Pulse

CDC public health data query CLI. Explore datasets, run bundled queries, and use Claude to build and refine custom XML queries — across CDC WONDER, NCI SEER cancer statistics, CDC Open Data, WISQARS injury data, ATSDR GRASP disease surveillance, NSSP ED visits, and NIS vaccination surveys.

What is this?

CDC WONDER (Wide-ranging ONline Data for Epidemiologic Research) is the government's primary interface for public health statistics: drug overdose deaths, maternal mortality, birth rates, COVID deaths by race, suicide trends, vaccine adverse events, and much more. Its XML API is powerful but opaque.

pulse makes it usable:

• Explore all datasets with clear descriptions of what they cover and when
• Search by topic to find the right dataset or a working example query
• Run bundled, validated XML queries directly against the CDC API
• Build new queries from natural language using Claude
• Refine existing queries with conversational feedback

Beyond WONDER, pulse gives direct access to six more live CDC/NCI/ATSDR sources — no LLM required for those, just a dataset lookup and a query: seer, cdc-open, wisqars, grasp, nssp, and nis.

Setup

# From PyPI (requires Python 3.14+)
pip install pulse-code

# Or from source
uv sync

# For build/query/refine/compare/chat commands, set your Anthropic API key:
export ANTHROPIC_API_KEY=sk-ant-...
# or put it in a .env file:
echo "ANTHROPIC_API_KEY=sk-ant-..." > .env

LLM provider

pulse defaults to Anthropic Claude but can also run against an Azure OpenAI Foundry deployment (e.g. GPT-5.4). Select the provider with LLM_PROVIDER (defaults to anthropic):

# Anthropic (default), needs ANTHROPIC_API_KEY as above

# Azure OpenAI Foundry
export LLM_PROVIDER=azure_openai
export AZURE_OPENAI_API_KEY=...
export AZURE_OPENAI_ENDPOINT=https://<your-resource>.openai.azure.com
export AZURE_OPENAI_DEPLOYMENT=<your-gpt-5.4-deployment-name>
export AZURE_OPENAI_API_VERSION=<api-version-your-resource-supports>

All four AZURE_OPENAI_* variables are required when LLM_PROVIDER=azure_openai; pulse will tell you which ones are missing. These can also go in a .env file alongside ANTHROPIC_API_KEY.

If the LLM endpoint isn't directly reachable (e.g. an Azure OpenAI resource with public network access disabled, requiring a private endpoint), bridge the connection through a proxy with LLM_HTTP_PROXY. Applies to both providers, and supports http://, https://, socks5://, and socks5h:// (DNS resolved through the proxy):

export LLM_HTTP_PROXY=socks5h://user:pass@host:port

Commands

The CLI has five top-level commands: topics (browse by subject across all sources), source (browse/query one source), search (free-text find), plus doctor and generate. Every data source lives under source: pulse source for an overview, pulse source <name> for its datasets, and pulse source <name> <verb> … to query it (e.g. pulse source seer mortality).

pulse source wonder datasets — what's available

pulse source wonder datasets                    # all datasets
pulse source wonder datasets --topic Mortality  # filter by topic
pulse source wonder datasets --json             # JSON output

Shows all 26+ CDC WONDER datasets with: topic, year range, what the data covers, number of bundled example queries, and whether age-adjusted rates are available.

Topics: Mortality · Infant Mortality · Natality · Environment · Vaccine Safety · Infectious Disease

pulse source wonder info <ID> — deep dive on a dataset

pulse source wonder info D176    # Provisional Mortality (2018–present)
pulse source wonder info D66     # Natality / birth data
pulse source wonder info D8      # VAERS vaccine adverse events

Shows: subject description, available measures, key grouping dimensions, and all bundled example queries for that dataset.

pulse search "<topic>" — find what you need

pulse search "opioid overdose deaths by state"
pulse search "maternal mortality by race"
pulse search "birth rates 2010 to 2020"
pulse search "tick-borne disease cases" --queries   # queries only
pulse search "recent COVID deaths" --datasets       # datasets only

pulse source wonder list-queries — all bundled example queries

pulse source wonder list-queries
pulse source wonder list-queries --dataset D176   # filter by dataset

23 working XML queries covering: drug/opioid/fentanyl deaths, maternal mortality, births, COVID deaths by race, suicide, tick-borne diseases, racial mortality gap, infant mortality, heart disease vs. cancer, and more.

pulse source seer — NCI SEER cancer statistics

pulse source seer sites --search breast              # look up a cancer site code
pulse source seer mortality --site 55 --sex female -f csv
pulse source seer mortality --site 47 --compare-by race -f csv
pulse source seer incidence --site 55 --stage 104 -f csv
pulse source seer by-age --site 1 -f csv
pulse source seer compare-sites 55 47 66 -f csv       # breast vs. lung vs. melanoma

Cancer incidence and U.S. mortality rates/counts by site, sex, race, and age group, back to 1975 — calls the same unauthenticated JSON endpoints SEER*Explorer itself uses. No API key needed.

