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Source code for galaxy.managers.histories
"""
Manager and Serializer for histories.
Histories are containers for datasets or dataset collections
created (or copied) by users over the course of an analysis.
"""
import logging
from typing import (
cast,
Dict,
List,
Optional,
Set,
)
from sqlalchemy import (
and_,
asc,
desc,
)
from galaxy import exceptions as glx_exceptions
from galaxy import model
from galaxy.managers import (
deletable,
hdas,
history_contents,
sharable,
)
from galaxy.managers.base import (
Serializer,
SortableManager,
)
from galaxy.schema.schema import (
HDABasicInfo,
ShareHistoryExtra,
)
from galaxy.structured_app import MinimalManagerApp
log = logging.getLogger(__name__)
[docs]class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMixin, SortableManager):
model_class = model.History
foreign_key_name = "history"
user_share_model = model.HistoryUserShareAssociation
tag_assoc = model.HistoryTagAssociation
annotation_assoc = model.HistoryAnnotationAssociation
rating_assoc = model.HistoryRatingAssociation
# TODO: incorporate imp/exp (or alias to)
[docs] def __init__(
self,
app: MinimalManagerApp,
hda_manager: hdas.HDAManager,
contents_manager: history_contents.HistoryContentsManager,
contents_filters: history_contents.HistoryContentsFilters,
):
super().__init__(app)
self.hda_manager = hda_manager
self.contents_manager = contents_manager
self.contents_filters = contents_filters
[docs] def copy(self, history, user, **kwargs):
"""
Copy and return the given `history`.
"""
return history.copy(target_user=user, **kwargs)
# .... sharable
# overriding to handle anonymous users' current histories in both cases
[docs] def by_user(self, user, current_history=None, **kwargs):
"""
Get all the histories for a given user (allowing anon users' theirs)
ordered by update time.
"""
# handle default and/or anonymous user (which still may not have a history yet)
if self.user_manager.is_anonymous(user):
return [current_history] if current_history else []
return super().by_user(user, **kwargs)
[docs] def is_owner(self, history, user, current_history=None, **kwargs):
"""
True if the current user is the owner of the given history.
"""
# anon users are only allowed to view their current history
if self.user_manager.is_anonymous(user):
if current_history and history == current_history:
return True
return False
return super().is_owner(history, user)
# TODO: possibly to sharable or base
[docs] def most_recent(self, user, filters=None, current_history=None, **kwargs):
"""
Return the most recently update history for the user.
If user is anonymous, return the current history. If the user is anonymous
and the current history is deleted, return None.
"""
if self.user_manager.is_anonymous(user):
return None if (not current_history or current_history.deleted) else current_history
desc_update_time = desc(self.model_class.update_time)
filters = self._munge_filters(filters, self.model_class.user_id == user.id)
# TODO: normalize this return value
return self.query(filters=filters, order_by=desc_update_time, limit=1, **kwargs).first()
# .... purgable
[docs] def purge(self, history, flush=True, **kwargs):
"""
Purge this history and all HDAs, Collections, and Datasets inside this history.
"""
self.hda_manager.dataset_manager.error_unless_dataset_purge_allowed()
# First purge all the datasets
for hda in history.datasets:
if not hda.purged:
self.hda_manager.purge(hda, flush=True)
# Now mark the history as purged
super().purge(history, flush=flush, **kwargs)
# .... current
# TODO: make something to bypass the anon user + current history permissions issue
# def is_current_users_current_history( self, history, trans ):
# pass
[docs] def get_current(self, trans):
"""
Return the current history.
"""
# TODO: trans
return trans.get_history()
[docs] def set_current(self, trans, history):
"""
Set the current history.
"""
# TODO: trans
trans.set_history(history)
return history
[docs] def set_current_by_id(self, trans, history_id):
"""
Set the current history by an id.
