pathling 9.3.0.dev0__tar.gz → 9.4.0__tar.gz

{pathling-9.3.0.dev0 → pathling-9.4.0}/LICENSE

@@ -183,11 +183,12 @@ agree to comply with the licence terms for these components as part of
 accessing the Software. Other third party software may also be identified in
 separate files distributed with the Software.
 
-* (Apache License, Version 2.0) FHIR Bulk Client (au.csiro.fhir:bulk-export:1.0.3 - https://github.com/aehrc/fhir-bulk-java)
+* (Apache License, Version 2.0) FHIR Bulk Client (au.csiro.fhir:bulk-export:1.0.4 - https://github.com/aehrc/fhir-bulk-java)
+* (Apache License, Version 2.0) FHIR Auth Client for Java (au.csiro.fhir:fhir-auth:1.0.0 - https://github.com/aehrc/fhir-auth-java)
 * (Apache License, Version 2.0) HAPI FHIR - Core Library (ca.uhn.hapi.fhir:hapi-fhir-base:8.6.0 - https://hapifhir.io/)
 * (Apache License, Version 2.0) HAPI FHIR - Client Framework (ca.uhn.hapi.fhir:hapi-fhir-client:8.6.0 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-client)
 * (Apache License, Version 2.0) HAPI FHIR Structures - FHIR R4 (ca.uhn.hapi.fhir:hapi-fhir-structures-r4:8.6.0 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-structures-r4)
-* (Eclipse Public License 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.5.18 - http://logback.qos.ch/logback-classic)
+* (Eclipse Public License 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.5.25 - http://logback.qos.ch/logback-classic)
 * (Apache License, Version 2.0) WireMock (com.github.tomakehurst:wiremock-jre8-standalone:2.35.2 - http://wiremock.org)
 * (Apache License, Version 2.0) FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.2 - http://findbugs.sourceforge.net/)
 * (Apache License, Version 2.0) Gson (com.google.code.gson:gson:2.10 - https://github.com/google/gson/gson)
@@ -213,6 +214,7 @@ separate files distributed with the Software.
 * (Apache License, Version 2.0) Infinispan Commons (org.infinispan:infinispan-commons:15.0.3.Final - http://www.infinispan.org)
 * (Apache License, Version 2.0) Infinispan Component Annotations (org.infinispan:infinispan-component-annotations:15.0.3.Final - http://www.infinispan.org)
 * (Apache License, Version 2.0) Infinispan Core (org.infinispan:infinispan-core:15.0.3.Final - http://www.infinispan.org)
+* (Public Domain) JSON in Java (org.json:json:20231013 - https://github.com/douglascrockford/JSON-java)
 * (Public Domain) JSON in Java (org.json:json:20240303 - https://github.com/douglascrockford/JSON-java)
 * (Eclipse Public License v2.0) JUnit Jupiter API (org.junit.jupiter:junit-jupiter-api:5.11.4 - https://junit.org/junit5/)
 * (Eclipse Public License v2.0) JUnit Jupiter Engine (org.junit.jupiter:junit-jupiter-engine:5.11.4 - https://junit.org/junit5/)
@@ -221,7 +223,8 @@ separate files distributed with the Software.
 * (GNU General Public License (GPL), version 2, with the Classpath exception) JMH Core (org.openjdk.jmh:jmh-core:1.37 - http://openjdk.java.net/projects/code-tools/jmh/jmh-core/)
 * (GNU General Public License (GPL), version 2, with the Classpath exception) JMH Generators: Annotation Processors (org.openjdk.jmh:jmh-generator-annprocess:1.37 - http://openjdk.java.net/projects/code-tools/jmh/jmh-generator-annprocess/)
 * (MIT License) Project Lombok (org.projectlombok:lombok:1.18.38 - https://projectlombok.org)
-* (Apache License, Version 2.0) Scala Library (org.scala-lang:scala-library:2.13.15 - https://www.scala-lang.org/)
+* (Apache License, Version 2.0) Scala Library (org.scala-lang:scala-library:2.13.16 - https://www.scala-lang.org/)
 * (Apache License, Version 2.0) JSONassert (org.skyscreamer:jsonassert:1.5.1 - https://github.com/skyscreamer/JSONassert)
+* (Apache License, Version 2.0) JSONassert (org.skyscreamer:jsonassert:1.5.3 - https://github.com/skyscreamer/JSONassert)
 * (MIT License) SLF4J API Module (org.slf4j:slf4j-api:2.0.17 - http://www.slf4j.org)
 * (Apache License, Version 2.0) spring-boot-starter-test (org.springframework.boot:spring-boot-starter-test:3.4.11 - https://spring.io/projects/spring-boot)

