feat(workflow-operator): volcano plot hover column by eugenegujing · Pull Request #9042 · apache/texera

eugenegujing · 2026-10-20T04:16:36Z

What changes were proposed in this PR?

The Volcano Plot uses hover_name=table.columns[0], so the tooltip label is whatever column comes first in the input. That is fine for a DESeq2 table starting with gene and useless for one starting with a composite id or a number, and there is no way to change it. This PR copies Scatter Plot's Hover column property over, one column only.

Hover column	Result
empty or whitespace-only (default)	`hover_name=table.columns[0]`, unchanged for saved workflows
set, present in the input	`hover_name=<that column>`
set, missing from the input	the operator's error page `Missing hover column in table.`, like the existing check for the two required columns (Scatter Plot lets plotly raise a `ValueError` here)

Since #8504 merged, the operator also exports a standalone script through generateStandaloneCode(), which had hover_name=table.columns[0] hard-coded. This PR mirrors the property there: the hover column goes in as an escaped Python literal, and a set column that the input lacks adds one more elif to the script's column checks, writing the same error page. Whether the field counts as empty is decided by one helper for both paths, so the exported figure and the engine's cannot disagree.

Independent of the PRs for the label fix (#9037) and the significance thresholds (#9039); all three touch neighbouring lines of VolcanoPlotOpDesc.scala, so whichever lands second needs a small rebase.

Figures below are the operator's generated Python from main and from this branch (Hover column = gene), run on the 430-gene example workflow from the issue whose first column is transcript|gene|chr|strand; the same point is hovered in both.

Before	After (Hover column = gene)

Any related issues, documentation, discussions?

Closes #9038

PR #8504 (merged) added the generateStandaloneCode() export path with the same hover_name=table.columns[0]; the mirroring described above is the follow-up it needed.

How was this PR tested?

New tests in VolcanoPlotOpDescSpec, written before the source change:

empty or whitespace-only field keeps hover_name=table.columns[0] and emits no hover check
a set field emits the decoded column as hover_name plus the presence check, and no table.columns[0]
a column name with quotes and non-ASCII text reaches the code only as a decode site
a workflow JSON saved before this change generates byte-for-byte the same code as a default-constructed operator
generateStandaloneCode: an empty field keeps hover_name=table.columns[0] and adds no check; a set field is emitted as a literal plus an exact five-line elif branch between the required-column check and the drawing branch; a name with quotes, non-ASCII text or a backslash comes out escaped rather than decoded; whitespace-only equals empty

sbt -Dsbt.server.forcestart=true "WorkflowOperator/testOnly *VolcanoPlotOpDescSpec"
# Tests: succeeded 15, 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 outside Texera (pytexera stubbed, pandas + plotly 5.24.1) on the 430-gene mock table: defaults hover-label the first point as ENST00000000000|GENE_0000|chr2|+; Hover column = gene gives GENE_0000; Hover column = no_such_column yields <h1>Volcano Plot failed</h1><p>Missing hover column in table.</p>. The exported script for the default and the gene 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.

Add an optional Hover column property, as on Scatter Plot, used as the hover label of each point. An empty or blank field keeps the first input column as before; a set column missing from the input yields the operator's error page.

github-actions · 2026-10-20T04:37:55Z

Automated Reviewer Suggestions

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

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

…over-column

… Plot too

codecov-commenter · 2026-10-24T23:35:48Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.72%. Comparing base (d6c9050) to head (bbc08a2).
⚠️ Report is 39 commits behind head on main.

Additional details and impacted files

@@             Coverage Diff              @@
##               main    #9042      +/-   ##
============================================
- Coverage     91.85%   91.72%   -0.14%     
- Complexity     5020     5033      +13     
============================================
  Files          1279     1269      -10     
  Lines         56192    55778     -414     
  Branches       7320     7202     -118     
============================================
- Hits          51615    51161     -454     
- Misses         2741     2778      +37     
- Partials       1836     1839       +3

Flag	Coverage Δ		*Carryforward flag
access-control-service	`77.44% <ø> (ø)`
agent-service	`99.53% <ø> (ø)`		Carriedforward from 6fa064b
amber	`85.80% <100.00%> (-0.10%)`	⬇️
computing-unit-managing-service	`64.05% <ø> (ø)`
config-service	`87.73% <ø> (+0.11%)`	⬆️
file-service	`82.31% <ø> (+0.01%)`	⬆️
frontend	`96.46% <ø> (-0.08%)`	⬇️	Carriedforward from 6fa064b
notebook-migration-service	`83.77% <ø> (ø)`
pyamber	`98.54% <ø> (+0.07%)`	⬆️	Carriedforward from 6fa064b
workflow-compiling-service	`78.30% <ø> (+0.34%)`	⬆️

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

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github-actions · 2026-10-24T23:39:25Z

