering-criteria">\n')
# SOURCE LINE 80
for i, filter in enumerate(column.get_accepted_filters()):
# SOURCE LINE 81
__M_writer(u' ')
# HACK: we know that each filter will have only a single argument, so get that single argument.
for key, arg in filter.args.items():
filter_key = key
filter_arg = arg
# SOURCE LINE 86
__M_writer(u'\n')
# SOURCE LINE 87
if i > 0:
# SOURCE LINE 88
__M_writer(u' |\n')
# SOURCE LINE 90
if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[
column.key] == filter.args[column.key]:
# SOURCE LINE 91
__M_writer(
u' <span class="categorical-filter '
)
__M_writer(unicode(column.key))
__M_writer(u'-filter current-filter">')
__M_writer(unicode(filter.label))
__M_writer(u'</span>\n')
# SOURCE LINE 92
else:
# SOURCE LINE 93
__M_writer(
u' <span class="categorical-filter '
)
__M_writer(unicode(column.key))
__M_writer(
u'-filter">\n <a href="'
)
# SOURCE LINE 94
__M_writer(unicode(url(filter.get_url_args())))
__M_writer(u'" filter_key="')
__M_writer(unicode(filter_key))
__M_writer(u'" filter_val="')
__M_writer(unicode(filter_arg))
__M_writer(u'">')
__M_writer(unicode(filter.label))
__M_writer(u'</a>\n </span>\n')
# SOURCE LINE 98
__M_writer(u' </span>\n')
# SOURCE LINE 100
__M_writer(u' </td>\n </tr>\n')
return ''
finally:
context.caller_stack._pop_frame()
class ExternalServiceGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, external_service):
return external_service.name
class ExternalServiceTypeColumn(grids.TextColumn):
def get_value(self, trans, grid, external_service):
try:
return trans.app.external_service_types.all_external_service_types[
external_service.external_service_type_id].name
except KeyError:
return 'Error in loading external_service type: %s' % external_service.external_service_type_id
# Grid definition
title = "External Services"
template = "admin/external_service/grid.mako"
model_class = model.ExternalService
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict(deleted="False")
columns = [
NameColumn("Name",
key="name",
link=(lambda item: iff(item.deleted, None,
dict(operation="view", id=item.id))),
attach_popup=True,
filterable="advanced"),
grids.TextColumn("Description",
key='description',
filterable="advanced"),
ExternalServiceTypeColumn("External Service Type"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Edit",
allow_multiple=False,
condition=(lambda item: not item.deleted)),
grids.GridOperation("Delete",
allow_multiple=True,
condition=(lambda item: not item.deleted)),
grids.GridOperation("Undelete", condition=(lambda item: item.deleted)),
]
global_actions = [
grids.GridAction(
"Reload external service types",
dict(controller='external_service',
action='reload_external_service_types')),
grids.GridAction(
"Create new external service",
dict(controller='external_service',
action='create_external_service'))
]
except KeyError, e:
return 'Error in loading external_service type: %s' % external_service.external_service_type_id
# Grid definition
title = "External Services"
template = "admin/external_service/grid.mako"
model_class = model.ExternalService
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict( deleted="False" )
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: iff( item.deleted, None, dict( operation="view", id=item.id ) ) ),
attach_popup=True,
filterable="advanced" ),
grids.TextColumn( "Description",
key='description',
filterable="advanced" ),
ExternalServiceTypeColumn( "External Service Type" ),
grids.GridColumn( "Last Updated",
key="update_time",
format=time_ago ),
grids.DeletedColumn( "Deleted",
key="deleted",
visible=False,
filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search",
def render_render_individual_tagging_element(context,user=None,tagged_item=None,elt_context=None,use_toggle_link=True,in_form=False,input_size='15',tag_click_fn='default_tag_click_fn',get_toggle_link_text_fn='default_get_toggle_link_text_fn',editable=True,render_add_tag_button=True):
context.caller_stack._push_frame()
try:
isinstance = context.get('isinstance', UNDEFINED)
unicode = context.get('unicode', UNDEFINED)
int = context.get('int', UNDEFINED)
h = context.get('h', UNDEFINED)
self = context.get('self', UNDEFINED)
dict = context.get('dict', UNDEFINED)
str = context.get('str', UNDEFINED)
trans = context.get('trans', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 122
__M_writer(u'\n')
# SOURCE LINE 124
__M_writer(u' ')
# Useful ids.
tagged_item_id = str( trans.security.encode_id ( tagged_item.id ) )
elt_id = int ( floor ( random()*maxint ) )
# Get list of user's item tags. TODO: implement owner_tags for all taggable objects and use here.
item_tags = [ tag for tag in tagged_item.tags if ( tag.user == user ) ]
# SOURCE LINE 131
__M_writer(u'\n \n')
# SOURCE LINE 134
__M_writer(u' ')
__M_writer(unicode(self.render_tagging_element_html(elt_id=elt_id, tags=item_tags, editable=editable, use_toggle_link=use_toggle_link, input_size=input_size, in_form=in_form, render_add_tag_button=render_add_tag_button)))
__M_writer(u'\n \n')
# SOURCE LINE 137
__M_writer(u' <script type="text/javascript">\n //\n // Set up autocomplete tagger.\n //\n\n //\n // Default function get text to display on the toggle link.\n //\n var default_get_toggle_link_text_fn = function(tags)\n {\n var text = "";\n var num_tags = obj_length(tags);\n if (num_tags != 0)\n {\n text = num_tags + (num_tags != 1 ? " Tags" : " Tag");\n /*\n // Show first N tags; hide the rest.\n var max_to_show = 1;\n \n // Build tag string.\n var tag_strs = new Array();\n var count = 0;\n for (tag_name in tags)\n {\n tag_value = tags[tag_name];\n tag_strs[tag_strs.length] = build_tag_str(tag_name, tag_value);\n if (++count == max_to_show)\n break;\n }\n tag_str = tag_strs.join(", ");\n \n // Finalize text.\n var num_tags_hiding = num_tags - max_to_show;\n text = "Tags: " + tag_str + \n (num_tags_hiding != 0 ? " and " + num_tags_hiding + " more" : "");\n */\n }\n else\n {\n // No tags.\n text = "Add tags";\n }\n return text;\n };\n \n // Default function to handle a tag click.\n var default_tag_click_fn = function(tag_name, tag_value) { };\n \n ')
# SOURCE LINE 185
## Build dict of tag name, values.
tag_names_and_values = dict()
for tag in item_tags:
tag_name = tag.user_tname
tag_value = ""
if tag.value is not None:
