@openfn/language-fhir-4 0.3.2 → 0.4.1

package/dist/index.cjs

@@ -129,7 +129,7 @@ var logResponse = (response, query) => {
 var request = (method, path, options) => {
   (0, import_util.assertRelativeUrl)(path);
   const { configuration, ...otherOptions } = options;
-  const fullPath = import_node_path.default.join(configuration.apiPath ?? "", path);
+  const fullPath = import_node_path.default.join(configuration.apiPath ?? "/fhir", path);
   const headers = addAuth(options);
   const opts = {
     ...otherOptions,
@@ -144,20 +144,79 @@ var request = (method, path, options) => {
     baseUrl: configuration.baseUrl,
     parseAs: "json"
   };
-  return (0, import_util.request)(method, fullPath, opts).then(logResponse).catch(async (e) => {
+  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/)) {
-      const error = JSON.parse(e.body);
-      e.body = error;
-      if (error.issue && error.issue.length) {
-        console.error("Error from FHIR server:");
-        error.issue.forEach((issue) => {
-          console.error(issue.diagnostics);
-        });
-      }
+      logValidationErrors(e);
     }
     throw e;
   });
 };
+function logValidationErrors(response, logger = console) {
+  const error = JSON.parse(response.body);
+  if (error.issue && error.issue.length) {
+    delete response.body;
+    logger.log();
+    logger.error("FHIR server reports validation issues:");
+    const errCount = error.issue.reduce(
+      (count, e) => e.severity === "error" ? count + 1 : count,
+      0
+    );
+    if (errCount) {
+      logger.error(` - ${errCount} Errors`);
+    }
+    const warnCount = error.issue.reduce(
+      (count, e) => e.severity === "error" ? count + 1 : count,
+      0
+    );
+    if (warnCount) {
+      logger.error(` - ${warnCount} Warnings`);
+    }
+    logger.log();
+    const groups = {};
+    error.issue.forEach((issue) => {
+      var _a, _b, _c;
+      try {
+        let id2 = "unidentified resource";
+        if (issue.location) {
+          id2 = issue.location[0];
+          if (id2.startsWith("Bundle")) {
+            id2 = id2.split("*").at(1) ?? id2;
+          }
+        } else {
+          console.log({ issue });
+        }
+        groups[id2] ?? (groups[id2] = {});
+        (_a = groups[id2])[_b = issue.severity] ?? (_a[_b] = []);
+        const path = issue.location[0];
+        (_c = groups[id2][issue.severity])[path] ?? (_c[path] = []);
+        groups[id2][issue.severity][path].push(issue.diagnostics);
+      } catch (e) {
+        logger.log("error parsing issue at ", issue.location);
+        console.log(e);
+      }
+    });
+    for (const resource in groups) {
+      logger.log(`${resource} issues:`);
+      ["error", "warning"].forEach((type) => {
+        if (type in groups[resource]) {
+          logger.log(`  ${type}s:`.toUpperCase());
+          for (const path in groups[resource][type]) {
+            logger.log();
+            logger.log("  ", path);
+            for (const message of groups[resource][type][path]) {
+              logger.log("    -", message);
+            }
+          }
+          logger.log();
+        }
+      });
+    }
+    response.validationIssues = groups;
+  } else {
+    response.body = error;
+  }
+  return response;
+}
 function collectRefs(value2) {
   if (!value2 || typeof value2 !== "object")
     return [];
@@ -740,6 +799,9 @@ var composite = (object, key, value2) => {
     k.push("CodeableConcept");
   } else if (value2.reference) {
     k.push("Reference");
+  }
+  if (value2.value && typeof value2.value === "number") {
+    k.push("Quantity");
   } else if (value2.id && value2.meta && value2.resourceType) {
     k.push("Reference");
     value2 = reference(value2);

