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Source code for galaxy.webapps.galaxy.controllers.history

import logging
import urllib

from markupsafe import escape
from six import string_types
from sqlalchemy import and_, false, func, null, true
from sqlalchemy.orm import eagerload, eagerload_all

import galaxy.util
from galaxy import exceptions
from galaxy import managers
from galaxy import model
from galaxy import web
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.util import nice_size, Params, parse_int
from galaxy.util.odict import odict
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import url_for
from galaxy.web.base.controller import BaseUIController
from galaxy.web.base.controller import ERROR, INFO, SUCCESS, WARNING
from galaxy.web.base.controller import ExportsHistoryMixin
from galaxy.web.base.controller import ImportsHistoryMixin
from galaxy.web.base.controller import SharableMixin
from galaxy.web.framework.helpers import grids, iff, time_ago


log = logging.getLogger(__name__)


[docs]class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, history): return escape(history.get_display_name())
[docs]class HistoryListGrid(grids.Grid): # Custom column types
[docs] class DatasetsByStateColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, history): # States to show in column. states_to_show = ('ok', 'running', 'queued', 'new', 'error') # Get dataset counts for each state in a state-count dictionary. state_counts = dict((state, count) for state, count in trans.sa_session.query(model.Dataset.state, func.count(model.Dataset.state)) .join(model.HistoryDatasetAssociation) .group_by(model.Dataset.state) .filter(model.HistoryDatasetAssociation.history_id == history.id, model.HistoryDatasetAssociation.visible == true(), model.HistoryDatasetAssociation.deleted == false(), model.Dataset.state.in_(states_to_show))) # Create HTML. rval = '' for state in states_to_show: count = state_counts.get(state) if count: rval += '<div class="count-box state-color-%s">%s</div> ' % (state, count) return rval
[docs] class HistoryListNameColumn(NameColumn):
[docs] class DeletedColumn(grids.DeletedColumn):
[docs] def get_value(self, trans, grid, history): if history == trans.history: return "<strong>current history</strong>" if history.purged: return "deleted permanently" elif history.deleted: return "deleted" return ""
[docs] def sort(self, trans, query, ascending, column_name=None): if ascending: query = query.order_by(self.model_class.table.c.purged.asc(), self.model_class.table.c.update_time.desc()) else: query = query.order_by(self.model_class.table.c.purged.desc(), self.model_class.table.c.update_time.desc()) return query
# Grid definition title = "Saved Histories" model_class = model.History default_sort_key = "-update_time" columns = [ HistoryListNameColumn("Name", key="name", attach_popup=True, filterable="advanced"), DatasetsByStateColumn("Datasets", key="datasets_by_state", sortable=False, nowrap=True), grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid"), grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False), grids.GridColumn("Size on Disk", key="disk_size", format=nice_size, sortable=False), grids.GridColumn("Created", key="create_time", format=time_ago), grids.GridColumn("Last Updated", key="update_time", format=time_ago), DeletedColumn("Status", key="deleted", filterable="advanced") ] columns.append( grids.MulticolFilterColumn( "search history names and tags", cols_to_filter=[columns[0], columns[2]], key="free-text-search", visible=False, filterable="standard") ) operations = [ grids.GridOperation("Switch", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=True), grids.GridOperation("View", allow_multiple=False, url_args=dict(action='view')), grids.GridOperation("Share or Publish", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(action='sharing')), grids.GridOperation("Copy", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False), grids.GridOperation("Rename", condition=(lambda item: not item.deleted), url_args=dict(action='rename')), grids.GridOperation("Delete", condition=(lambda item: not item.deleted), async_compatible=True), grids.GridOperation("Delete Permanently", condition=(lambda item: not item.purged), confirm="History contents will be removed from disk, this cannot be undone. Continue?", async_compatible=True), grids.GridOperation("Undelete", condition=(lambda item: item.deleted and not item.purged), async_compatible=True), ] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True)), grids.GridColumnFilter("All", args=dict(deleted='All')), ] default_filter = dict(name="All", deleted="False", tags="All", sharing="All") num_rows_per_page = 15 preserve_state = False use_async = True use_paging = True info_text = "Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted."