"""
return self.set_current(trans, self.by_id(history_id))
# order_by parsing - similar to FilterParser but not enough yet to warrant a class?
[docs] def parse_order_by(self, order_by_string, default=None):
"""Return an ORM compatible order_by using the given string"""
# TODO: generalize into class
# TODO: general (enough) columns
if order_by_string in ("create_time", "create_time-dsc"):
return desc(self.model_class.create_time)
if order_by_string == "create_time-asc":
return asc(self.model_class.create_time)
if order_by_string in ("update_time", "update_time-dsc"):
return desc(self.model_class.update_time)
if order_by_string == "update_time-asc":
return asc(self.model_class.update_time)
if order_by_string in ("name", "name-asc"):
return asc(self.model_class.name)
if order_by_string == "name-dsc":
return desc(self.model_class.name)
# TODO: history columns
if order_by_string in ("size", "size-dsc"):
return desc(self.model_class.disk_size)
if order_by_string == "size-asc":
return asc(self.model_class.disk_size)
# TODO: add functional/non-orm orders (such as rating)
if default:
return self.parse_order_by(default)
raise glx_exceptions.RequestParameterInvalidException(
"Unkown order_by", order_by=order_by_string, available=["create_time", "update_time", "name", "size"]
)
[docs] def non_ready_jobs(self, history):
"""Return the currently running job objects associated with this history.
Where running is defined as new, waiting, queued, running, resubmitted,
and upload.
"""
# TODO: defer to jobModelManager (if there was one)
# TODO: genericize the params to allow other filters
jobs = (
self.session()
.query(model.Job)
.filter(model.Job.history == history)
.filter(model.Job.state.in_(model.Job.non_ready_states))
)
return jobs
[docs] def queue_history_import(self, trans, archive_type, archive_source):
# Run job to do import.
history_imp_tool = trans.app.toolbox.get_tool("__IMPORT_HISTORY__")
incoming = {"__ARCHIVE_SOURCE__": archive_source, "__ARCHIVE_TYPE__": archive_type}
job, *_ = history_imp_tool.execute(trans, incoming=incoming)
trans.app.job_manager.enqueue(job, tool=history_imp_tool)
return job
# TODO: remove this function when the legacy endpoint using it is removed
[docs] def legacy_serve_ready_history_export(self, trans, jeha):
assert jeha.ready
if jeha.compressed:
trans.response.set_content_type("application/x-gzip")
else:
trans.response.set_content_type("application/x-tar")
disposition = f'attachment; filename="{jeha.export_name}"'
trans.response.headers["Content-Disposition"] = disposition
archive = trans.app.object_store.get_filename(jeha.dataset)
return open(archive, mode="rb")
[docs] def get_ready_history_export_file_path(self, trans, jeha) -> str:
"""
Serves the history export archive for use as a streaming response so the file
doesn't need to be loaded into memory.
"""
assert jeha.ready
return trans.app.object_store.get_filename(jeha.dataset)
[docs] def queue_history_export(
self, trans, history, gzip=True, include_hidden=False, include_deleted=False, directory_uri=None, file_name=None
):
# Convert options to booleans.
if isinstance(gzip, str):
gzip = gzip in ["True", "true", "T", "t"]
if isinstance(include_hidden, str):
include_hidden = include_hidden in ["True", "true", "T", "t"]
if isinstance(include_deleted, str):
include_deleted = include_deleted in ["True", "true", "T", "t"]
params = {
"history_to_export": history,
"compress": gzip,
"include_hidden": include_hidden,
"include_deleted": include_deleted,
}
if directory_uri is None:
export_tool_id = "__EXPORT_HISTORY__"
else:
params["directory_uri"] = directory_uri
params["file_name"] = file_name or None
export_tool_id = "__EXPORT_HISTORY_TO_URI__"
# Run job to do export.
history_exp_tool = trans.app.toolbox.get_tool(export_tool_id)
job, *_ = history_exp_tool.execute(trans, incoming=params, history=history, set_output_hid=True)
trans.app.job_manager.enqueue(job, tool=history_exp_tool)
return job
[docs] def get_sharing_extra_information(
self, trans, item, users: Set[model.User], errors: Set[str], option: Optional[sharable.SharingOptions] = None
) -> Optional[sharable.ShareWithExtra]:
"""Returns optional extra information about the datasets of the history that can be accessed by the users."""
