@datagrok/proteomics 1.0.1 → 1.2.1

package/docs/personas-and-capabilities.md

@@ -0,0 +1,165 @@
+# Personas & capabilities
+
+Who does what with a Proteomics dataset, what each persona is *allowed* to do, and
+**how that boundary is enforced** — today and where we are taking it.
+
+This doc is the reference behind the README's ["What you can achieve"](../README.md#what-you-can-achieve)
+section. The README leads with outcomes; this leads with the capability boundary and its
+enforcement, because a client requirement (see [Target state](#target-state)) needs that
+boundary to be real, not conventional.
+
+## The two personas
+
+| Persona | Role | Outcome they want |
+|---|---|---|
+| **Proteomics analyst** (data generator) | Builds the analysis: import → annotate → normalize → impute → differential expression | A defensible, reproducible, FDR-controlled result they can stand behind and hand off |
+| **Biology scientist** (data consumer / reviewer) | Interprets a finished analysis: volcano, enrichment, per-protein annotation | To understand *what changed and what it means* — without touching (or being able to change) the analysis itself |
+
+The dividing line is **"the interpretation"** — the set of decisions that determine what the
+result *says*: group assignment, normalization, imputation, the DE method, and the
+significance thresholds. The analyst owns these. The biologist reads the consequences and
+explores them, but must not alter them.
+
+## Capability matrix
+
+Legend: ✅ allowed · 🚫 must not · 👁 read-only interaction (view/filter/select, no state change)
+
+| Capability | Analyst | Biologist | Changes the interpretation? |
+|---|---|---|---|
+| Import a search-engine file | ✅ | — (receives a shared snapshot instead) | Produces it |
+| Annotate Experiment (assign groups) | ✅ | 🚫 | **Yes** |
+| Set Log2 Scale | ✅ | 🚫 | **Yes** |
+| Normalize | ✅ | 🚫 | **Yes** |
+| Impute Missing Values | ✅ | 🚫 | **Yes** |
+| Differential Expression | ✅ | 🚫 | **Yes** |
+| Compute SPC Status | ✅ | 🚫 | **Yes** |
+| Volcano Plot | ✅ | 👁 | No (view) |
+| Heatmap / PCA / Group-Mean Correlation / QC Dashboard | ✅ | 👁 | No (view) |
+| Enrichment Analysis & Charts | ✅ | ✅ (derives biology; non-destructive) | No |
+| UniProt protein panel | ✅ | ✅ | No |
+| Filter / select / cross-link in any viewer | ✅ | ✅ | No |
+| Share Analysis for Review | ✅ | 🚫 | N/A (publishes) |
+| Save changes to a shared snapshot | ✅ (own copy) | 🚫 | **Yes** |
+
+The 🚫 rows are the ones CK cares about: a biologist must not be able to re-run the pipeline
+or re-thresholds and thereby produce a *different* interpretation of the same data.
+
+## How the boundary is enforced today
+
+The package differentiates on **three axes** — none of which is the user's identity.
+
+### 1. By data shape — the only code-enforced line (`sampleOnly` grey-out)
+
+`src/menu.ts` gates every analysis-mutating action behind
+`sampleLevelDisabledReason(df)`. On a Spectronaut **Candidates** file (pre-computed DE, no
+per-sample intensities) these items grey out with an explanatory tooltip:
+
+> *Not applicable to a Spectronaut Candidates file — it already carries computed
+> differential expression and has no per-sample intensities. Use Volcano Plot, Enrichment
+> Analysis or the UniProt panel, or import the matching Spectronaut Report for sample-level
+> analyses.*
+
+Gated (sample-level): Annotate Experiment, Set Log2 Scale, Normalize, Impute, Differential
+Expression, Compute SPC Status, Heatmap, PCA, Group-Mean Correlation, QC Dashboard, Show All
+Visualizations.
+
+Always available: Import, Volcano Plot, Enrichment Analysis + Charts, Export Enrichment
+Inputs, SPC Dashboard, Share for Review, UniProt panel.
+
+**This gates on the *data*, not the *person*.** It happens to keep a biologist who only ever
+receives Candidates files in the interpretation lane — but it does nothing to stop a
+biologist who opens a **Report** file from running the whole pipeline.