[docs] def get_current_item(self, trans, **kwargs): return trans.get_history()
[docs] def apply_query_filter(self, trans, query, **kwargs): return query.filter_by(user=trans.user, importing=False)
[docs]class SharedHistoryListGrid(grids.Grid): # Custom column types
[docs] class DatasetsByStateColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, history): rval = '' for state in ('ok', 'running', 'queued', 'error'): total = sum(1 for d in history.active_datasets if d.state == state) if total: rval += '<div class="count-box state-color-%s">%s</div>' % (state, total) return rval
[docs] class SharedByColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, history): return escape(history.user.email)
# Grid definition title = "Histories shared with you by others" model_class = model.History default_sort_key = "-update_time" default_filter = {} columns = [ grids.GridColumn("Name", key="name", attach_popup=True), DatasetsByStateColumn("Datasets", sortable=False), grids.GridColumn("Created", key="create_time", format=time_ago), grids.GridColumn("Last Updated", key="update_time", format=time_ago), SharedByColumn("Shared by", key="user_id") ] operations = [ grids.GridOperation("View", allow_multiple=False, url_args=dict(action='view')), grids.GridOperation("Copy", allow_multiple=False), grids.GridOperation("Unshare", allow_multiple=False) ] standard_filters = []
[docs] def build_initial_query(self, trans, **kwargs): return trans.sa_session.query(self.model_class).join('users_shared_with')
[docs] def apply_query_filter(self, trans, query, **kwargs): return query.filter(model.HistoryUserShareAssociation.user == trans.user)
[docs]class HistoryAllPublishedGrid(grids.Grid):
[docs] class NameURLColumn(grids.PublicURLColumn, NameColumn): pass
title = "Published Histories" model_class = model.History default_sort_key = "update_time" default_filter = dict(public_url="All", username="All", tags="All") use_paging = True num_rows_per_page = 50 use_async = True columns = [ NameURLColumn("Name", key="name", filterable="advanced"), grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced"), grids.OwnerColumn("Owner", key="username", model_class=model.User, filterable="advanced"), grids.CommunityRatingColumn("Community Rating", key="rating"), grids.CommunityTagsColumn("Community Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid"), grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago) ] columns.append( grids.MulticolFilterColumn( "Search name, annotation, owner, and tags", cols_to_filter=[columns[0], columns[1], columns[2], columns[4]], key="free-text-search", visible=False, filterable="standard") ) operations = []
[docs] def build_initial_query(self, trans, **kwargs): # Join so that searching history.user makes sense. return trans.sa_session.query(self.model_class).join(model.User.table)
[docs] def apply_query_filter(self, trans, query, **kwargs): # A public history is published, has a slug, and is not deleted. return query.filter(self.model_class.published == true()).filter(self.model_class.slug != null()).filter(self.model_class.deleted == false())
[docs]class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, ExportsHistoryMixin, ImportsHistoryMixin):
[docs] def __init__(self, app): super(HistoryController, self).__init__(app) self.history_manager = managers.histories.HistoryManager(app) self.history_serializer = managers.histories.HistorySerializer(self.app)
[docs] @web.expose def index(self, trans): return ""
[docs] @web.expose def list_as_xml(self, trans): """XML history list for functional tests""" trans.response.set_content_type('text/xml') return trans.fill_template("/history/list_as_xml.mako")
# ......................................................................... lists stored_list_grid = HistoryListGrid() shared_list_grid = SharedHistoryListGrid() published_list_grid = HistoryAllPublishedGrid()
[docs] @web.expose @web.json def list_published(self, trans, **kwargs): kwargs['dict_format'] = True return self.published_list_grid(trans, **kwargs)
[docs] @web.expose @web.json @web.require_login("work with multiple histories") def list(self, trans, **kwargs): """List all available histories""" current_history = trans.get_history() status = message = None if 'operation' in kwargs: operation = kwargs['operation'].lower() history_ids = galaxy.util.listify(kwargs.get('id', [])) # Display no message by default status, message = None, None # Load the histories and ensure they all belong to the current user histories = [] for history_id in history_ids: history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history) if history: # Ensure history is owned by current user if history.user_id is not None and trans.user: assert trans.user.id == history.user_id, "History does not belong to current user" histories.append(history) else: log.warning("Invalid history id '%r' passed to list", history_id) if histories: if operation == "switch": status, message = self._list_switch(trans, histories) # Take action to update UI to reflect history switch. If # grid is using panels, it is standalone and hence a redirect # to root is needed; if grid is not using panels, it is nested # in the main Galaxy UI and refreshing the history frame # is sufficient. use_panels = kwargs.get('use_panels', False) == 'True' if use_panels: return trans.response.send_redirect(url_for("/")) else: kwargs['refresh_frames'] = ['history'] elif operation in ("delete", "delete permanently"): if operation == "delete permanently": status, message = self._list_delete(trans, histories, purge=True) else: status, message = self._list_delete(trans, histories) if current_history in histories: # Deleted the current history, so a new, empty history was # created automatically, and we need to refresh the history frame kwargs['refresh_frames'] = ['history'] elif operation == "undelete": status, message = self._list_undelete(trans, histories) elif operation == "unshare": for history in histories: for husa in trans.sa_session.query(trans.app.model.HistoryUserShareAssociation) \ .filter_by(history=history): trans.sa_session.delete(husa) elif operation == "enable import via link": for history in histories: if not history.importable: self._make_item_importable(trans.sa_session, history) elif operation == "disable import via link": if history_ids: histories = [] for history_id in history_ids: history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history) if history.importable: history.importable = False histories.append(history) trans.sa_session.flush() # Render the list view kwargs['dict_format'] = True return self.stored_list_grid(trans, status=status, message=message, **kwargs)