tag_value = tag.user_value
## Tag names and values may be string or unicode object.
if isinstance( tag_name, str ):
tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8')
else: ## isInstance( tag_name, unicode ):
tag_names_and_values[tag_name] = tag_value
# SOURCE LINE 198
__M_writer(u'\n var options =\n {\n tags : ')
# SOURCE LINE 201
__M_writer(unicode(h.to_json_string(tag_names_and_values)))
__M_writer(u',\n editable : ')
# SOURCE LINE 202
__M_writer(unicode(iff( editable, 'true', 'false' )))
__M_writer(u',\n get_toggle_link_text_fn: ')
# SOURCE LINE 203
__M_writer(unicode(get_toggle_link_text_fn))
__M_writer(u',\n tag_click_fn: ')
# SOURCE LINE 204
__M_writer(unicode(tag_click_fn))
__M_writer(u',\n')
# SOURCE LINE 206
__M_writer(u' ajax_autocomplete_tag_url: "')
__M_writer(unicode(h.url_for( controller='/tag', action='tag_autocomplete_data', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__ )))
__M_writer(u'",\n ajax_add_tag_url: "')
# SOURCE LINE 207
__M_writer(unicode(h.url_for( controller='/tag', action='add_tag_async', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )))
__M_writer(u'",\n ajax_delete_tag_url: "')
# SOURCE LINE 208
__M_writer(unicode(h.url_for( controller='/tag', action='remove_tag_async', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )))
__M_writer(u'",\n delete_tag_img: "')
# SOURCE LINE 209
__M_writer(unicode(h.url_for('/static/images/delete_tag_icon_gray.png')))
__M_writer(u'",\n delete_tag_img_rollover: "')
# SOURCE LINE 210
__M_writer(unicode(h.url_for('/static/images/delete_tag_icon_white.png')))
__M_writer(u'",\n use_toggle_link: ')
# SOURCE LINE 211
__M_writer(unicode(iff( use_toggle_link, 'true', 'false' )))
__M_writer(u"\n };\n \n $('#")
# SOURCE LINE 214
__M_writer(unicode(elt_id))
__M_writer(u"').autocomplete_tagging(options);\n </script>\n \n")
# SOURCE LINE 218
__M_writer(u' <style>\n .tag-area {\n display: ')
# SOURCE LINE 220
__M_writer(unicode(iff( use_toggle_link, "none", "block" )))
__M_writer(u';\n }\n </style>\n\n <noscript>\n <style>\n .tag-area {\n display: block;\n }\n </style>\n </noscript>\n')
return ''
finally:
context.caller_stack._pop_frame()
def render_render_tagging_element_html(context,elt_id=None,tags=None,editable=True,use_toggle_link=True,input_size='15',in_form=False,tag_type='individual',render_add_tag_button=True):
context.caller_stack._push_frame()
try:
h = context.get('h', UNDEFINED)
unicode = context.get('unicode', UNDEFINED)
isinstance = context.get('isinstance', UNDEFINED)
len = context.get('len', UNDEFINED)
str = context.get('str', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 20
__M_writer(u'\n')
# SOURCE LINE 22
__M_writer(u' ')
num_tags = len( tags )
# SOURCE LINE 24
__M_writer(u'\n <div class="tag-element"\n')
# SOURCE LINE 26
if elt_id:
# SOURCE LINE 27
__M_writer(u' id="')
__M_writer(unicode(elt_id))
__M_writer(u'"\n')
pass
# SOURCE LINE 30
if num_tags == 0 and not editable:
# SOURCE LINE 31
__M_writer(u' style="display: none"\n')
pass
# SOURCE LINE 33
__M_writer(u' >\n')
# SOURCE LINE 34
if use_toggle_link:
# SOURCE LINE 35
__M_writer(u' <a class="toggle-link" href="#">')
__M_writer(unicode(num_tags))
__M_writer(u' Tag')
__M_writer(unicode(iff( num_tags == 1, "", "s")))
__M_writer(u'</a>\n')
pass
# SOURCE LINE 37
__M_writer(u' <div class="tag-area \n')
# SOURCE LINE 38
if tag_type == 'individual':
# SOURCE LINE 39
__M_writer(u' individual-tag-area\n')
pass
# SOURCE LINE 41
__M_writer(u' ">\n\n')
# SOURCE LINE 44
for tag in tags:
# SOURCE LINE 45
__M_writer(u' ')
## Handle both Tag and ItemTagAssociation objects.
if isinstance( tag, Tag ):
tag_name = tag.name
tag_value = None
elif isinstance( tag, ItemTagAssociation ):
tag_name = tag.user_tname
tag_value = tag.user_value
## Convert tag name, value to unicode.
if isinstance( tag_name, str ):
tag_name = unicode( escape( tag_name ), 'utf-8' )
if tag_value:
tag_value = unicode( escape( tag_value ), 'utf-8' )
if tag_value:
tag_str = tag_name + ":" + tag_value
else:
tag_str = tag_name
# SOURCE LINE 62
__M_writer(u'\n <span class="tag-button">\n <span class="tag-name">')
# SOURCE LINE 64
__M_writer(unicode(tag_str))
__M_writer(u'</span>\n')
# SOURCE LINE 65
if editable:
# SOURCE LINE 66
__M_writer(u' <img class="delete-tag-img" src="')
__M_writer(unicode(h.url_for('/static/images/delete_tag_icon_gray.png')))
__M_writer(u'"/>\n')
pass
# SOURCE LINE 68
__M_writer(u' </span>\n')
pass
# SOURCE LINE 70
__M_writer(u' \n')
# SOURCE LINE 72
if editable:
# SOURCE LINE 73
if in_form:
# SOURCE LINE 74
__M_writer(u' <textarea class="tag-input" rows=\'1\' cols=\'')
__M_writer(unicode(input_size))
__M_writer(u"'></textarea>\n")
# SOURCE LINE 75
else:
# SOURCE LINE 76
__M_writer(u' <input class="tag-input" type=\'text\' size=\'')
__M_writer(unicode(input_size))
__M_writer(u"'/>\n")
pass
# SOURCE LINE 79
if render_add_tag_button:
# SOURCE LINE 80
__M_writer(u" <img src='")
__M_writer(unicode(h.url_for('/static/images/fugue/tag--plus.png')))
__M_writer(u'\' class="add-tag-button tooltip" title="Add tags"/>\n')
pass
pass
# SOURCE LINE 83
__M_writer(u' </div>\n </div>\n')
return ''
finally:
context.caller_stack._pop_frame()
class InstalledRepositoryGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
if tool_shed_repository.update_available:
return '<div class="count-box state-color-running">%s</div>' % tool_shed_repository.name
return tool_shed_repository.name
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.description
class OwnerColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.owner
class RevisionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.changeset_revision
class StatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
status_label = tool_shed_repository.status
if tool_shed_repository.status in [
trans.model.ToolShedRepository.installation_status.CLONING,
trans.model.ToolShedRepository.installation_status.
SETTING_TOOL_VERSIONS, trans.model.ToolShedRepository.
installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
trans.model.ToolShedRepository.installation_status.
INSTALLING_TOOL_DEPENDENCIES,
trans.model.ToolShedRepository.installation_status.
LOADING_PROPRIETARY_DATATYPES
]:
bgcolor = trans.model.ToolShedRepository.states.INSTALLING
elif tool_shed_repository.status in [
trans.model.ToolShedRepository.installation_status.NEW,
trans.model.ToolShedRepository.installation_status.
UNINSTALLED
]:
bgcolor = trans.model.ToolShedRepository.states.UNINSTALLED
elif tool_shed_repository.status in [
trans.model.ToolShedRepository.installation_status.ERROR
]:
bgcolor = trans.model.ToolShedRepository.states.ERROR
elif tool_shed_repository.status in [
trans.model.ToolShedRepository.installation_status.
DEACTIVATED
]:
bgcolor = trans.model.ToolShedRepository.states.WARNING
elif tool_shed_repository.status in [
trans.model.ToolShedRepository.installation_status.
INSTALLED
]:
if tool_shed_repository.missing_repository_dependencies:
bgcolor = trans.model.ToolShedRepository.states.WARNING
status_label = '%s, missing repository dependencies' % status_label
elif tool_shed_repository.missing_tool_dependencies:
bgcolor = trans.model.ToolShedRepository.states.WARNING
status_label = '%s, missing tool dependencies' % status_label
else:
bgcolor = trans.model.ToolShedRepository.states.OK
else:
bgcolor = trans.model.ToolShedRepository.states.ERROR
rval = '<div class="count-box state-color-%s">%s</div>' % (
bgcolor, status_label)
return rval
class ToolShedColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.tool_shed
class DeletedColumn(grids.DeletedColumn):
def get_accepted_filters(self):
""" Returns a list of accepted filters for this column. """
accepted_filter_labels_and_vals = {
"Active": "False",
"Deactivated or uninstalled": "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))
return accepted_filters
# Grid definition
title = "Installed tool shed repositories"
model_class = model.ToolShedRepository
template = '/admin/tool_shed_repository/grid.mako'
default_sort_key = "name"
