pulse-code 1.0.1__py3-none-any.whl

pulse/wonder_client.py

@@ -0,0 +1,161 @@
+"""CDC WONDER HTTP client and response parser."""
+
+from __future__ import annotations
+
+import re
+import xml.etree.ElementTree as ET
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any, Optional
+
+import requests
+
+
+@dataclass
+class ResponseCell:
+    label: Optional[str] = None
+    value: Optional[str] = None
+    data_total: Optional[str] = None
+
+    def numeric(self) -> Optional[float]:
+        raw = self.value or self.data_total
+        if raw is None:
+            return None
+        try:
+            return float(raw.replace(",", ""))
+        except ValueError, AttributeError:
+            return None
+
+
+@dataclass
+class ResponseRow:
+    cells: list[ResponseCell]
+    is_total: bool = False
+
+
+class WonderClient:
+    BASE_URL = "https://wonder.cdc.gov/controller/datarequest"
+
+    def __init__(self, timeout: int = 120) -> None:
+        self.timeout = timeout
+        self.session = requests.Session()
+
+    def query_from_xml(self, dataset_id: str, xml: str) -> str:
+        data = {"request_xml": xml, "accept_datause_restrictions": "true"}
+        resp = self.session.post(
+            f"{self.BASE_URL}/{dataset_id}", data=data, timeout=self.timeout
+        )
+        if resp.status_code != 200:
+            raise RuntimeError(
+                f"CDC WONDER returned HTTP {resp.status_code}: {resp.text[:400]}"
+            )
+        return resp.text
+
+    def execute_file(self, path: str | Path) -> str:
+        xml = Path(path).read_text()
+        dataset_id = self._extract_dataset_id(xml)
+        if not dataset_id:
+            raise ValueError(f"Could not find dataset_code in {path}")
+        return self.query_from_xml(dataset_id, xml)
+
+    @staticmethod
+    def _extract_dataset_id(xml: str) -> Optional[str]:
+        try:
+            root = ET.fromstring(xml)
+            el = root.find(".//parameter[name='dataset_code']/value")
+            return el.text if el is not None else None
+        except ET.ParseError:
+            return None
+
+    def parse_rows(self, xml: str) -> list[ResponseRow]:
+        root = ET.fromstring(xml)
+        table = root.find(".//data-table")
+        if table is None:
+            raise ValueError("No <data-table> found in CDC WONDER response")
+
+        rows: list[ResponseRow] = []
+        for r in table.findall("r"):
+            cells = []
+            is_total = False
+            for c in r.findall("c"):
+                dt = c.get("dt")
+                if dt is not None:
+                    is_total = True
+                cells.append(
+                    ResponseCell(label=c.get("l"), value=c.get("v"), data_total=dt)
+                )
+            rows.append(ResponseRow(cells=cells, is_total=is_total))
+        return rows
+
+    def get_headers(self, xml: str) -> list[str]:
+        root = ET.fromstring(xml)
+        var_labels: dict[str, str] = {}
+        for var in root.findall(".//*[@code]"):
+            code = var.get("code")
+            label = var.get("label")
+            if code and label:
+                var_labels[code] = label
+            for hier in var.findall("hier-level"):
+                h_code = hier.get("code")
+                h_label = hier.get("label")
+                if h_code and h_label:
+                    var_labels[h_code] = h_label
+
+        headers: list[str] = []
+        byvars = root.find(".//byvariables")
+        if byvars is not None:
+            for bv in byvars.findall("variable"):
+                code = bv.get("code")
+                headers.append(var_labels.get(code, code or ""))
+
+        measure_labels: dict[str, str] = {}
+        for m in root.findall(".//measure[@code]"):
+            c = m.get("code")
+            label = m.get("label")
+            if c and label:
+                measure_labels[c] = label
+
+        ms = root.find(".//response//measure-selections")
+        if ms is not None:
+            for m in ms.findall("measure"):
+                c = m.get("code")
+                if c and not re.search(r"\.M\d{2,}$", c):
+                    headers.append(measure_labels.get(c, c or ""))
+
+        return headers or [f"Col {i + 1}" for i in range(6)]
+
+    def to_records(self, xml: str) -> list[dict[str, Any]]:
+        headers = self.get_headers(xml)
+        rows = self.parse_rows(xml)
+        records = []
+        for row in rows:
+            record: dict[str, Any] = {}
+            for i, cell in enumerate(row.cells):
+                key = headers[i] if i < len(headers) else f"col_{i}"
+                if cell.label:
+                    record[key] = cell.label
+                else:
+                    num = cell.numeric()
+                    record[key] = (
+                        num if num is not None else (cell.value or cell.data_total)
+                    )
+            if record:
+                records.append(record)
+        return records
+
+    def to_arrays(self, xml: str) -> tuple[list[str], list[list[Any]]]:
+        headers = self.get_headers(xml)
+        rows = self.parse_rows(xml)
+        data: list[list[Any]] = []
+        for row in rows:
+            r: list[Any] = []
+            for cell in row.cells:
+                if cell.label:
+                    r.append(cell.label)
+                else:
+                    num = cell.numeric()
+                    r.append(
+                        num if num is not None else (cell.value or cell.data_total)
+                    )
+            data.append(r)
+        return headers, data

