Rename the Variation record to Variant; add a precomputed SNV characteristics search - #212

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jbrestel wants to merge 108 commits into

dnaseq-merge-experiments

Commits on Jul 30, 2026

Make the DNASeq injector dormant while dnaseq processing is redone

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9968576
Stop consuming communitycount, which this branch stopped producing

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60a3e36
Inject the DeRisi time series questions instead of hardcoding them

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28b06e4
Drop a dataset-specific attribute from a generic compound search

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e785390
Add VariationAttributes tuning table

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9ff6094
Add a minimal buildable variation record

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9bcf147
Add variation classification attributes from VariationFeature
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48f13bc
Add SNP and Indel allele attributes as separate sections
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d35e557
Add variation strain and call statistic attributes
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af9b2aa
Add variation gene aggregate, per-caller effect rollups, collapsed columns
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d8ccd76
Fix variation impact sorting and the collapsed-MAF help text
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e3571e2
Add variation record overview and default summary columns
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f9264c0
Add variation TranscriptProducts record table
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dd4efa6
Correct the TranscriptProducts strain_count help text

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9cc505b
Add variation PredictedEffects record table
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b19c82d
Categorize variation record attributes and tables
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cf0dd13
Label the overview allele rows by class instead of header rows

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d636b44
Assemble the "allele (frequency)" strings in SQL, not as textAttributes

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51cb41b
Fix ontology parenting and four review findings

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19b6527
Rename distinct_strain_count to "Called Strain Count (including reference)"

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e0bb106
Point the variation record at the real tuning table

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2723cda

Commits on Aug 5, 2026

Add the variation record design spec and implementation plan

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d3616c6
Reconcile the variation plan's progress with what actually shipped

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6be5539
Add the variation searches design spec (scaffolding + ID search)

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5fd66ca
Add the variation searches implementation plan

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f77d97a
Add variation search scaffolding and the VariationBySourceId search

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6130ef9
Disambiguate the spec reference in variationParams.xml

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ff563a5
Import the variation question, query, and param files

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cf87f9d
Categorize the VariationBySourceId search under Genetic Variation

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eaa4757
Mark the variation searches spec implemented

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6961842
Add the VariationsByIsolateGroup design spec

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3dc299a
Add VariationsByIsolateGroup implementation plan
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c1829d6
Point buildNumber at build-71 webservices files
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46e06f4
Add organismVQ.withVariationsTree for the variation searches

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a7a54fa
Add hidden eda_sample_table_suffix param and VariationVQ querySet
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1487112
Add EDA-driven variation_sample_meta filterParam and its two queries
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71bfa81
Fix illegal -- inside XML comments in the plan's code blocks
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e5946d4
Copy the four HSSS path and threshold params into variationParams

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dee13ba
Fix wdkXml grep patterns in the plan: single quotes, not double
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594c502
Add VariationsByIsolateGroup process query

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d870ea6
Fix the plugin source path in the plan (src/main/java, not lib/java)
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13c85bf
Add the VariationsByIsolateGroup question

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7ac703c
Add the required dynamicAttributes block to the plan's Task 7
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06cf403
Categorize VariationsByIsolateGroup under Genetic Variation
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cdd33e3
Design VariationsByLocation and VariationsByGeneIds
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f5345b4
Add implementation plan for VariationsByLocation and VariationsByGeneIds
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7b8501d
Fix the plan's installed-jar check: read the class, do not grep the lib dir
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87b5db5
Add chromosomeOptionalForVariations param and its vocabulary

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6b38902
Add the VariationsByLocation search
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ef12c77
Add the VariationsByGeneIds search

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45a2e2a
Categorize VariationsByLocation and VariationsByGeneIds
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fb976c0
Design VariationsByTwoIsolateGroups, the last of the five snp ports
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a74be0f
Add implementation plan for VariationsByTwoIsolateGroups
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4656225
Add the two-group sample filters and four thresholds
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9f6aae1
Fix the plan's expected param count: fourteen, not thirteen
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f087d78
Add the VariationsByTwoIsolateGroups search

