CSV review feedback - #843
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The CSV package respelled hgvs_nt/hgvs_splice/hgvs_pro in two places and restated the null-token set a third time. Both now come from validation.constants.general and mave.utils.NULL_VALUES. This also settles a disagreement inside columns.py: cells were rendered with `_is_output_null` while `drop_unused_hgvs_columns` judged emptiness with validation's `is_null`, which additionally counts "-" as null. A column of "-" therefore rendered as "-" but was eligible to be dropped. Both now use the export's own predicate, which drops the package's dependency on validation.utilities entirely. CORE_NAMESPACE's resolvers keep the three names spelled out rather than taking `hgvs_columns`: that dict's declaration order is the published header order, and `hgvs_columns` is sorted.
scores.csv was composed from ["scores"], which meant every score column while
`include_custom_columns` defaulted to True, and means only the required `score` column since the
namespace refactor. /score-sets/{urn}/scores was updated to name both score namespaces; the dump
was missed, so it would have shipped an archive contradicting its own README. Never released — the
namespace refactor is on this branch.
Also here, because they touch the same code:
- `annotation_export_namespaces` takes a required viewer, and `annotations_csv` threads one viewer
through both namespace selection and cell resolution, so a calibration cannot be offered as a
column group and then withheld as data.
- The archive's research-use-only rule is now stated rather than implied: annotations.csv carries
RUO calibrations flagged by `research_use_only`, va.ndjson does not, and the README documents the
asymmetry instead of claiming the dump excludes them.
- The README's claim that mapped/ retains superseded records was wrong — the query has always
filtered `current`. Corrected, with the contrast against the API endpoint that does return
history.
- The command is decomposed into per-artifact functions so each branch the README documents is
reachable without running the whole export. `counts_csv` also stops indexing
dataset_columns["count_columns"] directly, which would KeyError and abort the entire dump on a
score set lacking the key.
66 tests over the archive contract: which files appear for which score-set shape, the `accession`
join key across files, RUO included-and-flagged versus private excluded, every ClinVar release
present, NDJSON line count and newline termination, and the published + CC0 selection gate.
Fixtures build the published/CC0 shape explicitly rather than reusing the generic score-set
factories, whose license is deliberately not CC0. Two carry non-obvious constraints:
TEST_MINIMAL_MAPPED_VARIANT sets post_mapped={}, a shape production never stores and the annotation
layer cannot parse; and a private calibration may not be marked primary.
Coverage Report for CI Build 31729312761Coverage increased (+0.2%) to 88.879%Details
Uncovered Changes
Coverage Regressions25 previously-covered lines in 4 files lost coverage.
Coverage Stats
💛 - Coveralls |
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