extra = ShareHistoryExtra()
history = cast(model.History, item)
if history.empty:
errors.add("You cannot share an empty history.")
return extra
owner = trans.user
owner_roles = owner.all_roles()
can_change_dict = {}
cannot_change_dict = {}
share_anyway = option is not None and option == sharable.SharingOptions.no_changes
datasets = history.activatable_datasets
total_dataset_count = len(datasets)
for user in users:
if self.is_history_shared_with(history, user):
continue
user_roles = user.all_roles()
# TODO: Handle this is a more performant way
# Only deal with datasets that have not been purged
for hda in datasets:
if trans.app.security_agent.can_access_dataset(user_roles, hda.dataset):
continue
# The user with which we are sharing the history does not have access permission on the current dataset
owner_can_manage_dataset = (
trans.app.security_agent.can_manage_dataset(owner_roles, hda.dataset)
and not hda.dataset.library_associations
)
if option and owner_can_manage_dataset:
if option == sharable.SharingOptions.make_accessible_to_shared:
trans.app.security_agent.privately_share_dataset(hda.dataset, users=[owner, user])
elif option == sharable.SharingOptions.make_public:
trans.app.security_agent.make_dataset_public(hda.dataset)
else:
hda_id = trans.security.encode_id(hda.id)
hda_info = HDABasicInfo(id=hda_id, name=hda.name)
if owner_can_manage_dataset:
can_change_dict[hda_id] = hda_info
else:
cannot_change_dict[hda_id] = hda_info
extra.can_change = list(can_change_dict.values())
extra.cannot_change = list(cannot_change_dict.values())
extra.accessible_count = total_dataset_count - len(extra.can_change) - len(extra.cannot_change)
if not extra.accessible_count and not extra.can_change and not share_anyway:
errors.add(
"The history you are sharing do not contain any datasets that can be accessed by the users with which you are sharing."
)
extra.can_share = not errors and (extra.accessible_count == total_dataset_count or option is not None)
return extra
[docs] def make_members_public(self, trans, item):
"""Make the non-purged datasets in history public.
Performs permissions check.
"""
for hda in item.activatable_datasets:
dataset = hda.dataset
if not trans.app.security_agent.dataset_is_public(dataset):
if trans.app.security_agent.can_manage_dataset(trans.user.all_roles(), dataset):
try:
trans.app.security_agent.make_dataset_public(hda.dataset)
except Exception:
log.warning(f"Unable to make dataset with id: {dataset.id} public")
else:
log.warning(f"User without permissions tried to make dataset with id: {dataset.id} public")
[docs]class HistoryExportView:
[docs] def get_exports(self, trans, history_id):
history = self._history(trans, history_id)
matching_exports = history.exports
return [self.serialize(trans, history_id, e) for e in matching_exports]
[docs] def serialize(self, trans, history_id, jeha):
rval = jeha.to_dict()
encoded_jeha_id = trans.security.encode_id(jeha.id)
api_url = trans.url_builder("history_archive_download", id=history_id, jeha_id=encoded_jeha_id)
external_url = trans.url_builder("history_archive_download", id=history_id, jeha_id="latest", qualified=True)
external_permanent_url = trans.url_builder(
"history_archive_download", id=history_id, jeha_id=encoded_jeha_id, qualified=True
)
rval["download_url"] = api_url
rval["external_download_latest_url"] = external_url
rval["external_download_permanent_url"] = external_permanent_url
rval = trans.security.encode_all_ids(rval)
return rval
[docs] def get_ready_jeha(self, trans, history_id, jeha_id="latest"):
history = self._history(trans, history_id)
matching_exports = history.exports
if jeha_id != "latest":
decoded_jeha_id = trans.security.decode_id(jeha_id)
matching_exports = [e for e in matching_exports if e.id == decoded_jeha_id]
if len(matching_exports) == 0:
raise glx_exceptions.ObjectNotFound("Failed to find target history export")
jeha = matching_exports[0]
if not jeha.ready:
raise glx_exceptions.MessageException("Export not available or not yet ready.")
return jeha
def _history(self, trans, history_id):
if history_id is not None:
history = self.app.history_manager.get_accessible(
trans.security.decode_id(history_id), trans.user, current_history=trans.history
)
else:
history = trans.history
return history
[docs]class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSerializerMixin):
"""
Interface/service object for serializing histories into dictionaries.