columns = [
NameColumn("Name",
key="name",
link=(lambda item: iff(
item.status in
[model.ToolShedRepository.installation_status.CLONING],
None, dict(operation="manage_repository", id=item.id))),
attach_popup=True),
DescriptionColumn("Description"),
OwnerColumn("Owner"),
RevisionColumn("Revision"),
StatusColumn("Installation Status", filterable="advanced"),
ToolShedColumn("Tool shed"),
# Columns that are valid for filtering but are not visible.
DeletedColumn("Status",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = []
operations = [ grids.GridOperation( "Get updates",
allow_multiple=False,
condition=( lambda item: not item.deleted and item.status not in \
[ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ),
async_compatible=False,
url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='get updates' ) ),
grids.GridOperation( "Install",
allow_multiple=False,
condition=( lambda item: not item.deleted and item.status == model.ToolShedRepository.installation_status.NEW ),
async_compatible=False,
url_args=dict( controller='admin_toolshed', action='manage_repository', operation='install' ) ),
grids.GridOperation( "Deactivate or uninstall",
allow_multiple=False,
condition=( lambda item: not item.deleted and item.status not in \
[ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ),
async_compatible=False,
url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='deactivate or uninstall' ) ),
grids.GridOperation( "Reset to install",
allow_multiple=False,
condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ),
async_compatible=False,
url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='reset to install' ) ),
grids.GridOperation( "Activate or reinstall",
allow_multiple=False,
condition=( lambda item: item.deleted ),
async_compatible=False,
url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='activate or reinstall' ) ) ]
standard_filters = []
default_filter = dict(deleted="False")
num_rows_per_page = 50
preserve_state = False
use_paging = False
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query(self.model_class)
class HistoryDatasetAssociationListGrid(grids.Grid):
# Custom columns for grid.
class HistoryColumn(grids.GridColumn):
def get_value(self, trans, grid, hda):
return hda.history.name
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, hda):
if hda.deleted:
return "deleted"
return ""
def get_accepted_filters(self):
""" Returns a list of accepted filters for this column. """
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))
return accepted_filters
# Grid definition
title = "Saved Datasets"
model_class = model.HistoryDatasetAssociation
template = '/dataset/grid.mako'
default_sort_key = "-create_time"
columns = [
grids.TextColumn(
"Name",
key="name",
model_class=model.HistoryDatasetAssociation,
# Link name to dataset's history.
link=(lambda item: iff(item.history.deleted, None,
dict(operation="switch", id=item.id))),
filterable="advanced"),
HistoryColumn("History",
key="history",
link=(lambda item: iff(
item.history.deleted, None,
dict(operation="switch_history", id=item.id)))),
grids.TagsColumn("Tags",
"tags",
model.HistoryDatasetAssociation,
model.HistoryDatasetAssociationTagAssociation,
filterable="advanced",
grid_name="HistoryDatasetAssocationListGrid"),
StatusColumn("Status", key="deleted", attach_popup=False),
grids.GridColumn("Created", key="create_time", format=time_ago),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[2]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = []
standard_filters = []
default_filter = dict(name="All", deleted="False", tags="All")
preserve_state = False
use_paging = True
num_rows_per_page = 50
def apply_default_filter(self, trans, query, **kwargs):
# This is a somewhat obtuse way to join the History and HDA tables. However, it's necessary
# because the initial query in build_initial_query is specificied on the HDA table (this is reasonable)
# and there's no simple property in the HDA to do the join.
return query.select_from(
model.HistoryDatasetAssociation.table.join(
model.History.table)).filter(model.History.user == trans.user)
except KeyError, e:
return 'Error in loading external_service type: %s' % external_service.external_service_type_id
# Grid definition
title = "External Services"
template = "admin/external_service/grid.mako"
model_class = model.ExternalService
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict( deleted="False" )
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: iff( item.deleted, None, dict( operation="view", id=item.id ) ) ),
attach_popup=True,
filterable="advanced" ),
grids.TextColumn( "Description",
key='description',
filterable="advanced" ),
ExternalServiceTypeColumn( "External Service Type" ),
grids.GridColumn( "Last Updated",
key="update_time",
format=time_ago ),
grids.DeletedColumn( "Deleted",
key="deleted",
visible=False,
filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search",
def render_render_grid_column_filter(context,grid,column):
context.caller_stack._push_frame()
try:
basestring = context.get('basestring', UNDEFINED)
cur_filter_dict = context.get('cur_filter_dict', UNDEFINED)
url = context.get('url', UNDEFINED)
h = context.get('h', UNDEFINED)
list = context.get('list', UNDEFINED)
len = context.get('len', UNDEFINED)
dict = context.get('dict', UNDEFINED)
enumerate = context.get('enumerate', UNDEFINED)
isinstance = context.get('isinstance', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 7
__M_writer(u'\n <tr>\n ')
# SOURCE LINE 9
column_label = column.label
if column.filterable == "advanced":
column_label = column_label.lower()
# SOURCE LINE 13
__M_writer(u'\n')
# SOURCE LINE 14
if column.filterable == "advanced":
# SOURCE LINE 15
__M_writer(u' <td align="left" style="padding-left: 10px">')
__M_writer(unicode(column_label))
__M_writer(u':</td>\n')
pass
# SOURCE LINE 17
__M_writer(u' <td style="padding: 0;">\n')
# SOURCE LINE 18
if isinstance(column, TextColumn):
# SOURCE LINE 19
__M_writer(u' <form class="text-filter-form" column_key="')
__M_writer(unicode(column.key))
__M_writer(u'" action="')
__M_writer(unicode(url(dict())))
__M_writer(u'" method="get" >\n')
# SOURCE LINE 21
for temp_column in grid.columns:
# SOURCE LINE 22
if temp_column.key in cur_filter_dict:
# SOURCE LINE 23
__M_writer(u' ')
value = cur_filter_dict[ temp_column.key ]
__M_writer(u'\n')
# SOURCE LINE 24
if value != "All":
# SOURCE LINE 25
__M_writer(u' ')
if isinstance( temp_column, TextColumn ):
value = h.to_json_string( value )
# SOURCE LINE 28
__M_writer(u'\n <input type="hidden" id="')
# SOURCE LINE 29
__M_writer(unicode(temp_column.key))
__M_writer(u'" name="f-')
__M_writer(unicode(temp_column.key))
__M_writer(u'" value=\'')
__M_writer(unicode(value))
__M_writer(u"'/>\n")
pass
pass
pass
# SOURCE LINE 34
__M_writer(u' <span id="')
__M_writer(unicode(column.key))
__M_writer(u'-filtering-criteria">\n')
# SOURCE LINE 35
if column.key in cur_filter_dict:
# SOURCE LINE 36
__M_writer(u' ')
column_filter = cur_filter_dict[column.key]
__M_writer(u'\n')
# SOURCE LINE 37
if isinstance( column_filter, basestring ):
# SOURCE LINE 38
if column_filter != "All":
# SOURCE LINE 39
__M_writer(u" <span class='text-filter-val'>\n ")
# SOURCE LINE 40
__M_writer(unicode(cur_filter_dict[column.key]))
__M_writer(u'\n ')
# SOURCE LINE 41
filter_all = GridColumnFilter( "", { column.key : "All" } )
__M_writer(u'\n <a href="')
# SOURCE LINE 42
__M_writer(unicode(url(filter_all.get_url_args())))
__M_writer(u'"><span class="delete-search-icon" /></a>\n </span>\n')
pass
# SOURCE LINE 45
elif isinstance( column_filter, list ):
# SOURCE LINE 46
for i, filter in enumerate( column_filter ):
# SOURCE LINE 47
if i > 0:
# SOURCE LINE 48
__M_writer(u' ,\n')
pass
# SOURCE LINE 50
__M_writer(u" <span class='text-filter-val'>")
__M_writer(unicode(filter))
__M_writer(u'\n ')
# SOURCE LINE 51
new_filter = list( column_filter )
del new_filter[ i ]
new_column_filter = GridColumnFilter( "", { column.key : h.to_json_string( new_filter ) } )
# SOURCE LINE 55
__M_writer(u'\n <a href="')
# SOURCE LINE 56
__M_writer(unicode(url(new_column_filter.get_url_args())))
__M_writer(u'"><span class="delete-search-icon" /></a>\n </span>\n')
pass
pass
pass
# SOURCE LINE 61
__M_writer(u' </span>\n')
# SOURCE LINE 63
__M_writer(u' <span class="search-box">\n ')
# SOURCE LINE 64
# Set value, size of search input field. Minimum size is 20 characters.
value = iff( column.filterable == "standard", column.label.lower(), "")
size = len( value )
if size < 20:
size = 20
# +4 to account for search icon/button.
size = size + 4
# SOURCE LINE 72
__M_writer(u'\n <input class="search-box-input" id="input-')
# SOURCE LINE 73
__M_writer(unicode(column.key))
__M_writer(u'-filter" name="f-')
__M_writer(unicode(column.key))
__M_writer(u'" type="text" value="')
__M_writer(unicode(value))
__M_writer(u'" size="')
__M_writer(unicode(size))
__M_writer(u'"/>\n <button class="submit-image" type="submit" title=\'Search\'><span style="display: none;"></button>\n </span>\n </form>\n')
# SOURCE LINE 77
else:
# SOURCE LINE 78
__M_writer(u' <span id="')
__M_writer(unicode(column.key))
__M_writer(u'-filtering-criteria">\n')
# SOURCE LINE 79
for i, filter in enumerate( column.get_accepted_filters() ):
