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Remove hid window interface from api

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This commit is contained in:
guerler
2026-05-01 23:06:08 +03:00
parent 87fe6be8c1
commit 4fd1cbee4f
5 changed files with 27 additions and 174 deletions
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lib/galaxy/managers/history_graph.py
+19 -30
View File
@@ -79,8 +79,6 @@ class HistoryGraphBuilder:
seed: Optional[str] = None,
direction: str = "both",
depth: int = 5,
older_than_hid: Optional[int] = None,
newer_than_hid: Optional[int] = None,
seed_scope: Optional[str] = None,
):
self.sa_session = sa_session
@@ -92,9 +90,9 @@ class HistoryGraphBuilder:
self.seed = seed
self.direction = direction
self.depth = depth
self.older_than_hid = older_than_hid
self.newer_than_hid = newer_than_hid
self.seed_scope = seed_scope
self._older_than_hid: Optional[int] = None
self._newer_than_hid: Optional[int] = None
self._sort_keys: dict[str, tuple[int, int]] = {}
def build(self) -> HistoryGraphResponse:
@@ -102,14 +100,10 @@ class HistoryGraphBuilder:
if self.seed_scope:
truncation.scope_type = "seed_centered"
self._resolve_seed_scope()
elif self.older_than_hid is not None or self.newer_than_hid is not None:
truncation.scope_type = "window"
# 1. Select top-level items in scope.
dataset_ids, collection_ids, item_capped, oldest_hid, newest_hid = self._select_items()
dataset_ids, collection_ids, item_capped = self._select_items()
truncation.item_count_capped = item_capped
truncation.oldest_hid_included = oldest_hid
truncation.newest_hid_included = newest_hid
# 2. Remove hidden collection elements.
dataset_ids = self._remove_hidden_elements(dataset_ids)
@@ -202,10 +196,10 @@ class HistoryGraphBuilder:
if row is None or row.hid is None:
raise RequestParameterInvalidException(f"seed_scope {self.seed_scope} not found in history.")
half = self.limit // 2
self.older_than_hid = row.hid + half + (self.limit % 2)
self.newer_than_hid = row.hid - half - 1
self._older_than_hid = row.hid + half + (self.limit % 2)
self._newer_than_hid = row.hid - half - 1
def _select_items(self) -> tuple[set[int], set[int], bool, Optional[int], Optional[int]]:
def _select_items(self) -> tuple[set[int], set[int], bool]:
hda_q: Select = select(
HistoryDatasetAssociation.id,
HistoryDatasetAssociation.hid,
@@ -213,10 +207,10 @@ class HistoryGraphBuilder:
).where(HistoryDatasetAssociation.history_id == self.history_id)
if not self.include_deleted:
hda_q = hda_q.where(HistoryDatasetAssociation.deleted == False) # noqa: E712
if self.older_than_hid is not None:
hda_q = hda_q.where(HistoryDatasetAssociation.hid < self.older_than_hid)
if self.newer_than_hid is not None:
hda_q = hda_q.where(HistoryDatasetAssociation.hid > self.newer_than_hid)
if self._older_than_hid is not None:
hda_q = hda_q.where(HistoryDatasetAssociation.hid < self._older_than_hid)
if self._newer_than_hid is not None:
hda_q = hda_q.where(HistoryDatasetAssociation.hid > self._newer_than_hid)
hdca_q: Select = select(
HistoryDatasetCollectionAssociation.id,
@@ -225,22 +219,23 @@ class HistoryGraphBuilder:
).where(HistoryDatasetCollectionAssociation.history_id == self.history_id)
if not self.include_deleted:
hdca_q = hdca_q.where(HistoryDatasetCollectionAssociation.deleted == False) # noqa: E712
if self.older_than_hid is not None:
hdca_q = hdca_q.where(HistoryDatasetCollectionAssociation.hid < self.older_than_hid)
if self.newer_than_hid is not None:
hdca_q = hdca_q.where(HistoryDatasetCollectionAssociation.hid > self.newer_than_hid)
if self._older_than_hid is not None:
hdca_q = hdca_q.where(HistoryDatasetCollectionAssociation.hid < self._older_than_hid)
if self._newer_than_hid is not None:
hdca_q = hdca_q.where(HistoryDatasetCollectionAssociation.hid > self._newer_than_hid)
combined = union_all(hda_q, hdca_q).subquery()