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27ba528
Categorize VariationsByTwoIsolateGroups
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e131375

Commits on Aug 6, 2026

Design the port of the four remaining Genetic Variation searches

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f41a71b
Add implementation plan for the Genetic Variation searches port

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9a31137
Restore the GenesByNgsSnps process query on variationParams

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adb9ebe
Switch the plan's query verification to -showParams

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80189c9
Restore the GenesByNgsSnps question
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ebfb517
Fix the plan's service checks for the webapp context path

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382386a
Use -- not ## for SQL comments in GenesByNgsSnps postCacheUpdateSql

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0745c44
Add transitional apidbtuning CNV tables

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ea74772
Correct the webready CNV tables for the next workflow run

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8aa395e
Merge master into dnaseq-merge-experiments

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2ae20ca
Order needsUpdateProgram before program in the Pubmed tuning table

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7473351
Add CNV organism vocabularies and the cnv_sample_meta filter
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2d0a87b
Port GenesByCopyNumber onto the corrected CNV tables

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8eca4e9
Use percentile_cont, not Oracle median(), in the CNV medians CTEs
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9123b6a
Port GenesByCopyNumberComparison onto the corrected CNV tables
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6d32f8c
Restore the CNV summary columns on both gene CNV searches
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f95b152
Port SequencesByPloidy onto the corrected chromosome CNV table
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340d236
Categorize the three CNV searches under Genetic Variation
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afc84f3
Fix Task 14's unpassable gate in the port plan

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52a1b82
Retire the dead CNV organism and strain params

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e0bbc54
Compute ref_cn from the annotation, per chromosome

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63d6e80
Apply final code review findings

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b13b371

Commits on Aug 7, 2026

Add GeneVariationSummary tuning + webready tables

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d48ac7d
Add ungated piN/piS columns for display alongside their denominator

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9a38645
Fix: reference TranscriptAttributes unversioned, not with &1

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61e49a3
Wire the gene-record Genetic Variation attributes

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ed68d81
Group the gene variation attributes into six record subsections

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c6eddbb
Rename the genotype-ploidy attribute so it cannot be read as copy number

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1c3bd3b
Offer the reference strain in the HSSS sample filters

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f3f46c6
Show dataset display names in the sample filters, not DS_ IDs

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4266421

Commits on Aug 8, 2026

Rename the Variation record to Variant; display as "Short Variant"

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c8a99bd
Mark the four HSSS searches as SNV-only in their display names

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24935d7
Name the region and gene SNV searches for what they compute

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bfb8418
Merge branch 'feature/variant-rename' into dnaseq-merge-experiments
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652c1c2
Rename the GenesByNgsSnps display name to SNV Characteristics

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7312822
Add GenesByVariantCharacteristics, a precomputed SNV characteristics search

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0cf8251
Use the transcript record's own variation attributes, not new dynamic ones

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0520b48
Declare span_snp_density on the GenesByNgsSnps process query

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c319350
Label the GenesByNgsSnps result columns for what they now compute

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Label the GenesByNgsSnps params for what they now filter

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052be33
Point the GenesByNgsSnps description at the normalized ratio

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06cca80
Drop the synonymous-site-fraction figures from the GenesByNgsSnps description

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186d484
Mark the GenesByNgsSnps result columns as per-sample-group

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2dea527
Merge remote-tracking branch 'origin/master' into dnaseq-merge-experiments
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83974cb

Commits on Aug 10, 2026

Map EDA's date data_type in the sample ontology query

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37cc0e8
Inject only per-dataset dnaseq props, not per-sample

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58a5b93
Let coverage track callers override derived labels and metadata

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21047fd
Add variant glyph and effect-class colour functions

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Make the VCF glyph overridable and raise its rendering ceilings

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Build dnaseq tracks from the webservices tree

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Request the dnaseq tracks in the default JBrowse track set

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9e45584