allow _count paramater in search command. add bundle loading script f…

…rom connectathon

service/package.json

@@ -13,6 +13,7 @@
     "db:reset": "ts-node ./scripts/dbSetup.ts reset",
     "db:setup": "ts-node ./scripts/dbSetup.ts create",
     "db:loadBundle": "ts-node ./scripts/dbSetup.ts loadBundle",
+    "loadBundles": "ts-node ./scripts/loadBundles.ts",
     "lint": "eslint \"./src/**/*.{js,ts}\"",
     "lint:fix": "eslint \"./src/**/*.{js,ts}\" --fix",
     "prettier": "prettier --check \"./src/**/*.{js,ts}\"",

service/scripts/loadBundles.ts

@@ -0,0 +1,150 @@
+import * as fs from 'fs';
+import path from 'path';
+
+const SERVER_URL = 'https://abacus-demo.c3ib.org/mrs/4_0_1';
+//const SERVER_URL = 'http://localhost:3000/4_0_1';
+const ECQM_CONTENT_PATH = '/Users/hossenlopp/Downloads/May 2024 Connectathon';
+const MEASURES_PATH = path.join(ECQM_CONTENT_PATH);
+
+function getBundlePaths(): string[] {
+  const filePaths: string[] = [];
+
+  fs.readdirSync(MEASURES_PATH, { withFileTypes: true }).forEach(ent => {
+    // if this item is a directory, look for .json files under it
+    if (ent.isDirectory()) {
+      fs.readdirSync(path.join(MEASURES_PATH, ent.name), { withFileTypes: true }).forEach(subEnt => {
+        if (!subEnt.isDirectory() && subEnt.name.endsWith('.json')) {
+          filePaths.push(path.join(MEASURES_PATH, ent.name, subEnt.name));
+        } else if (subEnt.isDirectory()) {
+          fs.readdirSync(path.join(MEASURES_PATH, ent.name, subEnt.name), { withFileTypes: true }).forEach(
+            subSubEnt => {
+              if (!subSubEnt.isDirectory() && subSubEnt.name.endsWith('.json')) {
+                filePaths.push(path.join(MEASURES_PATH, ent.name, subEnt.name, subSubEnt.name));
+              }
+            }
+          );
+        }
+      });
+    }
+  });
+
+  return filePaths;
+}
+
+function loadBundle(path: string): fhir4.Bundle | null {
+  const bundle = JSON.parse(fs.readFileSync(path, 'utf8'));
+  if (bundle.resourceType === 'Bundle') {
+    return bundle as fhir4.Bundle;
+  } else {
+    console.warn(`${path} is not a Bundle`);
+    return null;
+  }
+}
+
+async function putLibraries(bundle: fhir4.Bundle) {
+  const libraries: fhir4.Library[] = bundle.entry
+    ?.filter(entry => entry.resource?.resourceType === 'Library')
+    .map(entry => entry.resource as fhir4.Library) as fhir4.Library[];
+  /*
+  console.log(`Fixing refs in ${measure?.id}`);
+  console.log(measure.relatedArtifact?.length);
+  measure.relatedArtifact?.forEach(ra => {
+    //console.log(ra);
+    if (ra.resource) {
+      if (!ra.resource.startsWith('http')) {
+        console.log(`  replacing ${ra.resource}`);
+        ra.resource = 'http://ecqi.healthit.gov/ecqms/' + ra.resource;
+      }
+    }
+  });
+  */
+  for (const library of libraries) {
+    try {
+      console.log(`  PUT ${SERVER_URL}/Library/${library.id}`);
+
+      const resp = await fetch(`${SERVER_URL}/Library/${library.id}`, {
+        method: 'PUT',
+        body: JSON.stringify(library),
+        headers: {
+          'Content-Type': 'application/json+fhir'
+        }
+      });
+      console.log(`    ${resp.status}`);
+    } catch (e) {
+      console.error(e);
+    }
+  }
+}
+
+async function fixAndPUTMeasure(bundle: fhir4.Bundle) {
+  const measure: fhir4.Measure = bundle.entry?.find(entry => entry.resource?.resourceType === 'Measure')
+    ?.resource as fhir4.Measure;
+  /*
+  console.log(`Fixing refs in ${measure?.id}`);
+  console.log(measure.relatedArtifact?.length);
+  measure.relatedArtifact?.forEach(ra => {
+    //console.log(ra);
+    if (ra.resource) {
+      if (!ra.resource.startsWith('http')) {
+        console.log(`  replacing ${ra.resource}`);
+        ra.resource = 'http://ecqi.healthit.gov/ecqms/' + ra.resource;
+      }
+    }
+  });
+  */
+  try {
+    console.log(`  PUT ${SERVER_URL}/Measure/${measure.id}`);
+
+    const resp = await fetch(`${SERVER_URL}/Measure/${measure.id}`, {
+      method: 'PUT',
+      body: JSON.stringify(measure),
+      headers: {
+        'Content-Type': 'application/json+fhir'
+      }
+    });
+    console.log(`    ${resp.status}`);
+  } catch (e) {
+    console.error(e);
+  }
+}
+
+async function transactBundle(bundle: fhir4.Bundle) {
+  if (bundle.entry) {
+    for (const entry of bundle.entry) {
+      if (entry.request?.method === 'POST') {
+        entry.request.method = 'PUT';
+      }
+    }
+  }
+
+  try {
+    console.log(`  POST ${SERVER_URL}`);
+
+    const resp = await fetch(`${SERVER_URL}`, {
+      method: 'POST',
+      body: JSON.stringify(bundle),
+      headers: {
+        'Content-Type': 'application/json+fhir'
+      }
+    });
+    console.log(`    ${resp.status}`);
+  } catch (e) {
+    console.error(e);
+  }
+}
+
+async function loadBundles(bundlePaths: string[]) {
+  for (const path of bundlePaths) {
+    const bundle = loadBundle(path);
+    if (bundle) {
+      console.log('FILE ' + path);
+      await transactBundle(bundle);
+      //await fixAndPUTMeasure(bundle);
+      //await putLibraries(bundle);
+    }
+  }
+}
+
+const bundlePaths = getBundlePaths();
+
+loadBundles(bundlePaths);

service/src/requestSchemas.ts

@@ -198,7 +198,8 @@ export const CoreSearchArgs = z
     // adding _summary for count (https://www.hl7.org/fhir/search.html#_summary)
     _summary: z.literal('count'),
     // adding _elements for a comma separated string (https://www.hl7.org/fhir/search.html#_elements)
-    _elements: z.string()
+    _elements: z.string(),
+    _count: z.string()
   })
   .partial()
   .strict();

service/src/util/queryUtils.ts

@@ -34,6 +34,8 @@ export function getMongoQueryFromRequest(query: RequestQuery): Filter<any> {
     } else if (key === '_elements') {
       const elements = query[key] as string;
       mf[key] = elements.split(',');
+    } else if (key === '_count') {
+      //blackhole _count for now
     } else {
       // Otherwise no parsing necessary
       mf[key] = query[key];