# Deterministic order: hid desc, then id desc as a stable tiebreaker
# so duplicate hids (theoretically possible across imported data) do
# not affect internal selection stability.
stmt = (
select(combined.c.id, combined.c.hid, combined.c.item_type)
.order_by(combined.c.hid.desc())
.order_by(combined.c.hid.desc(), combined.c.id.desc())
.limit(self.limit + 1)
)
dataset_ids: set[int] = set()
collection_ids: set[int] = set()
min_hid: Optional[int] = None
max_hid: Optional[int] = None
count = 0
for row in self.sa_session.execute(stmt):
count += 1
@@ -250,13 +245,7 @@ class HistoryGraphBuilder:
dataset_ids.add(row.id)
else:
collection_ids.add(row.id)
hid = row.hid
if hid is not None:
if min_hid is None or hid < min_hid:
min_hid = hid
if max_hid is None or hid > max_hid:
max_hid = hid
return dataset_ids, collection_ids, count > self.limit, min_hid, max_hid
return dataset_ids, collection_ids, count > self.limit
def _remove_hidden_elements(self, dataset_ids: set[int]) -> set[int]:
if not dataset_ids:
lib/galaxy/schema/history_graph.py
+1 -3
View File
@@ -28,9 +28,7 @@ class GraphEdge(BaseModel):
class TruncationInfo(BaseModel):
item_count_capped: bool = False
scope_type: Literal["recent", "window", "seed_centered"] = "recent"
oldest_hid_included: Optional[int] = None
newest_hid_included: Optional[int] = None
scope_type: Literal["recent", "seed_centered"] = "recent"
seed_in_scope: Optional[bool] = None
lib/galaxy/webapps/galaxy/api/histories.py
+1 -11
View File
@@ -390,17 +390,9 @@ class FastAPIHistories:
ge=1,
le=20,
),
older_than_hid: Optional[int] = Query(
default=None,
description="Pagination: select items with hid less than this value (older items).",
),
newer_than_hid: Optional[int] = Query(
default=None,
description="Pagination: select items with hid greater than this value (newer items).",
),
seed_scope: Optional[str] = Query(
default=None,
description="Center the selection window on this item's hid position. Format: d{encoded_id} or c{encoded_id}.",
description="Center the selection window on this item. Format: d{encoded_id} or c{encoded_id}.",
),
trans: ProvidesHistoryContext = DependsOnTrans,
) -> HistoryGraphResponse:
@@ -412,8 +404,6 @@ class FastAPIHistories:
seed=seed,
direction=direction,
depth=depth,
older_than_hid=older_than_hid,
newer_than_hid=newer_than_hid,
seed_scope=seed_scope,
)
lib/galaxy/webapps/galaxy/services/histories.py
-4
View File
@@ -389,8 +389,6 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
seed: Optional[str] = None,
direction: str = "both",
depth: int = 20,
older_than_hid: Optional[int] = None,
newer_than_hid: Optional[int] = None,
seed_scope: Optional[str] = None,
):
history = self.manager.get_accessible(history_id, trans.user, current_history=trans.history)
@@ -405,8 +403,6 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
seed=seed,
direction=direction,
depth=depth,
older_than_hid=older_than_hid,
newer_than_hid=newer_than_hid,
seed_scope=seed_scope,
)
return builder.build()
test/unit/app/managers/test_HistoryGraphBuilder.py
+6 -126
View File
@@ -43,8 +43,6 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
direction="both",
depth=20,
limit=500,
older_than_hid=None,
newer_than_hid=None,
seed_scope=None,
):
builder = HistoryGraphBuilder(
@@ -55,8 +53,6 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
seed=seed,
direction=direction,
depth=depth,
older_than_hid=older_than_hid,
newer_than_hid=newer_than_hid,
seed_scope=seed_scope,
)
return builder.build()
@@ -194,8 +190,6 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
assert len(graph.nodes) == 0
assert len(graph.edges) == 0
assert graph.truncated.scope_type == "recent"
assert graph.truncated.oldest_hid_included is None
assert graph.truncated.newest_hid_included is None
assert graph.truncated.seed_in_scope is None
def test_standalone_datasets_included(self):
@@ -206,9 +200,6 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
graph = self._build_graph(history)
assert len(graph.nodes) == 2
assert len(graph.edges) == 0
assert graph.truncated.oldest_hid_included is not None
assert graph.truncated.newest_hid_included is not None
assert graph.truncated.newest_hid_included >= graph.truncated.oldest_hid_included
def test_full_history_graph(self):
"""Full history graph includes all items and edges."""
