pp-clinical-trials — mvanhorn/printing-press-libra…

Oryginalny dokument Skill

Treść z repozytorium z zachowaniem nagłówków, przykładów, kodu, tabel, linków i obrazów.

ClinicalTrials.gov — Printing Press CLI

Prerequisites: Install the CLI

This skill drives the clinical-trials-pp-cli binary. You must verify the CLI is installed before invoking any command from this skill. If it is missing, install it first:

Install via the Printing Press installer. It defaults binaries to $HOME/.local/bin on macOS/Linux and %LOCALAPPDATA%\Programs\PrintingPress\bin on Windows:

bash

   npx -y @mvanhorn/printing-press-library install clinical-trials --cli-only

Verify: clinical-trials-pp-cli --version
Ensure the reported install directory is on $PATH for the agent/runtime that will invoke this skill.

If the npx install fails (no Node, offline, etc.), fall back to a direct Go install (requires Go 1.26.6 or newer). This installs into $GOPATH/bin (default $HOME/go/bin), so add that directory to $PATH instead:

bash

go install github.com/mvanhorn/printing-press-library/library/health/clinical-trials/cmd/clinical-trials-pp-cli@latest

If --version reports "command not found" after install, the runtime cannot see the binary directory on $PATH. Do not proceed with skill commands until verification succeeds.

Every other ClinicalTrials.gov tool is a single-source pass-through. This one merges registries into one normalized trial model, dedups across NCT/EUCTR/WHO IDs, and computes intelligence: emerging therapies, recruitment velocity, drug comparisons, abandonment risk, geographic hotspots, and sponsor dominance. It degrades gracefully down a fallback chain and never crashes, caching everything locally for offline, agent-native analysis.

When to Use This CLI

Reach for this CLI when the task is understanding the clinical-trials landscape — what is running, what is emerging, how two drugs compare, whether a trial is risky, or where recruitment is concentrated — across more than one registry. It is the right tool for evidence synthesis, competitive trial analysis, and weekly landscape reports.

Anti-triggers

Do not use this CLI for:

Do not use it to enroll patients or submit trial registrations — it is read-only.
Do not use it for full EHR or patient-record data — it covers public trial registries only.
Do not use --source who expecting live data — WHO ICTRP has no public API.

Unique Capabilities

These capabilities aren't available in any other tool for this API.

Intelligence engine

`emerging` — See the fastest-growing trial categories for a disease area, with percent change.

Pick this when the user asks where research is heading, not about one specific trial.

bash

  clinical-trials-pp-cli emerging cancer --json

`velocity` — Measure how fast a disease area's trials and enrollment are growing over time.

Use to quantify momentum in a field; buckets a sampled set of trials by start year and reports a recent-vs-prior growth rate (no prior snapshot needed).

bash

  clinical-trials-pp-cli velocity "alzheimer" --json

`compare` — Compare two drugs head-to-head across trial counts, phases, sponsors, and recruiting status.

Use to weigh two interventions by real trial activity, not marketing.

bash

  clinical-trials-pp-cli compare "Keytruda" "Opdivo" --json

`risk` — Get an explainable risk read on a single trial from termination, enrollment, site count, sponsor track record, and phase factor (earlier phases = higher risk).

Use to triage whether a trial is likely to complete and report.

bash

  clinical-trials-pp-cli risk NCT07011732 --json

`forecast` — Forward-looking completion outlook for a trial, derived from the same deterministic signals as risk.

Use to get a plain-language outlook band and the primary concerns behind it. **Caveat:** heuristic only — a read of registry signals, not a clinical prediction.

bash

  clinical-trials-pp-cli forecast NCT07011732 --json

`sponsors` — Rank who runs the most trials in an area, classified as industry, academic, or government.

Use to see who controls research in a field.

bash

  clinical-trials-pp-cli sponsors "diabetes" --json

`digest` — Compact "what's notable" snapshot for a condition or search term: total matched, recruiting count, newest trials, and recently-stopped ones.

