@openfn/language-fhir-4 0.4.1 → 0.5.0

package/configuration-schema.json

@@ -2,63 +2,56 @@
   "$schema": "http://json-schema.org/draft-07/schema#",
   "type": "object",
   "properties": {
-      "baseUrl": {
-          "title": "Base Url",
-          "type": "string",
-          "description": "The baseUrl",
-          "examples": [
-              "https://hapi.fhir.org"
-          ]
-      },
-      "apiPath": {
-          "title": "API Path",
-          "anyOf": [
-              {
-                  "type": "string"
-              },
-              {
-                  "type": "null"
-              }
-          ],
-          "placeholder": "R4",
-          "description": "FHIR api path",
-          "minLength": 1,
-          "examples": [
-              "baseR4",
-              "R3",
-              "R4"
-          ]
-      },
-      "username": {
-          "title": "Username",
-          "type": "string",
-          "description": "Username",
-          "examples": [
-              "openfn_test"
-          ]
-      },
-      "password": {
-          "title": "Password",
-          "type": "string",
-          "description": "Password",
-          "writeOnly": true,
-          "examples": [
-              "@some(!)Str0ngp4ss0w0rd"
-          ]
-      },
-      "access_token": {
-          "title": "Access Token",
-          "type": "string",
-          "description": "Your FHIR access token",
-          "writeOnly": true,
-          "minLength": 1,
-          "examples": [
-              "the-long-access-token-from-your-auth"
-          ]
-      }
+    "baseUrl": {
+      "title": "Base Url",
+      "type": "string",
+      "description": "The baseUrl",
+      "examples": ["https://hapi.fhir.org"]
+    },
+    "apiPath": {
+      "title": "API Path",
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "placeholder": "R4",
+      "description": "FHIR api path",
+      "minLength": 1,
+      "examples": ["baseR4", "R3", "R4"]
+    },
+    "username": {
+      "title": "Username",
+      "type": "string",
+      "description": "Username",
+      "examples": ["openfn_test"]
+    },
+    "password": {
+      "title": "Password",
+      "type": "string",
+      "description": "Password",
+      "writeOnly": true,
+      "examples": ["@some(!)Str0ngp4ss0w0rd"]
+    },
+    "access_token": {
+      "title": "Access Token",
+      "type": "string",
+      "description": "Your FHIR access token",
+      "writeOnly": true,
+      "minLength": 1,
+      "examples": ["the-long-access-token-from-your-auth"]
+    },
+    "authorization": {
+      "title": "Authorization Header",
+      "type": "string",
+      "description": "Custom Authorization header value",
+      "writeOnly": true,
+      "minLength": 1,
+      "examples": ["custom 12345"]
+    }
   },
-  "required": [
-      "baseUrl",
-      "apiPath"
-  ]
-}
+  "required": ["baseUrl", "apiPath"]
+}

package/dist/index.cjs

@@ -79,6 +79,7 @@ var import_util2 = require("@openfn/language-common/util");
 
