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Merge release-v0.7 into main - #88
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The generated Windows launcher shelled out to `powershell -Command Start-Process` to delay-open the browser after starting the server. That pattern - a freshly-written .bat spawning PowerShell - gets quarantined by some antivirus/Defender heuristics right after install.py creates it, leaving users with no Start.bat and no indication why (the installer log still reports success). Replace it with a plain cmd/ping/start sequence that achieves the same delayed browser-open without invoking PowerShell. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
The mcp_server/ integration was only described in CLAUDE.md; add a README section listing the read and write tools it exposes so non-Claude-Code contributors can find it. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Document the MCP server in README
…estart A leftover AlignmentJob row stuck in running_populate since a prior server restart tripped start_job()'s concurrency guard, so every click of "Start Alignment Run" was silently rejected with a 409 while the UI kept polling the stale job. - services/alignment_runner.py: add reconcile_stale_jobs(), which fails out any leftover non-terminal AlignmentJob row (background threads can't survive a process restart, so a non-terminal row left behind is always stale). - app.py: run reconcile_stale_jobs() at startup, before app.run(), so this can't recur. - tests/test_alignment_runner.py: cover non-terminal jobs getting marked failed, terminal jobs left untouched, and the no-jobs no-op case. - README-PROGRESS.md: changelog entry. - CLAUDE.md: carried-over edit from pi-add-mcp-readme. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Fix Windows Start.bat quarantined by antivirus
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Sep 16, 2026
_run_pipeline's except handler set status=failed but never touched completed_at, while both the success path and reconcile_stale_jobs() (added earlier on this branch) do set it. That left completed_at as an unreliable signal for "this job stopped running" — true for a completed or startup-reconciled job, but silently None for one that actually failed mid-run. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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As a BC/DSS curator, copy an existing BC or Specialization and tweak the group-level info while keeping its DECs/variables, per issue #83. Clone pre-fills the existing New BC / New Specialization form from a source record (group-level fields, DECs/variables) with the ID left blank, so nothing is saved until the curator edits and hits Save — reuses the existing create_bc()/save_decs() and specialization create() paths unchanged. Each cloned DEC's dec_id is blanked so save_decs() regenerates it under the new bc_id rather than keeping a stale "<old_bc_id>.DEC.N". BC clone is scoped to the BC + its DECs (not its linked specializations); specializations are cloned independently via their own action, matching the issue's treatment of BCs and specializations as parallel requests. - services/bc_service.py: add build_bc_clone(), returning a transient BC + DEC dicts copied from an existing bc_id. - routes/bc.py: /bc/new?clone_from=<bc_id> renders the New BC form pre-filled from the source. - routes/specializations.py: /specializations/?clone_from=<vlm_group_id> pre-fills the (already-collapsible) New Specialization panel from the source, without touching its vlm_group_id or the edit-in-place path. - templates/bc_detail.html: DEC table now renders from the `decs` route variable instead of `bc.decs`, so a transient (unsaved) clone object can be pre-filled; adds a Clone button and a "cloned from" banner. - templates/specializations.html: introduces a shared `fs` (edit_spec or clone_spec) template variable for prefill, keeping vlm_group_id and the published-lock checks scoped to true edit-in-place only; adds a Clone row action. - templates/bc_list.html: adds a Clone row action. - tests: services/bc_service, routes/bc, routes/specializations coverage for build_bc_clone() and both clone_from entry points. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Add issue templates
Clone Biomedical Concepts and Dataset Specializations (closes #83)
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Summary
mcp_server/) and its read/write tools inREADME.md, so non-Claude-Code contributors can discover the integration (previously only described inCLAUDE.md).AlignmentJobrow left in a non-terminal status blockedstart_job()'s concurrency guard forever, so "Start Alignment Run" silently failed. Addsreconcile_stale_jobs(), run at startup, to fail out any such stale row.Supersedes #86 (release-v0.6 -> main), which only carried the README doc change — this carries that plus the alignment fix from release-v0.7 in one step.
Test plan
pytest --tb=short(full suite, 484 tests) passesisort/black/flake8cleanTestReconcileStaleJobscoverage intests/test_alignment_runner.py/ncit-alignment/statusreports the last real completed job instead of the phantom stuck one