"""
model_manager_class = HistoryManager
SINGLE_CHAR_ABBR = "h"
[docs] def __init__(
self,
app: MinimalManagerApp,
hda_manager: hdas.HDAManager,
hda_serializer: hdas.HDASerializer,
history_contents_serializer: history_contents.HistoryContentsSerializer,
):
super().__init__(app)
self.history_manager = self.manager
self.hda_manager = hda_manager
self.hda_serializer = hda_serializer
self.history_contents_serializer = history_contents_serializer
self.default_view = "summary"
self.add_view(
"summary",
[
"id",
"model_class",
"name",
"deleted",
"purged",
# 'count'
"url",
# TODO: why these?
"published",
"annotation",
"tags",
"update_time",
],
)
self.add_view(
"detailed",
[
"contents_url",
"empty",
"size",
"user_id",
"create_time",
"update_time",
"importable",
"slug",
"username_and_slug",
"genome_build",
# TODO: remove the next three - instead getting the same info from the 'hdas' list
"state",
"state_details",
"state_ids",
"hid_counter",
# 'community_rating',
# 'user_rating',
],
include_keys_from="summary",
)
# in the Historys' case, each of these views includes the keys from the previous
#: ..note: this is a custom view for newer (2016/3) UI and should be considered volatile
self.add_view(
"dev-detailed",
[
"contents_url",
"size",
"user_id",
"create_time",
"update_time",
"importable",
"slug",
"username_and_slug",
"genome_build",
# 'contents_states',
"contents_active",
"hid_counter",
],
include_keys_from="summary",
)
# assumes: outgoing to json.dumps and sanitized
[docs] def add_serializers(self):
super().add_serializers()
deletable.PurgableSerializerMixin.add_serializers(self)
serializers: Dict[str, Serializer] = {
"model_class": lambda item, key, **context: "History",
"size": lambda item, key, **context: int(item.disk_size),
"nice_size": lambda item, key, **context: item.disk_nice_size,
"state": self.serialize_history_state,
"url": lambda item, key, **context: self.url_for(
"history", id=self.app.security.encode_id(item.id), context=context
),
"contents_url": lambda item, key, **context: self.url_for(
"history_contents", history_id=self.app.security.encode_id(item.id), context=context
),
"empty": lambda item, key, **context: (len(item.datasets) + len(item.dataset_collections)) <= 0,
"count": lambda item, key, **context: len(item.datasets),
"hdas": lambda item, key, **context: [self.app.security.encode_id(hda.id) for hda in item.datasets],
"state_details": self.serialize_state_counts,
"state_ids": self.serialize_state_ids,
"contents": self.serialize_contents,
"non_ready_jobs": lambda item, key, **context: [
self.app.security.encode_id(job.id) for job in self.manager.non_ready_jobs(item)
],
"contents_states": self.serialize_contents_states,
"contents_active": self.serialize_contents_active,
# TODO: Use base manager's serialize_id for user_id (and others)
# after refactoring hierarchy here?
"user_id": lambda item, key, **context: self.app.security.encode_id(item.user_id)
if item.user_id is not None
else None,
}
self.serializers.update(serializers)
# remove this
[docs] def serialize_state_ids(self, item, key, **context):
"""
Return a dictionary keyed to possible dataset states and valued with lists
containing the ids of each HDA in that state.
"""
history = item
state_ids: Dict[str, List[str]] = {}
for state in model.Dataset.states.values():
state_ids[state] = []
# TODO:?? collections and coll. states?
for hda in history.datasets:
# TODO: do not encode ids at this layer
encoded_id = self.app.security.encode_id(hda.id)
state_ids[hda.state].append(encoded_id)
return state_ids
# remove this
[docs] def serialize_state_counts(self, item, key, exclude_deleted=True, exclude_hidden=False, **context):
"""
Return a dictionary keyed to possible dataset states and valued with the number
of datasets in this history that have those states.