def _list_delete(self, trans, histories, purge=False): """Delete histories""" n_deleted = 0 deleted_current = False message_parts = [] status = SUCCESS for history in histories: if history.users_shared_with: message_parts.append("History (%s) has been shared with others, unshare it before deleting it. " % history.name) status = ERROR else: if not history.deleted: # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later history.deleted = True # If deleting the current history, make a new current. if history == trans.get_history(): deleted_current = True trans.log_event("History (%s) marked as deleted" % history.name) n_deleted += 1 if purge and trans.app.config.allow_user_dataset_purge: for hda in history.datasets: if trans.user: trans.user.adjust_total_disk_usage(-hda.quota_amount(trans.user)) hda.purged = True trans.sa_session.add(hda) trans.log_event("HDA id %s has been purged" % hda.id) trans.sa_session.flush() if hda.dataset.user_can_purge: try: hda.dataset.full_delete() trans.log_event("Dataset id %s has been purged upon the the purge of HDA id %s" % (hda.dataset.id, hda.id)) trans.sa_session.add(hda.dataset) except: log.exception('Unable to purge dataset (%s) on purge of hda (%s):' % (hda.dataset.id, hda.id)) history.purged = True self.sa_session.add(history) self.sa_session.flush() for hda in history.datasets: # Not all datasets have jobs associated with them (e.g., datasets imported from libraries). if hda.creating_job_associations: # HDA has associated job, so try marking it deleted. job = hda.creating_job_associations[0].job if job.history_id == history.id and not job.finished: # No need to check other outputs since the job's parent history is this history job.mark_deleted(trans.app.config.track_jobs_in_database) trans.app.job_manager.job_stop_queue.put(job.id) trans.sa_session.flush() 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 += " and removed %s dataset%s from disk" % (iff(n_deleted != 1, "their", "its"), iff(n_deleted != 1, 's', '')) elif purge: part += " but the datasets were not removed from disk because that feature is not enabled in this Galaxy instance" message_parts.append("%s. " % part) if deleted_current: # note: this needs to come after commits above or will use an empty history that was deleted above 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 _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) def _list_switch(self, trans, histories): """Switch to a new different history""" new_history = histories[0] galaxy_session = trans.get_galaxy_session() try: association = trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation) \ .filter_by(session_id=galaxy_session.id, history_id=new_history.id) \ .first() except: association = None new_history.add_galaxy_session(galaxy_session, association=association) trans.sa_session.add(new_history) trans.sa_session.flush() trans.set_history(new_history) # No message return None, None
[docs] @web.expose @web.json @web.require_login("work with shared histories") def list_shared(self, trans, **kwargs): """List histories shared with current user by others""" status = message = None if 'operation' in kwargs: ids = galaxy.util.listify(kwargs.get('id', [])) operation = kwargs['operation'].lower() if operation == 'unshare': if not ids: message = "Select a history to unshare" status = 'error' for id in ids: # No need to check security, association below won't yield a # hit if this user isn't having the history shared with her. history = self.history_manager.by_id(self.decode_id(id)) # Current user is the user with which the histories were shared association = (trans.sa_session.query(trans.app.model.HistoryUserShareAssociation) .filter_by(user=trans.user, history=history).one()) trans.sa_session.delete(association) trans.sa_session.flush() message = "Unshared %d shared histories" % len(ids) status = 'done' # Render the list view kwargs['dict_format'] = True return self.shared_list_grid(trans, status=status, message=message, **kwargs)
# ......................................................................... html
[docs] @web.expose def citations(self, trans): # Get history history = trans.history history_id = trans.security.encode_id(history.id) return trans.fill_template("history/citations.mako", history=history, history_id=history_id)
[docs] @web.expose def as_xml(self, trans, id=None, show_deleted=None, show_hidden=None): """ Return a history in xml format. """ if trans.app.config.require_login and not trans.user: return trans.fill_template('/no_access.mako', message='Please log in to access Galaxy histories.') if id: history = self.history_manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history) else: history = trans.get_history(most_recent=True, create=True) trans.response.set_content_type('text/xml') return trans.fill_template_mako( "history/as_xml.mako", history=history, show_deleted=galaxy.util.string_as_bool(show_deleted), show_hidden=galaxy.util.string_as_bool(show_hidden))
[docs] @web.expose def display_structured(self, trans, id=None): """ Display a history as a nested structure showing the jobs and workflow invocations that created each dataset (if any). """ # Get history if id is None: id = trans.history.id else: id = self.decode_id(id) # Expunge history from the session to allow us to force a reload # with a bunch of eager loaded joins trans.sa_session.expunge(trans.history) history = trans.sa_session.query(model.History).options( eagerload_all('active_datasets.creating_job_associations.job.workflow_invocation_step.workflow_invocation.workflow'), eagerload_all('active_datasets.children') ).get(id) assert history # TODO: formalize to trans.show_error assert (history.user and (history.user.id == trans.user.id) or (history.id == trans.history.id) or (trans.user_is_admin())) # Resolve jobs and workflow invocations for the datasets in the history # items is filled with items (hdas, jobs, or workflows) that go at the # top level items = [] # First go through and group hdas by job, if there is no job they get # added directly to items jobs = odict() for hda in history.active_datasets: if hda.visible is False: continue # Follow "copied from ..." association until we get to the original # instance of the dataset original_hda = hda # while original_hda.copied_from_history_dataset_association: # original_hda = original_hda.copied_from_history_dataset_association # Check if the job has a creating job, most should, datasets from # before jobs were tracked, or from the upload tool before it # created