Cumulative Fixes and Improvements

.github/scripts/read-binary-content-via-json-invalid.sh

@@ -0,0 +1,90 @@
+#!/bin/bash -e
+
+# This script creates a binary resource with invalid data and verifies that,
+# when trying to read its binary content, an error is generated.
+
+BASE="http://localhost:8080/fhir"
+
+# 10 KiB of random data, base64 encoded
+ORIGINAL_DATA="$(openssl rand -base64 10240 | tr -d '\n')"
+
+
+# Higher-order function to apply a transformation based on a condition
+apply_generic_transformation() {
+    local data="$1"
+    local transform_function="$2"
+
+    local result=""
+
+    # Iterate over the data and apply the transform function
+    for i in $(seq 0 ${#data}-1); do
+        result+=$(eval "$transform_function \"${data:$i:1}\" $i")
+    done
+
+    echo "$result"
+}
+
+remove_parts_transform() {
+    local char="$1"
+    local index="$2"
+
+    # Randomly decide whether to remove this character (skip it)
+    if (( RANDOM % 10 == 0 )); then
+        echo ""  # Skip (remove this character)
+    else
+        echo "$char"  # Keep the character
+    fi
+}
+
+insert_non_base64_transform() {
+    local char="$1"
+    local index="$2"
+
+    # Every 5th character, insert a random non-base64 character
+    if (( index % 5 == 0 )); then
+        echo "$((RANDOM % 10))"  # Insert a non-base64 digit
+    else
+        echo "$char"  # Keep the character
+    fi
+}
+
+# Apply Remove Parts of the Data
+FAULTY_DATA=$(apply_generic_transformation "$ORIGINAL_DATA" "remove_parts_transform")
+# echo "Faulty Data (Removed Parts): $FAULTY_DATA"
+
+# Apply Insert Non-Base64 Characters
+FAULTY_DATA=$(apply_generic_transformation "$FAULTY_DATA" "insert_non_base64_transform")
+# echo "Faulty Data (also with Non-Base64 Characters): $FAULTY_DATA"
+
+DATA=$FAULTY_DATA
+
+
+binary() {
+cat <<END
+{
+  "resourceType": "Binary",
+  "contentType": "application/pdf",
+  "data": "$DATA"
+}
+END
+}
+
+# Create a Binary resource that contains that faulty data, and get its ID (via JSON)
+ID_VIA_JSON=$(curl -s -H 'Content-Type: application/fhir+json' -d "$(binary)" "$BASE/Binary" | jq -r '.id')
+
+echo "Created Binary resource that contains the Random Data"
+echo "  - via JSON, with ID: $ID_VIA_JSON"
+
+
+# Retrieve the Binary resource, and Base64 encode it so it can be safely handled by Bash (JSON)
+BASE64_ENCODED_BINARY_RESOURCE_VIA_JSON=$(curl -s -H 'Accept: application/pdf' "$BASE/Binary/$ID_VIA_JSON" | base64 | tr -d '\n')
+
+
+echo "Binary data retrieved. Verifying content... (JSON version)"
+
+if [ "$DATA" = "$BASE64_ENCODED_BINARY_RESOURCE_VIA_JSON" ]; then
+    echo "✅ Base64 encoding of both the Original Data and the Retrieved Resource Data match (JSON)"
+else
+    echo "🆘 Base64 encoding of both the Original Data and the Retrieved Resource Data are different (JSON)"
+    exit 1
+fi

.github/workflows/build.yml

@@ -1069,6 +1069,9 @@ jobs:
     - name: Binary Content Download - not found
       run: .github/scripts/read-binary-content-not-found.sh
 
+    - name: Binary Content Download - invalid (via JSON)
+      run: .github/scripts/read-binary-content-via-json-invalid.sh
+
     - name: Binary Content Download - found (via JSON)
       run: .github/scripts/read-binary-content-via-json-found.sh
 

modules/rest-util/src/blaze/middleware/fhir/output.clj

@@ -29,8 +29,8 @@
 
 (def ^:private parse-accept (parse/fast-memoize 1000 parse/parse-accept))
 
-(defn- generate-error [generation-fn ex]
-  (-> ex
+(defn- generate-error-payload [generation-fn e]
+  (-> e
       ba/anomaly
       handler-util/operation-outcome
       generation-fn))
@@ -51,7 +51,7 @@
     (update response :body generate-xml**)
     (catch Throwable e
       (assoc response
-             :body (generate-error generate-xml** e)
+             :body (generate-error-payload generate-xml** e)
              :status 500))))
 
 (defn- generate-xml [response]
@@ -68,7 +68,7 @@
     (update response :body generate-binary**)
     (catch Throwable e
       (assoc response
-             :body (generate-error identity e)
+             :body (generate-error-payload generate-json e)
              :status 500))))
 
 (defn- generate-binary [response]

modules/rest-util/test/blaze/middleware/fhir/output_test.clj

@@ -214,12 +214,12 @@
           [:headers "Content-Type"] := nil
           :body := nil)))
 
-    (testing "failing binary emit (with invalid data)"
+    (testing "failing binary emit (with invalid data, using the JSON default)"
       (given (call (binary-resource-handler-200 {:content-type "application/pdf" :data "MTANjECg=="}) {:headers {"accept" "text/plain"}})
         :status := 500
         [:headers "Content-Type"] := "application/pdf"
-        [:body :fhir/type] := :fhir/OperationOutcome
-        [:body :issue 0 :diagnostics] := "Input byte array has wrong 4-byte ending unit"))))
+        [:body parse-json :fhir/type] := :fhir/OperationOutcome
+        [:body parse-json :issue 0 :diagnostics] := "Input byte array has wrong 4-byte ending unit"))))
 
 (deftest not-acceptable-test
   (is (nil? (call resource-handler-200-with-patient {:headers {"accept" "text/plain"}}))))