kert 4e9dc3d3d8 fix(dev): dedupe unlinks after commit; report removed keys (refs #615) ...

apply() deleted storage copies inside the BEGIN/COMMIT, so a failure
partway through rolled the rows back and left the surviving rows
pointing at files that were already gone. Collect the doomed paths
during the transaction, COMMIT, then unlink — rows and files can now
only be lost together.

--apply also prints how many keys it removed (first 20), and main()
closes the connection it opens.

2026-09-08 15:42:25 -04:00

..

backends

feat(bib,zot): deterministic URL lookup + nightly library-wide merge-dupes (refs #665)

2026-08-26 12:53:27 -04:00

_lake.py

fix(lake): M5 covered OPPS only — build out PFS (refs #514)

2026-07-10 23:47:51 -04:00

add_carrier_to_zotero.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

add_cf_history_to_zotero.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

add_pprrvu_historical_to_zotero.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

add_zipcode_to_zotero.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

analyze_coordination.py

feat(comments): coordination + form-letter detection, no LLM required (refs #255)

2026-07-10 22:17:42 -04:00

backfill_body_sha1.py

fix(bib,cli): durable merge-log path, empty-body alias guard, body_sha1 backfill (refs #665)

2026-08-26 15:46:34 -04:00

bootstrap_certs.py

feat(llm): SSO-guarded RAG chat UI at llm.fhirworx.io (P34)

2026-07-17 16:52:28 -04:00

bootstrap_secrets.py

remove: scrub all woodpecker references from codebase

2026-04-18 18:51:21 -04:00

bootstrap_sso.py

feat(llm): SSO-guarded RAG chat UI at llm.fhirworx.io (P34)

2026-07-17 16:52:28 -04:00

build_product_susceptibility.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

build_skin_subs_analytics.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

build_skin_subs_anomaly.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

build_skin_subs_evidence_base.py

chore: prune dead code and refresh stale docs

2026-07-08 10:12:24 -04:00

build_skin_subs_geo_setting.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

check_freshness.py

feat(infra): version-pin freshness check + Renovate auto-bump for ARG pins

2026-07-08 19:55:44 -04:00

check_pdf_coverage.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

classify_comments.py

feat(comments): coordination + form-letter detection, no LLM required (refs #255)

2026-07-10 22:17:42 -04:00

collect_grey_lit_skin_subs.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

coverage_badge.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

dedupe_attachments.py

fix(dev): dedupe unlinks after commit; report removed keys (refs #615)

2026-09-08 15:42:25 -04:00

dedupe_bib_legacy.py

feat(bib): legacy dedupe script — merge same-url and re-sent-email rows (refs #665)

2026-08-26 14:09:02 -04:00

download_opps_files.py

feat(opps): recover CY2014-2020 Addendum B + fix ingest finder

2026-07-08 14:48:17 -04:00

dump_zot_schema.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

enrich_entity_tags_and_load_duckdb.py

chore: prune dead code and refresh stale docs

2026-07-08 10:12:24 -04:00

extract_study_characteristics.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

fetch_fr_attachments.py

refactor(llm,rex): normalize FR text at capture; index-time strip becomes guard (refs #617)

2026-08-13 20:04:38 -04:00

fetch_nprm_addenda.py

feat(pfs): register NPRM Addendum E (proposed GPCIs) in bib (refs #629)

2026-08-17 12:13:57 -04:00

fetch_pdfs.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

file_concurrency_issues.py

fix(scripts): resolve Gitea label names to IDs in issue filer

2026-07-08 15:43:25 -04:00

fix_zotero_dates.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

fix_zotero_keys.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

gen_config.py

remove: scrub all woodpecker references from codebase

2026-04-18 18:51:21 -04:00

gen_readme.py

remove: scrub all woodpecker references from codebase

2026-04-18 18:51:21 -04:00

generate_alr_filenames.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_alr_reference_tables.py

reorg dev/ into scripts/ and seeds/, add PY2024 value sets

2026-03-03 22:05:49 -05:00

generate_alr_table_models.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_asr_table_models.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_cclf_docs.py

reorg dev/ into scripts/ and seeds/, add PY2024 value sets

2026-03-03 22:05:49 -05:00

generate_cclf_filenames.py

reorg dev/ into scripts/ and seeds/, add PY2024 value sets

2026-03-03 22:05:49 -05:00

generate_cclf_models.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_ccw_docs.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_ccw_models.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_cms_express.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_expressions.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_models.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_quality_measure_docs.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_reach_docs.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_reach_models.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_reach_participants.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

generate_skin_sub_claims.py

data: synthetic skin sub claims — 2,000 encounters, product + application codes

2026-03-25 10:09:20 -04:00

generate_ssp_county_models.py

reorg dev/ into scripts/ and seeds/, add PY2024 value sets

2026-03-03 22:05:49 -05:00

generate_zot_tables.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

ingest_asp.py

feat(conf): notebook read-replica aco.ro.duckdb (closes #510)

