feat(storage): delete whole row on vertex removal to reduce super-node tombstones

[porunov]

Removing a vertex previously issued one column-level delete per incident edge/property on the vertex's storage row. For super-nodes this produced thousands of cell tombstones on a single Cassandra partition, leading to read timeouts and TombstoneOverwhelmingException.

When a vertex is fully removed, JanusGraph now deletes its entire storage row in a single backend operation: on CQL a partition-level DELETE ... WHERE key = ? (one partition tombstone) instead of N per-column deletes. Because the per-column delete entries are no longer serialized, this also reduces client-side memory, batching, and network cost for large removals.

Implementation:

• New whole-row-deletion flag on Mutation, plumbed through BackendTransaction.mutateEdges -> KCVSCache.mutateEntries -> CacheTransaction -> KCVMutation -> KeyColumnValueStoreManager.mutateMany.
• New StoreFeatures.hasOptimizedWholeRowDeletion() capability (default false). The graph skips building per-column deletions only when the backend advertises the capability, so backends without it keep the previous per-column behavior (no data loss).
• Commit-time detection in StandardJanusGraph.prepareCommitAddRelationMutations, driven by StandardJanusGraphTx tracking the canonical ids of fully-removed vertices. Only the edge store is affected; the index store still deletes per-column (its rows are shared across vertices). Partitioned vertices wipe every representative row via canonical-id normalization.
• Backend support: CQL/Scylla (partition delete), in-memory (drop key), HBase (column-family delete). BerkeleyJE and others fall back to per-column deletes.
• Controlled by the new storage.drop-whole-row-on-vertex-removal option (default true).

Tests cover the Mutation flag, the write-path plumbing, each backend, and graph-level integration (super-node removal, flag-off fallback, partial-edge removal, and partitioned-vertex removal). Documented in docs/changelog.md (1.2.0) and docs/storage-backend/cassandra.md.

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[Copilot]

Pull request overview

This PR introduces an optimization to reduce tombstone and client-side overhead when fully removing vertices (especially super-nodes) by allowing storage backends to perform a single whole-row/partition delete instead of issuing per-column deletes.

Changes:

• Add a whole-row-deletion flag to mutations and plumb it through the edge-store write path to backend mutateMany.
• Track fully removed vertices in StandardJanusGraphTx and, when enabled + supported by the backend, skip per-column deletion serialization and issue a whole-row delete for the vertex’s edge-store row.
• Add backend capability advertisement + implementations (CQL, HBase, InMemory) and add tests/docs covering the new behavior.

Reviewed changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
janusgraph-inmemory/src/test/java/org/janusgraph/graphdb/inmemory/WholeRowDeletionOptimizationTest.java	Integration test asserting whole-row deletion is used for super-node removal when enabled.
janusgraph-inmemory/src/test/java/org/janusgraph/graphdb/inmemory/RemovedVertexTrackingTest.java	Test verifying transaction-level tracking of fully removed vertices.
janusgraph-inmemory/src/test/java/org/janusgraph/graphdb/inmemory/PartitionedVertexWholeRowDeletionTest.java	Integration test for whole-row deletion behavior on partitioned vertex removal.
janusgraph-inmemory/src/test/java/org/janusgraph/diskstorage/inmemory/WholeRowDeletionCapturingStoreManager.java	Test-only store manager capturing mutateMany calls for assertions.
janusgraph-inmemory/src/test/java/org/janusgraph/diskstorage/inmemory/InMemoryWholeRowDeletionTest.java	Unit tests for in-memory backend whole-row delete semantics.
janusgraph-inmemory/src/main/java/org/janusgraph/diskstorage/inmemory/InMemoryStoreManager.java	Advertises optimized whole-row deletion and implements it in mutateMany.
janusgraph-inmemory/src/main/java/org/janusgraph/diskstorage/inmemory/InMemoryKeyColumnValueStore.java	Adds deleteRow used by in-memory whole-row deletion.
janusgraph-hbase/src/test/java/org/janusgraph/diskstorage/hbase/HBaseStoreManagerMutationTest.java	Test ensuring HBase uses family-level delete for whole-row deletion mutations.
janusgraph-hbase/src/main/java/org/janusgraph/diskstorage/hbase/HBaseStoreManager.java	Advertises feature and emits HBase family delete when whole-row deletion is flagged.
janusgraph-cql/src/test/java/org/janusgraph/diskstorage/cql/CQLWholeRowDeletionTest.java	Test ensuring CQL backend advertises and executes partition-level deletes.
janusgraph-cql/src/main/java/org/janusgraph/diskstorage/cql/function/mutate/AbstractCQLMutateManyFunction.java	Emits DELETE ... WHERE key=? when whole-row deletion is requested.
janusgraph-cql/src/main/java/org/janusgraph/diskstorage/cql/CQLKeyColumnValueStore.java	Adds prepared statement + API for row/partition delete.
janusgraph-cql/src/main/java/org/janusgraph/diskstorage/cql/builder/CQLStoreFeaturesBuilder.java	Advertises optimized whole-row deletion for CQL store features.
janusgraph-core/src/test/java/org/janusgraph/diskstorage/MutationTest.java	Tests new mutation flag behavior (emptiness/merge/total mutation count).
janusgraph-core/src/test/java/org/janusgraph/diskstorage/keycolumnvalue/StandardStoreFeaturesTest.java	Tests default/enable/copy behavior for the new StoreFeatures capability.
janusgraph-core/src/test/java/org/janusgraph/diskstorage/keycolumnvalue/cache/CacheTransactionWholeRowDeletionTest.java	Ensures whole-row deletion flag reaches backend mutateMany.
janusgraph-core/src/main/java/org/janusgraph/graphdb/vertices/StandardVertex.java	Records vertex removal in the transaction for commit-time detection.
janusgraph-core/src/main/java/org/janusgraph/graphdb/transaction/StandardJanusGraphTx.java	Adds removed-vertex canonical-id tracking and query method for commit-time checks.
janusgraph-core/src/main/java/org/janusgraph/graphdb/database/StandardJanusGraph.java	Commit-time decision to issue whole-row delete and skip per-column deletions for fully removed vertices.
janusgraph-core/src/main/java/org/janusgraph/graphdb/configuration/GraphDatabaseConfiguration.java	Adds storage.drop-whole-row-on-vertex-removal config option and wiring.
janusgraph-core/src/main/java/org/janusgraph/diskstorage/Mutation.java	Adds whole-row deletion flag and merges/count semantics.
janusgraph-core/src/main/java/org/janusgraph/diskstorage/keycolumnvalue/StoreFeatures.java	Adds hasOptimizedWholeRowDeletion() capability contract.
janusgraph-core/src/main/java/org/janusgraph/diskstorage/keycolumnvalue/StandardStoreFeatures.java	Implements new feature flag in store features + builder.
janusgraph-core/src/main/java/org/janusgraph/diskstorage/keycolumnvalue/cache/KCVSCache.java	Plumbs whole-row deletion flag into cache transaction mutations.
janusgraph-core/src/main/java/org/janusgraph/diskstorage/keycolumnvalue/cache/CacheTransaction.java	Persists whole-row deletion flag into KCVMutation sent to backend.
janusgraph-core/src/main/java/org/janusgraph/diskstorage/BackendTransaction.java	Adds overload to carry whole-row deletion flag to edge-store mutation calls.
docs/storage-backend/cassandra.md	Documents super-node deletion using partition-level delete and the config toggle.
docs/configs/janusgraph-cfg.md	Documents the new storage.drop-whole-row-on-vertex-removal option.
docs/changelog.md	Adds changelog entry describing whole-row deletion optimization and how to disable it.

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