+
+### 2. By workflow stage — the menu grouping mirrors the roles
+
+`Import → Annotate → Analyze` is the analyst building the result; `Visualize → Share` is the
+consumer interpreting it. The volcano auto-opening on both DE-completion and Candidates
+import lands the interpreter on the deliverable without making them run the pipeline. This
+is a *convention*, not a restriction.
+
+### 3. By access — view-only sharing (the one real identity boundary)
+
+`Share Analysis for Review` publishes a frozen, versioned snapshot and grants the reviewer
+group **View only**. The publish flow's verify-and-rollback gate aborts if the reviewer
+group has any Edit / Share / Delete right at the project, child-space, or umbrella-space
+level. So through the **shared snapshot**, a biologist genuinely cannot change the
+interpretation — they get a read-only copy.
+
+## The gap
+
+Enforcement today is **data-shape + access**, not **identity**. Concretely:
+
+- A biology user who opens a **Report** file (not a Candidates file, not a shared snapshot)
+  sees the full analyst menu enabled and can run/redo DE, re-normalize, re-threshold, and
+  re-share. Nothing checks who they are.
+- The view-only guarantee exists **only** for analyses that arrived via Share for Review. A
+  biologist working on a live table is unconstrained.
+
+CK does not want their biologists to be able to change the interpretation *at all* — which
+data-shape gating cannot guarantee, because it depends on which file they happened to open.
+
+## Target state
+
+Add an **identity/role** axis on top of the existing data-shape and access gating, so the
+🚫 capabilities are unavailable to a biologist regardless of file type.
+
+### What the platform can and cannot enforce
+
+This constrains the design, so it comes first. Datagrok's permission model
+(`grok.dapi.permissions`) grants **View / Edit / Share / Delete** on *entities* — projects,
+connections, scripts, queries, packages. There is **no per-function "Execute" permission for
+client-side TypeScript package functions** (a `Func` extends `Entity` but carries no ACL). So
+you **cannot** express "grant the Proteomics group execute on `Normalize`, deny Biologics"
+as a native grant.
+
+That leaves two enforcement tiers, with very different strength:
+
+- **Application-level group gating (a deterrent, not a wall).** A package function can check
+  `grok.dapi.groups.currentUserGroups()` at runtime and refuse to run for non-analysts. This
+  is real and has precedent (PowerPack, Grokky), but it runs in the browser and the
+  DataFrame mutation is client-side — a determined user could invoke the function from the
+  console. It hides analyst actions from biologists; it does **not** guarantee they can't
+  change data locally.
+- **Server-enforced boundaries (the real walls).** Three exist: (a) the **view-only shared
+  snapshot** — already built (Share for Review); the reviewer group has only View on the
+  project, so the server blocks any *save*, and a locally re-run analysis can't be persisted;
+  (b) **package-level sharing** — deny the package to a group entirely, but that is
+  all-or-nothing and would also remove the volcano/enrichment/UniProt biologists legitimately
+  need; (c) **server-side Script/Query Execute permission** — real per-step gating, but only
+  for the R scripts, and the package's client-side fallbacks (`limma`/`vsn` → client t-test /
+  quantile) are a loophole that would have to be disabled for non-analysts.
+
+**The strongest guarantee that already exists is the view-only shared snapshot.** If
+biologists only ever receive analyses via Share for Review, the interpretation of record is
+server-protected today. Everything below is about the *live-table* case.
+
+### Direction (to be specified in an implementation phase)
+
+1. **A "Proteomics Analysts" Datagrok group.** Analyst-only actions key off membership.
+2. **Menu gating (UX layer).** Extend the `sampleOnly` predicate in `src/menu.ts` to an
+   `analystOnly` predicate that also greys out (with a clear reason) when the current user is
+   not in the analysts group — so interpretation-changing items disappear for biologists on
+   *any* table, not just Candidates. This is a deterrent, not a security boundary.
+3. **Handler gating (defense in depth, still client-side).** Guard the mutating handlers in
+   `src/package.ts` (where `requireSampleLevelData` already lives) so a directly-invoked
+   function also refuses for non-analysts. This closes the menu-bypass path but, being
+   client-side, is still not a hard wall — the console can reach the same code.