pulse source cdc-open — CDC Open Data (data.cdc.gov)

pulse source cdc-open list                            # 60+ datasets: mortality, vaccination, wastewater, NNDSS, HAI, and more
pulse source cdc-open list --search wastewater
pulse source cdc-open query leading_death --where "year='2015'" -f csv
pulse source cdc-open query bi63-dtpu --where "state='California'" --limit 500 -f json

Raw SODA queries (--where, --select, --group, --order) against any of the registered Socrata datasets, by registry key or by Socrata ID directly. No API key needed (set CDC_DATA_APP_TOKEN for a higher rate limit).

pulse source wisqars — WISQARS injury & violence data

pulse source wisqars list
pulse source wisqars mortality --intent Suicide --mechanism Firearm -f csv       # 1999-2016
pulse source wisqars national --intent FA_Deaths --type year -f csv             # 2019-present
pulse source wisqars state --intent Drug_OD --year 2023 -f table
pulse source wisqars county --state Texas --intent FA_Deaths --year 2023
pulse source wisqars tract --state Texas --intent All_Homicide --year 2022      # census-tract granularity
pulse source wisqars query t6u2-f84c --where "intent='Drug_OD' AND type='year'"

Fatal firearm/suicide/homicide/drug-overdose data from WISQARS at national, state, county, and census-tract granularity, backed by data.cdc.gov Socrata datasets (same client as cdc-open). No API key needed.

pulse source grasp — ATSDR GRASP disease surveillance

pulse source grasp list
pulse source grasp hantavirus cases --outcome Dead -f table              # pre-1993-present
pulse source grasp hantavirus by-year -f table
pulse source grasp hantavirus by-state -f table
pulse source grasp fluview ili-data --region nat --region ca --region tx --epiweeks 202001-202026
pulse source grasp fluview ili-by-region --epiweeks 201940-202020 -f table
pulse source grasp fluview clinical-data --region nat --epiweeks 202001-202026
pulse source grasp flusurv data --location CA --location OH --epiweeks 202001-202020 -f csv
pulse source grasp flusurv by-season --location CA -f table
pulse source grasp flusurv by-location --season 2019-20 -f table

Hantavirus case data, FluView ILINet influenza-like-illness activity, WHO/NREVSS clinical lab flu positivity, and FluSurv-NET hospitalization rates — sourced from gis.cdc.gov/grasp and the CMU Delphi Epidata API. No API key needed. Note: repeatable options like --region/--location take one value per flag (--region nat --region ca), unlike health's argparse CLI which accepts space-separated lists after a single flag.

pulse source nssp — emergency department visit surveillance

pulse source nssp query covid --geo-type state --geo-value ca -f csv
pulse source nssp query influenza --geo-type nation --geo-value us
pulse source nssp national --start 202401 -f csv                # all 4 pathogens, national
pulse source nssp hhs rsv --region 4 -f table

Weekly % of ED visits attributed to COVID/flu/RSV from the National Syndromic Surveillance Program, via the CMU Delphi Epidata API. Time values use epiweek format (YYYYWW, e.g. 202518 = week 18 of 2025). No API key needed.

pulse source nis — National Immunization Survey (vaccination coverage)

pulse source nis list child                                       # available years, 2011-2022
pulse source nis stream child 2022 --limit 10 -f json              # raw respondent microdata
pulse source nis rates child 2022 -f table                         # state-level UTD rates
pulse source nis rates teen 2022 --vaccines P_UTDHPV13 -f csv
pulse source nis national child 2022                                # national UTD summary

Childhood (19–35mo) and teen (13–17yr) vaccination coverage from CDC's annual random-digit-dial survey. Files are large fixed-width .dat files (50–200MB) streamed directly — nothing is written to disk. Known issue: CDC has restructured its NIS file hosting since this registry's URLs were last verified (some years now live under www.cdc.gov/nis/media/files/... or ftp.cdc.gov/pub/Vaccines_NIS/ instead of the legacy ftp.cdc.gov/.../nis/NISPUF{YY}-formats.sas path baked into nis_catalog.py), so live stream/rates/national calls currently 404 for at least the 2015+ years — the same pre-existing gap affects health's own nis module. The CLI plumbing and DAT-streaming parser are unit-tested and correct; only the hardcoded per-year URLs need refreshing against CDC's current hosting.

pulse source wonder run <query> — execute a query

# Run a bundled query by filename (no path needed)
pulse source wonder run drug-deaths-by-year-2018-2024-req.xml

# Output formats
pulse source wonder run opioid-overdose-deaths-2018-2024-req.xml -f csv
pulse source wonder run mortality-by-year-cause-2021-2024-req.xml -f json
pulse source wonder run births-by-year-2007-2024-req.xml -f table -o births.csv

# Run your own query file
pulse source wonder run /path/to/my-query.xml

Hits the live CDC WONDER API. No login required; CDC requires a ~2-minute cooldown between queries.

