Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.managers.history_contents
"""
Heterogenous lists/contents are difficult to query properly since unions are
not easily made.
"""
import json
import logging
from typing import (
Any,
Dict,
List,
)
from sqlalchemy import (
asc,
cast,
desc,
false,
func,
Integer,
literal,
nullsfirst,
nullslast,
select,
Select,
sql,
true,
UnaryExpression,
)
from sqlalchemy.orm import (
joinedload,
undefer,
)
from galaxy import (
exceptions as glx_exceptions,
model,
)
from galaxy.managers import (
annotatable,
base,
deletable,
genomes,
hdas,
hdcas,
taggable,
tools,
)
from galaxy.managers.job_connections import JobConnectionsManager
from galaxy.schema import ValueFilterQueryParams
from galaxy.structured_app import MinimalManagerApp
from galaxy.util import listify
from .base import (
parse_bool,
raise_filter_err,
Serializer,
)
log = logging.getLogger(__name__)
# into its own class to have it's own filters, etc.
# TODO: but can't inherit from model manager (which assumes only one model)
[docs]
class HistoryContentsManager(base.SortableManager):
root_container_class = model.History
contained_class = model.HistoryDatasetAssociation
contained_class_manager_class = hdas.HDAManager
contained_class_type_name = "dataset"
subcontainer_class = model.HistoryDatasetCollectionAssociation
subcontainer_class_manager_class = hdcas.HDCAManager
subcontainer_class_type_name = "dataset_collection"
#: the columns which are common to both subcontainers and non-subcontainers.
# (Also the attributes that may be filtered or orderered_by)
common_columns = (
"history_id",
"history_content_type",
"id",
"type_id",
"hid",
# joining columns
"extension",
"dataset_id",
"collection_id",
"name",
"state",
"object_store_id",
"size",
"deleted",
"purged",
"visible",
"create_time",
"update_time",
)
default_order_by = "hid"
[docs]
def __init__(self, app: MinimalManagerApp):
self.app = app
self.contained_manager = app[self.contained_class_manager_class]
self.subcontainer_manager = app[self.subcontainer_class_manager_class]
# ---- interface
[docs]
def contents(self, container, filters=None, limit=None, offset=None, order_by=None, **kwargs):
"""
Returns a list of both/all types of contents, filtered and in some order.
"""
# TODO?: we could branch here based on 'if limit is None and offset is None' - to a simpler (non-union) query
# for now, I'm just using this (even for non-limited/offset queries) to reduce code paths
return self._union_of_contents(
container, filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs
)
[docs]
def contents_count(self, container, filters=None, limit=None, offset=None, order_by=None, **kwargs):
"""
Returns a count of both/all types of contents, based on the given filters.
"""
return self.contents_query(
container, filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs
).count()
[docs]
def contents_query(self, container, filters=None, limit=None, offset=None, order_by=None, **kwargs):
"""
Returns the contents union query for subqueries, etc.
"""
return self._union_of_contents_query(
container, filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs
)
# 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"""
available = ["create_time", "extension", "hid", "history_id", "name", "update_time", "size"]
for attribute in available:
attribute_dsc = f"{attribute}-dsc"
attribute_asc = f"{attribute}-asc"
if order_by_string in (attribute, attribute_dsc):
order_by: UnaryExpression = desc(attribute)
if attribute == "size":
return nullslast(order_by)
return order_by
if order_by_string == attribute_asc:
order_by = asc(attribute)
if attribute == "size":
return nullsfirst(order_by)
return order_by
if default:
return self.parse_order_by(default)
raise glx_exceptions.RequestParameterInvalidException(
"Unknown order_by", order_by=order_by_string, available=available
)
# history specific methods
[docs]
def state_counts(self, history):
"""
Return a dictionary containing the counts of all contents in each state
keyed by the distinct states.
Note: does not include deleted/hidden contents.
"""
filters = [
base.ModelFilterParser.parsed_filter("orm", sql.column("deleted") == false()),
base.ModelFilterParser.parsed_filter("orm", sql.column("visible") == true()),
]
contents_subquery = self._union_of_contents_query(history, filters=filters).subquery()
statement: Select = (
select(sql.column("state"), func.count()).select_from(contents_subquery).group_by(sql.column("state"))
)
counts = self.app.model.session.execute(statement).fetchall()
return dict(counts) # type:ignore[arg-type]
[docs]
def active_counts(self, history):
"""
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.