+4. **The hard wall stays server-side.** For a genuine guarantee, rely on the view-only shared
+   snapshot as the default biologist entry point; a true block on *live* tables would require
+   moving the mutating steps to server-side Scripts with Execute permission **and** disabling
+   the client fallbacks for non-analysts (a larger architectural change — scope only if
+   biologists must edit live tables and still be hard-blocked).
+
+Open questions for the implementation phase: whether Enrichment re-runs count as "changing
+the interpretation" (currently treated as non-destructive exploration); where CK's biologists
+actually work (shared snapshots only vs. live files — this decides whether steps 2–4 are even
+needed); how the analysts group is provisioned per client/deployment; and whether to expose
+an explicit read-only "Reviewer mode" toggle vs. inferring it from group membership.
+
+## See also
+
+- [`README.md` → What you can achieve](../README.md#what-you-can-achieve) — the outcome-led persona intro
+- [`CLAUDE.md` → Menu architecture](../CLAUDE.md) — how the ribbon menu and `isEnabled` grey-out are built
+- `src/menu.ts` — `sampleLevelDisabledReason`, the `sampleOnly` gate
+- `src/package.ts` — `requireSampleLevelData`, the handler-level guards
+- `src/publishing/` — the Share for Review view-only publish flow

package/files/demo/README.md

@@ -0,0 +1,264 @@
+# Demo Datasets
+
+Sample search-engine outputs that exercise every import path and the full analysis
+pipeline (annotate → normalize → impute → differential expression → enrichment →
+visualize), plus the fixtures the package's tests pin against. They are browsable in the
+platform under **Files | App Data | Proteomics | demo**.
+
+Most carry an engineered or known-ground-truth signal — spike-in standards or species
+mixed at fixed ratios between conditions — so the differential-expression and volcano
+results are checkable against the truth, not just plausible.
+
+## Which dataset should I use?
+
+| Dataset | Vendor / format | Acquisition | Best for |
+|---------|-----------------|-------------|----------|
+| `cptac-spike-in.txt` | MaxQuant `proteinGroups.txt` | DDA | The full pipeline on a real benchmark with known UPS spike-in truth |
+| `proteinGroups.txt` | MaxQuant `proteinGroups.txt` | DDA | A fast, tiny MaxQuant import / UI smoke test |
+| `fragpipe-smoke-test.tsv` | FragPipe `combined_protein.tsv` | DDA | The FragPipe path + UniProt panel (real accessions) with an engineered volcano |
+| `spectronaut-hye-mix.tsv` | Spectronaut report (long) | DIA | Long-format DIA import and the three-species (HYE) ground-truth story |
+| `spectronaut-hye-demo.tsv` | Spectronaut report (long, slim) | DIA | **The registered `Proteomics Demo`** — the full pipeline's richest endpoint, run end to end |
+| `enrichment-demo.csv` | Engineered human DE result | — | **The registered `Proteomics Enrichment Demo`** — a single-organism pathway-enrichment story |
+| `spectronaut-hye-candidates.tsv` | Spectronaut Candidates | DIA | The pre-computed-DE shortcut (straight to volcano/enrichment) |
+| `spectronaut-hye-precursor*.{tsv,json}` | Spectronaut precursor / aggregated | DIA | Streaming-aggregation import and its golden-file equivalence tests |
+
+The two HYE files (`spectronaut-hye-mix.tsv` and `spectronaut-hye-candidates.tsv`) tell the
+same biological story from two angles — per-sample quantities vs. pre-computed
+fold-change — so they pair well for comparing the package's own DE against a vendor-shaped
+result.
+
+## proteinGroups.txt
+
+| Property | Value |
+|----------|-------|
+| **Format** | MaxQuant `proteinGroups.txt` (wide, tab-separated) |
+| **Source** | Synthetic — generated for development and testing |
+| **Organism** | Human |
+| **Proteins** | 27 |
+| **Samples** | 6 (Sample1–Sample6) |
+| **Quantification** | LFQ intensity |
+| **Columns** | 17 (Protein IDs, Gene names, Protein names, filter flags, LFQ intensities, coverage, peptide counts) |
+| **Size** | 3.7 KB |
+
+Minimal MaxQuant output suitable for quick import testing and UI development. Includes
+`Potential contaminant`, `Reverse`, and `Only identified by site` filter columns.
