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rfdouglas97/pharma-scrape

https://github.com/rfdouglas97/pharma-scrape · scanned 2026-06-15 23:50 UTC (2 months, 3 weeks ago)

25 raw signals (0 security + 25 graph)

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UNIFIED Repobility · multi-layer engine · AI coders

Complete repo analysis

Last scanned 2 months, 3 weeks ago · v1 · 24 actionable findings from 1 signal source. 1 repeated signal grouped for readability. Security checks, system graph analysis, and verified AI-agent feedback are merged into one review queue.

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Combined
86.1
/100
Security checks
86
0 findings
System graph
86
100.0% cov · 24 findings
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Severity: Critical 0 High 1 Medium 3 Low 18 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 24 Crowd 0 Layer: Hardware 1 Security 2 Quality 8 Api 13

All 454 nodes from the latest scan, grouped by kind. Each node is a unit the engine identified (file, function, endpoint, table…). Most users won't need this view — it's primarily for debugging the engine's graph extraction or for AI agents that want to enumerate the project structure.

LabelLayerStatusPath
test_local_storage_roundtrip software healthy tests/test_storage.py:4
db_available software healthy tests/conftest.py:9
require_db software healthy tests/conftest.py:19
tx software healthy tests/conftest.py:25
tree software healthy tests/test_adjacency.py:23
test_adjacent_descendants_and_ancestors software healthy tests/test_adjacency.py:37
test_ancestor_hop_limit software healthy tests/test_adjacency.py:51
test_programs_by_indication_expands_to_subtypes software healthy tests/test_adjacency.py:58
test_slug software healthy tests/test_run_helpers.py:4
test_load_fixtures_empty_dir_is_safe software healthy tests/test_eval_harness.py:10
test_load_labeled_fixture software healthy tests/test_eval_harness.py:14
test_unlabeled_template_dir_is_loaded_but_inert software healthy tests/test_eval_harness.py:43
test_model_seeded_draft_not_counted_until_labeled software healthy tests/test_eval_harness.py:52
uniq software healthy tests/test_loader.py:26
_make_extraction software healthy tests/test_loader.py:30
_asset software healthy tests/test_loader.py:46
test_load_creates_gold_and_is_idempotent software healthy tests/test_loader.py:57
test_phase_change_creates_scd2_history software healthy tests/test_loader.py:83
test_synonym_dedupes_to_one_asset software healthy tests/test_loader.py:118
test_seed_is_idempotent software healthy tests/test_seed_and_snapshot.py:19
test_hash_skip software healthy tests/test_seed_and_snapshot.py:32
test_clean_label_strips_noise software healthy tests/test_mapper.py:16
test_clean_label_drops_line_of_therapy_prefix software healthy tests/test_mapper.py:24
test_gene_family_threshold_is_sane software healthy tests/test_open_targets.py:9
test_drug_annotation_dataclass software healthy tests/test_open_targets.py:14
test_normalize_collapses_whitespace software healthy tests/test_hashing.py:4
test_hash_stable_across_cosmetic_whitespace software healthy tests/test_hashing.py:8
test_hash_changes_on_content_change software healthy tests/test_hashing.py:15
test_hash_is_sha256_hex software healthy tests/test_hashing.py:19
_asset software healthy tests/test_scorer.py:11
_prog software healthy tests/test_scorer.py:21
test_perfect_match_scores_one software healthy tests/test_scorer.py:25
test_phase_synonyms_count_as_match software healthy tests/test_scorer.py:35
test_phase_normalization_matches_verbatim_variants software healthy tests/test_scorer.py:51
test_synonym_matches_asset_identity software healthy tests/test_scorer.py:59
test_missed_asset_is_false_negative software healthy tests/test_scorer.py:68
test_wrong_phase_is_both_fp_and_fn software healthy tests/test_scorer.py:80
test_hallucinated_target_is_false_positive software healthy tests/test_scorer.py:88
health software healthy api/main.py:35
companies software healthy api/main.py:41
company software healthy api/main.py:47
programs software healthy api/main.py:56
asset software healthy api/main.py:76
facet_values software healthy api/main.py:85
coverage software healthy api/main.py:91
indications software healthy api/main.py:97
indication_adjacent software healthy api/main.py:103
screenshot software healthy api/main.py:113
list_extractions software healthy api/main.py:125
get_extraction software healthy api/main.py:149

