ENH: Initial working version

CNAME

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+clinicaltrialsapi.straive.app

LICENSE

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+Copyright 2024 Anand S
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

clinicaltrials.js

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+const BASE = "https://clinicaltrials.gov/api/v2";
+
+async function run(path, params = {}) {
+  const url = `${BASE}${path}${params ? `?${new URLSearchParams(params)}` : ""}`;
+  const res = await fetch(url);
+  if (!res.ok) throw new Error(`API Error ${res.status}: ${await res.text()}`);
+  return res.json();
+}
+
+function addFields(params) {
+  if (!params.fields) params.fields = [];
+  for (const module of ["identificationModule", "statusModule"]) {
+    const field = `protocolSection.${module}`;
+    if (!params.fields.includes(field)) params.fields.push(field);
+  }
+  return params;
+}
+
+export const api = {
+  studies: (params) => run("/studies", { pageSize: 10, ...addFields(params) }),
+  study: ({ nctId }) => run(`/studies/${nctId}`),
+  studiesMetadata: () => run("/studies/metadata"),
+  studiesSearchAreas: () => run("/studies/search-areas"),
+  studiesEnums: () => run("/studies/enums"),
+  statsSize: (params) => run("/stats/size", params),
+  statsFieldValues: (params) => run("/stats/field/values", params),
+  statsFieldSizes: (params) => run("/stats/field/sizes", params),
+};
+
+export const tools = {
+  studies: {
+    name: "studies",
+    description: "Search clinical trials with filters. Use AND, OR, NOT, and parentheses for grouping.",
+    parameters: {
+      type: "object",
+      required: ["fields"],
+      properties: {
+        "query.cond": { type: "string", description: "Search for condition or disease" },
+        "query.term": {
+          type: "string",
+          description: "Search other terms like age, phase, design, sponsor, keyword, etc.",
+        },
+        "query.locn": { type: "string", description: "Search for location (country, state, city, facility)" },
+        "query.titles": { type: "string", description: "Search in title" },
+        "query.intr": { type: "string", description: "Search in interventions, Arm Groups" },
+        "query.outc": { type: "string", description: "Search in outcome measures" },
+        "query.spons": { type: "string", description: "Search sponsors / collaborators" },
+        // "query.lead": { type: "string", description: 'Searches "LeadSponsorName" field' },
+        // "query.id": { type: "string", description: "Study IDs query" },
+        "query.patient": { type: "string", description: "Search all patient details" },
+        "filter.overallStatus": {
+          type: "array",
+          items: { type: "string" },
+          description:
+            "Can be ACTIVE_NOT_RECRUITING, COMPLETED, ENROLLING_BY_INVITATION, NOT_YET_RECRUITING, RECRUITING, SUSPENDED, TERMINATED, WITHDRAWN, AVAILABLE, NO_LONGER_AVAILABLE, TEMPORARILY_NOT_AVAILABLE, APPROVED_FOR_MARKETING, WITHHELD, UNKNOWN",
+        },
+        // "filter.geo": { type: "string", description: "Geo-function filter. Format: distance(lat, long, dist)" },
+        // "filter.ids": {
+        //   type: "array",
+        //   items: { type: "string" },
+        //   description: "List of NCT IDs",
+        // },
+        // "filter.advanced": { type: "string", description: "Essie expression filter. Examples: AREA[StartDate]2022" },
+        // "filter.synonyms": {
+        //   type: "array",
+        //   items: { type: "string" },
+        //   description: "Comma- or pipe-separated area:synonym_id pairs",
+        // },
+        // "postFilter.overallStatus": {
+        //   type: "array",
+        //   items: { type: "string" },
+        //   description: "Status filter. Examples: NOT_YET_RECRUITING, RECRUITING",
+        // },
+        // "postFilter.geo": {
+        //   type: "string",
+        //   description: "Geo-function filter. Examples: distance(39.0035707,-77.1013313,50mi)",
+        // },
+        // "postFilter.ids": {
+        //   type: "array",
+        //   items: { type: "string" },
+        //   description: "NCT ID filter. Examples: [ NCT04852770, NCT01728545 ]",
+        // },
+        // "postFilter.advanced": {
+        //   type: "string",
+        //   description: "Essie expression filter. Examples: AREA[StartDate]2022",
+        // },
+        // "postFilter.synonyms": {
+        //   type: "array",
+        //   items: { type: "string" },
+        //   description: "Area:synonym_id pairs filter",
+        // },
+        // aggFilters: { type: "string", description: "Aggregation filter. Format: filter_id:option keys" },
+        // geoDecay: {
+        //   type: "string",
+        //   description: "Proximity factor for geo-filtering. Examples: func:linear,scale:100km",
+        // },
+        fields: {
+          type: "array",
+          items: {
+            type: "string",
+            enum: [
+              "protocolSection.identificationModule",
+              "protocolSection.statusModule",
+              "protocolSection.sponsorCollaboratorsModule",
+              "protocolSection.oversightModule",
+              "protocolSection.descriptionModule",
+              "protocolSection.designModule",
+              "protocolSection.eligibilityModule",
+              "protocolSection.ipdSharingStatementModule",
+            ],
+          },
+          description: "Pick ALL modules relevant to answering the question",
+        },
+        sort: {
+          type: "array",
+          items: { type: "string" },
+          maxItems: 2,
+          description: "Sorting options. Examples: @relevance, LastUpdatePostDate, EnrollmentCount:desc, NumArmGroups",
+        },
+        // countTotal: { type: "boolean", description: "Returns totalCount with the first page if true" },
+        // page: {
+        //   type: "integer",
+        //   description: "Page number for pagination",
+        //   default: 1,
+        // },
+        // pageSize: {
+        //   type: "integer",
+        //   description: "Results per page (max 1000)",
+        //   default: 1000,
+        // },
+        // fields: {
+        //   type: "array",
+        //   items: { type: "string" },
+        //   description: "Specific fields to return in the response",
+        // },
+      },
+    },
+  },
+  study: {
+    name: "study",
+    description: "Get a single study by NCT ID",
+    parameters: {
+      type: "object",
+      properties: {
+        nctId: { type: "string", description: "NCT ID" },
+      },
+    },
+  },
+};