"""
history = item
# TODO: the default flags above may not make a lot of sense (T,T?)
state_counts = {}
for state in model.Dataset.states.values():
state_counts[state] = 0
# TODO:?? collections and coll. states?
for hda in history.datasets:
if exclude_deleted and hda.deleted:
continue
if exclude_hidden and not hda.visible:
continue
state_counts[hda.state] = state_counts[hda.state] + 1
return state_counts
# TODO: remove this (is state used/useful?)
[docs] def serialize_history_state(self, item, key, **context):
"""
Returns the history state based on the states of the HDAs it contains.
"""
history = item
states = model.Dataset.states
# (default to ERROR)
state = states.ERROR
# TODO: history_state and state_counts are classically calc'd at the same time
# so this is rel. ineff. - if we keep this...
hda_state_counts = self.serialize_state_counts(history, "counts", exclude_deleted=True, **context)
if history.empty:
state = states.NEW
else:
num_hdas = sum(hda_state_counts.values())
if (
hda_state_counts[states.RUNNING] > 0
or hda_state_counts[states.SETTING_METADATA] > 0
or hda_state_counts[states.UPLOAD] > 0
):
state = states.RUNNING
# TODO: this method may be more useful if we *also* polled the histories jobs here too
elif hda_state_counts[states.QUEUED] > 0 or hda_state_counts[states.NEW] > 0:
state = states.QUEUED
elif hda_state_counts[states.ERROR] > 0 or hda_state_counts[states.FAILED_METADATA] > 0:
state = states.ERROR
elif (hda_state_counts[states.OK] + hda_state_counts[states.DEFERRED]) == num_hdas:
state = states.OK
return state
[docs] def serialize_contents(self, item, key, trans=None, user=None, **context):
history = item
returned = []
for content in self.manager.contents_manager._union_of_contents_query(history).all():
serialized = self.history_contents_serializer.serialize_to_view(
content, view="summary", trans=trans, user=user
)
returned.append(serialized)
return returned
[docs] def serialize_contents_states(self, item, key, trans=None, **context):
"""
Return a dictionary containing the counts of all contents in each state
keyed by the distinct states.
Note: does not include deleted/hidden contents.
"""
history = item
return self.manager.contents_manager.state_counts(history)
[docs] def serialize_contents_active(self, item, key, **context):
"""
Return a dictionary keyed with 'deleted', 'hidden', and 'active' with values
for each representing the count of contents in each state.
Note: counts for deleted and hidden overlap; In other words, a dataset that's
both deleted and hidden will be added to both totals.
"""
history = item
return self.manager.contents_manager.active_counts(history)
[docs]class HistoryDeserializer(sharable.SharableModelDeserializer, deletable.PurgableDeserializerMixin):
"""
Interface/service object for validating and deserializing dictionaries into histories.
"""
model_manager_class = HistoryManager
[docs] def __init__(self, app: MinimalManagerApp):
super().__init__(app)
self.history_manager = self.manager
[docs] def add_deserializers(self):
super().add_deserializers()
deletable.PurgableDeserializerMixin.add_deserializers(self)
self.deserializers.update(
{
"name": self.deserialize_basestring,
"genome_build": self.deserialize_genome_build,
}
)
[docs]class HistoryFilters(sharable.SharableModelFilters, deletable.PurgableFiltersMixin):
model_class = model.History
model_manager_class = HistoryManager
def _add_parsers(self):
super()._add_parsers()
deletable.PurgableFiltersMixin._add_parsers(self)
self.orm_filter_parsers.update(
{
# history specific
"name": {"op": ("eq", "contains", "like")},
"genome_build": {"op": ("eq", "contains", "like")},
"create_time": {"op": ("le", "ge", "gt", "lt"), "val": self.parse_date},
"update_time": {"op": ("le", "ge", "gt", "lt"), "val": self.parse_date},
}
)