@@ -413,7 +404,7 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
assert e.source != e.target, f"Self-loop: {e.source}"
def test_seed_scope_centers_on_item(self):
"""seed_scope centers the selection window on the specified item's hid."""
"""seed_scope centers the selection window on the specified item."""
history, _ = self._create_history()
# Create 10 standalone datasets
hdas = [self._create_hda(history, name=f"dataset_{i}") for i in range(10)]
@@ -427,19 +418,7 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
# The seed item must be in scope
node_ids = {n.id for n in graph.nodes}
assert seed_scope in node_ids
# Scope metadata should reflect the window
assert graph.truncated.scope_type == "seed_centered"
assert graph.truncated.oldest_hid_included is not None
assert graph.truncated.newest_hid_included is not None
assert graph.truncated.oldest_hid_included <= middle.hid <= graph.truncated.newest_hid_included
def test_pagination_scope_type(self):
"""Pagination params produce scope_type='window'."""
history, _ = self._create_history()
for i in range(5):
self._create_hda(history, name=f"dataset_{i}")
graph = self._build_graph(history, older_than_hid=4)
assert graph.truncated.scope_type == "window"
def test_seed_in_scope_true(self):
"""seed_in_scope is true when seed is in the constructed graph."""
@@ -625,24 +604,6 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
graph = builder.build()
assert len(graph.nodes) == 1
def test_pagination_no_overlap(self):
"""Consecutive pages share no items."""
history, _ = self._create_history()
for i in range(10):
self._create_hda(history, name=f"ds_{i}")
# Page 1: most recent 5
page1 = self._build_graph(history, limit=5)
page1_ids = {n.id for n in page1.nodes}
oldest_hid = page1.truncated.oldest_hid_included
# Page 2: older than page 1's oldest
page2 = self._build_graph(history, limit=5, older_than_hid=oldest_hid)
page2_ids = {n.id for n in page2.nodes}
assert len(page1_ids & page2_ids) == 0, "Pages must not overlap"
assert len(page1_ids) + len(page2_ids) == 10
def test_determinism_identical_requests(self):
"""Identical requests produce identical output."""
history, _ = self._create_history()
@@ -1174,9 +1135,11 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
# 5-step chain: hda0 → tr0 → hda1 → tr1 → hda2 → tr2 → hda3 → tr3 → hda4 → tr4 → hda5
chain = self._build_linear_chain(history, length=5)
# Pick a small seed window in the middle of the chain.
middle_input_hid = chain[2][0].hid
graph = self._build_graph(history, older_than_hid=middle_input_hid + 1, newer_than_hid=middle_input_hid - 1)
# Center the seed window on the middle hda with limit=1, so the
# window holds just that one item and closure must complete the
# tool_request from there.
middle_hda = chain[2][0]
graph = self._build_graph(history, seed_scope=self._encode("d", middle_hda.id), limit=1)
node_ids = {n.id for n in graph.nodes}
tr_nodes = [n for n in graph.nodes if n.type == "tool_request"]
@@ -1198,22 +1161,6 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
"expected at least one input and one output after closure"
)
def test_pagination_newer_than_hid(self):
"""newer_than_hid selects only items with hid > N."""
history, _ = self._create_history()
hdas = [self._create_hda(history, name=f"ds_{i}") for i in range(6)]
# Get the middle item's hid as boundary
boundary_hid = hdas[2].hid
graph = self._build_graph(history, newer_than_hid=boundary_hid)
# Only items with hid > boundary_hid should be included
for n in graph.nodes:
assert n.hid is not None
assert n.hid > boundary_hid, f"Node hid {n.hid} should be > {boundary_hid}"
assert len(graph.nodes) == 3 # hdas[3], hdas[4], hdas[5]
def test_stability_new_items_shift_recent_window(self):
"""Adding new items shifts the recent-overview window.