a job, may not if not original_hda.creating_job_associations: items.append((hda, None)) # Attach hda to correct job # -- there should only be one creating_job_association, so this # loop body should only be hit once for assoc in original_hda.creating_job_associations: job = assoc.job if job in jobs: jobs[job].append((hda, None)) else: jobs[job] = [(hda, None)] # Second, go through the jobs and connect to workflows wf_invocations = odict() for job, hdas in jobs.iteritems(): # Job is attached to a workflow step, follow it to the # workflow_invocation and group if job.workflow_invocation_step: wf_invocation = job.workflow_invocation_step.workflow_invocation if wf_invocation in wf_invocations: wf_invocations[wf_invocation].append((job, hdas)) else: wf_invocations[wf_invocation] = [(job, hdas)] # Not attached to a workflow, add to items else: items.append((job, hdas)) # Finally, add workflow invocations to items, which should now # contain all hdas with some level of grouping items.extend(wf_invocations.items()) # Sort items by age items.sort(key=(lambda x: x[0].create_time), reverse=True) # return trans.fill_template("history/display_structured.mako", items=items, history=history)
[docs] @web.expose def structure(self, trans, id=None, **kwargs): """ """ unencoded_history_id = trans.history.id if id: unencoded_history_id = self.decode_id(id) history_to_view = self.history_manager.get_accessible(unencoded_history_id, trans.user, current_history=trans.history) history_dictionary = self.history_serializer.serialize_to_view(history_to_view, view='dev-detailed', user=trans.user, trans=trans) contents = self.history_serializer.serialize_contents(history_to_view, 'contents', trans=trans, user=trans.user) jobs = (trans.sa_session.query(trans.app.model.Job) .filter(trans.app.model.Job.user == history_to_view.user) .filter(trans.app.model.Job.history_id == unencoded_history_id)).all() jobs = map(lambda j: self.encode_all_ids(trans, j.to_dict('element'), True), jobs) tools = {} for tool_id in set(map(lambda j: j['tool_id'], jobs)): unquoted_id = urllib.unquote_plus(tool_id) tool = self.app.toolbox.get_tool(unquoted_id) if not tool: raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % tool_id) # TODO: some fallback for tool information tools[tool_id] = tool.to_dict(trans, io_details=True, link_details=True) return trans.fill_template("history/structure.mako", historyId=history_dictionary['id'], history=history_dictionary, contents=contents, jobs=jobs, tools=tools, **kwargs)
[docs] @web.expose def view(self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True): """ View a history. If a history is importable, then it is viewable by any user. """ show_deleted = galaxy.util.string_as_bool(show_deleted) show_hidden = galaxy.util.string_as_bool(show_hidden) use_panels = galaxy.util.string_as_bool(use_panels) history_dictionary = {} user_is_owner = False try: if id: history_to_view = self.history_manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history) user_is_owner = history_to_view.user == trans.user history_is_current = history_to_view == trans.history else: history_to_view = trans.history user_is_owner = True history_is_current = True # include all datasets: hidden, deleted, and purged history_dictionary = self.history_serializer.serialize_to_view(history_to_view, view='dev-detailed', user=trans.user, trans=trans) except Exception as exc: user_id = str(trans.user.id) if trans.user else '(anonymous)' log.exception('Error bootstrapping history for user %s', user_id) if isinstance(exc, exceptions.ItemAccessibilityException): error_msg = 'You do not have permission to view this history.' else: error_msg = ('An error occurred getting the history data from the server. ' + 'Please contact a Galaxy administrator if the problem persists.') return trans.show_error_message(error_msg, use_panels=use_panels) return trans.fill_template_mako("history/view.mako", history=history_dictionary, user_is_owner=user_is_owner, history_is_current=history_is_current, show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels)
[docs] @web.require_login("use more than one Galaxy history") @web.expose def view_multiple(self, trans, include_deleted_histories=False, order='update_time', limit=10): """ """ current_history_id = trans.security.encode_id(trans.history.id) # TODO: allow specifying user_id for admin? include_deleted_histories = galaxy.util.string_as_bool(include_deleted_histories) limit = parse_int(limit, min_val=1, default=10, allow_none=True) return trans.fill_template_mako("history/view_multiple.mako", current_history_id=current_history_id, include_deleted_histories=include_deleted_histories, order=order, limit=limit)
[docs] @web.expose def display_by_username_and_slug(self, trans, username, slug): """ Display history based on a username and slug. """ # Get history. session = trans.sa_session user = session.query(model.User).filter_by(username=username).first() history = trans.sa_session.query(model.History) \ .options(eagerload('tags')).options(eagerload('annotations')) \ .filter_by(user=user, slug=slug, deleted=False).first() if history is None: raise web.httpexceptions.HTTPNotFound() # Security check raises error if user cannot access history. self.history_manager.error_unless_accessible(history, trans.user, current_history=trans.history) # Get rating data. user_item_rating = 0 if trans.get_user(): user_item_rating = self.get_user_item_rating(trans.sa_session, trans.get_user(), history) if user_item_rating: user_item_rating = user_item_rating.rating else: user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, history) # create ownership flag for template, dictify models user_is_owner = trans.user == history.user history_dictionary = self.history_serializer.serialize_to_view(history, view='dev-detailed', user=trans.user, trans=trans) history_dictionary['annotation'] = self.get_item_annotation_str(trans.sa_session, history.user, history) return trans.stream_template_mako("history/display.mako", item=history, item_data=[], user_is_owner=user_is_owner, history_dict=history_dictionary, user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings)
