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fix(vdb): stop failing to read columns that a schema fills with a constant - #79
fg-sra fastq --defline with $sg failed on archives that store no SPOT_GROUP, such as ERR695638 (PacBio RS), with VDB error: the blob read for row 1 holds 0 rows from row -9223372036854775808. The v0.2.1 corpus check found it; v0.2.0 fails the same way.
Cause
The INSDC schema defines SPOT_GROUP = out_spot_group | .SPOT_GROUP | echo<''>(), so an archive that stores none gets the constant ''. VDB serves a nullary function's result as one blob spanning every row id, INT64_MIN..=INT64_MAX (prod-cmn.c), and VBlobIdRange reports its 2^64 rows as a count of 0, which blob_rows refused as a blob missing the row read. Schemas use the same pattern for other columns, e.g. the text PLATFORM (echo<'ILLUMINA'>()), so the fix is in the generic blob reader rather than specific to SPOT_GROUP.
Fix
blob_rows takes a blob starting at i64::MIN with a count of 0 as the whole id range. Only reads that previously always failed behave differently.
Testing
New unit test, and constant_column_blob_reads_match_cell_reads (runs with FG_SRA_TEST_TABLE_SRA, e.g. SRR2584863): reads the constant (ascii)PLATFORM through blobs and compares with cell reads. Without the fix it fails with the same BlobMissesRow { row: 1, first: i64::MIN, count: 0 }.
ERR695638 with --defline '$ac.$si sg=$sg length=$rl': output identical to fastq-dump --split-3 apart from the spots with more than two biological reads that fg-sra drops by design.
cargo ci-fmt, cargo ci-lint, cargo ci-test with the test archives set: all pass, except two whole-archive aligned tests that exceed nextest's 120 s limit in a debug build; both pass in the release profile (45 s and 100 s).
Summary by CodeRabbit
Bug Fixes
Blob reads now cover all row IDs for constant-column blobs, including ranges with no reported rows.
Tests
Added an opt-in archive test comparing blob reads with cell-by-cell reads across a large row range.
…stant
A schema column that falls back to a nullary function, such as SPOT_GROUP's
`echo<''>()` in archives that store none, is served as one blob spanning every
row id, INT64_MIN..=INT64_MAX. VBlobIdRange reports its 2^64 rows as a count
of 0, which blob reads refused as a blob missing the row read. `fastq
--defline` with `$sg` failed this way on ERR695638 (PacBio RS).
blob_rows now treats a blob with first == i64::MIN and count == 0 as covering every i64 row ID. Tests cover this case and compare blob and cell reads for (ascii)PLATFORM in an opt-in archive test.
blob_rows returns the full i64 row range for the specified zero-count blob. A unit test checks the range. An opt-in flat-table archive test compares blob reads with cell reads for (ascii)PLATFORM over rows 1 through 20,000.
Constant-column blobs now cover the full row-ID range. No merge-blocking issue was established.
Pre-merge checks: 4 · 1
Failed checks: 1 warning
Check name
Status
Explanation
Resolution
Docstring Coverage
Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documenta…
Write docstrings for the functions missing them to satisfy the coverage threshold.
Passed checks: 4 passed
Check name
Status
Explanation
Description Check
Check skipped - CodeRabbit’s high-level summary is enabled.
Title check
The title states the main change: VDB columns filled by a schema constant (nullary function blobs) were failing to read, and the fix stops those failures. The raw summary and objectives both describe …
Linked Issues check
Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check
Check skipped because no linked issues were found for this pull request.
Full details: Title check
Explanation
The title states the main change: VDB columns filled by a schema constant (nullary function blobs) were failing to read, and the fix stops those failures. The raw summary and objectives both describe a blob_rows change that treats first == i64::MIN with count == 0 as covering the full row-ID range, which addresses exactly this. The title is specific, uses the conventional prefix, and a teammate scanning history would understand the primary fix.
Full details: Docstring Coverage
Explanation
Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 2 functions across 2 files.
Resolution
Write docstrings for the functions missing them to satisfy the coverage threshold.
Finishing Touches
Generate docstrings
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A rabbit checks the row IDs wide, From smallest bounds to farthest side. The blob reads rows, the cells agree, PLATFORM hops through rows with glee. The rabbit rests beside the tree.
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only still-valid issues, skip the rest with a brief reason, keep changes
minimal, and validate.
Failed pre-merge checks:
- Docstring Coverage:
Write docstrings for the functions missing them to satisfy the coverage
threshold.
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Files selected for processing: 2
crates/fg-sra-vdb/src/cursor.rs
crates/fg-sra-vdb/tests/local_archives.rs
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Summary
fg-sra fastq --deflinewith$sgfailed on archives that store noSPOT_GROUP, such as ERR695638 (PacBio RS), withVDB error: the blob read for row 1 holds 0 rows from row -9223372036854775808. The v0.2.1 corpus check found it; v0.2.0 fails the same way.Cause
The INSDC schema defines
SPOT_GROUP = out_spot_group | .SPOT_GROUP | echo<''>(), so an archive that stores none gets the constant''. VDB serves a nullary function's result as one blob spanning every row id,INT64_MIN..=INT64_MAX(prod-cmn.c), andVBlobIdRangereports its 2^64 rows as a count of 0, whichblob_rowsrefused as a blob missing the row read. Schemas use the same pattern for other columns, e.g. the textPLATFORM(echo<'ILLUMINA'>()), so the fix is in the generic blob reader rather than specific toSPOT_GROUP.Fix
blob_rowstakes a blob starting ati64::MINwith a count of 0 as the whole id range. Only reads that previously always failed behave differently.Testing
constant_column_blob_reads_match_cell_reads(runs withFG_SRA_TEST_TABLE_SRA, e.g. SRR2584863): reads the constant(ascii)PLATFORMthrough blobs and compares with cell reads. Without the fix it fails with the sameBlobMissesRow { row: 1, first: i64::MIN, count: 0 }.--defline '$ac.$si sg=$sg length=$rl': output identical tofastq-dump --split-3apart from the spots with more than two biological reads that fg-sra drops by design.cargo ci-fmt,cargo ci-lint,cargo ci-testwith the test archives set: all pass, except two whole-archive aligned tests that exceed nextest's 120 s limit in a debug build; both pass in the release profile (45 s and 100 s).Summary by CodeRabbit