[eugenegujing]

What changes were proposed in this PR?

Root cause: VolcanoPlotOpDesc.generatePythonCode hard-codes the y column as the literal "-log10(pvalue)" and plots it under that name, so the y axis always says -log10(pvalue) even when the selected column is padj. The title is the literal "Volcano Plot" and the x axis and color bar show the raw effect column name. None of this can be changed from the property panel.

Before:  P-Value Column = padj  ->  y column "-log10(pvalue)"  ->  y axis "-log10(pvalue)"
After:   P-Value Column = padj  ->  y column "-log10(padj)"    ->  y axis "-log10(padj)", or the Y Label the user typed

The y column is now named after the selected p-value column, so the axis and the hover text say which column was transformed. Four optional label properties are added, empty by default:

Property	Empty	Set
Title	Volcano Plot	the text typed
X Label	effect column name	the text typed
Y Label	-log10(<p-value column>)	the text typed
Color Bar Label	effect column name	the text typed

The labels go through fig.update_layout(xaxis_title, yaxis_title, coloraxis_colorbar_title_text), same as Line Chart's X Label / Y Label. Each label is an EncodableString, so quotes and non-ASCII text are fine. A whitespace-only field counts as empty. The hover box still shows raw column names (plotly behaviour, same as Line Chart).

Behavior change for saved workflows: a workflow with padj as the p-value column now renders -log10(padj) instead of -log10(pvalue). That is the fix.

Since #8504 merged, the operator also has an export path, generateStandaloneCode(), which writes the same figure as a standalone script. It carried the same hard-coded "-log10(pvalue)" and title="Volcano Plot", so this PR applies the same change there: the y column is named after the selected p-value column and the four labels go through fig.update_layout as escaped Python literals (the export has no decoder, so pyStringLiteral escapes quotes and backslashes). The engine template and the exported script now label the figure the same way, and a spec checks that across the label combinations.

Rebase note: coloraxis_colorbar_title_text is emitted unconditionally, in both templates. Once the significance-coloring PR (#9039) lands, the categorical mode has no coloraxis, so whichever branch rebases second needs to make that entry conditional.

Figures below are the operator's generated Python from main and from this branch, run on the 430-gene example workflow from the issue; the third one has all four labels filled in.

Before	After (defaults)	After (labels set)

Any related issues, documentation, discussions?

Closes #9037

PR #8504 (merged) added the generateStandaloneCode() export path with the same hard-coded "-log10(pvalue)"; the mirroring described above is the follow-up it needed.

How was this PR tested?

New tests in VolcanoPlotOpDescSpec, written before the source change:

• y column and axis are named after the selected p-value column; the old literal is gone
• every label falls back to its default when empty or whitespace-only
• a set label replaces its default and reaches the code only as a decode site (sentinels with quotes, backslash, non-ASCII)
• one set label leaves the other three at their defaults
• a workflow JSON saved before this change (only the two column keys) generates byte-for-byte the same code as a default-constructed operator
• generateStandaloneCode: the y column and axis are named after the p-value column (including a name with a quote, p"adj), the labels fall back to the column-derived defaults, a set label is emitted as an escaped literal and the default title is gone, whitespace-only keeps the default, a saved workflow renders as a default-constructed operator, and a cross-path test checks that the engine template and the exported script carry the same title, axis and color bar labels

sbt -Dsbt.server.forcestart=true "WorkflowOperator/testOnly *VolcanoPlotOpDescSpec"
# Tests: succeeded 17, failed 0, canceled 0, ignored 0, pending 1   (the pending one is pre-existing)

sbt -Dsbt.server.forcestart=true "WorkflowOperator/scalafmtAll" "WorkflowOperator/Test/scalafmtAll"
sbt -Dsbt.server.forcestart=true "WorkflowOperator/scalafixAll --check"
# success

Smoke run: the generated code was executed outside Texera (pytexera stubbed, pandas + plotly 5.24.1) on the 430-gene mock table. Defaults give title Volcano Plot, x lfc_shrunk, y -log10(padj), color bar lfc_shrunk; with all four labels set the figure shows the typed text; whitespace-only title and y label fall back to the defaults. The exported script for the default and the all-labels configuration parses with ast.parse.

Was this PR authored or co-authored using generative AI tooling?

Yes. Generated-by: Claude Code (claude-fable-5-1). Co-authored with Claude; the author reviewed the change before submission.

[github-actions]

Automated Reviewer Suggestions

Based on the git blame history of the changed files, we recommend the following reviewers:

• Contributors with relevant context: @kz930, @Yicong-Huang
  You can notify them by mentioning @kz930, @Yicong-Huang in a comment.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.87%. Comparing base (98c6337) to head (ba9e78d).