Use for a fast read on a topic's current state; a read-only point-in-time snapshot (use `watch` for a persistent change feed). `--limit` bounds the newest and recently-stopped lists.

bash

  clinical-trials-pp-cli digest "type 2 diabetes" --limit 5 --json

Single-trial analysis

`similar` — Find trials similar to a given NCT ID by shared condition, phase, and intervention profile.

Use to surface comparable trials from registry signals only (no ML matching); `--limit` caps how many matches are returned.

bash

  clinical-trials-pp-cli similar NCT04280705 --limit 5 --json

`timeline` — Show a trial's key dates in chronological order: start, primary completion, completion, and last-update posted.

Use to see a single trial's schedule at a glance; dates with no posted value are omitted.

bash

  clinical-trials-pp-cli timeline NCT04280705 --json

`enrollment-check` — Heuristic plausibility check on a trial's posted enrollment target relative to its phase.

Reuses the `risk` command's enrollment signal. **Caveat:** this is a heuristic from observable registry signals only — not a clinical judgment or a prediction of whether the trial will enroll.

bash

  clinical-trials-pp-cli enrollment-check NCT04280705 --json

Interoperability

`export-fhir` — Export a trial's registry metadata as a minimal FHIR R4 ResearchStudy resource (JSON) or a flat CSV row.

Use to hand a trial's core metadata to a FHIR-aware system or a spreadsheet. `--format fhir` (default) emits the ResearchStudy JSON; `--format csv` emits one flat row. **Caveat:** this is a lightweight metadata export, not a full FHIR-conformant clinical dataset, and is not validated against a FHIR profile.

bash

  clinical-trials-pp-cli export-fhir NCT04280705
  clinical-trials-pp-cli export-fhir NCT04280705 --format csv

Local state that compounds

`watch` — Track a term and report new, changed, and terminated trials since the last run.

Use to monitor a topic over time instead of re-reading full result sets.

bash

  clinical-trials-pp-cli watch "vitamin d" --json

Multi-source aggregation

`search` — Search a single normalized trial model aggregated and deduplicated across ClinicalTrials.gov, EU CTIS, and OpenAlex.

Use as the default entry point; it queries the merged multi-source mirror, so it sees more than any single registry.

bash

  clinical-trials-pp-cli search "glioblastoma" --json

Enrichment

`evidence` — Link a trial to its publications and citation context via PubMed and OpenAlex.

Use to check whether a trial actually published results.

bash

  clinical-trials-pp-cli evidence NCT07011732 --json

`safety` — Surface FDA adverse-event signals for a trial's intervention drug.

Use to add a real-world safety lens to a trial's drug.

bash

  clinical-trials-pp-cli safety "pembrolizumab" --json

Output for humans

`report` — Compose search, emerging, hotspots, and sponsors into one markdown or CSV briefing for a topic.

Use for a weekly landscape summary a clinician can read at a glance.

bash

  clinical-trials-pp-cli report "long covid" --format md

Reliability

`health` — Show live status, latency, and failure rate for every data source in the fallback chain.

Use to know which sources are degraded before trusting a result.

bash

  clinical-trials-pp-cli health --json

Command Reference

clinicaltrials-gov-version — Manage clinicaltrials gov version

clinical-trials-pp-cli clinicaltrials-gov-version — API and data versions. API version follows Semantic Versioning 2.0.0 Schema.

stats — Data statistics

clinical-trials-pp-cli stats field-values — Value statistics of the study leaf fields.
clinical-trials-pp-cli stats list-field-sizes — Sizes of list/array fields. To search studies by a list field size, use AREA[FieldName:size] search operator.
clinical-trials-pp-cli stats size — Statistics of study JSON sizes.

studies — Related to clinical trial studies

clinical-trials-pp-cli studies enums — Returns enumeration types and their values.
clinical-trials-pp-cli studies fetch-study — Returns data of a single study.
clinical-trials-pp-cli studies list — Returns data of studies matching query and filter parameters. The studies are returned page by page.
clinical-trials-pp-cli studies metadata — Returns study data model fields.
clinical-trials-pp-cli studies search-areas — Search Docs and their Search Areas.