"""
hda_select = self._active_counts_statement(model.HistoryDatasetAssociation, history.id)
hdca_select = self._active_counts_statement(model.HistoryDatasetCollectionAssociation, history.id)
subquery = hda_select.union_all(hdca_select).subquery()
statement = select(
cast(func.coalesce(func.sum(subquery.c.deleted), 0), Integer).label("deleted"),
cast(func.coalesce(func.sum(subquery.c.hidden), 0), Integer).label("hidden"),
cast(func.coalesce(func.sum(subquery.c.active), 0), Integer).label("active"),
)
returned = self.app.model.context.execute(statement).one()
return dict(returned._mapping)
def _active_counts_statement(self, model_class, history_id):
deleted_attr = model_class.deleted
visible_attr = model_class.visible
table_attr = model_class.table
return (
select(
func.sum(cast(deleted_attr, Integer)).label("deleted"),
func.sum(cast(visible_attr == false(), Integer)).label("hidden"),
func.sum(func.abs(cast(visible_attr, Integer) * (cast(deleted_attr, Integer) - 1))).label("active"),
)
.select_from(table_attr)
.filter_by(history_id=history_id)
)
[docs]
def map_datasets(self, history, fn, **kwargs):
"""
Iterate over the datasets of a given history, recursing into collections, and
calling fn on each dataset.
Uses the same kwargs as `contents` above.
"""
returned = []
contents = self.contents(history, **kwargs)
for content in contents:
if isinstance(content, self.subcontainer_class):
processed_list = self.subcontainer_manager.map_datasets(content, fn)
returned.extend(processed_list)
else:
processed = fn(content)
returned.append(processed)
return returned
# ---- private
def _session(self):
return self.app.model.context
def _union_of_contents(self, container, expand_models=True, **kwargs):
"""
Returns a limited and offset list of both types of contents, filtered
and in some order.
"""
contents_results = self._union_of_contents_query(container, **kwargs).all()
if not expand_models:
return contents_results
# partition ids into a map of { component_class names -> list of ids } from the above union query
id_map: Dict[str, List[int]] = {self.contained_class_type_name: [], self.subcontainer_class_type_name: []}
for result in contents_results:
result_type = self._get_union_type(result)
contents_id = self._get_union_id(result)
if result_type in id_map:
id_map[result_type].append(contents_id)
else:
raise TypeError("Unknown contents type:", result_type)
# query 2 & 3: use the ids to query each component_class, returning an id->full component model map
contained_ids = id_map[self.contained_class_type_name]
id_map[self.contained_class_type_name] = self._contained_id_map(contained_ids)
subcontainer_ids = id_map[self.subcontainer_class_type_name]
serialization_params = kwargs.get("serialization_params", None)
id_map[self.subcontainer_class_type_name] = self._subcontainer_id_map(
subcontainer_ids, serialization_params=serialization_params
)
# cycle back over the union query to create an ordered list of the objects returned in queries 2 & 3 above
contents = []
filters = kwargs.get("filters") or []
# TODO: or as generator?
for result in contents_results:
result_type = self._get_union_type(result)
contents_id = self._get_union_id(result)
content = id_map[result_type][contents_id]
if self.passes_filters(content, filters):
contents.append(content)
return contents
[docs]
@staticmethod
def passes_filters(content, filters):
for filter_fn in filters:
if filter_fn.filter_type == "function":
if not filter_fn.filter(content):
return False
return True
def _union_of_contents_query(
self, container, filters=None, limit=None, offset=None, order_by=None, user_id=None, **kwargs
):
"""
Returns a query for a limited and offset list of both types of contents,
filtered and in some order.
