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Source code for galaxy.webapps.galaxy.controllers.history
import logging
from dateutil.parser import isoparse
from markupsafe import escape
from sqlalchemy import false
from sqlalchemy.orm import undefer
from galaxy import (
exceptions,
model,
web,
)
from galaxy.managers import histories
from galaxy.managers.sharable import SlugBuilder
from galaxy.model.item_attrs import (
UsesAnnotations,
UsesItemRatings,
)
from galaxy.structured_app import StructuredApp
from galaxy.util import (
listify,
sanitize_text,
string_as_bool,
unicodify,
)
from galaxy.web import (
expose_api_anonymous,
url_for,
)
from galaxy.web.framework.helpers import (
grids,
iff,
time_ago,
)
from galaxy.webapps.base.controller import (
BaseUIController,
ERROR,
INFO,
SharableMixin,
SUCCESS,
WARNING,
)
from ..api import depends
log = logging.getLogger(__name__)
[docs]class HistoryListGrid(grids.Grid):
# Custom column types
[docs] class HistoryListNameColumn(NameColumn):
[docs] def get_link(self, trans, grid, history):
link = None
if not history.deleted:
link = dict(operation="Switch", id=history.id, use_panels=grid.use_panels, async_compatible=True)
return link
[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.update_time.desc())
else:
query = query.order_by(self.model_class.table.c.purged.desc(), self.model_class.update_time.desc())
return query
[docs] def build_initial_query(self, trans, **kwargs):
# Override to preload sharing information used when fetching data for grid.
query = super().build_initial_query(trans, **kwargs)
query = query.options(undefer("users_shared_with_count"))
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"),
ItemCountColumn("Items", key="item_count", sortable=False),
grids.GridColumn("Datasets", key="datasets_by_state", sortable=False, nowrap=True, delayed=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, use_shared_with_count=True
),
grids.GridColumn("Size on Disk", key="disk_size", sortable=False, delayed=True),
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[3]],
key="free-text-search",
visible=False,
filterable="standard",
)
)
global_actions = [grids.GridAction("Import history", dict(controller="", action="histories/import"))]
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(controller="", action="histories/view")),
grids.GridOperation(
"Share or Publish",
allow_multiple=False,
condition=(lambda item: not item.deleted),
url_args=dict(controller="", action="histories/sharing"),
),
grids.GridOperation(
"Change Permissions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
url_args=dict(controller="", action="histories/permissions"),
),
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(controller="", action="histories/rename"),
target="top",
),
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
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 apply_query_filter(self, trans, query, **kwargs):
return query.filter_by(user=trans.user, importing=False)
[docs]class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings):
history_manager: histories.HistoryManager = depends(histories.HistoryManager)
history_serializer: histories.HistorySerializer = depends(histories.HistorySerializer)
slug_builder: SlugBuilder = depends(SlugBuilder)
[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()
[docs] @web.legacy_expose_api
@web.require_login("work with multiple histories")
def list(self, trans, **kwargs):
"""List all available histories"""
current_history = trans.get_history()
message = kwargs.get("message")
status = kwargs.get("status")
if "operation" in kwargs:
operation = kwargs["operation"].lower()
history_ids = 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"):
status, message = self._list_delete(trans, histories, purge=(operation == "delete permanently"))
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)
trans.sa_session.flush()
# Render the list view
if message and status:
kwargs["message"] = sanitize_text(message)
kwargs["status"] = status
return self.stored_list_grid(trans, **kwargs)
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 _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 Exception:
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
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=string_as_bool(show_deleted),
show_hidden=string_as_bool(show_hidden),
)
[docs] @expose_api_anonymous
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 = string_as_bool(show_deleted)
show_hidden = string_as_bool(show_hidden)
use_panels = string_as_bool(use_panels)
history_dictionary = {}
user_is_owner = False
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
)
return {
"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,
"allow_user_dataset_purge": trans.app.config.allow_user_dataset_purge,
}
[docs] @web.expose
def display_by_username_and_slug(self, trans, username, slug, **kwargs):
"""
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).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)
# Encode history id.
history_id = trans.security.encode_id(history.id)
# Redirect to client.
return trans.response.send_redirect(
web.url_for(
controller="published",
action="history",
id=history_id,
)
)
[docs] @web.legacy_expose_api
@web.require_login("changing default permissions")
def permissions(self, trans, payload=None, **kwd):
"""
Sets the permissions on a history.
"""
history_id = kwd.get("id")
if not history_id:
return self.message_exception(trans, f"Invalid history id ({str(history_id)}) received")
history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
if trans.request.method == "GET":
inputs = []
all_roles = trans.user.all_roles()
current_actions = history.default_permissions
for action_key, action in trans.app.model.Dataset.permitted_actions.items():
in_roles = set()
for a in current_actions:
if a.action == action.action:
in_roles.add(a.role)
inputs.append(
{
"type": "select",
"multiple": True,
"optional": True,
"individual": True,
"name": action_key,
"label": action.action,
"help": action.description,
"options": [(role.name, trans.security.encode_id(role.id)) for role in set(all_roles)],
"value": [trans.security.encode_id(role.id) for role in in_roles],
}
)
return {"title": "Change default dataset permissions for history '%s'" % history.name, "inputs": inputs}
else:
permissions = {}
for action_key, action in trans.app.model.Dataset.permitted_actions.items():
in_roles = payload.get(action_key) or []
in_roles = [
trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in in_roles
]
permissions[trans.app.security_agent.get_action(action.action)] = in_roles
trans.app.security_agent.history_set_default_permissions(history, permissions)
return {"message": "Default history '%s' dataset permissions have been changed." % history.name}
[docs] @web.legacy_expose_api
@web.require_login("make datasets private")
def make_private(self, trans, history_id=None, all_histories=False, **kwd):
"""
Sets the datasets within a history to private. Also sets the default
permissions for the history to private, for future datasets.