Finding the right command

When you know what you want to do but not which command does it, ask the CLI directly:

bash

clinical-trials-pp-cli which "<capability in your own words>"

which resolves a natural-language capability query to the best matching command from this CLI's curated feature index. Exit code 0 means at least one match; exit code 2 means no confident match — fall back to --help or use a narrower query.

Recipes

Bounded agent-friendly search

bash

clinical-trials-pp-cli search "glioblastoma" --json --limit 20

Searches the merged multi-source mirror and returns a bounded result set an agent can parse.

Emerging oncology

bash

clinical-trials-pp-cli emerging cancer --json

Ranks the fastest-growing oncology trial categories with percent change.

Head-to-head drug activity

bash

clinical-trials-pp-cli compare "pembrolizumab" "nivolumab" --json

Compares two drugs by trial counts, phases, and sponsors with RxNorm synonym resolution.

Triage a single trial

bash

clinical-trials-pp-cli risk NCT07011732 --json

Returns an explainable risk score with each contributing factor.

Weekly clinician report

bash

clinical-trials-pp-cli report "long covid" --format md

Composes search, emerging, hotspots, and sponsors into one markdown briefing.

Auth Setup

No credentials required for the core. ClinicalTrials.gov, EU CTIS, OpenAlex, RxNorm, and MeSH need no key. OpenFDA and PubMed accept an optional key purely for higher rate limits.

Run clinical-trials-pp-cli doctor to verify setup.

Agent Mode

Add --agent to any command. Expands to: --json --compact --no-input --no-color --yes.

Pipeable — JSON on stdout, errors on stderr
Filterable — --select keeps a subset of fields. Dotted paths descend into nested structures; arrays traverse element-wise. Critical for keeping context small on verbose APIs:

bash

  clinical-trials-pp-cli studies list --agent --select id,name,status

Previewable — --dry-run shows the request without sending
Offline-friendly — sync/search commands can use the local SQLite store when available
Non-interactive — never prompts, every input is a flag
Read-only — do not use this CLI for create, update, delete, publish, comment, upvote, invite, order, send, or other mutating requests

Response envelope

Commands that read from the local store or the API wrap output in a provenance envelope:

json

{
  "meta": {"source": "live" | "local", "synced_at": "...", "reason": "..."},
  "results": <data>
}

Parse .results for data and .meta.source to know whether it's live or local. A human-readable N results (live) summary is printed to stderr only when stdout is a terminal AND no machine-format flag (--json, --csv, --compact, --quiet, --plain, --select) is set — piped/agent consumers and explicit-format runs get pure JSON on stdout.

Paths and state

Agents should treat the CLI's path resolver as part of the runtime contract:

Use --home <dir> for one invocation, or set CLINICAL_TRIALS_HOME=<dir> to relocate all four path kinds under one root.
Use per-kind env vars only when a specific kind must diverge: CLINICAL_TRIALS_CONFIG_DIR, CLINICAL_TRIALS_DATA_DIR, CLINICAL_TRIALS_STATE_DIR, CLINICAL_TRIALS_CACHE_DIR.
Resolution order is per-kind env var, --home, CLINICAL_TRIALS_HOME, XDG (XDG_CONFIG_HOME, XDG_DATA_HOME, XDG_STATE_HOME, XDG_CACHE_HOME), then platform defaults.
config contains settings like config.toml and profiles. data contains credentials.toml, data.db, cookies, and auth sidecars. state contains persisted queries, jobs, and teach.log. cache contains regenerable HTTP/cache files.
Stored secrets live in credentials.toml under the data dir. Existing legacy config.toml secrets are read for compatibility and leave config.toml on the first auth write.
Run clinical-trials-pp-cli doctor --fail-on warn to surface path and credential-location warnings. agent-context exposes a schema v4 paths block for agents that need the resolved dirs.
For MCP, pass relocation through the MCP host config. The MCP binary does not inherit CLI flags:

json

  {
    "mcpServers": {
      "clinical-trials": {
        "command": "clinical-trials-pp-mcp",
        "env": {
          "CLINICAL_TRIALS_HOME": "/srv/clinical-trials"
        }
      }
    }
  }