"""
order_by = order_by if order_by is not None else self.default_order_by
order_by = order_by if isinstance(order_by, (tuple, list)) else (order_by,)
# TODO: 3 queries and 3 iterations over results - this is undoubtedly better solved in the actual SQL layer
# via one common table for contents, Some Yonder Resplendent and Fanciful Join, or ORM functionality
# Here's the (bizarre) strategy:
# 1. create a union of common columns between contents classes - filter, order, and limit/offset this
# 2. extract the ids returned from 1 for each class, query each content class by that id list
# 3. use the results/order from 1 to recombine/merge the 2+ query result lists from 2, return that
# note: I'm trying to keep these private functions as generic as possible in order to move them toward base later
# query 1: create a union of common columns for which the component_classes can be filtered/limited
contained_query = self._contents_common_query_for_contained(
history_id=container.id if container else None, user_id=user_id
)
subcontainer_query = self._contents_common_query_for_subcontainer(
history_id=container.id if container else None, user_id=user_id
)
filters = filters or []
# Apply filters that are specific to a model
for orm_filter in filters:
if orm_filter.filter_type == "orm_function":
contained_query = contained_query.filter(orm_filter.filter(self.contained_class))
subcontainer_query = subcontainer_query.filter(orm_filter.filter(self.subcontainer_class))
elif orm_filter.filter_type == "orm":
contained_query = self._apply_orm_filter(contained_query, orm_filter)
subcontainer_query = self._apply_orm_filter(subcontainer_query, orm_filter)
contents_query = contained_query.union_all(subcontainer_query)
contents_query = contents_query.order_by(*order_by)
if limit is not None:
contents_query = contents_query.limit(limit)
if offset is not None:
contents_query = contents_query.offset(offset)
return contents_query
def _apply_orm_filter(self, qry, orm_filter):
if isinstance(orm_filter.filter, sql.elements.BinaryExpression):
for match in filter(lambda col: col["name"] == orm_filter.filter.left.name, qry.column_descriptions):
column = match["expr"]
new_filter = orm_filter.filter._clone()
if orm_filter.case_insensitive:
column = func.lower(column)
new_filter.left = column
qry = qry.filter(new_filter)
return qry
def _contents_common_columns(self, component_class, **kwargs):
columns = []
# pull column from class by name or override with kwargs if listed there, then label
for column_name in self.common_columns:
if column_name in kwargs:
column = kwargs[column_name]
elif column_name == "model_class":
column = literal(component_class.__name__)
else:
column = getattr(component_class, column_name)
column = column.label(column_name)
columns.append(column)
return columns
def _contents_common_query_for_contained(self, history_id, user_id):
component_class = self.contained_class
# TODO: and now a join with Dataset - this is getting sad
columns = self._contents_common_columns(
component_class,
history_content_type=literal("dataset"),
size=model.Dataset.file_size,
state=model.Dataset.state,
object_store_id=model.Dataset.object_store_id,
quota_source_label=model.Dataset.object_store_id,
# do not have inner collections
collection_id=literal(None),
)
subquery = self._session().query(*columns)
# for the HDA's we need to join the Dataset since it has an actual state column
subquery = subquery.join(model.Dataset, model.Dataset.id == component_class.table.c.dataset_id)
if history_id:
subquery = subquery.filter(component_class.table.c.history_id == history_id)
else:
# Make sure we only return items that are user-accessible by checking that they are in a history
# owned by the current user.
# TODO: move into filter mixin, and implement accessible logic as SQL query
subquery = subquery.filter(
component_class.table.c.history_id == model.History.table.c.id, model.History.table.c.user_id == user_id
)
return subquery
def _contents_common_query_for_subcontainer(self, history_id, user_id):
component_class = self.subcontainer_class
columns = self._contents_common_columns(
component_class,
history_content_type=literal("dataset_collection"),
# do not have datasets
dataset_id=literal(None),
size=literal(None),
state=model.DatasetCollection.populated_state,
object_store_id=literal(None),
quota_source_label=literal(None),
# TODO: should be purgable? fix
purged=literal(False),
extension=literal(None),
)
subquery = self._session().query(*columns)
# for the HDCA's we need to join the DatasetCollection since it has the populated_state
subquery = subquery.join(model.DatasetCollection, model.DatasetCollection.id == component_class.collection_id)
if history_id:
subquery = subquery.filter(component_class.history_id == history_id)
else:
subquery = subquery.filter(
component_class.history_id == model.History.table.c.id, model.History.table.c.user_id == user_id
)
return subquery
def _get_union_type(self, union):
"""Return the string name of the class for this row in the union results"""
return str(union[1])
def _get_union_id(self, union):
"""Return the id for this row in the union results"""
return union[2]
def _contained_id_map(self, id_list):
"""Return an id to model map of all contained-type models in the id_list."""