"""
histories = []
all_histories = string_as_bool(all_histories)
if all_histories:
histories = trans.user.histories
elif history_id:
history = self.history_manager.get_owned(
self.decode_id(history_id), trans.user, current_history=trans.history
)
if history:
histories.append(history)
if not histories:
return self.message_exception(trans, "Invalid history or histories specified.")
private_role = trans.app.security_agent.get_private_user_role(trans.user)
user_roles = trans.user.all_roles()
private_permissions = {
trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS: [private_role],
trans.app.security_agent.permitted_actions.DATASET_ACCESS: [private_role],
}
for history in histories:
# Set default role for history to private
trans.app.security_agent.history_set_default_permissions(history, private_permissions)
# Set private role for all datasets
for hda in history.datasets:
if (
not hda.dataset.library_associations
and not trans.app.security_agent.dataset_is_private_to_user(trans, hda.dataset)
and trans.app.security_agent.can_manage_dataset(user_roles, hda.dataset)
):
# If it's not private to me, and I can manage it, set fixed private permissions.
trans.app.security_agent.set_all_dataset_permissions(hda.dataset, private_permissions)
if not trans.app.security_agent.dataset_is_private_to_user(trans, hda.dataset):
raise exceptions.InternalServerError("An error occurred and the dataset is NOT private.")
return {
"message": f"Success, requested permissions have been changed in {'all histories' if all_histories else history.name}."
}
# ......................................................................... actions/orig. async
[docs] @web.expose
def purge_deleted_datasets(self, trans):
count = 0
if trans.app.config.allow_user_dataset_purge and trans.history:
for hda in trans.history.datasets:
if not hda.deleted or hda.purged:
continue
hda.purge_usage_from_quota(trans.user)
hda.purged = True
trans.sa_session.add(hda)
trans.log_event(f"HDA id {hda.id} has been purged")
trans.sa_session.flush()
if hda.dataset.user_can_purge:
try:
hda.dataset.full_delete()
trans.log_event(
f"Dataset id {hda.dataset.id} has been purged upon the the purge of HDA id {hda.id}"
)
trans.sa_session.add(hda.dataset)
except Exception:
log.exception(f"Unable to purge dataset ({hda.dataset.id}) on purge of hda ({hda.id}):")
count += 1
return trans.show_ok_message(
"%d datasets have been deleted permanently" % count, refresh_frames=["history"]
)
return trans.show_error_message("Cannot purge deleted datasets from this session.")
[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 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.json
@web.require_login("get history name and link")
def get_name_and_link_async(self, trans, id=None):
"""Returns history's name and link."""
history = self.history_manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history)
if self.slug_builder.create_item_slug(trans.sa_session, history):
trans.sa_session.flush()
return_dict = {
"name": history.name,
"link": url_for(
controller="history",
action="display_by_username_and_slug",
username=history.user.username,
slug=history.slug,
),
}
return return_dict
# 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.legacy_expose_api
@web.require_login("rename histories")
def rename(self, trans, payload=None, **kwd):
id = kwd.get("id")
if not id:
return self.message_exception(trans, "No history id received for renaming.")
user = trans.get_user()
id = listify(id)
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 trans.request.method == "GET":
return {
"title": "Change history name(s)",
"inputs": [
{"name": "name_%i" % i, "label": f"Current: {h.name}", "value": h.name}
for i, h in enumerate(histories)
],
}
else:
messages = []
for i, h in enumerate(histories):
cur_name = h.get_display_name()
new_name = payload.get("name_%i" % i)
# validate name is empty
if not isinstance(new_name, str) or not new_name.strip():
messages.append("You must specify a valid name for History '%s'." % cur_name)
# skip if not the owner
elif h.user_id != user.id:
messages.append("History '%s' does not appear to belong to you." % cur_name)
# skip if it wouldn't be a change
elif new_name != cur_name:
h.name = new_name
trans.sa_session.add(h)
trans.sa_session.flush()
trans.log_event(f"History renamed: id: {str(h.id)}, renamed to: {new_name}")
messages.append(f"History '{cur_name}' renamed to '{new_name}'.")
message = sanitize_text(" ".join(messages)) if messages else "History names remain unchanged."
return {"message": message, "status": "success"}
# ------------------------------------------------------------------------- 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
@web.do_not_cache
def set_as_current(self, trans, id):
"""Change the current user's current history to one with `id`."""
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 as msg_exc:
trans.response.status = msg_exc.status_code
return {"err_msg": msg_exc.err_msg, "err_code": msg_exc.err_code.code}
[docs] @web.json
@web.do_not_cache
def current_history_json(self, trans, since=None):
"""Return the current user's current history in a serialized, dictionary form."""
history = trans.get_history(most_recent=True, create=True)
if since and history.update_time <= isoparse(since):
# Should ideally be a 204 response, but would require changing web.json
# This endpoint should either give way to a proper API or a SSE loop
return
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