Merge pull request #312 from OpenFn/improve-fhir

`fhir` improvements
OpenFn · Jul 28, 2023 · 04a9754 · 04a9754
2 parents 95da6f2 + 9e302a2
commit 04a9754
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diff --git a/.changeset/sixty-rockets-buy.md b/.changeset/sixty-rockets-buy.md
@@ -0,0 +1,5 @@
+---
+'@openfn/language-fhir': minor
+---
+
+Migrate from axios to using `fetch` from `undici` and add uniti tests
diff --git a/packages/fhir/ast.json b/packages/fhir/ast.json
@@ -17,7 +17,7 @@
           },
           {
             "title": "example",
-            "description": "create(\"/endpoint\", {\"foo\": \"bar\"})"
+            "description": "create(\"Bundle\", {...state.data: type: \"collection\"})"
           },
           {
             "title": "function",
@@ -79,7 +79,7 @@
           },
           {
             "title": "example",
-            "description": "createTransactionBundle( {\"entry\": [{...},, {...}]})"
+            "description": "createTransactionBundle({\n  resourceType: \"Bundle\",\n  type: \"transaction\",\n  entry: [\n    {\n      fullUrl: \"https://hapi.fhir.org/baseR4/Patient/592442\",\n      resource: {\n        resourceType: \"Patient\",\n        id: \"592442\",\n        name: [{ given: \"Caleb\", family: \"Cushing\" }],\n      },\n      request: {\n        method: \"POST\",\n        url: \"Patient\",\n      },\n    },\n  ],\n});"
           },
           {
             "title": "function",
@@ -133,7 +133,13 @@
           },
           {
             "title": "example",
-            "description": "get(\"/endpoint\", {\"foo\": \"bar\"})"
+            "description": "get(\"Claim\", { _include: \"Claim:patient\", _sort: \"-_lastUpdated\", _count: 200 })",
+            "caption": "Get Claim from FHIR with optional query"
+          },
+          {
+            "title": "example",
+            "description": "get('Patient');",
+            "caption": "Get Patient from FHIR"
           },
           {
             "title": "function",
@@ -178,6 +184,69 @@
         ]
       },
       "valid": true
+    },
+    {
+      "name": "getClaim",
+      "params": [
+        "claimId",
+        "query",
+        "callback"
+      ],
+      "docs": {
+        "description": "Get Claim in a FHIR system",
+        "tags": [
+          {
+            "title": "public",
+            "description": null,
+            "type": null
+          },
+          {
+            "title": "example",
+            "description": "getClaim({ _include: \"Claim:patient\", _sort: \"-_lastUpdated\", _count: 200 });"
+          },
+          {
+            "title": "function",
+            "description": null,
+            "name": null
+          },
+          {
+            "title": "param",
+            "description": "(optional) claim id",
+            "type": {
+              "type": "NameExpression",
+              "name": "string"
+            },
+            "name": "claimId"
+          },
+          {
+            "title": "param",
+            "description": "(optinal) query parameters",
+            "type": {
+              "type": "NameExpression",
+              "name": "object"
+            },
+            "name": "query"
+          },
+          {
+            "title": "param",
+            "description": "(Optional) callback function",
+            "type": {
+              "type": "NameExpression",
+              "name": "function"
+            },
+            "name": "callback"
+          },
+          {
+            "title": "returns",
+            "description": null,
+            "type": {
+              "type": "NameExpression",
+              "name": "Operation"
+            }
+          }
+        ]
+      },
+      "valid": true
     }
   ],
   "exports": [],

diff --git a/packages/fhir/package.json b/packages/fhir/package.json
@@ -21,17 +21,16 @@
   ],
   "dependencies": {
     "@openfn/language-common": "workspace:^1.8.1",
-    "axios": "0.21.4"
+    "undici": "^5.22.1"
   },
   "devDependencies": {
     "@openfn/buildtools": "workspace:^1.0.2",
     "@openfn/simple-ast": "^0.4.1",
-    "assertion-error": "^1.1.0",
-    "chai": "^3.5.0",
-    "deep-eql": "^0.1.3",
+    "assertion-error": "2.0.0",
+    "chai": "^4.3.6",
+    "deep-eql": "4.1.1",
     "esno": "^0.16.3",
-    "mocha": "^7.2.0",
-    "nock": "^12.0.3",
+    "mocha": "9.2.2",
     "rimraf": "^3.0.2"
   },
   "repository": {

diff --git a/packages/fhir/src/Adaptor.js b/packages/fhir/src/Adaptor.js
@@ -1,12 +1,7 @@
-import {
-  execute as commonExecute,
-  expandReferences,
-  http,
-} from '@openfn/language-common';
-import { handleError, handleResponse } from './Utils';
+import { execute as commonExecute } from '@openfn/language-common';
+import { expandReferences } from '@openfn/language-common/util';
 
-const { axios } = http;
-export { axios };
+import { handleResponse, request } from './Utils';
 