# SOURCE LINE 80
__M_writer(u' ')
# HACK: we know that each filter will have only a single argument, so get that single argument.
for key, arg in filter.args.items():
filter_key = key
filter_arg = arg
# SOURCE LINE 85
__M_writer(u'\n')
# SOURCE LINE 86
if i > 0:
# SOURCE LINE 87
__M_writer(u' |\n')
pass
# SOURCE LINE 89
if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[column.key] == filter.args[column.key]:
# SOURCE LINE 90
__M_writer(u' <span class="categorical-filter ')
__M_writer(unicode(column.key))
__M_writer(u'-filter current-filter">')
__M_writer(unicode(filter.label))
__M_writer(u'</span>\n')
# SOURCE LINE 91
else:
# SOURCE LINE 92
__M_writer(u' <span class="categorical-filter ')
__M_writer(unicode(column.key))
__M_writer(u'-filter">\n <a href="')
# SOURCE LINE 93
__M_writer(unicode(url(filter.get_url_args())))
__M_writer(u'" filter_key="')
__M_writer(unicode(filter_key))
__M_writer(u'" filter_val="')
__M_writer(unicode(filter_arg))
__M_writer(u'">')
__M_writer(unicode(filter.label))
__M_writer(u'</a>\n </span>\n')
pass
pass
# SOURCE LINE 97
__M_writer(u' </span>\n')
pass
# SOURCE LINE 99
__M_writer(u' </td>\n </tr>\n')
return ''
finally:
context.caller_stack._pop_frame()
def __call__(self, trans, **kwargs):
# Get basics.
# FIXME: pretty sure this is only here to pass along, can likely be eliminated
status = kwargs.get('status', None)
message = kwargs.get('message', None)
# Build a base filter and sort key that is the combination of the saved state and defaults.
# Saved state takes preference over defaults.
base_filter = {}
if self.default_filter:
# default_filter is a dictionary that provides a default set of filters based on the grid's columns.
base_filter = self.default_filter.copy()
base_sort_key = self.default_sort_key
# Build initial query
query = self.build_initial_query(trans, **kwargs)
query = self.apply_query_filter(trans, query, **kwargs)
# Maintain sort state in generated urls
extra_url_args = {}
# Determine whether use_default_filter flag is set.
use_default_filter_str = kwargs.get('use_default_filter')
use_default_filter = False
if use_default_filter_str:
use_default_filter = (use_default_filter_str.lower() == 'true')
# Process filtering arguments to (a) build a query that represents the filter and (b) build a
# dictionary that denotes the current filter.
cur_filter_dict = {}
for column in self.columns:
if column.key:
# Get the filter criterion for the column. Precedence is (a) if using default filter, only look there; otherwise,
# (b) look in kwargs; and (c) look in base filter.
column_filter = None
if use_default_filter:
if self.default_filter:
column_filter = self.default_filter.get(column.key)
elif f"f-{column.model_class.__name__}.{column.key}" in kwargs:
# Queries that include table joins cannot guarantee unique column names. This problem is
# handled by setting the column_filter value to <TableName>.<ColumnName>.
column_filter = kwargs.get(f"f-{column.model_class.__name__}.{column.key}")
elif f"f-{column.key}" in kwargs:
column_filter = kwargs.get(f"f-{column.key}")
elif column.key in base_filter:
column_filter = base_filter.get(column.key)
# Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings.
def loads_recurse(item):
decoded_list = []
if isinstance(item, str):
try:
# Not clear what we're decoding, so recurse to ensure that we catch everything.
decoded_item = loads(item)
if isinstance(decoded_item, list):
decoded_list = loads_recurse(decoded_item)
else:
decoded_list = [str(decoded_item)]
except ValueError:
decoded_list = [str(item)]
elif isinstance(item, list):
for element in item:
a_list = loads_recurse(element)
decoded_list = decoded_list + a_list
return decoded_list
# If column filter found, apply it.
if column_filter is not None:
# TextColumns may have a mix of json and strings.
if isinstance(column, TextColumn):
column_filter = loads_recurse(column_filter)
if len(column_filter) == 1:
column_filter = column_filter[0]
# Interpret ',' as a separator for multiple terms.
if isinstance(column_filter, str) and column_filter.find(',') != -1:
column_filter = column_filter.split(',')
# Check if filter is empty
if isinstance(column_filter, list):
# Remove empty strings from filter list
column_filter = [x for x in column_filter if x != '']
if len(column_filter) == 0:
continue
elif isinstance(column_filter, str):
# If filter criterion is empty, do nothing.
if column_filter == '':
continue
# Update query.
query = column.filter(trans, trans.user, query, column_filter)
# Upate current filter dict.
# Column filters are rendered in various places, sanitize them all here.
cur_filter_dict[column.key] = sanitize_text(column_filter)
# Carry filter along to newly generated urls; make sure filter is a string so
# that we can encode to UTF-8 and thus handle user input to filters.
if isinstance(column_filter, list):
# Filter is a list; process each item.
column_filter = [str(_).encode('utf-8') if not isinstance(_, str) else _ for _ in column_filter]
extra_url_args[f"f-{column.key}"] = dumps(column_filter)
else:
# Process singleton filter.
if not isinstance(column_filter, str):
column_filter = str(column_filter)
extra_url_args[f"f-{column.key}"] = column_filter.encode("utf-8")
# Process sort arguments.
sort_key = None
if 'sort' in kwargs:
sort_key = kwargs['sort']
elif base_sort_key:
sort_key = base_sort_key
if sort_key:
ascending = not(sort_key.startswith("-"))
# Queries that include table joins cannot guarantee unique column names. This problem is
# handled by setting the column_filter value to <TableName>.<ColumnName>.
table_name = None
if sort_key.find('.') > -1:
a_list = sort_key.split('.')
if ascending:
table_name = a_list[0]
else:
table_name = a_list[0][1:]
column_name = a_list[1]
elif ascending:
column_name = sort_key
else:
column_name = sort_key[1:]
# Sort key is a column key.
for column in self.columns:
if column.key and column.key.find('.') > -1:
column_key = column.key.split('.')[1]
else:
column_key = column.key
if (table_name is None or table_name == column.model_class.__name__) and column_key == column_name:
query = column.sort(trans, query, ascending, column_name=column_name)
break
extra_url_args['sort'] = sort_key
# There might be a current row
current_item = self.get_current_item(trans, **kwargs)
# Process page number.
if self.use_paging:
if 'page' in kwargs:
if kwargs['page'] == 'all':
page_num = 0
if self.allow_fetching_all_results:
page_num = 0
else:
# Should make it harder to return all results at once
page_num = 1
else:
page_num = int(kwargs['page'])
else:
page_num = 1
if page_num == 0:
# Show all rows in page.
total_num_rows = query.count()
page_num = 1
num_pages = 1
else:
# Show a limited number of rows. Before modifying query, get the total number of rows that query
# returns so that the total number of pages can be computed.
total_num_rows = query.count()
query = query.limit(self.num_rows_per_page).offset((page_num - 1) * self.num_rows_per_page)
num_pages = int(math.ceil(float(total_num_rows) / self.num_rows_per_page))
else:
# Defaults.
page_num = 1
num_pages = 1
# There are some places in grid templates where it's useful for a grid
# to have its current filter.
self.cur_filter_dict = cur_filter_dict
# Log grid view.
context = str(self.__class__.__name__)
params = cur_filter_dict.copy()
params['sort'] = sort_key
params['async'] = ('async' in kwargs)
