SQL on FHIR view runner

.editorconfig

@@ -900,7 +900,7 @@ ij_json_keep_indents_on_empty_lines = false
 ij_json_keep_line_breaks = true
 ij_json_space_after_colon = true
 ij_json_space_after_comma = true
-ij_json_space_before_colon = true
+ij_json_space_before_colon = false
 ij_json_space_before_comma = false
 ij_json_spaces_within_braces = true
 ij_json_spaces_within_brackets = false

.github/workflows/test.yml

@@ -239,12 +239,23 @@ jobs:
   fhir-server-3:
     name: FHIR server (tranche 3)
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: write
+      actions: write
+      checks: write
     steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::865780493209:role/PathlingBenchmarkUpload
+          aws-region: ap-southeast-2
       - name: Checkout code
         uses: actions/checkout@v4
         with:
           # This is required so that git-commit-id-plugin can find the latest tag.
           fetch-depth: 0
+          submodules: recursive
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
@@ -324,6 +335,8 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           check_name: FHIR server test report 3
           fail_on_test_failures: true
+      - name: Upload SQL on FHIR test report to S3
+        run: aws s3 cp fhirpath/target/fhir-view-compliance-test.json s3://pathling-benchmark/test-reports/${{ github.ref }}/sof-test-results.json
 
   # This job builds, tests and scans the FHIR server Docker image.
   docker-image:
@@ -591,7 +604,7 @@ jobs:
           ${{ env.PATHLING_OPTS }}
         timeout-minutes: 60
       - name: Upload check logs
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         if: always()
         with:
           name: r-check-logs
@@ -600,7 +613,7 @@ jobs:
             lib/R/target/pathling.Rcheck/*.out
             lib/R/target/pathling.Rcheck/*.fail
       - name: Upload package as artifact
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: r-package
           path: lib/R/target/pathling_*.tar.gz

.gitignore

@@ -29,6 +29,7 @@ _version.py
 metastore_db
 derby.log
 spark-warehouse
+.*.crc
 
 
 #R

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "sql-on-fhir"]
+	path = sql-on-fhir
+	url = https://github.com/aehrc/sql-on-fhir-v2.git

.trivyignore

@@ -64,3 +64,12 @@ CVE-2022-1471
 # This vulnerability relates to privilege management using spark-submit, which is outside of the
 # scope of this solution.
 CVE-2023-22946
+
+
+# This vulnerability relates to WebFlex applications, which are not used in Pathling.
+CVE-2024-38821
+
+# This vulnerability relates to avro support in hadoop client runtime, which is not shipped 
+# with pathling but with Spark. The server docker image which used this version does not use 
+# avro.
+CVE-2024-47561

NOTE.md

@@ -0,0 +1,13 @@
+
+
+
+
+
+
+### For build to work (with Java17):
+
+```bash
+export MAVEN_OPTS="-Xmx4g -ea -Duser.timezone=UTC --add-exports=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED"
+```
+
+Possibly change the way test data are generated to use 'exec' instead of java and pass the options there.

deployment/helm/pom.xml

@@ -24,7 +24,7 @@
   <parent>
     <groupId>au.csiro.pathling</groupId>
     <artifactId>pathling</artifactId>
-    <version>7.0.1</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
   <artifactId>helm</artifactId>

encoders/pom.xml

@@ -30,7 +30,7 @@
   <parent>
     <groupId>au.csiro.pathling</groupId>
     <artifactId>pathling</artifactId>
-    <version>7.0.1</version>
+    <version>7.1.0-SNAPSHOT</version>
   </parent>
   <artifactId>encoders</artifactId>
   <packaging>jar</packaging>

encoders/src/main/java/au/csiro/pathling/config/EncodingConfiguration.java

@@ -26,6 +26,7 @@
 import jakarta.validation.constraints.Min;
 import jakarta.validation.constraints.NotNull;
 import java.util.Set;
+import au.csiro.pathling.encoders.FhirEncoders;
 import lombok.Builder;
 import lombok.Data;
 
@@ -59,19 +60,5 @@ public class EncodingConfiguration {
    */
   @NotNull
   @Builder.Default
-  private Set<String> openTypes = Set.of(
-      "boolean",
-      "code",
-      "date",
-      "dateTime",
-      "decimal",
-      "integer",
-      "string",
-      "Coding",
-      "CodeableConcept",
-      "Address",
-      "Identifier",
-      "Reference"
-  );
-
+  private Set<String> openTypes = FhirEncoders.STANDARD_OPEN_TYPES;
 }

encoders/src/main/java/au/csiro/pathling/encoders/FhirEncoders.java

@@ -41,6 +41,37 @@
  */
 public class FhirEncoders {
 
+  /**
+   * The reasonable default set of open types to encode with extension values.
+   */
+  public static final Set<String> STANDARD_OPEN_TYPES = Set.of(
+      "boolean",
+      "code",
+      "date",
+      "dateTime",
+      "decimal",
+      "integer",
+      "string",
+      "Coding",
+      "CodeableConcept",
+      "Address",
+      "Identifier",
+      "Reference"
+  );
+
+  /**
+   * All possible open types in FHIR R4.
+   */
+  public static final Set<String> ALL_OPEN_TYPES = Set.of("base64Binary", "boolean", "canonical",
+      "code", "date", "dateTime", "decimal", "id", "instant", "integer", "markdown", "oid",
+      "positiveInt", "string", "time", "unsignedInt", "uri", "url", "uuid", "Address", "Age",
+      "Annotation", "Attachment", "CodeableConcept", "Coding", "ContactPoint", "Count", "Distance",
+      "Duration", "HumanName", "Identifier", "Money", "Period", "Quantity", "Range", "Ratio",
+      "Reference", "SampledData", "Signature", "Timing", "ContactDetail", "Contributor",
+      "DataRequirement", "Expression", "ParameterDefinition", "RelatedArtifact",
+      "TriggerDefinition", "UsageContext", "Dosage", "Meta");
+
+
   /**
    * Cache of Encoders instances.
    */
@@ -308,6 +339,24 @@ public Builder withOpenTypes(final Set<String> openTypes) {
       return this;
     }
 
+    /**
+     * Sets the reasonable default list of types to be encoded for open types, such as extensions.
+     *
+     * @return this builder
+     */
+    public Builder withStandardOpenTypes() {
+      return withOpenTypes(STANDARD_OPEN_TYPES);
+    }
+
+    /**
+     * Sets the list of all types to be encoded for open types, such as extensions.
+     *
+     * @return this builder
+     */
+    public Builder withAllOpenTypes() {
+      return withOpenTypes(ALL_OPEN_TYPES);
+    }
+
     /**
      * Switches on/off the support for extensions in encoders.
      *

encoders/src/main/scala/au/csiro/pathling/encoders/EncoderBuilder.scala

@@ -34,8 +34,8 @@ import scala.reflect.ClassTag
  */
 object EncoderBuilder {
 
-  val UNSUPPORTED_RESOURCES: Set[String] = Set("Parameters",
-    "Task", "StructureDefinition", "StructureMap", "Bundle")
+  val UNSUPPORTED_RESOURCES: Set[String] = Set("Parameters", "StructureDefinition", "StructureMap",
+    "Bundle")
 
   /**
    * Returns an encoder for the FHIR resource implemented by the given class