index.html

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+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+  <meta charset="UTF-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <title>Clinical Trials API Agent</title>
+  <link rel="icon" href="https://raw.githubusercontent.com/gramener/assets/main/straive-favicon.svg">
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" crossorigin="anonymous">
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.min.css">
+  <style>
+    .narrative {
+      max-width: 40rem;
+    }
+
+    .pre-wrap {
+      white-space: pre-wrap;
+    }
+
+    #summary details {
+      margin-bottom: 1.5rem;
+    }
+  </style>
+</head>
+
+<body>
+
+  <nav class="navbar navbar-expand-lg bg-body-tertiary" data-bs-theme="dark">
+    <div class="container-fluid">
+      <a class="navbar-brand" href=".">Clinical Trials API Agent</a>
+      <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
+        <span class="navbar-toggler-icon"></span>
+      </button>
+      <div class="collapse navbar-collapse" id="navbarSupportedContent">
+        <div class="nav-item dropdown ms-auto" role="group" aria-label="Toggle dark mode" title="Toggle Dark Mode">
+          <button class="dark-theme-toggle btn btn-outline-light dropdown-toggle" type="button" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Toggle theme (auto)">
+            <i class="bi bi-circle-half"></i> <span class="d-lg-none ms-2">Toggle theme</span>
+          </button>
+          <ul class="dropdown-menu dropdown-menu-end">
+            <li><button class="dropdown-item" data-bs-theme-value="light"><i class="me-2 bi bi-sun-fill"></i> Light</button></li>
+            <li><button class="dropdown-item" data-bs-theme-value="dark"><i class="me-2 bi bi-moon-stars-fill"></i> Dark</button></li>
+            <li><button class="dropdown-item" data-bs-theme-value="auto"><i class="me-2 bi bi-circle-half"></i> Auto</button></li>
+          </ul>
+        </div>
+      </div>
+    </div>
+  </nav>
+
+  <div class="container">
+    <h1 class="display-1 my-4 text-center">Clinical Trials API Agent</h1>
+    <h2 class="display-6 text-center">Answer questions from the <a href="https://www.clinicaltrials.gov/data-api/api">ClinicalTrials.gov API</a></h2>
+    <div class="mx-auto my-3 narrative">
+      <p>This application is designed for the Clinical Trials API Agent, allowing users to answer questions based on the <a href="https://www.clinicaltrials.gov/data-api/api">ClinicalTrials.gov API</a>.</p>
+      <p>Enter a question below. The agent will:</p>
+      <ul>
+        <li>Convert the question into a structured query</li>
+        <li>Fetch the relevant studies from the ClinicalTrials.gov API</li>
+        <li>Show the summary of these studies</li>
+        <li>Create a plan to answer the question using the data</li>
+        <li>Present a final answer, citing studies to support the answer</li>
+      </ul>
+    </div>
+
+    <form id="query-form" class="d-flex gap-2">
+      <div class="flex-grow-1">
+        <input type="text" class="form-control" id="query" placeholder="Enter your question here" aria-label="Question" list="sample-questions">
+        <datalist id="sample-questions">
+          <option value="What are inclusion-exclusion criteria for a diabetes trial on 65+ patients?">
+          <option value="What are primary and secondary outcomes for breast cancer patients?">
+          <option value="Which interventions are being tested in 50+ Alzheimer's patients?">
+          <option value="What are the eligibility criteria for pediatric asthma trials?">
+          <option value="What is the average duration of depression medications trials?">
+        </datalist>
+      </div>
+      <button type="submit" class="btn btn-primary">Submit</button>
+    </form>
+
+    <div id="search-params" class="my-3 table-responsive"></div>
+    <div id="error" class="narrative mx-auto my-5"></div>
+    <div id="summary" class="narrative mx-auto my-5"></div>
+  </div>
+
+  <div class="container-fluid">
+    <div id="search-documents" class="my-3 table-responsive"></div>
+  </div>
+
+  <footer class="my-5 vh-100 d-flex align-items-center justify-content-center">
+    <h1 class="display-4">Designed by <a href="https://gramener.com/" class="text-reset link-offset-3 link-underline link-underline-opacity-25">Gramener</a></h1>
+  </footer>
+
+  <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" type="module"></script>
+  <script src="https://cdn.jsdelivr.net/npm/@gramex/[email protected]/dist/dark-theme.js" type="module"></script>
+  <script src="script.js" type="module"></script>
+</body>
+
+</html>