# ......................................................................... sharing & publishing
[docs] @web.expose @web.require_login("share Galaxy histories") def sharing(self, trans, id=None, histories=[], **kwargs): """ Handle history sharing. """ # Get session and histories. session = trans.sa_session # Id values take precedence over histories passed in; last resort is current history. if id: ids = galaxy.util.listify(id) if ids: histories = [self.history_manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history) for history_id in ids] elif not histories: histories = [trans.history] # Do operation on histories. for history in histories: if 'make_accessible_via_link' in kwargs: self._make_item_accessible(trans.sa_session, history) elif 'make_accessible_and_publish' in kwargs: self._make_item_accessible(trans.sa_session, history) history.published = True elif 'publish' in kwargs: if history.importable: history.published = True else: # TODO: report error here. pass elif 'disable_link_access' in kwargs: history.importable = False elif 'unpublish' in kwargs: history.published = False elif 'disable_link_access_and_unpublish' in kwargs: history.importable = history.published = False elif 'unshare_user' in kwargs: user = trans.sa_session.query(trans.app.model.User).get(self.decode_id(kwargs['unshare_user'])) # Look for and delete sharing relation for history-user. deleted_sharing_relation = False husas = trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=user, history=history).all() if husas: deleted_sharing_relation = True for husa in husas: trans.sa_session.delete(husa) if not deleted_sharing_relation: history_name = escape(history.name) user_email = escape(user.email) message = "History '%s' does not seem to be shared with user '%s'" % (history_name, user_email) return trans.fill_template('/sharing_base.mako', controller_list='histories', item=history, message=message, status='error', use_panels=True) # Legacy issue: histories made accessible before recent updates may not have a slug. Create slug for any histories that need them. for history in histories: if history.importable and not history.slug: self._make_item_accessible(trans.sa_session, history) session.flush() return trans.fill_template("/sharing_base.mako", controller_list='histories', item=history, use_panels=True)
[docs] @web.expose @web.require_login("share histories with other users") def share(self, trans, id=None, email="", **kwd): # If a history contains both datasets that can be shared and others that cannot be shared with the desired user, # then the entire history is shared, and the protected datasets will be visible, but inaccessible ( greyed out ) # in the copyd history params = Params(kwd) user = trans.get_user() # TODO: we have too many error messages floating around in here - we need # to incorporate the messaging system used by the libraries that will display # a message on any page. err_msg = galaxy.util.restore_text(params.get('err_msg', '')) if not email: if not id: # Default to the current history id = trans.security.encode_id(trans.history.id) id = galaxy.util.listify(id) send_to_err = err_msg histories = [] for history_id in id: history_id = self.decode_id(history_id) history = self.history_manager.get_owned(history_id, trans.user, current_history=trans.history) histories.append(history) return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err) histories = self._get_histories(trans, id) send_to_users, send_to_err = self._get_users(trans, user, email) if not send_to_users: if not send_to_err: send_to_err += "%s is not a valid Galaxy user. %s" % (email, err_msg) return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err) if params.get('share_button', False): # The user has not yet made a choice about how to share, so dictionaries will be built for display can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \ self._populate_restricted(trans, user, histories, send_to_users, None, send_to_err, unique=True) send_to_err += err_msg if cannot_change and not no_change_needed and not can_change: send_to_err = "The histories you are sharing do not contain any datasets that can be accessed by the users with which you are sharing." return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err) if can_change or cannot_change: return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err, can_change=can_change, cannot_change=cannot_change, no_change_needed=unique_no_change_needed) if no_change_needed: return self._share_histories(trans, user, send_to_err, histories=no_change_needed) elif not send_to_err: # User seems to be sharing an empty history send_to_err = "You cannot share an empty history. " return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err)
[docs] @web.expose def adjust_hidden(self, trans, id=None, **kwd): """ THIS METHOD IS A TEMPORARY ADDITION. It'll allow us to fix the regression in history-wide actions, and will be removed in the first release after 17.01 """ action = kwd.get('user_action', None) if action == 'delete': for hda in trans.history.datasets: if not hda.visible: hda.mark_deleted() elif action == 'unhide': trans.history.unhide_datasets() trans.sa_session.flush()
[docs] @web.expose @web.require_login("share restricted histories with other users") def share_restricted(self, trans, id=None, email="", **kwd): if 'action' in kwd: action = kwd['action'] else: err_msg = "Select an action. " return trans.response.send_redirect(url_for(controller='history', action='share', id=id, email=email, err_msg=err_msg, share_button=True)) user = trans.get_user() user_roles = user.all_roles() histories = self._get_histories(trans, id) send_to_users, send_to_err = self._get_users(trans, user, email) send_to_err = '' # The user has made a choice, so dictionaries will be built for sharing can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \ self._populate_restricted(trans, user, histories, send_to_users, action, send_to_err) # Now that we've populated the can_change, cannot_change, and no_change_needed dictionaries, # we'll populate the histories_for_sharing dictionary from each of them. histories_for_sharing = {} if no_change_needed: # Don't need to change anything in cannot_change, so populate as is histories_for_sharing, send_to_err = \ self._populate(trans, histories_for_sharing, no_change_needed, send_to_err) if cannot_change: # Can't change anything in cannot_change, so populate as is histories_for_sharing, send_to_err = \ self._populate(trans, histories_for_sharing, cannot_change, send_to_err) # The action here is either 'public' or 'private', so we'll continue to populate the # histories_for_sharing dictionary from the can_change dictionary. for send_to_user, history_dict in can_change.items(): for history in history_dict: # Make sure the current history has not already been shared with the current send_to_user if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation) \ .filter(and_(trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id)) \ .count() > 