pulse source wonder build "<description>" — build a query with Claude

# Requires ANTHROPIC_API_KEY
pulse source wonder build "drug overdose deaths by state and year 2018-2023"
pulse source wonder build "maternal mortality by race, 2018-2023" -o maternal-race.xml
pulse source wonder build "birth rates by age of mother 2010 to 2024" --no-suggest

Suggests closest existing queries first, then calls Claude to build a new XML query. The LLM selects the right dataset and generates overrides merged onto a validated base template.

pulse source wonder query "<description>" — build and run in one step

pulse source wonder query "fentanyl deaths by state 2020-2024" -f csv
pulse source wonder query "infant mortality by race 2018-2023" --save-xml infant-race.xml

pulse source wonder refine <file> "<feedback>" — iterate on a query

pulse source wonder refine opioid-overdose-deaths-2018-2024-req.xml "break it down by state"
pulse source wonder refine drug-deaths-by-year-2018-2024-req.xml "add sex breakdown" -o drug-sex.xml
pulse source wonder refine drug-deaths-by-year-2018-2024-req.xml "show monthly not yearly" --run -f csv

Testing

uv run pytest                  # unit tests only, fast, no network (default)
uv run pytest -m integration   # + integration tests (see below)

Unit tests cover catalog/matcher lookups, XML template merging (including the CDC WONDER radio-button-trap regression), AAR constraints, provider selection, and the offline-network-free CLI commands.

Integration tests (tests/integration/) are excluded by default and split into two kinds:

• test_socks_proxy_integration.py: always runs. Spins up a local SOCKS5 relay and a local mock LLM HTTP server, so it actually exercises LLM_HTTP_PROXY end-to-end (real SOCKS handshake, real HTTP request/response) without needing real Azure/Anthropic credentials.
• test_llm_provider_live.py: hits whatever ANTHROPIC_API_KEY / LLM_PROVIDER=azure_openai + AZURE_OPENAI_* / LLM_HTTP_PROXY you actually have configured. Skips if credentials aren't set; also skips (rather than fails) if the provider is reachable but blocked at the network layer (e.g. an Azure OpenAI resource with public access disabled and no working proxy). That's an environment gap, not a code defect.

Bundled Datasets (with base templates)

Public Health Questions You Can Answer

• How did opioid overdose deaths trend from 1999 to today, broken down by drug type?
• What is the racial gap in COVID-19 mortality?
• How does maternal mortality differ by race and state?
• Which states have the highest suicide rates by sex?
• How have birth rates changed by age of mother since 1995?
• Are tick-borne disease cases increasing?
• How do PM2.5 air quality levels correlate with where people live?
• What are the most common adverse events reported after COVID vaccines?

Releasing

Releases are cut by pushing a tag. publish.yml (single workflow, one run per tag) handles the rest as three sequential jobs:

1. Bump version in pyproject.toml, commit it.
2. git tag vX.Y.Z && git push origin vX.Y.Z
3. build builds the sdist/wheel, failing fast if the tag doesn't match pyproject.toml's version.
4. release (needs build) creates the GitHub Release with the built artifacts attached, the source of truth for what shipped.
5. publish (needs release) publishes those same artifacts to PyPI (pulse-code) via trusted publishing (OIDC) against the prod environment, with no API tokens stored in the repo.

The needs: chain means a failure at any step blocks everything after it. For example, a PyPI hiccup can't leave a GitHub Release around for a package that isn't actually installable. If the publish job fails after release succeeds, use "Re-run failed jobs" on that workflow run rather than re-tagging. PyPI publishing is immutable: once a version is published it can't be re-uploaded, so a bad release means bumping to a new version.

Related projects

pulse is the exploration layer of a three-repo pipeline:

pulse-code  →  health  →  health-charts
(explore)      (archive)   (visualize)

• fartbagxp/health, a collection of CDC data pipelines (WONDER, data.cdc.gov, NCHS, SEER, WISQARS, GRASP, NSSP, NIS, and more) and the CDC WONDER XML API client and LLM query builder this tool builds on. pulse's SEER, CDC Open Data, WISQARS, GRASP, NSSP, and NIS clients are lightweight, standalone reimplementations of health's equivalent modules — kept dependency-free (just requests) rather than depending on health directly, which also pulls in pandas/playwright/lxml for its archival pipelines. pulse now covers every source health does. Where pulse is for one-off, ad hoc exploration, health is where a query graduates once someone wants it archived on a recurring schedule: 23 of the 36 saved WONDER queries in src/pulse/queries/ are also saved in health's src/wonder/queries/, each wrapped there in a small fetch_*.py script that runs on a schedule and commits the result as a CSV under data/raw/wonder/. The other 13 (cancer incidence/mortality by site, fetal deaths, PM2.5, TB, STI cases, heat-wave days, etc.) are exploration-only for now, candidates for health if any of them turn into a recurring need.
• fartbagxp/health-charts, the dashboard at the end of the pipeline. It reads the CSVs health archives (including the ones seeded by pulse's queries above) directly from GitHub and renders them as an interactive chart site.