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

LabelLayerStatusPath
README.md software healthy README.md
pharma-pipeline-intelligence-brief.md software healthy pharma-pipeline-intelligence-brief.md
ENGINEERING_PLAN.md software healthy ENGINEERING_PLAN.md
.env.example software healthy .env.example
pyproject.toml software healthy pyproject.toml
docker-compose.yml software healthy docker-compose.yml
companies.seed.yaml software healthy config/companies.seed.yaml
modality.yaml software healthy config/vocab/modality.yaml
phase.yaml software healthy config/vocab/phase.yaml
test_storage.py software healthy tests/test_storage.py
conftest.py software healthy tests/conftest.py
test_adjacency.py software healthy tests/test_adjacency.py
test_run_helpers.py software healthy tests/test_run_helpers.py
test_eval_harness.py software healthy tests/test_eval_harness.py
test_loader.py software healthy tests/test_loader.py
test_seed_and_snapshot.py software healthy tests/test_seed_and_snapshot.py
test_mapper.py software healthy tests/test_mapper.py
test_open_targets.py software healthy tests/test_open_targets.py
test_hashing.py software healthy tests/test_hashing.py
test_scorer.py software healthy tests/test_scorer.py
expected.json software healthy tests/golden/eli-lilly/expected.json
meta.json software healthy tests/golden/eli-lilly/meta.json
expected.json software healthy tests/golden/bristol-myers-squibb/expected.json
meta.json software healthy tests/golden/bristol-myers-squibb/meta.json
expected.json software healthy tests/golden/moderna/expected.json
meta.json software healthy tests/golden/moderna/meta.json
expected.json software healthy tests/golden/gsk/expected.json
meta.json software healthy tests/golden/gsk/meta.json
main.py software healthy api/main.py
package.json software healthy web/package.json
next-env.d.ts software healthy web/next-env.d.ts
package-lock.json software healthy web/package-lock.json
tsconfig.json software healthy web/tsconfig.json
next.config.mjs software healthy web/next.config.mjs
components.tsx software healthy web/app/components.tsx
globals.css software healthy web/app/globals.css
page.tsx software healthy web/app/page.tsx
layout.tsx software healthy web/app/layout.tsx
page.tsx software healthy web/app/review/page.tsx
page.tsx software healthy web/app/review/[id]/page.tsx
page.tsx software healthy web/app/assets/[id]/page.tsx
page.tsx software healthy web/app/companies/page.tsx
page.tsx software healthy web/app/companies/[id]/page.tsx
api.ts software healthy web/lib/api.ts
__init__.py software healthy pipeline_intel/__init__.py
db.py software healthy pipeline_intel/db.py
config.py software healthy pipeline_intel/config.py
cli.py software healthy pipeline_intel/cli.py
golden.py software healthy pipeline_intel/quality/golden.py
__init__.py software healthy pipeline_intel/quality/__init__.py