Additional details and impacted files

@@            Coverage Diff            @@
##               main    #9040   +/-   ##
=========================================
  Coverage     91.87%   91.87%           
  Complexity     5049     5049           
=========================================
  Files          1265     1265           
  Lines         54915    54913    -2     
  Branches       6940     6940           
=========================================
- Hits          50453    50452    -1     
+ Misses         2769     2768    -1     
  Partials       1693     1693           

Flag	Coverage Δ		*Carryforward flag
access-control-service	77.38% <ø> (ø)
agent-service	99.16% <ø> (ø)		Carriedforward from 98c6337
amber	86.07% <ø> (+<0.01%)	⬆️	Carriedforward from 98c6337
computing-unit-managing-service	60.48% <ø> (ø)
config-service	87.37% <ø> (ø)
file-service	82.00% <ø> (ø)
frontend	96.50% <ø> (ø)		Carriedforward from 98c6337
notebook-migration-service	83.73% <ø> (ø)
pyamber	98.54% <ø> (ø)		Carriedforward from 98c6337
workflow-compiling-service	72.43% <ø> (ø)

*This pull request uses carry forward flags. Click here to find out more.

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[github-actions]

⚠️ Benchmark changes need a look

🟢 2 better · 🔴 7 worse · ⚪ 6 noise (<±5%) · 0 without baseline

Compared against main 98c6337 benchmarked on this same runner, so the delta is largely free of cross-runner hardware noise. The "7d avg" column still reflects the gh-pages dashboard. Treat <±5% as noise unless repeated.

Dashboard · Run

	config	throughput	MB/s	latency	max Δ latest / 7d
🔴	bs=10 sw=10 sl=64	526	0.321	18,053/28,515/28,515 us	🔴 +12.6% / 🔴 +100.3%
🟢	bs=100 sw=10 sl=64	1,233	0.752	80,266/90,358/90,358 us	🟢 -40.9% / 🟢 -12.1%
🔴	bs=1000 sw=10 sl=64	1,443	0.88	691,544/763,007/763,007 us	🔴 +6.7% / 🟢 +22.1%

Baseline details

Latest main 98c6337 from same runner

config	metric	PR	latest main	7d avg	Δ latest	Δ 7d
bs=10 sw=10 sl=64	throughput	526 tuples/sec	592 tuples/sec	879.16 tuples/sec	-11.1%	-40.2%
bs=10 sw=10 sl=64	MB/s	0.321 MB/s	0.361 MB/s	0.537 MB/s	-11.1%	-40.2%
bs=10 sw=10 sl=64	p50	18,053 us	16,032 us	11,504 us	+12.6%	+56.9%
bs=10 sw=10 sl=64	p95	28,515 us	26,442 us	14,234 us	+7.8%	+100.3%
bs=10 sw=10 sl=64	p99	28,515 us	26,442 us	17,338 us	+7.8%	+64.5%
bs=100 sw=10 sl=64	throughput	1,233 tuples/sec	1,219 tuples/sec	1,147 tuples/sec	+1.1%	+7.5%
bs=100 sw=10 sl=64	MB/s	0.752 MB/s	0.744 MB/s	0.7 MB/s	+1.1%	+7.4%
bs=100 sw=10 sl=64	p50	80,266 us	77,479 us	88,987 us	+3.6%	-9.8%
bs=100 sw=10 sl=64	p95	90,358 us	152,989 us	96,473 us	-40.9%	-6.3%
bs=100 sw=10 sl=64	p99	90,358 us	152,989 us	102,791 us	-40.9%	-12.1%
bs=1000 sw=10 sl=64	throughput	1,443 tuples/sec	1,489 tuples/sec	1,182 tuples/sec	-3.1%	+22.1%
bs=1000 sw=10 sl=64	MB/s	0.88 MB/s	0.909 MB/s	0.721 MB/s	-3.2%	+22.0%
bs=1000 sw=10 sl=64	p50	691,544 us	673,998 us	872,751 us	+2.6%	-20.8%
bs=1000 sw=10 sl=64	p95	763,007 us	714,851 us	910,151 us	+6.7%	-16.2%
bs=1000 sw=10 sl=64	p99	763,007 us	714,851 us	941,479 us	+6.7%	-19.0%

Raw CSV

config_idx,batch_size,schema_width,string_len,num_batches,total_ms,total_tuples,total_bytes,tuples_per_sec,mb_per_sec,lat_p50_us,lat_p95_us,lat_p99_us
0,10,10,64,20,380.06,200,128000,526,0.321,18053.36,28514.66,28514.66
1,100,10,64,20,1622.43,2000,1280000,1233,0.752,80265.87,90357.90,90357.90
2,1000,10,64,20,13863.99,20000,12800000,1443,0.880,691544.10,763007.41,763007.41