{pathling-9.3.0.dev0 → pathling-9.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pathling
-Version: 9.3.0.dev0
+Version: 9.4.0
 Summary: Python API for Pathling
 Project-URL: Homepage, https://github.com/aehrc/pathling
 Author-email: "Australian e-Health Research Centre, CSIRO" <pathling@csiro.au>

{pathling-9.3.0.dev0 → pathling-9.4.0}/pathling/_version.py

@@ -2,8 +2,8 @@
 # Auto generated from POM project version.
 # Please do not modify.
 #
-__version__="9.3.0.dev0"
-__java_version__="9.3.0-SNAPSHOT"
+__version__="9.4.0"
+__java_version__="9.4.0"
 __scala_version__="2.13"
 __delta_version__="4.0.0"
 __hadoop_version__="3.4.1"

{pathling-9.3.0.dev0 → pathling-9.4.0}/pathling/context.py

@@ -33,6 +33,14 @@ if TYPE_CHECKING:
 __all__ = ["PathlingContext"]
 
 
+def _convert_java_value(value):
+    """Converts a Java value from Py4J to an equivalent Python type."""
+    if isinstance(value, (str, int, float, bool)):
+        return value
+    # For other types (e.g., Java BigDecimal, Row), convert to string.
+    return str(value)
+
+
 class StorageType:
     MEMORY: str = "memory"
     DISK: str = "disk"
@@ -415,6 +423,59 @@ class PathlingContext:
         jcolumn = self._jpc.fhirPathToColumn(resource_type, fhirpath_expression)
         return Column(jcolumn)
 
+    def evaluate_fhirpath(
+        self,
+        resource_type: str,
+        resource_json: str,
+        fhirpath_expression: str,
+        context_expression: Optional[str] = None,
+        variables: Optional[dict] = None,
+    ) -> dict:
+        """
+        Evaluates a FHIRPath expression against a single FHIR resource and returns
+        materialised typed results.
+
+        The resource is encoded into a one-row Spark Dataset internally, and the
+        existing FHIRPath engine is used to evaluate the expression. Results are
+        collected and returned as typed values.
+
+        Example usage::
+
+            pc = PathlingContext.create(spark)
+            result = pc.evaluate_fhirpath("Patient", patient_json, "name.family")
+            for value in result["results"]:
+                print(f"{value['type']}: {value['value']}")
+
+        :param resource_type: the FHIR resource type (e.g., "Patient", "Observation")
+        :param resource_json: the FHIR resource as a JSON string
+        :param fhirpath_expression: the FHIRPath expression to evaluate
+        :param context_expression: an optional context expression; if provided, the main
+               expression is composed with the context expression
+        :param variables: optional named variables available via %variable syntax, or None
+        :return: a dict with ``results`` (list of dicts with ``type`` and ``value``
+                 keys) and ``expectedReturnType`` (string)
+        :raises: Exception if the expression is invalid or evaluation fails
+        """
+        jresult = self._jpc.evaluateFhirPath(
+            resource_type,
+            resource_json,
+            fhirpath_expression,
+            context_expression,
+            variables,
+        )
+        # Convert Java FhirPathResult to Python dict.
+        results = []
+        for jtyped_value in jresult.getResults():
+            value = jtyped_value.getValue()
+            # Convert Java types to Python types.
+            if value is not None:
+                value = _convert_java_value(value)
+            results.append({"type": jtyped_value.getType(), "value": value})
+        return {
+            "results": results,
+            "expectedReturnType": jresult.getExpectedReturnType(),
+        }
+
     def search_to_column(self, resource_type: str, search_expression: str) -> Column:
         """
         Converts a FHIR search expression to a boolean filter column.