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

LabelLayerStatusPath
GoldenSave software healthy api/main.py:168
Settings software healthy pipeline_intel/config.py:6
Fixture software healthy pipeline_intel/quality/eval_harness.py:34
FixtureResult software healthy pipeline_intel/quality/eval_harness.py:76
CategoryScore software healthy pipeline_intel/quality/scorer.py:97
ScoreReport software healthy pipeline_intel/quality/scorer.py:119
Storage software healthy pipeline_intel/ingest/storage.py:16
LocalStorage software healthy pipeline_intel/ingest/storage.py:21
S3Storage software healthy pipeline_intel/ingest/storage.py:35
RenderResult software healthy pipeline_intel/ingest/render.py:19
RenderError software healthy pipeline_intel/ingest/render.py:100
ExtraField software healthy pipeline_intel/extract/schemas.py:24
Partner software healthy pipeline_intel/extract/schemas.py:31
ExtractedProgram software healthy pipeline_intel/extract/schemas.py:42
ExtractedAsset software healthy pipeline_intel/extract/schemas.py:59
ExtractionResult software healthy pipeline_intel/extract/schemas.py:90
ExtractionOutcome software healthy pipeline_intel/extract/extractor.py:32
ClosureStats software healthy pipeline_intel/ontology/closure.py:41
TermCandidate software healthy pipeline_intel/ontology/ols_client.py:31
TAStats software healthy pipeline_intel/ontology/therapeutic_area.py:53
DrugAnnotation software healthy pipeline_intel/ontology/open_targets.py:37
BackfillStats software healthy pipeline_intel/ontology/open_targets.py:81
Normalization software healthy pipeline_intel/ontology/mapper.py:91
Adjudication software healthy pipeline_intel/ontology/mapper.py:100
MapStats software healthy pipeline_intel/ontology/mapper.py:129
LoadStats software healthy pipeline_intel/gold/upsert.py:59
Base software healthy pipeline_intel/gold/models.py:34
Company software healthy pipeline_intel/gold/models.py:49
CompanySource software healthy pipeline_intel/gold/models.py:65
Snapshot software healthy pipeline_intel/gold/models.py:81
Extraction software healthy pipeline_intel/gold/models.py:99
Asset software healthy pipeline_intel/gold/models.py:117
AssetSynonym software healthy pipeline_intel/gold/models.py:140
Indication software healthy pipeline_intel/gold/models.py:155
IndicationMapping software healthy pipeline_intel/gold/models.py:161
Target software healthy pipeline_intel/gold/models.py:176
AssetTarget software healthy pipeline_intel/gold/models.py:185
Program software healthy pipeline_intel/gold/models.py:198
ProgramVersion software healthy pipeline_intel/gold/models.py:211
Partnership software healthy pipeline_intel/gold/models.py:232
PhaseVocab software healthy pipeline_intel/gold/models.py:248
ModalityVocab software healthy pipeline_intel/gold/models.py:256
VocabMapping software healthy pipeline_intel/gold/models.py:263
OntologyTerm software healthy pipeline_intel/gold/models.py:278
OntologyEdge software healthy pipeline_intel/gold/models.py:287
OntologyClosure software healthy pipeline_intel/gold/models.py:293
ProgramEmbedding software healthy pipeline_intel/gold/models.py:302
ReviewQueue software healthy pipeline_intel/gold/models.py:310
JobRun software healthy pipeline_intel/gold/models.py:323

LabelLayerStatusPath
Base data healthy pipeline_intel/gold/models.py
Company data healthy pipeline_intel/gold/models.py
CompanySource data healthy pipeline_intel/gold/models.py
Snapshot data healthy pipeline_intel/gold/models.py
Extraction data healthy pipeline_intel/gold/models.py
Asset data healthy pipeline_intel/gold/models.py
AssetSynonym data healthy pipeline_intel/gold/models.py
Indication data healthy pipeline_intel/gold/models.py
IndicationMapping data healthy pipeline_intel/gold/models.py
Target data healthy pipeline_intel/gold/models.py
AssetTarget data healthy pipeline_intel/gold/models.py
Program data healthy pipeline_intel/gold/models.py
ProgramVersion data healthy pipeline_intel/gold/models.py
Partnership data healthy pipeline_intel/gold/models.py
PhaseVocab data healthy pipeline_intel/gold/models.py
ModalityVocab data healthy pipeline_intel/gold/models.py
VocabMapping data healthy pipeline_intel/gold/models.py
OntologyTerm data healthy pipeline_intel/gold/models.py
OntologyEdge data healthy pipeline_intel/gold/models.py
OntologyClosure data healthy pipeline_intel/gold/models.py
ProgramEmbedding data healthy pipeline_intel/gold/models.py
ReviewQueue data healthy pipeline_intel/gold/models.py
JobRun data healthy pipeline_intel/gold/models.py
company data healthy pipeline_intel/gold/models.py
company_source data healthy pipeline_intel/gold/models.py
snapshot data healthy pipeline_intel/gold/models.py
extraction data healthy pipeline_intel/gold/models.py
asset data healthy pipeline_intel/gold/models.py
asset_synonym data healthy pipeline_intel/gold/models.py
indication data healthy pipeline_intel/gold/models.py
indication_mapping data healthy pipeline_intel/gold/models.py
target data healthy pipeline_intel/gold/models.py
asset_target data healthy pipeline_intel/gold/models.py
program data healthy pipeline_intel/gold/models.py
program_version data healthy pipeline_intel/gold/models.py
partnership data healthy pipeline_intel/gold/models.py
phase_vocab data healthy pipeline_intel/gold/models.py
modality_vocab data healthy pipeline_intel/gold/models.py
vocab_mapping data healthy pipeline_intel/gold/models.py
ontology_term data healthy pipeline_intel/gold/models.py
ontology_edge data healthy pipeline_intel/gold/models.py
ontology_closure data healthy pipeline_intel/gold/models.py
program_embedding data healthy pipeline_intel/gold/models.py
review_queue data healthy pipeline_intel/gold/models.py
job_run data healthy pipeline_intel/gold/models.py