pulse_code-1.0.1.dist-info/METADATA

@@ -0,0 +1,249 @@
+Metadata-Version: 2.4
+Name: pulse-code
+Version: 1.0.1
+Summary: CDC WONDER query CLI — explore, build, and refine public health data queries
+Requires-Python: >=3.14
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: anthropic==0.115.1
+Requires-Dist: openai==2.44.0
+Requires-Dist: pydantic==2.13.4
+Requires-Dist: python-dotenv==1.2.2
+Requires-Dist: requests==2.34.2
+Requires-Dist: rich==15.0.0
+Requires-Dist: socksio==1.0.0
+Requires-Dist: typer==0.26.8
+Dynamic: license-file
+
+# pulse
+
+CDC WONDER public health query CLI — explore datasets, run bundled queries, and use Claude to build and refine custom XML queries for public health data that Americans should care about.
+
+## What is this?
+
+[CDC WONDER](https://wonder.cdc.gov/) (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
+
+## Setup
+
+```bash
+# Install (requires Python 3.12+)
+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`):
+
+```bash
+# 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):
+
+```bash
+export LLM_HTTP_PROXY=socks5h://user:pass@host:port
+```
+
+## Commands
+
+### `pulse datasets` — what's available
+
+```bash
+pulse datasets                    # all datasets
+pulse datasets --topic Mortality  # filter by topic
+pulse 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 info <ID>` — deep dive on a dataset
+
+```bash
+pulse info D176    # Provisional Mortality (2018–present)
+pulse info D66     # Natality / birth data
+pulse 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
+
+```bash
+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 list-queries` — all bundled example queries
+
+```bash
+pulse list-queries
+pulse 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 run <query>` — execute a query
+
+```bash
+# Run a bundled query by filename (no path needed)
+pulse run drug-deaths-by-year-2018-2024-req.xml
+
+# Output formats
+pulse run opioid-overdose-deaths-2018-2024-req.xml -f csv
+pulse run mortality-by-year-cause-2021-2024-req.xml -f json
+pulse run births-by-year-2007-2024-req.xml -f table -o births.csv
+
+# Run your own query file
+pulse run /path/to/my-query.xml
+```
+
+Hits the live CDC WONDER API. No login required; CDC requires a ~2-minute cooldown between queries.
+
+### `pulse build "<description>"` — build a query with Claude
+
+```bash
+# Requires ANTHROPIC_API_KEY
+pulse build "drug overdose deaths by state and year 2018-2023"
+pulse build "maternal mortality by race, 2018-2023" -o maternal-race.xml
+pulse 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 query "<description>"` — build and run in one step
+
+```bash
+pulse query "fentanyl deaths by state 2020-2024" -f csv
+pulse query "infant mortality by race 2018-2023" --save-xml infant-race.xml
+```
+
+### `pulse refine <file> "<feedback>"` — iterate on a query
+
+```bash
+pulse refine opioid-overdose-deaths-2018-2024-req.xml "break it down by state"
+pulse refine drug-deaths-by-year-2018-2024-req.xml "add sex breakdown" -o drug-sex.xml