if not id_list:
return []
component_class = self.contained_class
stmt = (
select(component_class)
.where(component_class.id.in_(id_list))
.options(undefer(component_class._metadata))
.options(joinedload(component_class.dataset).joinedload(model.Dataset.actions))
.options(joinedload(component_class.tags))
.options(joinedload(component_class.annotations)) # type: ignore[attr-defined]
)
result = self._session().scalars(stmt).unique()
return {row.id: row for row in result}
def _subcontainer_id_map(self, id_list, serialization_params=None):
"""Return an id to model map of all subcontainer-type models in the id_list."""
if not id_list:
return []
component_class = self.subcontainer_class
stmt = (
select(component_class)
.where(component_class.id.in_(id_list))
.options(joinedload(component_class.collection))
.options(joinedload(component_class.tags))
.options(joinedload(component_class.annotations))
)
result = self._session().scalars(stmt).unique()
return {row.id: row for row in result}
[docs]
class HistoryContentsSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin):
"""
Interface/service object for serializing histories into dictionaries.
"""
model_manager_class = HistoryContentsManager
[docs]
def __init__(self, app: MinimalManagerApp, **kwargs):
super().__init__(app, **kwargs)
self.default_view = "summary"
self.add_view(
"summary",
[
"id",
"type_id",
"history_id",
"hid",
"history_content_type",
"visible",
"dataset_id",
"collection_id",
"name",
"state",
"deleted",
"purged",
"create_time",
"update_time",
],
)
# assumes: outgoing to json.dumps and sanitized
[docs]
def add_serializers(self):
super().add_serializers()
deletable.PurgableSerializerMixin.add_serializers(self)
serializers: Dict[str, Serializer] = {
"type_id": self.serialize_type_id,
"history_id": self.serialize_id,
"dataset_id": self.serialize_id_or_skip,
"collection_id": self.serialize_id_or_skip,
}
self.serializers.update(serializers)
[docs]
def serialize_id_or_skip(self, item: Any, key: str, **context):
"""Serialize id or skip if attribute with `key` is not present."""
if not hasattr(item, key):
raise base.SkipAttribute("no such attribute")
return self.serialize_id(item, key, **context)
[docs]
class HistoryContentsFilters(
base.ModelFilterParser,
annotatable.AnnotatableFilterMixin,
deletable.PurgableFiltersMixin,
genomes.GenomeFilterMixin,
taggable.TaggableFilterMixin,
tools.ToolFilterMixin,
):
# surprisingly (but ominously), this works for both content classes in the union that's filtered
model_class = model.HistoryDatasetAssociation
[docs]
def parse_query_filters_with_relations(self, query_filters: ValueFilterQueryParams, history_id):
"""Parse query filters but consider case where related filter is included."""
has_related_q = [q for q in ("related-eq", "related") if query_filters.q and q in query_filters.q]
if query_filters.q and query_filters.qv and has_related_q:
qv_index = query_filters.q.index(has_related_q[0])
qv_hid = query_filters.qv[qv_index]
# Type check whether hid is int
if not qv_hid.isdigit():
raise glx_exceptions.RequestParameterInvalidException(
"unparsable value for related filter",
column="related",
operation="eq",
value=qv_hid,
ValueError="invalid type in filter",
)
query_filters_with_relations = self.get_query_filters_with_relations(
query_filters=query_filters, related_q=has_related_q[0], history_id=history_id
)
return super().parse_query_filters(query_filters_with_relations)
return super().parse_query_filters(query_filters)
def _parse_orm_filter(self, attr, op, val):
# we need to use some manual/text/column fu here since some where clauses on the union don't work
# using the model_class defined above - they need to be wrapped in their own .column()
# (and some of these are *not* a normal columns (especially 'state') anyway)
# TODO: genericize these - can probably extract a _get_column( attr, ... ) or something
# special cases...special cases everywhere
def get_filter(attr, op, val):
if attr == "history_content_type" and op == "eq":
if val in ("dataset", "dataset_collection"):
return sql.column("history_content_type") == val
raise_filter_err(attr, op, val, "bad op in filter")
if attr == "related":
if op == "eq":
# unclear if multiple related values make sense, maybe this should be `.eq_` instead
return sql.column("hid").in_(listify(json.loads(val)))
