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BaranziniLab/CDWAgent

https://github.com/BaranziniLab/CDWAgent · scanned 2026-06-17 01:19 UTC (1 month, 2 weeks ago)

14 raw signals (0 security + 14 graph)

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UNIFIED Repobility · multi-layer engine · AI coders

Complete repo analysis

Last scanned 1 month, 2 weeks ago · v2 · last Δ -14.8 (diff) · 13 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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66.7% cov · 13 findings

Severity distribution — click a segment to filter

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Severity: Critical 0 High 0 Medium 7 Low 4 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 13 Crowd 0 Layer: Software 1 Security 2 Cicd 2 Quality 8

Exclude dismissed / FP Exclude test files

All 129 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.

Label	Layer	Status	Path
`.env.example`	software	healthy	`.env.example`
`manifest.json`	software	healthy	`manifest.json`
`AGENTS.md`	software	healthy	`AGENTS.md`
`CHANGELOG.md`	software	healthy	`CHANGELOG.md`
`README.md`	software	healthy	`README.md`
`pyproject.toml`	software	healthy	`pyproject.toml`
`parse_data_dictionary.py`	software	healthy	`scripts/parse_data_dictionary.py`
`ci.yml`	software	healthy	`.github/workflows/ci.yml`
`validation.py`	software	healthy	`src/cdwagent/validation.py`
`cli.py`	software	healthy	`src/cdwagent/cli.py`
`server.py`	software	healthy	`src/cdwagent/server.py`
`__init__.py`	software	healthy	`src/cdwagent/__init__.py`
`__main__.py`	software	healthy	`src/cdwagent/__main__.py`
`config.py`	software	healthy	`src/cdwagent/config.py`
`sql_log.py`	software	healthy	`src/cdwagent/sql_log.py`
`db.py`	software	healthy	`src/cdwagent/db.py`
`notes.py`	software	healthy	`src/cdwagent/tools/notes.py`
`__init__.py`	software	healthy	`src/cdwagent/tools/__init__.py`
`stats.py`	software	healthy	`src/cdwagent/tools/stats.py`
`queries.py`	software	healthy	`src/cdwagent/tools/queries.py`
`export.py`	software	healthy	`src/cdwagent/tools/export.py`
`concepts.py`	software	healthy	`src/cdwagent/tools/concepts.py`
`schema.py`	software	healthy	`src/cdwagent/tools/schema.py`
`BIOROUTER.md`	software	healthy	`docs/BIOROUTER.md`
`biorouter-cdwagent.md`	software	healthy	`docs/upstream/biorouter-cdwagent.md`
`05-disambiguation-matrix.md`	software	healthy	`docs/agent-flows/05-disambiguation-matrix.md`
`INDEX.md`	software	healthy	`docs/agent-flows/INDEX.md`
`04-schema-interaction-map.md`	software	healthy	`docs/agent-flows/04-schema-interaction-map.md`
`01-routing-decision-tree.md`	software	healthy	`docs/agent-flows/01-routing-decision-tree.md`
`18-omop-cdw-bridge.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/18-omop-cdw-bridge.md`
`16-care-gap-detection.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/16-care-gap-detectio…`
`01-cohort-by-codes.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/01-cohort-by-codes.md`
`02-cohort-by-phenotype.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/02-cohort-by-phenoty…`
`11-notes-phenotype-extraction.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/11-notes-phenotype-e…`
`13-stratified-disparities.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/13-stratified-dispar…`
`14-vulnerable-population.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/14-vulnerable-popula…`
`06-drug-exposure-trajectory.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/06-drug-exposure-tra…`
`README.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/README.md`
`04-time-restricted-cohort.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/04-time-restricted-c…`
`12-sdoh-research.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/12-sdoh-research.md`
`15-trial-feasibility.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/15-trial-feasibility…`
`08-healthcare-utilization.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/08-healthcare-utiliz…`
`03-multi-criteria-cohort.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/03-multi-criteria-co…`
`09-adverse-drug-event.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/09-adverse-drug-even…`
`19-write-rejection.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/19-write-rejection.md`
`05-lab-trajectory.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/05-lab-trajectory.md`
`10-polypharmacy.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/10-polypharmacy.md`
`17-readmission-analysis.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/17-readmission-analy…`
`07-disease-progression.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/07-disease-progressi…`
`20-disambiguation.md`	software	healthy	`docs/agent-flows/03-clinical-workflows/20-disambiguation.md`