LabelLayerStatusPath
config software healthy config
vocab software healthy config/vocab
tests software healthy tests
golden software healthy tests/golden
eli-lilly software healthy tests/golden/eli-lilly
bristol-myers-squibb software healthy tests/golden/bristol-myers-squibb
moderna software healthy tests/golden/moderna
gsk software healthy tests/golden/gsk
api software healthy api
web software healthy web
app software healthy web/app
review software healthy web/app/review
[id] software healthy web/app/review/[id]
assets software healthy web/app/assets
[id] software healthy web/app/assets/[id]
companies software healthy web/app/companies
[id] software healthy web/app/companies/[id]
lib software healthy web/lib
pipeline_intel software healthy pipeline_intel
quality software healthy pipeline_intel/quality
ingest software healthy pipeline_intel/ingest
registry software healthy pipeline_intel/registry
search software healthy pipeline_intel/search
extract software healthy pipeline_intel/extract
prompts software healthy pipeline_intel/extract/prompts
ontology software healthy pipeline_intel/ontology
gold software healthy pipeline_intel/gold
normalize software healthy pipeline_intel/normalize
migrations software healthy migrations
versions software healthy migrations/versions
.github software healthy .github
workflows software healthy .github/workflows

LabelLayerStatusPath
GET /v1/health api healthy api/main.py
GET /v1/companies api healthy api/main.py
GET /v1/companies/{company_id} api healthy api/main.py
GET /v1/programs api healthy api/main.py
GET /v1/assets/{asset_id} api healthy api/main.py
GET /v1/facets api healthy api/main.py
GET /v1/meta/coverage api healthy api/main.py
GET /v1/indications api healthy api/main.py
GET /v1/indications/adjacent api healthy api/main.py
GET /v1/snapshots/{snapshot_id}/screenshot api healthy api/main.py
GET /v1/review/extractions api healthy api/main.py
GET /v1/review/extractions/{extraction_id} api healthy api/main.py
POST /v1/review/golden api healthy api/main.py

LabelLayerStatusPath
ExplorePage frontend healthy web/app/page.tsx
RootLayout frontend healthy web/app/layout.tsx
ReviewListPage frontend healthy web/app/review/page.tsx
ReviewEditor frontend healthy web/app/review/[id]/page.tsx
AssetPage frontend healthy web/app/assets/[id]/page.tsx
CompaniesPage frontend healthy web/app/companies/page.tsx
CompanyPage frontend healthy web/app/companies/[id]/page.tsx

LabelLayerStatusPath
env.py data healthy migrations/env.py
25dbd5dfee09_add_enrichment_provenance_asset_.py data healthy migrations/versions/25dbd5dfee09_add_enrichment_provenance_…
be165f264480_add_indication_mapping_therapeutic_area.py data healthy migrations/versions/be165f264480_add_indication_mapping_the…
9f5de3fc7bf0_add_asset_mechanism_verbatim_disclosed_.py data healthy migrations/versions/9f5de3fc7bf0_add_asset_mechanism_verbat…
09b9ab596a73_add_asset_extras.py data healthy migrations/versions/09b9ab596a73_add_asset_extras.py
6ea3b1b88744_schema_v1.py data healthy migrations/versions/6ea3b1b88744_schema_v1.py

LabelLayerStatusPath
/page.tsx frontend healthy web/app/page.tsx
/review frontend healthy web/app/review/page.tsx
/review/[id] frontend healthy web/app/review/[id]/page.tsx
/assets/[id] frontend healthy web/app/assets/[id]/page.tsx
/companies frontend healthy web/app/companies/page.tsx
/companies/[id] frontend healthy web/app/companies/[id]/page.tsx

LabelLayerStatusPath
postgres data healthy README.md
postgresql data healthy .env.example

LabelLayerStatusPath
port:5433 network healthy docker-compose.yml
port:5432 network healthy docker-compose.yml

LabelLayerStatusPath
repobility-clone-j57xu12l software healthy /tmp/repobility-clone-j57xu12l

LabelLayerStatusPath
127.0.0.1 network healthy api/main.py

LabelLayerStatusPath
db hardware healthy docker-compose.yml

LabelLayerStatusPath
gha::ci cicd healthy .github/workflows/ci.yaml

LabelLayerStatusPath
test cicd healthy .github/workflows/ci.yaml
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