# TODO:??
# commenting this out; when this fn calls session.add( action ) and session.flush the query from this fn
# is effectively 'wiped' out. Nate believes it has something to do with our use of session( autocommit=True )
# in mapping.py. If you change that to False, the log_action doesn't affect the query
# Below, I'm rendering the template first (that uses query), then calling log_action, then returning the page
# trans.log_action( trans.get_user(), text_type( "grid.view" ), context, params )
# Render grid.
def url(*args, **kwargs):
route_name = kwargs.pop('__route_name__', None)
# Only include sort/filter arguments if not linking to another
# page. This is a bit of a hack.
if 'action' in kwargs:
new_kwargs = dict()
else:
new_kwargs = dict(extra_url_args)
# Extend new_kwargs with first argument if found
if len(args) > 0:
new_kwargs.update(args[0])
new_kwargs.update(kwargs)
# We need to encode item ids
if 'id' in new_kwargs:
id = new_kwargs['id']
if isinstance(id, list):
new_kwargs['id'] = [trans.security.encode_id(i) for i in id]
else:
new_kwargs['id'] = trans.security.encode_id(id)
# The url_for invocation *must* include a controller and action.
if 'controller' not in new_kwargs:
new_kwargs['controller'] = trans.controller
if 'action' not in new_kwargs:
new_kwargs['action'] = trans.action
if route_name:
return url_for(route_name, **new_kwargs)
return url_for(**new_kwargs)
self.use_panels = (kwargs.get('use_panels', False) in [True, 'True', 'true'])
self.advanced_search = (kwargs.get('advanced_search', False) in [True, 'True', 'true'])
async_request = ((self.use_async) and (kwargs.get('async', False) in [True, 'True', 'true']))
# Currently, filling the template returns a str object; this requires decoding the string into a
# unicode object within mako templates. What probably should be done is to return the template as
# utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid
# results via a controller method, which is require substantial changes. Hence, for now, return grid
# as str.
page = trans.fill_template(iff(async_request, self.async_template, self.template),
grid=self,
query=query,
cur_page_num=page_num,
num_pages=num_pages,
num_page_links=self.num_page_links,
allow_fetching_all_results=self.allow_fetching_all_results,
default_filter_dict=self.default_filter,
cur_filter_dict=cur_filter_dict,
sort_key=sort_key,
current_item=current_item,
ids=kwargs.get('id', []),
url=url,
status=status,
message=message,
info_text=self.info_text,
use_panels=self.use_panels,
use_hide_message=self.use_hide_message,
advanced_search=self.advanced_search,
show_item_checkboxes=(self.show_item_checkboxes
or kwargs.get('show_item_checkboxes', '') in ['True', 'true']),
# Pass back kwargs so that grid template can set and use args without
# grid explicitly having to pass them.
kwargs=kwargs)
trans.log_action(trans.get_user(), "grid.view", context, params)
return page
class ToolDependencyGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_dependency):
return tool_dependency.name
class VersionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_dependency):
return tool_dependency.version
class TypeColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_dependency):
return tool_dependency.type
class StatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_dependency):
if tool_dependency.status in [
trans.install_model.ToolDependency.installation_status.
INSTALLING
]:
bgcolor = trans.install_model.ToolDependency.states.INSTALLING
elif tool_dependency.status in [
trans.install_model.ToolDependency.installation_status.
NEVER_INSTALLED, trans.install_model.ToolDependency.
installation_status.UNINSTALLED
]:
bgcolor = trans.install_model.ToolDependency.states.UNINSTALLED
elif tool_dependency.status in [
trans.install_model.ToolDependency.installation_status.
ERROR
]:
bgcolor = trans.install_model.ToolDependency.states.ERROR
elif tool_dependency.status in [
trans.install_model.ToolDependency.installation_status.
INSTALLED
]:
bgcolor = trans.install_model.ToolDependency.states.OK
rval = '<div class="count-box state-color-%s" id="ToolDependencyStatus-%s">%s</div>' % \
( bgcolor, trans.security.encode_id( tool_dependency.id ), tool_dependency.status )
return rval
title = "Tool Dependencies"
template = "admin/tool_shed_repository/tool_dependencies_grid.mako"
model_class = tool_shed_install.ToolDependency
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = False
columns = [
NameColumn("Name",
link=(lambda item: iff(
item.status in [
tool_shed_install.ToolDependency.installation_status
.NEVER_INSTALLED, tool_shed_install.ToolDependency.
installation_status.INSTALLING, tool_shed_install.
ToolDependency.installation_status.UNINSTALLED
], None,
dict(action="manage_tool_dependencies",
operation='browse',
id=item.id))),
filterable="advanced"),
VersionColumn("Version", filterable="advanced"),
TypeColumn("Type", filterable="advanced"),
StatusColumn("Installation Status", filterable="advanced"),
]
def build_initial_query(self, trans, **kwd):
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids(
as_string=False, **kwd)
if tool_dependency_ids:
clause_list = []
for tool_dependency_id in tool_dependency_ids:
clause_list.append(self.model_class.table.c.id == trans.
security.decode_id(tool_dependency_id))
return trans.install_model.context.query( self.model_class ) \
.filter( or_( *clause_list ) )
return trans.install_model.context.query(self.model_class)
def apply_query_filter(self, trans, query, **kwd):
tool_dependency_id = kwd.get('tool_dependency_id', None)
if tool_dependency_id:
return query.filter_by(tool_dependency_id=trans.security.decode_id(
tool_dependency_id))
return query
def __call__(self, trans, **kwargs):
# Get basics.
# FIXME: pretty sure this is only here to pass along, can likely be eliminated
status = kwargs.get('status', None)
message = kwargs.get('message', None)
dict_format = kwargs.get('dict_format', False)
# Build a base filter and sort key that is the combination of the saved state and defaults.
# Saved state takes preference over defaults.
base_filter = {}
if self.default_filter:
# default_filter is a dictionary that provides a default set of filters based on the grid's columns.
base_filter = self.default_filter.copy()
base_sort_key = self.default_sort_key
if self.preserve_state:
pref_name = text_type(self.__class__.__name__ +
self.cur_filter_pref_name)
if pref_name in trans.get_user().preferences:
saved_filter = loads(trans.get_user().preferences[pref_name])
base_filter.update(saved_filter)
pref_name = text_type(self.__class__.__name__ +
self.cur_sort_key_pref_name)
if pref_name in trans.get_user().preferences:
base_sort_key = loads(trans.get_user().preferences[pref_name])
# Build initial query
query = self.build_initial_query(trans, **kwargs)
query = self.apply_query_filter(trans, query, **kwargs)
# Maintain sort state in generated urls
extra_url_args = {}
# Determine whether use_default_filter flag is set.
use_default_filter_str = kwargs.get('use_default_filter')
use_default_filter = False
if use_default_filter_str:
use_default_filter = (use_default_filter_str.lower() == 'true')
# Process filtering arguments to (a) build a query that represents the filter and (b) build a
# dictionary that denotes the current filter.
cur_filter_dict = {}
for column in self.columns:
if column.key:
# Get the filter criterion for the column. Precedence is (a) if using default filter, only look there; otherwise,
# (b) look in kwargs; and (c) look in base filter.
column_filter = None
if use_default_filter:
if self.default_filter:
column_filter = self.default_filter.get(column.key)
elif "f-" + column.model_class.__name__ + ".%s" % column.key in kwargs:
# Queries that include table joins cannot guarantee unique column names. This problem is
# handled by setting the column_filter value to <TableName>.<ColumnName>.
column_filter = kwargs.get("f-" +
column.model_class.__name__ +
".%s" % column.key)
elif "f-" + column.key in kwargs:
column_filter = kwargs.get("f-" + column.key)
elif column.key in base_filter:
column_filter = base_filter.get(column.key)
# Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings.