+
+## cptac-spike-in.txt
+
+| Property | Value |
+|----------|-------|
+| **Format** | MaxQuant `proteinGroups.txt` (wide, tab-separated) |
+| **Source** | CPTAC spike-in study — processed through MaxQuant |
+| **Organism** | Human (with UPS spike-in standards) |
+| **Proteins** | 1,569 |
+| **Samples** | 6 (two conditions: 6A and 6B, 3 replicates each) |
+| **Quantification** | LFQ intensity and raw Intensity |
+| **Columns** | 80 (full MaxQuant output including peptide counts, sequence coverage, identification types, MS/MS counts) |
+| **Size** | 4.6 MB |
+
+Full-scale MaxQuant output from the CPTAC spike-in benchmark. Two conditions (6A vs 6B) with
+known differentially abundant UPS proteins spiked into a constant yeast background. Ideal for
+testing the complete pipeline: import, normalization, imputation, and differential expression.
+
+## fragpipe-smoke-test.tsv
+
+| Property | Value |
+|----------|-------|
+| **Format** | FragPipe `combined_protein.tsv` (wide, tab-separated) |
+| **Source** | Synthetic — generated to exercise the FragPipe parser |
+| **Organism** | Human (plus one bovine contaminant) |
+| **Proteins** | 10 (8 targets + 1 `contam_` + 1 `rev_` decoy) |
+| **Samples** | 4 (Ctrl_1, Ctrl_2, Treat_1, Treat_2 — two conditions × two replicates) |
+| **Quantification** | MaxLFQ Intensity, Intensity, Razor Intensity (all three per sample) |
+| **Columns** | 19 (Protein, Protein ID, Entry Name, Gene, Length, Organism, Description + 3 × 4 sample intensity columns) |
+| **Size** | 2.1 KB |
+
+Minimal FragPipe output for smoke-testing import and the full analysis pipeline. Real UniProt
+accessions (TP53, BRCA1, EGFR, AKT1, MTOR, F2, PRKCD, HRAS) so the UniProt context panel
+resolves. Includes a `contam_BOVIN_CASEIN` row and a `rev_sp|P12345|...` decoy row to exercise
+the parser's contaminant/decoy filter. Differential abundance is engineered: TP53/AKT1/F2 up
+in Treat, BRCA1/PRKCD down, EGFR/MTOR/HRAS unchanged — gives a predictable volcano-plot pattern.
+
+## spectronaut-hye-mix.tsv
+
+| Property | Value |
+|----------|-------|
+| **Format** | Spectronaut report (long, tab-separated) |
+| **Source** | [SpectroPipeR](https://github.com/stemicha/SpectroPipeR) — HYE species mix benchmark (`inst/extdata/SN_test_HYE_mix_file.tsv`) |
+| **Organism** | Human / Yeast / *E. coli* three-species mix |
+| **Proteins** | 93 protein groups |
+| **Samples** | 8 runs (two conditions: HYE mix A and HYE mix B, 4 replicates each) |
+| **Quantification** | PG.Quantity (protein group), FG.MS2Quantity (fragment), PG.IBAQ |
+| **Columns** | 35 (R.FileName, R.Condition, R.Replicate, PG.ProteinGroups, PG.Organisms, EG.Qvalue, EG.ModifiedPeptide, FG.Charge, and more) |
+| **Instrument** | timsTOF Pro2 |
+| **Size** | 5.0 MB |
+
+Native Spectronaut DIA-MS long-format report from a three-species spike-in experiment. Each row
+is a peptide precursor measurement across runs. Human, yeast, and *E. coli* proteins are mixed at
+known ratios between conditions A and B, providing ground-truth differential abundance. Useful for
+testing long-format import and DIA-specific workflows.