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

Label	Layer	Status	Path
`parse_data_dictionary`	software	healthy	`scripts/parse_data_dictionary.py:9`
`_is_write_query`	software	healthy	`src/cdwagent/validation.py:6`
`_strip_comments`	software	healthy	`src/cdwagent/validation.py:18`
`is_read_only_clinical_query`	software	healthy	`src/cdwagent/validation.py:23`
`main`	software	healthy	`src/cdwagent/cli.py:11`
`_format_namespace`	software	healthy	`src/cdwagent/server.py:149`
`create_cdw_server`	software	healthy	`src/cdwagent/server.py:156`
`clinical_data_exploration`	software	healthy	`src/cdwagent/server.py:177`
`cohort_building`	software	healthy	`src/cdwagent/server.py:202`
`notes_analysis`	software	healthy	`src/cdwagent/server.py:241`
`main`	software	healthy	`src/cdwagent/server.py:260`
`_default_log_path`	software	healthy	`src/cdwagent/sql_log.py:27`
`log_sql`	software	dead	`src/cdwagent/sql_log.py:35`
`get_log_path`	software	dead	`src/cdwagent/sql_log.py:48`
`get_connection`	software	healthy	`src/cdwagent/db.py:13`
`_query_to_csv`	software	healthy	`src/cdwagent/tools/notes.py:42`
`_validate_cohort`	software	healthy	`src/cdwagent/tools/notes.py:65`
`_cohort_in_clause`	software	healthy	`src/cdwagent/tools/notes.py:83`
`_escape_keyword`	software	healthy	`src/cdwagent/tools/notes.py:88`
`register_notes_tools`	software	healthy	`src/cdwagent/tools/notes.py:95`
`search_note_concepts`	software	healthy	`src/cdwagent/tools/notes.py:116`
`search_note_sdoh`	software	healthy	`src/cdwagent/tools/notes.py:308`
`search_notes`	software	healthy	`src/cdwagent/tools/notes.py:409`
`get_note`	software	healthy	`src/cdwagent/tools/notes.py:484`
`register_stats_tools`	software	healthy	`src/cdwagent/tools/stats.py:19`
`summarize_table`	software	healthy	`src/cdwagent/tools/stats.py:32`
`cohort_summary`	software	healthy	`src/cdwagent/tools/stats.py:84`
`_execute_readonly_query`	software	healthy	`src/cdwagent/tools/queries.py:21`
`register_query_tools`	software	healthy	`src/cdwagent/tools/queries.py:47`
`query`	software	healthy	`src/cdwagent/tools/queries.py:60`
`get_patient_demographics`	software	healthy	`src/cdwagent/tools/queries.py:99`
`crossmap_patient`	software	healthy	`src/cdwagent/tools/queries.py:130`
`get_encounters`	software	healthy	`src/cdwagent/tools/queries.py:182`
`get_medications`	software	healthy	`src/cdwagent/tools/queries.py:207`
`get_diagnoses`	software	healthy	`src/cdwagent/tools/queries.py:232`
`get_labs`	software	healthy	`src/cdwagent/tools/queries.py:255`
`register_export_tools`	software	healthy	`src/cdwagent/tools/export.py:21`
`export_query_to_csv`	software	healthy	`src/cdwagent/tools/export.py:34`
`_run_query`	software	healthy	`src/cdwagent/tools/concepts.py:19`
`register_concept_tools`	software	healthy	`src/cdwagent/tools/concepts.py:40`
`search_diagnoses_by_code`	software	healthy	`src/cdwagent/tools/concepts.py:53`
`search_medications_by_code`	software	healthy	`src/cdwagent/tools/concepts.py:81`
`search_labs_by_code`	software	healthy	`src/cdwagent/tools/concepts.py:108`
`search_procedures_by_code`	software	healthy	`src/cdwagent/tools/concepts.py:142`
`_get_schema_ref`	software	healthy	`src/cdwagent/tools/schema.py:19`
`register_schema_tools`	software	healthy	`src/cdwagent/tools/schema.py:29`
`get_database_overview`	software	healthy	`src/cdwagent/tools/schema.py:42`
`describe_table`	software	healthy	`src/cdwagent/tools/schema.py:97`
`search_schema`	software	healthy	`src/cdwagent/tools/schema.py:133`

Label	Layer	Status	Path
`scripts`	software	healthy	`scripts`
`.github`	software	healthy	`.github`
`workflows`	software	healthy	`.github/workflows`
`src`	software	healthy	`src`
`cdwagent`	software	healthy	`src/cdwagent`
`tools`	software	healthy	`src/cdwagent/tools`
`docs`	software	healthy	`docs`
`upstream`	software	healthy	`docs/upstream`
`agent-flows`	software	healthy	`docs/agent-flows`
`03-clinical-workflows`	software	healthy	`docs/agent-flows/03-clinical-workflows`
`02-tool-flows`	software	healthy	`docs/agent-flows/02-tool-flows`

Label	Layer	Status	Path
`ClinicalQueryValidator`	software	healthy	`src/cdwagent/validation.py:14`
`ClinicalDBConfig`	software	healthy	`src/cdwagent/config.py:13`
`CDWConfig`	software	healthy	`src/cdwagent/config.py:21`

Label	Layer	Status	Path
`vps::azure`	hardware	healthy	`README.md`
`vps::aws`	hardware	healthy	`README.md`

Label	Layer	Status	Path
`BaranziniLab__CDWAgent`	software	healthy	`/data/fable5_failed_archive/BaranziniLab__CDWAgent`

Label	Layer	Status	Path
`127.0.0.1`	network	healthy	`src/cdwagent/server.py`

Label	Layer	Status	Path
`password_literal::README.md`	security	healthy	`README.md`

Label	Layer	Status	Path
`gha::ci`	cicd	healthy	`.github/workflows/ci.yml`

Label	Layer	Status	Path
`smoke`	cicd	healthy	`.github/workflows/ci.yml`

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BaranziniLab/CDWAgent

Complete repo analysis

file 50+

function 49

directory 11

class 3

vps 2

repo 1

service 1

secret 1

pipeline 1

job 1