@@ -1242,29 +1189,6 @@ class TestHistoryGraphBuilder(BaseTestCase, CreatesCollectionsMixin):
for hda in original[1:]:
assert self._encode("d", hda.id) in ids2
def test_stability_hid_window_does_not_mutate(self):
"""A fixed hid-based window returns the same results even after new items are added."""
history, _ = self._create_history()
for i in range(5):
self._create_hda(history, name=f"ds_{i}")
# Take a snapshot with older_than_hid to define a fixed window
snapshot = self._build_graph(history, older_than_hid=4)
snapshot_ids = {n.id for n in snapshot.nodes}
snapshot_hids = sorted(n.hid for n in snapshot.nodes if n.hid is not None)
# Add new items to the history (higher hids)
for i in range(5, 10):
self._create_hda(history, name=f"ds_{i}")
# Same window query returns identical results
after = self._build_graph(history, older_than_hid=4)
after_ids = {n.id for n in after.nodes}
after_hids = sorted(n.hid for n in after.nodes if n.hid is not None)
assert snapshot_ids == after_ids
assert snapshot_hids == after_hids
# ── Scalability / Boundedness Tests ──
@@ -1409,9 +1333,6 @@ class TestHistoryGraphBuilderBoundedness(BaseTestCase, CreatesCollectionsMixin):
assert len(graph.nodes) == min(n, limit)
assert len(graph.edges) == 0
assert graph.truncated.item_count_capped == (n > limit)
assert graph.truncated.oldest_hid_included is not None
assert graph.truncated.newest_hid_included is not None
assert graph.truncated.oldest_hid_included <= graph.truncated.newest_hid_included
def test_deep_linear_chain(self):
"""N-step linear chain: A→tr→B→tr→C→...
@@ -1530,42 +1451,6 @@ class TestHistoryGraphBuilderBoundedness(BaseTestCase, CreatesCollectionsMixin):
# Total edge count bounded: not m*k element edges
assert len(graph.edges) <= 2 * len(tr_nodes)
def test_pagination_non_overlapping_windows(self):
"""Two consecutive pages on a large history.
Assert: no overlap, deterministic ordering, expected hid ranges.
"""
n = GRAPH_SCALE_HISTORY_SIZE
limit = n // 2
history, _ = self._create_history()
for i in range(n):
self._create_hda(history, name=f"ds_{i}")
# Page 1: most recent
page1 = self._build_graph(history, limit=limit)
page1_ids = {nd.id for nd in page1.nodes}
page1_hids = sorted(nd.hid for nd in page1.nodes if nd.hid is not None)
assert len(page1.nodes) == limit
assert page1.truncated.item_count_capped is True
oldest_hid_p1 = page1.truncated.oldest_hid_included
# Page 2: older items
page2 = self._build_graph(history, limit=limit, older_than_hid=oldest_hid_p1)
page2_ids = {nd.id for nd in page2.nodes}
page2_hids = sorted(nd.hid for nd in page2.nodes if nd.hid is not None)
# No overlap
assert len(page1_ids & page2_ids) == 0, "Pages must not overlap"
# Deterministic ordering: page1 has higher hids than page2
if page1_hids and page2_hids:
assert min(page1_hids) > max(page2_hids), "Page 1 should contain newer items than page 2"
# Expected hid ranges
assert page1.truncated.newest_hid_included >= page1.truncated.oldest_hid_included
assert page2.truncated.newest_hid_included >= page2.truncated.oldest_hid_included
def test_seed_scope_on_older_item(self):
"""seed_scope on an early item in a large history.
@@ -1590,12 +1475,7 @@ class TestHistoryGraphBuilderBoundedness(BaseTestCase, CreatesCollectionsMixin):
# Response bounded
assert len(graph.nodes) <= limit
# Scope metadata valid
assert graph.truncated.scope_type == "seed_centered"
assert graph.truncated.oldest_hid_included is not None
assert graph.truncated.newest_hid_included is not None
assert graph.truncated.oldest_hid_included <= early.hid <= graph.truncated.newest_hid_included
def test_recent_overview_shift_after_append(self):
"""Recent overview shifts predictably when new items are appended.