Fleet precedence: an inherited per-kind env var overrides an explicit --home for that kind. Use CLINICAL_TRIALS_HOME or per-kind vars as durable fleet levers, and use --home only for a single invocation. Relocation is not reversible by unsetting env vars; move files manually before clearing CLINICAL_TRIALS_HOME, or doctor will not find credentials left under the former root.

Agent Feedback

When you (or the agent) notice something off about this CLI, record it:

clinical-trials-pp-cli feedback "the --since flag is inclusive but docs say exclusive"
clinical-trials-pp-cli feedback --stdin < notes.txt
clinical-trials-pp-cli feedback list --json --limit 10

Entries are stored locally as feedback.jsonl under the resolved data dir. They are never POSTed unless CLINICAL_TRIALS_FEEDBACK_ENDPOINT is set AND either --send is passed or CLINICAL_TRIALS_FEEDBACK_AUTO_SEND=true. Default behavior is local-only.

Write what surprised you, not a bug report. Short, specific, one line: that is the part that compounds.

Output Delivery

Every command accepts --deliver <sink>. The output goes to the named sink in addition to (or instead of) stdout, so agents can route command results without hand-piping. Three sinks are supported:

Sink	Effect
`stdout`	Default; write to stdout only
`file:<path>`	Atomically write output to `<path>` (tmp + rename)
`webhook:<url>`	POST the output body to the URL (`application/json` or `application/x-ndjson` when `--compact`)

Unknown schemes are refused with a structured error naming the supported set. Webhook failures return non-zero and log the URL + HTTP status on stderr.

Named Profiles

A profile is a saved set of flag values, reused across invocations. Use it when a scheduled agent calls the same command every run with the same configuration - HeyGen's "Beacon" pattern.

clinical-trials-pp-cli profile save briefing --json
clinical-trials-pp-cli --profile briefing studies list
clinical-trials-pp-cli profile list --json
clinical-trials-pp-cli profile show briefing
clinical-trials-pp-cli profile delete briefing --yes

Explicit flags always win over profile values; profile values win over defaults. agent-context lists all available profiles under available_profiles so introspecting agents discover them at runtime.

Exit Codes

Code	Meaning
0	Success
2	Usage error (wrong arguments)
3	Resource not found
5	API error (upstream issue)
7	Rate limited (wait and retry)
10	Config error

Argument Parsing

Parse $ARGUMENTS:

Empty, `help`, or `--help` → show clinical-trials-pp-cli --help output
Starts with `install` → ends with mcp → MCP installation; otherwise → see Prerequisites above
Anything else → Direct Use (execute as CLI command with --agent)

MCP Server Installation

Install the MCP server:

bash

   go install github.com/mvanhorn/printing-press-library/library/health/clinical-trials/cmd/clinical-trials-pp-mcp@latest

bash

   claude mcp add clinical-trials-pp-mcp -- clinical-trials-pp-mcp

Verify: claude mcp list

Direct Use

Check if installed: which clinical-trials-pp-cli

If not found, offer to install (see Prerequisites at the top of this skill).

Match the user query to the best command from the Unique Capabilities and Command Reference above.
Execute with the --agent flag:

bash

   clinical-trials-pp-cli <command> [subcommand] [args] --agent

If ambiguous, drill into subcommand help: clinical-trials-pp-cli <command> --help.