0: send_to_err += "History (%s) already shared with user (%s)" % (history.name, send_to_user.email) else: # Only deal with datasets that have not been purged for hda in history.activatable_datasets: # If the current dataset is not public, we may need to perform an action on it to # make it accessible by the other user. if not trans.app.security_agent.can_access_dataset(send_to_user.all_roles(), hda.dataset): # The user with which we are sharing the history does not have access permission on the current dataset if trans.app.security_agent.can_manage_dataset(user_roles, hda.dataset) and not hda.dataset.library_associations: # The current user has authority to change permissions on the current dataset because # they have permission to manage permissions on the dataset and the dataset is not associated # with a library. if action == "private": trans.app.security_agent.privately_share_dataset(hda.dataset, users=[user, send_to_user]) elif action == "public": trans.app.security_agent.make_dataset_public(hda.dataset) # Populate histories_for_sharing with the history after performing any requested actions on # its datasets to make them accessible by the other user. if send_to_user not in histories_for_sharing: histories_for_sharing[send_to_user] = [history] elif history not in histories_for_sharing[send_to_user]: histories_for_sharing[send_to_user].append(history) return self._share_histories(trans, user, send_to_err, histories=histories_for_sharing)
def _get_histories(self, trans, ids): if not ids: # Default to the current history ids = trans.security.encode_id(trans.history.id) ids = galaxy.util.listify(ids) histories = [] for history_id in ids: history_id = self.decode_id(history_id) history = self.history_manager.get_owned(history_id, trans.user, current_history=trans.history) histories.append(history) return histories def _get_users(self, trans, user, emails_or_ids): send_to_users = [] send_to_err = "" for string in galaxy.util.listify(emails_or_ids): string = string.strip() if not string: continue send_to_user = None if '@' in string: email_address = string send_to_user = self.user_manager.by_email(email_address, filters=[trans.app.model.User.table.c.deleted == false()]) else: try: decoded_user_id = self.decode_id(string) send_to_user = self.user_manager.by_id(decoded_user_id) if send_to_user.deleted: send_to_user = None # TODO: in an ideal world, we would let this bubble up to web.expose which would handle it except exceptions.MalformedId: send_to_user = None if not send_to_user: send_to_err += "%s is not a valid Galaxy user. " % string elif send_to_user == user: send_to_err += "You cannot send histories to yourself. " else: send_to_users.append(send_to_user) return send_to_users, send_to_err def _populate(self, trans, histories_for_sharing, other, send_to_err): # This method will populate the histories_for_sharing dictionary with the users and # histories in other, eliminating histories that have already been shared with the # associated user. No security checking on datasets is performed. # If not empty, the histories_for_sharing dictionary looks like: # { userA: [ historyX, historyY ], userB: [ historyY ] } # other looks like: # { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} } for send_to_user, history_dict in other.items(): for history in history_dict: # Make sure the current history has not already been shared with the current send_to_user if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation) \ .filter(and_(trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id)) \ .count() > 0: send_to_err += "History (%s) already shared with user (%s)" % (history.name, send_to_user.email) else: # Build the dict that will be used for sharing if send_to_user not in histories_for_sharing: histories_for_sharing[send_to_user] = [history] elif history not in histories_for_sharing[send_to_user]: histories_for_sharing[send_to_user].append(history) return histories_for_sharing, send_to_err def _populate_restricted(self, trans, user, histories, send_to_users, action, send_to_err, unique=False): # The user may be attempting to share histories whose datasets cannot all be accessed by other users. # If this is the case, the user sharing the histories can: # 1) action=='public': choose to make the datasets public if he is permitted to do so # 2) action=='private': automatically create a new "sharing role" allowing protected # datasets to be accessed only by the desired users # This method will populate the can_change, cannot_change and no_change_needed dictionaries, which # are used for either displaying to the user, letting them make 1 of the choices above, or sharing # after the user has made a choice. They will be used for display if 'unique' is True, and will look # like: {historyX : [hda, hda], historyY : [hda] } # For sharing, they will look like: # { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} } can_change = {} cannot_change = {} no_change_needed = {} unique_no_change_needed = {} user_roles = user.all_roles() for history in histories: for send_to_user in send_to_users: # Make sure the current history has not already been shared with the current send_to_user if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation) \ .filter(and_(trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id)) \ .count() > 0: send_to_err += "History (%s) already shared with user (%s)" % (history.name, send_to_user.email) else: # Only deal with datasets that have not been purged for hda in history.activatable_datasets: if trans.app.security_agent.can_access_dataset(send_to_user.all_roles(), hda.dataset): # The no_change_needed dictionary is a special case. If both of can_change # and cannot_change are empty, no_change_needed will used for sharing. Otherwise # unique_no_change_needed will be used for displaying, so we need to populate both. # Build the dictionaries for display, containing unique histories only if history not in unique_no_change_needed: unique_no_change_needed[history] = [hda] else: unique_no_change_needed[history].append(hda) # Build the dictionaries for sharing if send_to_user not in no_change_needed: no_change_needed[send_to_user] = {} if history not in no_change_needed[send_to_user]: no_change_needed[send_to_user][history] = [hda] else: no_change_needed[send_to_user][history].append(hda) else: # The user with which we are sharing the history does not have access permission on the current dataset if trans.app.security_agent.can_manage_dataset(user_roles, hda.dataset): # The current user has authority to change permissions on the current dataset