def loads_recurse(item):
decoded_list = []
if isinstance(item, string_types):
try:
# Not clear what we're decoding, so recurse to ensure that we catch everything.
decoded_item = loads(item)
if isinstance(decoded_item, list):
decoded_list = loads_recurse(decoded_item)
else:
decoded_list = [text_type(decoded_item)]
except ValueError:
decoded_list = [text_type(item)]
elif isinstance(item, list):
for element in item:
a_list = loads_recurse(element)
decoded_list = decoded_list + a_list
return decoded_list
# If column filter found, apply it.
if column_filter is not None:
# TextColumns may have a mix of json and strings.
if isinstance(column, TextColumn):
column_filter = loads_recurse(column_filter)
if len(column_filter) == 1:
column_filter = column_filter[0]
# Interpret ',' as a separator for multiple terms.
if isinstance(
column_filter,
string_types) and column_filter.find(',') != -1:
column_filter = column_filter.split(',')
# Check if filter is empty
if isinstance(column_filter, list):
# Remove empty strings from filter list
column_filter = [x for x in column_filter if x != '']
if len(column_filter) == 0:
continue
elif isinstance(column_filter, string_types):
# If filter criterion is empty, do nothing.
if column_filter == '':
continue
# Update query.
query = column.filter(trans, trans.user, query,
column_filter)
# Upate current filter dict.
# Column filters are rendered in various places, sanitize them all here.
cur_filter_dict[column.key] = sanitize_text(column_filter)
# Carry filter along to newly generated urls; make sure filter is a string so
# that we can encode to UTF-8 and thus handle user input to filters.
if isinstance(column_filter, list):
# Filter is a list; process each item.
column_filter = [
text_type(_).encode('utf-8')
if not isinstance(_, string_types) else _
for _ in column_filter
]
extra_url_args["f-" +
column.key] = dumps(column_filter)
else:
# Process singleton filter.
if not isinstance(column_filter, string_types):
column_filter = text_type(column_filter)
extra_url_args[
"f-" + column.key] = column_filter.encode("utf-8")
# Process sort arguments.
sort_key = None
if 'sort' in kwargs:
sort_key = kwargs['sort']
elif base_sort_key:
sort_key = base_sort_key
if sort_key:
ascending = not (sort_key.startswith("-"))
# Queries that include table joins cannot guarantee unique column names. This problem is
# handled by setting the column_filter value to <TableName>.<ColumnName>.
table_name = None
if sort_key.find('.') > -1:
a_list = sort_key.split('.')
if ascending:
table_name = a_list[0]
else:
table_name = a_list[0][1:]
column_name = a_list[1]
elif ascending:
column_name = sort_key
else:
column_name = sort_key[1:]
# Sort key is a column key.
for column in self.columns:
if column.key and column.key.find('.') > -1:
column_key = column.key.split('.')[1]
else:
column_key = column.key
if (table_name is None
or table_name == column.model_class.__name__
) and column_key == column_name:
query = column.sort(trans,
query,
ascending,
column_name=column_name)
break
extra_url_args['sort'] = sort_key
# There might be a current row
current_item = self.get_current_item(trans, **kwargs)
# Process page number.
if self.use_paging:
if 'page' in kwargs:
if kwargs['page'] == 'all':
page_num = 0
else:
page_num = int(kwargs['page'])
else:
page_num = 1
if page_num == 0:
# Show all rows in page.
total_num_rows = query.count()
page_num = 1
num_pages = 1
else:
# Show a limited number of rows. Before modifying query, get the total number of rows that query
# returns so that the total number of pages can be computed.
total_num_rows = query.count()
query = query.limit(self.num_rows_per_page).offset(
(page_num - 1) * self.num_rows_per_page)
num_pages = int(
math.ceil(float(total_num_rows) / self.num_rows_per_page))
else:
# Defaults.
page_num = 1
num_pages = 1
# There are some places in grid templates where it's useful for a grid
# to have its current filter.
self.cur_filter_dict = cur_filter_dict
# Preserve grid state: save current filter and sort key.
if self.preserve_state:
pref_name = text_type(self.__class__.__name__ +
self.cur_filter_pref_name)
trans.get_user().preferences[pref_name] = text_type(
dumps(cur_filter_dict))
if sort_key:
pref_name = text_type(self.__class__.__name__ +
self.cur_sort_key_pref_name)
trans.get_user().preferences[pref_name] = text_type(
dumps(sort_key))
trans.sa_session.flush()
# Log grid view.
context = text_type(self.__class__.__name__)
params = cur_filter_dict.copy()
params['sort'] = sort_key
params['async'] = ('async' in kwargs)
# TODO:??
# commenting this out; when this fn calls session.add( action ) and session.flush the query from this fn
# is effectively 'wiped' out. Nate believes it has something to do with our use of session( autocommit=True )
# in mapping.py. If you change that to False, the log_action doesn't affect the query
# Below, I'm rendering the template first (that uses query), then calling log_action, then returning the page
# trans.log_action( trans.get_user(), text_type( "grid.view" ), context, params )
# Render grid.
def url(*args, **kwargs):
route_name = kwargs.pop('__route_name__', None)
# Only include sort/filter arguments if not linking to another
# page. This is a bit of a hack.
if 'action' in kwargs:
new_kwargs = dict()
else:
new_kwargs = dict(extra_url_args)
# Extend new_kwargs with first argument if found
if len(args) > 0:
new_kwargs.update(args[0])
new_kwargs.update(kwargs)
# We need to encode item ids
if 'id' in new_kwargs:
id = new_kwargs['id']
if isinstance(id, list):
new_kwargs['id'] = [
trans.security.encode_id(i) for i in id
]
else:
new_kwargs['id'] = trans.security.encode_id(id)
# The url_for invocation *must* include a controller and action.
if 'controller' not in new_kwargs:
new_kwargs['controller'] = trans.controller
if 'action' not in new_kwargs:
new_kwargs['action'] = trans.action
if route_name:
return url_for(route_name, **new_kwargs)
return url_for(**new_kwargs)
self.use_panels = (kwargs.get('use_panels', False)
in [True, 'True', 'true'])
self.advanced_search = (kwargs.get('advanced_search', False)
in [True, 'True', 'true'])
async_request = ((self.use_async) and (kwargs.get('async', False)
in [True, 'True', 'true']))
# Currently, filling the template returns a str object; this requires decoding the string into a
# unicode object within mako templates. What probably should be done is to return the template as
# utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid
# results via a controller method, which is require substantial changes. Hence, for now, return grid
# as str.
if not dict_format:
page = trans.fill_template(
iff(async_request, self.async_template, self.template),
grid=self,
query=query,
cur_page_num=page_num,
num_pages=num_pages,
num_page_links=self.num_page_links,
default_filter_dict=self.default_filter,
cur_filter_dict=cur_filter_dict,
sort_key=sort_key,
current_item=current_item,
ids=kwargs.get('id', []),
url=url,
status=status,
message=message,
info_text=self.info_text,
use_panels=self.use_panels,
use_hide_message=self.use_hide_message,
advanced_search=self.advanced_search,
show_item_checkboxes=(self.show_item_checkboxes or kwargs.get(
'show_item_checkboxes', '') in ['True', 'true']),
# Pass back kwargs so that grid template can set and use args without
# grid explicitly having to pass them.
kwargs=kwargs)
trans.log_action(trans.get_user(), text_type("grid.view"), context,
params)
return page
grid_config = {
'title':
self.title,
'url_base':
trans.request.path_url,
'async':
self.use_async,
'async_ops': [],
'categorical_filters': {},
'filters':
cur_filter_dict,
'sort_key':
sort_key,
'show_item_checkboxes':
self.show_item_checkboxes
or kwargs.get('show_item_checkboxes', '') in ['True', 'true'],
'cur_page_num':
page_num,
'num_pages':
num_pages,
'num_page_links':
self.num_page_links,
'status':
status,
'message':
restore_text(message),
'global_actions': [],
'operations': [],
'items': [],
'columns': [],
'model_class':
str(self.model_class),
'use_paging':
self.use_paging,
'legend':
self.legend,
'current_item_id':
False,
'use_hide_message':
self.use_hide_message,
'default_filter_dict':
self.default_filter,
'advanced_search':
self.advanced_search,
'info_text':
self.info_text,
'url':
url(dict()),
'refresh_frames':
kwargs.get('refresh_frames', [])
}
if current_item:
grid_config['current_item_id'] = current_item.id
for column in self.columns:
href = None
extra = ''
if column.sortable:
if sort_key.endswith(column.key):
if not sort_key.startswith("-"):
href = url(sort=("-" + column.key))
extra = "↓"
else:
href = url(sort=(column.key))
extra = "↑"
else:
href = url(sort=column.key)
grid_config['columns'].append({
'key':
column.key,
'visible':
column.visible,
'nowrap':
column.nowrap,
'attach_popup':
column.attach_popup,
'label_id_prefix':
column.label_id_prefix,
'sortable':
column.sortable,
'label':
column.label,
'filterable':
column.filterable,
'is_text':
isinstance(column, TextColumn),
'href':
href,
'extra':
extra
})
for operation in self.operations:
grid_config['operations'].append({
'allow_multiple':
operation.allow_multiple,
'allow_popup':
operation.allow_popup,
'target':
operation.target,
'label':
operation.label,
'confirm':
operation.confirm,
'href':
url(**operation.url_args) if isinstance(
operation.url_args, dict) else None,
'global_operation':
False
})
if operation.allow_multiple:
grid_config['show_item_checkboxes'] = True
if operation.global_operation:
grid_config['global_operation'] = url(
**(operation.global_operation()))
for action in self.global_actions:
grid_config['global_actions'].append({
'url_args':
url(**action.url_args),
'label':
action.label,
'target':
action.target
})
for operation in [op for op in self.operations if op.async_compatible]:
grid_config['async_ops'].append(operation.label.lower())
for column in self.columns:
if column.filterable is not None and not isinstance(
column, TextColumn):
grid_config['categorical_filters'][column.key] = dict([
(filter.label, filter.args)
for filter in column.get_accepted_filters()
])
for i, item in enumerate(query):
item_dict = {
'id': item.id,
'encode_id': trans.security.encode_id(item.id),
'link': [],
'operation_config': {},
'column_config': {}
}
for column in self.columns:
if column.visible:
link = column.get_link(trans, self, item)
if link:
link = url(**link)
else:
link = None
target = column.target
value = column.get_value(trans, self, item)
if isinstance(value, str):
value = text_type(value, 'utf-8')
value = value.replace('/', '//')
item_dict['column_config'][column.label] = {
'link': link,
'value': value,
'target': target
}
for operation in self.operations:
item_dict['operation_config'][operation.label] = {
'allowed': operation.allowed(item),
'url_args': url(**operation.get_url_args(item)),
'target': operation.target
}
grid_config['items'].append(item_dict)
trans.log_action(trans.get_user(), text_type("grid.view"), context,
params)
return grid_config
def __call__( self, trans, **kwargs ):