+
+## spectronaut-hye-demo.tsv
+
+| Property | Value |
+|----------|-------|
+| **Format** | Spectronaut report (long, tab-separated) — slimmed to the 7 columns the parser reads |
+| **Source** | **Derived** from `spectronaut-hye-mix.tsv`: kept `R.FileName, R.Condition, R.Replicate, PG.ProteinGroups, PG.Organisms, PG.IBAQ, EG.Qvalue`, and scaled `PG.IBAQ` ×1000 into realistic intensity magnitudes. |
+| **Organism** | Human / Yeast / *E. coli* three-species mix |
+| **Proteins** | 93 protein groups |
+| **Samples** | 8 runs (HYE mix A and HYE mix B, 4 replicates each) |
+| **Quantification** | PG.IBAQ (scaled to realistic magnitude) |
+| **Columns** | 7 |
+| **Signal** | client-side Welch t-test + BH FDR yields ~45 significant (E. coli 27 + yeast 17 + human 1), log2FC up to ≈ 2.5 |
+| **Size** | 1.1 MB |
+
+Backs the package's single registered **`Proteomics Demo`** (`meta.demoPath: Bioinformatics |
+Proteomics Differential Expression`). The demo imports this file and runs the whole pipeline —
+import → impute → differential expression → volcano + heatmap — landing on the richest analysis
+endpoint with no R environment and no manual steps. It also opens a **QC dashboard** on a second
+tab and pre-selects the top-significant protein so its **UniProt** entry is already showing in the
+context panel. Enrichment is intentionally excluded: g:Profiler enrichment assumes one organism,
+and this is a three-species mix, so it would only map the human subset and mislead.
+
+Why a separate file rather than reusing `spectronaut-hye-mix.tsv`: that fixture's `PG.IBAQ`
+values were scaled *down* for size (max ≈ 34 k), which lands them in the ambiguous band where the
+parser's log2-vs-raw heuristic (`detectLog2Status`) wrongly concludes the data is already
+log2-transformed and skips the transform — producing meaningless linear "fold changes" (± thousands).
+Scaling every intensity by a constant leaves fold-changes and significance **unchanged** (log2FC is
+a difference of logs) but restores realistic magnitudes so the parser log2-transforms correctly.
+The result is the textbook HYE outcome: the two spiked species (E. coli, yeast) separate on the
+volcano while the constant human background stays flat. Regenerate with:
+
+```
+awk -F'\t' 'BEGIN{OFS="\t"; split("R.FileName,R.Condition,R.Replicate,PG.ProteinGroups,PG.Organisms,PG.IBAQ,EG.Qvalue", w, ",")}
+NR==1{for(i=1;i<=NF;i++)h[$i]=i; s=""; for(k=1;k<=length(w);k++)s=s (k>1?OFS:"") w[k]; print s; next}
+{o=""; for(k=1;k<=length(w);k++){c=w[k]; v=(c in h)?$(h[c]):""; if(c=="PG.IBAQ"&&v!=""&&v!="NA"&&v!="NaN")v=v*1000; o=o (k>1?OFS:"") v} print o}' \
+  spectronaut-hye-mix.tsv > spectronaut-hye-demo.tsv
+```
+
+## enrichment-demo.csv
+
+| Property | Value |
+|----------|-------|
+| **Format** | Pre-computed DE result (CSV): `Protein ID, Gene, log2FC, p-value, adj.p-value, significant` |
+| **Source** | **Engineered for demonstration.** Real HGNC gene symbols + UniProt accessions; fold-changes and p-values are synthetic. |
+| **Organism** | Human (single organism — enrichment requires one) |
+| **Proteins** | 119 (30 up, 25 down, 64 non-significant background) |
+| **Signal** | UP = cell cycle / mitosis; DOWN = oxidative phosphorylation; background = a diverse, unrelated set |
+| **Size** | 4.5 KB |
+
+Backs the registered **`Proteomics Enrichment Demo`** (`meta.demoPath: Proteomics | Enrichment
+Analysis`). The demo loads this as a pre-computed DE result, opens the volcano, runs g:Profiler
+over-representation analysis (GO / KEGG / Reactome / WikiPathways), and docks the enrichment
+charts cross-linked to the volcano — selecting a term highlights its proteins.