 // src/util.ts
 var import_node_path = __toESM(require("path"), 1);
+var import_lodash_es = __toESM(require("lodash-es"), 1);
 var import_language_common = require("@openfn/language-common");
 var import_util = require("@openfn/language-common/util");
 function assertValidResourceId(id2) {
@@ -91,18 +92,22 @@ function assertValidResourceId(id2) {
 }
 function addAuth(options) {
   var _a;
-  if ((_a = options == null ? void 0 : options.headers) == null ? void 0 : _a.Authorization)
+  if ((_a = options.headers) == null ? void 0 : _a.Authorization) {
     return;
-  const { username, password, access_token } = options.configuration;
-  if (access_token) {
+  }
+  const { username, password, access_token, authorization } = options.configuration;
+  if (authorization) {
+    return { Authorization: authorization };
+  }
+  if (access_token || authorization) {
     return { Authorization: `Bearer ${access_token}` };
-  } else if (username && password) {
+  }
+  if (username && password) {
     return { ...(0, import_util.makeBasicAuthHeader)(username, password) };
   }
-  return {};
 }
 var prepareNextState = (state, response) => {
-  const { body, ...responseWithoutBody } = response;
+  const { body, validationErrors, ...responseWithoutBody } = response;
   return {
     ...(0, import_language_common.composeNextState)(state, body),
     response: responseWithoutBody
@@ -130,15 +135,15 @@ var request = (method, path, options) => {
   (0, import_util.assertRelativeUrl)(path);
   const { configuration, ...otherOptions } = options;
   const fullPath = import_node_path.default.join(configuration.apiPath ?? "/fhir", path);
-  const headers = addAuth(options);
   const opts = {
     ...otherOptions,
     headers: Object.assign(
-      headers,
+      {},
       {
         accept: "application/fhir+json",
         "content-type": "application/fhir+json"
       },
+      addAuth(options),
       options.headers
     ),
     baseUrl: configuration.baseUrl,
@@ -146,12 +151,12 @@ var request = (method, path, options) => {
   };
   return (0, import_util.request)(method, fullPath, opts).then(logResponse).then().catch(async (e) => {
     if (e.headers && "content-type" in e.headers && e.headers["content-type"].match(/fhir\+json/)) {
-      logValidationErrors(e);
+      logValidationErrors(e, opts.body);
     }
     throw e;
   });
 };
-function logValidationErrors(response, logger = console) {
+function logValidationErrors(response, payload, logger = console) {
   const error = JSON.parse(response.body);
   if (error.issue && error.issue.length) {
     delete response.body;
@@ -176,20 +181,35 @@ function logValidationErrors(response, logger = console) {
     error.issue.forEach((issue) => {
       var _a, _b, _c;
       try {
-        let id2 = "unidentified resource";
+        let resourceId = "unidentified resource";
         if (issue.location) {
-          id2 = issue.location[0];
-          if (id2.startsWith("Bundle")) {
-            id2 = id2.split("*").at(1) ?? id2;
+          let idx = issue.location[0].match(/Bundle.entry\[(\d+)\]/);
+          if (idx && idx.length >= 2) {
+            idx = idx[1];
+            const resource = (_a = import_lodash_es.default.get(payload, `entry[${idx}]`)) == null ? void 0 : _a.resource;
+            if (resource) {
+              resourceId = `${resource.resourceType}/${resource.id}`;
+            }
+          } else {
+            if (payload.resourceType && payload.id) {
+              resourceId = `${payload.resourceType}/${payload.id}`;
+            }
           }
-        } else {
-          console.log({ issue });
         }
-        groups[id2] ?? (groups[id2] = {});
-        (_a = groups[id2])[_b = issue.severity] ?? (_a[_b] = []);
-        const path = issue.location[0];
-        (_c = groups[id2][issue.severity])[path] ?? (_c[path] = []);
-        groups[id2][issue.severity][path].push(issue.diagnostics);
+        const type = `${issue.severity}s`;
+        groups[resourceId] ?? (groups[resourceId] = {});
+        let path = "*";
+        if (issue.location[0].match(/\.resource\./)) {
+          path = issue.location[0].split(/\.resource\./)[1];
+        } else if (issue.location.includes(`*${resourceId}*`)) {
+          const suffix = issue.location[0].split(/\.resource\./)[1];
+          if (suffix && suffix.length > 1) {
+            path = suffix;
+          }
+        }
+        (_b = groups[resourceId])[type] ?? (_b[type] = {});
+        (_c = groups[resourceId][type])[path] ?? (_c[path] = []);
+        groups[resourceId][type][path].push(issue.diagnostics);
       } catch (e) {
         logger.log("error parsing issue at ", issue.location);
         console.log(e);
@@ -197,26 +217,36 @@ function logValidationErrors(response, logger = console) {
     });
     for (const resource in groups) {
       logger.log(`${resource} issues:`);
-      ["error", "warning"].forEach((type) => {
+      ["errors", "warnings"].forEach((type) => {
         if (type in groups[resource]) {
-          logger.log(`  ${type}s:`.toUpperCase());
+          logger.log(`  ${type}:`.toUpperCase());
           for (const path in groups[resource][type]) {
             logger.log();
             logger.log("  ", path);
             for (const message of groups[resource][type][path]) {
-              logger.log("    -", message);
+              const fn2 = type === "error" ? console.error : console.warn;
+              fn2("    -", message);
             }
           }
           logger.log();
         }
       });
     }
-    response.validationIssues = groups;
+    logger.log("Issues will be written to state.fhirValidationIssues");
+    response.$validationIssues = groups;
   } else {
     response.body = error;
   }
   return response;
 }
+function cleanResponseObject(state, response) {
+  if (response.$validationIssues) {
+    state.fhirValidationIssues ?? (state.fhirValidationIssues = {});
+    Object.assign(state.fhirValidationIssues, response.$validationIssues);
+    delete response.$validationIssues;
+  }
+  return state;
+}
 function collectRefs(value2) {
   if (!value2 || typeof value2 !== "object")
     return [];
@@ -383,6 +413,9 @@ function create(resource) {
     const response = await request("POST", $resource.resourceType, {
       configuration: state.configuration,
       body: $resource
+    }).catch((e) => {
+      cleanResponseObject(state, e);
+      throw e;
     });
     console.log(`Created ${response.body.id}`);
     return prepareNextState(state, response);
@@ -447,6 +480,9 @@ function uploadBundle(bundle = "bundle") {
     const response = await request("POST", "/", {
       configuration: state.configuration,
       body: data
+    }).catch((e) => {
+      cleanResponseObject(state, e);
+      throw e;
     });
     return prepareNextState(state, response);
   };