raise_filter_err(attr, op, val, "bad op in filter")
if attr == "type_id":
if op == "eq":
return sql.column("type_id") == val
if op == "in":
return sql.column("type_id").in_(self.parse_type_id_list(val))
raise_filter_err(attr, op, val, "bad op in filter")
if attr in ("update_time", "create_time"):
if op == "ge":
return sql.column(attr) >= self.parse_date(val)
if op == "le":
return sql.column(attr) <= self.parse_date(val)
if op == "gt":
return sql.column(attr) > self.parse_date(val)
if op == "lt":
return sql.column(attr) < self.parse_date(val)
raise_filter_err(attr, op, val, "bad op in filter")
if attr == "state":
valid_states = model.Dataset.states.values()
if op == "eq":
if val not in valid_states:
raise_filter_err(attr, op, val, "invalid state in filter")
return sql.column("state") == val
if op == "in":
states = [s for s in val.split(",") if s]
for state in states:
if state not in valid_states:
raise_filter_err(attr, op, state, "invalid state in filter")
return sql.column("state").in_(states)
raise_filter_err(attr, op, val, "bad op in filter")
if attr == "object_store_id":
if op == "eq":
return sql.column("object_store_id") == val
if op == "in":
object_store_ids = [s for s in val.split(",") if s]
return sql.column("object_store_id").in_(object_store_ids)
raise_filter_err(attr, op, val, "bad op in filter")
if attr == "quota_source_label":
if op == "eq":
ids = self.app.object_store.get_quota_source_map().ids_per_quota_source(
include_default_quota_source=True
)
if val == "__null__":
val = None
if val not in ids:
raise ValueError(f"Could not find key {val} in object store keys {list(ids.keys())}")
object_store_ids = ids[val]
return sql.column("object_store_id").in_(object_store_ids)
raise_filter_err(attr, op, val, "bad op in filter")
if (column_filter := get_filter(attr, op, val)) is not None:
return self.parsed_filter(filter_type="orm", filter=column_filter)
return super()._parse_orm_filter(attr, op, val)
[docs]
def get_query_filters_with_relations(self, query_filters: ValueFilterQueryParams, related_q: str, history_id):
"""Return `query_filters_with_relations` changing `related:hid` to `related:[hid1, hid2, ...]`."""
if query_filters.q and query_filters.qv:
qv_index = query_filters.q.index(related_q)
qv_hid = query_filters.qv[qv_index]
# Make new q and qv excluding related filter
new_q = [x for i, x in enumerate(query_filters.q) if i != qv_index]
new_qv = [x for i, x in enumerate(query_filters.qv) if i != qv_index]
# Get list of related item hids from job_connections manager
job_connections_manager = JobConnectionsManager(self.app.model.session)
related = job_connections_manager.get_related_hids(history_id, int(qv_hid))
# Make new query_filters with updated list of related hids for given hid
new_q.append("related-eq")
new_qv.append(json.dumps(related))
query_filters_with_relations = ValueFilterQueryParams(
q=new_q,
qv=new_qv,
)
return query_filters_with_relations
return query_filters
[docs]
def decode_type_id(self, type_id):
TYPE_ID_SEP = "-"
split = type_id.split(TYPE_ID_SEP, 1)
return TYPE_ID_SEP.join((split[0], str(self.app.security.decode_id(split[1]))))
[docs]
def parse_type_id_list(self, type_id_list_string, sep=","):
"""
Split `type_id_list_string` at `sep`.
"""
return [self.decode_type_id(type_id) for type_id in type_id_list_string.split(sep)]
def _add_parsers(self):
super()._add_parsers()
annotatable.AnnotatableFilterMixin._add_parsers(self)
genomes.GenomeFilterMixin._add_parsers(self)
deletable.PurgableFiltersMixin._add_parsers(self)
taggable.TaggableFilterMixin._add_parsers(self)
tools.ToolFilterMixin._add_parsers(self)
self.orm_filter_parsers.update(
{
"history_content_type": {"op": ("eq")},
"type_id": {"op": ("eq", "in"), "val": self.parse_type_id_list},
"hid": {"op": ("eq", "ge", "le", "gt", "lt"), "val": int},
# TODO: needs a different val parser - but no way to add to the above
# 'hid-in' : { 'op': ( 'in' ), 'val': self.parse_int_list },
"name": {"op": ("eq", "contains", "like")},
"state": {"op": ("eq", "in")},
"object_store_id": {"op": ("eq", "in")},
"quota_source_label": {"op": ("eq")},
"visible": {"op": ("eq"), "val": parse_bool},
"create_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
"update_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
}
)