# Get basics.
# FIXME: pretty sure this is only here to pass along, can likely be eliminated
status = kwargs.get( 'status', None )
message = kwargs.get( 'message', None )
# Build a base filter and sort key that is the combination of the saved state and defaults.
# Saved state takes preference over defaults.
base_filter = {}
if self.default_filter:
# default_filter is a dictionary that provides a default set of filters based on the grid's columns.
base_filter = self.default_filter.copy()
base_sort_key = self.default_sort_key
if self.preserve_state:
pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name )
if pref_name in trans.get_user().preferences:
saved_filter = loads( trans.get_user().preferences[pref_name] )
base_filter.update( saved_filter )
pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name )
if pref_name in trans.get_user().preferences:
base_sort_key = loads( trans.get_user().preferences[pref_name] )
# Build initial query
query = self.build_initial_query( trans, **kwargs )
query = self.apply_query_filter( trans, query, **kwargs )
# Maintain sort state in generated urls
extra_url_args = {}
# Determine whether use_default_filter flag is set.
use_default_filter_str = kwargs.get( 'use_default_filter' )
use_default_filter = False
if use_default_filter_str:
use_default_filter = ( use_default_filter_str.lower() == 'true' )
# Process filtering arguments to (a) build a query that represents the filter and (b) build a
# dictionary that denotes the current filter.
cur_filter_dict = {}
for column in self.columns:
if column.key:
# Get the filter criterion for the column. Precedence is (a) if using default filter, only look there; otherwise,
# (b) look in kwargs; and (c) look in base filter.
column_filter = None
if use_default_filter:
if self.default_filter:
column_filter = self.default_filter.get( column.key )
elif "f-" + column.model_class.__name__ + ".%s" % column.key in kwargs:
# Queries that include table joins cannot guarantee unique column names. This problem is
# handled by setting the column_filter value to <TableName>.<ColumnName>.
column_filter = kwargs.get( "f-" + column.model_class.__name__ + ".%s" % column.key )
elif "f-" + column.key in kwargs:
column_filter = kwargs.get( "f-" + column.key )
elif column.key in base_filter:
column_filter = base_filter.get( column.key )
# Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings.
def loads_recurse(item):
decoded_list = []
if isinstance( item, basestring):
try:
# Not clear what we're decoding, so recurse to ensure that we catch everything.
decoded_item = loads( item )
if isinstance( decoded_item, list):
decoded_list = loads_recurse( decoded_item )
else:
decoded_list = [ unicode( decoded_item ) ]
except ValueError:
decoded_list = [ unicode( item ) ]
elif isinstance( item, list):
for element in item:
a_list = loads_recurse( element )
decoded_list = decoded_list + a_list
return decoded_list
# If column filter found, apply it.
if column_filter is not None:
# TextColumns may have a mix of json and strings.
if isinstance( column, TextColumn ):
column_filter = loads_recurse( column_filter )
if len( column_filter ) == 1:
column_filter = column_filter[0]
# Interpret ',' as a separator for multiple terms.
if isinstance( column_filter, basestring ) and column_filter.find(',') != -1:
column_filter = column_filter.split(',')
# Check if filter is empty
if isinstance( column_filter, list ):
# Remove empty strings from filter list
column_filter = [x for x in column_filter if x != '']
if len(column_filter) == 0:
continue
elif isinstance(column_filter, basestring):
# If filter criterion is empty, do nothing.
if column_filter == '':
continue
# Update query.
query = column.filter( trans, trans.user, query, column_filter )
# Upate current filter dict.
# Column filters are rendered in various places, sanitize them all here.
cur_filter_dict[ column.key ] = sanitize_text(column_filter)
# Carry filter along to newly generated urls; make sure filter is a string so
# that we can encode to UTF-8 and thus handle user input to filters.
if isinstance( column_filter, list ):
# Filter is a list; process each item.
for filter in column_filter:
if not isinstance( filter, basestring ):
filter = unicode( filter ).encode("utf-8")
extra_url_args[ "f-" + column.key ] = dumps( column_filter )
else:
# Process singleton filter.
if not isinstance( column_filter, basestring ):
column_filter = unicode(column_filter)
extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8")
# Process sort arguments.
sort_key = None
if 'sort' in kwargs:
sort_key = kwargs['sort']
elif base_sort_key:
sort_key = base_sort_key
if sort_key:
ascending = not( sort_key.startswith( "-" ) )
# Queries that include table joins cannot guarantee unique column names. This problem is
# handled by setting the column_filter value to <TableName>.<ColumnName>.
table_name = None
if sort_key.find( '.' ) > -1:
a_list = sort_key.split( '.' )
if ascending:
table_name = a_list[0]
else:
table_name = a_list[0][1:]
column_name = a_list[1]
elif ascending:
column_name = sort_key
else:
column_name = sort_key[1:]
# Sort key is a column key.
for column in self.columns:
if column.key and column.key.find( '.' ) > -1:
column_key = column.key.split( '.' )[1]
else:
column_key = column.key
if ( table_name is None or table_name == column.model_class.__name__ ) and column_key == column_name:
query = column.sort( trans, query, ascending, column_name=column_name )
break
extra_url_args['sort'] = sort_key
# There might be a current row
current_item = self.get_current_item( trans, **kwargs )
# Process page number.
if self.use_paging:
if 'page' in kwargs:
if kwargs['page'] == 'all':
page_num = 0
else:
page_num = int( kwargs['page'] )
else:
page_num = 1
if page_num == 0:
# Show all rows in page.
total_num_rows = query.count()
page_num = 1
num_pages = 1
else:
# Show a limited number of rows. Before modifying query, get the total number of rows that query
# returns so that the total number of pages can be computed.
total_num_rows = query.count()
query = query.limit( self.num_rows_per_page ).offset( ( page_num - 1 ) * self.num_rows_per_page )
num_pages = int( math.ceil( float( total_num_rows ) / self.num_rows_per_page ) )
else:
# Defaults.
page_num = 1
num_pages = 1
# There are some places in grid templates where it's useful for a grid
# to have its current filter.
self.cur_filter_dict = cur_filter_dict
# Preserve grid state: save current filter and sort key.
if self.preserve_state:
pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name )
trans.get_user().preferences[pref_name] = unicode( dumps( cur_filter_dict ) )
if sort_key:
pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name )
trans.get_user().preferences[pref_name] = unicode( dumps( sort_key ) )
trans.sa_session.flush()
# Log grid view.
context = unicode( self.__class__.__name__ )
params = cur_filter_dict.copy()
params['sort'] = sort_key
params['async'] = ( 'async' in kwargs )