⚠️ Benchmark changes need a look

🟢 0 better · 🔴 9 worse · ⚪ 6 noise (<±5%) · 0 without baseline

Compared against main d6c9050 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	428	0.261	22,456/32,344/32,344 us	🔴 +29.9% / 🔴 +122.7%
🔴	bs=100 sw=10 sl=64	964	0.588	100,071/128,656/128,656 us	🔴 +11.4% / 🔴 +33.7%
🔴	bs=1000 sw=10 sl=64	1,125	0.687	877,562/1,085,247/1,085,247 us	🔴 +16.7% / 🔴 +19.9%

Baseline details

Latest main d6c9050 from same runner

config	metric	PR	latest main	7d avg	Δ latest	Δ 7d
bs=10 sw=10 sl=64	throughput	428 tuples/sec	512 tuples/sec	901.09 tuples/sec	-16.4%	-52.5%
bs=10 sw=10 sl=64	MB/s	0.261 MB/s	0.313 MB/s	0.55 MB/s	-16.6%	-52.5%
bs=10 sw=10 sl=64	p50	22,456 us	20,175 us	11,350 us	+11.3%	+97.9%
bs=10 sw=10 sl=64	p95	32,344 us	24,897 us	14,525 us	+29.9%	+122.7%
bs=10 sw=10 sl=64	p99	32,344 us	24,897 us	17,637 us	+29.9%	+83.4%
bs=100 sw=10 sl=64	throughput	964 tuples/sec	1,005 tuples/sec	1,205 tuples/sec	-4.1%	-20.0%
bs=100 sw=10 sl=64	MB/s	0.588 MB/s	0.613 MB/s	0.735 MB/s	-4.1%	-20.0%
bs=100 sw=10 sl=64	p50	100,071 us	98,408 us	88,882 us	+1.7%	+12.6%
bs=100 sw=10 sl=64	p95	128,656 us	115,516 us	96,205 us	+11.4%	+33.7%
bs=100 sw=10 sl=64	p99	128,656 us	115,516 us	120,754 us	+11.4%	+6.5%
bs=1000 sw=10 sl=64	throughput	1,125 tuples/sec	1,144 tuples/sec	1,245 tuples/sec	-1.7%	-9.6%
bs=1000 sw=10 sl=64	MB/s	0.687 MB/s	0.698 MB/s	0.76 MB/s	-1.6%	-9.6%
bs=1000 sw=10 sl=64	p50	877,562 us	869,864 us	862,870 us	+0.9%	+1.7%
bs=1000 sw=10 sl=64	p95	1,085,247 us	929,807 us	905,485 us	+16.7%	+19.9%
bs=1000 sw=10 sl=64	p99	1,085,247 us	929,807 us	948,588 us	+16.7%	+14.4%

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
0,10,10,64,20,467.79,200,128000,428,0.261,22456.09,32344.09,32344.09
1,100,10,64,20,2075.08,2000,1280000,964,0.588,100070.91,128656.03,128656.03
2,1000,10,64,20,17781.30,20000,12800000,1125,0.687,877561.99,1085247.22,1085247.22

kz930

LGTM. The empty default keeps saved workflows unchanged, and the missing-column error page is nicer than Scatter Plot's ValueError.

…over-column # Conflicts: # common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/visualization/volcanoPlot/VolcanoPlotOpDesc.scala

…over-column

kunwp1

LGTM!

Remove the export saved-workflow test, compare the engine whitespace and saved-workflow tests against the default operator, and file the two required-field tests back under generatePythonCode.

feat(workflow-operator): volcano plot hover column

e7cd89d

Add an optional Hover column property, as on Scatter Plot, used as the hover label of each point. An empty or blank field keeps the first input column as before; a set column missing from the input yields the operator's error page.

github-actions Bot added feature common labels Oct 20, 2026

github-actions Bot assigned eugenegujing Oct 20, 2026

eugenegujing added 2 commits October 24, 2026 16:32

Merge remote-tracking branch 'upstream/main' into feat/volcano-plot-h…

85d38b3

…over-column

feat(workflow-operator): use the hover column in the exported Volcano…

b2126f8

… Plot too

kz930 approved these changes Oct 26, 2026

View reviewed changes

Merge remote-tracking branch 'upstream/main' into feat/volcano-plot-h…

79f3e5b

…over-column # Conflicts: # common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/visualization/volcanoPlot/VolcanoPlotOpDesc.scala

eugenegujing mentioned this pull request Nov 6, 2026

CI: every job that sets up sbt fails at "Setup sbt launcher" since 2026-11-05, so Required Checks is red on main and on every PR #9345

Closed

Merge remote-tracking branch 'upstream/main' into feat/volcano-plot-h…

6fa064b

…over-column

kunwp1 approved these changes Nov 13, 2026

View reviewed changes

Comment thread ...scala/org/apache/texera/amber/operator/visualization/volcanoPlot/VolcanoPlotOpDescSpec.scala Resolved

test(workflow-operator): trim redundant volcano plot hover tests

bbc08a2

Remove the export saved-workflow test, compare the engine whitespace and saved-workflow tests against the default operator, and file the two required-field tests back under generatePythonCode.

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What changes were proposed in this PR?

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