Internal strain-genomic-segment record class (model side) - #209

Merged

bgajria merged 43 commits into

strain-segment-record

Aug 5, 2026

Commits on Jul 31, 2026

Add design spec for internal strain genomic segment record

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3fdc46d
Resolve the ontology-visibility question in the strain segment spec

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91c5989
Add implementation plan for the strain genomic segment record

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d33a8f5
Drop all project scoping from the new strain segment record

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a98ddaa
Sync spec and plan with the shipped StrainSegmentId grammar

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84f9735
Add organism-dependent strain vocabulary param for strain segments
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37350e5
Dedupe strain vocabulary on node id and drop the project-restricted organism vocab
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fb5666e
Add validating ID query for strain genomic segments
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b9d7872
Remove the organism param: a sequence ID already determines its organism

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f91996c
Drop the organism param from strain segment queries
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dce329e
Add strain coordinate conversion attribute query
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1fd3f08
Drive strain vocabulary from protocolappnode and clarify query comments
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2589a39
Key strain offsets on the primary key to stop cross-sequence contamination
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0281aa9
Record the PK-keying and deletion-inversion decisions in the spec

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b2deb6c
Make strain-offset derivation duplicate-safe; correct false underscore claim

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889f023
Correct the spec's attribute list and the node-count claims
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8396af3
Refuse to mint a primary key for a colon-bearing reference sequence
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0787ef1
Add strain segment record class and question, and import the model files

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c062fc5
Fix plan and spec defects that would have broken Tasks 6 and 7
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d41cfb6
Apply Task 5 review findings to the strain segment record and question

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47f9e14
Correct comment claims found in the Task 5 re-review
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06c656f
Register the BED reporter on the strain segment record class

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db185b8
Record that wb model does not compile ApiCommonWebsite/Model
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5431e02
Correct the illustrative defline to what DeflineBuilder actually emits
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6c0bfd8
Update the three comments Task 6 falsified
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2c60a74
Record that the dev instance's appDb has no apidb.indel
jbrestel
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9686013

Commits on Aug 1, 2026

Record the new appDb, its test cases, and why the first gated rebuild failed
jbrestel
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0b2272b
Make the DNASeq injector dormant while dnaseq processing is redone

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59d56ed
Stop consuming communitycount, which this branch stopped producing

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a09d8da
Inject the DeRisi time series questions instead of hardcoding them

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0d24155
Drop a dataset-specific attribute from a generic compound search

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4656a38
Stop the id-SQL macro from expanding inside a comment
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a27fd49
Record that apidb.indel.location is the VCF anchor base
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aab2436
Gate strain segments on organism, not exact sequence

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acbc27d
Add the shareable end-to-end test report
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707b838
Drop apidb.indel coordinates from the shareable test report
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f05574e
Stamp provenance on the strain-segment numbers and correct the wrong ones

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cf8c49c
Tighten the shareable test report
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14d852a
Convert the end-to-end test report to markdown
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1c8cc32
Make the strain-segment search multi-strain: one search, N BED lines

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4265007
Note that the strain list is a comma-delimited string, not a JSON array
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fa8fc20
Show the mito SNP the identity figure refers to
jbrestel
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4357458

Commits on Aug 5, 2026

Merge branch 'master' into strain-segment-record
bgajria
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d31885f