2026-07-10 22:23:57 -04:00

ingest_opps.py

fix(lake): M5 covered OPPS only — build out PFS (refs #514)

2026-07-10 23:47:51 -04:00

ingest_pfs.py

feat(pfs): NPRM Addendum E loader -> pfs.gpci_proposed + ingest wiring (closes #629)

2026-08-17 12:16:17 -04:00

install_certs.sh

feat: public SSO — fhirworx.io domain, Gitea OAuth2, Cloudflare tunnel

2026-04-09 19:06:33 -04:00

llm_bakeoff.py

feat(llm): embed bake-off harness + P33 outcomes in spec (refs #564 #567)

2026-07-17 14:37:34 -04:00

migrate_fr_txt.py

refactor(llm,rex): normalize FR text at capture; index-time strip becomes guard (refs #617)

2026-08-13 20:04:38 -04:00

migrate_zotero.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

nb_fe_smoke.py

fix(ci): unbreak notebook quality gates first CI exercise

2026-07-10 11:36:25 -04:00

nb_integration.py

fix(notebooks): drop cascade errors from snapshot parsing

2026-07-10 11:38:30 -04:00

nb_issue_filer.py

feat(notebooks): quality gates — headless integration test, FE smoke gate, dedup issue auto-filer

2026-07-10 10:14:46 -04:00

nb_watcher.py

feat(notebooks): quality gates — headless integration test, FE smoke gate, dedup issue auto-filer

2026-07-10 10:14:46 -04:00

pkg_drift.py

feat: package supply chain — inventory, mirrors, drift, vuln scanning (refs #159–#168)

2026-03-24 17:02:30 -04:00

pkg_inventory.py

fix(ci): finish gitea→git container rename in pkg scripts; skip gitignored Dockerfiles in inventory

2026-07-09 21:27:02 -04:00

pkg_issues.py

fix(ci): finish gitea→git container rename in pkg scripts; skip gitignored Dockerfiles in inventory

2026-07-09 21:27:02 -04:00

pkg_mirror_sync.py

fix(ci): finish gitea→git container rename in pkg scripts; skip gitignored Dockerfiles in inventory

2026-07-09 21:27:02 -04:00

populate_quality_measure_value_sets.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

publish_reference_to_lake.py

feat(lake): publish gpci_proposed + primary_care_service_code to DuckLake (closes #630)

2026-08-17 12:17:35 -04:00

refarm_cms_2026_2377.sh

chore(comments): re-farm script is the plain chain now that every stage is incremental (refs #615)

2026-09-08 14:37:13 -04:00

register_seeds.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

scrape_cms_data.py

reorg dev/ into scripts/ and seeds/, add PY2024 value sets

2026-03-03 22:05:49 -05:00

search_pubmed_palliative_rfi.py

feat(bib,notebooks): uncapped palliative identification + standards snowball + proposed code family (refs #644, #652)

2026-08-18 11:48:36 -04:00

search_pubmed_skin_subs.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

seed_col_tags.py

implement P6 bibliography: col tags, bib sync, generate models, lineage (fix #22, fix #23, fix #24, fix #25)

2026-03-12 17:25:30 -04:00

setup_unity_catalog.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

snowball_citations.py

fix(bib): elink snowball merged all seeds into one LinkSet; criteria clause (f) for code-family arm (refs #652)

2026-08-18 12:10:58 -04:00

sync_secrets.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

tag_palliative_comments.py

feat(comments): palliative-mention sweep — topic:palliative tags + extra_json snippets (refs #660)

2026-08-19 12:25:53 -04:00

test_network_isolation.sh

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

unity_catalog_example.py

chore: clean sweep — lint, format, stale refs, generated artifacts

2026-03-24 17:33:55 -04:00

zotero_archive_migrate.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00

zotero_fix_fields.py

feat: full session — mail servers, comment pipeline, PRISMA fetch, email ingest

2026-04-16 09:04:38 -04:00