+
+Why engineered rather than a real dataset: enrichment assumes a **single organism**, which rules
+out the three-species HYE files, and it needs a **coherent** regulated set so the returned terms
+are recognizable. The two regulated sets are drawn from textbook, strongly-annotated pathways
+(cell cycle up, oxidative phosphorylation down), so g:Profiler returns crisp terms — e.g. KEGG
+"Cell cycle" and "Oxidative phosphorylation" at FDR < 1e-15. Gene symbols are real (g:Profiler
+maps them); accessions are real (the UniProt panel resolves); only the statistics are synthetic.
+Regenerate with `bash tools/generate-enrichment-fixture.sh` (the gene lists live in that script).
+
+## spectronaut-hye-candidates.tsv
+
+| Property | Value |
+|----------|-------|
+| **Format** | Spectronaut Candidates report (wide, tab-separated, pre-computed DE) |
+| **Source** | **Derived** from `spectronaut-hye-mix.tsv` via this package's own Welch's t-test + BH FDR. Regenerate with `node tools/generate-spectronaut-candidates-fixture.mjs`. |
+| **Comparison** | HYE mix B / HYE mix A (single comparison) |
+| **Proteins** | 93 protein groups (30 Human + 30 Yeast + 30 *E. coli* + 3 other) |
+| **Columns** | 18 (Valid, Comparison, Condition Numerator/Denominator, # of Ratios, Group, AVG Group Quantity Num/Den, AVG Log2 Ratio, Absolute AVG Log2 Ratio, % Change, Ratio, Pvalue, Qvalue, ProteinGroups, Genes, UniProtIds, Organisms) |
+| **Signal** | log2FC range ≈ [−2.46, +3.66]; 43 significant at \|log2FC\| ≥ 1 ∧ q ≤ 0.05 (26 up, 17 down) |
+| **Size** | 20 KB |
+
+Exercises the `Proteomics | Import | Spectronaut Candidates...` path with values that line up
+with the source PG file, so the two HYE fixtures tell the same biological story from different
+angles. **Not a verbatim Spectronaut export** — we don't have Spectronaut here, so the script
+does its own DE math and lays it out in Spectronaut's Candidates column shape. Schema matches
+real Spectronaut Candidates output closely enough to round-trip through the importer; numerical
+values are ours, not Biognosys's.
+
+## spectronaut-hye-precursor.tsv
+
+| Property | Value |
+|----------|-------|
+| **Format** | Spectronaut report (long, tab-separated, precursor/fragment-level) |
+| **Source** | Synthetic — generated to exercise the streaming Spectronaut import path. Regenerate with `node tools/generate-spectronaut-precursor-fixture.mjs`. |
+| **Organism** | Human / Yeast / *E. coli* three-species mix (synthetic) |
+| **Proteins** | 41 protein groups (39 passing + 1 `CON__` + 1 `REV__`) |
+| **Samples** | 6 runs (two conditions: CondA / CondB, 3 replicates each) |
+| **Quantification** | PG.Quantity (constant per protein × condition × replicate) |
+| **Columns** | 11 (R.FileName, R.Condition, R.Replicate, PG.ProteinGroups, PG.Organisms, PG.Quantity, EG.Qvalue, PEP.StrippedSequence, EG.ModifiedPeptide, FG.Charge, FG.Id) |
+| **Size** | ~44 KB |
+
+Small synthetic precursor-level Spectronaut report: ≥2 distinct precursor/fragment
+rows per protein × sample. Carries the D-01 precursor signature columns
+(`EG.ModifiedPeptide` / `FG.Charge` / `PEP.StrippedSequence`) so the header-sniff
+routes it to the streaming aggregator, uses `CondA`/`CondB`, and carries **no**
+`PG.Genes`/`PG.ProteinAccessions` columns (the real `spectronaut-hye-mix.tsv`
+lacks them too). Deliberately includes one `CON__` row, one `REV__` row, one
+protein mixing a passing precursor with a >0.01 sub-threshold one, one
+non-numeric (`Profiled`) q-value protein, and one empty-string q-value protein so
+every Spectronaut filter branch is exercised by a single fixture.