package/dist/index.js

@@ -87,7 +87,7 @@ var logResponse = (response, query) => {
 var request = (method, path, options) => {
   assertRelativeUrl(path);
   const { configuration, ...otherOptions } = options;
-  const fullPath = nodepath.join(configuration.apiPath ?? "", path);
+  const fullPath = nodepath.join(configuration.apiPath ?? "/fhir", path);
   const headers = addAuth(options);
   const opts = {
     ...otherOptions,
@@ -102,20 +102,79 @@ var request = (method, path, options) => {
     baseUrl: configuration.baseUrl,
     parseAs: "json"
   };
-  return commonRequest(method, fullPath, opts).then(logResponse).catch(async (e) => {
+  return commonRequest(method, fullPath, opts).then(logResponse).then().catch(async (e) => {
     if (e.headers && "content-type" in e.headers && e.headers["content-type"].match(/fhir\+json/)) {
-      const error = JSON.parse(e.body);
-      e.body = error;
-      if (error.issue && error.issue.length) {
-        console.error("Error from FHIR server:");
-        error.issue.forEach((issue) => {
-          console.error(issue.diagnostics);
-        });
-      }
+      logValidationErrors(e);
     }
     throw e;
   });
 };
+function logValidationErrors(response, logger = console) {
+  const error = JSON.parse(response.body);
+  if (error.issue && error.issue.length) {
+    delete response.body;
+    logger.log();
+    logger.error("FHIR server reports validation issues:");
+    const errCount = error.issue.reduce(
+      (count, e) => e.severity === "error" ? count + 1 : count,
+      0
+    );
+    if (errCount) {
+      logger.error(` - ${errCount} Errors`);
+    }
+    const warnCount = error.issue.reduce(
+      (count, e) => e.severity === "error" ? count + 1 : count,
+      0
+    );
+    if (warnCount) {
+      logger.error(` - ${warnCount} Warnings`);
+    }
+    logger.log();
+    const groups = {};
+    error.issue.forEach((issue) => {
+      var _a, _b, _c;
+      try {
+        let id2 = "unidentified resource";
+        if (issue.location) {
+          id2 = issue.location[0];
+          if (id2.startsWith("Bundle")) {
+            id2 = id2.split("*").at(1) ?? id2;
+          }
+        } else {
+          console.log({ issue });
+        }
+        groups[id2] ?? (groups[id2] = {});
+        (_a = groups[id2])[_b = issue.severity] ?? (_a[_b] = []);
+        const path = issue.location[0];
+        (_c = groups[id2][issue.severity])[path] ?? (_c[path] = []);
+        groups[id2][issue.severity][path].push(issue.diagnostics);
+      } catch (e) {
+        logger.log("error parsing issue at ", issue.location);
+        console.log(e);
+      }
+    });
+    for (const resource in groups) {
+      logger.log(`${resource} issues:`);
+      ["error", "warning"].forEach((type) => {
+        if (type in groups[resource]) {
+          logger.log(`  ${type}s:`.toUpperCase());
+          for (const path in groups[resource][type]) {
+            logger.log();
+            logger.log("  ", path);
+            for (const message of groups[resource][type][path]) {
+              logger.log("    -", message);
+            }
+          }
+          logger.log();
+        }
+      });
+    }
+    response.validationIssues = groups;
+  } else {
+    response.body = error;
+  }
+  return response;
+}
 function collectRefs(value2) {
   if (!value2 || typeof value2 !== "object")
     return [];
@@ -710,6 +769,9 @@ var composite = (object, key, value2) => {
     k.push("CodeableConcept");
   } else if (value2.reference) {
     k.push("Reference");
+  }
+  if (value2.value && typeof value2.value === "number") {
+    k.push("Quantity");
   } else if (value2.id && value2.meta && value2.resourceType) {
     k.push("Reference");
     value2 = reference(value2);

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@openfn/language-fhir-4",
   "label": "FHIR r4",
-  "version": "0.3.2",
+  "version": "0.4.1",
   "description": "OpenFn FHIR r4 adaptor",
   "author": "Open Function Group",
   "license": "LGPLv3",