# TODO:??
# commenting this out; when this fn calls session.add( action ) and session.flush the query from this fn
# is effectively 'wiped' out. Nate believes it has something to do with our use of session( autocommit=True )
# in mapping.py. If you change that to False, the log_action doesn't affect the query
# Below, I'm rendering the template first (that uses query), then calling log_action, then returning the page
# trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params )
# Render grid.
def url( *args, **kwargs ):
# Only include sort/filter arguments if not linking to another
# page. This is a bit of a hack.
if 'action' in kwargs:
new_kwargs = dict()
else:
new_kwargs = dict( extra_url_args )
# Extend new_kwargs with first argument if found
if len(args) > 0:
new_kwargs.update( args[0] )
new_kwargs.update( kwargs )
# We need to encode item ids
if 'id' in new_kwargs:
id = new_kwargs[ 'id' ]
if isinstance( id, list ):
new_kwargs[ 'id' ] = [ trans.security.encode_id( i ) for i in id ]
else:
new_kwargs[ 'id' ] = trans.security.encode_id( id )
# The url_for invocation *must* include a controller and action.
if 'controller' not in new_kwargs:
new_kwargs['controller'] = trans.controller
if 'action' not in new_kwargs:
new_kwargs['action'] = trans.action
return url_for( **new_kwargs)
self.use_panels = ( kwargs.get( 'use_panels', False ) in [ True, 'True', 'true' ] )
self.advanced_search = ( kwargs.get( 'advanced_search', False ) in [ True, 'True', 'true' ] )
async_request = ( ( self.use_async ) and ( kwargs.get( 'async', False ) in [ True, 'True', 'true'] ) )
# Currently, filling the template returns a str object; this requires decoding the string into a
# unicode object within mako templates. What probably should be done is to return the template as
# utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid
# results via a controller method, which is require substantial changes. Hence, for now, return grid
# as str.
page = trans.fill_template( iff( async_request, self.async_template, self.template ),
grid=self,
query=query,
cur_page_num=page_num,
num_pages=num_pages,
num_page_links=self.num_page_links,
default_filter_dict=self.default_filter,
cur_filter_dict=cur_filter_dict,
sort_key=sort_key,
current_item=current_item,
ids=kwargs.get( 'id', [] ),
url=url,
status=status,
message=message,
info_text=self.info_text,
use_panels=self.use_panels,
use_hide_message=self.use_hide_message,
advanced_search=self.advanced_search,
show_item_checkboxes=( self.show_item_checkboxes or
kwargs.get( 'show_item_checkboxes', '' ) in [ 'True', 'true' ] ),
# Pass back kwargs so that grid template can set and use args without
# grid explicitly having to pass them.
kwargs=kwargs )
trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params )
return page
def render_render_individual_tagging_element(context,user=None,tagged_item=None,elt_context=None,use_toggle_link=True,in_form=False,input_size='15',tag_click_fn='default_tag_click_fn',get_toggle_link_text_fn='default_get_toggle_link_text_fn',editable=True,render_add_tag_button=True):
context.caller_stack._push_frame()
try:
isinstance = context.get('isinstance', UNDEFINED)
unicode = context.get('unicode', UNDEFINED)
int = context.get('int', UNDEFINED)
h = context.get('h', UNDEFINED)
self = context.get('self', UNDEFINED)
dict = context.get('dict', UNDEFINED)
str = context.get('str', UNDEFINED)
trans = context.get('trans', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 122
__M_writer(u'\n')
# SOURCE LINE 124
__M_writer(u' ')
# Useful ids.
tagged_item_id = str( trans.security.encode_id ( tagged_item.id ) )
elt_id = int ( floor ( random()*maxint ) )
# Get list of user's item tags. TODO: implement owner_tags for all taggable objects and use here.
item_tags = [ tag for tag in tagged_item.tags if ( tag.user == user ) ]
# SOURCE LINE 131
__M_writer(u'\n \n')
# SOURCE LINE 134
__M_writer(u' ')
__M_writer(unicode(self.render_tagging_element_html(elt_id=elt_id, tags=item_tags, editable=editable, use_toggle_link=use_toggle_link, input_size=input_size, in_form=in_form, render_add_tag_button=render_add_tag_button)))
__M_writer(u'\n \n')
# SOURCE LINE 137
__M_writer(u' <script type="text/javascript">\n //\n // Set up autocomplete tagger.\n //\n\n //\n // Default function get text to display on the toggle link.\n //\n var default_get_toggle_link_text_fn = function(tags)\n {\n var text = "";\n var num_tags = obj_length(tags);\n if (num_tags != 0)\n {\n text = num_tags + (num_tags != 1 ? " Tags" : " Tag");\n /*\n // Show first N tags; hide the rest.\n var max_to_show = 1;\n \n // Build tag string.\n var tag_strs = new Array();\n var count = 0;\n for (tag_name in tags)\n {\n tag_value = tags[tag_name];\n tag_strs[tag_strs.length] = build_tag_str(tag_name, tag_value);\n if (++count == max_to_show)\n break;\n }\n tag_str = tag_strs.join(", ");\n \n // Finalize text.\n var num_tags_hiding = num_tags - max_to_show;\n text = "Tags: " + tag_str + \n (num_tags_hiding != 0 ? " and " + num_tags_hiding + " more" : "");\n */\n }\n else\n {\n // No tags.\n text = "Add tags";\n }\n return text;\n };\n \n // Default function to handle a tag click.\n var default_tag_click_fn = function(tag_name, tag_value) { };\n \n ')
# SOURCE LINE 185
## Build dict of tag name, values.
tag_names_and_values = dict()
for tag in item_tags:
tag_name = tag.user_tname
tag_value = ""
if tag.value is not None:
tag_value = tag.user_value
## Tag names and values may be string or unicode object.
if isinstance( tag_name, str ):
tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8')
else: ## isInstance( tag_name, unicode ):
tag_names_and_values[tag_name] = tag_value
# SOURCE LINE 198
__M_writer(u'\n var options =\n {\n tags : ')
# SOURCE LINE 201
__M_writer(unicode(h.to_json_string(tag_names_and_values)))
__M_writer(u',\n editable : ')
# SOURCE LINE 202
__M_writer(unicode(iff( editable, 'true', 'false' )))
__M_writer(u',\n get_toggle_link_text_fn: ')
# SOURCE LINE 203
__M_writer(unicode(get_toggle_link_text_fn))
__M_writer(u',\n tag_click_fn: ')
# SOURCE LINE 204
__M_writer(unicode(tag_click_fn))
__M_writer(u',\n')
# SOURCE LINE 206
__M_writer(u' ajax_autocomplete_tag_url: "')
__M_writer(unicode(h.url_for( controller='/tag', action='tag_autocomplete_data', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__ )))
__M_writer(u'",\n ajax_add_tag_url: "')
# SOURCE LINE 207
__M_writer(unicode(h.url_for( controller='/tag', action='add_tag_async', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )))
__M_writer(u'",\n ajax_delete_tag_url: "')
# SOURCE LINE 208
__M_writer(unicode(h.url_for( controller='/tag', action='remove_tag_async', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )))
__M_writer(u'",\n delete_tag_img: "')
# SOURCE LINE 209
__M_writer(unicode(h.url_for('/static/images/delete_tag_icon_gray.png')))
__M_writer(u'",\n delete_tag_img_rollover: "')
# SOURCE LINE 210
__M_writer(unicode(h.url_for('/static/images/delete_tag_icon_white.png')))
__M_writer(u'",\n use_toggle_link: ')
# SOURCE LINE 211
__M_writer(unicode(iff( use_toggle_link, 'true', 'false' )))
__M_writer(u"\n };\n \n $('#")
# SOURCE LINE 214
__M_writer(unicode(elt_id))
__M_writer(u"').autocomplete_tagging(options);\n </script>\n \n")
# SOURCE LINE 218
__M_writer(u' <style>\n .tag-area {\n display: ')
# SOURCE LINE 220
__M_writer(unicode(iff( use_toggle_link, "none", "block" )))
__M_writer(u';\n }\n </style>\n\n <noscript>\n <style>\n .tag-area {\n display: block;\n }\n </style>\n </noscript>\n')
return ''
finally:
context.caller_stack._pop_frame()