because # they have permission to manage permissions on the dataset. # NOTE: ( gvk )There may be problems if the dataset also has an ldda, but I don't think so # because the user with which we are sharing will not have the "manage permission" permission # on the dataset in their history. Keep an eye on this though... if unique: # Build the dictionaries for display, containing unique histories only if history not in can_change: can_change[history] = [hda] else: can_change[history].append(hda) else: # Build the dictionaries for sharing if send_to_user not in can_change: can_change[send_to_user] = {} if history not in can_change[send_to_user]: can_change[send_to_user][history] = [hda] else: can_change[send_to_user][history].append(hda) else: if action in ["private", "public"]: # The user has made a choice, so 'unique' doesn't apply. Don't change stuff # that the user doesn't have permission to change continue if unique: # Build the dictionaries for display, containing unique histories only if history not in cannot_change: cannot_change[history] = [hda] else: cannot_change[history].append(hda) else: # Build the dictionaries for sharing if send_to_user not in cannot_change: cannot_change[send_to_user] = {} if history not in cannot_change[send_to_user]: cannot_change[send_to_user][history] = [hda] else: cannot_change[send_to_user][history].append(hda) return can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err def _share_histories(self, trans, user, send_to_err, histories=None): # histories looks like: { userA: [ historyX, historyY ], userB: [ historyY ] } histories = histories or {} msg = "" shared_histories = [] if not histories: send_to_err += "No users have been specified or no histories can be sent without changing permissions or associating a sharing role. " else: for send_to_user, send_to_user_histories in histories.items(): for history in send_to_user_histories: share = trans.app.model.HistoryUserShareAssociation() share.history = history share.user = send_to_user trans.sa_session.add(share) self.create_item_slug(trans.sa_session, history) trans.sa_session.flush() if history not in shared_histories: shared_histories.append(history) if send_to_err: msg += send_to_err return self.sharing(trans, histories=shared_histories, msg=msg) # ......................................................................... actions/orig. async
[docs] @web.expose def purge_deleted_datasets(self, trans): count = 0 if trans.app.config.allow_user_dataset_purge: for hda in trans.history.datasets: if not hda.deleted or hda.purged: continue if trans.user: trans.user.adjust_total_disk_usage(-hda.quota_amount(trans.user)) hda.purged = True trans.sa_session.add(hda) trans.log_event("HDA id %s has been purged" % hda.id) trans.sa_session.flush() if hda.dataset.user_can_purge: try: hda.dataset.full_delete() trans.log_event("Dataset id %s has been purged upon the the purge of HDA id %s" % (hda.dataset.id, hda.id)) trans.sa_session.add(hda.dataset) except: log.exception('Unable to purge dataset (%s) on purge of hda (%s):' % (hda.dataset.id, hda.id)) count += 1 return trans.show_ok_message("%d datasets have been deleted permanently" % count, refresh_frames=['history'])
[docs] @web.expose def delete(self, trans, id, purge=False): """Delete the history -- this does not require a logged in user.""" # TODO: use api instead try: # get the history with the given id, delete and optionally purge current_history = self.history_manager.get_current(trans) history = self.history_manager.get_owned(self.decode_id(id), trans.user, current_history=current_history) if history.users_shared_with: raise exceptions.ObjectAttributeInvalidException( "History has been shared with others. Unshare it before deleting it." ) self.history_manager.delete(history, flush=(not purge)) if purge: self.history_manager.purge(history) # 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 if history == current_history: 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() except Exception as exc: return trans.show_error_message(exc) return trans.show_ok_message("History deleted", refresh_frames=['history'])
[docs] @web.expose def resume_paused_jobs(self, trans, current=False, ids=None): """Resume paused jobs the active history -- this does not require a logged in user.""" if not ids and galaxy.util.string_as_bool(current): histories = [trans.get_history()] refresh_frames = ['history'] else: raise NotImplementedError("You can currently only resume all the datasets of the current history.") for history in histories: history.resume_paused_jobs() trans.sa_session.add(history) trans.sa_session.flush() return trans.show_ok_message("Your jobs have been resumed.", refresh_frames=refresh_frames)
# TODO: used in index.mako
[docs] @web.expose @web.require_login("rate items") @web.json def rate_async(self, trans, id, rating): """ Rate a history asynchronously and return updated community data. """ history = self.history_manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history) if not history: return trans.show_error_message("The specified history does not exist.") # Rate history. self.rate_item(trans.sa_session, trans.get_user(), history, rating) return self.get_ave_item_rating_data(trans.sa_session, history)
# TODO: used in display_base.mako
[docs] @web.expose # TODO: Remove require_login when users are warned that, if they are not # logged in, this will remove their current history. @web.require_login("use Galaxy histories") def import_archive(self, trans, **kwargs): """ Import a history from a file archive. """ # Set archive source and type. archive_file = kwargs.get('archive_file', None) archive_url = kwargs.get('archive_url', None) archive_source = None if hasattr(archive_file, 'file'): # archive_file.file is a TemporaryFile and will be deleted once it is closed. # We prevent this by setting `delete` to `False`. archive_file.file.delete = False archive_source = archive_file.file.name archive_type = 'file' elif archive_url: archive_source = archive_url archive_type = 'url' # If no source to create archive from, show form to upload archive or specify URL. if not archive_source: form = web.FormBuilder(web.url_for(controller='history', action='import_archive'), "Import a History from an Archive", submit_text="Submit") form.add_input("text", "Archived History URL", "archive_url", value="", error=None) form.add_input("file", "Archived History File", "archive_file", value="", error=None) return trans.show_form(form) self.queue_history_import(trans, archive_type=archive_type, archive_source=archive_source) return trans.show_message("Importing history from '%s'. \ This history will be visible when the import is complete" % archive_source)
