feat(apollo): rebuild the Apollo release package as a tested CLI - #224

Open

jbrestel wants to merge 46 commits into

feat/apollo-configs

Commits on Aug 21, 2026

Apollo release package: fix jbrowseOrganismList, add design spec

John Brestelli
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3f29059
Apollo spec: record faToTwoBit resolution on cedar

John Brestelli
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e6d0a68
Apollo spec: replace release-68 diff with live-site equivalence

John Brestelli
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e1ee52e
Apollo: add implementation plan

John Brestelli
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3ac106a

Commits on Aug 22, 2026

fix(jbrowse): repair organismList history query and Postgres key casing

John Brestelli
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eed177e
feat(apollo): add Portal module for the UniDB organism list

John Brestelli
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aa8bb30
fix(apollo): coerce Portal flags and build numbers numerically

John Brestelli
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e2c564f
test(apollo): make the build_number ordering assertion discriminate

John Brestelli
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6424d56
feat(apollo): add Apollo module for the live prod roster

John Brestelli
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3ec2195
Apollo: an update must never change an organism's visibility

John Brestelli
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00acbf9
test(apollo): pin the non-numeric build_number skip path

John Brestelli
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0eeeabc
feat(apollo): add roster overlay parser and seeded overlay file

John Brestelli
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d2229d4
test(apollo): assert the unparseable-directory warning, rename a loose test

John Brestelli
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4df20cd
refactor(apollo): collect Portal warnings instead of writing to stderr

John Brestelli
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57c5413
feat(apollo): add reconciliation with add/prune/rename invariant

John Brestelli
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4cd7d6d
Apollo plan: report the redundant_overlay bucket

John Brestelli
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50fdc30
fix(apollo): trim whitespace from directory, report a non-JSON body as itself

John Brestelli
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76d8803
fix(apollo): sharper overlay parse errors, cite both lines, hermetic test

John Brestelli
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3e3c4fd
test(apollo): cover hidden publicMode, rename dies, rename-shadowed overlay

John Brestelli
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a0c870c
feat(apollo): detect taxonomic renames by assembly identity

John Brestelli
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69db985
feat(apollo): add URL absolutization with a mandatory post-condition check

John Brestelli
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d55a18a
fix(apollo): report unreadable indexes instead of reading them as a changed genome

John Brestelli
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242ee5e
polish(apollo): tighten base validation, a loose assertion, and exception shape

John Brestelli
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cb80d44
Apollo spec: record the measured jbrowse script baseline, and two defects

John Brestelli
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69e4c98
fix(jbrowse): remove the dead refSeqs cache path that killed jbrowseRefSeqs

jbrestel
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8337a23
feat(apollo): carry the internal organism abbrev alongside the public one

jbrestel
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648d9bd
Apollo spec: detect renames from the database, not the genome

John Brestelli
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1b93b69
Apollo: derive refSeqs.json from the .fai; jbrowseRefSeqs is orphaned

John Brestelli
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d026a81
Apollo spec: Apollo owns its fasta copy; organismSpecific needs a strip and has junk

John Brestelli
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f80cfb0
Merge master: refSeqs cache removal and organismSpecific integer fix

jbrestel
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5c43b5e
feat(apollo): generate the per-organism Apollo package

John Brestelli
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b5434f5
Apollo spec: record provenance and settle apollo_gene_tracks.conf

John Brestelli
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5e41435
fix(apollo): close the spec-review gaps in Generate

John Brestelli
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f8d27ef
feat(apollo): emit Apollo update, rename, prune and add commands

John Brestelli
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8deb571
Apollo: command-file verification counts non-comment lines; flag groovy URLs

John Brestelli
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8688436
feat(apollo): render the reconciliation report

John Brestelli
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49621e7
test(apollo): pin the organism-name quoting guards

John Brestelli
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6742712
fix(apollo): count every annotated prune, not just the unapproved ones

John Brestelli
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eb60a59
feat(apollo): add the createApolloReleasePackage CLI

John Brestelli
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0c4a7f6
test(apollo): cover the assembly merge-decline and positive narrowing

John Brestelli
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3d4e4ff
fix(apollo): print collected warnings before the gates that die

John Brestelli
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c3aeefb
fix(apollo): refuse to --generate an empty package, even under --force

John Brestelli
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2ec66d6
docs(apollo): trim the commentary to the load-bearing why

John Brestelli
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95f1030

Commits on Aug 24, 2026

Merge remote-tracking branch 'origin/master' into feat/apollo-configs
jbrestel
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ada6e76
Add --roster-overlay to override the installed roster overlay

jbrestel
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3ab53df
Generate twoBit under data/ instead of beside it

jbrestel
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dc50050