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

.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/FHIR/sql-on-fhir-v2.git

deployment/helm/pom.xml

@@ -24,7 +24,7 @@
   <parent>
     <groupId>au.csiro.pathling</groupId>
     <artifactId>pathling</artifactId>
-    <version>6.4.2</version>
+    <version>6.5.0-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>6.4.2</version>
+    <version>6.5.0-SNAPSHOT</version>
   </parent>
   <artifactId>encoders</artifactId>
   <packaging>jar</packaging>

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

@@ -26,6 +26,7 @@
 import java.util.Set;
 import javax.validation.constraints.Min;
 import javax.validation.constraints.NotNull;
+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 +41,25 @@
  */
 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"
+  );
+
+
   /**
    * Cache of Encoders instances.
    */
@@ -308,6 +327,15 @@ 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 withStandardOenTypes() {
+      return withOpenTypes(STANDARD_OPEN_TYPES);
+    }
+
     /**
      * Switches on/off the support for extensions in encoders.
      *