# TODO: used in this file and index.mako
[docs] @web.expose def export_archive(self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False, preview=False): """ Export a history to an archive. """ # # Get history to export. # if id: history = self.history_manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history) else: # Use current history. history = trans.history id = trans.security.encode_id(history.id) if not history: return trans.show_error_message("This history does not exist or you cannot export this history.") # If history has already been exported and it has not changed since export, stream it. jeha = history.latest_export if jeha and jeha.up_to_date: if jeha.ready: if preview: url = url_for(controller='history', action="export_archive", id=id, qualified=True) return trans.show_message("History Ready: '%(n)s'. Use this link to download " "the archive or import it to another Galaxy server: " "<a href='%(u)s'>%(u)s</a>" % ({'n': history.name, 'u': url})) else: return self.serve_ready_history_export(trans, jeha) elif jeha.preparing: return trans.show_message("Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>" % ({'n': history.name, 's': url_for(controller='history', action="export_archive", id=id, qualified=True)})) self.queue_history_export(trans, history, gzip=gzip, include_hidden=include_hidden, include_deleted=include_deleted) url = url_for(controller='history', action="export_archive", id=id, qualified=True) return trans.show_message("Exporting History '%(n)s'. You will need to <a href='%(share)s'>make this history 'accessible'</a> in order to import this to another galaxy sever. <br/>" "Use this link to download the archive or import it to another Galaxy server: " "<a href='%(u)s'>%(u)s</a>" % ({'share': url_for(controller='history', action='sharing'), 'n': history.name, 'u': url}))
# TODO: used in this file and index.mako # TODO: used in page/editor.mako
[docs] @web.expose @web.require_login("set history's accessible flag") def set_accessible_async(self, trans, id=None, accessible=False): """ Set history's importable attribute and slug. """ history = self.history_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history) # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed. importable = accessible in ['True', 'true', 't', 'T'] if history and history.importable != importable: if importable: self._make_item_accessible(trans.sa_session, history) else: history.importable = importable trans.sa_session.flush() return
# TODO: used in page/editor.mako
[docs] @web.expose @web.require_login("rename histories") def rename(self, trans, id=None, name=None, **kwd): user = trans.get_user() if not id: # Default to the current history history = trans.get_history() if not history.user: return trans.show_error_message("You must save your history before renaming it.") id = trans.security.encode_id(history.id) id = galaxy.util.listify(id) name = galaxy.util.listify(name) histories = [] for history_id in id: history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history) if history and history.user_id == user.id: histories.append(history) if not name or len(histories) != len(name): return trans.fill_template("/history/rename.mako", histories=histories) change_msgs = [] for i in range(len(histories)): cur_name = histories[i].get_display_name() new_name = name[i] # skip if name is empty if not isinstance(new_name, string_types) or not new_name.strip(): change_msgs.append("You must specify a valid name for History: " + cur_name) continue # skip if not the owner # ??: isn't this already handled in get_history/if statement above? if histories[i].user_id != user.id: change_msgs.append("History: " + cur_name + " does not appear to belong to you.") continue # skip if it wouldn't be a change if new_name == cur_name: change_msgs.append("History: " + cur_name + " is already named: " + new_name) continue # escape, sanitize, set, and log the change new_name = escape(new_name) histories[i].name = sanitize_html(new_name) trans.sa_session.add(histories[i]) trans.sa_session.flush() trans.log_event("History renamed: id: %s, renamed to: '%s'" % (str(histories[i].id), new_name)) change_msgs.append("History: " + cur_name + " renamed to: " + new_name) change_msg = '<br />'.join(change_msgs) return trans.show_message(change_msg, refresh_frames=['history'])
# ------------------------------------------------------------------------- current history
[docs] @web.expose @web.require_login("switch to a history") def switch_to_history(self, trans, hist_id=None): """Change the current user's current history to one with `hist_id`.""" # remains for backwards compat self.set_as_current(trans, id=hist_id) return trans.response.send_redirect(url_for("/"))
[docs] def get_item(self, trans, id): return self.history_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history)
# TODO: override of base ui controller?
[docs] def history_data(self, trans, history): """Return the given history in a serialized, dictionary form.""" return self.history_serializer.serialize_to_view(history, view='dev-detailed', user=trans.user, trans=trans)
# TODO: combine these next two - poss. with a redirect flag # @web.require_login( "switch to a history" )
[docs] @web.json def set_as_current(self, trans, id): """Change the current user's current history to one with `id`.""" # Prevent IE11 from caching this, since we actually use it via GET. trans.response.headers['Cache-Control'] = ["max-age=0", "no-cache", "no-store"] try: history = self.history_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history) trans.set_history(history) return self.history_data(trans, history) except exceptions.MessageException, msg_exc: trans.response.status = msg_exc.err_code.code return {'err_msg': msg_exc.err_msg, 'err_code': msg_exc.err_code.code}
[docs] @web.json def current_history_json(self, trans): """Return the current user's current history in a serialized, dictionary form.""" # Prevent IE11 from caching this trans.response.headers['Cache-Control'] = ["max-age=0", "no-cache", "no-store"] history = trans.get_history(most_recent=True, create=True) return self.history_data(trans, history)
[docs] @web.json def create_new_current(self, trans, name=None): """Create a new, current history for the current user""" new_history = trans.new_history(name) return self.history_data(trans, new_history)
# TODO: /history/current to do all of the above: if ajax, return json; if post, read id and set to current