+pulse refine drug-deaths-by-year-2018-2024-req.xml "show monthly not yearly" --run -f csv
+```
+
+## Testing
+
+```bash
+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 genuinely 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)
+
+| ID | Subject | Years |
+|----|---------|-------|
+| D176 | Provisional mortality — opioids, COVID, suicide, heart disease | 2018–present |
+| D157 | Final mortality, single race (MCD+UCD) | 2018–2023 |
+| D158 | Underlying cause of death, single race — maternal mortality | 2018–2023 |
+| D77 | Multiple cause of death — drug deaths (historical) | 1999–2020 |
+| D76 | Underlying cause of death — suicide, cancer (historical) | 1999–2020 |
+| D141 | MCD with US-Mexico border regions | 1999–2020 |
+| D140 | Compressed mortality ICD-10 | 1999–2016 |
+| D16 | Compressed mortality ICD-9 | 1979–1998 |
+| D74 | Compressed mortality ICD-8 | 1968–1978 |
+| D69 | Linked birth/infant death records | 2007–2023 |
+| D159 | Linked birth/infant death, expanded race | 2017–2023 |
+| D31/D18/D23 | Linked birth/infant death (historical) | 1995–2006 |
+| D66 | Natality — birth rates, birth outcomes | 2007–2024 |
+| D149 | Natality, expanded race detail | 2016–2024 |
+| D192 | Provisional natality (monthly) | 2023–present |
+| D27/D10 | Natality (historical) | 1995–2006 |
+| D8 | VAERS vaccine adverse events | 1990–present |
+| D104 | Heat wave days by county | 1981–2010 |
+| D60/D80/D81 | NLDAS temperature, sunlight, precipitation | 1979–2011 |
+| D73 | PM2.5 fine particulate matter | 2003–2011 |
+| D61 | MODIS land surface temperature | 2003–2008 |
+
+## 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 — no API tokens stored in the repo.
+
+The `needs:` chain means a failure at any step blocks everything after it —
+e.g. 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.
+
+## Based On
+
+Built using [fartbagxp/health](https://github.com/fartbagxp/health) as reference — a comprehensive collection of CDC data pipelines and the CDC WONDER XML API client and LLM query builder this tool builds on.

pulse_code-1.0.1.dist-info/RECORD

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+pulse_code-1.0.1.dist-info/licenses/LICENSE,sha256=ogEPNDSH0_dhiv_lT3ifVIdgIzHAqNA_SemnxUfPBJk,7048
+pulse_code-1.0.1.dist-info/METADATA,sha256=-0l2XjjcWEWdIJqo-jJuBFtgx1bSbCLtuZ5qSHr4Jtk,10388
+pulse_code-1.0.1.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+pulse_code-1.0.1.dist-info/entry_points.txt,sha256=8JmklTqLTsHiCLSeKJx-55gnt1mYNFfKuE2rwz3efyo,40
+pulse_code-1.0.1.dist-info/top_level.txt,sha256=gQdwpJBbAgjgx7qW49yUgv8h89nOedqh1oGgfnxmR_g,6
+pulse_code-1.0.1.dist-info/RECORD,,

pulse_code-1.0.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

pulse_code-1.0.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+pulse = pulse.cli:app

pulse_code-1.0.1.dist-info/licenses/LICENSE

@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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pulse_code-1.0.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+pulse