+
+## spectronaut-hye-precursor-golden.tsv
+
+| Property | Value |
+|----------|-------|
+| **Format** | Aggregated Spectronaut report (one row per protein × condition × replicate, tab-separated) |
+| **Source** | **Derived** — verbatim duckdb output of `tools/spectronaut-aggregate.sh` over `spectronaut-hye-precursor.tsv`. Regenerate with `tools/spectronaut-aggregate.sh files/demo/spectronaut-hye-precursor.tsv files/demo/spectronaut-hye-precursor-golden.tsv`. |
+| **Proteins** | 39 (the `CON__`/`REV__` decoys are dropped by the WHERE filter) |
+| **Samples** | 6 (CondA / CondB × 3 replicates) |
+| **Rows** | 234 data rows + header |
+| **Columns** | 6 (PG.ProteinGroups, R.Condition, R.Replicate, R.FileName, PG.Quantity, EG.Qvalue) |
+| **Size** | ~12 KB |
+
+The D-04 equivalence oracle: the real duckdb aggregation of the fixture, not a
+hand-derived approximation. The Plan-03 golden test compares the streaming
+TypeScript aggregator's output against this file.
+
+## spectronaut-hye-precursor-golden.json
+
+| Property | Value |
+|----------|-------|
+| **Format** | JSON map `{ "<protein><condition>_<replicate>": { "quantity": number, "qvalue": number } }` |
+| **Source** | **Transcribed verbatim** from `spectronaut-hye-precursor-golden.tsv` — no re-aggregation. Regenerate with `node tools/derive-precursor-golden-sidecar.mjs`. |
+| **Entries** | 234 (one per surviving protein × condition × replicate) |
+| **Size** | ~9 KB |
+
+Read by `grok test` as the in-test oracle when committed-file reads are
+unavailable in the test runner. It is **derived FROM** the golden `.tsv` and
+never re-aggregated, so the equivalence test stays pinned to real duckdb output;
+re-running the deriver against an unchanged golden produces a byte-identical JSON.
+
+### Flip caveat & regeneration order
+
+The committed `tools/spectronaut-aggregate.sql` carries a **reference-file-only**
+DMD↔WT `R.Condition` correction (a one-off fix for the mislabeled
+`2026-05-13 BP DMD WT.tsv` reference file). It is a structural **no-op** on this
+`CondA`/`CondB` fixture, which is exactly why the same script doubles as both the
+documented manual fallback **and** the test oracle without perturbing the golden.
+The committed SQL also **drops** the two unused `any_value` carry-along SELECT
+terms for the gene-symbol and protein-accession columns present in the `/tmp`
+original — a documented divergence, because the package's Spectronaut data does
+not carry those columns and keeping them would Binder-Error duckdb over this
+fixture.
+
+The fixture → golden `.tsv` → golden `.json` chain **must be regenerated in
+order**, or the artifacts silently drift:
+
+1. `node tools/generate-spectronaut-precursor-fixture.mjs`
+2. `tools/spectronaut-aggregate.sh files/demo/spectronaut-hye-precursor.tsv files/demo/spectronaut-hye-precursor-golden.tsv`
+3. `node tools/derive-precursor-golden-sidecar.mjs`
+
+## License
+
+- **proteinGroups.txt** — Synthetic data, no restrictions.
+- **cptac-spike-in.txt** — Public benchmark data from the Clinical Proteomic Tumor Analysis Consortium.
+- **fragpipe-smoke-test.tsv** — Synthetic data, no restrictions.
+- **spectronaut-hye-mix.tsv** — From SpectroPipeR, licensed under MIT.
+- **spectronaut-hye-candidates.tsv** — Derived from `spectronaut-hye-mix.tsv` (MIT). DE values computed by this package; no restrictions.
+- **spectronaut-hye-precursor.tsv** — Synthetic data, no restrictions.
+- **spectronaut-hye-precursor-golden.tsv** — Derived (duckdb aggregation) from `spectronaut-hye-precursor.tsv` (synthetic); no restrictions.
+- **spectronaut-hye-precursor-golden.json** — Transcribed from `spectronaut-hye-precursor-golden.tsv` (synthetic); no restrictions.