 /**
  * Execute a sequence of operations.
@@ -38,7 +33,7 @@ export function execute(...operations) {
  * Creates a resource in a destination system using a POST request
  * @public
  * @example
- * create("/endpoint", {"foo": "bar"})
+ * create("Bundle", {...state.data: type: "collection"})
  * @function
  * @param {string} path - Path to resource
  * @param {object} params - data to create the new resource
@@ -47,50 +42,67 @@ export function execute(...operations) {
  */
 export function create(path, params, callback) {
   return state => {
-    const resolvedpath = expandReferences(path)(state);
-    const resolvedParams = expandReferences(params)(state);
+    const [resolvedpath, resolvedParams] = expandReferences(
+      state,
+      path,
+      params
+    );
 
     const { baseUrl, apiPath } = state.configuration;
 
     const url = `${baseUrl}/${apiPath}/${resolvedpath}`;
 
-    const config = {
-      url,
+    const options = {
       headers: {
         accept: 'application/fhir+json',
         'Content-Type': 'application/fhir+json',
       },
-      data: resolvedParams,
+      ...resolvedParams,
     };
 
-    return http
-      .post(config)(state)
-      .then(response => handleResponse(response, state, callback))
-      .catch(handleError);
+    return request(url, options, 'POST').then(response =>
+      handleResponse(response, state, callback)
+    );
   };
 }
 
 /**
  * Creates a transactionBundle for HAPI FHIR
  * @public
  * @example
- * createTransactionBundle( {"entry": [{...},, {...}]})
+ * createTransactionBundle({
+ *   resourceType: "Bundle",
+ *   type: "transaction",
+ *   entry: [
+ *     {
+ *       fullUrl: "https://hapi.fhir.org/baseR4/Patient/592442",
+ *       resource: {
+ *         resourceType: "Patient",
+ *         id: "592442",
+ *         name: [{ given: "Caleb", family: "Cushing" }],
+ *       },
+ *       request: {
+ *         method: "POST",
+ *         url: "Patient",
+ *       },
+ *     },
+ *   ],
+ * });
  * @function
  * @param {object} params - data to create the new transaction
  * @param {function} callback - (Optional) callback function
  * @returns {Operation}
  */
 export function createTransactionBundle(params, callback) {
   return state => {
-    const resolvedParams = expandReferences(params)(state);
+    const [resolvedParams] = expandReferences(state, params);
 
     const { baseUrl, apiPath, authType, token } = state.configuration;
 
     const url = `${baseUrl}/${apiPath}`;
     const auth = `${authType} ${token}`;
 
-    const config = {
-      url,
+    const options = {
       body: {
         resourceType: 'Bundle',
         type: 'transaction',
@@ -99,45 +111,69 @@ export function createTransactionBundle(params, callback) {
       auth,
     };
 
-    return http
-      .post(config)(state)
-      .then(response => handleResponse(response, state, callback))
-      .catch(handleError);
+    return request(url, options, 'POST').then(response =>
+      handleResponse(response, state, callback)
+    );
   };
 }
 
 /**
  * Get a resource in a FHIR system
  * @public
- * @example
- * get("/endpoint", {"foo": "bar"})
+ * @example <caption>Get Claim from FHIR with optional query</caption>
+ * get("Claim", { _include: "Claim:patient", _sort: "-_lastUpdated", _count: 200 })
+ * @example <caption>Get Patient from FHIR</caption>
+ * get('Patient');
  * @function
  * @param {string} path - Path to resource
  * @param {object} query - data to get the new resource
  * @param {function} callback - (Optional) callback function
  * @returns {Operation}
  */
-export function get(path, query, callback = false) {
+export function get(path, query, callback = s => s) {
   return state => {
-    const resolvedPath = expandReferences(path)(state);
-    const resolvedQuery = expandReferences(query)(state);
+    const [resolvedPath, resolvedQuery] = expandReferences(state, path, query);
 
     const { baseUrl, apiPath } = state.configuration;
     const url = `${baseUrl}/${apiPath}/${resolvedPath}`;
 
-    const config = {
-      url,
-      query: resolvedQuery,
-    };
+    return request(url, { ...resolvedQuery }).then(response =>
+      handleResponse(response, state, callback)
+    );
+  };
+}
+
+/**
+ * Get Claim in a FHIR system
+ * @public
+ * @example
+ * getClaim({ _include: "Claim:patient", _sort: "-_lastUpdated", _count: 200 });
+ * @function
+ * @param {string} claimId - (optional) claim id
+ * @param {object} query - (optinal) query parameters
+ * @param {function} callback - (Optional) callback function
+ * @returns {Operation}
+ */
+export function getClaim(claimId, query, callback = s => s) {
+  return state => {
+    const [resourcedclaimId, resolvedQuery] = expandReferences(
+      state,
+      claimId,
+      query
+    );
+
+    const { baseUrl, apiPath } = state.configuration;
+    const url = resourcedclaimId
+      ? `${baseUrl}/${apiPath}/Claim/${resourcedclaimId}`
+      : `${baseUrl}/${apiPath}/Claim`;
 
-    return http
-      .get(config)(state)
-      .then(response => handleResponse(response, state, callback))
-      .catch(handleError);
+    return request(url, { ...resolvedQuery }).then(response =>
+      handleResponse(response, state, callback)
+    );
   };
 }
+export { request } from './Utils';
 
-// What functions do you want from the common adaptor?
 export {
   alterState,
   dataPath,
@@ -147,7 +183,6 @@ export {
   field,
   fields,
   fn,
-  http,
   lastReferenceValue,
   merge,
   sourceValue,